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@@ -53,3 +53,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
+full_texts-2024-04-25-update.json filter=lfs diff=lfs merge=lfs -text
+full_texts.json filter=lfs diff=lfs merge=lfs -text

eval/task1_eval.py

@@ -0,0 +1,107 @@
+import argparse
+import json
+import csv
+import math
+import os
+
+
+def compute_dcg(pred_docs, gold_docs):
+    dcg_score = 0.0
+    for i, doc in enumerate(pred_docs):
+        position = i + 1
+        discount = 1.0 / math.log2(position + 1)
+        relevance = 0.0
+        if doc in gold_docs:
+            # If predicted image is present in gold list, set relevance to 1.0
+            relevance = 1.0
+        else:
+            for gdoc in gold_docs:
+                # If predicted image is a sub-image or parent image of an image in gold list,
+                # we set relevance to 0.5 to provide partial credit
+                if doc in gdoc or gdoc in doc:
+                    relevance = 0.5
+                    break
+        dcg_score += (discount * relevance)
+    return dcg_score
+
+
+def compute_idcg(relevance_ranking, rank):
+    sorted_relevance_ranking = list(sorted(relevance_ranking.items(), key=lambda x: x[1], reverse=True))
+    # Only consider top k relevant items for IDCG@k
+    sorted_relevance_ranking = sorted_relevance_ranking[:min(len(sorted_relevance_ranking), rank)]
+    idcg_score = sum([ (1.0 / (math.log2(i + 2))) * x[1] for i, x in enumerate(sorted_relevance_ranking)])
+    return idcg_score
+
+
+def run_eval(pred_labels, gold_labels, parse_folder, claim_citekeys, debug):
+    ranks_to_eval = [5, 10]
+    ndcg_scores = {n: {} for n in ranks_to_eval}
+    non_empty_samples = 0
+
+    for claim_id in pred_labels:
+        if claim_id not in gold_labels:
+            print(f"Warning: Claim ID {claim_id} not found in gold data - skipping!")
+            continue
+        if not gold_labels[claim_id]:
+            print(f"Warning: Claim ID {claim_id} has no associated evidence figures/tables - skipping!")
+            continue
+
+        non_empty_samples += 1
+        for rank in ranks_to_eval:
+            # If #predictions < rank in predicted ranking, include all for evaluation
+            pred_images = pred_labels[claim_id][:min(len(pred_labels[claim_id]), rank)]
+            gold_images = gold_labels[claim_id]
+
+            # Compute DCG score
+            dcg_score = compute_dcg(pred_images, gold_images)
+
+            # Compute ideal DCG score
+            # First need to get relevance scores for all possible images
+            # Images in gold list get relevance score of 1.0
+            relevance_ranking = {x: 1.0 for x in gold_images}
+            for file in os.listdir(os.path.join(parse_folder, claim_citekeys[claim_id])):
+                if 'CAPTION' in file:
+                    continue
+                image_id = file.split('.png')[0]
+                if image_id not in gold_images:
+                    relevance_ranking[image_id] = 0.0
+                    # All images that are parent/sub-images of a gold image get relevance of 0.5
+                    for gold_image in gold_images:
+                        if image_id in gold_image or gold_image in image_id:
+                            relevance_ranking[image_id] = 0.5
+                            break
+            idcg_score = compute_idcg(relevance_ranking, rank)
+
+            # Finally compute and store NDCG score@k
+            ndcg_score = dcg_score / idcg_score
+            ndcg_scores[rank][claim_id] = ndcg_score
+    
+    # Display final evaluation scores
+    for rank in ranks_to_eval:
+        final_ndcg = sum(list(ndcg_scores[rank].values())) / len(gold_labels)
+        print(f'NDCG@{rank}: {final_ndcg}')
+    
+    if debug:
+        json.dump(ndcg_scores, open("task1_scores.json", "w"))
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--pred_file", type=str, required=True, help="Path to prediction file")
+    parser.add_argument("--gold_file", type=str, required=True, help="Path to gold data file")
+    parser.add_argument("--parse_folder", type=str, required=True, help="Path to folder containing parsed images/tables")
+    parser.add_argument("--debug", type=bool, default=False, help="Dump per-prediction scores for debuggin/analysis")
+    args = parser.parse_args()
+
+    gold_data = json.loads(open(args.gold_file).read())
+    gold_labels = {x["id"]: x["findings"] for x in gold_data}
+    claim_citekeys = {x["id"]: x["citekey"] for x in gold_data}
+    
+    reader = csv.reader(open(args.pred_file))
+    next(reader, None)
+    pred_labels = {}
+    for row in reader:
+        pred_labels[row[0]] = row[1].split(',')
+    
+    run_eval(pred_labels, gold_labels, args.parse_folder, claim_citekeys, args.debug)

eval/task2_eval.py

@@ -0,0 +1,87 @@
+import argparse
+import json
+import itertools
+from collections import defaultdict
+
+import bert_score
+from bert_score import score
+from rouge_score import rouge_scorer
+
+
+def get_best_scores(candidates, score_list):
+    per_pair_scores = defaultdict(list) 
+    for cand, score in zip(candidates, score_list): 
+        per_pair_scores[cand].append(score)
+    best_match_scores = {cand: max(scores) for cand, scores in per_pair_scores.items()}
+    return best_match_scores
+
+
+def run_snippet_eval(pred_snippets, gold_snippets, debug):
+    bert_scores = {}
+    rouge_scores = {"rouge1": {}, "rouge2": {}, "rougel": {}}
+    rscorer = rouge_scorer.RougeScorer(['rouge1', 'rouge2', 'rougeL'], use_stemmer=True)
+
+    for claim_id in pred_snippets:
+        if claim_id not in gold_snippets:
+            print(f"Warning: Claim ID {claim_id} not found in gold data - skipping!")
+            continue
+        if not gold_snippets[claim_id]:
+            print(f"Warning: Claim ID {claim_id} has no associated evidence snippets - skipping!")
+            continue
+
+        # Generate all possible combinations of gold x predicted snippets for overlap computation
+        eval_pairs = itertools.product(pred_snippets[claim_id], gold_snippets[claim_id])
+        candidates, references = zip(*list(eval_pairs))
+
+        # Compute BERT scores for all gold x predicted snippets and retain best match score per prediction
+        P, R, F1 = score(candidates, references, lang='en', verbose=True)
+        best_scores = get_best_scores(candidates, F1.numpy().tolist())
+        mean_bert_score = sum(best_scores.values()) / len(pred_snippets[claim_id])
+        bert_scores[claim_id] = mean_bert_score
+
+        # Similarly compute ROUGE-1,2,L scores
+        r1_list, r2_list, rl_list = [], [], []
+        for cand, ref in zip(candidates, references):
+            score_output = rscorer.score(ref, cand)
+            r1_list.append(score_output['rouge1'].fmeasure)
+            r2_list.append(score_output['rouge2'].fmeasure)
+            rl_list.append(score_output['rougeL'].fmeasure)
+        best_rouge1 = get_best_scores(candidates, r1_list)
+        best_rouge2 = get_best_scores(candidates, r2_list)
+        best_rougel = get_best_scores(candidates, rl_list)
+        rouge_scores["rouge1"][claim_id] = sum(best_rouge1.values()) / len(pred_snippets[claim_id])
+        rouge_scores["rouge2"][claim_id] = sum(best_rouge2.values()) / len(pred_snippets[claim_id])
+        rouge_scores["rougel"][claim_id] = sum(best_rougel.values()) / len(pred_snippets[claim_id])
+    
+    # Print final score report
+    final_bert_score = sum(bert_scores.values()) / len(gold_snippets)
+    print(f"BERT Score: {final_bert_score}")
+    final_rouge1_score = sum(rouge_scores["rouge1"].values()) / len(gold_snippets)
+    print(f"ROUGE-1 Score: {final_rouge1_score}")
+    final_rouge2_score = sum(rouge_scores["rouge2"].values()) / len(gold_snippets)
+    print(f"ROUGE-2 Score: {final_rouge2_score}")
+    final_rougel_score = sum(rouge_scores["rougel"].values()) / len(gold_snippets)
+    print(f"ROUGE-L Score: {final_rougel_score}")
+    # TODO: Allow dumping of per-prediction scores for analysis?
+
+    if debug:
+        json.dump(bert_scores, open("task2_bertscores.json", "w"))
+        json.dump(rouge_scores, open("task2_rougescores.json", "w"))
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--pred_file", type=str, required=True, help="Path to prediction file")
+    parser.add_argument("--gold_file", type=str, required=True, help="Path to gold data file")
+    parser.add_argument("--debug", type=bool, default=False, help="Dump per-prediction scores for debuggin/analysis")
+    args = parser.parse_args()
+
+    gold_data = json.loads(open(args.gold_file).read())
+    gold_snippets = {x["id"]: x["context"] for x in gold_data}
+
+    pred_data = json.loads(open(args.pred_file).read())
+    pred_snippets = {x["id"]: x["context"] for x in pred_data}
+
+    # Run ROUGE and BERTScore evaluation for grounding snippets
+    run_snippet_eval(pred_snippets, gold_snippets, args.debug)

extracted_captions/Kueh2008.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'Figure 1: **Actin filaments disassemble in bursts in cofilin, coromin, and Aip1.** [A] Time-lapse wide-field epifluorescence images of fluorescently labeled actin filaments in the presence of 2 \\\\(\\\\mu\\\\)M cofilin, 1 \\\\(\\\\mu\\\\)M comin, 200 nM Aip1, 5 \\\\(\\\\mu\\\\)M of actin monomer, and 2 mM ATP. Filaments shorten and disappear from the field of view. Bar, 3 \\\\(\\\\mu\\\\)m. [B] Successive time-lapse images showing a single actin filament [f] over time, along with laryngographs drawn along the contours of representative filaments [f1-4]. The red lines on the image of 1 \\\\(\\\\mu\\\\)t = 0 denote the contour on which the kymograph was drawn. Time is given on the x axis of the kymograph, whereas the position along the filament contour is given on the y axis. Mean integration time for a single image was 400 ms for _H1-f3_ and 16 ms for _I4_. Triangles denote endwise bursting [f1-3]; yellow triangles denote initial burst [f1-f3], red triangles denote successive proximal bursts [f1] and _I2_, and green triangle denotes a successive distal burst [f3]. Some-side bursts occurred more frequently (78%) than opposite-side bursts (22%; \\\\(\\\\tau\\\\) < 0.001, one-tailed 2 test). The square denotes internal disassembly event counted as a severing event [f3]. Bar, 1 \\\\(\\\\mu\\\\)m. [C] Histogram of filament burst size. The mean burst size was 260 subunits. [D] Histogram of waiting times between successive bursts [red], fit to a single exponential [black]. Single exponential fit gave characteristic decay time of \\\\(\\\\tau\\\\) = 14 s.\\n\\n'", "CAPTION FIG2.png": "'Figure 2. **Filament bursting is distinct from eefilin-mediated severing. [\\\\(\\\\mu\\\\)A] Time-lapse images of two actin filaments disassembling in 10 mM cefilin, 5 mM of actin monomer, and 2 mM ATP. Long filaments were chosen to illustrate the accurrenca of multiple severing events within a single filament. Bar, 1 pm. [B] Bar graph showing the fraction of disassembly events scored as bursting (red) or severing [green], either in the full desobymarizing system (left) or in cefilin alone (right). In the full system, bursting occurred with significantly higher frequency than severing [\\\\(\\\\chi^{2}=190\\\\), df = 1, P < 0.01]. However, in the presence of high concentrations of actin, severing occurred with significantly higher frequency than bursting [\\\\(\\\\chi^{2}=55\\\\), df = 1, P < 0.01] and was the predominant disassembly mechanism observed under these conditions. We note that mean inel filament length did not differ significantly between different experiments and was not the cause of the differences observed.**\\n\\n'", "CAPTION FIG3.png": "'Figure 3: **Actin filaments disassemble with similar kinetics from both ends.**[_A_] Time-lapse images of actin filament bundles grown off fragments of _l._ acyl-phyrins accrosomal processes. Filaments in the long bundle have exposed barbed ends (b), whereas filaments in the short bundle have exposed pointed ends (c). The two bundles shown were elongated from opposite ends of the same _L._ poly-phyrins accrosomal fragment. The brightness of the shorter bundle was increased relative to the longer one for ease of visualization. _At_ 0 s, filament bundles were perfused with 2 mM cocillin, 1 mM cocrinin, 300 mM Ag1, 5 mM of actin monomer, and 2 mM ATP. Bar, 1 \u03bcm. (B) Total actin polymer mass in the filament bundles as a function of time measured for all bundles (red), bundles with exposed barbed ends (green), and bundles with exposed pointed ends (blue). To compare the rates of rapid disassembly, the slowly varying component of each decay curve was removed (Fig. S1, available at http://www.jcb.org/cgi/content/full/jcb.200801027/DC1; see Materials and methods). [_C_] Bar graph comparing decay rates for bundles with exposed barbed ends (b) with those with exposed pointed ends (b). Data represent mean and standard deviation of three independent experiments.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: **Bursting disassembly generates barbed ends not recognized by CapZ.** Fluorescence images show Alaxa 647 actin (left) and Alexa 488 CapZ. (right) in filament bundles. Barbed ends are oriented toward to the right. The bar graph shows the CapZ/actin filament ratio, a measure of the fraction of copper barbed ends in the bundle. Data represent mean and standard deviation of eight filament bundles. (A) Filament bundles polymerized from L. _Polyg\u00e8mes_ acrossal fragments were incubated directly with Alexa 488 CapZ. [B] Filament bundles were partially disassembled with _\u03b2_ null actin for 90 s then incubated with CapZ. [C] Filament bundles were partially disassembled with 2.5 \u03bcM actin, 1.5 \u03bcM coronin, and 50 \u03bcM Ap1 for 25 s, then incubated with CapZ. (D) Filament bundles were partially disassembled with cofilin, coronin, and _Aip1_ as in C, incubated in buffer for 10 s, then incubated with CapZ. Bar, 1 \u03bcm.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: **Barbed end-copping factors inhibit actin disassembly by coffin, coronin, and Aip1.** [A] Mean filament length over time under the following conditions: 2 \u03bcM cells, 1 \u03bcM actin, 1 \u03bcM coronin, 5 \u03bcM of actin monomer, and 2 \u03bcM ATP, as well as 200 \u03bcM \u03bcM (red), no Aip1 [green], 5 \u03bcM CorpZ [yellow], 200 \u03bcM Ap1 + 1 \u03bcM CytOb [black], or 200 \u03bcM Ap1 + 5 \u03bcM CapZ [blue]. Fast non-linear-insensitive disassembly required Aip1 [red vs. green, yellow]. CytoD and CopZ inhibited disassembly in the full system [black, blue vs. red]. [B] Bor graph showing the percentage of filaments that underwent endwise bursting or severing. The number of filaments analyzed is given below the bars. The percentages of filaments that either underwent endwise bursting or severing increased significantly in the presence of Aip1 [red vs. green, yellow] and decreased significantly when the barbed-end coopers CytO and CopZ were added to the full system [black, blue vs. red]; severing frequency of ~CopZ vs. ~CopZ, _kh_ = 4.9, _df_ = 1, \\\\(p\\\\) < 0.05, all other pairwise comparisons, _kh_ > 40, _df_ = 1, \\\\(p\\\\) < 0.001). [C] Polymer mass decay for bundles with either exposed barbed ends or pointed ends in 3 \u03bcM CytOb (brown and purple) or 10 \u03bcM CapZ (blue and green), as well as polymer mass decay for all filament bundles in the absence of barbed-end coopers [red]. Dissensembly of bundles with either exposed barbed ends or pointed ends were inhibited by CytoD/CopZ with equal efficacy. [D] fraction of polymer mass diisassembled as a function of CytoD concentration (red circles). Best fit of the data to a hyperbolic [red curve] shows an C_x_50 of 90 \u03bcM inhibition of disassembly. Length of filament bundles polymerized for a fixed period of time in the presence of varying concentrations of C_x_50 is also shown (blue squares). Hyperbolic best fit [blue curve] shows an C_x_50 of 30 \u03bcM inhibition of polymerization. [E] Fraction of polymer diisassembled as a function of CapZ concentration [red squares]. The situation curve did not reach saturation; the red curve denotes best fit of the data to a straight line. The length of filament actin bundle polymerized in the presence of varying concentrations of CapZ is also shown (blue circles). Polymerization conditions were identical to those in D. Hyperbolic best fit [blue curve] gave an C_x_50 of 30 \u03bcM for inhibition of polymerization. Error bars indicate SD. [F] CytoD does not inhibit coffin-mediated severing. The bars graph shows the percentage of filaments that served during a 400 s video either in the absence of CytoD [left] or in the presence of 1 \u03bcM CytOb (right). Conditions: 8 \u03bcM cclilin and 5 \u03bcM of actin monomer in assay buffer.\\n\\n'", "CAPTION FIG6.png": "'Figure 6: **Barbed end-capping drugs inhibit actin disassembly in mammalian tissue-culture cells.** (A) Images of suspension Hela S3 calls showing F-actin stained with TRIT-cpholdolin (top) and DNA stained with Hoechst Bottom). Images show unreacted cells [left], cells treated with 10 \u03bcM Cyph0] for 480 s (middle), and cells treated with 10 \u03bcM Limb Left for 480 s (right). All images used identical acquisition settings and contrast levels. 20, 100 rpm. (B) The level F-actin per cell at different times after treatment with either Cyph0 [blue] or LofR [red]. F-actin levels remained high after Cyph0 Treatment. In contrast, F-actin levels left rapidly upon LofR treatment. Each point represents the mean and SD of at least 10 fields of cells. (C) Images of actin content tails in \\\\(\\\\cdot\\\\) monocytogenes-inflicted BSC-1 cells taken at successive times after drug treatment. In the absence of any drugs [control], comet tails disassembled with 50 s (open left). Upon LofR treatment, comet tails also disassembled within 50 s, which suggests that there is no effect of LofR on comet tail disassembly kinetics. In contrast, comet tails did not disassemble in Cyph0- and KabC-exceeded cells for at least 50 s after drug addition, which implies that Cyph0 and KabC-exhibited comet tail disassembly. All drugs were added at time 0. Bar, 5 \u03bcM. (D) Curves showing decay of actin polymer mass from \\\\(L\\\\). monocytogenes comet tails. In the absence of drugs, actin disassembled at an initial rate of \\\\(k_{\\\\text{model}}=[2.3\\\\pm 0.2]\\\\times 10^{-3}\\\\)-1. LofR did not change the disassembly rate, with \\\\(k_{\\\\text{model}}=[2.6\\\\pm 0.2]\\\\times 10^{-2}\\\\)-1. LofR in contrast, Cyph0 reduced the L. monocytogenes content tail decay rate to \\\\(k_{\\\\text{model}}=[1.9\\\\pm 6]\\\\times 10^{-4}\\\\)-s\\\\({}^{-1}\\\\). Data represent the mean of polymer mass in multiple trials [control], 27 s/cis; Cyph0 treatment, 40 tails; LofR treatment, 27 tails). Disassembly rates were obtained by fitting the initial slope of the decay curve to a straight line.\\n\\n'", "CAPTION FIG7.png": "'Figure 7: **Borbed-end and coppers inhibit disassembly of dynamic actin at the ruffling cell edge.** (A\u2013C) Time-lapse images of ruffling edges in BSC-1 cells expressing mRFP-PAGE/PAGP-actin taken before CytoD addition (A), after LofI addition (B), or after CytoD addition [C]. The red channel shows bulk actin, and the green channel shows photoactivated fluorescence. Images were taken before activation [left], immediately after activation (middle), and 100 s after activation (right). [D\u2013F] Xymographs taken along the lines shown in A, B, and C, respectively. The color symograph shows bulk actin in red and photoactivated actin in green. The black and white kymograph shows photoactivated actin alone. Arrows show the time of CytoD addition [O and E] for LofI addition [E]. (A and D) Before drug treatment, photoactivated subpopulations of actin decayed within 100 s. [B and E] LofI did not inhibit actin disassembly. Both bulk and photoactivated subpopulations of actin disappeared within 100 s. [C and F] CytoD inhibited disassembly of dynamic actin assemblies at the ruffling edge. Photoactivated actin subpopulations remained visible for >100 s, and bulk actin fluorescence persisted at the ruffling cell edge. Bar, 5 \u03bcm.\\n\\n'", "CAPTION FIG8.png": "'Figure 8. **Candidate mechanisms for actin filament disassembly by co-filin, ceronian, and Aip1. [A] Cooperative strand separation. [B] Filament scavenging. Black lines denote filament strands. The blue box denotes CapZ. The red bar denotes inhibition of CapZ binding. Successive illustrations depict reaction intermediates in each disassembly pathway.**\\n\\n'"}

extracted_captions/Owen2020Cterminal.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n**Figure 1: Talin-1 ABS3 binding to actin is stabilized by force**. (**Ai**) No-load three bead optical trap experimental setup. ABS3 (light blue) is immobilized via an N-terminal HaloTag domain on a microscope coverslip sparsely decorated with 1.5 \\\\(\\\\upmu\\\\)m diameter platform beads. A single actin filament (orange) is stretched between two optically trapped 1 \\\\(\\\\upmu\\\\)m diameter beads. The microscope stage is positioned such that a platform bead is positioned directly underneath the actin filament. (**Aii**) Sample trace of the position of the trapped beads to detect binding of ABS3 to F-actin. In the absence of applied load, ABS3 binding to F-actin can be detected by a damping of high-frequency Brownian fluctuations (cumulative power spectrum, C.P.S. \\\\(>\\\\) 0.3-10 kHz) in the trapped beads. (**Aiii**) Binding lifetimes detected with this method. N=291 binding events detected from sampling the ABS3 construct from 1,419 seconds of recorded data. N=8 binding events detected from sampling an eGFP-coated surface from 2,188 seconds. (**Bi**) Loaded three bead optical trap experimental setup. Same as **Ai**, except the stage is translated parallel to the actin filament in a trapezoidal wave form. (**Bii**) If one or more ABS3 molecules on the platform bead bind to the actin filament while the stage is moving, one of the trapped beads is pulled out of its equilibrium position (demarcated by the blue force trace), thus applying load to the ABS3-F-actin bond. When this occurs the stage motion is halted until all of the protein complexes unbind and the trapped beads return to their equilibrium positions (marked with purple notch, gray trace). Reported lifetimes are last steps of binding events, which for this sample trace is the time between yellow and purple arrows, or the full lifetime of single-step events.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Figure 2:****Talin-1 forms a catch bond with F-actin when force is applied towards the pointed end of the actin filament (A)** An asymmetry in bond lifetimes is observed for a single actin filament. (**Ai, Aii**) Load on the _right_ (**Ai**) or _left_ (**Aii**) trapped bead. (**Aiii**) Sample force trace. Load on the right bead is indicated in orange, while load on the left bead is shown in blue. (**B**) (**Bi**) A myosin VI construct steps along actin filaments, pulling the bead attached to the (-) end of the filament out of the trap. (**Bii**) Sample myosin trace. In this example, the left bead is attached to the F-actin (-) end. (**C**) ABS3 binding dwell times measured as a function of force. Forces directed towards the pointed (-) end of the filament correspond to negative force values and forces directed towards the barbed (+) end correspond to positive force values. _Dark gray_: binding lifetimes of events measured in the directionality assay in which the actin filament polarity was explicitly measured for each dumbbell (N=2 flow cells, N=3 dumbbells, N=47 events). _Lavender_: binding dwell times for which the actin filament polarity was statistically inferred. _Orange_: mean dwell times (20 data points per bin), with 95% confidence intervals shown in thinner lines (N = 777 binding events, N=42 dumbbells, N=18 flow cells). (**D**) Fold-difference in bond lifetime for forces applied towards the pointed vs. barbed end of the actin filament, with 95% confidence intervals per 1 pN bin.\\n\\n'", "CAPTION FIG3.png": "'\\n\\n**Figure 3: The C-terminal dimerization domain (DD) is required for F-actin binding under load. (A)** The constructs used in this study (see text). (B) Native PAGE of BSA (MW=66.5 as monomer), ABS3 (64.2 kDa if monomeric), ABS3\\\\(\\\\Delta\\\\)DD (58.5 kDa, monomer) and NTD-ABS3\\\\(\\\\Delta\\\\)DD (113 kDa). Note the gradual shift in apparent molecular weight as a function of ABS3 concentration, suggestive of a dynamic equilibrium of dimerization. \\\\(\\\\bullet\\\\) and \\\\(\\\\overline{\\\\textbf{V}}\\\\)denote distances traveled of peaks in different replicates. (C) Actin cosedimentation of 4 uM ABS3, 2 uM NTD-ABS3, or 2 uM NTD-ABS3\\\\(\\\\Delta\\\\)DD with 20 uM actin. N=3 replicates. (D) Force-lifetime plots of binding events detected for the NTD-ABS3 construct (lavender) with mean lifetime and confidence intervals on the mean plotted in orange (20 data points per bin). N=386 binding events, N=18 dumbbells, N=8 flow cells.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Talin ABS3 functions as a molecular AND gate (see text). Integrin cartoon modified from Zhu _et al._, 2017.\\n\\n'"}

extracted_captions/alfonzomendez2022dual.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n**Fig. 1 EGF modifies the ultrastructure of clathrin at the plasma membrane.****a**_N_Montaged PREM image of an unroofed control HCS-EGFR-GFP cell and the mask created after segmentation of the full membrane outlined (yellow). Flat, dome, and sphere clathrin-coated structures (CCCs) are shown in green, blue, and magenta, respectively. **b** High-magnification image of the cropped PREM in (**a**); the different segmented CCSs are color-coded as in (**a**), with grayscale in magnified insets. **c**_Montaged PREM image of an unroofed HCS-EGFR-GFP cell treated with 50 ng/mL EGF for 15 min and the mask created after the segmentation. **d**_High-magnification of a representative region of the PREM in (**c**), the magnification insets are shown at the same scale and are outlined with dashed squares in each image. **e**_Representative clathrin masks of the EGF stimulation time course for 0, 2, 5, 15, 30, and 60 min. PREM images corresponding to the masks and cropped images are shown in Supplementary Fig. 1. **f-h**_Morphometric analysis of the percentage of plasma membrane (PM) area occupation for each CCS subtype. 1-_N_Morphometric analysis of the percentage of plasma maximum data point markers with a coefficient value of 1.5. **f-k**_Morphometric analysis of the size of flat, dome, and sphere CCSs during the EGF time course for three clathrin subtypes. Dot plots show every structure segmented, the bar is the median, \\\\(N\\\\) = 2 biologically independent experiments in (**a**-**a**); 0 min: \\\\(N_{\\\\text{Max}}\\\\) = 141, \\\\(N_{\\\\text{dena}}\\\\) = 46, \\\\(N_{\\\\text{dena}}\\\\) = 68, \\\\(N_{\\\\text{exta}}\\\\) = 4; 2 min: \\\\(N_{\\\\text{Int}}\\\\) = 164, \\\\(N_{\\\\text{dena}}\\\\) = 32, \\\\(N_{\\\\text{dena}}\\\\) = 30, \\\\(N_{\\\\text{exta}}\\\\) = 3; 5 min: \\\\(N_{\\\\text{Max}}\\\\) = 184, \\\\(N_{\\\\text{dena}}\\\\) = 26, \\\\(N_{\\\\text{dena}}\\\\) = 36, \\\\(N_{\\\\text{dena}}\\\\) = 4; 15 min: \\\\(N_{\\\\text{Int}}\\\\) = 559, \\\\(N_{\\\\text{dena}}\\\\) = 67, \\\\(N_{\\\\text{dena}}\\\\) = 207, \\\\(N_{\\\\text{exta}}\\\\) = 4; 30 min: \\\\(N_{\\\\text{Int}}\\\\) = 395, \\\\(N_{\\\\text{dena}}\\\\) = 149, \\\\(N_{\\\\text{dena}}\\\\) = 113, \\\\(N_{\\\\text{exta}}\\\\) = 3; 60 min: \\\\(N_{\\\\text{int}}\\\\) = 81, \\\\(N_{\\\\text{dena}}\\\\) = 57, \\\\(N_{\\\\text{exta}}\\\\) = 5 examined over the indicated independent experiments. Scale bars in (**a**) and (**c**) are 5 min. Scale bars in (**b**, **d**, **e**) are 1 min insets are 200 nm. EGF epidermal growth factor, EGFR epidermal growth factor receptor, PREM platinum replica electron microscopy.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Fig. 2 Flat clathrin lattice formation requires EGFR.****a** Representative PREM images of control HSC3-EGFR-GFP cells (Ctrl), **b** cells treated either with ESO ng/mL EGF alone (EGF) for 15 min, or in presence of (**c**) 10 \u03bcM gefitinib (Gefi + EGF), and **d** EGFR siRNA (EGFR siRNA + EGF). EGFR siRNA validation is shown in Supplementary Fig. 3. The magnification insets are shown at the same scale and are outlined with dashed squares in each image. Flat, dome, and sphere clathrin-coated structures (CCSs) are shown in transparent green, blue, and magenta, respectively, with native grayscale in magnified insets. **e** Representative masks of segmented cells treated as in (**a-d**). PREM images corresponding to the masks and cropped images are shown in Supplementary Fig. 4. **f** Morphometric analysis of the percentage of plasma membrane (PM) area occupation for flat clathrin structures. 1-shaped box plots show median extended from 25th to 75th percentiles, and minimum and maximum data point whiskers with a coefficient value of 15. **g** Morphometric analysis of the size of flat structures of cells treated as indicated in (**a-d**). Dot plots show every structure segmented the bar indicates the median. Ctrl: _N_Hua = 14L \\\\(N_{\\\\text{cells}}\\\\) = 4; EGF: _N_Hua = 559, _N_cells = 4; Gefi + EGF: _N_Hua = 160, _N_cells = 4; EGFR siRNA + EGF: _N_Hua = 346, _N_cells = 4. Number of biologically independent experiments = 2. Scale bars in (**a-e**) are 1 \u03bcm; insets are 200 nm. Ctrl and EGF data were from Fig. 1 and shown for reference. EGF epidermal growth factor receptor, PREM platinum replica electron microscopy.\\n\\n'", "CAPTION FIG3.png": "'Fig. 3: **Flat clathrin lattice formation requires Src.****a** Representative PREM images of control HSC3-EGFR-GFP cells (CtrU), **b** cells treated either with 50 ng/mL EGF alone (EGF) for TS min, or in presence of **c**10 \u03bcM PP2 (PP2 + EGF), and **d** Src siRNA (Src siRNA + EGF). Src siRNA validation is shown in Supplementary Fig. 3. The magnification insets are shown at the same scale and are outlined with dashed squares in each image. Flat, dome, and sphere clathrin-coated structures (CCSs) are shown in green, blue, and magenta, respectively, with native grayscale in magnified insets. **e** Representative masks of segmented cells treated as in (**a\u2013d**). PREM images corresponding to the masks and cropped images are shown in Supplementary Fig. 4. **f** Morphometric analysis of the percentage of plasma membrane (PM) area occupation for flat clathrin structure. **i**-shaped box plots show median extended from 25th to 75th percentiles, and minimum and maximum data point whiskers with a coefficient value of 1.5. **g** Morphometric analysis of the size of flat structures of cells treated as indicated in (**a\u2013d**). Dot plots show every structure segmented the bar indicates the median. CtrU \\\\({}_{\\\\text{Mat}}\\\\) = 141, \\\\(N_{\\\\text{cells}}\\\\) = 4; EGF: \\\\(N_{\\\\text{Mat}}\\\\) = 559, \\\\(N_{\\\\text{cells}}\\\\) = 4; PP2 + EGF: \\\\(N_{\\\\text{Mat}}\\\\) = 267, \\\\(N_{\\\\text{cells}}\\\\) = 8; Src KD + EGF: \\\\(N_{\\\\text{Mat}}\\\\) = 71, \\\\(N_{\\\\text{cells}}\\\\) = 7. Number of biologically independent experiments - 2. Scale bars in (**a\u2013e**) are 1 \u03bcm; insets are 200 nm. CtrU and EGF data were from Fig. 1 and shown for reference. EGF epidermal growth factor, EGFR epidermal growth factor receptor, PREM platinum replica electron microscopy.\\n\\n'", "CAPTION FIG4.png": "'\\nFig. 4: **Flat clathrin lattice formation requires \\\\(\\\\beta\\\\)S-integrin.** A Representative PREMs of control HSC3-EGR-GFP cells (Ctrl), **b** treated either with 50 ng/mL EGF alone (EGF) for 15 min, or in presence of **e** 10 \u03bcM clengicide acid (CTA + EGF), and **d** \\\\(\\\\beta\\\\)S-integrin siRNA (Q5 siRNA + EGF). \\\\(\\\\beta\\\\)S-integrin siRNA isolation is shown in Supplementary Fig. 3. The magnification insets are shown at the same scale and are outlined with dashed squares in each image. Flat, _red_, and sphere clathrin-coated structures (CCSs) are shown in green, blue, and magenta, respectively, with native grayscale in magnified insets. **e** Representative masks of segmented cells treated as in (**a\u2013d**). PREM images corresponding to the masks and creoped images are shown in Supplementary Fig. 4. **f** Morphometric analysis of the percentage of plasma membrane (PM) area occupation for flat clathrin structures. 1-shaped box plots show median extended from 25th to 75th percentiles, and minimum and maximum data point whiskers with a coefficient value of 15. **g** Morphometric analysis of the size of flat structures of cells treated as indicated in (**a\u2013d**). Dot plots show every structure segmented the bar indicates the median. Ctrl: \\\\(N_{\\\\text{int}}\\\\) = 14U, \\\\(N_{\\\\text{cells}}\\\\) = 4; EGF: \\\\(N_{\\\\text{tot}}\\\\) = 559, \\\\(N_{\\\\text{cells}}\\\\) = 4; CTA + EGF: \\\\(N_{\\\\text{tot}}\\\\) = 244, \\\\(N_{\\\\text{cells}}\\\\) = 4; pS siRNA + EGF: \\\\(N_{\\\\text{tot}}\\\\) = 304, \\\\(N_{\\\\text{cells}}\\\\) = 7. Number of biologically independent experiments = 2. Scale bars in (**a\u2013e**) are 1 \u03bcm; insets are 200 nm. Ctrl and EGF data were from Fig. 1 and shown for reference. EGF epidermal growth factor receptor, PREM platinum replica electron microscopy.\\n\\n'", "CAPTION FIG5.png": "'\\n\\n**Fig. 5 Differential location of EGFR; Src, and (BS-integrin in clathrin-coated structures.****a** Representative two-calar TIRF images of genome-edited HSC3 expressing EGFR-GFP and transfected with mScarlet-CLCa or HSC3 WT cells co-transfected with mScarlet-CLCa + Src-GFP or DESIGN-GFP before (Ctrl) or after 50 ng/ml EGF stimulation for 15 mm. Scale bar is 10 mm; insets are 7.3 mm x 7.3 mm. **b** Automated correlation analysis between clathrin and EGFR, Src, and (BS-integrin. Dot box plots show median extended from 25th to 75th percentiles, mean (square), and minimum and maximum data paint whiskers with a coefficient value of 1.5. Significance was tested by a two-tailed _t_-test. EGFR, ***_P_ = 5.9 x 10-7. Src ***_P_ = 1.7 x 10-11; (BS-integrin. rnp = 0.358. \\\\(N\\\\) = 4 biologically independent experiments with consistent results. \\\\(N_{\\\\text{EGFR-Ca}} = 23\\\\) cells - 3728 spots, \\\\(N_{\\\\text{ECF-ECF}} = 22\\\\) cells - 2173 spots, \\\\(N_{\\\\text{exc-CH}} = 28\\\\) cells - 1394 spots, \\\\(N_{\\\\text{exc}}\\\\). \\\\(\\\\text{EGF} = 27\\\\) cells - 1407 spots, \\\\(N_{\\\\text{EG-CH}} = 21\\\\) cells - 1037 spots; \\\\(N_{\\\\text{EG-CH}} = 20\\\\) cells - 1011 spots examined over the indicated independent experiments. EGFR epidermal growth factor receptor, TIRF total internal reflection fluorescence, CLCa clathrin light chain a, WT wild type, EGF epidermal growth factor.\\n\\n'", "CAPTION FIG6.png": "'\\n\\n**Fig. 6****BS-integrin phosphorylation controls spatial correlation with clathrin.****a** Diagram of \\\\(\\\\beta\\\\)S-integrin and magnification of the cytoplasmic domain showing different mutants. Numbers indicate the residue positions, and letters identify the amino acid. The truncated line in the diagram indicates deletion of the sequence coding for amino acids 743-799. Other constructs are wild type (WT), carboxyl-truncated (\\\\(\\\\Delta\\\\)C), none-phosphorylatable (3Y-F), phosphomimetic (3Y-E), and PAK-targeted (2S-A). **b** In vitro phosphorylation assay using purified Src or PAK4 and peptides corresponding to the B5-integrin carboxyl domain (742-799) WT and mutants in (**a**). Significance was tested by a one-way ANOVA test: \\\\({}^{*}P\\\\) = 1.51 x 10-4, \\\\({}^{**}p\\\\) = 0.002, \\\\({}^{***}P\\\\) = 1.09 x 10-5, \\\\({}^{**}p\\\\) = 0.020S. \\\\(N\\\\) = 3 biologically independent experiments with consistent results. **c** Representative TIRF images of HSC3 WT cells can transfected with mScarlet-CLCa and B5-integrin-GFP WT or containing the different mutations shown in (**a**), either before (Ctrl) or after 50 ng/mL EGF stimulation for 15 min. Scale bars are 10 min; insets are 2.3 mm x 7.3 mm. **d** Automated two-color correlation analysis of (**a**). Dot box lists show median extended from 25th to 75th percentiles, mean (square), and minimum and maximum data point whiskers with a coefficient value of 1.5. Significance was tested by a two-tailed _t_-test, \\\\({}^{**}p_{\\\\text{E-WT}}\\\\) = 0.0811, \\\\({}^{***}p_{\\\\text{B5-AC}}\\\\) = 4.03 x 10-7, \\\\({}^{***}p_{\\\\text{E-WT}}\\\\) = 8.9 x 10-5, \\\\({}^{***}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 0.9149, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 0.5331. \\\\(N\\\\) = 4 biologically independent experiments with consistent results. \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 193 cells - 1492 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 16 cells - 872 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 16 cells - 872 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 16 cells - 872 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 18 cells - 1099 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 17 cells - 1245 spots, \\\\({}^{**}p_{\\\\text{E-WT},\\\\text{C}}\\\\) = 16 cells - 1122 spots,'", "CAPTION FIG7.png": "'\\n\\n**Fig. 7 Flat clathrin lattices partition sustained signals at the plasma membrane.****a** Representative TIRF images of control (Ctrl) unroofed genome-edited HSC3 cells expressing EGFR-GFP transfected with mScarlet-CLCa and immunelabeled with anti-phospho EGFR (P-EGFR) coupled to Alexa 647, treated with 50 ng/ml EGF alone (EGF) or in the presence of bSintegrin mRNA (05 siRNA + EGF). **b** Automated correlation analysis of (**a**). \\\\({}^{*}\\\\)P = 3.67 x 10-21, \\\\({}^{**}\\\\)P = 4.84 x 10-8, \\\\({}^{***}\\\\)P = 6.31 x 10-9. \\\\(N\\\\) = 4 biologically independent experiments with consistent results. _N_(c)(c)(c)(c)(c)(c) = 19 cells - 1770 spots, _N_(c)(c)(c)(c) = 19 cells - 1240 spots, _N_(c)(c)(c) = 20 cells - 1660 spots, _N_(c)(c)(c) = 19 cells - 1678 spots examined over the indicated independent experiments. **c** Fluorescence intensity measurements of the signal from membrane P-EGFR. \\\\({}^{*}\\\\)P = 4.71 x 10-23, \\\\({}^{**}\\\\)P = 2.6 x 10-5, \\\\({}^{**}\\\\)P = 0.052. _N_(c)(c)(c)(c)(c)(c)(c) = 30 cells, _N_(c)(c)(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells. **d** Fluorescence intensity measurements of the signal from membrane total EGFR-GFP (T-EGFR). \\\\({}^{*}\\\\)P = 1.45 x 10-4, \\\\({}^{**}\\\\)P = 2.46 x 10-4, \\\\({}^{***}\\\\)P = 8.53 x 10-9. _N_(c)(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells. **e** Representative TIRF images of HSC3 WT cells transfected with mScarlet-CLCa and immunelabeled with anti-Grb2 coupled to Alexa 647 before (Ctrl) and treated as in (**a**). **f** Automated correlation analysis of (**e**). \\\\({}^{*}\\\\)P = 3.44 x 10-7, \\\\({}^{**}\\\\)P = 3.54 x 10-5, \\\\({}^{***}\\\\)P = 4.47 x 10-3. \\\\(N\\\\) = 4 biologically independent experiments with consistent results. _N_(c)(c)(c)(c)(c) = 19 cells - 1965 spots, _N_(c)(c)(c)(c)(c) = 20 cells - 1532 spots, _N_(c)(c)(c)(c) = 19 cells - 2165 spots, _N_(c)(c)(c)(c) = 14 cells - 801 spots. **g** Fluorescence intensity measurements of the signal coming from immunelabeled Grb2. \\\\({}^{*}\\\\)P = 2.69 x 10-14, \\\\({}^{**}\\\\)P = 2.67 x 10-7, \\\\({}^{***}\\\\)P = 0.089 _N_(c)(c)(c)(c) = 30 cells, _N_(c)(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells, _N_(c)(c)(c) = 30 cells. Scale bars are 10 \\\\(\\\\mu\\\\)m\\\\(\\\\times\\\\) insets are 7.3 \\\\(\\\\mu\\\\)m\\\\(\\\\times\\\\) 7.3 \\\\(\\\\mu\\\\)m. Dot and box plots show median extended from 25th to 75th percentiles, mean (square) and minimum and maximum data point whiskers with a coefficient value of 1.5. Significance between groups was evaluated by a one-way ANOVA test. Number of independent experiments = 4 (**c**, **d**, **g**). AU fluorescence arbitrary units, EGFR epidermal growth factor receptor, CLCa clathrin light chain a, WT wild type, EGF epidermal growth factor, TIRF total internal reflection fluorescence.\\n\\n'", "CAPTION FIG8.png": "'\\n\\n**Fig. 8****Model of flat clathrin lattices expansion during growth factor response.** **a** Small flat clathrin lattices are in proximity to Src and are enriched with HS-integrin. **b** EGF triggers the dimerization, clustering, and cross-phosphorylation of EGFR at growing FCLs. This in parallel allows the biding of the downstream scaffold Grb2 and locally activates Src, which in turn phosphorylates BS-integrin cytoplasmic domain. The maintenance of the EGFR/Src/BS-integrin axis promotes flat clathrin lattice growth. A key implication of this model is that two different receptor systems are spatially organized at the nanoscale within flat clathrin lattices. EGF epidermal growth factor, EGFR epidermal growth factor receptor, FCLs flat clathrin lattices.\\n\\n'"}

extracted_captions/allcottWelfareEffectsSocial2020.json

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+{"CAPTION FIG1.png": "'\\n\\n**C.\\n\\n'", "CAPTION FIG10.png": "'\\n_Notes:_ This figure presents the moderators of local average treatment effects of Facebook deactivation estimated using equation (4). For each of the six outcomes, we present the five moderators with the largest moderation coefficients \\\\(\\\\hat{\\\\alpha}^{k}\\\\). All outcome variables are normalized so that the Control group ending distribution has a standard deviation of 1, and all moderators are also normalized to have a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions.\\n\\nFigure 10. Heterogeneous Treatment Effects for All Moderators\\n\\n'", "CAPTION FIG11.png": "'_Notes:_ This figure presents the distribution of willingness-to-accept to deactivate Facebook between midline and endline. All responses above $525 are plotted at $525.\\n\\n'", "CAPTION FIG12.png": "'_Notes:_ This figure presents the mean willingness-to-accept \\\\(\\\\langle\\\\)WTA\\\\(\\\\rangle\\\\) to deactivate Facebook in Treatment and Control, for the impact evaluation sample: participants who were willing to accept less than $102 to deactivate Facebook for the four weeks after midline and were offered \\\\(p=$102$\\\\) or \\\\(p=$0\\\\) to do so. The first pair of bars is the mean WTA for deactivation in weeks 1-4, the four weeks after the midline survey. The second pair of bars is mean WTA for deactivation in weeks 5-8, the four weeks after the midline survey, as elicited in the midline survey. The third pair of bars is mean WTA for deactivation in weeks 5-8, as elicited in the midline survey.\\n\\nFigure 12. Average Valuation of Facebook in Treatment and Control.\\n\\n'", "CAPTION FIG2.png": "'_Notes:_ This figure presents local average treatment effects of Facebook deactivation estimated using equation (1). All variables are normalized so that the Control group ending distribution has a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions. _Facebook minutes_ is not included in the substitute time uses index, and _Facebook news_ is not included in the substitute news sources index, so we visually separate these two variables from the other variables in their respective families. We also visually separate online and offline time uses and news sources, although all online and offline substitutes enter their respective indexes.\\n\\n'", "CAPTION FIG3.png": "'_Notes:_ This figure presents local average treatment effects of Facebook deactivation estimated using equation (1). All variables are normalized so that the Control group endline distribution has a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions.\\n\\nFigure 3. Effects on News and Political Outcomes\\n\\n'", "CAPTION FIG4.png": "'_Notes:_ This figure presents kernel density plots of issue opinions for Democrats and Republicans in Treatment and Control at endline. Issue opinions are attitudes about nine current political issues on a scale from \\\\(-5\\\\) to \\\\(+5\\\\), such as \"To what extent do you think that free trade agreements between the US and other countries have been a good thing for a bad thing for the United States.\" See online Appendix B for a list of all nine issue questions. To construct the issue opinions measure, for each issue question \\\\(q\\\\), we normalize responses by the standard deviation in the Control group, determine Democrats\\' and Republicans\\' average responses \\\\(\\\\mu_{q}^{D}\\\\) and \\\\(\\\\mu_{q}^{R}\\\\), researcher so that \\\\(\\\\mu_{q}^{D}+\\\\mu_{q}^{R}=0\\\\), and design so that \\\\(\\\\mu^{R}>0\\\\). Define \\\\(\\\\hat{y}_{\\\\text{eg}}\\\\) as individual \\\\(i\\\\)\\'s normalized, recentered, and re-signed response to question \\\\(q\\\\). Thus \\\\(\\\\hat{y}_{\\\\text{eg}}\\\\) reflects the strength of individual \\\\(i\\\\)\\'s agreement with the average Repablican. Define \\\\(\\\\sigma_{q}\\\\) as the Control group within-person standard deviation of \\\\(\\\\hat{y}_{\\\\text{eg}}\\\\) for question \\\\(q\\\\). This measures how much people\\'s views change between baseline and endline, and allows us to place higher weight on issues about which views are malleable over the deactivation period. The preliminary issue opinion measure is \\\\(Y_{i}=\\\\sum_{q}\\\\hat{y}_{\\\\text{eg}}\\\\sigma_{q}\\\\), and the final issue opinion measure plotted in the figure is \\\\(Y_{i}\\\\) divided by the Control group standard deviation.\\n\\nFigure 4. Issue opinions by Party at Endline\\n\\n'", "CAPTION FIG5.png": "'_Notes:_ This figure presents local average treatment effects of Facebook deactivation estimated using equation (1). All variables are normalized so that the Control group endline distribution has a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions.\\n\\n'", "CAPTION FIG6.png": "'_Notes:_ This figure presents local average treatment effects of Facebook deactivation estimated using equation (1). All variables are normalized so that the Control group endline distribution has a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions.\\n\\n'", "CAPTION FIG7.png": "'_Notes:_ This figure shows the share of the Treatment and Control groups that had their Facebook accounts described, by day of the experiment, for the impact evaluation sample: participants who were willing to accept less than $102 to deactivate Facebook for the four weeks after midline and were offered \\\\(p=$102\\\\) or \\\\(p=$0\\\\) to do so. The vertical gray areas reflect the 24-hour periods after midline and endline during which both Treatment and Control were instructed to deactivate.\\n\\n'", "CAPTION FIG8.png": "''", "CAPTION FIG9-1.png": "'[_Continued_]'", "CAPTION FIG9.png": "'\\nFigure 9. Heterogeneous Treatment Effects (Continued)\\n\\n_Notes:_ This figure presents local average treatment effects of Facebook deactivation estimated using equation \\\\(\\\\langle 1\\\\rangle\\\\), for subgroups defined by the primary moderators in our pre-analysis plan. All variables are normalized so that the Control group ending distribution has a standard deviation of 1. Error bars reflect 95 percent confidence intervals. See Section IC for variable definitions.\\n\\n'", "CAPTION TAB2.png": "'_Notes:_ Column 1 presents average demographics for the impact evaluation sample: participants who were willing to accept less than $102 to deactivate Facebook for the four weeks after midline and were offered \\\\(p~{}=~{}\\\\$102\\\\) or \\\\(p~{}=~{}\\\\$0\\\\) to do so. Column 2 presents our estimate of average demographics of American adults with a Facebook account. The top five numbers in column 2 are inferred from a Few Research Center (2018f) survey of social media use by demographic group. The bottom number in column 2 (the average of 45 minutes of Facebook use per day) is approximated on those basis of sources such as Facebook (2016) and Molla and Wagner (2018). Column 3 presents average demographics of American adults. The top five numbers are from the 2017 American Community Survey (US Census Bureau 2017), and the Repabikan and Democrat shares are from the 2016 American National Election Study (American National Election Studies 2016).\\n\\n'", "CAPTION TAB3.png": "'_Notes:_ Columns 1 and 2 present survey response and treatment compliance rates for the Treatment and Control groups in the impact evaluation sample: participants who were willing to accept less than $102 to deactivate Facebook for the four weeks after midline and were offered \\\\(p~{}=~{}\\\\$102\\\\) or \\\\(p~{}=~{}\\\\$0\\\\) to do so. Column 3 presents \\\\(p\\\\)-values of tests of differences in response rates between the two groups.\\n\\n'", "CAPTION TAB4.png": "'_Notes:_ The post-endline survey included the following question with an open response text box: \"How has the way you use Facebook changed, if at all, since participating in this study?\" For all responses, we stemmed words, filtered out stop words, then constructed all phrases of length \\\\(l\\\\ =\\\\ \\\\left\\\\{1,2,3,4\\\\right\\\\}\\\\) words. For each phrase \\\\(p\\\\) of length \\\\(l\\\\), we calculated the number of occurrences of that phrase in Treatment and Control group responses (\\\\(f_{p\\\\text{GT}}\\\\) and \\\\(f_{p\\\\text{GT}}\\\\)) and the number of occurrences of length-\\\\(l\\\\) phrases that are _not_ phrase \\\\(p\\\\) in Treatment and Control responses (\\\\(f_{-\\\\mu\\\\text{GT}}\\\\) and \\\\(f_{-p\\\\text{GT}}\\\\)). We then constructed Pearson\\'s \\\\(\\\\chi^{2}\\\\)-statistic:\\n\\n\\\\[\\\\chi^{2}\\\\ =\\\\ \\\\frac{\\\\left(f_{p\\\\text{GT}}f_{-p\\\\text{GT}}-f_{p\\\\text{GT}}f_{-p \\\\text{GT}}\\\\right)^{2}}{\\\\left(f_{p\\\\text{GT}}+f_{p\\\\text{GT}}\\\\right)\\\\left(f_{p \\\\text{GT}}+f_{-\\\\mu\\\\text{GT}}\\\\right)\\\\left(f_{p\\\\text{GT}}+f_{-\\\\mu\\\\text{GT}} \\\\right)\\\\left(f_{-p\\\\text{GT}}+f_{-p\\\\text{GT}}\\\\right)}.\\\\]\\n\\nThis table presents the 20 phrases with the highest \\\\(\\\\chi^{2}\\\\) that were most commonly written by the Treatment and Control groups. The % Treatment and % Control columns present the share of people in the respective group whose responses included each phrase.\\n\\n'", "CAPTION TAB5.png": "'_Notes:_ The endline survey asked, \"Do you think the researchers in this study had an agenda?\" Columns 1 and 2 present the share of the Treatment and Control groups who gave each possible response. Column 3 presents \\\\(\\\\rho\\\\)-values of tests of differences in means between the two groups.\\n\\n'", "CAPTION TAB6.png": "'_Notes:_ This table presents estimates of equation \\\\(\\\\langle 5\\\\rangle\\\\). The dependent variable is the change in WTA for post-endline deactivation measured at endline versus midline. Standard errors are in parentheses.\\n\\n'"}

extracted_captions/althuizenSupportingCreativeProblem2014.json

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+{"CAPTION FIG1.png": "'Figure 1: Study 1: Interaction Between Creative Ability and the Use of a CBR System\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Study 2: Interaction Between Creative Ability and Type of Cases in the CBR System\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Study 3: Interaction Between Creative Ability and Number of Cases in the CBR System\\n\\n'", "CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB3.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline  & \\\\\\\\ \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 3: The Effects of the Number of Cases Stored in the CBR System (Study 3).\\n\\n'", "CAPTION TAB4.png": "'\\n\\n**Abstract**\\n\\nWe study the relationship between the two-dimensional and the two-dimensional case of a two-dimensional system of coupled equations. We show that the two-dimensional case is equivalent to the two-dimensional case. We show that the two-dimensional case is equivalent to the two-dimensional case.\\n\\n'", "CAPTION TAB5.png": "'* [16] A.\\n\\n'"}

extracted_captions/andrianantoandro2006mechanism.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'Figure 1: Actin filament Severing by Collins Observed by Evanescent Wave Fluorescence Microscopy Conditions were as follows: 50 mM KCl, 10 mM imidazole, 1 mM MgCl2, 1 mM EGTA, 0.2 mM ATP, 0.25% methyl ceHulose, 100 mM DTT, 15 mM glucose, 20 mg/mL catalase, and 100 mg/mL glucose oxidase at 22\u00b0 C and pH 7.0. (A) Fluorescence micrographs of entire microscopic fields of 25% Oregon Green-labeled actin filaments polymerized for 6 min taken at indicated time points after wash in from time-lapse movies of actin filament severing. First row, actin filaments washed with S. pombe coffin at the optimal severing concentration of 10 nM. Filaments were attached to the glass surface at their barbed ends by S. pombe GST-CdCl21[FH1FH2]p. Second row, actin filaments washed with actophorin at the optimal severing concentration of 100 nM. Filaments were attached to the glass surface by NEM-inactivated muscle myosin II. (B) Detailed mortgage of one actin filament being sewered by 100 nM actophorin over time.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Analysis of Actin Filament Severing by Collins (A) Dependence of severing activity on the concentration of _S. pombe_ cofflin under the conditions of Figure 1. Degree of saturation of the subunits in the filaments was calculated by using Equation. 2. The units of severing activity are severing events per um of actin filament per second. Optimal severing activity occurs at 10 nM _S. pombe_ cofflin with cofflin bound to 0.12% of the actin subunits. No severing occurred without cofflin or with 1 \u03bcM S. pombe cofflin, which saturates 49% of the actin subunits.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Effect of Collins on Actin Filament Elongation and Nucleation (A\u2013C) Elongation was observed by evanescent wave fluorescence microscopy with 50% Oregon Green-labeled ATP-actin. Conditions as in Figure 3. Dependence of the elongation rate on the concentration of unlabeled actin: (A) actin alone, (B) actin with 32 \u03bcM human coffin, and (C) actin with 24 \u03bcM _M_S_._pombe coffin. Filled circles represent barbed-end rates and filled triangles represent pointed-and rates. Slope = k_v_-int_ = k_v_-, and x-int = Cc. (D\u2013F) nucleation of actin filaments by coffins. Evanescent wave fluorescence micrographs of filaments formed by 0.8 \u03bcM 50% Oregon Green-labeled ATP-actin after 400 s in polymerization buffer. Conditions as in Figure 1. (D) Actin alone, (E) actin with 32 \u03bcM human coffin, and (F) actin with 24 \u03bcM _M_S_. pombe coffin. (G\u2013I) Quantitation of barbed ends formed by nucleation by dilution of samples into 2 \u03bcM 25% pyrenyl ATP-actin monomers and measurement of the rate of elongation. Conditions for nucleation and subsequent elongation were as in Figures 2C and 2D. (G) Time course of barbed-end formation by 6 \u03bcM ATP-actin with 10 \u03bcM _M_S_._pombe coffin fit with a hyperbola. Inset, time course of ends formed by 6 \u03bcM ATP-actin with 10 \u03bcM _M_S_. pombe coffin (filled circles), or with 10 \u03bcM _M_S_._pombe coffin and 10 \u03bcM _M_S_._pombe profilin (filled triangles). (H) Dependence of and formation on actin monomer concentration. A range of ATP-actin concentrations was polymerized for 30 s with 10 \u03bcM _M_S_._pombe coffin. (I) Dependence of the rate of end formation by 10 \u03bcM _M_S_._pombe coffin concentration. Samples were polymerized for 60 s before dilution.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: Concentration Dependence of Codlin Activity\\n\\nVery low concentrations of codlin (blue ovals) do not bind actin filaments (green). At an optimal low concentration of codlin, single codlins bind and sever actin filaments. Capping of severed filament barbed ends promotes dissociation of actin monomers (green circles) from pointed ends, leading to filament disassembly. Higher concentrations of codlin bind cooperatively to actin filaments and promote the release of inorganic phosphate (P\\\\({}_{\\\\beta}\\\\)) but do not sever them. Very high concentrations of codlin bind actin monomers and stimulate nucleation, leading to actin filament assembly.\\n\\n'", "CAPTION FIG7.png": "'Figure 3: Depolymerization of Actin Filaments in the Presence of Collins Observed by Evanescent Wave Fluorescence Microscopy Conditions as in Figure 1. ATP-actin filaments were grown for 6 min from 1.5 \u03bcM 50% Oregon Green-labeled actin alone, or with 32 \u03bcM human coffin, or with 24 \u03bcM S, pombe coffin. These samples were washed with buffer alone or with 10 \u03bcM human coffin or with 10 \u03bcM S, pombe coffin, and observed. The data are presented in two ways: (A)\u2013(F), time course of length versus time, where dark gray lines are the global fit rates with dark dotted lines at 95% confidence intervals and light gray lines are the average individual filament rates with light dotted lines at minimum and maximum slopes and dashed lines indicating standard deviations, and (B)\u2013(L), histograms of the distribution of measured length changes during each 9 s interval. (A\u2013C) Barbed ends. (A) Actin filaments alone, (B) actin with 10 \u03bcM human coffin, and (C) actin with 10 \u03bcM S, pombe coffin. (D\u2013F), Pointed ends. (D) Actin filaments alone, (E) actin with 10 \u03bcM human coffin, and (F) actin with 10 \u03bcM S, pombe coffin. (G\u2013L) Barbed ends. (G) Actin filaments alone, (F) actin with 10 \u03bcM human coffin, and (I) actin with 10 \u03bcM S, pombe coffin. (J\u2013L) Pointed ends. (J) Actin filaments alone, (K) actin with 10 \u03bcM human coffin, and (L) actin with 10 \u03bcM S, pombe coffin.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{**Table 1.**} & \\\\multicolumn{1}{c}{**S**over**} \\\\\\\\ \\\\multicolumn{1}{c}{**and**} & \\\\multicolumn{1}{c}{**Optimal**} & \\\\multicolumn{1}{c}{**S**over**} \\\\\\\\ \\\\multicolumn{1}{c}{**and**} & \\\\multicolumn{1}{c}{**Optimal**} & \\\\multicolumn{'", "CAPTION TAB2.png": "'* [19]'", "SUPP CAPTION FIGS1.png": "'\\n\\n**Fig. S1.** X-ray crystal structure of S. pombe cofilin. (A) Stereo ribbon diagram of S. pombe cofilin with residues R78 and K80 highlighted, and sulfate ion bound to N-terminus. Residues 2-123 shown. (B) Model and electron density for residues surrounding the bound sulfate.\\n\\n'", "SUPP CAPTION FIGS2-1.png": "'\\n\\n**Fig. S2.** Inhibition of nucleotide exchange on actin monomer by S. pombe cofllin. Conditions: 10 mM imidazole, 1 mM MgCl\\\\({}_{2}\\\\), 1 mM EGTA, 0.5 mM DTT, 1 mM NaN\\\\({}_{3}\\\\) at 22 degC and pH 7.0. Actin concentrations were'", "SUPP CAPTION FIGS2-2.png": "'0.2 uM. Observed rate constant for etheno-ATP or etheno-ADP dissociation from actin monomer upon addition of 0.5 mM ATP or ADP plus S. pombe cofilin is plotted versus S. pombe cofilin concentration. Black circles, dashed line: ADP-actin. Open circles, dashed line: ATP-actin. Grey triangles, solid line: ADP-actin plus 50 mM KCl. Open triangles, solid line, ATP-actin plus 50 mM KCl.\\n\\n'", "SUPP CAPTION FIGS2.png": "''", "SUPP CAPTION FIGS3.png": "'\\n\\n**Fig. S3.** Time course of fluorescence change following the mixing of 0.2 \\\\(\\\\upmu\\\\)M S. pombe cofilin with 6 \\\\(\\\\upmu\\\\)M pyrene-labeled skeletal muscle ADP-actin filaments. The inset shows the initial rapid decrease in fluorescence on a faster time scale, fit to a single-exponential. Conditions: 10 mM imidazole, 2 mM Tris-HCl pH 8.0, 50 mM KCl, 1 mM MgCl\\\\({}_{2}\\\\), 1 mM EGTA, 0.2 mM ATP, 0.5 mM DTT, 1 mM NaN\\\\({}_{3}\\\\) at 22 \\\\({}^{\\\\circ}\\\\)C and pH 7.0'", "SUPP CAPTION FIGS4-1.png": "'Fig. S4. Raw data of 2 \\\\(\\\\mu\\\\)M pyrene actin elongating from actin nucleated in the presence and absence of human, S. pombe, and R78E K80E S. pombe cofilin mutant. Conditions: 10 mM imidazole, 2 mM Tris-HCl pH 8.0, 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 0.2 mM ATP, 0.5 mM DTT, 1 mM NaN3 at 22 \\\\({}^{\\\\circ}\\\\)C and pH 7.0. The slopes of the fluorescence traces indicate the number of ends formed under each condition: no seeds (heavy black line), 6 mM actin seeds (light black line), 6 mM actin/10 mM S. pombe cofilin seeds (light dotted line), 6 mM actin/10 mM Human cofilin'", "SUPP CAPTION FIGS4-2.png": "'seeds (grey line), 6 uM actin/10 uM R78E K80E S. pomhe cofilin mutant seeds (heavy dotted line).\\n\\n'", "SUPP CAPTION FIGS4.png": "'Figure 44: Raw data of 2 \\\\(\\\\mu\\\\)M prime actin elongating from actin nucleated in the presence and absence of human, S. pombe, and R79E K80E S. pombe for actin mutant seeds (heavy dotted line). 6 mM actin most seeds (light black line), 6 mM actin most seeds (light black line), 6 mM actin/10 mM S. pombe cofflin mutant. Conditions: 10 mM imidazole, 2 mM Tris-HCl pH 8.0, 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 0.2 mM ATP, 0.5 mM DTT, 1 mM NaN, at 22 \u00b0C and pH 7.0. The slopes of the fluorescence traces indicate the number of ends formed under each condition: no seeds (heavy black line), 6 mM actin seeds (light black line), 6 mM actin most seeds (light black line), 6 mM actin/10 mM S. pombe cofflin seeds (light dotted line), 6 mM actin/10 mM Human cofflin\\n\\n'", "SUPP CAPTION FIGS5.png": "'\\n\\n**Fig. S5.** Predicted spatial compartmentalization of ADF/cofilin activities.\\n\\n'", "SUPP CAPTION TABS1.png": "'\\n\\n**Table S1.** Data Collection and Refinement Statistics'"}

extracted_captions/aoki2016rhoa.json

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+{"CAPTION FIG1.png": "'\\nFig. 1: Epss locally accumulations at the initial phase of membrane extraction in the membrane bath. (_A_) (LDD) cells exhibit membrane blocking when cultured in a single region (_k_igth). (Scale bar, 20 \\\\(\\\\mu\\\\)m) (_B_ and C) Membrane blebbing of DLD1 cells transfected with LHeat-RFP and GFP-tagged PLCs-PH. Timing relative to the first image is indicated in white text. Actin cortex reassembly started from multiple sites of the protruded membrane (arrowheads). (Scale bar: \\\\(B\\\\), 5 \\\\(\\\\mu\\\\)m; \\\\(C\\\\), 2 \\\\(\\\\mu\\\\)m). (_D_) Localization of GFP-MRC1 during membrane bleb expansion and retraction. MRC1 accounts/ates at multiple regions of membrane blebs (arrowheads). (Scale bar: 1 \\\\(\\\\mu\\\\)m). (_E_) Localization of GFP-tagged Epss in membrane blebs of DLD1 cells. Epss accumulates in multiple foci at the protruded membrane (arrowheads). (Scale bar: 2 \\\\(\\\\mu\\\\)m). (_F_ and _G_) Extrapogrsk showing actin localization (red) with respect to actin cytoskeleton-related proteins (green) during bleb retraction. Blob extension is shown on the horizontal axis, and time is shown on the vertical axis. Epss-B (_F_, green) localizes to the protruded membrane before actin filaments. MRC1 (_G_, green) is executed after actin filaments. (_H_) Timing of arrival of Epss and MRC1 relative to that of actin filaments (_f_ = 0 s). Data are the mean \\\\(\\\\pm\\\\) SD.\\n\\n'", "CAPTION FIG2.png": "\"\\nFig. 2: The end-tapping and actin-burdling activities of Epsl are required for continuous membrane blebbing. (A) Expression of Epsl is greatly reduced in Epsl-KD DLD1 cells. (B) Epsl-KD DLD1 cells are spherical and do not exhibit membrane blebbing when cultured in a type I collagen matrix. (Scale bar, 10 \u03bcm.) [C] Exogenous expression of GFP-tagged mouse Epsl restores membrane blebbing (arrow) in Epsl-KD DLD1 cells. (Scale bar, 10 \u03bcm.) (D) Schematic drawings of mutant Epsl constructs. The number of amino acid residues of Epsl is shown. (F) Total cell lysates of DLD1 cells expressing each construct separated by SDS9AGE and immunoblotted with an anti-GFP mAb. (F) The percentages of GFP-positive cells showing membrane blebbing relative to the total number of GFP-positive cells in a given field were calculated. In each experiment, the total cell number was 100 (\\\\(n=3\\\\)). Data are the mean \\\\(\\\\pm 5\\\\). \\\\(\\\\pm P<0.05\\\\) (Student's t test). (G) Localization of GFP-tagged mutant Epsl8 in Epsl-KD DLD1 cells. Expression of the GFP-tagged Epsl mutant lacking the proline-rich region (GFP-Epsl8APR) or the GFP-tagged Epsl mutant lacking the SH3 domain (GFP-Epsl8APR34) restores membrane blebbing in Epsl8-KD DLD1 cells (arrow). (Scale bar, 10 \u03bcm.)\"", "CAPTION FIG3.png": "'Figure 3: Activation of azaft occurs at retracting membranes and is required for the rapid retraction of membrane blebs. (_A_) Membrane blebbing in DLD1 cells transfected with GFP-ezrin. GFP-ezrin localizes uniformly at the protruded membrane. (Scale bar, 2 \u03bcm.) (_E_) DLD1 cells were fixed and stained with an anti-phospho-ER antibody (red) and an anti-total ERM antibody (green). Nuclei were stained with DAPI (blue). The asterisk indicates a membrane bleb in which ERM proteins were not activated. (Scale bar, 2 \u03bcm.) (_C_) DLD1 cells were fixed and stained with an anti-phospho-ERM antibody (green) and an anti-Epr8 antibody (red). The arrowheads indicate the colocalization of Epr8 and phosphorylated ERM proteins. (Scale bar, 2 \u03bcm.) (_D_) DLD1 cells were fixed and stained with an anti-phospho-ERM antibody (green) and Alexa 594-phalloidin (red). The boxed area shows the membrane blebs with growing actin filaments. High-magnification image of the boxed area is shown in the right panels. The asterisks indicate a membrane bleb covered with actin cortex. (Scale bar, 10 \u03bcm.) (_E_) Total cell lysates of wild-type DLD1 cells and azaft-KO DLD1 cells separated by SDSPAGE and immunohistolated with an anti-total ERM antibody, an anti-Epr8 antibody, and an anti-tubulin antibody. (_F_) Membrane blebbing of wild-type DLD1 cells and azaft-KO DLD1 cells transfected with Histcard-RFP and GFP-tagged Epr8. (Scale bar, 10 \u03bcm.) (_G_) Tricolor map of membrane blebs in wild-type DLD1 cells and azaft-KO DLD1 cells. Angular coordinates are shown on the horizontal axis, and time is shown on the vertical axis. Red zones represent expansion, blue zones represent retraction, and white zones represent no movement. (_H_) Histogram of bleb expansion and retraction velocities in wild-type DLD1 cells and azaft-KO DLD1 cells. (_I_) The frequencies of membrane blebs in wild-type DLD1 cells and azaft-KO DLD1 cells during 10 min were quantified. **_P_\\\\(<\\\\) 0.01 (Student\u2019s t test). (_J_) The sizes of membrane blebs in wild-type DLD1 cell and in azaft-KO DLD1 cells during 10 min were quantified. **_P_\\\\(<\\\\) 0.01 (Student\u2019s t test).\\n\\n'", "CAPTION FIG4.png": "'\\nFig. 4: The RhoA-ROCK-Rn3 feedback loop determines the actin reassembly sites of retracting membranes. (A) GFP-ROCK-It is recruited to the retracting protruded membrane in DLD1 cells. (Scale bar, 2 \\\\(\\\\mu\\\\)m) (B) GFP-ROCK is recruited to the retracting protruded membrane in azin-KO DLD1 cells (arrowhead). (Scale bar, 2 \\\\(\\\\mu\\\\)m). (C) Membrane blebbing of DLD1 cells transfected with Lifcat-RFP and GFP-tagged AHD. (Scale bar, 2 \\\\(\\\\mu\\\\)m) (D) Membrane blebbing of DLD1 cells transfected with Lifcat-RFP and GFP-tagged AHD. (Scale bar, 2 \\\\(\\\\mu\\\\)m). (D) Membrane blebbing of DLD1 cells transfected with Lifcat-RFP and GFP-tagged Rnds. (Rad accumulation gradually disappears upon the initiation of membrane blebbing retraction (\\\\(t=25\\\\) S. (Scale bar, 2 \\\\(\\\\mu\\\\)m).) (E) Kymographs showing the localization of actin (red) with respect to that of Rnds (green) during bleb retraction. (B) Extension is shown on the horizontal axis, and time is shown on the vertical axis. (F) Kymographs showing the localization of Rnds (red) with respect to that of Exp8 (green) during bleb retraction. (B) Extension is shown on the horizontal axis, and time is shown on the vertical axis. (G) GFP-D1908-Rho-GAP localizes only at expanding blebs that lack the actin cortex. The membrane localization of p1908 Rho-GAP is gradually lost upon the initiation of actin cortex recovery. (Scale bar, 2 \\\\(\\\\mu\\\\)m.)'", "CAPTION FIG5.png": "'\\n\\n## References\\n\\nFig. 5: A model of Rnd3- and RhoA-mediated regulation of actin cytoskeleton during membrane-bleibbing cycle. (_A_) Localization of Ep8 in DLD1 cells expressing GFP-wild type Rnd3 (Upper) and GFP-Rrd3 S240A mutant. (Scale bar, 10 \u03bcm.) (_B_) Tricolor map of membrane blobs in DLD1 cells expressing GFP-wild type Rnd3 or GFP-Rnd3 S240A mutant. Angular coordinates are shown on the horizontal axis, and time is shown on the vertical axis. Red zones represent expansion, blue zones represent retraction, and white zones represent no movement. (_C_) Histogram of bleib expansion and retraction velocities in DLD1 cells expressing wild-type Rnd3 or the Rnd3 S240A mutant. (_D_) The frequencies of membrane bleibs in DLD1 cells expressing GFP-wild type Rnd3 or GFP-Rnd3 S240A mutant during 10 min were quantified. *_P_< 0.01 (Student\u2019s test). (_E_) The sizes of membrane blebs in DLD1 cells expressing GFP-wild type Rnd3 or GFP-Rnd3 S240A mutant during 10 min were quantified. *_P_< 0.05 (Student\u2019s test). (_P_) In the expansion phase of membrane bleibbing, Rnd3 and p1968\u2013Rho-GAP inhibit the activation of RhoA. As the protruded membrane areas become enlarged, the relative concentration of Rnd3 decreases. Sporadic activation of RhoA leads to ROCK phosphorylation of Rnd3 and removal of p1968\u2013Rho-GAP from the membrane. Thus, RhoA activation is amplified and sustained by the positive-feedback loop. ROCK also phosphorylates earin and activated earin recruits, which leads to reassembly of the actin cortex.\\n\\n'"}

extracted_captions/artsParadiseNoveltyLoss2018a.json

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+{"CAPTION TAB1.png": "'\\n\\n## Table 1: Summary Statistics'", "CAPTION TAB2.png": "'\\n\\n**Table 2**.: Inventor-Firm Fixed Effects Models Exploring New Fields'", "CAPTION TAB3.png": "'\\n\\n**Abstract**\\n\\nWe study the relationship between the \\\\(\\\\beta\\\\)-function and the \\\\(\\\\beta\\\\)-function of the \\\\(\\\\beta\\\\)-'", "CAPTION TAB4.png": "'\\n\\n**Table 4. Summary Statistics** MAKA Sample'", "CAPTION TAB5.png": "'\\n\\n**Table 5.** Difference-ir-Diferences Average Rate of Exploring New Fields'", "CAPTION TAB6.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB7.png": "'\\n## References\\n\\n* [1] A. A. K. K. Aarseth, and A. A. K. Aarseth, \"The 2-Darket: A New Approach to the Evolution of the Galaxy,\" _Astrophys. J._ **584**, 103 (2008).\\n\\n[MISSING_PAGE_POST]\\n\\n'"}

extracted_captions/bailExposureOpposingViews2018.json

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+{"CAPTION FIG1.png": "'\\n\\n**Fig. 1.** Operator at reaction depth.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Abstract**\\n\\nThe thesis is based on the work of'", "CAPTION FIG3.png": "\"Figure 3: Effect of following Twitter hosts that retweet messages by elected officials, organizations, and opinion leaders with opposing political ideologies for 1 mo, on a seven-point liberalKonservative scale where larger values indicate more conservative opinions about social policy issues, for experiments with Democrats (\\\\(n\\\\) = 697) and Republicans (\\\\(n\\\\) = 542). Models predict posttreatment liberalconservative scale score and control for pretreatment score on this scale as well as 12 other covariates described in _SI Appendix_. Circles describe unstandardized point estimates, and bars describe 90% and 95% confidence intervals. Respondents Assigned to Treatment\u201d describes the IT effect for Democrats (\\\\(\\\\text{ITT}=-0.02\\\\), \\\\(\\\\text{IT}=-0.76\\\\), \\\\(\\\\text{p}=0.45\\\\), \\\\(n=416\\\\)) and Republicans (\\\\(\\\\text{ITT}=0.12\\\\), \\\\(\\\\text{E}=2.68\\\\), \\\\(\\\\text{p}=0.008\\\\), \\\\(n=316\\\\)). Minimally-Compliant Respondents\u2019 describes the CACE for respondents who followed one of the study's box for Democrats (\\\\(\\\\text{CACE}=-0.04\\\\), \\\\(\\\\text{r}=-0.75\\\\), \\\\(\\\\text{p}=0.45\\\\), \\\\(n\\\\) of compliant respondents = 271) and Republicans (\\\\(\\\\text{CACE}=0.19\\\\), \\\\(\\\\text{r}=2.73\\\\), \\\\(\\\\text{p}<0.007\\\\), \\\\(n\\\\) of compliant respondents = 181). \u201cPartially-Compliant Respondents\u201d describes the CACE for respondents who correctly answered at least one question, but not all questions, about the content of a hot's tweets during weekly surveys throughout the study period for Democrats (\\\\(\\\\text{CACE}=-0.05\\\\), \\\\(\\\\text{r}=-0.75\\\\), \\\\(\\\\text{p}=0.45\\\\), \\\\(n\\\\) of compliant respondents = 211) and Republicans (\\\\(\\\\text{CACE}=0.31\\\\), \\\\(\\\\text{r}=2.73\\\\), \\\\(\\\\text{p}<0.007\\\\), \\\\(n\\\\) of compliant respondents = 211). \u201cFully-Compliant Respondents\u2019 describes the CACE for respondents who answered all questions about the content of the hot's tweets correctly for Democrats (\\\\(\\\\text{CACE}=-0.14\\\\), \\\\(\\\\text{r}=-0.75\\\\), \\\\(\\\\text{p}=0.46\\\\), \\\\(n\\\\) of compliant respondents = 66) and Republicans (\\\\(\\\\text{CACE}=0.60\\\\), \\\\(\\\\text{r}=2.53\\\\), \\\\(\\\\text{p}<0.01\\\\), \\\\(n\\\\) of compliant respondents = 53). Although treated Democrats exhibited slightly more liberal attitudes posttreatment that increase in size with level of compliance, none of these effects were statistically significant. In contrast, treated Republicans exhibited substantially more conservative views posttreatment that increase in size with level of compliance, and these effects are highly significant.\\n\\n\""}

extracted_captions/bakerComplexInstructionalAnalogies2001.json

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+{"CAPTION TAB2.png": "'\\n\\n## 4 The \\\\(\\\\chi\\\\) value of \\\\(2.12\\\\) has a value of \\\\(0.034\\\\).\\n\\n'", "CAPTION TAB4.png": "'\\\\({}^{\\\\rm a}\\\\) Likert items used the following 1 - 5 scale: 1 - strongly disagree, 2 - disagree, 3 - not sure, 4 - agree, 5 - strongly agree.\\n\\n'"}

extracted_captions/banksPolarizedFeedsThreeExperiments2021.json

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+{"CAPTION FIG1.png": "'Figure 1: Assimilation and contrast in the 2016 presidential election, The American National Election Study (2016).\\n\\nNote: Positive slopes describe assimilation, where voters report an ideological location that is shifted in the direction of their own ideological preferences. Negative slopes describe context effects, where respondents perceive the candidate as further away from their own ideological preference. Our estimation from the Cooperative Congressional Election Study, 2016 data, Ansolabehere and Schaffner (2017).\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Tweets of Donald Trump and Hillary Clinton criticizing their opponents. Note. Tweet posted by Hillary Clinton (Tweet ID: 790606692547452932, left) on October 24, 2016, and by Donald J. Trump (Tweet ID: 789594671387447297, right) on October 21, 2016. Dates of the tweets were not included in the experiment.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Perceived polarization and tweet exposure, Clinton and Trump.\\n\\nNote. Perceived polarization describes the difference between the reported placement of Trump and Clinton for each respondent. Figures correspond to Table 1, Models 2 and 4. Point estimates with 95 percent confidence intervals.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Perceived polarization, tweet exposure, and vote choice.\\n\\nNote. Perceived polarization describes the difference between the reported placement of Donald Trump- and Hilary Clinton for each respondent. Point estimates with 95 percent confidence intervals.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: Identification of selected tweets in the observational data of the #TravelBan Network.\\n\\nNote. Selection of tweets was based on Twitter network analyses collected between January 31 and February 2, 2017. The primary connected network included 241,271 users and posted 2,031,518 tweets. The largest community (anti-ban in dark gray) included 137,858 users in the primary connected network, representing 37 percent of the network. The second largest community (pro-ban in light gray) included 41,181 users, representing 17 percent of the network. In the anti-ban community, the account of the NYT was the most reweeted authority. In the pro-ban community, Fox News was the second most reweeted account, after PrisonPlanet. Tweets of Fox News and the NYT circulated in very different areas of Twitter\u2019s social network, with 80.5 percent of Fox News retweets by supporters of the #TravelBan and 92 percent of NYT reweets by opponents of the #TravelBan (see SIF for details). NYT = New York Times; SIF = Supplementary Information File.\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Perceived polarization, time of exposure (attention), and party ID. Note. Exposure to sweet by party ID and by treatment. Point estimates with 95 percent confidence intervals.\\n\\n'", "CAPTION FIG7.png": "'Figure 7: Distance from Democrats and Republicans by party ID and tweet exposure. Note. Exposure to tweet by party ID and by treatment. Point estimates with 95 percent confidence intervals.\\n\\n'", "CAPTION FIG8.png": "'Figure 8: Marginal effect (dy/dx) of time of tweet exposure on perceived ideological polarization, by treatment and party.\\n\\nNote. Results describe the marginal effect (slope) of time of exposure on polarization, conditional on the party of the respondent and the news organization of the tweet.\\n\\n'", "CAPTION FIG9.png": "'Figure 9: Perceived polarization and tweet exposure, Mauricio Macri (president) and Cristina Fernandez de Kirchner (former president).\\n\\nNote. Perceived polarization describes the difference between the reported placement of Mauricio Macri (president) and Cristina Fernandez de Kirchner (former president) for each respondent. Three groups, one exposed to a tweet by Lamata (journalist aligned with Macri), another group exposed to a tweet by Navarro (journalist aligned with Fernandez), and a control group.\\n\\n'", "CAPTION TAB1-1.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB1-2.png": "''", "CAPTION TAB1.png": "''", "CAPTION TAB2-1.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K. (1999) The mathematical theory of the mathematical theory'", "CAPTION TAB2-2.png": "'\\n\\n**Acknowledgement**'", "CAPTION TAB2-3.png": "'* [19]'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{c c c} \\\\hline \\\\hline \\\\multicolumn{1}{c}{\\\\multirow{2}{*}{**Table 2.** Perceived Polarization and Attention, Second Experiment.}} & **Table 2.** (Continued) & **Table 2.** (Continued) & **Table 2.** (Continued) \\\\\\\\  & \\\\(\\\\varphi<0.5^{\\\\circ}\\\\) & \\\\(\\\\varphi<0.1\\\\) & \\\\(\\\\varphi<0.1\\\\) \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 2: Perceived Polarization and Attention, Second Experiment.\\n\\n'"}

extracted_captions/baschieri2018frustrated.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\nFig. 1: Clathrin-coated plaques are mechanosensitive structures. **a** HeLa cells were seeded on collagen-coated glass or polyacrylamide gels of indicated stiffness and fixed 24 h later before being stained for \u03b1-adaptin. Scale bar: 15 \u03bcm. Higher magnifications of boxed regions are shown. **b** Kymographs showing CCS dynamics in genome-edited HeLa cells expressing endogenous GFP-tagged \u03bcM2-adaptin seeded on the indicated collagen-coated substrate and imaged by spinning disk microscopy every 5 s for 5 min. **c** Quantification of the dynamics of CCSs observed as in **b** (\u201c+P < 0.001, as compared to 0.1 kPa condition, one-way analysis of variance\u2014ANOVA = 3). **d** HeLa cells seeded on collagen-coated glass were treated with Bleblithian or Cytokthalasian D as indicated for 30 min before being fixed and stained for \u03b1-adaptin. Scale bar: 10 \u03bcm. Higher magnifications of boxed regions are shown. **e** Quantification of the dynamics of CCSs observed as in **d** (\u201cP < 0.01, \u201cP < 0.05, ANOVA = 3). **f** EM micrographs of unrooted HeLa cells that were cultured on glass and treated for 30 min with blebbistatin before being fixed and processed. Clathrin-coated plaques are highlighted in green. Scale bar: 200 nm. All results are expressed as mean \u00b1 SD'", "CAPTION FIG2.png": "'\\nFig. 2: avlv5 integrin localizes to plaques and is required for their assembly. **a** HeLa cells were seeded on collagen-coated glass and fixed 24 h later before being stained for \u03b1-adaptin and avl/b5-integrin. Scale bar: 10 \u03bcm. Higher magnifications of boxed regions are shown. Arrows point to clathrin-coated plaques arrowheads point to CCPs. **b** Quantification of avl/b5 enrichment at plaques versus CCPs (*P < 0.005, two tailed Student\u2019s t-test. _n = 3_; 100 structures per experiment were counted). **c** Quantification of colocalization (Pearson\u2019s coefficient) between \u03b1/b5 and \u03b1-adaptin in cells cultured on the indicated collagen-coated substrate (*P < 0.005; *P < 0.001, one-way analysis of variance\u2013ANOVA _n = 3_). **d** HeLa cells treated with control (upper panel) or b5-specific (lower panel) siRNA were seeded on collagen-coated glass and fixed 24 h later before being stained for \u03b1-adaptin. Scale bar: 15 \u03bcm. **c** Kymgtaphs showing CCS dynamics in genome-edited HeLa cells treated with the indicated siRNA, seeded on collagen-coated glass, and imaged by spinning disk microscopy every 5 s for 5 min. **f** Quantification of the dynamics of CCSs observed as **in****e** and treated with the indicated siRNA (**_n_ < 0.001, ANOVA _n = 3_). **g** HeLa cells treated with b5-specific siRNAs were transfected with a siRNA-resistant \u03b2 5-GFP encoding construct and then fixed 24 h later before being stained for \u03b1-adaptin. Scale bar: 10 \u03bcm. The star marks a cell that is not transfected by b5-GFP. Higher magnifications of boxed regions are shown. All results are expressed as mean \u00b1 SD'", "CAPTION FIG3.png": "'\\nFig. 3: Clathrin-coated plaques assemble as a consequence of frustrated endocytosis. **a** Genome-edited HeLa cells expressing endogenous mCherry-tagged \\\\(\\\\mu^{2}\\\\)-adaptiv, seeded on collagen-coated glass, were treated with trypsin and imaged by spinning disk microscopy every 5 s. Time after trypsin addition is indicated in seconds. Arrowheads point to dot-like structure emanating from the disassembling plaques. Scale bar: 1 \u03bcm. **b** Kymographs showing plaque disassembly dynamics and concomitant GFP-auxillin bursts in HeLa cell treated and imaged as in **a**. Note that loss of \\\\(\\\\mu^{2}\\\\)-adaptiv-associated fluorescence is correlated with auxillin flashes. **c** Quantification of the number of auxillin flashes per plaque and per minute in HeLa cells before and after incubation with trypsin. Results are expressed as mean \\\\(\\\\pm\\\\) SD (\\\\(\\\\text{P}\\\\)\\\\(\\\\text{P}\\\\)\\\\(\\\\text{<}\\\\)\\\\(\\\\text{0.001}\\\\), Mann-Whitney rank sum test. **d** Total of 90 structures from three independent experiments was quantified). **d** Genome-edited HeLa cells expressing endogenous mCherry-tagged \\\\(\\\\mu^{2}\\\\)-adaptiv, seeded on collagen-coated glass, were treated with. Clingentide and imaged by spinning disk microscopy every 5 s. Time after Clingentide addition is indicated in seconds. Arrowheads point to dot-like structure emanating from the disassembling plaques. Scale bar: 1 \u03bcm. **e** Genome-edited HeLa cells treated with \\\\(\\\\text{P}\\\\)5-specific siRNA and transfected with a construct encoding mCherry-tagged TIR were seeded on anti-mCherry antibodies-coated glass and imaged 24 h later by spinning disk microscopy every 5 s. Scale bar: 10 \u03bcm. **f** Kymograph showing CCS dynamics in the region corresponding to the boxed area in **e**. Note that the cell on the left is not transfected by the TIR-mCherry construct and only display dynamic CCSs. **g** Quantification of the dynamics of CCSs observed as in **e** in genome-edited HeLa cells expressing the TIR-mCherry construct and treated as indicated (\\\\(\\\\text{P}\\\\)\\\\(\\\\text{P}\\\\)\\\\(\\\\text{<}\\\\)\\\\(\\\\text{0.001}\\\\), one-way analysis of variance--ANOVA. \\\\(n\\\\)\\\\(\\\\text{=}\\\\)\\\\(\\\\text{3}\\\\)). Results are expressed as mean \\\\(\\\\pm\\\\) SD'", "CAPTION FIG4.png": "'\\nFig. 4: Clathrin-coated plaques regulate stiffness-dependent Erk signaling. **a** Western-bit analysis of phospho-Erk (P-Erk) levels in HeLa cells growing on collagen-coated glass and treated with control or \\\\(\\\\beta\\\\)S-specific siRNAs as indicated (representative image of four independent experiments). Total-Erk was used as a leading control. **b** Densitometry analysis of bands obtained in western-blots as in **a** Results are expressed as mean \\\\(\\\\pm 5\\\\)D from four independent experiments (\u201cP < 0.05, one-way analysis of variance\u2014ANOVA). **c** Western-bit analysis of phospho-Erk (P-Erk) levels in HeLa cells growing on collagen-coated, 0.1 kPa polyacrylamide gels and treated with control or integrin \\\\(\\\\beta\\\\)S-specific siRNAs, as indicated. Total-Erk was used as a loading control (representative image of three independent experiments) **d** Densitometry analysis of bands obtained in western-blots as in **e** Results are expressed as mean \\\\(\\\\pm 5\\\\)D from three independent experiments. **e** GP-Erk-expressing HeLa cells treated or not with a \\\\(\\\\beta\\\\)S-specific siRNA and transfected or not with TRIzolCherry, as indicated, were seeded on anti-mCherry antibodies-coated glass and imaged 24 h later. Scale bar: 10 \u03bcm. A color-coded scale for low and high signal intensity is shown. **f** Quantification of GP-Erk nuclear enrichment index in cells as in **e** and cultured on control antibody- or anti-mCherry antibody-coated glass, as indicated, and treated or not with indicated siRNAs. Results are expressed as mean \\\\(\\\\pm 5\\\\)D (\u201cP < 0.01, \u201cP < 0.001, ANOVA, ControlAb-siCtr: 144 cells from \\\\(n=5\\\\) independent experiments; mCherryAb-siCtr: 19 cells from \\\\(n=5\\\\) independent experiments; ControlAb-siCtr: 146 cells from \\\\(n=5\\\\) independent experiments; mCherryAb-siCtr: 120 cells from \\\\(n=5\\\\) independent experiments; ControlAb-siCtr: 1- siRNA-2: 69 cells from \\\\(n=3\\\\) independent experiments; mCherryAb-siCtr: 1- siRNA-2: 68 cells from \\\\(n=3\\\\) independent experiments; ControlAb-siCtr: 1- siRNA-2: 67 cells from \\\\(n=3\\\\) independent experiments)'", "CAPTION FIG5.png": "'\\nFig. 5: Clathrin-coated plaques: totally regulate receptor-dependent Ek: signaling. **a** HeLa cells seeded on collagen-coated glass were starved for 4 h and then treated or not with 10 ng/ml EGF for 5 min alone or added after 30 min preincubation with 10 \u03bcM Gefitinib. Cells were then fixed and stained for a-adaptin and phosphotyrosine. The arrowhead points to one CCP and the star marks a plaque. Scale bar: 2 \u03bcM. **b** Quantification of phosphotyrosine accumulation at plaques or CCPs in the indicated conditions. Results are expressed as mean +- SOD (*_P_ < 0.05, *_P_ < 0.001, one-way analysis of variance\u2013ANOVA. \\\\(n\\\\) = 3. Number of structures analyzed per condition: Starved 160 plaques; EGF: 452 plaques, EGF + Gefitinib: 301 plaques, CCPs/EGF: 200 pits). **c** Western-blot analysis of phospho-Ek (P-Ek) levels in starved HeLa cells treated with control or b5-specific siRNA as indicated, and stimulated for the indicated time with 10 ng/ml EGF. Total-Ek was used as a leading control (representative image of three independent experiments. **d** Derstimometry analysis of bands obtained in western-blots as in **e**. Results are expressed as mean +- SOD (*_P_ < 0.05, ANOVA. \\\\(n\\\\) = 3). **e** HeLa cells treated with b5-specific siRNA were transfected with plasmids encoding for TIR-mCherry and EGFR-GFP and seeded on anti-mCherry antibodies-coated glass. Cells were serum-starved for 4 h and then treated with 10 ng/ml EGF for 470 s. Scale bar: 0.5 \u03bcM. Arrowheads point to plaques positive for EGFR-GFP. **f** HeLa cells treated with b5-specific siRNA were transfected with plasmids encoding for TIR-mCherry and HGFR-GFP and seeded on anti-mCherry antibodies-coated glass. Cells were serum-starved for 4 h and then treated with 50 ng/ml HGF for 570 s. Scale bar: 0.5 \u03bcM. Arrowheads point to plaques positive for HGFR-GFP. **g** HeLa cells treated with b5-specific siRNA were transfected with plasmids encoding for TIR-mCherry and seeded on anti-mCherry antibodies-coated glass. Cells were serum-starved for 4 h and then treated with 10 ng/ml EGF for 5 min prior to fixation and staining for phosphotyrosine. Scale bar: 1.5 \u03bcM. Arrowheads point to plaques positive for P-Tyr'", "CAPTION FIG6.png": "'\\nFig. 6: Signaling at plaques is contractility-independent and regulate cell proliferation. **a** HeLa cells on collagen-coated glass were treated for 1 h with 10 \u03bcM Blebbistatin or 10 \u03bcM Cytochalasin D prior to be fixed and stained for \u03b1-adaptin (red) and phosphotyrosines (P-Tyr, green). Scale bar: 3 \u03bcM. **b**, Quantification of phosphotyrosines accumulation at plaques in cells treated as in a, as indicated (*P < 0.05, one-way analysis of variance\u2014ANOVA). Control: 402 plaques from \\\\(n=3\\\\) independent experiments; Blebbistatin: 303 plaques from \\\\(n=3\\\\) independent experiments; Cytochalasin: 302 plaques from \\\\(n=3\\\\) independent experiments. **c** Western-blot analysis of phospho-Frk (P-Frk) levels in HeLa cells cultured on collagen- or vitronectin-coated glass or 0.1 \u03bcM kPa polyvinylamide gels, as indicated. Total-Erk was used as a loading control (representing image of three independent experiments). **d** Densimetry analysis of bands obtained in western-blots as in **e** (*P < 0.05, ANOVA. \\\\(n=3\\\\)). **e** Western-blot analysis of phospho-Frk (P-Erk) levels in HeLa cells growing on collagen-coated glass and treated with control or integrin b5-specific siRNAs and incubated or not with 10 \u03bcM Blebbistatin for 1 h, as indicated. Total-Erk was used as a loading control (representative image of three independent experiments). **f** Densitometry analysis of bands obtained in western-blots as in **e** (*P < 0.05, *P < 0.01, ANOVA. \\\\(n=5\\\\)). **g** Equal numbers of HeLa cells were plated on non-coated glass (open squares), or on collagen-coated (purple open circles) or vitronectin-coated glass (black open circles), as indicated. Cells were harvested and counted 24 and 48 h after plating (***P < 0.001, ANOVA. \\\\(n=3\\\\)). **h** HeLa cells treated with control (circles), b5-specific (triangles and crosses), or any-specific siRNAs (diamonds and hexagons) for 48 h were seeded on vitronectin-coated glass in equal numbers. 24 and 48 h later, cells were harvested and counted (*P < 0.05, ANOVA. \\\\(n=3\\\\)). **i** HeLa cells treated with b5-specific siRNAs were transfected with a plasmid encoding TIR-mCherry and seeded in equal numbers on glass coated with either anti-mCherry (black circles) or control antibodies (open circles). 24 and 48 h later, cells were harvested and counted (*P < 0.05, ANOVA. \\\\(n=3\\\\)). All results are expressed as mean \u00b1 SD'"}

extracted_captions/blakeCollaborativeInformationSynthesis2006a.json

@@ -0,0 +1 @@
+{"CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'"}

extracted_captions/cattaniDeconstructingOutsiderPuzzle2017.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'Source: Royal Museum Greenwich (http://prints.rng.co.uk/art/)\\n\\n515403/harrisons-marine-timkeeper-hd4.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: (Color online) Harrison\u2019s Transition Across \u201cLayers of Legitimacy\u201d Over Time.\\n\\n'", "CAPTION FIG3.png": "'Note. Solid lines indicate the boundaries of the action and attention spaces _before_ the jolt, while dotted lines indicate the expansion of these boundaries _after_ the jolt.\\n\\n'", "CAPTION FIG4.png": "'* [19]'", "CAPTION TAB1.png": "'Source. Adapted from Andrecus (1996a, p. 234).\\n\\n'"}

extracted_captions/champion2006role.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n## 2 The \\\\(\\\\beta\\\\)-function\\n\\nThe \\\\(\\\\beta\\\\)-function is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (1)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (2)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (3)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (4)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (5)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (6)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (7)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (8)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (9)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (10)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (11)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (12)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (13)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (14)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (15)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (16)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (17)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (18)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (19)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\(\\\\beta\\\\). The function \\\\(\\\\beta(x)\\\\) is defined as\\n\\n\\\\[\\\\beta(x)=\\\\frac{1}{\\\\beta(x)}\\\\exp\\\\left(-\\\\frac{1}{\\\\beta(x)}\\\\right)\\\\] (20)\\n\\nwhere \\\\(\\\\beta(x)\\\\) is the \\\\(\\\\beta\\\\)-function of the function \\\\('", "CAPTION FIG2.png": "'Figure 2: Time-lapse video microscopy clips spanning 39 min of macrophages interacting with identical nonopinionized ED particles (major axis 14 \\\\(\\\\mu\\\\)m, minor axis 3 \\\\(\\\\mu\\\\)m) from two different orientations. (A) Cell attaches along the major axis of an ED and internalizes it completely in 3 min. (B) Cell attaches to the flat side of an identical ED and spreads but does not internalize the particle. Continued observation indicated that this particle was not internalized for \\\\(>\\\\)10 min. (Scale bars: 10 \\\\(\\\\mu\\\\)m.) See Movies 1 and 2.) At least three cells were observed for each orientation of each particle type and size. Similar results were observed in all repetitions.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Scanning electron micrographs and actin staining confirm time-lapse video microscopy observations. Micrographs (\\\\(A\\\\)\u2013C) of cells and particles were colored brown and purple, respectively. (\\\\(A\\\\)) The cell body can be seen at the end of an organized ED, and the membrane has progressed down the length of the particle. (Scale bar: 10 \\\\(\\\\mu\\\\)m.) (\\\\(B\\\\)) A call has attached to the flat side of an organized ED and has spread on the particle. (Scale bar: 5 \\\\(\\\\mu\\\\)m.) (\\\\(C\\\\)) An organized spherical particle has attached to the top of a cell, and the membrane has progressed over approximately half the particle. (Scale bar: 5 \\\\(\\\\mu\\\\)m.) (\\\\(D\\\\)\u2013\\\\(F\\\\)) Overlays of bright-field and fluorescent images after fixing the calls and staining for polymerized actin with rhodamine phalloidin. (\\\\(D\\\\)) Actin ring forms as remodeling and depolymerization enable membrane to progress over an organized ED by new actin polymerization at the leading edge of the membrane. (\\\\(E\\\\)) Actin polymerization in the call at site of attachment to flat side of an organized ED, but no actin cup or ring is visible. (\\\\(F\\\\)) Actin cup surrounds the end of an organized sphere as internalization begins after attachment. (Scale bars in \\\\(D\\\\)\u2013\\\\(F\\\\): 10 \\\\(\\\\mu\\\\)m.) At least five calls were observed for each orientation of each particle. Similar results were observed in all repetitions.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Definition of \\\\(\\\\Omega\\\\) and its relationship with membrane velocity. (\\\\(A\\\\)) A schematic diagram illustrating how membrane progresses tangentially around an ED. \\\\(\\\\overline{\\\\Omega}\\\\) represents the average of tangential angles from \\\\(\\\\theta=0\\\\,\\\\theta=\\\\pi/2\\\\,\\\\Pi\\\\) is the angle between \\\\(T\\\\) and membrane normal at the site of attachment, \\\\(\\\\Omega\\\\). (\\\\(B\\\\)) Membrane velocity (distance traveled by the membrane divided by time to internalize, \\\\(n\\\\simeq 3\\\\); error bars represent SD) decreases with increasing \\\\(\\\\Omega\\\\) for a variety of shapes and sizes of particles. Nonsponsized particles are indicated by filled circles, and IgG-opsonized particles are indicated by open squares. Each data point represents a different shape, size, or aspect ratio particle. The internalization velocity is positive for \\\\(\\\\Pi\\\\simeq 45^{\\\\circ}\\\\) (\\\\(P\\\\leq 0.001\\\\)). Above a critical value of \\\\(\\\\Pi\\\\), \\\\(\\\\sim\\\\)45\\\\({}^{\\\\circ}\\\\), the internalization velocity is zero (\\\\(P\\\\leq 0.001\\\\)) and there is only membrane spreading after particle attachments, not internalization. The arrows above the plot indicate the point of attachment for each shape that corresponds to the value of \\\\(\\\\Omega\\\\) on the \\\\(x\\\\) axis. Error in \\\\(\\\\Omega\\\\) is due to the difference in the actual point of contact in time-lapse microscopy from that used to calculate \\\\(\\\\Pi\\\\). Only points of contact within 10\\\\({}^{\\\\circ}\\\\) of that used to calculate \\\\(\\\\Omega\\\\) were selected. All data points at the critical point, \\\\(\\\\Pi=45^{\\\\circ}\\\\), except UFOs, do not have error associated with \\\\(\\\\Pi\\\\) because of their symmetry.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: Phagocytosis phase diagram with \\\\(\\\\Omega\\\\) and dimensionless particle volume \\\\(V^{*}\\\\) (particle volume divided by 7.5 \\\\(\\\\mu\\\\)m radius spherical cell volume) as governing parameters (\\\\(\\\\Omega=5\\\\) for each point). Initialization of internalization is judged by the presence of an actin cup or ring as described in the text. There are three regions. Cells attaching to particles at areas of high \\\\(\\\\Omega\\\\), \\\\(>\\\\)45\\\\({}^{\\\\circ}\\\\), spread but do not initiate internalization (region \\\\(\\\\Omega\\\\)). Cells attaching to particles at areas of low \\\\(\\\\Omega\\\\), \\\\(<\\\\)45\\\\({}^{\\\\circ}\\\\), initiate internalization (regions \\\\(A\\\\) and \\\\(B\\\\)). If \\\\(V^{*}\\\\) is \\\\(\\\\leq\\\\)1, internalization is completed (region \\\\(A\\\\)). If \\\\(V^{*}\\\\) > 1, internalization is not completed because of the size of the particle (region \\\\(B\\\\)). The arrows above the plot indicate the point of attachment for each shape that corresponds to the value of \\\\(\\\\Omega\\\\) on the \\\\(x\\\\) axis. Each case was classified as phagocytosis or no phagocytosis if \\\\(>\\\\)95% of observations were consistent. Each data point represents a different shape, size, or aspect ratio particle.\\n\\n'"}

extracted_captions/chanImpactAnalogiesCreative2015.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K. _et al._, \"The \\\\(\\\\beta\\\\)-decay of the \\\\(\\\\gamma\\\\)-ray emission from the \\\\(\\\\gamma'", "CAPTION FIG2.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION FIG3.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K. (1999) The'", "CAPTION TAB1.png": "'\\n\\n## Appendix A Proof of Theorem 1\\n\\n### Proof of Theorem 1\\n\\nProof of Theorem 1\\n'", "CAPTION TAB10.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB11.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} \\\\\\\\ \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}\\n\\n'", "CAPTION TAB12.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{Odds ratios by lag type for logistic regressions of new concept on fair analogy} \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 12: Olds ratios by lag type for logistic regressions of new concept on fair analogy'", "CAPTION TAB13.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB14.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} &'", "CAPTION TAB2.png": "'\\n\\n## Chapter 6 Conclusions\\n\\nIn this thesis we have presented a new method for the calculation of the \\\\(\\\\Delta\\\\)-meson coupling constant in the \\\\(\\\\Delta\\\\)-meson coupling constant. We have shown that the \\\\(\\\\Delta\\\\)-meson coupling constant is a function of the form factors of the'", "CAPTION TAB3.png": "'\\n\\n## Chapter 3 Example of problem identification analogy\\n'", "CAPTION TAB4.png": "'\\n\\n## Chapter 4 Example of concept generation and history'", "CAPTION TAB5.png": "'\\n\\n## Chapter 5 Example of explain'", "CAPTION TAB6.png": "'\\n\\n## Table 6 Example of function-finding analogy'", "CAPTION TAB7.png": "'Table 7: Example of concept for \"keep the point head level\"\\n\\n'", "CAPTION TAB8.png": "'\\n\\n## Table 5 Example of current pair tuning'", "CAPTION TAB9.png": "'\\n\\n## Table 9\\n\\nSubproblems by number of concepts'"}

extracted_captions/chen2006roles.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n**Fig. 1 Knock-down of cortactin in MDA-MB-231 cells attenuates transferrin endocytosis**\\n\\n(A) Cortactin protein in siRNA treated cells was not detected by immunoblot assay. (B) Only about 50% of cells subjected to cortactin siRNA treatment. had normal transferrin (Tfri) uptake. (C) Tfri fluorescent intensity in cytoplasm in cortactin siRNA treated-cells was apparently reduced (lower panel, arrow head) in comparison to neighboring cells with relatively high cortactin levels (lower panel, arrow), or to mock-treated cells (upper panel). Magnification, 600\\\\(\\\\times\\\\).\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Fig. 2** **Introduction of coractin immunoreagents into live cells suppresses transferrin uptake**\\n\\nNIHGT3 cells were subjected to coractin immunoreagent infinduction mediated by the BioPORTER-resistance system. Quantitation of endocytic biotinylated-labeled transferrin (Tf) by ELISA-based transferrin uptake assay was performed 5 h after the start of the tratment. BioPORTER only (column 1)\\\\({}_{r}\\\\) rahit IgG (column 4) and labeled mouse IgG (column 5) with kit were used as control. Endocyteis is cells with either coctactin antibody (column 2) or 4F11 (column 3) was repaired.\\n\\n'", "CAPTION FIG3.png": "'\\n\\n**Fig. 3**: **Perturbation of actin dynamics by cytochalasin D affects the association of cortactin with dynamin at endocytosis sites** NIH/3T3 cells were treated with cytochalasin D in serum-free medium. The association of cortactin (red) with dynamin (green) was obvious in control cells without cytochalasin D treatment (A), and became invisible after cytochalasin D exposure (B), then was restored after the drug was washed out (C). Compared with the control (D), transferrin (green) endocytosis was reduced by cytochalasin D treatment for 1 h (E) and restored within 1 h after the drug was washed out (F). Magnification, 600x.\\n\\n'", "CAPTION FIG4.png": "'NH(3T 3 cells were seeded on fibronectin-coated coverslips the day before DNA transfection. Contraction was performed using Lipofectamine reagent. Red fluorescent protein (RFP)-contactin (A), dynamic-green fluorescent protein (GFP) (B) and AP-2 (C) co-distributed in cytoplasm and formed granular structure (D). In cells cotransfected with RFP-tagged wild-type outardin (E) and proline rich domain (PRD) depleted dynamin (F), the association of contraction with dynamin and AP-2 (G) was abolished (H). This phenomenon also happened in cells cotransfected with SH3 domain-deleted outardin and wild-type dynamin. Unlike wild-type outardin, RFP-ContASH3 (I) is not associated with dynamin (J) and AP-2 (K) any more, while the latter two still co-distributed in cytoplasm (L). In contactin SH3 domain only expressing cells, RFP-tagged outardin SH3 (M), GFP-tagged wild-type dynamin (N) and AP-2 (Q) were co-distributed as puncta-like structure in cytoplasm (P). When cells were cotransfected with coordinate SH3 and PRD-depleted dynamin, contactin SH3 domain (Q) lost its association with PRD-depleted dynamin (R) and AP-2 (S), while PRD-depleted dynamin (P-2 co-distribution was still present (T). Cells expressing RFP (U) and wild-type dynamin (V) were used as the control, no colocalization was found (X), and the colocalization between dynamin and AP-2 was not affected by GFP expression (W, X). Bars=10 \\\\(\\\\mu\\\\)m.\\n\\nFig. 4: In vivo recruitment of cortactin to endocytosis sites by dynamin'", "CAPTION FIG5.png": "'(A) Full-down assay of the interaction of GST-proline rich domain of dynamic and cortactin. (B) Purified contraction was mixed with different amounts of immobilized GST-tagged dynamic proline rich domain (Dyn PRD) protein. After incubation, samples were centrifuged (800 g) and the supernatants were collected for immunoblot assay to detect the amount of remaining cortactin with contractile antibody dF11. Amount of cortactin was quantified by digital scanning and normalized to the percentage of depletion. The resulting data were used to fit a rectangular hyperbola, yielding apparent _K_x values of 0.964 \u03bcM. (C) Fluorescent carboxylated polystyrene beads were coated with GST-Dyn-PRD by including beads in protein solution (5 mg/ml). Branched actin filaments were recruited to Dyn-PRD coated beads (a, b and c), but not to non-contact beads (d). Cort, cortactin. Magnification, 600%.\\n\\nFig. 5: Cortactin-mediated actin assembly is recruited to dynamin-coated beads in vitro (A) Full-down assay of the interaction of GST-proline rich domain of dynamic and cortactin. (B) Purified contraction was mixed with different amounts of immobilized GST-tagged dynamic proline rich domain (Dyn PRD) protein. After incubation, samples were centrifuged (800 g) and the supernatants were collected for immunoblot assay to detect the amount of remaining cortactin with contractile antibody dF11. Amount of cortactin was quantified by digital scanning and normalized to the percentage of depletion. The resulting data were used to fit a rectangular hyperbola, yielding apparent _K_x values of 0.964 \u03bcM. (C) Fluorescent carboxylated polystyrene beads were coated with GST-Dyn-PRD by including beads in protein solution (5 mg/ml). Branched actin filaments were recruited to Dyn-PRD coated beads (a, b and c), but not to non-contact beads (d). Cort, cortactin. Magnification, 600%.\\n\\n'", "CAPTION FIG6.png": "'\\n\\n**Fig. 6** **C ortactin functions in the late stage of clathrin coated vesicle (CCV) formation**\\n\\n(A) Western blot analysis of mtDNA cytosol before and after treatment with contractile antibody-coupled beads. Equivalent volumes of supernatants (lane 1 and lane 4) or beads after incubation (lane 5) and before incubation (lane 6), 1/2 loading volume (lane 2) and 1/4 loading volume of supernatants (lane 3) were probed with anti-contraction antibody 001. More than 95% cortactin was depleted (lane 4). (B) Permeabilized 3T3-L1 cells were incubated with mock-depleted cytosol (mock, column 1), cortactin, only (Cort, column 2), or cortactin-depleted cytosol (Cort D, column 3), or cortactin-depleted cytosol supplemented with recombinant cortactin SH3 domain (Cort D+Cort-SH3, column 4), N-terminal-depleted cortactin (Cort D+Cort-NTD, column 5) or wild-type contraction (Cort D+Cort, column 6). Endocytosis was measured by MetaNa resistance in specially detect internalization of B-SS-transferrin (Tfru) into sealed vesicles.\\n\\n'"}

extracted_captions/choInfluencingMyselfSelfReinforcement2018.json

@@ -0,0 +1 @@
+{"CAPTION FIG1.png": "'\\n\\n**Abstract**\\n\\nThe thesis deals with the study of the role of the \"weak\" and \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \"strong\" \" \"strong\" \"strong\"'", "CAPTION FIG2.png": "'Figure 2: Unconditional model: Longitudinality of candidate preference. Note. \\\\(\\\\chi^{\\\\perp}_{\\\\zeta}=0.42\\\\); df = 1; normed fit index (NFI) = .9%; Tucker\u2013Lewis index (TLU) = 1.00; comparative fit index (CFI) = 1.00; root mean square error of approximation (RMSEA) = .00.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Conditional model: Political expression and candidate preference. Note. Enries are unstandardized coefficients with standard errors in parentheses. Estimated coefficients for control variables are not presented in this figure for parsimony, but full results are available upon request. \\\\(\\\\chi^{2}\\\\) = 18.96; df = 13; normed fit index (NFI) = .98; Tucker-Lewis index (TLI) = .95; comparative fit index (CFI) = .99; root mean square error of approximation (RMSEA) = .03.\\n\\n'", "CAPTION TAB1.png": "'* [10] A.\\n\\n'"}

extracted_captions/cmmidcovid19workinggroupAgedependentEffectsTransmission2020.json

@@ -0,0 +1 @@
+{"CAPTION FIG1\"(NOISY)\".png": "'\\n\\n**Fig. 11 Fit of different model variants to data from Wuhan City, China.**,**,**. Model diagram and duration of disease states in days, where \\\\(d\\\\) parameters represent the duration of time in each disease state (see Methods), \\\\(y\\\\), is the fraction of infections that manifest as clinical cases in age group \\\\(\\\\downarrow\\\\lambda\\\\) is the force of infection in age group \\\\(\\\\downarrow P\\\\), is the incubation period and \\\\(\\\\rho_{i}\\\\) is the serial interval (see Methods). **b**, Susceptibility by age for the three models, with mean (lines), 50% (darker shading) and 95% (lighter shading) credible intervals shown. Age-specific values were estimated for model 1 (orange). Susceptibility is defined as the probability of infection on contact with an infectious person. **c**, Clinical fraction (\\\\(y\\\\)) by age for the three models. Age-specific values were estimated for model 2 (blue) and fixed at 0.5 for models 1 and 3. **d**, Fitted contact multipliers for holiday (\\\\(q_{0}\\\\)) and restricted periods (\\\\(q_{1}\\\\)) for each model showed an increase in non-school contacts beginning on 12 January (start of the Lunar New Year) and a decrease in contacts following restrictions on 23 January. **e**, Estimated \\\\(R_{0}\\\\) values for each model. The red barplot shows the inferred window of spillover of infection. **f**, Incident reported cases (black) and modeled incidence of reported clinical cases for the three models fitted to cases reported by China Centers for Disease Control (CCDCY) with onset on or before 1 February 2020. Lines mark the mean and the shaded window is the 95% highest density interval (HDI). **g**, Age distribution of cases by onset date as fitted to the age distributions reported by Li et al.2(first three panels) and CCDC (fourth panel). Data are shown in open bars and model predictions in filled bars, where the dot marks the mean posterior estimate. **h**, Implied distribution of subclinical cases by age for each model. Credible intervals on modeled values show the 95% HDIs; credible intervals on data for **g** and **h** show 95% HDIs for the proportion of cases in each age group.\\n\\n'", "CAPTION FIG1.png": "'\\n\\n**Fig. 11 Fit of different model variants to data from Wuhan City, China.**,**,**. Model diagram and duration of disease states in days, where \\\\(d\\\\) parameters represent the duration of time in each disease state (see Methods), \\\\(y\\\\), is the fraction of infections that manifest as clinical cases in age group \\\\(\\\\downarrow\\\\lambda\\\\) is the force of infection in age group \\\\(\\\\downarrow P\\\\), is the incubation period and \\\\(\\\\rho_{i}\\\\) is the serial interval (see Methods). **b**, Susceptibility by age for the three models, with mean (lines), 50% (darker shading) and 95% (lighter shading) credible intervals shown. Age-specific values were estimated for model 1 (orange). Susceptibility is defined as the probability of infection on contact with an infectious person. **c**, Clinical fraction (\\\\(y\\\\)) by age for the three models. Age-specific values were estimated for model 2 (blue) and fixed at 0.5 for models 1 and 3. **d**, Fitted contact multipliers for holiday (\\\\(q_{0}\\\\)) and restricted periods (\\\\(q_{1}\\\\)) for each model showed an increase in non-school contacts beginning on 12 January (start of the Lunar New Year) and a decrease in contacts following restrictions on 23 January. **e**, Estimated \\\\(R_{0}\\\\) values for each model. The red barplot shows the inferred window of spillover of infection. **f**, Incident reported cases (black) and modeled incidence of reported clinical cases for the three models fitted to cases reported by China Centers for Disease Control (CCDCY) with onset on or before 1 February 2020. Lines mark the mean and the shaded window is the 95% highest density interval (HDI). **g**, Age distribution of cases by onset date as fitted to the age distributions reported by Li et al.2(first three panels) and CCDC (fourth panel). Data are shown in open bars and model predictions in filled bars, where the dot marks the mean posterior estimate. **h**, Implied distribution of subclinical cases by age for each model. Credible intervals on modeled values show the 95% HDIs; credible intervals on data for **g** and **h** show 95% HDIs for the proportion of cases in each age group.\\n\\n'", "CAPTION FIG10.png": "'\\n\\n**Extended Data Fig. 10 | Contact matrices used in transmission model.** Contact matrices used for Figs. 1-3 of the main text. We have not shown matrices for all 12 regions of Italy modeled, nor for all 13 provinces of China modeled, as these show similar patterns to the matrices for Milan and for Wuhan, Beijing and Shanghai, respectively.\\n\\n'", "CAPTION FIG2 \"(NOISY)\".png": "'\\nFigure 2: **Estimating the age-specific symptomatic rate from age-specific case counts for six countries.****a.** Age-specific reported cases from 13 provinces of China, 12 regions of Italy, Japan, Singapore, South Korea and Ontario, Canada. Open bars are data and the colored lines are model fits with 95% HD. **b.** Fitted mean (lines) and 95% HD (shaded areas) for the age distribution in the clinical fraction (solid lines) and the age distribution of susceptibility (dashed lines) for all countries. The overall consensus fit is shown in gray. **c.** Fitted incidence of confirmed cases and resulting age distribution of cases using either the consensus (gray) or country-specific (color) age-specific clinical fraction from **b.**\\n\\n'", "CAPTION FIG2.png": "'\\nFigure 2: **Estimating the age-specific symptomatic rate from age-specific case counts for six countries.****a.** Age-specific reported cases from 13 provinces of China, 12 regions of Italy, Japan, Singapore, South Korea and Ontario, Canada. Open bars are data and the colored lines are model fits with 95% HD. **b.** Fitted mean (lines) and 95% HD (shaded areas) for the age distribution in the clinical fraction (solid lines) and the age distribution of susceptibility (dashed lines) for all countries. The overall consensus fit is shown in gray. **c.** Fitted incidence of confirmed cases and resulting age distribution of cases using either the consensus (gray) or country-specific (color) age-specific clinical fraction from **b.**\\n\\n'", "CAPTION FIG3.png": "'\\n\\n**Fig. 3 [Effect of school closure under different demographics and subclinical infectiousness.****a**, Age dependence in clinical fraction (severity) and susceptibility to infection on contact for COVID-19 and for the influenza-like scenarios (simplified, based on ref. [4]) considered here. **b**, Age structure for the three exemplar cities. **c**, Age-specific clinical case rate for COVID-19 and influenza-like infections, assuming \\\\(\\\\leq\\\\)50% infectiousness of subclinical infections. **d**, Daily incidence of clinical cases in exemplar cities for COVID-19 versus influenza-like infections. \\\\(R_{0}\\\\) is fixed at 2.4. The rows show the effect of varying the infectiousness of subclinical infections to be 0%, 50% or 100% as infectious as clinical cases while keeping \\\\(R_{0}\\\\) fixed **e**, Change in peak timing and peak cases for the three cities, for either COVID-19 or influenza-like infections. **f**, Change in median COVID-19 peak timing and peak cases for the three cities, depending on the infectiousness of subclinical infections.\\n\\n'", "CAPTION FIG4.png": "'\\n\\n**Fig. 4 : Implications for global preparedness.****a**, Expected clinical case attack rate (mean and 95% HDD) and peak in clinical case incidence for 146 countries in the Global Burden of Disease (GBD) country groupings(r) for an unmitigated epidemic. **b**, Expected subclinical case attack rate and peak in subclinical cases. **c**, Estimated basic reproduction number (_R_o) in the capital city of each country assuming the age-specific clinical fraction shown in Fig. 2b and 50% infectiousness of subclinically infected people. **d**, Proportion of clinical cases in each age group at times relative to the peak of the epidemic. The 146 city epidemics were aligned at the peak, and colors mark the GBD groupings in **a**, **e**, Age distribution of the first and last thirds of clinical cases for 146 countries in GBD country groupings.\\n\\n'", "CAPTION FIG5.png": "\"\\n\\n**Extended Data Fig. 5 Posterior distributions for Beijing, Shanghai, South Korea, and Lombardy.** Prior and posterior distributions for the epidemics in a, Beijing and Shanghai, **b**, South Korea and **c**, Lombardy using the 'consensus' fit for age-specific clinical fraction and assuming subclinical infections are 50% as infectious as clinical infections (see Fig. 2c, main text). For (**a**), times are in days after December 1st, 2019; for (**b**) and (**c**), times are in days after January 1st, 2019. Note, seed_d is the inferred duration of the seeding event. See also Supplementary Table 4.\\n\\n\"", "CAPTION FIG6.png": "'\\n\\n**Extended Data Fig. 6 [ Global projections assuming greater severity in lower-income countries.****a**. Schematic age-specific clinical fraction for higher-income and lower-income countries. **b-f**, illustrative results of the projections for 146 capital cities assuming a higher age-varying clinical fraction in lower-income countries. See Fig. 4 (main text) for details.\\n\\n'", "CAPTION FIG7.png": "'\\n\\n**Extended Data Fig. 7 [ Consensus age-specific clinical fraction and susceptibility under varying assumptions for subclinical infectiousness.** Line and rhobens show mean and 95% HDI for clinical fraction and susceptibility, assuming subclinical infections are 0%, 25%, 50%, 75%, or 100% as infectious as clinical infections.\\n\\n'", "CAPTION FIG8.png": "'\\n\\n**Extended Data Fig. 8 | Projections for capital cities depending upon subclinical infectiousness.****a**, Projected total and peak clinical case attack rate for 146 capital cities, under different assumptions for the infectiousness of subclinical infections. **b**, Projected total and peak subclinical infection attack rate for 146 capital cities, under different assumptions for the infectiousness of subclinical infections. **c**, Projected differences in \\\\(R_{a}\\\\) among 146 capital cities, under different assumptions for the infectiousness of subclinical infections. Mean and 95% HDI shown.\\n\\n'", "CAPTION FIG9.png": "'\\n\\n**Extended Data Fig. 9 | School closures with fixed susceptibility across cities.** Comparison of school closures in three exemplar cities when susceptibility is fixed across settings instead of 80. See main text Fig. 3 for details.\\n\\n'", "CAPTION FIGS1.png": "'\\n\\n**Extended Data Fig. 1 Posterior distributions for Wuhan.** Prior distributions (gray dotted lines) and posterior distributions (colored histograms) for model parameters fitting to the early epidemic in Wuhan (Fig. 1, main text); seed_start is measured in days after November 1st, 2019. **a**, Model 1(age-varying contact patterns and susceptibility); **b**, Model 2 (age-varying contact patterns and clinical fraction); **c**, Model 3 (age-varying contact patterns only). See also Supplementary Table 4.\\n\\n'", "CAPTION FIGS10.png": "'\\n\\n**Extended Data Fig. 10 | Contact matrices used in transmission model.** Contact matrices used for Figs. 1-3 of the main text. We have not shown matrices for all 12 regions of Italy modeled, nor for all 13 provinces of China modeled, as these show similar patterns to the matrices for Milan and for Wuhan, Beijing and Shanghai, respectively.\\n\\n'", "CAPTION FIGS2.png": "'\\n\\n**Extended Data Fig. 2 [ Simultaneous estimation of age-varying susceptibility and clinical fraction to epidemic data from Wuhan City, China.** This figure replicates Fig. 1 of the main text, but comparing model variants 1 and 2 to a fourth model variant in which both susceptibility and clinical fraction vary by age. **a**, Model diagram (see Fig. 1, main text). **b**, Susceptibility by age for the three models. Age-specific values were estimated for models 1 (orange) and 4 (pink). Susceptibility is defined as the probability of infection on contact with an infectious person. Mean (lines), 50% (darker shading) and 95% (lighter shading) credible intervals shown. **c**, Clinical fraction (_y_) by age for the three models. Age-specific values were estimated for model 2 (blue) and 4 (pink), and fixed at 0.5 for model 1. **d**, Fitted contact multiplex for holiday (_a_b_) and restricted periods (_a_b_) for each model showed an increase in non-school contacts beginning on January 12th (start of Lunar New Year) and a decrease in contacts following restrictions on January 23rd. **e**, Estimated \\\\(R\\\\) values for each model. The red barplot shows the inferred window of spillover of infection. **f**, Incident reported cases (black), and modeled incidence of reported clinical cases for the three models fitted to cases reported by China Centers for Disease Control (CCDC) with onset on or before February 1st, 2020. Line marks mean and shaded window is the 95% highest density interval (HDI). **g**, Age distribution of cases by onset date as fitted to the age distributions reported by Li et al. (first three panels) and CCDC (fourth panel). Data are shown in the hollow bars, and model predictions in filled bars, where the dot marks the mean posterior estimate. **h**, Implied distribution of subclinical cases by age for each model. Credible intervals on modeled values show the 95% HDIs; credible intervals on data for panels g and h show 95% HDIs for the proportion of cases in each age group.\\n\\n'", "CAPTION FIGS3.png": "'\\n\\n**Extended Data Fig. 3 | Impact of data sources used.** _Analysis showing how the inferred age-varying susceptibility (first column) and age-varying clinical fraction (second column) depend upon the additional data sources used.\\n\\n'", "CAPTION FIGS4.png": "'\\n\\n**Extended Data Fig. 4 -- Posterior estimates for the consensus susceptibility and clinical fraction from 6 countries.** Note that susceptibility is a relative measure.\\n\\n'", "CAPTION FIGS5.png": "\"\\n\\n**Extended Data Fig. 5 Posterior distributions for Beijing, Shanghai, South Korea, and Lombardy.** Prior and posterior distributions for the epidemics in a, Beijing and Shanghai, **b**, South Korea and **c**, Lombardy using the 'consensus' fit for age-specific clinical fraction and assuming subclinical infections are 50% as infectious as clinical infections (see Fig. 2c, main text). For (**a**), times are in days after December 1st, 2019; for (**b**) and (**c**), times are in days after January 1st, 2019. Note, seed_d is the inferred duration of the seeding event. See also Supplementary Table 4.\\n\\n\"", "CAPTION FIGS6.png": "'\\n\\n**Extended Data Fig. 6 [ Global projections assuming greater severity in lower-income countries.****a**. Schematic age-specific clinical fraction for higher-income and lower-income countries. **b-f**, illustrative results of the projections for 146 capital cities assuming a higher age-varying clinical fraction in lower-income countries. See Fig. 4 (main text) for details.\\n\\n'", "CAPTION FIGS7.png": "'\\n\\n**Extended Data Fig. 7 [ Consensus age-specific clinical fraction and susceptibility under varying assumptions for subclinical infectiousness.** Line and rhobens show mean and 95% HDI for clinical fraction and susceptibility, assuming subclinical infections are 0%, 25%, 50%, 75%, or 100% as infectious as clinical infections.\\n\\n'", "CAPTION FIGS8.png": "'\\n\\n**Extended Data Fig. 8 | Projections for capital cities depending upon subclinical infectiousness.****a**, Projected total and peak clinical case attack rate for 146 capital cities, under different assumptions for the infectiousness of subclinical infections. **b**, Projected total and peak subclinical infection attack rate for 146 capital cities, under different assumptions for the infectiousness of subclinical infections. **c**, Projected differences in \\\\(R_{a}\\\\) among 146 capital cities, under different assumptions for the infectiousness of subclinical infections. Mean and 95% HDI shown.\\n\\n'", "CAPTION FIGS9.png": "'\\n\\n**Extended Data Fig. 9 | School closures with fixed susceptibility across cities.** Comparison of school closures in three exemplar cities when susceptibility is fixed across settings instead of 80. See main text Fig. 3 for details.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Figure Captions**'"}

extracted_captions/dunbarHowScientistsThink1997.json

@@ -0,0 +1 @@
+{"CAPTION TAB1.png": "\"\\n\\n**Scientists' Goals for Within-Organism, Other-Organism, and Nonbiological Analogies**\"", "CAPTION TAB2.png": "'\\n\\n**Types of Knowledge Retrieved by Analogies on the Basis of Homology and Nonhomology for Other-Organism Analogies**'"}

extracted_captions/eckertAdaptationSourcesInspiration2003.json

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+{"CAPTION FIG1.png": "'Figure 1. Outline of the hurricane design process\\n\\n'", "CAPTION FIG10.png": "'Figure 10. Assistance to the natural context of the source.\\n\\n'", "CAPTION FIG11.png": "'\\n\\n## Appendix A Appendix\\n\\nAppendix B: The derivation of'", "CAPTION FIG12.png": "'\\n\\n**Figure 12.** Structural role drive source stringy.\\n\\n'", "CAPTION FIG13.png": "'Figure 14: Structural role drives source design.\\n\\n'", "CAPTION FIG14.png": "'\\n\\n**Figure 14.** Emergent read drives source strategy.\\n\\n'", "CAPTION FIG15.png": "'\\n\\n**Figure 15.**_Middle hot \"target.\"'", "CAPTION FIG16.png": "'Chapter 4 Future'", "CAPTION FIG17.png": "'\\n\\n**Figure 17.** Sufence priority barrier.\\n\\n'", "CAPTION FIG18.png": "'\\n\\n**Figure 18**. _Source dimer_ amine structural role strategy.\\n\\n'", "CAPTION FIG19.png": "'Figure 19. Source driven same structural rule design.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Figure 2.** Single acetyl design with asymmetric shapes.\\n\\n'", "CAPTION FIG20.png": "'Figure 20. Source drives different structural role strategy.\\n\\n'", "CAPTION FIG21.png": "'\\n\\n**Figure 11.**_Source driven different structural role design_'", "CAPTION FIG22.png": "'\\n\\n## Chapter 3 Main of source strategy'", "CAPTION FIG23.png": "'\\n\\n**Figure 3.** Continued of source density.\\n\\n'", "CAPTION FIG24.png": "'\\n\\n## Abstract\\n\\nIn this thesis we study the effect of the \\\\(\\\\pi\\\\)-particle interaction on the \\\\(\\\\pi\\\\)-particle interaction. We show that the \\\\(\\\\pi\\\\)-particle interaction is a \\\\(\\\\pi\\\\)-particle interaction.\\n\\n'", "CAPTION FIG25.png": "'Figure 25: _Professional: Strategy frequencies in rng and tagery maks._\\n\\n'", "CAPTION FIG26.png": "'Figure 26: Frequencies of strange used by professionals and students.\\n\\n'", "CAPTION FIG3.png": "'Figure 1.: Adaptation of a source of inspiration for an individual design.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: The ring stimulus given to the subjects. Afshar rug (S. E. Iran). Scanned from Oriental Rays: A Buyer\u2019s Guide (p. 42), by Lee Alliance, Lookou: Thames and Hudson, 1988. Copyright 1988 Thames and Hudson. Reprinted with permission.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: The top-city stimulus given to the subjects. Out and Pigcom, designed by John Henry Deurle, c. 1895. Scanned from William Morris (p. 250), edited by Linda Parry, 1996, Loudoua: Philip Wilson Publishers/Victoria and Albert Miseau. Copyright 1996 V & A Images/Victoria and Albert Museum. Reprinted with permission.\\n\\n'", "CAPTION FIG6.png": "'\\n\\n## Chapter 4. Analytical driven current'", "CAPTION FIG7.png": "'Figure 7. Abstraction of the source design element.\\n\\n'", "CAPTION FIG8.png": "'Figure 1: Abstraction from a usual property of the source.\\n\\n'", "CAPTION FIG9.png": "'\\n\\n**Figure 1.** Schematic diagram for the case of a \\\\(\\\\pi\\\\)-particle.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n## Table 1. Cluster of Motif Arrangements'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{**Table 2**.: _Number and Frequency of Strategies Used with the Ring Source_} \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 2: _Number and Frequency of Strategies Used with the Ring Source_'", "CAPTION TAB3.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K.\\n\\n'", "CAPTION TAB4.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K.\\n\\n'", "CAPTION TAB5.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB6.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{**Table 6.**_Occurrences of Strategies Used by Professionals and Students in the Rug Task (Excluding Evolution Designs)_} \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 6: _Occurrences of Strategies Used by Professionals and Students in the Rug Task (Excluding Evolution Designs)_'", "CAPTION TAB7.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB8.png": "'\\n\\n**Table 6.**_More and Less Direct Strategies and Transformations_'"}

extracted_captions/fasler2020novel.json

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+{"CAPTION FIG S1.png": "'\\n\\n**Fig. S1.: Cryo-ET of the actin network in a NIH3T3 fibroblast lamellipodium. (a) Computational slice through a binned, non-CTF corrected tomogram (17.096A/px) of a NIH3T3 fibroblast lamellipodium. Protein density is black. The dense actin network is visible and the helical appearance of individual actin filaments can be clearly appreciated. Several branch junctions are highlighted in red circles. The dashed line indicates the cell edge. Scale bar is 100nm. (b) Gallery of selected branch junctions. The density corresponding to the Arp2/3 complex at branch junctions is visible in the individual examples.**'", "CAPTION FIG S2.png": "'\\n\\n**Fig. S2.: Graphical workflow of image processing.** Flow chart indicating the data processing steps involved in generating the structure of the active Arp2/3 complex within the branch junction. Colored boxes indicate usage of specific software packages. For simplicity, the procedure to produce a reference for template matching via manual picking and averaging branch junctions is not depicted here, but is described within the material and methods section.\\n\\n'", "CAPTION FIG S5.1.png": "'\\n\\n**Fig. S5.: Comparison of the active Arp2/3 complex conformation in branch junctions in cells to the _in vitro_ Dip1-activated Arp2/3 complex and to a previously published MD-derived _in vitro_ branch model. (a) Molecular models of the Arp2/3 complex in the active conformation (shown as density maps filtered to 9.5A resolution) as observed in cells (left, this study), the _in vitro_ Dip1-activated Arp2/3 complex (middle) [29], and a MD-derived active Arp2/3 complex [12], which is based on a low-resolution negative stain ET reconstruction (right) [9]. The models were aligned on the ArpC2 subunits to visualize the different conformations of the Arp2/3 complex and in case for the branch junction also the varying position on the mother filament between the _in situ_ and _in vitro_'", "CAPTION FIG S5.2.png": "'model. **(b-c)** RMSD values (in A) calculated between the subunits of the three models shown in **(a)**. Rows indicate which subunit was used for aligning full models to each other, prior to measurements between individual subunits (indicated in the columns) of the different models of the active Arp2/3 complex. **(b)** RMSD values of differences between the Arp2/3 complex in branch junctions in cells and the _in vitro_ Dip1-activated Arp2/3 complex. In order to calculate C-alpha RMSD values between our model and pdb 6W17 only primary structure areas are considered, in which the _B. Taurus_ (as used in our model) and _S. pombe_ protein sequences are in the same register, hence omitting inserts present in only one species. This comparison reveals differences between the Dip1-activated Arp2/3 complex in vitro and the activated state of the Arp2/3 complex in cells, in particular with respect to ArpC3. **(c)** RMSD values of differences between the Arp2/3 complex in branch junctions in cells and the MD-derived _in vitro_ branch junction model.\\n\\n'", "CAPTION FIG S6.png": "'\\n\\n**Fig. S6.: Mother actin filament conformation in the actin-Arp2/3 complex branch junction. (a) Fit of the final model of the mother actin filament after MD-refinement into the EM density of the branch junction using ISOLDE. The empty density close to M4, corresponding to the helix of ArpC1 is annotated with a green ellipsoid. (b) Superimposition between the starting model used for fitting (pdb 6T20, pink) and the final model after MD-refinement. Small deviations between the filament assemblies can be observed. (c) Superimposition between one monomer of pdb 6T20 (pink) and monomer M4 of the mother filament in our branch junction model. No large-scale deviations in the monomer conformation are observed. (d) RMSD calculations between the C-alpha atoms of one monomer of pdb 6T20 and the monomers of the mother filament. The average RMSD value is 1.76A.**'", "CAPTION FIG.S4.png": "'\\n\\n**Fig. S4.: Comparison of the short pitch actin dimer conformation to Arp2 and Arp3 in their inactive and active conformation.** Density maps of molecular models of an actin dimer, or of Arp2 and Arp3 in their active and inactive conformation, respectively, filtered to a resolution of 15A. The models of the active Arp2/3 conformation were derived from our model of the actin filament Arp2/3 complex structure in cells described in this manuscript and the _in vitro_ Dip1-activated _S. pombe_ Arp2/3 complex (pdb 6W17) [29]. The shown models of filamentous actin were derived from pdb 6T20 [30], and for the inactive ATP-bound Arp2/3 complex from pdb 1TYQ [8]. Maps were oriented by fitting Arp3 subunits and the actin monomer M1 to each other. While Arp2 and Arp3 of the active complex adopt a similar short pitch conformation as the monomers of the actin dimer, this is not the case for the subunits of the inactive complex. Subunit identity is indicated by the color scheme.\\n\\n'", "CAPTION FIG1.png": "'\\nFigure 1: **Subnanometer Structure of the actin filament Arp2/3 complex branch junction in cells.****(a)** Isosurface representation of the actin filament Arp2/3 complex branch junction in cells at 9\u00c5 resolution. The structure is shown from three orientations. A guide for orientation is given in (b). **(b)** The electron microscopy density map (shown transparent) with the flexibly fitted models of the Arp2/3 complex subunits and actin filaments. Schematic guides indicate the positions of the individual subunits of the complex and the monomers of both the mother and daughter filaments. A colour legend provides the color code for the fitted models. The color code and legend are used throughout the manuscript to aid the reader.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Fig. 2: Comparison of Arp2/3 complex in its inactive conformation and in the branch junction in cells. (a) Molecular models of the Arp2/3 complex in the inactive (derived from pdb 1TYQ) and the active conformation shown as density maps filtered to 9.5A resolution. The models are shown from three orientations, corresponding to the views in figure 1. (b) RMSD values (in A) calculated between the inactive and active conformations of the individual Arp2/3 subunits (based on the models used in (a)). Rows indicate which subunit was used for aligning the full models against each other, prior to measurements between individual subunits of the inactive and active Arp2/3 complexes (indicated in the columns). The RMSD analysis reveals that the structural transition upon complex activation is accommodated by two subcomplexes consisting of Arp2, ArpC1, ArpC4 and ArpC3, ArpC2 and ArpC3, respectively, that rotate against each other along an axis formed by the large helices of ArpC2 and ArpC4 (Movie S4). RMSD variations between the same subunits in the inactive and active conformations derive from changes upon MD-based modelling of the x-ray crystal structure-derived model into the electron microscopy density map of the branch junction.**'", "CAPTION FIG3.png": "'\\n\\n**(a)** Interaction surfaces between the Arp2/3 complex and the actin mother and daughter filament. The surfaces for the Arp2/3 complex, mother and daughter filament are shown as density maps at 9.5A resolution generated from their respective models. Grey coloring on the surface of Arp2/3 subunits indicates contact sites with actin and coloring of actin monomers in a specific color indicates a contact site with the associated Arp2/3 subunit (color code is given within the figure). Coloring was applied via the color zone command in ChimeraX in a 5.5A radius around each C-alpha atom of the underlying model, which was positioned in a 10A radius to a C-alpha atom of its putative interactor. **(b)** Surface representation of the interaction of ArpC2 and ArpC4 with the mother filament monomers M6 and M7 (the interaction of ArpC2 with M5 is omitted for clarity). **(c)** The protrusion helix of ArpC1 fitted into its density close to subdomains 1 and 3 of M4. **(d)** Surface representation of the interactions of Arp3 and ArpC3 with the mother filament. Note the cavity below Arp2, where no contacts between the Arp2 subunit and the mother filament are observed. ArpC3 acts as a linker between Arp2 and the mother filament. **(e)** Surface representation of the interaction between Arp2, Arp3 and the first two monomers of the daughter filament.\\n\\nFig. 3: **Actin-Arp2/3 complex interaction surfaces within the branch junction**\\n\\n**(a)** Interaction surfaces between the Arp2/3 complex and the actin mother and daughter filament. The surfaces for the Arp2/3 complex, mother and daughter filament are shown as density maps at 9.5\u00c5 resolution generated from their respective models. Grey coloring on the surface of Arp2/3 subunits indicates contact sites with actin and coloring of actin monomers in a specific color indicates a contact site with the associated Arp2/3 subunit (color code is given within the figure). Coloring was applied via the color zone command in ChimeraX in a 5.5\u00c5 radius around each C-alpha atom of the underlying model, which was positioned in a 10\u00c5 radius to a C-alpha atom of its putative interactor. **(b)** Surface representation of the interaction of ArpC2 and ArpC4 with the mother filament monomers M6 and M7 (the interaction of ArpC2 with M5 is omitted for clarity). **(c)** The protrusion helix of ArpC1 fitted into its density close to subdomains 1 and 3 of M4. **(d)** Surface representation of the interactions of Arp3 and ArpC3 with the mother filament. Note the cavity below Arp2, where no contacts between the Arp2 subunit and the mother filament are observed. ArpC3 acts as a linker between Arp2 and the mother filament. **(e)** Surface representation of the interaction between Arp2, Arp3 and the first two monomers of the daughter filament.\\n\\n'", "CAPTION FIG4.png": "'\\n\\n**Fig. 4: Structural changes in Arp3 and ArpC5 upon branch junction formation**\\n\\n**(a)** Comparison of the conformation of the Arp3 C-terminal tail in the inactive and active conformation. No density is observed for the C-terminal tail of Arp3 in its inactive conformation (top). Instead, the C-terminal tail can flip towards Arp2 and ArpC4, where it is accommodated by an empty density present in the branch junction structure (bottom). **(b)** No density is observed for the ArpC5 N-terminus at its binding side in the inactive complex (top). Instead, the ArpC5 N-terminus can be fitted into a density between ArpC1 and Arp2. **(c)** Positively charged residues in ArpC1 and Arp2 could coordinate the negatively charged N-terminus of ArpC5. **(d)** Electrostatic potential map of the area shown in **(c)**.\\n\\n'", "CAPTION FIGS1.png": "'\\n\\n**Table S1.**\\n\\n**Data acquisition and image processing parameters**'", "CAPTION FIGS3.png": "'\\n\\n**Fig. S3.: Structural details of the actin filament Arp2/3 complex branch junction.** Densities for the individual subunits of the Arp2/3 complex plus their fitted models are shown. Subunit colors are annotated and identical to the schematic guide given in Figure 1. Secondary structure detail (i.e. alpha helices) are clearly visualized, for example for Arp3, ArpC2 and ArpC4. The beta-propellers of ArpC1 allow unambiguous fitting of the subunit into the density of the branch junction. The increased apparent flexibility at the N-terminus of the ArpC5 helical core (annotated by an arrow) is visible, resulting in reduced density for the N-terminal helices of this subunit. The subnanometer resolution of our structure also allows to clearly visualize secondary structure details in the actin filament, further highlighted by the visibility of an additional density accommodating Phalloidin (annotated by an arrow).\\n\\n'", "CAPTION TABS2.png": "'\\n\\n**Table S2.**\\n\\n**Summary of model content**\\n\\nThe pdb files used to generate the final model of the active Arp2/3 complex are listed. Residues that had to be added or removed from the original models are indicated. Residue stubs in the original models were completed to contain their entire side chains for MD-modelling in ISOLDE.\\n\\n'", "CAPTION TABS3.png": "'\\n\\n**Table 53.**\\n\\n**Modelling parameters and statistics**'", "CAPTION TABS4.png": "'\\n\\n**Table S4. Arp2/3 complex residues contacting the actin mother and daughter filaments**\\n\\nSummary of residues forming interactions between the Arp2/3 complex and the actin filaments, defined by a 10A C-alpha to C-alpha distance cutoff. The UniProt identifiers for the individual proteins are given.\\n\\n'"}

extracted_captions/feldEgonetsSystematicallyBiased2020.json

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+{"CAPTION FIG1.png": "\"Figure 1. A small social network drawn from the example given in Feld (1991) of Coleman's Adolescent Society (1961) data of reciprocated friendships. This includes seven of the eight girls in the original example-presented by Feld.\\n\\n\"", "CAPTION FIG2.png": "'Figure 2: The degree distribution for the 60,483 Facebook users in the New Orleans regional dataset who had at most 100 friends.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: The degree distribution for the 3,307 Facebook users in the New Orleans regional dataset who had at least 100 friends.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Median and quartiles of egonet mean degree, by the ego\u2019s degree. A diagonal dashed line shows the points where ego\u2019s degree is equal to egonet\u2019s degree. For instance, the 25% quantile intersects the dashed line where 75% of egonets have a higher mean degree than the ego. The solid horizontal line indicates the mean degree in the population.\\n\\n'", "CAPTION TABA1.png": "''", "CAPTION TABA2.png": "''"}

extracted_captions/ferguson2017mechanoregulation.json

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+{"CAPTION 2.png": "'Figure 1: **Cell processing blocks that and assemble skeletons in multiple cell operators.** (3) (Cutter and temperature) and temperature levels of a 3DCT cell are shown. **Fig. 2:**_Cell processing blocks that and assemble skeletons in multiple cell operators.** (4) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 3:**_Cell processing blocks that and assemble skeletons in multiple cell operators.** (5) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 4:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (6) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 5:**_Cell processing blocks that and assemble skeletons in multiple cell operators.** (7) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 6:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (8) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 7:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (9) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 8:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (10) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 9:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (11) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 10:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (12) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 11:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (13) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 12:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (14) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 13:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (15) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 14:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (16) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 15:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (17) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 16:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (18) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 17:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 18:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (10) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 19:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (11) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 10:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (12) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 11:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (13) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 12:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (14) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 13:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (15) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 14:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (16) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 15:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (17) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 16:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (18) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 17:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 18:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 19:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (11) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 11:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (12) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 12:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (13) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 13:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (14) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 14:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (15) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 16:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (16) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 17:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (17) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 18:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (18) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 19:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 10:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 11:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 12:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 13:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 14:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 15:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 16:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and temperature levels of a 3DCT cell are shown). **Fig. 17:**_Cell processing blocks and assemble skeletons in multiple cell operators.** (19) (Cutter and\\n\\n'", "CAPTION 2F.png": "'\\n\\n## References\\n\\nFig. 2: **Cell squeezing induces fast and reversible alterations in clathrin coat dynamics.** (A) Cartoon and representative frames of a BSC1 cell are shown at different stages of squeezing (Movie 2). (B) Kymograph showing the temporal evolution of the clathrin traces detected at the ventral surface of the cell shown in A. Dashed lines mark the squeezing steps. (C) For the cell in A, normalized distributions of clathrin growth rates are plotted for different squeezing levels (Fig. S1). The standard deviation of the distribution reduces as the tension increases. (D) For the same cell, the time variation of the ventral surface area (upper) and the standard deviation of the clathrin growth rates (lower). The stepwise changes in these parameters are due to discrete levels of squeezing. (E) The response of the same cell to squeezing is shown as the mean clathrin lifetime (upper) and initiation and conclusion densities (lower). Dashed lines indicate changes in squeezing (\\\\(n_{\\\\text{vacuum}}\\\\)=8217). (F) Standard deviation of clathrin growth rates (upper), mean lifetime (middle), and initiation and conclusion densities (lower) from a cell that undergoes increased stepwise squeezing (orange dashed lines) and relaxation (blue dashed lines) (Movie 3) (\\\\(n_{\\\\text{vacuum}}\\\\)=8255).\\n\\n'", "CAPTION FIG1.png": "'\\nFigure 1: **Aspiration of the plasma membrane slows down clathrin coat dynamics.** (A) Kymograph showing the clathrin activity at the ventral surface of a BSC1 cell expressing AP2-eGFP. Clathrin coat traces elongate gradually upon microsuspension (dashed line; Movie 1). Blue and red arrowheads mark the initiation and conclusion of a clathrin-coated structure, respectively. _A)_ its its lifetime. (B) Clathrin coat lifetime distributions are shown for nine BSC1 cells imaged before and during microsuspension (\\\\(n_{\\\\text{max}}\\\\)=40,943). (C) For the same nine cells, the standard deviation of the clathrin growth rate distributions are shown in koptics. Lines connect the standard deviation values obtained from the same cell before and during aspiration. The narrower growth rate distributions indicate slower clathrin coat dynamics. (D) Box plots are the initiation and conclusion densities of clathrin-coated structures before and during aspiration. In the koptics, the box represents the 25\u201375th percentiles, and the median is indicated. The whiskers show the 10\u201390th percentiles. _P_-values were obtained with a two-tailed _I_-test.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Hypetemic swelling inhibits clathrin coat dynamics temporarily. (A) Change in the volume (normalized to the radial value) is placed for three ESC1 cells during hypotonic swelling (i.e. osmachock). (B) Mean clathrin coat lifetime (upper), and initiation and conclusion densities (lower) are plotted against time for a ESC1 cell treated with hypotonic shock (dashed line). (C) Clathion lifetime distributions are assembled pre- and post-osmachock for 12 gene-edited SUM159 cells xenrazing AP2-EGFP (\\\\(n_{\\\\mathrm{tracea}}\\\\)=\\\\(34,113\\\\)). (DE) For the same cells, the standard deviation of clathrin growth rates [0] and initiation and conclusion densities of clathrin-coated structures pre- and post-osmotic shock(E) are shown in boxplots. Lines centered the standard deviation values obtained from the same cell pre- and post-osmachock. In the boxplots, the box represents the 25-75th percentiles, and the median is indicated. The whiskers show the 10-90th percentiles. Values were obtained with a two-tailed \\\\(t\\\\)-test.\\n\\n'", "CAPTION FIG4.png": "'\\nFigure 4: **Acth dynamics mediate the inward movement of clathrin coats prior to disassembly.** (A) Means-s.e.m. values for of normalized AP2 intensity traces (determined for a SUM159 cell before and after hypotonic swelling; \\\\(n_{\\\\text{max}}\\\\)=3728). The traces are aligned at the end point before averaging. (B) Mean-s.e.m. z. displacements are shown for the two trace groups in A. (C) Top, growth rate distributions are assembled for eight SUM159 cells before and after hypotonic swelling (\\\\(n_{\\\\text{max}}\\\\)=30,409). Different growth phases (ff, fast formation; sf, slow formation; p, plateau; sd, slow dissolution; fd, fast dissolution) were determined by quantifying the change in the clathrin coat signal over 25-s long time windows (Ferguson et al., 2016). Bottom, for the same cells, bar plots show the mean-s.e.m. of the z. velocities of the trace fragments (12 s long) that are used to generate the growth rate distributions above. Trace fragments that have the highest z velocity are found in the fast dissolution (1fd) phase. (D) Top, representative intensity traces of AP2 (green) and LifeAct (red) fluorescence during the formation of a clathrin-coated vesicle at the ventral surface of a BSC1 cell. Bottom, the relative LifeAct intensity (mean-s.e.m.) colocalizing with clathrin coats is shown for different growth phases (\\\\(n_{\\\\text{total}}\\\\)=4, \\\\(n_{\\\\text{max}}\\\\)=28,796). Note that the growth phases are determined by using the master (AP2=EGFP) signal. (E) Bar plots show the z velocities (mean-s.e.m.) corresponding to different growth phases for AP2 traces obtained from BSC1 cells in the absence and presence of jasplakinolide (Jase) (Control, \\\\(n_{\\\\text{total}}\\\\)=7, \\\\(n_{\\\\text{max}}\\\\)=20,204; Jase, \\\\(n_{\\\\text{max}}\\\\)=6, \\\\(n_{\\\\text{max}}\\\\)=25,972). *P-O0.0001; *P-O0.001 (two-tailed Hest).\\n\\n'"}

extracted_captions/fernandes2019cell.json

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+{"CAPTION FIG1.png": "'Figure 1: A quantitative treatment of TCS triggering relying on receptor dual time at phosphatase-depicted close contacts. (_A_) Top and side views of the close contact depicting contact topography (with contact radius \u201cr\u201d) and CD45 exclusion. The first box (solid line) shows the region of the cell magnified below it. The second box (dotted line) shows the region depicted in the top view on the right. (_B_) According to the model, a TCR (TCR) is triggered, i.e., phosphorylated because its residence time in the contact is >=2 s. TCR\\\\({}_{2}\\\\) is not triggered because it diffuses out of the contact in less than 2 s. (_C_) Also according to the model, a receptor (TCR) that engages ligand is likely to be held in the contact \u22652 s and become triggered. In \\\\(B\\\\) and \\\\(C\\\\), the margins of the contact are marked by the average positions of excluded CD45 molecules (green). (_D_) Snapshots from the simulation of the TCR density probability evolution in dose-contacts as they grow over time (_S_ Appendix_ _A_).\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Parameterization of the model. (A) Experimental approach. High-density labeling of CD45 (Gap 8.3 Fab, Alexa Fluor 488) was used to indicate sites of close-contact formation between T cells and a rat CD2-presenting SIs (Ledt), and this was combined with simultaneous low-density labeling of CD45 (Gap 8.3 Fab, Alexa Fluor SBE), Lck (Halo tag, tetramethylrhodamine [TM&]), or TCR (Halo tag, TMR) (right) to enable TIRFM-based single-molecule tracking. (B-D, Left) TERM-based single-molecule tracking of CD45 (B), Lck (C), and TCR (D). Well-separated individual trajectories were recorded for >280 ms and colored according to position in the contact (orange in CD45-rich region and blue in CD45-depleted regions). (Right) Close-up views of trajectories in regions marked by white rectangles CD45-rich regions are shown in gray. (Scale bar, 2 \u03bcm.) Data are representative of three independent experiments with \\\\(n>10\\\\) cells.\\n\\n'", "CAPTION FIG4.png": "'\\nFig. 4: Why the TCR can be triggered in the absence of ligands. (A) Probability that a TCR remains inside a dose contact for time, \\\\(\\\\tau\\\\), for close contacts of varying fixed radius, \\\\(\\\\tau_{0}\\\\) (B) Probability that a single TCR stays inside a dose contact >2 s as a function of final close-contact radius for growing contacts. (C) Total number of TCRs that remain inside the close contact for >2 s, incorporating the estimates shown in \\\\(A\\\\), the density of TCRs in Jurkat T cells, and the degree of exclusion of the TCR from close contacts for cells interacting with rCD2-presenting SLBs. (_D_) Total contact area (region of CD45 exclusion) at the time of calcium release for T cells interacting with rCD2-presenting SLBs (13 cells, 5 independent experiments). Central lines indicate the median; small squares indicate the mean; boxes show interquartile range; whiskers indicate SD.\\n\\n'", "CAPTION FIG5.png": "'\\nFig. 5: Self-finensifel discrimination. (_A_) Probability distribution of close-contact residence times for TCRs in the presence and absence of agonist and self pMHC, for a close contact of radius \\\\(\\\\tau_{0}=220\\\\) nm, showing that discrimination of ligands is not dependent on a threshold value for \\\\(\\\\tau_{\\\\rm exc}\\\\). (_B_) Probability that at least one TCR will be triggered, i.e., stay in the contact for \\\\(\\\\tau_{0}\\\\geq 2.5\\\\), as a function of contact duration in the presence and absence of agonist pMHC with a low \\\\(k_{\\\\rm int}\\\\) (\\\\(k_{\\\\rm int}=1^{-1}\\\\), 30 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)), or a self pMHC with a larger \\\\(k_{\\\\rm int}\\\\) present at higher pMHC densities (\\\\(k_{\\\\rm int}=50\\\\)\\\\(\\\\times\\\\)\\\\(1^{-1}\\\\), 300 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)). (_C_) Comparison of the triggering probability in the absence of pMHC for close contacts of 220 and 440 nm. (_D_) Triggering probability as a function of pMHC densities and pMHC of rates for a single contact of 220 nm radius with a duration of \\\\(\\\\tau_{0}=120\\\\) s. (_F_) Triggering probability as a function of close contact radius for pMHC with varying off rates for a contact duration of \\\\(\\\\tau_{0}=120\\\\) s. (_F_) Contribution to the overall signal of TCRs that are triggered without binding to pMHC, in the presence of agonist pMHC with varying \\\\(k_{\\\\rm int}\\\\) (30 pMHC\\\\(\\\\mu\\\\)m\\\\(\\\\lambda\\\\)).\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Prediction of the relative signaling potentials of well-characterized TCR ligands. Peptide-stimulation potentials (EC48 and EC5E values for IL-2 selection) for CD4\\\\({}^{+}\\\\) (Left) and CD8\\\\({}^{+}\\\\) T cells (Right) (determined elsewhere in refs. 11, 33, and 53), plotted against the probability that at least one TCR triggering event (\\\\(t_{\\\\rm{oxin}}\\\\geq 2\\\\) s) occurs at a single contact of \\\\(r_{\\\\rm{a}}=220\\\\) nm, that persists for \\\\(t_{\\\\rm{f}}=120\\\\) s.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table 1.** Experimental parameters used in this study.\\n\\n'"}

extracted_captions/goldenbogen2016dynamics.json

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+{"CAPTION FIG1.png": "'Figure 1: Elastic shell model of the shmoo predicts a spatially inhomogeneous distribution of the lateral cell wall stresses and the Young\u2019s modulus. (a) _M/Ta_ cells synthesize **a**-factor and grow a mating projection towards _M/Ta_ cells upon sensing **a**-factor, and vice versa. (b) Scheme of a shmooing cell divided in base (0), neck (II), shaft (III) and tip (IV) with considered contributing elements, i.e. elastic cell wall (blue) with locally varying Young\u2019s modulus (white hatched), turgor pressure \\\\(\\\\bar{P}\\\\), and material insertion at the tip. (c) Description of coordinates given an axisymmetric geometry: circumferential angle \\\\(\\\\theta\\\\), meridional length \\\\(s\\\\) with corresponding distance to the axis \\\\(r\\\\), relaxed radii for the mating projection \\\\(R_{\\\\text{synch}}\\\\), and the spherical part \\\\(R_{\\\\text{base}}\\\\) as well as cell wall thickness \\\\(d\\\\). (d,e) Distribution of von Mises stress \\\\(\\\\sigma_{\\\\text{M/t}}\\\\) and volumetric strain \\\\(e_{\\\\mu}\\\\), respectively, with red indicating high and blue low values. (f) Resulting spatial distribution of the Young\u2019s modulus \\\\(\\\\bar{E}\\\\), dark green shows low values and shades of light-green to white high values. White area at the tip shows region of undefined \\\\(e_{\\\\mu}\\\\) and \\\\(\\\\bar{E}\\\\). Contour plots of stress, strain and elastic modulus shown in electronic supplementary material, figure S2. We used a cell with relaxed radius of \\\\(R_{\\\\text{base}}=1.9\\\\)\\\\(\\\\mu\\\\)m, expanded radius of \\\\(r_{\\\\text{base}}=2.5\\\\)\\\\(\\\\mu\\\\)m, relaxed radius of \\\\(R_{\\\\text{synch}}=0.4\\\\)\\\\(\\\\mu\\\\)m, cell wall thickness of \\\\(d=115\\\\) nm, turgor pressure of \\\\(\\\\bar{P}=0.2\\\\) MPa and Poisson\u2019s ratio of \\\\(\\\\nu=0.5\\\\). The values of stresses and the Young\u2019s modulus itemized by the base, neck, shaft and tip are shown in electronic supplementary material, table S1.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: **\u03b1**-factor treatment of _MMTA_ bar1\u0394 cells induced a localized softening of the cell wall in the region of the emerging mating projection. (_a,b_) Three-dimensional images with textures representing the elasticity for two individual _MMTA_ bar1\u0394 cells without (_a_) and with (_b_) 1 h treatment with 10 \u03bcM\u03b1\u03b1\u03b1\u03c4\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Dynamics of cell wall elasticity during shinooning, measured by live cell wall nano-indentation experiments and simulations of the dynamic cell wall model (DMI). Softening of the cell wall starts early, continues with elongation of the mating projection and forms a ring around its base. MTA bar\\\\(\\\\Delta\\\\) cells were induced with 10 \\\\(\\\\mu\\\\)M er-factor for 64 min before the first image was acquired. (_a,b_) Sequences of height and elasticity developments during formation of a mating projection, from a continuous AFM measurement (\\\\([d]\\\\) consecutive images of the \\\\(E\\\\)-distribution and \\\\([b]\\\\) three-dimensional reconstruction with elasticity pattern, see electronic supplementary material, movie S1). Arrows indicate a region of non-softened cell wall material at the tip; scale bar, 1 \\\\(\\\\mu\\\\)m. Elasticity pattern controls shape of the evolving shinoo in the dynamic model. (\\\\(e-e\\\\)) Simulation snapshots of DMI (electronic supplementary material, movie S2), showing the pattern of the Young\u2019s modulus (\\\\([c]\\\\), black/green/white), the von Mises stress \\\\(\\\\sigma_{\\\\text{MI}}\\\\) (\\\\([d]\\\\), blue/red) and the volumetric strain \\\\(e_{\\\\text{T}}\\\\) (\\\\([e]\\\\), blue/red); scale bar, 1 \\\\(\\\\mu\\\\)m. Note that colour scale for the elasticity in (\\\\(a\\\\)) ranges from 0 to 10 MPa in order to distinguish the cell from its stiffer surrounding (orange spectrum). Contour plots of stress, strain and elastic modulus are shown in electronic supplementary material, figure S11.\\n\\n'", "CAPTION FIG4.png": "\"Figure 4: The influence of elasticity patterns on cell wall growth for two variants of the dynamic cell wall model, DM1 and DM2. Snapshots of the dynamic cell wall model DM1 (electronic supplementary material, movie S2) and DM2 (electronic supplementary material, movie S3) after 1 h of simulated time, where the shape (column 1), the Young's modulus \\\\(\\\\xi\\\\), the von Mises stress \\\\(\\\\sigma_{\\\\text{WI}}\\\\), the volumetric strain \\\\(e_{\\\\text{V}}\\\\) and expansion rates \\\\(\\\\alpha\\\\) or \\\\(\\\\alpha^{*}\\\\) is shown for different model assumption; scale bar, 2 \\\\(\\\\mu\\\\)m. (\\\\(a\\\\),\\\\(b\\\\)) Simulations of DM1 assuming growth under yield stress. (\\\\(c\\\\),\\\\(d\\\\)) Simulations of DM2 assuming growth under yield strain. (\\\\(e\\\\)) Simulation of pure elastic expansion without cell wall growth. (\\\\(f\\\\)) Spherical reference shape. The elasticity pattern (\\\\(a\\\\),\\\\(c\\\\)) results in a longer mating projection than for homogeneous elasticity (\\\\(b\\\\),\\\\(d\\\\)). The effect of elasticity pattern on cell growth is even larger for DM2 (\\\\(c\\\\)) than for DM1 (\\\\(g\\\\)). Growth showed a ring-like pattern around the tip for the DM2 (\\\\(\\\\xi\\\\)), column 5), whereas for the DM1 ((\\\\(a\\\\)), column 5) growth was focused to the centre of the tip. Contour plots of stress, strain and elastic modulus for DM1 and DM2 are shown in electronic supplementary material, figure S11.\\n\\n\"", "CAPTION FIG5.png": "'Figure 5: Osmotic stress experiments confirmed strain profiles of the dynamic models. (_a_) Modelled shapes under yield stress (left) and yield strain assumption, before (grey) and after (blue) reduction of turgor pressure, respectively. (_b_) Time series of bright-field microscopy images of shmooing MMa bar/\\\\(\\\\Delta\\\\) cells rapidly exposed to high extracellular osmolyte concentration (2 M sorbitol) in a microfluidic device (MFD). (_c_) Scheme of a shmooing cell with indicated dimensions: length of protrusion and longest axis, radii of base, neck and tip. (_d_) Scheme of the MFD set-up. The interface between normal (SD) and high osmolarity (SD + 2 M sorbitol) media can be shifted by varying the input pressures, which allows to rapidly exchange the cellular environment. (_e_,_f_) Measured relative expansion \\\\(\\\\Delta t/t_{0}\\\\) and \\\\(\\\\Delta t/t_{0}\\\\) in black and simulated volumetric strain obtained from yield stress model (DM1) as yellow triangles or from yield strain model (DM2) as blue triangles, for base, neck and tip, respectively. The deformation \\\\(\\\\Delta t/t_{0}\\\\) (_e_) at the neck was significantly higher than at the base or at the tip (_t_-test, ***_p_\\\\(<\\\\) 0.001, \\\\(n\\\\) = 119), whereas longest axis and protrusion show only a slight relative expansion \\\\(\\\\Delta t/t_{0}\\\\) (_f_).\\n\\n'", "CAPTION FIGS1.png": "'\\n\\n**Figure S1. Geometrical considerations and principal in plane stresses and strains.****A** shows the used coordinates: circumferential angle \\\\(\\\\theta\\\\), meridional distance s, radius r and shell thickness d **B** shows principal stresses and strains for a given shell element. **C** circumferential and meridional stresses (\\\\(\\\\sigma_{\\\\theta}\\\\), \\\\(\\\\sigma_{s}\\\\)) and strains (\\\\(\\\\varepsilon_{\\\\theta}\\\\), \\\\(\\\\varepsilon_{s}\\\\)) are equal for a sphere, while \\\\(\\\\sigma_{\\\\theta}\\\\) is twice as high as \\\\(\\\\sigma_{s}\\\\) for the lateral surface of a cylinder. Additionally, \\\\(\\\\varepsilon_{\\\\theta}\\\\) exceeds \\\\(\\\\varepsilon_{s}\\\\), given that \\\\(v\\\\leq 0.5\\\\).\\n\\n'", "CAPTION FIGS10-1.png": "'\\n\\n**Figure S10. The DM is based on the elasto-plastic deformations of the triangular surface elements.****A** shows the triangular meshed surface of the simulated shmooing cell, concentric rings at the protrusion results from mesh refinement steps during the simulation. **B** In each simulation step the triangles deform according to the applied stresses. [caption continued, next page]'", "CAPTION FIGS10-2.png": "'If the triangle is not in the defined growth zone or \\\\(\\\\sigma_{VM}<\\\\sigma_{y}\\\\), the triangle deforms purely elastically. \\\\(L_{1},L_{2},\\\\ L_{3}\\\\) are the relaxed lengths of the unstressed triangle \\\\(T\\\\) and \\\\(l_{1},l_{2},\\\\ l_{3}\\\\) are the elastically expanded length of the resulting triangle \\\\(T^{\\\\prime}\\\\). Correspondingly, \\\\(\\\\alpha_{1},\\\\alpha_{2},\\\\ \\\\alpha_{3}\\\\) represent the relaxed angles and \\\\(\\\\beta_{1},\\\\beta_{2},\\\\ \\\\beta_{3}\\\\) the angles of the deformed triangle. Additionally, triangles in the defined growth zone deform plastically if \\\\(\\\\sigma_{VM}\\\\geq\\\\sigma_{y}\\\\). Thereby, the relaxed lengths expand to new relaxed lengths, \\\\(L_{1}^{new}\\\\), \\\\(L_{2}^{new}\\\\) and \\\\(L_{3}^{new}\\\\), respectively while the angles remain unaltered.\\n\\n'", "CAPTION FIGS10.png": "'Figure 33. The 50% based on the stable-plastic deformations of the triangular surface elements. A shows the triangular nested surface of the simulated shimming cell, concentric rings at the protrusion results from mesh refinement steps during the simulation. **B** in each simulation step the shrouges deformation according to the applied stresses. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **C**errespondingly, \\\\(\\\\sigma_{\\\\mathrm{raw}},\\\\sigma_{\\\\mathrm{y}}\\\\) represent the relaxed angles and \\\\(\\\\sigma_{\\\\mathrm{f}},\\\\sigma_{\\\\mathrm{y}}\\\\), \\\\(\\\\sigma_{\\\\mathrm{y}}\\\\), the angles define scattering angles. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **C**errespondingly, \\\\(\\\\sigma_{\\\\mathrm{raw}},\\\\sigma_{\\\\mathrm{y}}\\\\) represent the relaxed angles and \\\\(\\\\sigma_{\\\\mathrm{f}},\\\\sigma_{\\\\mathrm{y}}\\\\), \\\\(\\\\sigma_{\\\\mathrm{y}}\\\\), the angles define scattering angles. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **C**errespondingly, \\\\(\\\\sigma_{\\\\mathrm{raw}},\\\\sigma_{\\\\mathrm{y}}\\\\) represent the relaxed angles and \\\\(\\\\sigma_{\\\\mathrm{f}},\\\\sigma_{\\\\mathrm{y}}\\\\), \\\\(\\\\sigma_{\\\\mathrm{y}}\\\\), the angles define scattering angles. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **C**errespondingly, \\\\(\\\\sigma_{\\\\mathrm{raw}},\\\\sigma_{\\\\mathrm{y}}\\\\) represent the relaxed angles and \\\\(\\\\sigma_{\\\\mathrm{f}},\\\\sigma_{\\\\mathrm{y}}\\\\), \\\\(\\\\sigma_{\\\\mathrm{y}}\\\\), the angles define scattering angles. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **C**errespondingly, \\\\(\\\\sigma_{\\\\mathrm{raw}},\\\\sigma_{\\\\mathrm{y}}\\\\) represent the relaxed angles and \\\\(\\\\sigma_{\\\\mathrm{f}},\\\\sigma_{\\\\mathrm{y}}\\\\), \\\\(\\\\sigma_{\\\\mathrm{y}}\\\\), the angles define scattering angles. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{raw}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle. **J**ation curves, red-spiel \\\\(f\\\\) The triangle is not the defined growth zone at \\\\(\\\\sigma_{\\\\mathrm{y}}<\\\\sigma_{\\\\mathrm{y}}\\\\), the triangle follows purely elastically, \\\\(L_{1},L_{2}\\\\), in the relaxed lengths of the unstressed triangle and \\\\(L_{1},L_{2}\\\\), in the relaxedly expanded length of the moving triangle.\\n\\n'", "CAPTION FIGS11.png": "\"\\n\\n**Figure S11. Simulated stress, strain and elasticity profiles along the cell contour.****A** The contours of the resulting cell shape of DM1 (yellow) and DM2 (blue) at time 3250 s with indicated regions: base (I), shaft (II), neck (III) and tip (IV). **B, C, D** Contour plots along the arc length \\\\(s\\\\) of the resulting von Mises stress \\\\(\\\\sigma_{VM}\\\\), the resulting volumetric strain \\\\(\\\\varepsilon_{V}\\\\) and the assumed Young's modulus \\\\(E\\\\).\\n\\n\"", "CAPTION FIGS12.png": "'\\n\\n**Figure S12. Sensitivity analysis of the yield limit for DM1 and DM2. A and B show cell shapes obtained from simulations with various limits for yield stress \\\\(\\\\sigma_{Y}\\\\) and yield strain \\\\(\\\\varepsilon_{Y}\\\\), respectively at 1000 s, 1500 s and 2000 s. Lower \\\\(\\\\sigma_{Y}\\\\) or lower \\\\(\\\\varepsilon_{Y}\\\\) result in faster growth. When varying parameters in a certain range, similar shapes are obtained at different times.**'", "CAPTION FIGS13.png": "\"\\n\\n**Figure S13. Decrease in Young's modulus with increasing indentation velocity was negligible within the scope of this study (v=67um/s)**. The mean Young's modulus of a selected 400nm x 400nm region in the center of a trapped cell (left) plotted against the applied indentation velocity (dots with error bars). Linear regression showed a significant but minor decrease in E (slope = -0.0046 +-0.0008 MPa/(um/s), R2=0.85, F(1, 6)=33.93 p=0.001).\\n\\n\"", "CAPTION FIGS2.png": "\"\\n\\n**Figure S2. Stress, strain and elasticity profiles of the SM. A** Contours for the relaxed (dashed line) and expanded (solid line) cell shape. Tip was the origin of the meridional coordinate, indicated with dashed arrow. The regions tip (I), shaft (III), neck (III) and base (IV) are separated by dashed lines for orientation. For the cell shape in **A** profiles of: **B** Young's modulus E, von Mises stress \\\\(\\\\sigma_{\\\\text{VM}}\\\\) and volumetric strain \\\\(\\\\varepsilon_{\\\\text{V}}\\\\), **C** meridional stress \\\\(\\\\sigma_{s}\\\\), circumferential stress \\\\(\\\\sigma_{\\\\emptyset}\\\\) and \\\\(\\\\sigma_{\\\\text{VM}}\\\\), **D** meridional strain \\\\(\\\\varepsilon_{s}\\\\), circumferential strain \\\\(\\\\varepsilon_{\\\\emptyset}\\\\) and \\\\(\\\\varepsilon_{\\\\text{V}}\\\\) are shown. **E, F**\\\\(\\\\varepsilon_{\\\\text{V}}\\\\)- and E-profiles for different relaxed shapes with varying radius \\\\(R_{\\\\text{shaft.}}\\\\) were calculated. **G, H** Profiles of \\\\(\\\\varepsilon_{s}\\\\) and \\\\(\\\\varepsilon_{\\\\emptyset}\\\\) or E and \\\\(\\\\sigma_{\\\\text{VM}}\\\\) assuming a constant volumetric strain \\\\(\\\\varepsilon_{\\\\text{V}}\\\\) and the expanded cell shape in **A**.\\n\\n\"", "CAPTION FIGS3.png": "'\\n\\n**Figure S3. Mapping the cell wall elasticity of entrapped haploid S. cerevisiae cells**. **A** Scheme of the experimental setup: the previously trapped yeast cell is scanned by an AFM in Q\\\\({}^{\\\\rm{ITM}}\\\\) Mode. For each pixel a nano-indentation measurement was carried out. **B** 3D representation of the shape detected in **A**. **C** Hypothetic approach curve for one pixel in **A**, along with a Sneddon fit (green) of these data assuming a conical indenter. The resulting spatial information on the elasticity (0 MPa - 20 MPa) of the probed material was displayed in 2D images **D** or used as a texture for 3D representations **B**. **B** and **D** show the same MAT**a** bar1\\\\(\\\\Delta\\\\) cell with characteristically stiffer bud scar regions (indicated by arrows); scale bar is 1 \\\\(\\\\mu\\\\)m.\\n\\n'", "CAPTION FIGS4.png": "'\\n\\n**Figure S4. Indentation depth varies between stiffer and softer regions.****A** Exemplary force-distance curves of nano-indentation measurements at the marked region in **B** and **C**. **B** shows elasticity map and **C** indentation map of shmooing MATa bar1\\\\(\\\\Delta\\\\) cell shown in Figure 2. If both curves reached similar maximum force, the conical tip of the cantilever indented the cell wall in softer region (shaft, green dots) deeper than the stiffer region (base, orange squares), due to the smaller slope of the curve **B**. The indentation depth \\\\(\\\\delta\\\\) (mean +- Ra, N=900) of a quadratic region (550 nm x 550 nm) at the top of the cell was at the shaft (\\\\(\\\\delta_{\\\\rm shaft}\\\\) = 97 nm +- 26 nm) and at the base (\\\\(\\\\delta_{\\\\rm base}\\\\) = 38nm +- 10 nm) less or equal than 115 nm, which is supposed to be the thickness of the cell wall.\\n\\n'", "CAPTION FIGS5.png": "'\\n\\n**Figure S5. Comparison of height and elasticity patterns between \\\\(\\\\alpha\\\\)-factor treated and non-treated MATa bar\\\\(\\\\Delta\\\\) cells.****A, B** Height images and **E, F** elasticity maps of two non-treated cells and **C, D** height images and **G, H** elasticity maps of two individual MATa bar\\\\(\\\\Delta\\\\) cells treated with 10 \\\\(\\\\mu\\\\)M \\\\(\\\\alpha\\\\)-factor; black and white bars correspond to 1\\\\(\\\\mu\\\\)m. The white arrows represent position length and direction of the selected cross-sections in **I, J, K, L**. Manually selected regions for base (I), shaft (II) and tip (IV) are framed with white rectangles.\\n\\n'", "CAPTION FIGS6.png": "'\\n\\n**Figure S6. The cell wall, at shaft of the mating projection, showed significant lower E-values. A Scatter Dot Plot of the mean E-values of selected regions at the base, shaft and tip, respectively; bar represents the mean. B Mean E-values of selected regions at the shaft, the base and the tip plotted against the mean E-values at the base for each measured cell. Lines correspond to linear regressions forced through (0,0) with a slope of E\\\\({}_{\\\\text{shaft}}\\\\)/E\\\\({}_{\\\\text{base}}\\\\) = 0.28 \\\\(\\\\pm\\\\) 0.06 (Sy.x=0.41, DF 6), E\\\\({}_{\\\\text{Tip}}\\\\)/E\\\\({}_{\\\\text{Base}}\\\\)=0.71 \\\\(\\\\pm\\\\) 0.2 (Sy.x=1.7, DF 6) and E\\\\({}_{\\\\text{Base}}\\\\)/E\\\\({}_{\\\\text{Base}}\\\\)=1.00 \\\\(\\\\pm\\\\) 0.00 (Sy.x=0.00, DF 6). Broken lines correspond to the respective confidence intervals (95%). C Elasticity profiles over tip, shaft and base for all analyzed shmooing cells showed a reduction of E from base to shaft and tip to shaft for every cell.**'", "CAPTION FIGS7.png": "'\\n\\n**Figure S7. Time series replica for estimation of the cell wall dynamics during mating projection formation.****A, B** Time-lapse sequence of the height and elasticity development during the formation of a mating projection, obtained with AFM; from left to right, consecutive images of the E-distribution (top) and 3D reconstruction with elasticity pattern (bottom), from a continuous measurement. MAT**a** bar1\\\\(\\\\Delta\\\\) cells were induced with 12 mM **A** and 10 mM **B** \\\\(\\\\alpha\\\\)-factor for 122 min **A** and 42 min **B**, respectively, before the first image was acquired. White arrows indicate a region of stiffer cell wall material at the tip. Note, the first image of sequence B shows a barely noticeable reduction in E at the side of the emerging protrusion. Both time-laps series show typical AFM-artifacts for high objects (in **A** a doubling of the tip shape and in **B** a height \"shadow\"), indicated with black arrows.\\n\\n'", "CAPTION FIGS8.png": "'\\n\\n**Figure S8. Cell stiffness saturated at 1.5 N/m for high loading forces and large indentations.** The cell stiffness, obtained with indentation experiments of three untreated _bar1_\\\\(\\\\Delta\\\\) cells, was plotted against the loading forces and the corresponding indentation depths. The plotted stiffness k (mean, RMS, N=1024), represents the maximal slope of the indentation curve, using a cantilever with k of 0.64 N/m. The fitted maximum, assuming a Hill function, was used to calculate the turgor pressure applying the formula: \\\\(P=k/\\\\pi r\\\\).\\n\\n'", "CAPTION FIGS9.png": "'\\n\\n**Figure S9. Relaxed shell volume rapidly declines at higher turgor pressure.****A** shows the relaxed radius of the spherical shell with resting radius 2.5 \\\\(\\\\mu\\\\)m, **B** shows the relative volume confined by the relaxed shell, **C** the relative circumferential strain depending on turgor pressure.\\n\\n'", "CAPTION TABS1.png": "'\\n\\n**Table S1 Parameters values used in the models**'"}

extracted_captions/goyalEffectsSensemakingTranslucence2016.json

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+{"CAPTION FIG1.png": "'Figure 1: The Document Space showing (clockwise, from top-left) the directory of crime case documents, a tabbed reader panel for reading case documents, a visual graph of connections based on common entities in the dataset, a map to identify locations of crimes and events, and a timeline to track events.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: The Analysis Space showing (clockwise, from top-left) the chat for explicit sharing, connected sticklies for Implicit Sharing, hypothesis window in the middle with columns to add new Hypotheses, confirming evidence, and disconfirming evidence for explicit Hypothesis Tracking, and Suspect Visualization at the bottom with 4 Avatars: Dennis Rathbone. Marilyn Stokes, Steve Gramming, and Lousie for Suspect Tracking. Note: Chat, Visualization, Sticky, and Hypothesis Window have been magnified to improve readability.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Sample sensemaking trajectory 1. Sensemaking-Translucence reminds users to consider suspects by showing empty Avatars at the start 2. Avatars are automatically populated by names detected from implicitly shared stickies. 3, 4 & 5. Avatars show distribution of name-reference by getting darker for names mentioned in stickies, chat and hypothesis window. The last mentioned suspect in hypothesis window is marked red 6. With use, visualization depicts distribution of attention at suspect level, based on explicit mentions. Note: Chat, Visualization, Sticky, and Hypothesis Window have been magnified to improve readability in 2, 3, 4 and 5. 1 and 6 represent non-magnified versions of the Sensemaking Translucence interface.\\n\\n'", "CAPTION FIG4.png": "'Figure 4. Serial killer identification and number of correct clues identified by interface condition.\\n\\n'", "CAPTION FIG5.png": "'Figure S. Perception of interface usefulness by interface condition\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Self-reported workload and team experience by interface condition.\\n\\n'"}

extracted_captions/gressin2015architecture.json

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+{"CAPTION FIG1.png": "'Figure 1: Effect of ADF/Cofilin on Different Actin Network Architectures (A) Schematic description of the experiment performed in Figure 1. (B) Left: time course of Alexa-568-labeled actin (2 \u03bcM assembly on Las-17-coated micropatterns in the presence of Arp2/3 complex (20 nM), prior to the addition of ADF/cofilin. Right: color-coded cartoon of actin network architectures. (C) Quantification of (B). Actin network normalized fluorescence intensity along the yellow linescan indicated in (B) after a 115 min polymerization time is shown. (D) Left: time course of Alexa-488-labeled ADF/cofilin (2 \u03bcM; gravel) binding to actin networks (red). Right: quantification of actin (red) and ADF/cofilin (green) fluorescence intensities, normalized to their peak intensities. Scale bars represent 30 \u03bcm. See also Figure S1 and Movie S1.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Effect of Alp1 on ADF/Cofilin-Bound Actin Networks (**A**) Schematic description of the experiment performed in Figures 2A and 2B and 2C. (**B**) Left panels: Trna course of Alp1-SAAP-Alaxa-647 (1 uM; in black) binding to ADF/cofilin-decorated actin networks. Right panels: Quantification of actin (_n_ red, Alp2/cofilin (_n_ green) and Alp1 (_n_ blue) fluorescence intensities, normalized to their peak intraclassics. Scale Bar represents 30 \u03bcm. See abs More S9.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: **Quantitative Measurement of ADF/Cofflin Accumulation along the Side of Individual Actin Filaments** (A) Time course of Alexa-488-labeled ADF/cofflin (green) binding to individual actin filaments (800 nM; red), at the indicated concentrations. White arrowheads show representative examples of ADF/cofflin cooperative binding to actin filaments. Blue arrowheads show a representative example of a swerving event, where ADF/cofflin molecules remain mainly on one and of the fragments. The scale bar represents 5 \\\\(\\\\mu\\\\)m. (B) Quantification of (A). A time course of four representative molecular accumulations of ADF/cofflin along actin filaments for 180 nM (dotted lines) or 360 nM (continuous line) or ADF/cofflin is shown. Curves are plotted in blue prior to fragmentation and in red after fragmentation occurred. (C) Quantification of (A) and (B). Distribution of the number of ADF/cofflin molecules bound to actin filaments prior to sevaring is shown (23 = 11 molecules; n = 46). Error bars indicate the SD. (D) Representative field of observation after many fragmentation events with 360-_n_M ADF/cofflin. The scale bar represents 10 \\\\(\\\\mu\\\\)m. (E) Fluorescence recovery after photobleaching (FRAP) of ADF/cofflin accumulations after sevaring. (F) Time course of actin filament elongation after sevaring. The scale bar represents 5 \\\\(\\\\mu\\\\)m. (B) Kymograph of (D), plotted along the axis of the filament. See also Figures S2\u2013S4 and (A). (B). Distribution of the number of ADF/cofflin molecules bound to actin filaments prior to sevaring is shown (23 = 11 molecules; n = 46). Error bars indicate the SD.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Effect of Alp1 on Individual ADF/Cofilin-Bound Actin Filaments (A) Schematic description of the experiment performed in Figure 4.\\n\\n(B) Time course of Alp1*s (1 mM) effect on individual actin filaments (800 mM; red) decorated with various amounts of ADF/cofilin (green). White arrowheads track representative examples of ADF/cofilin stretches bound to the side of actin filaments (non-sewaving events). Red arrowheads track representative examples of ADF/cofilin stretches bound to the parload end of actin filaments (subsequent to a sawering event). Scale bars represent 5 mM.\\n\\n(C) Quantification of (B). A time course of three representative ADF/cofilin stretches along actin filaments at 180 mM (black curve) and 360 nM (red and blue curves) at ADF/cofilin after injection of Alp1 is shown. Clusters of ADF/cofilin are obscured either before (blue curve) or after (red curve) the fragmentation occurred. Fluorescence signal decrease of end-binding ADF/cofilin clusters were fitted with a microenvironmental decay (\\\\(\\\\Gamma_{\\\\text{disc}}=1.3\\\\pm 1.1\\\\); \\\\'", "CAPTION FIG5.png": "'Figure 6: **Actin Filament Elongation Assay in the Presence of ADF/Cotfillin and Alp1**(A) Time course of Alexa-558-actin filament (800 nM; red) elongation in the presence of 360 nM ADF/cotfin after injection of 800 nM Alexa-647-actin monomers (blue) and 20 nM capping protein. (B) Time course of Alexa-558-actin filament (800 nM; red) elongation in the presence of 360 nM ADF/cotfin after injection of 800 nM Alexa-647-actin monomers (blue) and 1 uM Alp1. The scale bar represents 5 um.\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Effect of ADF/Cotfilin and Alp1 on Actin Filaments Blocked by Capping Protein\\n\\nTop: time course of actin filament (800 nM) elongation in the presence of 2-uM Alexa-488-ADF/cotfilin for 4 min, followed by a first injection of 20-nM capping protein for 16 min and a second injection of 1-uM Aipt. The scale bar represents 5 \u03bcm. Bottom: kymograph of the experiment plotted along the axis of an representative actin filament.\\n\\n'", "CAPTION FIG7-1.png": "'Figure 7: Models for the DIsassembly of Actin by ADF/Cofilin and Alp1 (A) Bioassembly at the whole-network scale: architecture dependence. In this model, binding of ADF/cofilin to actin cables does not trigger their disassembly, but switches actin filaments (blue filaments) to a pre-diassembly state (red filaments) (top). However, ADF/cofilin has an important effect for the dismantling of branched networks, through its de-branching activity (bottom). For all actin networks, presence of Alp1 turns these stable ADF/cofilin-decorated structures into unstable assemblies, prone to stochastic disassembly. (B) Swarming and disassembly at the single-filament scale. In this model, binding of ADF/cofilin needs to reach a threshold level of 23 molecules to trigger a conformational change of the filaments (represented by a change in their color, from blue to red). At a low concentration of ADF/cofilin (left), the threshold level is not reached. At an intermediate concentration of ADF/cofilin (center), actin filaments decorated by sub-stoichiometric densities of ADF/cofilin but with N > 23.\\n\\n'", "CAPTION FIG7-2.png": "'molecules of ADF/coffin are prone to an asymmetric swearing event. After fragmentation, ADF/coffin stretches remain near the pointed ends (PO), while barbed ends (BA) remain free to elongate. At a high concentration of ADF/coffin (right), filaments decorated by stoichiometric densities of ADF/coffin are stable. In this model, the conformation of actin filaments regulates the activity of Aip1. Only actin filaments decorated with N > 23 molecules of ADF/coffin undergo a fast stochastic disassembly.\\n\\n'", "CAPTION FIG7.png": "'* [18] J. M. C. _et al._, \"The \\\\(\\\\pi^{+}\\\\pi^{-}\\\\)'"}

extracted_captions/grozaSALTWeavingClaim2007.json

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+{"CAPTION FIG1.png": "'\\n\\n**Fig. 1.** Example of instantiation of the claim identification tree'", "CAPTION FIG2.png": "'Figure 2: Improved SALT semantic layer to support better identification\\n\\n'", "CAPTION FIG3.png": "'\\n\\n**Fig. 3. Example of rhetorical elements in a scientific document**'", "CAPTION FIG4.png": "'\\n\\n**Fig. 4. Example of test encoded in PDF format**'", "CAPTION FIG5.png": "'Figure 5: Example of transformation of a claim identification tree into a CBIB item.\\n\\n'", "CAPTION FIG6.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n G. 1990. The evolution of the density of the gas in the central region. _Phys. Rev. Lett._**78**,'", "CAPTION FIG7.png": "'\\n\\n**Fig. 1.** A. **Annotation** **tack** **evaluation**'", "CAPTION FIG8.png": "'\\n\\n**Fig. 8. A.** Soundness evaluation; **B.** Benefit uncertainty evaluation'"}

extracted_captions/harsDesigningScientificKnowledge2001.json

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+{"CAPTION FIG1.png": "'Figure 1: Conceptual model of paper-based scientific knowledge [semi-plified by excluding paper copies].\\n\\n'", "CAPTION FIG2.png": "\"\\n\\n**Fig. 2.**_Pugner's epistemology (class diagram).\\n\\n\"", "CAPTION FIG3.png": "'\\n\\n**Fig. 1.** A single-particle (Cas diagram).\\n\\n'", "CAPTION FIG4.png": "\"\\n\\n**Fig. 4.** Chain's epidemiology (Case diagram).\\n\\n\"", "CAPTION FIG5.png": "\"\\n\\n**Fig. 5.** Range's epistemology [class diagram].\\n\\n\"", "CAPTION FIG6.png": "'\\n\\n**Fig. 6.** Synthesized conceptual model of scientific knowledge.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table I.** Competency questions for a body of scientific knowledge'", "CAPTION TAB2.png": "'\\n\\n## Chapter 2 Core term related to research methodology\\n\\n### 2.1 Core term related to research methodology\\n\\n#### 2.1.1 Core term related to research methodology\\n\\nThe core term related to research methodology is a core term related to research methodology.\\n\\n'"}

extracted_captions/hassinger2017design.json

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+{"CAPTION FIG1.png": "'Figure 1: Schematic depiction of the main mechanical steps in CME. A multicomponent protein coat forms on the plasma membrane and causes the membrane to bend inward, forming a shallow pit. As the coat matures, the membrane becomes deeply irradiated to form an open, U-shaped pit before constricting to form a closed, \\\\(\\\\Omega\\\\)-shaped bud. The bud subsequently undergoes incision to form an internalized vesicle, and the coat is recycled. Actin polymerization is thought to provide a force, \\\\(\\\\mathbf{f}_{\\\\text{s}}\\\\) to facilitate these morphological changes, particularly at high membrane tensions [5]. Our study is focused on understanding the impact of membrane tension on the morphological changes affected by the coat and actin polymerization, as indicated by the dashed box.\\n\\n'", "CAPTION FIG2.png": "'\\nFig. 2: Membrane tension inhibits the ability of curvature generating costs to induce budding. (**a**) Profile views of membrane morphologies generated by simulations in which the area of a curvature-generating coat progressively increases, covering more of the bare membrane. The curvature-generating capability, or spontaneous curvature, of the coat is set at \\\\(C_{0}=0.02\\\\,\\\\mathrm{r}\\\\mathrm{m}^{-1}\\\\), corresponding to a preferred radius of curvature of \\\\(50\\\\,\\\\mathrm{n}\\\\mathrm{m}\\\\) (12, (**a**, _Upper_**) High membrane tension, \\\\(\\\\lambda_{3}=0.2\\\\,\\\\mathrm{p}\\\\mathrm{N}\\\\mathrm{/}\\\\mathrm{n}\\\\mathrm{m}\\\\). The membrane remains nearly flat as the area of the coat increases. (**a**, _Lower_**) Low membrane tension, \\\\(\\\\lambda_{3}=0.02\\\\,\\\\mathrm{p}\\\\mathrm{N}\\\\mathrm{/}\\\\mathrm{n}\\\\mathrm{m}\\\\). Addition of coat produces a smooth evolution from a flat membrane to a closed bud. (**b**) Membrane profiles for simulations with a constant coat area in which the spontaneous curvature of the coat progressively increases. The area of the coat is \\\\(A_{\\\\mathrm{cat}}=20.106\\\\,\\\\mathrm{n}\\\\mathrm{m}^{2}\\\\). (**b**, _Upper_**) High membrane tension, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\mathrm{p}\\\\mathrm{N}\\\\mathrm{/}\\\\mathrm{n}\\\\mathrm{m}\\\\). The membrane remains nearly flat with increasing spontaneous curvature. (**b**, _Lower_**) Low membrane tension, \\\\(\\\\lambda_{0}=0.002\\\\,\\\\mathrm{p}\\\\mathrm{N}\\\\mathrm{/}\\\\mathrm{n}\\\\mathrm{m}\\\\). Increasing the spontaneous curvature of the coat induces a smooth evolution from a flat membrane to a closed bud.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: A snap-through instability exists at intermediate, physiologically relevant (S4), membrane tensions, \\\\(\\\\lambda_{6}=0.02\\\\,\\\\mathrm{n}\\\\mathrm{M}/\\\\mathrm{r}\\\\mathrm{n}\\\\). (A) Membrane profiles showing bud morphology before (dashed line, \\\\(\\\\mathcal{A}_{\\\\mathrm{coat}}=20,0.65\\\\,\\\\mathrm{n}\\\\mathrm{m}^{2}\\\\)) and after (solid line, \\\\(\\\\mathcal{A}_{\\\\mathrm{coat}}=20,105\\\\,\\\\mathrm{r}\\\\mathrm{m}^{2}\\\\)) addition of a small amount of area to the coat, \\\\(C_{\\\\mathrm{q}}=0.02\\\\,\\\\mathrm{r}\\\\mathrm{m}^{-1}\\\\). (B) Mean curvature at the tip of the bud as a function of the coat area. There are two stable branches of solutions of the equilibrium membrane shape equations. The lower branch consists of open, U-shaped buds, whereas the upper branch consists of closed, G-shaped buds. The dashed portion of the curve indicates \u201cunstable\u201d solutions that are not accessible by simply increasing and decreasing the area of the coat. The marked positions on the curve denote the membrane profiles shown in \\\\(A\\\\). The transition between these two shapes is a snap-through instability, in which the bud maps closed upon a small addition to area of the coat. (C) Bud morphologies before (dashed line) and after (solid line) a snap-through instability with increasing spontaneous curvature, \\\\(\\\\mathcal{A}_{\\\\mathrm{coat}}=20,106\\\\,\\\\mathrm{r}\\\\mathrm{m}^{2}\\\\), \\\\(C_{0}=0.02\\\\,\\\\mathrm{r}\\\\mathrm{m}^{2}\\\\). (D) Mean curvature at the tip of the bud as a function of the spontaneous curvature of the coat. (E) Bud morphology before (dashed line) and after (solid line) a snap-through instability with decreasing membrane tension, \\\\(\\\\mathcal{A}_{\\\\mathrm{coat}}=20,106\\\\,\\\\mathrm{r}\\\\mathrm{m}^{2}\\\\), \\\\(C_{0}=0.02\\\\,\\\\mathrm{r}\\\\mathrm{m}^{2}\\\\), \\\\(\\\\lambda_{6}=0.02\\\\,\\\\mathrm{r}\\\\mathrm{n}\\\\mathrm{M}/\\\\mathrm{r}\\\\mathrm{n}\\\\). (F) Mean curvature at the tip of the bud as a function of the membrane-fension.\\n\\n'", "CAPTION FIG4.png": "'\\nFig. 4: Bud morphology depends on bending rigidity, membrane tension, spontaneous curvature, and coat area. (A) Coat spontaneous curvature (\\\\(\\\\zeta_{0}\\\\)) vs. membrane tension (\\\\(\\\\lambda_{0}\\\\)) phase diagram. The regions of the diagram are color coded according to the final shape of the membrane for coat \u201cgrowing\u201d simulations performed with the specified values for edge membrane tension and coat spontaneous curvature. Blue denotes closed, \\\\(\\\\Omega\\\\)-buds; red denotes open, U-shaped pits; and green are situations in which closed buds are obtained via a snap-through transition. The snap-through solutions cluster about the dashed line, \\\\(\\\\text{Ves}=1\\\\), which separates the high and low membrane tension regimes (for details, see the Instability _Evists over a Range of Membrane Tensions_, Coat Areas, and Spontaneous Curvature). The lines labeled B and C, respectively, indicate the phase diagrams at right. (B) Coat area vs. membrane tension phase diagram, \\\\(\\\\zeta_{0}=0.02\\\\) nm\\\\({}^{-1}\\\\). Blue denotes closed buds, red denotes open buds, and green denotes parameters that have both open and closed bud solutions. The dashed line, \\\\(\\\\text{Ves}=1\\\\), marks the transition from low to high membrane tension. The solid line represents the theoretical area of a sphere that minimizes the Heifrich energy at the specified membrane tension (_SI Appendix, 3. Radius of a Vesicle from Energy Minimization_). (C) Coat area vs. spontaneous curvature phase diagram, \\\\(\\\\lambda_{0}=0.02\\\\) pN/nm. The dashed line, \\\\(\\\\text{Ves}=1\\\\), marks the transition between spontaneous curvatures that are capable and incapable of overcoming the membrane tension to form a closed bud. The solid line represents the theoretical area of a sphere that minimizes the Heifrich energy at the specified spontaneous curvature (_SI Appendix, 3. Radius of a Vesicle from Energy Minimization_).\\n\\n'", "CAPTION FIG5.png": "'Figure 5: The snap-through instability at physiological tension, \\\\(\\\\lambda_{0}=0.02\\\\,\\\\mathrm{pN/nm}\\\\), is abolished when the bending rigidity of the coat is increased relative to the bare membrane, \\\\(\\\\kappa_{\\\\mathrm{bare}}=320\\\\,\\\\mathrm{pN}\\\\cdot\\\\mathrm{nm}\\\\), \\\\(\\\\kappa_{\\\\mathrm{coatt}}=2400\\\\,\\\\mathrm{pN}\\\\cdot\\\\mathrm{nm}\\\\). (\\\\(A\\\\)) Membrane profiles showing a smooth progression of bud morphologies as the area at the coat is increased (\\\\(\\\\Delta_{\\\\mathrm{cat}}=10,000\\\\,\\\\mathrm{nm}^{2}\\\\), \\\\(20,000\\\\,\\\\mathrm{nm}^{2}\\\\), \\\\(28,000\\\\,\\\\mathrm{nm}^{2}\\\\)), \\\\(\\\\xi_{0}=0.02\\\\,\\\\mathrm{nm}^{-1}\\\\). (\\\\(B\\\\)) Mean curvature at the bud tip as a function of the area of the coat. The marked positions denote the membrane profiles shown in \\\\(A\\\\). There is new only a single branch of solutions (compared with Fig. 3B), indicating a smooth evolution from a flat membrane to a closed bud. (\\\\(C\\\\)) Membrane profiles showing a smooth progression of bud morphologies as spontaneous curvature of the coat is increased (\\\\(C_{0}=0.01\\\\,\\\\mathrm{nm}^{-1},0.02\\\\,\\\\mathrm{nm}^{-1},0.024\\\\,\\\\mathrm{nm}^{-1}\\\\)), \\\\(\\\\Delta_{\\\\mathrm{coatt}}=20,106\\\\,\\\\mathrm{nm}^{2}\\\\). (\\\\(D\\\\)) Mean curvature at the bud tip as a function of the spontaneous curvature of the coat showing a single branch of solutions (compare with Fig. 3D).\\n\\n'", "CAPTION FIG6.png": "'Figure 6: A force from actin assembly can mediate the transition from a U- to \\\\(\\\\Omega\\\\)-shaped bud, avoiding the instability at intermediate membrane tension, \\\\(\\\\lambda_{0}=0.02\\\\) pN/rem. Two orientations of the actin force were chosen based on experimental evidence from yeast [31] and mammalian [45] cells. (A) Schematic depicting actin polymerization in a ring at the base of the pit with the network attached to the coat, causing a net inward force on the bud. (B) At constant coat area, \\\\(A_{\\\\text{can}}=17,593\\\\) nm\\\\({}^{2}\\\\), and spontaneous curvature, \\\\(C_{0}=0.02\\\\) nm\\\\({}^{-1}\\\\), a force (red dash) adjacent to the coat drives the shape transition from a U-shaped (dashed line) to \\\\(\\\\Omega\\\\)-shaped bud (solid line). The force intensity was homogeneously applied to the entire coat, and the force intensity at the base of the pit was set such that the total force on the membrane integrates to zero. The final applied inward force on the bud was \\\\(\\\\mathbf{f}=15\\\\) pN, well within the capability of a polymerizing actin network [60]. (C) Schematic depicting actin assembly in a collar at the base, directly providing a constricting force [45]. (D) A constricting force (red dash) localized to the coat drives the shape transition from a U-shaped (dashed line) to \\\\(\\\\Omega\\\\)-shaped bud (solid line), \\\\(A_{\\\\text{coat}}=17,593\\\\) nm\\\\({}^{2}\\\\), \\\\(C_{0}=0.02\\\\) nm\\\\({}^{-1}\\\\). The force intensity was homogeneously applied perpendicular to the membrane to an area of 5,027 nm\\\\({}^{2}\\\\) immediately adjacent to the coated region. The final applied force on the membrane was \\\\(\\\\mathbf{f}<1\\\\) pN.\\n\\n'", "CAPTION FIG7.png": "'Figure 7: A combination of increased coat rigidity and force from actin polymerization ensures robust vesiculation, even at high membrane tension, \\\\(A_{0}=0.2\\\\) pN/nm, \\\\(C_{0}=0.02\\\\) nm\\\\({}^{-1}\\\\). (A) Application of the inward directed actin force (as in Fig. 6a) induces tubulation, but not vesiculation, at high tension. (B) Increasing the stiffness of the coat alone is insufficient to overcome high membrane tension (dashed line). However, increasing the coat stiffness enables the applied force to induce vesiculation and decreases the magnitude of the force required by a factor of 3. (C) Application of the constricting actin force (as in Fig. 6C) is sufficient to induce vesiculation, even at high tension. The magnitude of the applied force required is likely unrealistically high in a biologically relevant setting. (D) Increasing the coat stiffness decreases the force required to induce vesiculation by an order of magnitude.\\n\\n'", "CAPTION FIG8.png": "'Figure 8: Design principles for robust vesiculation. The rigidity of the plasma membrane, as well as the membrane tension, resists budding by curvature-generating coats. In the low tension regime, as defined by the vesiculation number, increasing the coat area or spontaneously curvature is sufficient to induce a smooth evolution from a flat membrane to a closed bud. A combination of increased coat rigidity and force from actin polymerization is necessary to ensure robust vesiculation in the high memoranderation regime.\\n\\n'", "CAPTION FIGMOVIES1.png": "'\\n\\n**Movie 51**.: Membrane tension membrane budding in which the area of a curvature-generating coat progressively increases, covering more of the bare membrane. The curvature-generating capability, or spontaneous curvature, of the coat is set at \\\\(C_{3}=0.02\\\\,\\\\mathrm{nm}^{-1}\\\\), corresponding to a preferred radius of curvature of \\\\(50\\\\,\\\\mathrm{nm}\\\\) (\\\\(12\\\\), \\\\(45\\\\)). (_Left_) High membrane tension, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\mathrm{pN/nm}\\\\). The membrane remains nearly flat as the area of the coat increases. (_Right_) Low membrane tension, \\\\(\\\\lambda_{3}=0.002\\\\,\\\\mathrm{pN/nm}\\\\). Addition of coat produces a smooth evolution from a flat membrane to a closed bud.\\n\\n'", "CAPTION FIGMOVIES2.png": "'\\n\\n**Movie 52**.: Membrane tension inhibits membrane budding in which the spontaneous curvature of a curvature-generating coat progressively increases at fixed area, \\\\(A_{\\\\text{last}}=20,106\\\\,\\\\text{nm}^{2}\\\\). (_Left_) High membrane tension, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\text{pN}/nm\\\\). The membrane remains nearly flat with increasing spontaneous curvature. (_Right_) Low membrane tension, \\\\(\\\\lambda_{4}=0.002\\\\,\\\\text{pN}/nm\\\\). Increasing the spontaneous curvature of the coat induces a smooth evolution from a flat membrane to a closed bud.\\n\\n'", "CAPTION FIGMOVIES3.png": "'\\n\\n**Movie 53**.: A snap-through instability occurs with increasing coat area at intermediate, physiologically relevant (54), membrane tensions, \\\\(\\\\lambda_{0}=0.02\\\\) pH/_nm_. (Left) Membrane profiles showing bud morphology as the area to the coat increases, \\\\(\\\\mathcal{C}_{0}=0.02\\\\) nm\\\\({}^{-1}\\\\). (Right) Mean curvature at the tip of the bud as a function of the coat area. There are two stable branches of solutions of the equilibrium membrane shape equations. The marked position on the curve denotes the membrane profile shown on the left.\\n\\n'", "CAPTION FIGMOVIES4.png": "'\\n\\n**Movie 54**.: A snap-through instability occurs with increasing coat spontaneous curvature at intermediate, physiologically relevant (54), membrane tensions, \\\\(\\\\lambda_{0}=0.02\\\\) pN/nm. (_Left_) Bud morphology with increasing coat spontaneous curvature, \\\\(A_{\\\\text{last}}=20,106\\\\) nm\\\\({}^{2}\\\\). (_Right_) Mean curvature at the tip of the bud as a function of the spontaneous curvature of the coat. There are two stable branches of solutions of the equilibrium membrane shape equations. The marked position on the curve denotes the membrane profile shown on the left.\\n\\n'", "CAPTION FIGMOVIES5.png": "'\\n\\n**Movie 55**.: A snap-through instability occurs with decreasing membrane tension at intermediate, physiologically relevant [54], membrane tensions, \\\\(\\\\lambda_{b}=0.02\\\\) pN/nm. (_Left_) Bud morphology with decreasing membrane tension, \\\\(A_{\\\\text{test}}=20,106\\\\) nm\\\\({}^{2}\\\\), \\\\(\\\\text{C}_{b}=0.02\\\\) nm\\\\({}^{2}\\\\). (_Right_) Mean curvature at the tip of the bud as a function of the membrane tension. There are two stable branches of solutions of the equilibrium membrane shape equations. The marked position on the curve denotes the membrane profile shown on the left.\\n\\n'", "CAPTION FIGMOVIES6.png": "'\\n\\n**Movie 56**.: The snap-through instability with increasing coat area at physiological tension, \\\\(\\\\lambda_{b}=0.02\\\\,\\\\mathrm{pH/nm}\\\\), is abolished when the bending rigidity of the coat is increased relative to the bare membrane, \\\\(k_{\\\\mathrm{bare}}=320\\\\,\\\\mathrm{pH}\\\\cdot\\\\mathrm{nm}\\\\), \\\\(k_{\\\\mathrm{coac}}=2400\\\\,\\\\mathrm{pH}\\\\cdot\\\\mathrm{nm}\\\\). (_Left_/_f_) Membrane profiles showing a smooth progression of bud morphologies as the area of the coat is increased, \\\\(C_{\\\\mathrm{A}}=0.02\\\\,\\\\mathrm{nm}^{-1}\\\\). (_Right_) Mean curvature at the bud tip as a function of the area of the coat. The marked position denotes the membrane profile shown at left.\\n\\n'", "CAPTION FIGMOVIES7.png": "'\\n\\n**Movie 57**.: The snap-through instability with increasing cost spontaneous curvature at physiological tension, \\\\(\\\\lambda_{b}=0.02\\\\,\\\\text{pH}/\\\\text{nm}\\\\), is abolished when the bending rigidity of the coat is increased relative to the bare membrane, \\\\(k_{\\\\text{base}}=320\\\\,\\\\text{pH}\\\\cdot\\\\text{nm}\\\\), \\\\(k_{\\\\text{cast}}=2400\\\\,\\\\text{pH}\\\\cdot\\\\text{nm}\\\\). (_Left_) Membrane profiles showing a smooth progression of bud morphologies as spontaneous curvature of the coat is increased, \\\\(A_{\\\\text{cast}}=20\\\\), \\\\(106\\\\,\\\\text{nm}^{2}\\\\). (_Right_) Mean curvature at the bud tip as a function of the spontaneous curvature of the coat. The marked position denotes the membrane profile shown at left.\\n\\n'", "CAPTION FIGMOVIES8.png": "'\\n\\n**Movie S5.** A force from actin assembly can mediate the transition from a U- to \\\\(\\\\Omega\\\\)-shaped bud, avoiding the instability at intermediate membrane tension, \\\\(\\\\lambda_{b}=0.02\\\\) mN/nm. (_Left_) at constant coat area, \\\\(A_{\\\\text{coat}}=17,593\\\\) nm\\\\({}^{2}\\\\), and spontaneous curvature, \\\\(C_{b}=0.02\\\\) nm\\\\({}^{-1}\\\\), a force (red dash) localized to the coat drives the shape transition from a U-shaped to \\\\(\\\\Omega\\\\)-shaped bud. The applied force on the membrane remains below \\\\(\\\\mathbf{f}=20\\\\) pN, well within the capability of a polymerizing actin network (_Sol_). (_Right_) A constricting force (red dash) adjacent to the coat drives the shape transition from a U-shaped to \\\\(\\\\Omega\\\\)-shaped bud, \\\\(A_{\\\\text{coat}}=17,593\\\\) nm\\\\({}^{2}\\\\), \\\\(C_{b}=0.02\\\\) nm\\\\({}^{-1}\\\\). The force intensity was homogeneously applied perpendicular to the membrane to an area of \\\\(5,027\\\\) nm\\\\({}^{2}\\\\) immediately adjacent to the coated region. The applied force on the membrane remains below \\\\(\\\\mathbf{f}=1\\\\) pH.\\n\\n'", "CAPTION FIGMOVIES9.png": "'\\n\\n**Movie 59.** Comparison of actin ring forces as implemented in this study and by Walani et al. (42), \\\\(\\\\lambda_{6}=0.2\\\\) pN/nm. (_Left_) Membrane profiles showing morphology during tubulation with constant inner and outer radii (\\\\(\\\\dot{n}_{\\\\rm inner}=100\\\\) nm and \\\\(R_{\\\\rm outer}=150\\\\) nm) for the ring of upward directed force at the base of the invagination. Force initially increases with increasing depth of the invagination but remains constant after tubulation. (_Right_) Membrane during tubulation. Rather than the actin force ring being fixed with inner and outer radii \\\\(R_{\\\\rm core}=100\\\\) nm and \\\\(R_{\\\\rm outer}=150\\\\) nm, it tracks the same area of the membrane (between \\\\(A_{\\\\rm outer}=31,416\\\\) nm\\\\({}^{2}\\\\)\\\\(A_{\\\\rm outer}=70,686\\\\) nm\\\\({}^{2}\\\\)) as it is pulled into the tube. We believe that the counterforce in Walani et al. (42) was implemented in this manner. Force initially increases with increasing depth of the invagination, decreases upon tubulation, and subsequently increases as the length of the tube increases.\\n\\n'", "CAPTION FIGS1.png": "'Figure S1: Schematic of the axisymmetric geometry adopted for the simulations as described in Section 1.3 The boundary conditions at the tip of the bud and the boundary of the patch were implemented as indicated. The optional boundary conditions (\\\\(\\\\lx@sectionsign\\\\)30) and (\\\\(\\\\lx@sectionsign\\\\)31) were used to obtain the value of applied force in actin-mediated inward-directed force (Figure S2) and constriction force (Figure S3) simulations, respectively (see Section 1.3.3.\\n\\n'", "CAPTION FIGS2.png": "'Figure S2: A hyperbolic tangent functional form was used to implement heterogeneous membrane properties. As an example, \\\\(y=\\\\frac{1}{2}\\\\left[\\\\tanh(\\\\gamma(x-3))-\\\\tanh(\\\\gamma(x-7))\\\\right]\\\\) is plotted with \\\\(\\\\gamma=20\\\\). The sharp transitions were ideal for specifying the boundaries of the coated region or regions of applied force, and the smoothness of the tanh function allowed for straightforward implementation into the numerical scheme.\\n\\n'", "CAPTION FIGS3.png": "'Figure S3: High membrane tension, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\)pN/nm, \\\\(C_{0}=0.02\\\\,\\\\)nm\\\\({}^{-1}\\\\). At high membrane tension, the coat can grow arbitrarily large without causing a substantial deformation of the membrane. **(A)**\\\\(A_{\\\\rm cont}=251\\\\),\\\\(327\\\\,\\\\)nm\\\\({}^{2}\\\\), **(B)**\\\\(A_{\\\\rm cont}=1\\\\),\\\\(256\\\\),\\\\(637\\\\,\\\\)nm\\\\({}^{2}\\\\), **(C)**\\\\(A_{\\\\rm coat}=2\\\\),\\\\(513\\\\),\\\\(274\\\\,\\\\)nm\\\\({}^{2}\\\\)\\n\\n'", "CAPTION FIGS4.png": "'Figure S4: The size of the membrane patch has essentially no effect on the observed deformations of the membrane as long as it is sufficiently large. **(A)** Membrane profiles for identical coat areas and differing total patch areas. \\\\(\\\\lambda_{0}=0.002\\\\,\\\\)pN/nm, \\\\(A_{\\\\rm cost}=25,133\\\\,\\\\)nm\\\\({}^{2}\\\\), \\\\(C_{0}=0.02\\\\,\\\\)nm\\\\({}^{-1}\\\\). The deformations are identical for very large membrane patches. **(B-D)** Z-position of the bud tip, mean curvature of the bud tip, and energy to deform the membrane, respectively, as a function of the dimensionless area of the membrane patch. The deformation of the membrane is sensitive to small membrane patches, but is essentially identical beyond \\\\(\\\\alpha_{\\\\rm max}\\\\approx 200\\\\), particularly in terms of the tip mean curvature and the deformation energy.\\n\\n'", "CAPTION FIGS6.png": "'Figure S6: Mean curvature at the bud tip as a function of the area of the coat for the three different membrane tension cases. High membrane tension, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\)pN/nm: The mean curvature at the bud tip drops to nearly \\\\(0\\\\,\\\\)nm\\\\({}^{-1}\\\\) as the size of the coat increases and the membrane stays essentially flat at the center of the patch (Figure 11-C). Low membrane tension, \\\\(\\\\lambda_{0}=0.002\\\\,\\\\)pN/nm: The mean curvature at the bud tip remains at approximately \\\\(0.02\\\\,\\\\)nm\\\\({}^{-1}\\\\) as the size of the coat increases and the membrane adopts the spontaneous curvature of the coat (Figure 12-F). Intermediate membrane tension, \\\\(\\\\lambda_{0}=0.002\\\\,\\\\)pN/nm: Reproduced from Figure 13. The mean curvature at the bud tip is lower for open buds (lower solution branch) relative to the low tension case, indicating that tension is inhibiting curvature generation by the coat. In contrast, the curvature is higher in the closed buds (upper solution branch) relative to closed buds in the low tension case, showing that membrane tension serves to shrink the size (and hence increase the curvature) of closed buds.\\n\\n'", "CAPTION FIGS7.png": "'Figure S7: Comparison of actin ring forces as implemented in this study and by Walani et al. [19], \\\\(\\\\lambda_{0}=0.2\\\\,\\\\)pN/nm. **(A)** Membrane profiles showing morphology before (dashed line, \\\\(Z_{p}=-100\\\\,\\\\)nm) and after (solid line, \\\\(Z_{p}=-500\\\\,\\\\)nm) tubulation with constant inner and outer radii (\\\\(R_{\\\\mathrm{inner}}=100\\\\,\\\\)nm and \\\\(R_{\\\\mathrm{outer}}=150\\\\,\\\\)nm) for the ring of upward directed force at the base of the invagination. This implementation of the actin force was used in Figures S9 and A&B. **(B)** Applied force as a function of the tip displacement. Force initially increases with increasing depth of the invagination, but remains constant after tubulation. This behavior is also observed in the absence of a ring force [19]. **(C)** Membrane morphology before (dashed line, \\\\(Z_{p}=-100\\\\,\\\\)nm) and after (solid line, \\\\(Z_{p}=-500\\\\,\\\\)nm) tubulation. The ring force is applied such that it is always applied between \\\\(A_{\\\\mathrm{inner}}=31,416\\\\,\\\\)nm\\\\({}^{2}\\\\)\\\\(A_{\\\\mathrm{outer}}=70,686\\\\,\\\\)nm\\\\({}^{2}\\\\) in the area-dependent parametrization (Section I.4). Rather than being fixed at a ring with inner and outer radii\\\\(R_{\\\\mathrm{inner}}=100\\\\,\\\\)nm and \\\\(R_{\\\\mathrm{outer}}=150\\\\,\\\\)nm, the ring tracks the same area of the membrane as it is pulled into the tube. The net effect of this is to limit the amount of membrane that can enter the tube. We believe that the counter force in Walani et al. [19] was implemented in this manner. **(D)** Applied force as a function of the tip displacement. Force initially increases with increasing depth of the invagination, decreases upon tubulation, and subsequently increases as the length of the tube increases, leading to a snapthrough instability with increasing force, as found by Walani et al. This instability is occurs independent of the membrane tension or the presence of a curvature-generating coat (data not shown). The physiological relevance of this implementation of the actin force and the snapthrough instability that results is unclear for two reasons: 1) It is unclear whether actin or other proteins at the base of the invagination would limit the ability of the membrane to flow into the invagination as implicitly assumed by this implementation, and 2) Because force from actin polymerization is a reaction force established through a Brownian ratchet mechanism, it is not clear that the snapthrough would occur, though the increase in the stress in the bilayer as the tube extends certainly could cause rupture, as hypothesized by Walani et al.\\n\\n'", "CAPTION FIGS8.png": "'Figure S8: Effect of Gaussian modulus variation on membrane budding via increasing coat area, \\\\(\\\\lambda_{0}=0.2\\\\,\\\\mathrm{pN/nm}\\\\). We define \\\\(\\\\Delta\\\\kappa_{G}\\\\equiv\\\\left(\\\\kappa_{G,\\\\mathrm{coat}}-\\\\kappa_{G,\\\\mathrm{bare}} \\\\right)/\\\\kappa_{0}\\\\) as the difference in the Gaussian modulus between the coated and bare membrane normalized by the bending modulus. **(A)** Membrane morphology in which there is no difference between the Gaussian modulus in the coated region and in the bare membrane, \\\\(A_{\\\\mathrm{coat}}=23,859\\\\,\\\\mathrm{nm}^{2}\\\\). The boundary between the coated region and the bare membrane lies at the bud neck. **(B)** Membrane morphology in which the Gaussian modulus is lower in the coated region than in the bare membrane, \\\\(A_{\\\\mathrm{coat}}=21,278\\\\,\\\\mathrm{nm}^{2}\\\\). The boundary between the coat and the bare membrane does not reach the bud neck, even for a vanishing neck radius. This is in agreement with the findings of Julicher and Lipowsky **[**20**]****. **(C)** Membrane morphology in which the Gaussian modulus is higher in the coated region than in the bare membrane (dashed line, \\\\(A_{\\\\mathrm{coat}}=21,278\\\\,\\\\mathrm{nm}^{2}\\\\); solid line, \\\\(A_{\\\\mathrm{coat}}=57,733\\\\,\\\\mathrm{nm}^{2}\\\\)). Note the difference in the axes as compared to (A) and (B). Closed buds do not form for typical ranges of coat area, though a deep U-shaped bud was present at the end of the solution branch (see (D)). This indicates that an additional solution branch of closed bud solutions may exist, but we were unable to obtain any closed bud solutions by our numerical scheme (see SOM Section **E**). **(D)** Mean curvature at the bud tip as a function of coat area for several values of \\\\(\\\\Delta\\\\kappa_{G}\\\\). The marked positions indicate the membrane profiles shown in (A), (B), and (C). Increasing the Gaussian modulus of the coated region relative to the bare membrane inhibits bud formation at typical coat areas, whereas decreasing the coat Gaussian modulus relative to the bare membrane can abolish the snapthrough transition otherwise present at intermediate membrane tension.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table 1.** Notation used in the model'", "CAPTION TAB2.png": "'\\n\\n**Table 2.** Parameter used in the model'", "CAPTION TAB3.png": "'\\n\\n**Table 3: Parameters used in the model**'"}

extracted_captions/he2015src.json

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+{"CAPTION FIG1.png": "\"FIGURE 1: Src2 and cortactin increase the length of lamellipodia. (A\u2013E) DIC live-cell images of _Aplyxia_ growth cones in control condition (CTL; A) and expressing CASrc2 (B), MDSrc2 (C), cortactin (D), or CortF (E). (F) Quantification of lamellipodial length, measured as the distance between the T zone and the leading edge (double-headed arrow in A\u2013E). Mean values +- SEM. Numbers in parentheses are number of growth cones selected from at least three experiments. One-way ANOVA with Dunnett's post hoc test separately performed for Src2 and cortactin groups; **p < 0.01, ***p < 0.001. Scale bar as indicated.\\n\\n\"", "CAPTION FIG2.png": "'Figure 2: Src2 and cortactin positively regulate lamellipodial protrusion persistence. (A) DIC montages of 5-min time-lapse recordings at 10-s intervals showing lamellipodial leading-edge dynamics (red dashed line) in control growth cones or after expression of CASrc2, MDSrc2, cortactin, or CortF. Scale bar as indicated. (B, B\u2019) Respective protrusion and retraction frequencies of lamellipodia. (C, C\u2019) Respective average percentages of time lamellipodia spent in protrusion and retraction phases. (D, D\u2019) Respective average lamellipodial protrusion and retraction rates. Mean values +- SEM. Numbers in parentheses are number of growth cones selected from at least three experiments. One-way ANOVA with Dunnett\u2019s post hoc test was separately performed for Src2 and cortactin conditions; *_p_ < 0.05, **_p_ < 0.01, ***_p_ < 0.001.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Src2 and cortactin regulate filipodial density and stability. (A\u2013E) DIC images depicting the P domain of control (A) and CASrc2- (B), MDSrc2- (C), cortactin- (D), and CortF-expressing (E) growth cones. (F, G) DIC montages of a region of interest in the periphery of CASrc2- and CortF-expressing growth cones showing small-scale (F) and large-scale (G) lateral movements of filopodia traced with yellow, red, and green lines. Time interval between each image is 20 s; total time, 220 s. Scale bars as indicated. (H\u2013J) Quantifications of filipodial density (H) along growth cone perimeter, as well as small-scale (I) and large-scale (J) filopodial lateral movements, respectively. Small-scale lateral movements were defined as filopodia that moved sideways no further than two adjacent filopodia. Large-scale lateral movements were defined as filopodia that moved sideways further than two adjacent filopodia. Mean values \u00b1 SEM; numbers are numbers of growth cones selected from at least three experiments. One-way ANOVA with Dunnett\u2019s post hoc test was separately performed for Src2 and cortactin conditions; **_p_ < 0.01, ***_p_ < 0.001.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Src2 and cortactin facilitate protrusion of filopodia. (A) One representative filopodium is shown for each experimental condition. Filopodial length was measured from the T zone (red line) to tip of the filopodium (red dot). The position of leading edge is marked with a white line. Scale bar as indicated. (B) Quantification of average filopodial length after Src2 and cortactin up- and down-regulation, respectively. (C) Distance vs. time plots of five representative filopodial tips for each experimental condition. (D, D) Filopodial protrusion and retraction frequencies were determined as the frequency of entering into protrusion and retraction phase, respectively, from any other phases. (E, E) Percentage of time filopodia spent in protrusion or retraction phase, respectively. (F, F) Filopodial protrusion and retraction rates, respectively. Mean values +- SEM; numbers in parentheses are number of growth cones selected from at least three experiments; one-way ANOVA with Dunnett\u2019s post hoc test was separately performed for Src2 and cortactin conditions; *p < 0.05, **p < 0.01, ***p < 0.001.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: CortF abolishes CASrc2-induced lamellipodial and filopodial effects. (A) DIC live-cell image of Aplysia growth cone expressing CASrc2 and CortF; (B) Average lamellipodial length, (C) average filopodial length, (D) filopodial density, (E) fraction of filopodia undergoing small-scale lateral movement (cross two or fewer filopodia), and (F) fraction of filopodia undergoing large-scale lateral movement (cross more than two filopodia) in Aplysia growth cones expressing CASrc2, CortF, or both together compared with control (CTL) growth cones. Data are means \u00b1 SEM; numbers in parentheses are number of growth cones selected from at least three experiments. The \\\\(p\\\\) values are determined by one-way ANOVA with Dunnett\u2019s post hoc test, comparing each experimental group against a pooled control group. **p < 0.01, ***p < 0.001.\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Actin dynamics in filopodia. (A) Processed actin FSM image of an _Aplysia_ neuronal growth cone. (B) Representative time-lapse montage of a single filopodial actin bundle labeled with Alexa 568\u2013G-actin. Internal speckles (dashed line) are tracked to calculate the retrograde flow rate. Similarly, the positions of newly added speckles (arrowhead) are determined to calculate the actin assembly rate. (C\u2013C\u201d) Actin assembly rates in filopodial tips in protrusion (C), retraction (C\u201d), or pausing (C\u201d) phases. (D\u2013D\u201d) Actin retrograde flow rates near filopodial tips in protrusion (D), retraction (D\u201d), or pausing (D\u201d) phases. Mean values \\\\(\\\\pm\\\\) SEM; numbers in parentheses are number of growth cones selected from at least three experiments. One-way ANOVA with Dunnett\u2019s post hoc test was separately performed for _Src2_ and cortactin conditions. No significant differences were determined between the different conditions.\\n\\n'", "CAPTION FIG7.png": "\"Figure 7: Src2 and cortactin increase the density of actin networks. (A) SEM image of control and (B) CortF-expressing growth cone. Control growth cones had regularly spaced filopodia with dense actin networks in between, whereas CortF-expressing growth cones showed fewer and curved filopodia, as well as lamellipodia that were retracted and contained disorganized actin networks of reduced density. (C) Quantification of actin filament occupancy as indicator of network density in lamellipodia with different Src and cortactin activity levels. _CASrc2_ and cortactin expression increased network density, whereas MDSrc2 and CortF expression had opposite effects. Mean values +- SEM; numbers in parentheses are number of growth cones selected from at least three experiments. One-way ANOVA with Dunnett\u2019s post hoc test separately performed for Src2 and cortactin groups; ***_p_ < 0.001. (D-H) High- magnification SEM images of actin meshwork and F-actin bundles from control and _CASrc2-_, MDSrc2-_, cortactin-, and CortF-expressing growth cones. (D'-H) Higher-magnification SEM images of actin network in the lamellipodia leading edge of control and _CASrc2-_, MDSrc2-_, cortactin-, and CortF-expressing growth cones. (I-K) Low-magnification SEM images of _CASrc2-_, CortF-, and _CASrc2_+CortF-expressing growth cones. Lamellipodial and filopodial orientation phenotypes induced by CortF were restored by _CASrc2_ coexpression. Scale bars as indicated.\\n\\n\"", "CAPTION FIG8.png": "'Figure 8: STORM imaging reveals partial colocalization of cortactin with activated Src2 and Arp2/3 complex. (A) STORM image depicting localization of activated Src2 (pSrc2; red) and cortactin (green) in an Aplysia growth cone. (B) Higher-magnification STORM image of activated Src2 and cortactin showing colocalization along filopodia and leading edge (arrowheads). (C) Clusters of cortactin labels were detected at regular intervals along a growth cone filopodia. (D) Another example of filopodium with double labeling of cortactin and activated Src2. Periodic pattern was detected in both channels, and stronger colocalization can be seen toward the tip of filopodium (right). (E) Partial colocalization of Arp3 (red) and cortactin (green) in growth cone lamellipodia and along filopodia (arrowheads). (F) Colocalization quantification of cortactin, activated Src2, or Arp2/3 complex in growth cone lamellipodia or along filopodia. Data are presented as Manders coefficient (mean values \\\\(\\\\pm\\\\) SEM). Numbers in parentheses refer to the number of growth cones analyzed in the case of lamellipodia and to the number of filopodia analyzed (13 cells). Cortactin/pSrc2 represents the ratio of cortactin signal overlapping with activated Src2 signal. pSrc2/cortactin represents the ratio of activated Src2 labeling overlapping with cortactin labeling. See Materials and Methods for details. Scale bars as indicated.\\n\\n'", "CAPTION FIG9.png": "'Figure 9: Model for Src/cortactin-mediated regulation of dynamics and morphology of growth cone lamellipodia and filopodia. Schematic depicting leading edge of lamellipodia and filopodia of neuronal growth cone in control condition (left), with up-regulated Src activation and cortactin levels (middle), and with down-regulated Src activation and cortactin tyrosine phosphorylation levels (right). 1) In lamellipodia, Src phosphorylation of cortactin facilitates Arp2/3 complex-dependent actin nucleation and branching, which results in lamellipodial protrusion. 2) Src and cortactin contribute to filopodia formation and positioning within the actin network by facilitating Arp2/3-mediated actin branch formation and stabilization. 3) In filopodia, Src phosphorylation of cortactin stabilizes bundles of actin filaments, resulting in straight filopodia. 4) Src and cortactin regulate the transition between different states of actin assembly at the plus end of filaments, thereby controlling persistence of protrusions. High rates of assembly occur during protrusion, whereas low rates of assembly occur during retraction. Up-regulation of Src activation and cortactin levels results in longer filopodia and lamellipodia, higher density of filopodia and actin network in lamellipodia, and more persistent actin-driven protrusions (middle). Down-regulation of Src activation and cortactin phosphorylation results in shorter filopodia and lamellipodia, reduced density of filopodia and actin network in lamellipodia, less persistent protrusions, and increased lateral movements of filopodia (right).\\n\\n'"}

extracted_captions/helmsCompoundAnalogicalDesign2008.json

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+{"CAPTION FIG1.png": "'Figure 1. A simple case of compound solution generation: 1) presentation of the problem, 2) elaboration of the problem space, 3) retrieval of the analogue, and 4) application of the analogous solution. Repeat for each leaf in the problem decomposition (not shown).\\n\\n'", "CAPTION FIG2.png": "'Figure 2. Iterative analogical generation of a problem space: 1) presentation of the problem and retrieval of the analogue, including the solution decomposition, 2) elaboration of problem space, and retrieval of a new analogue, 3) continued elaboration of problem space.\\n\\n'", "CAPTION FIG3.png": "'Figure 3. Design Trajectory of the Eye in the Sea.\\n\\n'", "CAPTION FIG4.png": "'Figure 4. Design trajectory for the InvisiBoard.\\n\\n'", "CAPTION TAB1.png": "'Table 1. Design projects from the cognitive study.\\n\\n'"}

extracted_captions/hoshino2019adp.json

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+{"CAPTION EXTENDEDFIG1.png": "'\\n\\n**Extended Data Fig. 1** (**CRISPR library screening for PINK1- paraffin-mediated mitophagy. a, b,** Mitophagy was induced in paraffin- and mt-mKelima-expressing cells by treatment with the mitochondrial membrane potential uncoupler CCGP or a cocktail of suppressors of oxidative phosphorylation (OAK).\\n\\nMithophagy was analysed by flow cytometry for mt-mKelima (**a**) and western blotting for mitochondrial protein in the outer membrane (TOM20), inner membrane (ATFB), or matrix (PDH) (**b**).\\n\\n'", "CAPTION EXTENDEDFIG2.png": "\"\\n\\n**Extended Data Fig. 2 [Integration of seven mitophagy screens.****a**, GSEAof mitophagy accelerators. The top 1% of genes in aggregate _Z_-score were analysed using TopPGene Suite1n1. Representative functional categories and Bonferroni-corrected _P_values are shown. **b**, Proportion of genes encoding mitochondrial proteins annotated in MitoCart2.0*in the top 1% of mitophagy accelerators and decelerators (left), and percentage of MitoCart2.0 member genes identified as being either accelerators (green) or decelerators (red) of mitophagy (right). **c**, Five functional classes of proteins, based on MitoCart2.0 annotations, were present in the top 1% of mitophagy accelerators. The representation of each class within the top 1% was compared to its representation in MitoCart2.0*in vivo-tailed Fisher's exact test. **d**, Box-and-whisker plots of contrast significant mitophagy accelerator hits in each of the seven screens. Line, median; box; 75th-25th percentiles; whiskers (blue dots), 99th-18 percentiles. Genes involved in oxidative phosphorylation (OXPHOS) are indicated in yellow. Pathway enrichment was calculated using a Kolmogorov-Smirnov test. **e**, GSEA enrichment plot for OXPHOS (top) and ranked aggregate _Z_-scores of all genes (bottom). OXPHOS genes are indicated in yellow. **f**, GSEA of mitophagy accelerators analysed as in a. **g**-**1**, Genes in the KEGG endosomal sorting complexes required for transport (ESCRT) (**g**), homotypic fusion and vacuole protein sorting (HOPS) (**h**), and autophagosomes (**i**) pathways. Genes identified as mitophagy accelerators or decelerators are indicated in green and red, respectively. The diameter of each circle is proportional to the _Z_-score of the indicated gene. **j**, Principal component (PC) analysis isblot summarizing variation across the seven screens based on cumulative _Z_-scores of the top 100 genes, displayed as arrows. Autophagy-related genes are indicated. **k**, Mitochondrial membrane potential assessed by flow cytometry for TMRE is disrupted in CCCP treatment, but is increased after treatment with OAR cocktail. Similar results were obtained in two biological replicates.\\n\\n\"", "CAPTION EXTENDEDFIG3.png": "'\\n\\n**Extended Data Fig. 3 EssentialLC3 receptors for mitophagy in C2C12 mouse myoblasts.****a, b**, Validation as mitophagy decelerators of the indicated LC3 receptor geneRNAs, using one library gRNA and one non-library gRNA and using the m-mckemia assay (**a**) or western blotting of mitochondrial proteins in the outer membrane (TOM20 and TOM70), inner membrane (ATP8), or matrix (PPIH) (**b**): \\\\(n\\\\) = 3 biological replicates per gRNA, _P_values calculated by two-sided unpaired r-test relative to NTC_1. Mitophagic degradation of mitochondrial inner membrane and matrix proteins, but not outer membrane proteins, was blocked by gRNAtargeting _Tax1bp1_ for _Tbl1_, consistent with the notion that ubiquitinated outer membrane proteins can be degraded by the ubiquitin proteasome system. Similar results were obtained in two biological replicates. **c, d, LC3 receptor redundancy and TBK1 contribution.** **The indicated gRNAs were transduced singly or in combination by lentivirus infection, followed by analysis by flow cytometry for m-mckemia. Multiple gRNAs were superimposed on cells already targeted by _Tax1bp1_ gRNA (**d**), as indicated. \\\\(n\\\\) = 3 biological replicates per gRNA. _P_values calculated by one-way ANOVA with post hoc Tukey test, \"P_ < 0.05, \"P_ < 0.01, \"*P_ < 0.001 Data are mean +-x.d.\\n\\n'", "CAPTION EXTENDEDFIG4.png": "'\\n\\n**Extended DataFig. 4** **ANT is required in paraffin-mediated mitophagy.** A, Impaired mitophagy in the absence of ANT is confirmed by flux analysis using a lysosome inhibitor, bafilomycin A (\\\\(\\\\frac{1}{2}\\\\)M). Similar results were obtained in two biological replicates. **b**, **c**, Inhibition of mitophagy by CRISPR-mediated deletion of the indicated genes in mouse N2A (**b**) and human SH-SYSY (**c**) neuroblastoma cell lines. Representative flow tracings are shown on left, and quantification onright; \\\\(n\\\\) = 3biological replicates per gRNA, \\\\(P\\\\) values calculated by two-sided unpaired _t_-test relative to NTC, 1. Data are mean +- \\\\(s\\\\).d.\\n\\n'", "CAPTION EXTENDEDFIG5.png": "'\\n\\n**Extended Data Fig. 5**: **ANT is required for stabilization of PINK1.****a**, inhibition of ADP/ATP exchange worsens the loss of membrane potential in response to CCCP. TMR fluorescence intensity following treatment with CCCP was analysed by confocal laser scanning microscopy with the application of live time-series program. Cells were pretreated with control and boxykete acid (BA); \\\\(n\\\\) = 4 biological replicates per group. \\\\(P\\\\) values calculated by two-way repeated measures ANOVA. **b**, Mitophagy was induced by OXPHOS inhibitors (antimycin A and oligomycin) in the presence of the indicated concentration of the ADP/ATP transport inhibitor bongkeickacid, followed by flow cytometry for m-mecium. \\\\(n\\\\) = 3 biological replicates per group. \\\\(P\\\\) values calculated by one-way ANOVA with post hoc Tukey test; _\"P_ < 0.01. **c**, Genetic inhibition of ADP/ATP exchange worsens the loss of membrane potential in response to CCCP. _Ant_(_r_) cells were rescued by human wild-type (WT) or mutant ANTI; \\\\(n\\\\) = 3 biological replicates per group. \\\\(P\\\\) values calculated by two-way repeated measures ANOVA relative to NTC. **c**, ADP/ATP exchange rates is impaired in ADP/ATP-binding mutants (K330, K43E), but not in disease-causing mutants (A90D, V289M); \\\\(n\\\\) = 3 biological replicates per group. \\\\(P\\\\) values calculated by two-sided unpaired test relative to WT. **e**, Loss of ANT impairs PINK1-dependent mitophagy induced by oxidative stress, but does not impair PINK1-independent mitophagy caused by hypoxia or starvation; \\\\(n\\\\) = 3 biological replicates per gRNA. \\\\(P\\\\) values calculated by two-sided unpaired \\\\(t\\\\) test relative to NTC. \\\\(E\\\\), PINK1 accumulation in mitochondria is impaired in cells lacking ANT. Cells bearing gRNAs targeting the indicated genes were transduced with PINK1-GFP, followed by treatment with CCCP versus control, and then immunostained using anti-TOM20 antibody (red). GFP fluorescence is shown in green, and merged signal yellow. Scale bar, 20 \u03bcm. \\\\(g\\\\), PINK1 stabilization by CCCP treatment is preserved with wild-type ANT and ADP/ATP-binding double mutant (K43E/B24E), but not in known disease-causing mutants (A90D, A123D). **h**, Phosphorylation of PINK1 after CCCP treatment is preserved in the absence of ANT1 or ANTI. **l**, PINK1 transcription (b) and translation (j) are not changed by loss of ANT. **n** = 4 biological replicates per group. \\\\(P\\\\) values calculated by one-way ANOVA. **k**, The activities of the PINK1-cleaving proteases PARL and OMA1 are not changed by loss of ANT. **l**, General autophagy fluxis preserved in the absence of ANT. **n** = 3 biological replicates per group, \\\\(P\\\\) values calculated by two-sided unpaired \\\\(t\\\\) test relative to NTC. **m**, Suppression of TIM23-mediated protein translocation response to CCCP treatment is impaired in the absence of ANT1 or ANTI. **m**, as shown by import of SU9-GFP into intact cells; \\\\(n\\\\) = 3 biological replicates per gRNA, \\\\(P\\\\) values calculated by two-sided unpaired \\\\(t\\\\) test relative to NTC. Scale bar, 20 \u03bcm. Data are mean +- s.d. Similar results were obtained in two biological replicates (**f** - **h**, **j**, **k**). For gel source data, see Supplementary Fig. 1.\\n\\n'", "CAPTION EXTENDEDFIG6.png": "'\\n\\n**Extended Data Fig. 6**: **ANT mediates closure of TIM23 via TIM44.4**, Deletion of _Ant1_ or _Ant2_ does not affect expression of TIM or TOM proteins (right) or destabilize TIM and TOM complexes, as assessed by blue native PAGE (left). **b**, **c**, ANTI and ANTI2 bind to TIM23 and TIMM44, as assessed by corimmunoprecipitation (**b**) and blue native PAGE (**c**). The ANTI-TIM23 complex is marked with an asterisk asterisk. **d**, Wild-type ANTI and the ADP/ATP binding double mutant (K43/K2445) bind to the TIM23 complex component TIM23, whereas disease-causing mutants (A990D, A123D) do not. **c**, Closure of TIM23in response to CCCP treatment is impaired in the presence of disease-causing mutants (A90D, A123D), but is preserved in the presence of the ADP/ATP binding double mutant (K43E/R244E), as shown by import of SU9-GFP into mitochondria: \\\\(n\\\\) = 3 biological replicates per group. \\\\(P\\\\) values calculated by two-sided unpaired \\\\(t\\\\) test relative to empty. Scale bar, 40 um. **f**, ANTI binds to both TIMM23 and TIMM44. **g**, Mittophagys impaired in cells lacking TIMM44; \\\\(n\\\\) = 3 biological replicates per gRNA, \\\\(P\\\\) values calculated by two-sided unpaired \\\\(t\\\\) test relative to MC, **l**, **b**, PINI stabilization by CCCP treatment is abrogated in the absence of TIMM44. **l**, Rescue of mitophagy with wild-type ANT and ADP/ATP exchange mutants (K330, K43E/R244E), but not with known disease-causing mutants (A90D, A123D) and TIMM44-binding site mutant (G146E/K147D). Top left, schematic of ANT and sites of mutations. Bottom, western blotting demonstrating equivalent expression of ANT constructs. Right, quantification of mitophagy: \\\\(n\\\\) = 3 biological replicates per group, \\\\(P\\\\) values calculated by one-way ANOVA with post the Tukey test, \"_p_ < 0.01, \"_p_ < 0.001. **J**, Mutation of the predicted ANTI interactions site in TIMM44 abrogates binding to ANTI. **k**, Rescue of mitophagy with wild-type TIMM44, but not with binding site mutant (K43E/R244E); \\\\(n\\\\) = 3 biological replicates per group, \\\\(P\\\\) values calculated by one-way ANOVA with post hoc Tukey test, \"_p_ < 0.01, \"_p_ < 0.001. **I**, Mutation in TIMM44 of the ANTI interaction site does not abrogate TIMM44 binding to TIMM23. **Dataera** mean = s. d. Similar results were obtained in two biological replicates (**a**\u2013**d**, **f**, **b**\u2013**l**). For gel source data, see Supplementary Fig. 1.\\n\\n'", "CAPTION EXTENDEDFIG7.png": "'\\n\\n**Extended Data Fig. 7** **ANT is required for mitophagy in vivo, independently of transcriptional regulation.** Equivalent amounts of PINK1 and higher parkins transcription in _Antf_20 heart and skeletal muscle (SM); \\\\(n\\\\) = 4 per group, _P_values calculated by two-sided unpaired _k_-test. Data are mean +s.d.\\n\\n'", "CAPTION FIG1.png": "'relative to non-targeting control;NTC) or by western blotting of mitochondrial proteins in the outer membrane (OMM-TOM20), inner membrane (IMM-ATPB), or matrix (PDH) (**e**). Similar results were obtained in two biological replicates. For gel source data, see Supplementary Fig. 1.**f**, Suppression of mitophagy in primary ratneurons. Left, visualization of neuronal mitochondria with tetramethylrhodamine ethylester (TMRF) dye. Middle, representative image showing coating of mitochondria (labelled with Mirc-Snap) with the mitophagy receptor OPTN, indicating active mitophagy. Right, quantification of cells undergoing active mitophagy: \\\\(n\\\\) = 6 (untreated control), 6 (treated control), 4 (_Ant1_), and 5biological replicates (_Ant2_), \\\\(P\\\\) values calculated by one-way ANOVA with post hoc Dunnett\\'s multiple comparison test; \\\\(P\\\\) < 0.05, \"_P_ < 0.01. Scale bars, 5 \u03bcm, 0.8 \u03bcm (inset). Data are mean +-s.d.\\n\\nFig. 1: **Multidimensional mitophagy screen reveals that ANT is required for mitophagy.****a**. Outline of CRISPR\u2013Cas9 genome-wide genetic screen, using four reporter assays and two modes of mitophagy induction. **b**, Most significant hits in each of the seven screens. MT, MitoTracker; OM-G, outer membrane GFP; Mat-G, matrix GFP. Representative previously known genes shown by open symbols, previously unknown genes by coloured symbols; line, median; box, 75th\u201325th percentiles; \u2018whiskering\u2019, 99th\u20131st percentiles; duplicate experiments. **c**, Ranked aggregate _z_\u2019scores of all genes. Representative previously known genes labelled in grey, previously unknown in black. **d**, **e**, Validation as mitophagy decelerators of the indicated genes, using both a gRNA chosen from the screening library, and an independent non-library gRNA, followed by flow cytometry for matrix-targeted mkcima (**d**, \\\\(n\\\\) = 3 biological replicates per gRNA, \\\\(P\\\\) values calculated by two-sided unpaired _d_-test'", "CAPTION FIG2.png": "'Fig. 2 **ANT mediates suppression of TIM23 via TIM44.****a**, Inhibition of ADP/ATP transport with the indicated inhibitors accelerates mitophagy, in sharp contrast to genetic deletion of ANTI (bottom right); \\\\(n\\\\) = 3 per group., Mitochondrial admi is elevated in cells lacking ANT, and reduced in response to CCCP, compared to control cells, consistent with reverse ADP/ATP exchange in low admi: \\\\(n\\\\) = 3 per gRNA. \\\\(P\\\\) values calculated by two-way repeated measures ANOVA relative to NTC. **c**, Rescue of mitophagy with wild type (WT) ANT and ADP/ATP-binding mutant (K43k/R244K), but not with disease-causing mutants (A90D, A123D). Top left, schematic of ANT mutations. Bottom, equivalent expression of constructs. Right, quantification of mitophagy; \\\\(n\\\\) = 3 per group. **d**, PINK1 stabilization by CCCP treatment is abrogated in the absence of ANTI or 2. **e**, Suppression of TIM23-mediated import of [**15**S]Sup-DHFR into isolated mitochondria in response to CCCP is impaired in the absence of ANTI (p., precursor; m, mature). **f**, Interaction between ANTI and TIM44 identified in the mitochondrial interactome database XlinkDB. **g**, Deletion of TIMM44 impairs binding of ANTI to TIMM23. **h**, Mutation of the predicted TIMM44 interaction site in ANTI or disease-causing ANTI mutation (A90D) abrogates binding of ANTI to TIMM44, while ADP/ATP exchange mutants (K43K/R244E and K330) do not. **i**, Model of ANTI-mediated suppression of TIM23 in response to compromise of mitochondrial bioenergetics. Data are mean +- \\\\(x\\\\) < .d_.\\\\(P\\\\) values by one-way ANOVA with post hoc Tukey test (**a**, **c**); \\\\(p\\\\) < 0.05, \"_p_ < 0.01, \"_p_ < 0.001. Similar results were obtained in two biological replicates. For gel source data, see Supplementary Fig. 1(**c**\u2013**e**, **g**, **h**).\\n\\n'", "CAPTION FIG3.png": "'_Ant_20 mice. Scale bars, 2 \u03bcm. Similar results were obtained from three mice in each group. B, Dilated cardiomyopathy in _Ant_20 mice: heart weights (top left), sample images (top right) and quantification (bottom) of echocardiography; \\\\(n\\\\) = 7 per group. LVID, left ventricle internal diameter systolic (s) and diastolic (d); LVDW, left ventricle posterior wall; EF, ejection fraction. **1**. Echocardiography of patient bearing homozygous loss-of-function. _ANTI_ mutations. Left, systolic; right, diastole, **3**. Electron micrographs of endomyocardial biopsy from same patient as in L. Localized distension of outer membrane (blue arrows) with apparent release of mitochondrial matrix content (green) into the cytoplasm. Scale bars, 1 \u03bcm. Data are mean +-s.d. (**a**, **e**). _P_values by two-sided unpaired \\\\(t\\\\) test (**a**, **d**, **h**), one-way ANOVA with post hoc Tukey test (**b**); \\\\(P\\\\) < 0.05, \"_P_ < 0.01, \"_P_ < 0.001. For gel source data, see Supplementary Fig. 1.\\n\\nFig. 3: **ANTI is required for mitophagy in vivo.****a**, Blunted mitophagy in heart and brain of _Ant_20 mice, illustrate at by reduced coating of mitochondria by p62, PINK1 and parin. **b**, Blunted mitophagy in skeletal muscle of _Ant_20 mice, shown by intramuscular transfection of mitoQC plasmid. Line, mean; \\\\(n\\\\) = 4 mice, 47 fibres (WT) and 4 mice, 50 fibres (_Ant_20). Scale bars, 10 \u03bcm. **c**, Rescue or mitophagy with wild type (WT) ANTI and mutant lacking mCherry exchange activity (K3IQ), but not with disease-causing mutant (A900). Line, mean; \\\\(n\\\\) = 3 mice, 24 fibres (WT), 3 mice, 16 fibres (Luc), 3 mice, 23 fibres (k33Q) and 3 mice, 21 fibres (A90D). Scale bars, 10 \u03bcm. **d**, Accumulation of mitochondrial DNA (right) in heart (top) and muscle (bottom) of _Ant_20 mice despite absence of nuclear-encoded biogenesis (left): \\\\(n\\\\) = 4 per group. **e\u2013g**. Accumulation of mitochondrial proteins (**e**) and of disorganized and aberrant mitochondria (**f**) in heart, and deep red colouring of mitochondria in skeletal muscle (**g**) of _Ant_20 mice. Scale bars, 2 \u03bcm. Similar results were obtained from three mice in each group. **b**, Dilated cardiomyopathy in _Ant_20 mice: heart weights (top left), sample images (top right) and quantification (bottom) of echocardiography; \\\\(n\\\\) = 7 per group. LVID, left ventricle internal diameter systolic (s) and diastolic (d); LVDW, left ventricle posterior wall; EF, ejection fraction. **1**. Echocardiography of patient bearing homozygous loss-of-function. _ANTI_ mutations. Left, systolic; right, diastole, **3**. Electron micrographs of endomyocardial biopsy from same patient as in L. Localized distension of outer membrane (blue arrows) with apparent release of mitochondrial matrix content (green) into the cytoplasm. Scale bars, 1 \u03bcm. Data are mean +-s.d. (**a**, **e**). _P_values by two-sided unpaired \\\\(t\\\\) test (**a**, **d**, **h**), one-way ANOVA with post hoc Tukey test (**b**); \\\\(P\\\\) < 0.05, \"_P_ < 0.01, \"_P_ < 0.001. For gel source data, see Supplementary Fig. 1.\\n\\n'"}

extracted_captions/irwinForecastingArgumentationFrameworks2022.json

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+{"CAPTION FIG1.png": "'Figure 1: The step-by-step process of a FAF over its lifetime.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: A graphical representation of arguments and relations in the update framework from Example 3. Nodes represent proposal (\\\\(\\\\mathcal{P}\\\\)), increase (\\\\(\\\\uparrow\\\\)), decrease (\\\\(\\\\downarrow\\\\)), pro (\\\\(+\\\\)) and con (\\\\(-\\\\)) arguments, while dashed/solid edges indicate, resp., the \\\\(\\\\mathcal{R}^{\\\\mathcal{P}}\\\\mathcal{R}\\\\) relations.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K. (1999) The structure of the \\\\(\\\\mathbb{R}^{3}\\\\)-structure of the \\\\(\\\\mathbb{R}^{3}\\\\)-structure. _Journal of Computational Physics_, 123(1):1-12, 1994.\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'", "CAPTION TAB3.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline  & \\\\\\\\ \\\\end{tabular}\\n\\\\end{table}\\nTable 3: Auxiliary results from the experiment, where \\\\(\\\\overline{C}\\\\) is the average confidence score, \u2018Forecasts\u2019 is number of forecasts made in each question and \u2018Irrational Forecasts\u2019 the number in each question which violated each constraint in \u00a74.1.\\n\\n'"}

extracted_captions/isambert1995flexibility.json

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+{"CAPTION FIG1.png": "'Figure 1: **Schematic representation of thermal fluctuations of an actin filament.**_A_, transverse fluctuation. For each point of abscissa \\\\(S\\\\), the distance \\\\(D\\\\) from the tangent at the origin is measured on a series of images. Two typical shapes, \\\\(I\\\\) and \\\\(\\\\hat{z}\\\\), are shown. Note that \\\\(D\\\\) varies appreciably while the longitudinal distance \\\\(r\\\\) does not vary much. \\\\(B\\\\), correlation of the tangential directions. For each point of abscissa \\\\(S\\\\), the angle \\\\(\\\\theta s\\\\)) of the tangent with the tangent at the origin is measured.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Fig. 2. Recorded shapes of actin filaments undergoing thermal fluctuations.**_a_-_cf_, tetramethylrhodamine-phalloidin-stabilized actin filaments observed at 6-a time intervals (left to right), bar = 5 \\\\(\\\\mu\\\\)m. c-A, unstabilized tetramethylrhodamine-F-ADP-actin filaments observed in physiological ionic conditions at 6-a intervals in the presence of 0.2 mM ATP and 0.1 \\\\(\\\\mu\\\\)m unlabeled G-actin.\\n\\n'", "CAPTION FIG3.png": "'\\n\\n**Fig. 3. Analysis of filament flexibility.**\\\\(a\\\\), cosine correlation function. Dashed lines, rhodamine-phalloidin-stabilized F-ADP-actin (conditions as under Fig. 2, \\\\(a\\\\)-\\\\(d\\\\)). Solid lines, rhodamine-F-ADP-actin in the absence of phalloidin (conditions as under Fig. 2, \\\\(e\\\\)-\\\\(h\\\\)). \\\\(b\\\\), analysis of the average transverse fluctuations. Solid and dashed lines correspond to the data shown in \\\\(a\\\\). Nocay curves are experimental data (dashed line, average of 268 filaments; solid line, average of 110 filaments). Smooth curves represent the best fits to Equations 3 (\\\\(a\\\\)) and 7 (\\\\(b\\\\)), respectively.\\n\\n'", "CAPTION TAB1.png": "''"}

extracted_captions/jeppesenMarginalityProblemsolvingEffectiveness2010.json

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+{"CAPTION FIG1.png": "'\\n\\n**Figure 1** **Broadcast Search Procedure**'", "CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline\\n**Table 1** & **Contracts** (Mean Based) **Between Survey** \\\\\\\\\\n**Respondents and Nonexpondents in Submitter** \\\\\\\\\\n**Population** \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 1: Contracts (Mean Based) Between Survey Respondents and Nonexpondents in Submitter Population'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l l l} \\\\hline \\\\hline  & & & \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 2: Descriptive Statistics for Variables in First Stage of Heckman Probit Regression (\\\\(N=12,786\\\\))'", "CAPTION TAB3.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB4.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'"}

extracted_captions/jingHouseholdSecondaryAttack2020.json

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+{"CAPTION FIG1.png": "'Figure 1: **Spatial distribution of COVID-19 case clusters on the basis of contact tracing data from Guangzhou, China, from Jan 7, 2020, to Feb 18, 2020**\\n\\nOverall distribution of COVID-19 case clusters in Guangzhou (A), and distribution in the submissions defined in panel A (B-G). Individuals were considered as primary cases if their symptom onset dates were the earliest or 1 day (14) days for an imported case) after the earliest in the cluster and as secondary cases otherwise. Non-infected contacts are not shown. The displayed location of such case is randomly perturbed away from the actual residential address.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Figure 2:** Epidemic curve based on symptom onset dates of COVID-19 crisis in Guangzhou from Jan &, 2020, to Feb 18, 2020\\n\\n**Estimated \\\\(R\\\\), for those scenarios: scenario 1, all imported cities (who traveled to or resided in Huisei province 14 days before symptom onset) considered as primary cities, and all secondary cities were infected by primary cases in the same case district; scenario 2, which is identical to scenario 1, with the additional assumption that local primary cases might have been infected by earlier cases in other clusters; and scenario 3, which is identical to scenario 2, with the additional assumption that imported secondary cases were considered as infected by primary cases in the same cluster. \\\\(R\\\\)=effective reproductive number.**'", "CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'", "CAPTION TAB2.png": "'Estimates were reported using two-different definitions of household contact (cken r luthen or individuals sharing the same rouletental address) and for selected settings of the natural history of disease. This model was not adjusted for age group, epidermis phase, or household size. E-response-active number.\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l l l} \\\\hline \\\\hline  & & & \\\\\\\\ \\\\end{tabular}\\n\\\\end{table}\\nTable 2: **Model-based estimates of secondary attack rates among household and non-household contacts, and local R with and without quarantine**'", "CAPTION TAB3.png": "'Data are estimating (95% C). Estimation of the daily probability of infection from an external source and the GHR for the relative infectivity during the disease versus irradiation period are also provided. Extrusion as reported using two different definitions of household contact (dose relation, or only individual sharing the same residential address) and for selected setting of the natural history of disease (no mean incubation and maximum infectious period). This model was not adjusted for age group, epidemic phase, or household use. D6-odds ratio.\\n\\n'", "CAPTION TAB4.png": "'Data are 00 [95% CI]. Initration were repeated for selected settings of the natural history of disease (in, mean incubation and maximum infectious periods). The model was adjusted for age groups, epidemic phase, and household size. (Q1=odds ratio).\\n\\n'"}

extracted_captions/kaneCommunitiesWeChoose2018.json

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+{"CAPTION FIG1.png": "'Figure 1: The anatomy of a typical Reddit comamet section.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Average UMass topic coherence at each \\\\(\\\\$\\\\)-topic increment in number of topics.\\n\\n'", "CAPTION FIG3.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION FIG4.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB1.png": "'TABLE I\\n\\nA sample of far-IRASEN PHASES used by candidates'", "CAPTION TAB2.png": "'\\n\\n## Table II A sample of bicrams and trigrams found in each political volume\\n\\n'", "CAPTION TAB3.png": "'\\n\\n**Acknowledgement**'"}

extracted_captions/kaplanSearchInsight1990.json

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+{"CAPTION FIG1.png": "'\\n\\n**Fig. 1.** The classic mutilated checkerboard (MC) problem.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Fits 1.** **Experiment 3 at a time.**'", "CAPTION FIG3.png": "'\\n\\n**Fig. 1. The AHAI experience (three protocol excerpts).**'", "CAPTION FIG4.png": "'\\n\\n**Fig. 4. A sample production from switch.**'", "CAPTION FIG5.png": "'\\n\\n**Eto - A prototypical solution path.**'", "CAPTION FIG6.png": "'Figure 6: Frequencies of different types of invariants (first 10 min).\\n\\n'", "CAPTION FIG7.png": "'Figure 7: Number and type of invariants noticed in first and second halves of protocol.\\n\\n'", "CAPTION FIG8.png": "'\\n\\n**Fig. 8.** Categories covered (first \\\\(\\\\xi\\\\) min).\\n\\n'", "CAPTION TAB1.png": "'TABLE I\\n\\nSome Frablem Spaces Used by Subsets'", "CAPTION TAB10.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'", "CAPTION TAB11.png": "'TABLE 11\\n\\nRank Orders of Times to First Mention Perceptual Invariant and to solution (\\\\(n=8\\\\) Salje\\\\(\\\\cdot\\\\)ts)'", "CAPTION TAB2.png": "'TABLE 2\\n\\nBreakdown of Time Spent after First Mention of Parity, before Rough Proof'", "CAPTION TAB3.png": "'TABLE 3\\n\\nMean Times to Points on Solution Path and Mean Number of Approaches Tried.\\n\\n'", "CAPTION TAB4.png": "'TABLE 4\\n\\nPairwise Co'", "CAPTION TAB5-1.png": "'TABLE 3\\n\\nMean Number of Relevant Parity Statements before/after Hints'", "CAPTION TAB5-2.png": "'\\n\\n## Chapter 4 Conclusion'", "CAPTION TAB5.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l c c}  & \\\\(\\\\pi=8\\\\) Subjects. \\\\\\\\ Mean Number of Relevant Parity Statements before/after Hints & Mean Number of Relevant Parity Statements before/after Hints \\\\\\\\ \\\\end{tabular}\\n\\\\end{table}\\nTable 5: Mean Number of Relevant Parity Statements before/after Hints'", "CAPTION TAB6-1.png": "'TABLE 6\\n\\nNumber of Subjects Solving after Various Hints (No. of Subjects in Each Group Who Re-ceived Each Hint; \\\\(n\\\\) = 23 Subjects)'", "CAPTION TAB6-2.png": "'* Other hints included the COUNT hint, and other very specific hints which were given only if the PARITY hint proved ineffective.\\n\\n'", "CAPTION TAB6.png": "'\\\\(\\\\bullet\\\\)\\n\\n\\\\(\\\\bullet\\\\)\\n'", "CAPTION TAB7-1.png": "'\\n\\n## Chapter 1 Introduction\\n\\nThe Standard Model (SM) is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics, which is a model of particle physics. The SM is a model of particle physics, which is a model of particle physics,'", "CAPTION TAB7-2.png": "'* \\\\(p\\\\leq 10\\\\), **\\\\(p\\\\leq .01\\\\) (one failed \\\\(r\\\\) test). Difference compared with BI_ANK group.\\n\\n'", "CAPTION TAB7.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l c c c c} \\\\hline \\\\hline  & & & & \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 7: * \\\\(p<10\\\\), **\\\\(p<11\\\\)** (one failed \\\\(t\\\\) test). Differences compared with BLANK group.\\n\\n'", "CAPTION TAB8.png": "'TABLE 8\\n\\nOverall Frequency of Use (and Rate of Use) of Heuristics (\\\\(n=8\\\\) Subjects)'", "CAPTION TAB9-1.png": "'TABLE 9\\n\\nInvariant Properties Mentioned Repeatedly by Subjects (\\\\(\\\\alpha=8\\\\) Subjects)'", "CAPTION TAB9-2.png": "'_Note_. Listed first are all the invariants on the direct path to the insightful parity solution (i.e. the relevant invariants). Listed second are some common invariants that are not on the direct path to the insightful parity solution (i.e. the irrelevant invariants).\\n\\n'", "CAPTION TAB9.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l c c} \\\\hline \\\\hline  & & \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 9: Isoperimetric Method Revisited by Subjects (\\\\(n=8\\\\) Subjects) Invariant Properties Mentioned Repeoriately by Subjects (\\\\(n=8\\\\) Subjects)'"}

extracted_captions/kibetSociallyNetworkedHeterogeneity2019.json

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+{"CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{} & \\\\multicolumn{1}{c}{} & \\\\multicolumn{'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline  & WhatsApp and social network heterogeneity: Posting, discussing and commenting \\\\\\\\  & as mediating factors \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 2: WhatsApp and social network heterogeneity: Posting, discussing and commenting as mediating factors'", "CAPTION TAB3.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{**Table 3:**} & \\\\multicolumn{1}{c}{Regression analysis on use of WhatsApp, social networking heterogeneity and polarisation} \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 3: Regression analysis on use of WhatsApp, social networking heterogeneity and polarisation'"}

extracted_captions/kirkham2005ultrastructural.json

@@ -0,0 +1 @@
+{"CAPTION 1.png": "'Figure 1: **Ultrastructural characterization of caveolae endocytosis.** (A and B) WT MEFs with bound CTBHRP were warmed for 1 [A] or 5 _min_ [B]. The DAB fraction was performed on ice in the presence [+AA] or absence [-AA] of AA, and then cells were processed for immunoelectron microscopy detection of Cow1. A and B are representative of areas enriched in caveolae. (A) DAB reaction product is present in a small subset of buddingal (inoxarloc-connected). Cavi-positive caveolae (arrows) in cells treated with AA during the DAB reaction. A large number of caveolae were DAB negative and thus surface-connected [small arrowheads]. Putative budded clathrin vesicles were also observed (large arrowhead). (B) After 5 min of CTBHRP uptake, Cow1 also localized to DAB-positive internal structures [+AA], which had an irregular tubular morphology [defined operationally as clustered caveolae in E-G]. (C) WT MEFs with CTBHRP internalized for either 1 or 5 min were treated with DAB in the presence of AA, labelled for Cav1, and processed for whole-mount visualization. Budden (DAB-positively caveolae [arrowhead], surface-connected [DAB-negative]) caveolae (arrowhead), and internal Cav1-positive larger structures were observed. (D) WT MEFs were treated as in A but warmed for 5 min in the presence or absence of either DA or locCar before the DAB reaction in the presence of AA. (E\u2013G) Quantitation of internal caveolae (single or clustered) as compared with the total number of caveolae present in the same area with increasing time of incubation at 37\u00b0C (E) or after 5 min at 37\u00b0C in the presence/absence of OA (F) or locCar (G). Error bars indicate standard error. Bars: (A and B) 500 nm; (C and D) 200 nm.\\n\\n'", "CAPTION FIG2.png": "'\\n\\n**Figure 2.** **Inernalization of CTB by WT and Cav1\\\\(-\\\\)/ - MEFs.** {A-F} CTB-FITC was internalized in WT MEFs {A-F} CTB-FITC was internalized in WT MEFs {A-F} CTB-FITC was internalized in WT MEFs {C} at 37degC for various times, and then fixed and labeled for GM130 {A-F} CTB-FITC was accumulation of CTB within the Golgi complex in both WT MEFs and Cav1\\\\(-\\\\)/ - MEFs was quantified {C}; no significant differences were seen. Bars indicate standard error. Cav1\\\\(-\\\\)/ - MEFs were microinjected with pIRES-Cav1 using standard conditions {B and E} and short expression conditions {B and E}. {B} Injected calls {*} were marked by the production of cytosolic GFP coded for by the same message as untagged Cav1. CTB-Alexa Fluor 594 was internalized and CTB fluorescence intensity in the GM130-positive region was quantified {D-F}. WT MEFs were microinjected with pIRES-Cav1 using short expression conditions {F}. Only short expression of Cav1 reduced CTB trafficking to the Golgi complex as compared with nonexpreasing cells in both WT and Cav1\\\\(-\\\\)/ - MEFs (D-F). [G] Cav1\\\\(-\\\\)/ - MEFs were microinjected with vectors encoding for EPS15-DN-GFP and TIR for short expression. CTB-FITC was internalized simultaneously with TT for 40 min. CTB-FITC was labeled with an anti-CT antibody and a secondary antibody conjugated to Alexa Fluor 660. In cells that were injected with EPS15-DN-GFP, Tf uptake was inhibited, but CTB still accumulated in a perinuclear compartment. [H] Cav1\\\\(-\\\\)/ - MEFs were microinjected with vectors encoding TIR and either GFP or EPS15-DN-GFP [short expression], and then Tf uptake for 20 min was performed. Internal Tf was quantified in injected cells, and EPS15-DN-GFP inhibited Tf uptake by 90%. [I] Cav1\\\\(-\\\\)/ - MEFs were microinjected with vectors encoding for EPS15-DN-GFP [short expression], and CTB-Alexa Fluor 594 was internalized for various times. Quantification of CTB accumulation in the GM130-positive Golgi complex revealed that EPS15-DN-GFP reduced CTB trafficking by only 40%. Bars indicate standard error; *, P < 0.01; **, P < 0.001. Bars, 25 um.**'", "CAPTION FIG3.png": "'Figure 3. **Dyeamin and ARf4 mutants inhibit CTH-transpert to the Golgi complex.**_Cav1-f-MEFs_ were micrinjected with cDNA for DynKA4A4A [A] or ARFA T27N [B and C; short expression]. CTB Alexa Floc 594 was internalized for 40 nm [A and B. DynKA4A4A and A&F6 T27N heat contained NH2-terminal HA tags were labeled with eachHA [A and B]. CTB colocalizes with DynKA4A [A] and A&F6 T27N [B] in an extensive tubular network. This is highlighted in enlargements in between panels of A. [C] Cav1-f-MEFs were micrinjected with A&F6 T27N and HRF, and CTHHRF was internalized for 40 min at 37C. Cells were prepared for EM and CTHHRF was revealed by DNA cytochanatry. CTHHRF reacted product was evident within a network of 40-nm-diameter tubular structures in the injected cells, some of which connect to multi-axial regions [arawheads]. Bars [A, top, and B] 25 mm; [A, bottom] 5 mm; [C, left] 1 mm; [C, right] 200 mm.\\n\\n'", "CAPTION FIG4.png": "'Figure 4. Ultrastructural characterization of early carriers in Cav1\\\\(-\\\\)/\\\\(-\\\\) MEFs. Cav1\\\\(-\\\\)/\\\\(-\\\\) MEFs were incubated with CTB+RP [A and B] or TH+RP [C] at 4\\\\({}^{\\\\circ}\\\\)C. They were warmed for 15 s at 37\\\\({}^{\\\\circ}\\\\)C and DAB treated in the presence of AA [A and C] or were DAB treated in the absence of AA without a warming step to reveal the surface distribution of CTB+RP [B]. All samples were fixed and processed for EM without permabilization. [A] CTB+RP reaction product is evident within vesicular profiles [arrows] and tubular/rings-shaped profiles [arrows] close to the plasma membrane [PM]. Note the groups of labeled structures as most clearly evident in the low magnification serum [log]. [B] CTB+RP reaction product is evident over the entire local surface but tubular/rings-shaped profiles of similar morphology to those detached from the surface after warming are evident [arrows]. Also note the labeling of vesicular profiles connected to the call surface [arrows]. [C] in contrast to the structures labeled by CTB+RP after 15 s, TH+RP labels vesicular profiles [arrows] close to the PM. Bars, 200 nm.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: **Ultrasructural characterization of early noncaveolar carriers in Cav1\\\\(-\\\\)/\\\\(-\\\\) MFs and WT MFs.** WT (A, B, and E) and Cav1\\\\(-\\\\)/\\\\(-\\\\) (D and E) MEFs with bound CTBHRP were warmed for 15 s, 1 min, or 5 min at 37\u00b0C and DAB treated in the presence of AA. Samples were immunolabeled for Cav1 (A\u2013C) or dynamic (clathrin-pit panels) and processed for EM. In both WT (A) and Cav1\\\\(-\\\\)/\\\\(-\\\\) (D) MEFs, CTBHRP reaction product was observed after 15 s, 1 min, and 5 min in tubular structures, ringlike structures, clathrin coated vesicles, and smaller vesicular structures. [B] in WT MFs, CTBHRP-positive noncaveolar structures partly colocalized with Cav1. The percentage of noncaveolar structures labeled with Cav1 was quantified [F. (C)] WT MFs were grown on grids, and CTBHRP was internalized for 5 min. Calls were prepared for whole-mount visualization. CTBHRP labeled short tubular or ringshaped structures, some of which are Cav1 positive. [E] thermal CTBHRP-positive structures in WT and Cav1\\\\(-\\\\)/\\\\(-\\\\) MEFs was classified according to morphology (see Materials and methods) and quantitated as a percentage of total labeled structures. Most CTBHRP-labeled internal structures in both WT and Cav1\\\\(-\\\\)/\\\\(-\\\\) MEFs were nonvascular. Note that visualized structures of <70 nm diamond included caveolae. Bars, 200 nm.\\n\\n'", "CAPTION FIG6.png": "'Figure 6. Analysis of update of CTB, fluid phase meters, and GP-AB. (A) WT MEF, were re-selected with 10 mg/ml HBP as a fluid phase meter for 15 s, and then QAB tranded in the presence of AA betare being processed for EAA. Tue\\n\\n'", "SUPP CAPTION FIGS2.png": "'Figure S2: **Ultrastructural analysis of the nova-formed envelope.** To confirm that the transient expression of Cav1 in Cav1 -/- MEFs can cause the de novo formation of caveolue, Cav1 was expressed in Cav1 -/- MEFs using standard expression conditions. Cav1 -/- MEFs were microinjected with pRERS-Caw1 vector [100-150 mg/ml] together with HRP (which labels only the cell nucleus), incubated for 18\u201320 h at 37\u00b0C, and then CTBHRP was internalized for 40 min at 37\u00b0C. Cells were then fixed and processed for EM and CTBHRP was revealed by DAB. De novo formation of CTBHRP-positive caveolue was seen at the surface of injected cels. Bars, 200 nm.\\n\\n'", "SUPP CAPTION FIGS3-1.png": "'Figure 51. Cell update in Cav1-1-10\\n\\n'", "SUPP CAPTION FIGS3-2.png": "'there was no significant difference between treated and control cells. [C] CTB Alexa Fluor 594 was internalized for 40 min using the same conditions as in \\\\(\\\\AA\\\\). In untreated cells, CTB strongly colocalized with GM130. In cholesterol-depleted cells. This colocalization was reduced as shown in the quantitation in D. P \\\\(<\\\\) 1 \\\\(\\\\times\\\\) 1Q\\\\({}^{-T}\\\\); bars indicate standard error. Bars, 25.\\n\\n'", "SUPP CAPTION FIGS3.png": "'Figure S3. **CIB uptake in Cav1/\\\\(-\\\\)/MEFs is partly sensitive to cholesterol depletion. Cav1/\\\\(-\\\\)/MEFs were coincided with GFP and TR and incubated for 18-20 h. Calls were treated with cyclodextrin for 30 min, and Tf was internalized before immunofluorescence processing (A and B). Tf internalization occurred in both cholesterol-depleted calls and control cells, and quantification [B] revealed that there was no significant difference between treated and control cells. [C] CTR Alexa Fluor 594 was internalized for 40 min using the same conditions as in A. In unrelated cells, CTR strongly colocalized with GM130. In cholesterol-depleted cells. This colocalization was reduced as shown in the quantitation in D. P < 1x 10-2; bars indicate standard error. Bars, 25\\n\\n'", "SUPP CAPTION FIGS4.png": "'Figure S4. **A dynamic mutant inhibits CTB transport to the Golgi complex but not internalization.**_Cav1-/- MEFs_ were microinjected with HA-tagged DynK44A_ [B and C], DynK44A and TfR, or GFP and TfR [A]. DynK44A was expressed using the acute expression conditions (see Materials and methods). [A] Tf internalization [20 min at 37degC] was severely inhibited in \\\\(\\\\text{Ca}\\\\nu 1-/\\\\prime-\\\\) MEFs injected with DynK44A but not those injected with GFP. [B] CTB-Alexa Flucr 594 internalized for 40 min calculated with DynK44A in an extensive tubular network. The DynK44A-positive structures were not extensions of the Golgi, as GM130 did not colocalize with DynK44A or CTB. Tharefera, DynK44A severely inhibited CTB trafficking to the GM130-positive structures. [C] To investigate whether the tubular structures are surface-connected or intracellular, a time coarse of CTB internalization was performed in \\\\(\\\\text{Ca}\\\\nu 1-/\\\\prime-\\\\) MEFs transiently expressing DynK44A. CTB bound to the surface of cells at 4degC did not label the DynK44A tubular structures. However, the dynamic mutant and CTB were partially colocalized within tubular structures after 1 min of internalization, and this increased after 10 min. This suggests that dynamic is not involved in the initial entry step but affects early compartments on route to the Golgi complex. It also provides further evidence for a nonexwolce, nonclathrin pathway as DynK44A inhibits both clathrin- and Cav1-dependent endocytosis. Therefore, any CTB entering the cell should do so through the proposed nonclathrin, nonexwolce pathway.\\n\\n'", "SUPP CAPTION FIGS5.png": "'Figure S5. An ARF6 mutant inhibits CTB transport to the Golgi complex but not internalized. \\\\(\\\\text{Cav1}-\\\\text{/}\\\\text{/}-\\\\text{MEFs}\\\\) were microinjected with ARF6 T27N [B] and coincided with the transferrin receptor and HA-tagged ARF6 T27N (A). ARF6 T27N was expressed using the acute expression coordinates. (A) To investigate the effect of ARF6 in clathrin-mediated endocytosis. If was internalized for 20 min in \\\\(\\\\text{Cav1}-\\\\text{/}\\\\text{/}-\\\\text{MEFs}\\\\) that were expressing the transferrin receptor and ARF6 T27N. If uptake was severely inhibited by ARF6 T27N. (B) The formation of a tubular network was caused by overexpression of ARF6 T27N in \\\\(\\\\text{Cav1}-\\\\text{/}\\\\text{/}-\\\\text{MEFs}\\\\); CTB Alexa Fluor 59.4 internalized for 40 min accumulated in the tubular network. To determine whether or not the tubular network formed by the expression of ARF6 T27N was intracellular, a time course of CTB uptake was performed in \\\\(\\\\text{Cav1}-\\\\text{/}\\\\text{/}-\\\\text{MEFs}\\\\) expressing ARF6 T27N. CTB did not colocalize with ARF6 T27N after binding at 4degC but showed strong colocalization after 10 min at 37degC. Thus, these studies show that, like dynamic, ARF6 is not required for CTB entry. However, both proteins are involved in CTB trafficking at a post-entry step.\\n\\n'", "SUPP CAPTION S1.png": "'Figure S1: **Ultrastructural analysis of early endocytic carriers in WT-MFs and Cav1\\\\(-\\\\)/\\\\(-\\\\)MFs: development and validation.** CTB entry was examined using a modified method that distinguishes internal carriers at very early times of internalization [before fusion with other possible compartments] from surface-connected structures. In the case of caveolae, it is a considerable problem to distinguish between structures connected to the extracellular media and internal structures because caveolae and groups of caveolae can be connected to the cell surface by very narrow nacks (Porten et al., 1994). These nacks could exclude pretenaceous extracellular markers, as is the case for deeply invagorated clathrin-coated pits (Schmidt and Smythe, 1991). To prevent labeling of externally connected structures, we used the reducing agent ascorbic acid (AA) to quench the HRP-DAB reaction product on an extracellular surface (Sborovgogl et al., 1996). This necessitates carrying out the DAB reaction on cells before fixation. WT MEFs were labeled with CTB-HRP on ice, and then the HRP reaction was performed immediately or after warming to 37\u00b0C for 2.5 or 30 min. In each case, the DAB reaction was performed on ice in the presence or absence of ascorbic acid (=AA) and subsequently fixed and processed for EM. In addition, we optimized conditions to allow immunogold labeling of the CTB-HRP-labeled elements so that individual structures could be identified as surface connected or internal and identified using well-defined markers such as Cav1 and dynamin. [A] Cells maintained at 4\u00b0C and DAB reacted in the absence of AA [-AA] show an electron-dense layer of reaction product over the entire cell surface [a and b], including clearly surface-connected caveolae and putative caveolae structure that appear to be some disconnects from the PM but are obviously surface connected outside the plane of section [b]. The morphology was similar to that seen in cells in which the DAB reaction was performed after fixation [standard conditions; see Fig. S2). In the presence of AA [+AA] staining was completely abolished [c\u2013b], indicating that the AA is able to efficiently quench the surface reaction product even in deeply invagorated structures (e and f]. [B] WT MEFs were warmed to 37\u00b0C for 30 min and stained in the presence or absence of AA. Staining can be seen in putative endosomal structures and the Golgi [G] in both samples, although cells processed in the presence of AA show no surface labeling [compare to d [-C] for examine the non-surface-connected carriers involved in the earliest stages of CTB-HRP uptake, WT MEFs internalized CTB-HRP for 2.5 min at 37\u00b0C, and were DAB treated in the presence of AA to remove surface reaction. Note that structures within 50 nm from the surface show CTB-HRP/DAB staining but are clearly not surface connected. Thus, this method can be used to identify and characterize budding all intermediates in the CTB entry pathway for the first time. [D] A second method for sample preparation was also used in which cells were not sectioned after processing but were prepared as whole mount specimens using a modification of the method described previously (Stoovvagel et al., 1996). WT MEFs were grown on EM grids, which had internalized CTB-HRP for 5 min at 37\u00b0C. Cells were treated with DAB in the presence of AA. This method allowed the call pariphery to be observed without sectioning, and so facilitated the visualization of complex structures in three dimensions. When compared to C, similar structures observed in the section are observed in the whole mount calls. Bars: [Aa, Ac, Ba, and Bc] 1 mm; [Ab, Ad, Bb, Bd, C, and D] 500 nm; [Aa and Af] 100 nm.\\n\\n'"}

extracted_captions/kirshMultitaskingCostStructure2005.json

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+{}

extracted_captions/kneelandExploringUnchartedTerritory2020.json

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+{"CAPTION FIG1.png": "'Figure 1: (Color online) Knowledge Creation Processes for Outlying Technological Positions\\n\\n'", "CAPTION FIGA.1..png": "'\\n\\n**Figure A.1.** Example of Network Diagram with New Unconnected Node'", "CAPTION TAB1.png": "'\\n\\n[MISSING_PAGE_POST]\\n\\n'", "CAPTION TAB2.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline\\n**Table 2.** Top 10 NBER Technological Subcategories for Outlier and Nonoutlier Patents, 1990\u20132000 \\\\\\\\ \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 2: Top 10 NBER Technological Subcategories for Outlier and Nonoutlier Patents, 1990\u20132000'", "CAPTION TAB3.png": "'\\n\\n**Table 3. Search Processes, Definitions, Indicators, and Quotes'", "CAPTION TAB4.png": "'\\n\\n**Table 4.** Descriptive Statistics and Correlations'", "CAPTION TAB5.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K.\\n\\n'", "CAPTION TAB6.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline\\n**Table 6.** Logit Regressions Predicting Outlier Patents with Distant Recombination and Full Model \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 6: Logit Regressions Predicting Outlier Patents with Distant Recombination and Full Model'", "CAPTION TABB.1.-2.png": "'\\n\\n**Acknowledgement**'", "CAPTION TABB.1..png": "'\\n\\n**Table B.1. Additional Interview Information**'", "CAPTION TABC.1..png": "'\\n\\n**Table C.1.** **Kobustance Analysis**'"}

extracted_captions/knoblichConstraintRelaxationChunk1999.json

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+{"CAPTION FIG1.png": "'Figure 1: Two matchstick arithmetic problems in the format used in the experiments.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Cumulative solution rates for Problem Types A-C in Block 1 of Experiment 1A.\\n\\n'", "CAPTION FIG3.png": "'Figure 3: Cumulative solution rates for Problem Types A and D in Block 1 of Experiment 1A.\\n\\n'", "CAPTION FIG4.png": "'Figure 4: Cumulative solution rates for Problem Types A\u2013D in Block 2 of Experiment IA.\\n\\n'", "CAPTION FIG5.png": "'Figure 5: Cumulative solution rates for Problem Types \\\\(\\\\mathbf{A\\\\mbox{\\\\sf C}}\\\\) in Experiment 1B.\\n\\n'", "CAPTION FIG6.png": "'Figure 6: Cumulative solution rates for Problem Types A and D in Experiment 1B.\\n\\n'", "CAPTION FIG7.png": "'Figure 7: Cumulative solution rates for Problem Types A-C in Block 1 of Experiment 2.\\n\\n'", "CAPTION FIG8.png": "'Figure 8: Cumulative solution rates for Problem Types A and D in Block 1 of Experiment 2.\\n\\n'", "CAPTION FIG9.png": "'Figure 8: Cumulative solution rates for Problem Types A\u2013D in Block 2 of Experiment 2.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l'", "CAPTION TAB10.png": "'Table 10\\n\\n_Percentage Solutions in Experiment 3 by Coordination, Problem Type, and Block_'", "CAPTION TAB11.png": "'Table 11\\n\\nSolution Times (in Seconds) in Experiment 3 for Regular Problems'", "CAPTION TAB12.png": "'Table 12\\n\\nSolution Times (In Seconds) in Experiment 3 for Tautological Problems'", "CAPTION TAB13.png": "'\\n\\n\\\\begin{table}\\n\\\\begin{tabular}{l l} \\\\hline \\\\hline \\\\multicolumn{1}{c}{_Main Effects of Task Difficulty in Experiments IA. IB. and 23_} \\\\\\\\ \\\\hline \\\\hline \\\\end{tabular}\\n\\\\end{table}\\nTable 13: _Main Effects of Task Difficulty in Experiments IA. IB. and 23_'", "CAPTION TAB14.png": "'\\n\\n## Table 1: Transfer on Extratering IA and 2'", "CAPTION TAB2.png": "'\\n\\n## Table 2\\n\\nSolarflora Times (Hor Seconds) for Black 1 of Experiment IA (N = 20)'", "CAPTION TAB3.png": "'\\n\\n## Table 3 Solution Times (in Seconds) for Black 2 of Experiment IA (\\\\(\\\\Omega\\\\) = 20)'", "CAPTION TAB4.png": "'\\n\\n## Table 4 Problems Used in Experiment I'", "CAPTION TAB5.png": "'\\n\\n**Table 5**\\n\\nSolution Times (in Seconds) in Experiment 1B'", "CAPTION TAB6.png": "'Table 6: Problems Used in Experiment 2 by Type and Condition\\n\\n'", "CAPTION TAB7.png": "'\\n\\n## Table 1: Percentage Solutions in Experiment 2 by Condition and Block'", "CAPTION TAB8.png": "'Table 8\\n\\n_Solation Times (in Seconds) for Block 1 of Experiment 2_'", "CAPTION TAB9.png": "'Table 9\\n\\n_Solution Times (in Seconds) for Block 2 of Experiment 2_'"}

extracted_captions/kobayashiDepolarizationSocialMedia2020.json

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+{"CAPTION FIG1.png": "'\\n\\n**Figure I.** **Moderated effects of political use of social media.** Shaded areas indicate 95% CI.\\n\\n'", "CAPTION FIG2.png": "'Figure 2: Partisan selectivity among single and dual identifiers. Error bars indicate 95% CI.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table I. Regression models predicting partisan selectivity, polarization, and political participation.**'", "CAPTION TAB2.png": "'\\n\\n## References\\n\\n* [1] A. A. K. K. (1999) The mathematical theory of the mathematical theory'"}

extracted_captions/kobayashiNewsAudienceFragmentation2019.json

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+{"CAPTION FIG1.png": "'Figure 1. Distribution of estimated ideology.\\n\\n'", "CAPTION FIG2.png": "\"Figure 2. Distributions of Twitter users' ideology per media account.\\n\\n\"", "CAPTION FIG3.png": "'Figure 3. Overlap in followers of major Japanese media accounts.\\n\\n'", "CAPTION TAB1.png": "'\\n\\n**Table 1.** The list of media accounts.\\n\\n'", "CAPTION TAB2.png": "'\\n\\n**Table 2.** MSE of classifiers (10-fold cross-validation).\\n\\n'"}