task2-train-dev.json

[
    {
        "id": "akamatsulab-WbWLJVWcF",
        "claim": "Knockout of __Dictyostelium__ WASP (__wasA-__) led to bipolar localization of WAVE rather than WT localization of WAVE to the leading edge.",
        "citekey": "amato2019wasp",
        "context": [
            "Super-resolution microscopy was adopted to investigate the ability of WASP CRIB mutants to localize to clathrin-coated pits and to recruit the Arp2/3 complex. Images were acquires using a Zeiss LSM880 equipped with a 63x/1.40 NA objective. GFP was excited at 488 nm, RFP at 561 nm. Images were acquired using the ZEN imaging software every 1 or 2 s. TIRF microscopy was utilized to monitor the dynamics of clathrin, WASPs, Arp2/3 complex and actin on the ventral surface of the cells. Images were acquired using a modified Nikon Eclipse TE 2000-U microscope equipped with a photometrics Evolve 512 camera and a DualView DV2 emission splitter. GFP and RFP were excited using 473 nm and 561 nm wavelengths respectively. A 100x/1.40 NA TIRF objective was used. Images were acquired every 1 or 2 s using the MetaMorph software. (p. 18)",
            "Dictyostelium wild-type, wasA knockout, and inducible double null cells were grown at 22\u000eC on Petri dishes in HL5 supplemented with vitamins and micro-elements (Formedium). (p. 17)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-dFhjWUgD7",
        "claim": "TIRF revealed that Cortactin, Hip1R, and Clathrin were simultaneously recruited to endocytic sites in 3T3 cell.",
        "citekey": "leclainche2007hip1r",
        "context": [
            "We show that the complex contributes to the regulation of actin assembly in HeLa cells and we establish the relative timing of recruitment of these proteins to endocytic sites. Specifically, we show that the Hip1R\u2013cortactin complex inhibits actin assembly by capping filament barbed ends.",
            "Real-time imaging of Hip1R and cortactin at CCPs",
            "To determine when this Hip1R\u2013cortactin complex might function during endocytosis, we quantitatively analyzed the temporal appearance of Hip1R and cortactin at endocytic sites. Previous immuno-EM studies revealed that both proteins are present during all stages of CCP formation (Engqvist-Goldstein et al, 2001; Cao et al, 2003). In addition, Hip1R appeared to link actin filaments to CCPs, whereas cortactin was found on actin filaments and actin filament branches throughout the plasma membrane (EngqvistGoldstein et al, 2001; Cao et al, 2003). Total internal reflection fluorescence microscopy (TIR-FM) was performed to image Hip1R-GFP or cortactin-GFP on the surfaces of cells stably expressing DsRed-clathrin (Figure 4). Consistent with previous reports, Hip1R appeared at essentially all of the clathrin patches, whereas cortactin appeared at about onethird of the clathrin patches (Engqvist-Goldstein et al, 2004; Merrifield et al, 2005). We found that Hip1R recruitment follows the course of CCP growth, albeit with a small delay compared to clathrin (Figure 4A, C and E). When a CCP started to disappear, Hip1R behavior was essentially the same as that of clathrin. These observations are consistent with previous observations, but with greater time resolution (Engqvist-Goldstein et al, 2001; Keyel et al, 2004). In contrast, cortactin recruitment was more precipitous, occurring close to the time of CCV formation, and cortactin fluorescence lingered slightly longer after clathrin disappeared (Figure 4B, D and E).",
            "Live cell imaging TIR-FM was performed using an Olympus IX81 microscope equipped with a \b 60/NA1.45. lens and 488 nm argon ion laser (Melles Griot). The temperature was maintained at 27.51C using a Bioptechs chamber. The 488 nm laser was used to excite both GFP and DsRed. Simultaneous two-color imaging was performed using an image splitter (Optical Insight) to separate the red and green emission signals to two sides of the camera sensor using a 565 nm dichroic mirror, and 530/30 and 630/50 nm emission filters. No bleed-through between the red and the green channel was detected under our conditions. Swiss 3T3 cells that stably express DsRedmLCa (mouse clathrin light chain a) were transiently transfected with Hip1R-GFP or cortactin-GFP using Lipofectamine reagent (Invitrogen) 48 h before imaging. Each cell was imaged every 2 s for 200\u2013300 frames. After each experiment, images of immobilized microbeads that fluoresce at both green and red wavelengths were captured. These images were used to align the cell images.",
            "(C) Average fluorescence of clathrin (dark green) and Hip1R (red) plotted against time from 30 CCPs in eight cells. The error bars represent the s.d. from 30 events. Time 0 corresponds to the moment at which the clathrin signal started to dim. All data were normalized (see Materials and methods) before averaging. (D) Average fluorescence for clathrin (light green) and cortactin (blue) plotted against time from 30 CCPs in 14 cells. (E) Summary of panels C and D without the error bars. Time 0 is marked by a yellow line."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-5i2BACcCn",
        "claim": "Pyrene-actin binding assays between human myo1e and actin plateaued at a dissociation rate of 440 \u00b1 9 s-1 for ATP concentrations > 2 \u00b5M",
        "citekey": "mezgueldi2002kinetic",
        "context": [
            "Myosin-I Expression and Purification\u2014The cDNA for human myosin-IC (accession NM 004998), kindly provided by W. M. Bement (University of Wisconsin), was truncated at Glu720, generating a construct containing the motor domain and the only IQ motif (referred to as myo1eIQ throughout the paper). A FLAG peptide sequence was inserted at the C terminus and subcloned into the baculovirus transfer vector pVL1392 (Invitrogen). Recombinant baculovirus was generated using standard procedures. Myo1eIQ with bound calmodulin was purified from Sf9 cells that were coinfected with virus containing recombinant myo1eIQ and CaM (Fig. 1). Four liters of log phase cells (2 & 106 cells/ml) were infected and incubated at 27 \u00b0C for 60 h with shaking. Cells were harvested by centrifugation; suspended in lysis buffer (10 mM Tris, pH 7.0, 200 mM NaCl, 2 mM MgCl2,5mM DTT, 1 mM phenylmethylsulfonyl fluoride, 0.01 mg/ml aprotinin, 0.01 mg/ml leupeptin), 2 mM MgATP, and 0.05% Igepal at 4 \u00b0C; and homogenized with five strokes in a Dounce homogenizer. Cell extract was centrifuged at 100,000 & g for 1 h. The supernatant was loaded onto anti-FLAG antibody columns (Sigma). Columns were washed with 5 column volumes of lysis buffer ' 2mM MgATP and 5 column volumes of lysis buffer. Myo1eIQ was eluted with 10 mM Tris, pH 8.0, 100 mM NaCl, 1 mM DTT, 5 \"M CaM, 0.2 mg/ml FLAG peptide (Sigma), 0.01 mg/ml aprotinin, 0.01 mg/ml leupeptin. Eluted protein was loaded directly on to an 8-ml Mono Q column (Amersham Biosciences) equilibrated in column buffer (10 mM Tris, pH 8.0, 25 mM KCl, 1mM DTT) and eluted with a linear 25 mM\u20131 M KCl gradient. The Mono Q column separated myo1eIQ from FLAG peptide, ADP, ATP, and free CaM. Fractions containing myo1eIQ were dialyzed versus storage buffer (10 mM Tris, pH 7.5, 100 mM KCl, 1 mM EGTA, 1 mM DTT, 50% glycerol), which concentrated the protein and allowed for storage at $20 \u00b0C. Quantitative densitometry showed that myo1eIQ was (95% pure, and the CaM:myo1eIQ ratio was 1:1. Approximately 2 mg of pure myo1e protein was obtained from 4 liters of cells. (p. 2)",
            "Stopped Flow, Quenched Flow, and Kinetic Modeling\u2014Transient kinetic measurements were made at 25 \u00b0C with an Applied Photophysics (Surrey, UK) SX.18MV stopped flow having a 1.2-ms dead time. Tryptophan fluorescence (#ex # 295 nm) was measured using a 320 nm WG long pass emission filter (Oriel). A 400 nm long pass filter (Oriel) was used to monitor pyrene (#ex # 365 nm), and mantADP and mantATP (#ex # 295 nm) fluorescence. Usually three to five transients were averaged before nonlinear least square fitting. The time courses presented in the figures show the average of one to four individual traces. Transients were fitted to exponential functions using the software supplied with the stopped flow. (p. 2)",
            "Rabbit skeletal muscle actin was prepared and gel filtered (22). Actin concentrations were determined by absorbance at 290 nm, !259 # 26,600 M$1 cm$1 (23). Actin was labeled with pyrenyl iodoacetamide (pyreneactin) and gel filtered (24). All actin was stabilized with a molar equivalent of phalloidin (Sigma). Calmodulin (CaM) was expressed in bacteria and purified as described (25). (Pp. 1-2)",
            "Tryptophan fluorescence (#ex # 295 nm) was measured using a 320 nm WG long pass emission filter (Oriel). (p. 2)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-W8Zi3Y46u",
        "claim": "Overexpression of GFP-GRAF1 in HeLa cells showed long (1-5um) tubules that turn over completely within 10 minutes based on fluorescence microscopy",
        "citekey": "lundmark2008gtpaseactivating",
        "context": [
            "HeLa cells were grown in RPMI 1640 or MEM media (GIBCO) supplemented with LGlutamine, 10% foetal bovine serum, non-essential amino acids (for MEM), and transfected using Genejuice (Novagen) for transient protein expression. For primary cultures, rat hippocampal neurons/astrocytes were prepared by trypsin digestion and mechanical trituration from E18 or P1 Sprague-Dawley rats and plated onto poly L-lysine coated coverslips. Cells were cultured in B27-supplemented Neurobasal media. (Supplemental materials p. 2)",
            "For real time microscopy of the dynamics of GRAF1- and GRAF1 BAR+PH- positive tubules, transfected cells on glass-bottom Petri dishes (WillCo Wells BV, Amsterdam) were washed with buffer (125mM NaCl, 5mM KCl, 10mM Dglucose, 1mM MgCl2, 2mM CaCl2 and 25mM HEPES) and images were taken using a 5-live scanning microscope (Zeiss) or spinning disc confocal system (Improvision) with subsequent analysis in LSM Image Browser (Zeiss), ImageJ (freeware) or Volocity (Improvision) (Supplemental materials p.3)",
            "We found GRAF1-positive tubular structures to be spectacularly dynamic (Figure 1E and Movie S1)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-MIpYGNa-U",
        "claim": "WAVE2 and IRSp53 both localized at ruffles and cell-cell junctions in A431 cells.",
        "citekey": "suetsugu2006optimization",
        "context": [
            "**Cells and purification of the WAVE2 complex** A431 cells were transfected with FLAG-tagged WAVE2 in pCMV-Tag 2 (Stratagene) or with vector alone. FLAG-tagged WAVE2 is functional because the transfection of FLAG-tagged WAVE2 into WAVE2 knockout cells eliminated WAVE2 deficits. After selection with G418, cells with stable FLAG-WAVE2 expression were grown. These cells did not show any significant change in growth or appearance compared with vector-transfected cells or parental cells. The amount of FLAG-WAVE2 expression was similar to the amount of endogenous WAVE2. 106 cells were plated onto 15-cm dishes and cultured for 5 d. After serum starvation overnight, some cultures were stimulated with EGF. To purify the WAVE2 complex from the cytosol (cytosol fraction), cells were harvested in buffer A containing 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 150 mM NaCl, 5 mM NaF, 1 mM Na3VO4, 1 mM PMSF, 10 \u03bcg/ml aprotinin, and 10 \u03bcg/ml leupeptin.",
            "Figure 1. **Localization of WAVE2 and IRSp53 in A431 cells.** (A) Localization of WAVE2 and IRSp53 in EGF-stimulated A431 cells treated with control, IRSp53, or IRTKS stealth RNAi was examined by immunofluorescence with anti-WAVE2 antibody or anti-IRSp53 antibody (M051-3). Actin filaments stained with phalloidin are also shown. WAVE2 and IRSp53 were localized at ruffles (arrowheads) and cell\u2013cell junctions (arrows).",
            "All fluorescent images were taken through a microscope (Eclipse E600; Nikon) with a confocal microscopy system (Radiance 2000; Bio-Rad Laboratories) at room temperature. Fluorochromes used include AlexaFluor488, 546, and 647 and rhodamine (all purchased from Invitrogen). A 60× NA 1.40 oil immersion objective (Nikon) was used. Images were assembled with Adobe Photoshop. In each plate, photographs were cropped, and each fluorochrome was adjusted identically for brightness and contrast to represent the observed images. Time-lapse images were taken through a phase-contrast microscope (Axiovert S100; Carl Zeiss MicroImaging, Inc.) with a camera (CCD-782-Y/HS; Princeton Instruments). A 40× NA 1.30 FLUAR oil immersion objective (Carl Zeiss MicroImaging, Inc.) was used."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-6wkebK9Rb",
        "claim": "Depletion of \u03b21 or \u03b23 integrins by siRNA in HeLa cells showed no difference in the percentage of dynamic or static CCSs as compared to siCTRL cells.",
        "citekey": "baschieri2018frustrated",
        "context": [
            "Spinning disk microscopy of live cells. Cells were imaged at 5 s intervals for the indicated time using a spinning disk microscope (Andor) based on a CSU-W1 Yokogawa head mounted on the lateral port of an inverted IX-83 Olympus microscope equipped with a \u00d760 1.35NA UPLSAPO objective lens and a laser combiner system, which included 491 and 561 nm 100 mW DPSS lasers (Andor). Images were acquired with a Zyla sCMOS camera (Andor). The system was steered by IQ3 software (Andor). For CCS dynamics quantification, we measured the lifetime of CCSs using the TrackMate plugin of ImageJ47. Tracks below 5 s of duration (detected on only 1 frame) were discarded. Measured individual lifetimes were pooled into two groups: the \u201cdynamic\u201d group corresponding to structures with a lifetime below the duration of the movie (5 min) and the \u201cstatic\u201d group with a lifetime of 5 min. Of note, the relative percentage of dynamic versus static structures depends on the duration of the movie because static structures are only counted once while dynamic structures continuously nucleate and disappear during the movie. For this reason, all quantifications of CCS dynamics represent the relative number of static or dynamic events detectable at the plasma membrane at a given time point. At least 1000 CCSs from at least five cells per conditions and per experiments were tracked in 3\u20135 independent experiments. Data are expressed as mean \u00b1 SD. (p. 11)",
            "HeLa cells (a gift from P. Chavrier, Institut Curie, Paris, France; ATCC CCL-2), genome-edited HeLa cells engineered to expressed an endogenous GFP-tagged or mCherry-tagged \u03bc2 subunit, HepG2 cells (ATCC HB8065), Caco-2 cells (ATCC HTB-37), MDA-MB-231 cells (a gift from P. Chavrier, Institut Curie, Paris, France; ATCC HTB-26), or genome-edited MDA-MB-231 cells engineered to expressed an endogenous GFP-tagged \u03bc2 subunit (a gift from D. Drubin, University of California-Berkeley, California, USA) were grown in DMEM Glutamax supplemented with 10% foetal calf serum at 37 \u00b0C in 5% CO2. All cell lines have been tested for mycoplasma contaminations. For most experiments, cells were grown on substrates coated with a 50 \u03bcg/ml solution of collagen-I (Thermo Fisher Scientific\u2014Cat. Nr. A10483-01) unless otherwise stated. (p. 10)",
            "For siRNA depletion, 200,000 cells were plated in six well plates. After 24 h, cells were treated with the indicated siRNA (30 nM) using RNAimax (Invitrogen, Carlsbad, CA) according to the manufacturer\u2019s instruction. Protein depletion was maximal after 72 h of siRNA treatment as shown by immunoblotting analysis with specific antibodies. To deplete CHC or \u03bc2-adaptin, cells were transfected once as described above and then a second time, 48 h later, with the same siRNAs. In this case, cells were analyzed 96 h after the first transfection. The following siRNAs were used: \u03b25-1, 5\u2032-GCUCGCAGGUCUCAACA UA-3\u2032; \u03b25-2, 5\u2032-GGUCUAAAGUGGAGUUGUC-3\u2032; \u03bc2-adaptin, 5\u2032-AAGUGGA UGCCUUUCGGGUCA-3\u2032; Clathrin heavy chain (CHC), 5\u2032-GCUGGGAA AACUCUUCAGATT-3\u2032; \u03b1v-1, 5\u2032-CCUCUGACAUUGAUUGUUA-3\u2032; \u03b1v-2, 5\u2032-C CGAAACAAUGAAGCCUUA-3\u2032; DAB2, 5\u2032-GAGCAUGAACAUCCAGAU AATT-3\u2032; Numb, 5\u2032-GAUAGUCGUUGGUUCAUCATT-3\u2032; Integrin \u03b21 ON-TARGET plus SMART pool (Dharmacon L-004506-00), Integrin \u03b23 siGENOME Human ITGB3 siRNA (Dharmacon M-004124-02); Talin1, 5\u2032-AC AAGAUGGAUGAAUCAAUUUU-3\u2032; non-targeting siRNAs (siControl), ONTARGET plus Non-Targeting SMART pool siRNAs (Dharmacon D-001810-01) (p. 11)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-NU1hryH_8",
        "claim": "GRAF1-depletion by siRNA knockdown in HeLa cells has no effect on transferrin uptake",
        "citekey": "lundmark2008gtpaseactivating",
        "context": [
            "For immunofluorescence trafficking assays, biotinylated holo-transferrin, (Sigma Aldrich), Alexa Fluor 647- conjugated transferrin (Invitrogen), Alexa Fluor 546/555- conjugated CTxB (Invitrogen), DiI (Invitrogen), FITCdextran (10kDa MW, used for fluorimetric uptake assay, Invitrogen), and biotinylated dextran (10kDa MW, used for immunofluorescent uptake assays, Invitrogen), were diluted in pre-warmed media, added to cells and incubated for time periods and temperatures as described in figure legends. After washing, cells were fixed and subjected to immunofluorescence analysis as described",
            "GRAF1-depleted cells were assessed for their ability to endocytose dextran (allowing assessment of total endocytic capacity), both by epifluorescence microscopy and by a quantitative fluorimetric assay (Figures 4B and 4C).",
            "HeLa cells were grown in RPMI 1640 or MEM media (GIBCO) supplemented with LGlutamine, 10% foetal bovine serum, non-essential amino acids (for MEM), and transfected using Genejuice (Novagen) for transient protein expression. For primary cultures, rat hippocampal neurons/astrocytes were prepared by trypsin digestion and mechanical trituration from E18 or P1 Sprague-Dawley rats and plated onto poly L-lysine coated coverslips. Cells were cultured in B27-supplemented Neurobasal media. For GRAF1 depletion, HeLa cells were transfected with Stealth siRNAs specific against human GRAF1 using Lipofectamine 2000 (Invitrogen) according to manufacturers instructions. The Invitrogen siRNA duplex sequences used were siRNAa (UUA UCU CCC AUU CAG CAC AGA UAU C/ GAU AUC UGU GCU GAA UGG GAG AUA A), and siRNAb (UUU GAA ACU GGU ACA UCA UGA GUG G/CCA CUC AUG AUG UAC CAG UUU CAA A). Cells were cultured for an additional 48 hours for efficient silencing of the GRAF1 expression. Stealth Block-it siRNA (Invitrogen) was used as a control. AP2 siRNA was used as previously described [3]. (Supplemental materials p. 2)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-FxTUmxjh2",
        "claim": "Simulated fission yeast endocytic actin networks produced ~3000 pN of force, while simulated budding yeast endocytic actin networks produced ~1000 pN of force",
        "citekey": "nickaeen2022model",
        "context": [
            "To determine the time-dependent driving force fdrive (t), we integrate over the surface of the invagination, for each t, the active and viscous forces exerted on the invagination by actin flow and then project the resultant force on the invagination axis [see Supplemental Material, Eq (S4)].",
            "Our model, described in detail in Nickaeen et al. (2019), couples kinetics of actin nucleation, polymerization, and turnover constrained by counts of each participating protein over time (Berro et al., 2010), with the mechanics of the assembling filamentous meshwork approximated as that of a visco-active gel (Kruse et al. 2005; Prost et al., 2015). Mathematically, the model consists of advection-reaction equations governing densities of proteins involved in patch assembly (see Eq (S1) in the Supplemental Material), and a force-balance equation yielding actin velocities [Eq (S2) of the Supplemental Material].",
            "The coupled system of the reaction-transport equations [Eqs (S1), (S1*), and (S1**)], force-balance equation [Eq (S2)], and Eq (1) was solved using a moving-mesh solver of COMSOL Multiphysics, a software package for solving spatial multiphysics problems on finite element meshes (COMSOL Multiphysics, 2015).",
            "Figure 4 compares results for budding and fission yeast obtained with the optimized parameter sets. Graphs in panels A and B illustrate how turgor pressure affects fdrive (t) and fnet(t) = fdrive(t) \u2013 fresist(t)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-45WDQVJkn",
        "claim": "ABI2 formed a complex with GRAF1 based on immunoprecipitation of HeLa cell lysates, in a manner dependent on GRAF1 phosphorylation and treatment with mitochondrial damaging agent oligomycin-A and antimycin-A",
        "citekey": "zhu2023graf1",
        "context": [
            "GRAF1b isoform full length or various GRAF1 domains were cloned into pGEX-6P-1 vector and expressed as glutathione-s-transferase (GST) fusion proteins in BL21 E. coli. The expressed GST-fusion proteins were purified with Glutathione Sepharose 4B (Cytiva). For GST pull-down assays, Hela/YFP-Parkin cells were collected in lysis buffer (20 mM Tris HCl, 150 mM NaCl, 10% glycerol, 0.5 % Triton X100 pH7.4 with 1x HALT phosphatase & protease inhibitor cocktail). Cell lysates were incubated on ice for 15 min and centrifuged at 20,000xg for 15 min. The supernatants were incubated with GST-fusion protein-loaded beads for 1 hr end-over-end rotation at 4 \u00b0C. Beads were washed 5 times with cell lysis buffer and stored 4 \u00b0C until use or up to 7 days.",
            "a Co-IP of endogenous ABI2 with Flag-GRAF1 WT or phosphor-deficient AAA variant in GRAF1 KO Hela/YFP-Parkin cells. EV: empty vector.",
            "For western blot analysis, Hela cells or NRVCMs in 6 well plates with indicated treatment were lysed in Triton X-100 lysis buffer (25 mM Tris-HCL pH7.4, 150 mM NaCl, 10% glycerol, 1% Triton X-100 with 1x HALT phosphatase & protease inhibitor cocktail). Lysate concentration was measured by Pierce BCA protein assay kit. Approximately 25 ~ 50 \u03bcg protein per sample was separated on SDS-PAGE and then wet transferred in Tris-glycine transfer buffer to 0.2 \u03bcm pore size nitrocellulose membranes (Bio-Rad). HRP-conjugated secondary antibodies and ECL chemiluminescent substrate (GE Healthcare) were used to detect target proteins in blots.",
            "To perform co-immunoprecipitation of target proteins from COS7 cell lysates, COS7 cells were transfected with the specified plasmids and expressed the target proteins for a duration of 20 h. Subsequently, transfected COS7 cells were treated with a combination of Oligomycin A (2.5 \u03bcM) and Antimycin A (250 nM) for a period of 6 h to induce mitophagy. Cell lysates were prepared in lysis buffer (50 mM HEPES-HCl pH7.4, 150 mM NaCl, 1 mM EDTA, 10% glycerol, 0.8% Chaps and 1x HALT phosphatase & protease inhibitor cocktail). For co-immunoprecipitation of target proteins from Hela cells, cell lysates were prepared in lysis buffer (20 mM Tris HCl, 150 mM NaCl, 10% glycerol, 0.5 % Triton X100 pH7.4 with 1x HALT phosphatase & protease inhibitor cocktail). Cell lysates were incubated on ice for 15 min and centrifuged at 20,000 rcf for 15 min. Protein concentration was measured by Pierce BCA protein assay kit (Thermo Fisher). Protein lysates (500 ~ 800 \u03bcg) were incubated with mouse anti-Flag M2 (F1804,Sigma) or rabbit anti-GFP (A11122, Thermo Fisher) bound with Dynabeads\u00ae Protein G (Thermo Fisher) with end-over-end rotation for 3 h at 4 \u00b0C. Magnetic beads were washed 4 times with lysis buffer and were transferred to a clean tube for one more wash. Co-IPd protein complexes were eluted by boiling in Laemmli buffer plus \u03b2-mercaptoethanol for 5 min."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-JvW-piCf8",
        "claim": "Cortactin mutants lacking phosphorylatable Tyrosine site could not rescue the Knockdown of endogenous cortactin in Hela Cell",
        "citekey": "zhu2007receptormediated",
        "context": [
            "FIGURE 2. Cortactin mutant deficient in tyrosine phosphorylation fails to rescue uptake of Tfn in cortactin knockdown cells. A, MDA-MB-231 cells were infected with retroviruses carrying GFP or GFP-tagged murine cortactin variants (cortactin-GFP, Cort-F-GFP, and Cort\u0003SH3-GFP). The infected cells were treated with either human cortactin (C) or HS1 (H) siRNA for 2 days. The total cell lysates were prepared and analyzed for cortactin expression by immunoblotting using monoclonal cortactin antibody. The samples were also immunoblotted by actin antibody. B, siRNA-treated cells were subjected to Tfn uptake analysis after 2 days of treatment as described under \u201cExperimental Procedures.\u201d The data shown are the mean \b S.D. of three independent experiments. The p values of Student\u2019s t test refer to the difference between cortactin- and HS1 siRNA-treated cells (*) and the difference between cortactin-siRNA-treated cells expressing cortactin-GFP and those expressing CortF-GFP or Cort\u0003SH3-GFP (**).",
            "To study the role of cortactin tyrosine phosphorylation in receptor-mediated endocytosis, HeLa cells were infected with a retroviral vector, MGIN (39), encoding a murine cortactin construct tagged by GFP at the C terminus (cortactinGFP), a mutant of Y421F/Y466F/Y482F (Cort-F-GFP), and a mutation with deletion of the SH3 domain (Cort\u0003SH3-GFP) (Fig. 1A).",
            "Analysis of the Effect of Tyrosine Phosphorylation on the Affinity of Cortactin for Dynamin-2\u2014Cortactin was phosphorylated by Src kinase (Upstate) in a reaction buffer containing 100 mM Tris, pH 7.4, 125 mM MgCl2,25mM MnCl2,2mM EGTA, 1 mM ATP, and 0.2 mM Na3VO4 at 30 \u00b0C for 30 min, the modified condition recommended by the manufacture. To analyze the affinity of cortactin for dynamin, 18 pmol of cortactin, either phosphorylated or nonphosphorylated, was incubated with different amounts of GST-dynamin-2 immobilized on glutathione-Sepharose in buffer",
            "As shown in Fig. 2A, the human cortactin siRNA inhibited cortactin expression by \u000560 \u2013 80% as compared with that of the cells treated with the HS1 siRNA. When biotinTfn uptake was analyzed, a nearly 70% reduction in endocytosis was found in the cells treated with cortactin siRNA (Fig. 2B, left), which is consistent with our previous report (22) and a report from others (23). To determine whether the decrease in Tfn endocytosis was due to the specific loss of cortactin in the siRNA-treated cells, we treated the cells expressing murine cortactin-GFP with HS1 and cortactin siRNAs, respectively. In addition to the endogenous cortactin, the human cortactin siRNA also showed a slight inhibition of the exogenous murine cortactin (Fig. 2B, right), presumably because of the 95% identity between human and mouse mRNAs in the region targeted by the siRNA. Nevertheless, the overall level of exogenous cortactin proteins was greater than or similar to that of the endogenous cortactin of the control cells. At this level cortactin siRNA failed to inhibit Tfn uptake in the cortactinGFP-expressing cells, indicating that cortactin-GFP protein maintains its endocytic function similar to the endogenous cortactin. However, the same cortactin siRNA retained inhibitory activity for Tfn uptake in the cells expressing either mutant Cort-F-GFP or Cort\u0003SH3GFP (Fig. 2B)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-UlZY0Mnwt",
        "claim": "hiPSCs at the colony edges showed large, paxillin-positive focal adhesions with thick actin stress fibers parallel to the colony edge.",
        "citekey": "narva2017strong",
        "context": [
            "Cells were plated on VTNcoated glass plates and fixed after 24 hr with 4% paraformaldehyde for 15 min, permeabilized with 0.5% (v/v) Triton X-100 in PBS for 15 min, and stained with the appropriate antibodies, prepared in 30% (v/v) horse serum (Gibco), in addition to DAPI and attophalloidin-647 (Sigma) staining.",
            "HiPSC lines HEL24.3, HEL11.4, HEL24.3-SOX2-ntdT reporter, hESC line H9, and parental fibroblasts were obtained from the University of Helsinki. Cells were grown on MG (Corning) or on 5 mg/mL VTN (Life Technologies) in Essential 8 medium (Life Technologies). HiPSCs were differentiated in 10 mM RA (Sigma).",
            "Surprisingly, hiPSCs displayed large, PAXILLIN-positive FAs at the edges ofthe colonies (\u2018\u2018cornerstone\u2019\u2019 FAs) in stark contrast to the"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-iLicutBoX",
        "claim": "Fluid uptake as measured by fluorescent 10kDa Dextran increased upon relaxation after mechanically induced stretch by vacuum-based equi-bi-axial stretching device in CHO cells.",
        "citekey": "thottacherry2018mechanochemical",
        "context": [
            "For the stretch\u2013relax experiments, cells plated on PDMS membrane were loaded on the cell stretcher system (Fig. 1b) within a temperature-controlled chamber at 37 \u00b0C. Vacuum was applied beneath the ring containing the PDMS sheet, deforming the membrane and stretching the cells plated on the PDMS. The setup was calibrated to stretch cells equi-biaxially to cause 6% strain for 90 s.",
            "The quantification of endocytic uptake for a population is done by imaging on 20\u00d7, 0.75 NA on a Nikon TE300 widefield inverted microscope. For the stretch experiments, an upright microscope (Nikon eclipse Ni\u2013U) was used with a water immersion objective (60\u00d7, 1.0 NA). For endosome size calculation, spinning disk confocal microscope (100\u00d7, 1.4 NA) was used with ANDOR iQ software followed by analysis using 3D object counter plugin in Fiji61. The images were analyzed using MetaMorph\u00ae or MicroManager software and were processed for presentation using Adobe Illustrator. All images displayed are equally scaled for intensity unless otherwise mentioned. The integrated intensities, spread area and thus average uptake per cell were determined by drawing regions around each cell using the region measurement option in Fiji61. For plotting endocytic uptake, all values are normalized to the mean value of the control and plotted as a box plot using Origin software (OriginLab, Northampton, MA). Box plot shows uptake per cell (each data point) and it also shows median (middle line), standard deviation (whiskers), 25th percentile (lower line of box) and 75th percentile (upper line of box) value. The box plot contains points pooled from two separate experiments with technical duplicates in each and normalized to their respective controls. The total number of cells in each condition (pooled from all experiments) is mentioned in the legends. Statistical significance was tested using the Mann\u2013Whitney test and p values used to determine significance are reported in the legends. The scale bar is 10 \u03bcm, unless otherwise mentioned.",
            "CHO (Chinese Hamster Ovary) cells stably expressing FR-GPI and human transferrin receptor TfR (IA2.2 cells)8, HeLa9, MEF (Mouse embryonic fibroblasts) cells10, Caveolin null MEF10, conditional null dynamin triple knockout MEF11, vinculin null MEF12, FR-AGS (Human adenogastric carcinoma cells stably transfected with FR-GPI)13,14, IRSp53 null MEFs14 and IRSp53 null MEFs stably expressing WT-IRSp5314 were used for the assays. HF12 media (HiMEDIA, Mumbai, India) and DMEM (Invitrogen) supplemented with NaHCO3 and L-Glutamine/Penicillin/Streptomycin solution (Sigma Aldrich) were used for growing CHO/FR-AGS cells and the different MEF lines respectively. (supplemental materials p. 22)",
            "Fluid uptake (90 s) in CHO cells at steady state (steady state), immediately on relaxing the stretch (stretch\u2013relax), or after a waiting time of 90 s on relaxing the stretch (stretch\u2013relax\u2013wait) (n = control (316), stretch\u2013relax (257), stretch\u2013relax\u2013wait (277))."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-1Orp-fkjH",
        "claim": "Cells injected with anti-cortactin antibodies decreased the degree of transferrin internalization into clone 9 cells",
        "citekey": "cao2003cortactin",
        "context": [
            "both the cortactin AB3 and C-Tyr antibodies exhibited a profound inhibitory effect on ligand uptake (Fig. 4b and c). In over 80% (AB3-injected) and 70% (C-Tyr-injected) of the cells counted, transferrin internalization appeared completely ablated (Fig. 4e)",
            "For immunofluorescence microscopy and confocal microscopy, cells were grown on coverslips for 1 to 2 days and prepared as described previously (2). Clone 9 cells were double stained with anti-cortactin (AB3) polyclonal antibody or anti-cortactin (C-Tyr) polyclonal antibody with clathrin (X-22) monoclonal antibody. Transiently transfected cortactin-RFP-expressing cells were also costained with clathrin (X-22). The anticortactin and anti-SH3 antibodies were used to identify the Cort SH3-pCR3.1expressing cells. For the transferrin uptake experiments, the cells were permeabilized with 0.01% digitonin (Fluka, Ronkonkoma, N.Y.). Cells were viewed with an Axiovert 35 epifluorescence microscope (Carl Zeiss, Inc., Thornwood, N.Y.) equipped with a 100-W mercury lamp and a 100\u0006 objective lens (Zeiss Plan-Neofluar 1.30) and a confocal microscope (LSM-310 or 510; Carl Zeiss, Inc.) equipped with an argon\u2013krypton laser and a 100\u0006 objective lens.",
            "Clone 9 cells, an epithelial cell line isolated from normal rat liver (ATCC CRL-1439), were maintained in Ham\u2019s F-12K medium supplemented with 10% fetal bovine serum (Invitrogen), 100 U of penicillin/ml, and 100 \u0005g of streptomycin/ml in 5% CO2\u201395% air at 37\u00b0C. Cells were cultured in T-75 flasks (Fisher Scientific, Pittsburgh, Pa.) or on 22- by 22-mm glass coverslips for transfections and immunocytochemistry, respectively.",
            "Images for quantitation were acquired by using a cooled charge-coupled device camera (Photometrics SenSys, Tuscon, Ariz.) driven by Metamorph (Universal Imaging, West Chester, Pa.). All images of microinjected cells were taken at full resolution (1,024 by 1,024 pixels) with the same acquisition settings (exposure time, 5 s; 12-bit grayscale). The percentage of cells demonstrating an inhibition of transferrin or dextran uptake was determined by visual inspection. The mean percentage of cells showing reduced internalization was determined from three separate experiments and at least 150 cells for each condition. Fluorescence intensity quantitation was performed with IPLab (Scanalytics, Inc., Fairfax, Va.). The area occupied by each cell was traced, and the mean fluorescence intensity per unit area was determined for at least 100 cells in each injection condition."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-1B3Jax3yY",
        "claim": "Without clathrin-mediated endocytosis, flat-clathrin lattices and reticular adhesions could not form.",
        "citekey": "hakanpaa2023reticular",
        "context": [
            "Cell culture and reagents U2Os, U2Os-AP2-GFP, U2Os-AP2-halo, U2Os-AP2-GFP-ITGB5mScarlet, HeLa-AP2-GFP, and HeLa-AP2-halo were cultured in MEM supplemented with 10% FBS (Gibco) and penicillinstreptomycin (100 U/ml, Thermo Fisher Scientific). HDF-AP2halo and Caco2-AP2-halo were cultured in DMEM supplemented with 10% FBS (Gibco) and penicillin\u2013streptomycin (100 U/ml, Thermo Fisher Scientific). MCF7-AP2-halo was cultured in DMEM supplemented with 10% FBS (Gibco) and penicillinstreptomycin (100 U/ml, Thermo Fisher Scientific), 2 mM glutamine, 5 \u03bcg/ml human insulin, and 1 \u03bcM sodium pyruvate. hMEC-AP2-GFP was cultured in MEGM complete medium (Lonza).",
            "B) Analysis of RA coverage from samples in A. N (images): control = 12, shAP2A1#1 = 8, shAPA1#2 = 11, shAPS1#1 = 10, shAPS1#2 = 19, shAPS1#3 = 10. Data were obtained from two individual experiments and similar results were observed in five independent experiments. One-way ANOVA with Tukey\u2019s multiple comparison, F(5, 64) = 43.11, P < 0.001.",
            "These experiments were performed using U2Os cells with an endogenously GFP-tagged \u03b1 adaptin 2 Sigma-Aldrich subunit (AP2S1, hereafter referred to simply as AP2). AP2 is a widely used CME marker that faithfully mirrors clathrin dynamics (Almeida-Souza et al., 2018; Ehrlich et al., 2004; Rappoport and Simon, 2008). We used endogenously tagged cell lines throughout this study as the expression level of the AP2 complex was shown to modulate the amount of FCLs (Dambournet et al., 2018).",
            "Manipulation of CME machinery to study RA formation Clathrin assembly at the cell membrane was reduced by silencing two subdomains of AP2 or by overexpressing AP180 ct, which acts as a dominant negative for AP2. U2Os AP2-GFP cells silenced for AP2A1 shRNA #1 and #2 or AP2S1 shRNA #1, #2, and #3, and control shRNA, and plated on non-coated imaging dishes were fixed and stained for integrin \u03b1v\u03b25 and FA marker p-Pax. Alternatively, AP180 ct was overexpressed in U2Os AP2-GFP cells, and cells were plated on non-coated imaging dishes, fixed the next day, and stained for integrin \u03b1v\u03b25 and p-Pax. RA formation (integrin \u03b1v\u03b25 adhesions without FA marker) and FAs (integrin \u03b1v\u03b25 colocalizing with FA marker) were imaged using TIRF microscopy.",
            "While all FCLs colocalize to RAs, FCL-free areas of larger RAs are rather common (e.g., Fig. 2 A; Fig. 3, A\u2013C;andFig. S2 D), which may give the impression that FCLs are formed on preexisting RAs. Nevertheless, the fact that both structures are inhibited independently by FN suggests a deeper relationship and led us to ask if RAs can exist without the CME machinery. To answer this question, we quantified the RA coverage in U2OsAP2-GFP cells silenced for the clathrin adaptor AP2 complex subunits \u03b11 (AP2A1) or Sigma-Aldrich 1 (AP2S1) in cells plated on non-coated dishes, a condition where we observe large RAs. Consistent with an important role played by the CME machinery in RA formation, AP2A1- or AP2S1-silenced cells (easily recognizable as cells with little to no AP2-GFP signal) did not display RAs. Instead, integrin \u03b1v\u03b25 localized to FAs (Fig. 4, A and B)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-6-XC7noR7",
        "claim": "siRNA silenced Swip1 showed reduced internalization of B1-integrin in MDA-MB-231 cells.",
        "citekey": "morenolayseca2021cargospecific",
        "context": [
            "Fig. 5 | Swip1 is a cargo adaptor for the CG pathway. ... b, Representative micrographs (top), and levels of dextran\u2013TMR (bottom right) and \u03b21-integrin\u2013AF488 (bottom left) internalization in control-, Swip1- and IRSp53-silenced MDA-MB-231 at 15 min. Swip1 siRNA1, n = 157 cells; Swip1 siRNA2 and siCTRL, n = 160 cells; siCTRL, n = 121 cells; IRSp53 siRNA1, n = 177 cells; and IRSp53 siRNA2, n = 121 cells. ***P = 0.0001 and **P = 0.0004.",
            "Screening for Rab21 interaction partners by GFP-pulldown. Each mass-spectrometry experiment consisted of a mixture of a GFP-pulldown in active GFP\u2013Rab21-expressing MDA-MB-231 cells (WT or active Rab21 Q76L mutant) cultured in heavy medium and a GFP-pulldown in control cells (expressing GFP or the inactive GFP\u2013Rab21 T33N mutant) cultured in light medium (forward experiment). In the reverse experiment, the heavy and light media were exchanged (label-swap experiment). Briefly, co-immunoprecipitation samples were prepared as follows. Cells (two 15 cm dishes) were cultured until they reached 60\u201380% confluence, washed with ice-cold PBSM (PBS + 5 mM MgCl2), harvested in PBSM, pooled and washed again. The cell pellets were resuspended in 600 \u03bcl lysis buffer LB (50 mM Tris, pH 7.5, 5 mM MgCl2, 150 mM KCl, 1.3% n-beta-octyl-d-glucopyranoside, 10% glycerol, protease and phosphatase inhibitors, and 500 \u03bcM GppNHp for GFP-active Rab21-expressing cells or 500 \u03bcM GDP for GFP-inactive Rab21-expressing cells) and lysed by douncing 40\u00d7 in a tissue grinder (dounce homogenizer) and incubating on ice for 20 min. The insoluble fraction was removed by centrifugation at 18,000g and the supernatant was incubated with 20 \u03bcl GFP-Trap agarose beads (Chromotek) for 60 min at 4 \u00b0C by overhead rotation. The beads were then washed three times with 500\u03bcl washing buffer WB (50 mM Tris, pH 7.5, 5 mM MgCl2, 300 mM KCl and 10% glycerol), combining the heavy, GFP-active Rab21 immunoprecipitation with the light, GFP-inactive Rab21 immunoprecipitation (forward experiment) during the second wash step. Proteins were eluted from the beads in 100 \u03bcl of U/T buffer (6 M urea + 2 M thiourea in 10mM HEPES, pH 8.0) for 15 min with shaking in a bacterial shaker at room temperature and an agitation rate of 1,400 r.p.m. The eluted proteins were collected and the process was repeated to maximize the protein yield. The eluted proteins were precipitated by adding 70 \u03bcl of 2.5 M Na-acetate, pH 5.0, 1 \u03bcl GlycoBlue (Thermo Fisher) and 1,700 \u03bcl ethanol to the pooled elution fractions (200 \u03bcl) in a 2 ml tube. After an overnight incubation at 4 \u00b0C, the precipitation mixture was centrifuged for 50 min at 20,000g and the resulting pellet was dried for 15\u201320 min at 60\u201370 \u00b0C.",
            "Here we identify Swiprosin-1 (Swip1, EFHD2) as an interactor of Rab21 and a cargo-specific adaptor for CG-endocytosis.",
            "To assess whether Swip1 is a cargo adaptor or an integral member of the CG pathway, we investigated whether it regulates the endocytosis of other CG cargos. Swip1 silencing had no effect on the uptake of 10 kDa dextran or major histocompatibility complex I (MHCI; Fig. 5b,c).",
            "For visualization purposes, all of the identified proteins from each experiment were plotted (Fig. 1a and Extended Data Fig. 1a\u2013d), where each spot corresponds to a protein identified by mass spectrometry. Each plot is representative of two independent experiments (forward and reverse, x and y axis), where every experiment consists of two independent immunoprecipitations. The mean log2-transformed fold-change values from both experiments were plotted against the absolute protein intensities (intensity-based absolute quantification, iBAQ) and significance B was calculated according to Cox and Mann52. The error function was estimated using the erfc as is implemented in the pracma package53 (R package version 2.2.9). Abundance bins were defined by including 100 proteins in a subsequent order.",
            "To identify Rab21-interacting proteins, we performed proteomic analyses by stable isotope labelling with amino acids in cell culture (SILAC) of cells expressing wild-type (WT) Rab21, the constitutively active Rab21Q76L mutant (CA-Rab21) or the Rab21T31N inactive mutant16,17."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-Pu_eipQdq",
        "claim": "Matrigel stiffness can be tuned between ~10 Pa to ~300 Pa",
        "citekey": "slater2018tuning",
        "context": [
            "Collagen I Preparation Corning Collagen I High Concentration, rat tail (Collagen HC rat tail, Corning Cat. No. 354249) gelation is pH- and temperature-dependent, and the product must be neutralized in order to polymerize. Collagen HC rat tail was diluted using the alternate gelation procedure included in the lot-specific Certificate of Analysis30,31. All dilutions were prepared on ice in pre-chilled glass tubes. To prepare the desired volume and protein concentration of Collagen I solutions, 0.1X the final volume of 10X Dulbecco\u2019s Phosphate Buffered Saline (10X DPBS, Thermo Fisher), 0.023 mL of 1N Sodium Hydroxide (JT Baker) per mL of Collagen I were added and the final volume was adjusted using ice-cold DI-water. The contents of the tube were mixed by vortexing and the required volume of Collagen I was added to the solution using a positive displacement pipet, mixed by vortexing gently and held on ice. All diluted samples were mixed by inversion immediately before loading the test samples onto the rheometer using a positive displacement pipet (0.680 mL). Each protein concentration was measured in triplicate.",
            "To investigate whether varying the protein concentration alters the elastic modulus of the Matrigel matrix gels, Corning Matrigel High Concentration, Growth Factor Reduced (Matrigel HC GFR; at a concentration of 19.1 mg/mL) was diluted using ice-cold DMEM and liquid samples were directly added to the rotational rheometer.",
            "Over a range of concentrations from 3 to 19.1 mg/mL for Matrigel HC GFR, the elastic component of the shear modulus increased from 9.1 \u00b1 0.3 Pa to 288.2 \u00b1 9 Pa.",
            "Figure 1. Increase of elastic modulus as a function of Corning Matrigel HC GFR concentration. (B) Plateau values of G' (in Pa) shown as a function of Matrigel matrix concentration (n = 3).",
            "The temperature of the bottom plate (Peltier-controlled) was ramped from 5\u00b0C to 37\u00b0C and then held at 37\u00b0C, which is the recommended gelation temperature for Matrigel matrix. The evolution of the elastic component (G') and the viscous component (G\") of the complex shear modulus were observed over time and the sample was allowed to reach a state of equilibrium."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-7ioUQ5iO3",
        "claim": "The percentage clathrin-coated structures with visible actin overlap decreased from ~50% to ~20% from flat to curved pits in four cell types by platinum-replica electron microscopy",
        "citekey": "yang2022actin",
        "context": [
            "The shape of CCSs in most cases was obvious in 2D PREM images. In uncertain cases, the degree of CCS invagination was determined using images tilted at \u00b110\u201320 degrees. Based on the degree of invagination, CCSs were classified into three categories: (i) flat CCSs with no obvious invagination; (ii) dome-shaped CCSs that had a hemispherical or less invaginated shape with visible edges of the clathrin lattice; and (iii) spherical CCSs that had a round shape with the clathrin lattice edges not visible in 2D projection images. Dome-shaped subdomains of flat CCSs were quantified separately from the contiguous flat CCSs. The CCS area in PREM images was measured using ImageJ software.",
            "Branched actin networks in PREM samples were identified by the presence of two or more of the following characteristics: the presence of at least several Y-shaped configurations, short filament lengths, a wide range of filament orientations, and an abundance of actin filament ends. CCSs were considered to be actin-positive if branched actin networks were located no farther than 20 nm from the edge of the clathrin lattice. (p. 16)",
            "Fraction of the actin-positive CCSs with any amount of branched actin extending over their lattice in 2D projection images in the indicated cell types. (p. 4)",
            "Genome-edited human osteosarcoma U2OS cells and human cervical cancer HeLa cells, both endogenously expressing RFP-tagged clathrin light chain A (CLTA) and EGFP-tagged dynamin2 (DNM2), were a kind gift from Dr. David Drubin, University of California-Berkeley, California, USA41,93. Conditional epsin DKO MEFs with deleted epsin2 and epsin3 genes and floxed epsin1 gene were a kind gift of Dr. Pietro De Camilli, Yale University, Connecticut, USA33. U2OS, HeLa, potoroo epithelial kidney PtK2 cells and DKO MEFs were cultured at 37 \u00b0C with 5% CO2 in Dulbecco\u2019smodified Eagle\u2019s medium (DMEM) supplemented with GlutaMAX (#10569010, Thermo Fisher Scientific), 10% fetal bovine serum (FBS) (#F2442, Sigma-Aldrich) and 1% penicillin\u2212streptomycin. Mouse melanoma B16F1 cells were cultured in DMEM/F12 (#11330-032, Thermo Fisher Scientific) supplemented with 10% FBS and 1% penicillin\u2212streptomycin at 37 \u00b0C and 5% CO2 (p. 16)",
            "For unroofing experiments, B16F1 cells were seeded on coverslips coated with laminin (25 \u03bcg/ml, #L2020, Sigma-Aldrich), and Ptk2, U2OS and Hela cells were seeded on coverslips coated with poly-Dlysine (0.2 mg/ml, #P6407, Sigma-Aldrich) or HistoGrip (1:50 dilution, #008050, Thermo Fisher Scientific)94,95.EpsinDKOandTKOMEFs were cultured on uncoated glass coverslips. B16F1 cells were unroofed as described previously18. For unroofing of other cells, coverslips with cells were quickly transferred into ice-cold PEM buffer (100 mM PIPES \u2212 KOH, pH 6.9, 1 mM MgCl2 and 1 mM EGTA) containing 2 \u03bcM unlabeled phalloidin (#P2141, Sigma) and, in some experiments, 10 \u03bcM taxol (#T7402, Sigma-Aldrich) and unroofed by a brief (1 s) ultrasonic burst from a 1/8-inch microprobe positioned at ~45\u00b0 angle ~3 mm above the coverslip and operated by Misonix XL2020 Ultrasonic Processor at 17\u201320% of output power. After sonication, the coverslips were immediately fixed with 2% glutaraldehyde in 0.1 M Na-cacodylate buffer, pH 7.3 for at least 20 min at room temperature. Sample processing for PREM was performed as described previously96,97. In brief, glutaraldehyde-fixed cells were post-fixed by sequential treatment with 0.1% tannic acid and 0.2% uranyl acetate in water, critical-point dried, coated with platinum and carbon, and transferred onto EM grids for observation. PREM samples were examined using JEM 1011 transmission electron microscope (JEOL USA, Peabody, MA) operated at 100 kV. Images were acquired by an ORIUS 832.10 W CCD camera driven by Gatan Digital Micrograph 1.8.4 software (Gatan, Warrendale, PA) and presented in inverted contrast (p. 16)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-F0N83vxEe",
        "claim": "Knockdown of Dyn2 decreased the length of filopodia in H1299 cells",
        "citekey": "yamada2016actin",
        "context": [
            "Filopodial formation. H1299 cells were serum-starved for 16 h. Thereafter, the cells were transfected with dynamin 2 siRNAs, cortactin siRNAs, or the control siRNA, followed by incubation with DMEM supplemented with 10% FBS for 45 min. For the rescue experiments, cortactin was silenced in H1299 cells with oligo 3, and the cells were cultured for 24 h. The cells (1x105/coverslip) were then transfected with rat wild-type cortactin or cortactin W525K (0.25 \u03bcg each) cloned into the pIRES2-AcGFP1 expression vector (Clontech Laboratories, Santa Clara, CA, USA). Thereafter, the cells were stimulated with serum for 45 min, fixed, and stained with Alexa Fluor 488 or rhodamine-labeled phalloidin for visualization of filopodia.",
            "The human non-small cell lung carcinoma cell line H1299 (Cat. no. ATCC CRL-5803; American Type Culture Collection, Manassas, VA, USA) was cultured in Dulbecco's modified Eagle's medium (DMEM, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) at 37 \u030aC in an atmosphere of 5% CO2.",
            "Compared with the length of filopodia in serum-stimulated control cells (10.2\u00b10.5 \u03bcm), dynamin 2 knockdown decreased filopodial extension in silenced cells (4.7\u00b10.6 \u03bcm) (Fig. 3B and C)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-j0UGLJ3e6",
        "claim": "Cells treated with the WASP-inhibitor wiskostatin showed a time-dependent increase of GFP\u2013GRAF1-decorated tubes at the cell surface",
        "citekey": "francis2015endocytic",
        "context": [
            "Estimations of the fraction of fixed cells with GFPGRAF1 proteins in abundant or tubular structures were performed by epifluorescent visual assessment.  (p. 11)",
            "HeLa cells (ATCC-CRM-CCL-2) were cultured in Dulbecco\u2019s modified Eagle\u2019s medium (DMEM; low glucose, L-glutamine, sodium pyruvate, HEPES and Phenol Red), supplemented with 10% fetal bovine serum (FBS; Gibco). Flp-In T-REx HeLa cell lines with tetracycline-inducible expression of GRAF1, GRAF1\u2013GFP, GFP\u2013GRAF1 and GFP\u2013GRAF1-R412D were generated as previously described (Mohan et al., 2015). Established cultures were grown in the mentioned DMEM, exceptions being during 800CW-SS-cargo internalisation assays and live-cell acquisitions when basic medium containing 4.5 g/l glucose was used (Gibco). The culturing media were further supplemented with 100 \u03bcg/ml hygromycin B and 5 \u03bcg/ml blasticidin S HCl (Gibco) for plasmid selection, and recombinant protein expression was induced by incubation in doxycycline hyclate (Sigma-Aldrich) for 20\u00b14 h.  (p. 11)",
            "The Imaris Software V7.5 (Bitplane) was utilised to analyse micrographs captured from fixed and live-cell samples as specified in Table S3. (p. 11)",
            "The effects of actin polymerisation drugs on GRAF1 structures were analysed by fluorescence microscopy of fixed cells after treatment with 2 \u03bcM cytochalasin D, 2 \u03bcM latrunculin A (Sigma-Aldrich), 5 \u03bcM wiskostatin (Calbiochem) or DMSO.\" (p. 11)",
            "Cells were fixed and prepared for immunofluorescence analysis as previously described (Lundmark et al., 2008). Images of fixed cell samples were captured using an epifluorescence Axioimager Z1 system (AxioCam MRm camera) (Zeiss) with the ZEN Software and a 63\u00d7 lens (Plan-Apochromat 1.40 Oil DIC 0.17) or an A1 R Laser Scanning Confocal Microscope system (ANDOR iXon EMCCD camera) (Nikon Instruments) under control of the NIS-Elements Microscope Imaging Software and a 60\u00d7 lens (Apochromat 1.40 Oil \u03bbS 0.17 WD 0.14, Nikon), at the appropriate excitation and emission wavelengths. Live-cell confocal movies were recorded using the 63\u00d7 lens in the Nikon system or the 63\u00d7 lens (Plan-Apochromat 1.40 Oil DIC M27) in a Cell Observer Spinning Disc Confocal Microscope system (ANDOR iXon Ultra) (Zeiss) controlled by the ZEN Software. Real-time TIRF acquisitions were captured by employing the 100\u00d7 lens in respective system [Apochromat 1.49 Oil 0.13-0.20 DIC N2 (Nikon) or Plan-Apochromat 1.46 Oil DIC M27 (Zeiss)]. Micrographs and the acquired movies were prepared (cropped, rotated, linearly adjusted for intensity and converted) using Adobe Photoshop or ImageJ. (p. 11)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-Ke0qFhkQL",
        "claim": "Cortactin Knockdown by siRNA decreased the degree of transferrin endocytosis in MDA-MB-231 cells",
        "citekey": "chen2006roles",
        "context": [
            "While GFP knock-down as a mock treatment had no effect on transferrin uptake, knock-down of cortactin substantially attenuated the ligand uptake [Fig. 1(B,C)]",
            "MDA-MB-231, 3T3-L1 cells and NIH/3T3 cells were obtained from ATCC (Maryland, USA). Cells were cotransfected with Dyn-GFP (or Dyn-PRD-GFP) and RFP-Cort (or RFP-Cort-SH3, RFP-Cort\u2206SH3) using the Lipofectamine reagent according to the manufacturer\u2019s instructions. Cells for further experiment",
            "Cells were incubated with 10 \u03bcg/ml Oregon green labeled transferrin. The percentages of cells showing normal levels of internalized transferrin were determined by visual inspection in three independent experiments. Cells treated with BioPORTER (Sigma-Aldrich, St. Louis, USA) to introduce immunoreagents were subjected to ELISA-based endocytosis assay. The BioPORTER introduction of immunoreagents was performed according to the manufacturer\u2019s protocol. Capture-ELISA assay to measure endocytic transferrin was performed exactly as described [20,27]. Biotinylated human transferrin (10 \u03bcg/ml) was used in this assay. Each assay point was performed in duplicate.",
            "For immunofluorescence microscopy, cells were either permeabilized with P-buffer (0.02% Triton X-100, 0.1 M Mes, pH 7.4, 1 mM MgCl2, 1 mM EGTA and 4% PEG8000) for 10 s or directly fixed with 4% paraformaldehyde for 20 min at room temperature followed by permeabilization with 0.2% Triton X-100, then blocked with 2.5% bovine serum albumin-phosphate-buffered saline (BSA-PBS). After immunostaining, cells were viewed using an inverted Nikon ECLIPSE TE2000-U with a digital camera controlled by Nikon ACT-1 V.2.51 software (Nikon, Tokyo, Japan)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-OT8BRD36j",
        "claim": "Clathrin Light chains gives the clathrin lattice more stronger bending power.",
        "citekey": "dannhauser2015effect",
        "context": [
            "H6-tagged epsin 1 lacking the ENTH-domain (H6-epsin144\u2013575)and His-tagged AP180 lacking the ANTH-domain (H6-AP180328\u2013896)from rat brain were expressed and purified as previously described (44).",
            "Liposomes from Brain polar lipid extract (BPLE; Avanti) containing 5% (w/w) Ni2+-NTA-DOGS lipid (Avanti) were prepared and coated with H6-epsin144\u2013575 and clathrin as described before (18).",
            "In a two-stage binding assay, first H6-epsin144\u2013575 at 1.8 \u03bcM was attached to the liposomes at 4\u2218C in buffer G. Unbound protein was removed by centrifugation at 6.000 g and 4\u2218C, and in the second stage the resuspended liposomes were incubated with either clathrin (0.15 \u03bcM) or CHC triskelia (0.15 \u03bcM)for30minat15or25\u2218C, respectively, in a thermocycler. For ultrathin sectioning, liposomes were pelleted at 6000 g and 4\u2218C, fixed with 3% glutaraldehyde and further processed for embedding in Epon and staining as described previously (50). For the quantification of clathrin- or CHC-coated profiles images from ultrathin sections of plastic, embedded liposomes were analyzed using NIH ImageJ. Membrane buds were identified as coated outlines of liposomes with an inner diameter \u2264150 nm. The analysis of membrane budding at 15\u2218Cwas based on three independent experiments. Four ultrathin sections from pelleted membranes were examined in detail, and the percentile of coated membrane buds was determined from a total of 608.216-nm coated profiles. A membrane pellet from the 25\u2218Cincubationwasanalyzed in the same way. From three sections, 513.096-nm coated membrane profiles were quantitatively evaluated.",
            "at 15\u2218C a marked inhibition of budding by the light-chain-free clathrin supervened (Figure 3).",
            "After fixation of the protein on the electron microscope grids, the grids wererinsed,firstwithbufferG,thenwith100mM MES, 1 mM EGTA, 0.5 mM MgCl2, pH 6.4, blotted and then incubated for 1 min with 5% uranylacetateinH2O. Excess staining solution was carefully removed with moist filter paper. Clathrin assemblies on glass were visualized after critical point drying and PT/C-shadowing as described elsewhere (52). The specimens were examined with a Tecnai\u2122 G2 (FEI) electron microscope at an acceleration voltage of 200 kV or with a Morgagni (FEI) electron microscope at 80 kV. Digital images were generated with the TIA-Software (FEI), processed with the program NIH ImageJ and Adobe Photoshop CS.X."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-_N-gQJ0eV",
        "claim": "Expressing WT GFP-WASP in __wasA-__ mutants rescues confinement of active Rac to the leading edge of __Dictyostelium__ cells.",
        "citekey": "amato2019wasp",
        "context": [
            "At a given time, a subset of puncta in WASP CRIB mutants is also enriched in active Rac. WASP-CRIB-mutants and active Rac appear to have distinct dynamics: active Rac appears to remain at the plasma membrane for longer than CRIB-mutated WASPs. Therefore, although some active Rac-positive structures are not enriched in CRIB-mutated WASPs, we cannot exclude that they were enriched in CRIB-mutated WASP at some stage. Representative plots showing active Rac marker localization from front to rear are shown in Figure 5E. Quantification (Figure 5F) reveals that cells expressing CRIB-mutated WASPs accumulate active Rac at the rear to the same degree as wasA\u0001 cells, while wild-type WASP rescues the spatial confinement of active Rac at the leading edge. In line with previous reports from wasA\u0001 cells [6], cells expressing either WASP CRIB mutant are significantly slower than those expressing wild-type WASP",
            "Dictyostelium cells lacking Wiskott-Aldrich syndrome protein (WASP)",
            "(F) Frequency of active Rac accumulation at the back of wasA\u0001 cells and wasA\u0001 cells expressing wild-type WASP or WASP CRIB mutants. wasA\u0001 (n = 11 cells): 88.2% \u00b1 3.5%; wasA\u0001/GFP-WASP (n = 28 cells): 12.7% \u00b1 1.0%; wasA\u0001/GFP-WASPDCRIB (n = 24 cells): 78.1% \u00b1 2.0%; wasA\u0001/GFPWASP*CRIB (n = 28 cells): 76.7% \u00b1 2.2%; means \u00b1 SEM. One-way ANOVA; wasA\u0001/GFP-WASP versus wasA\u0001/GFP-WASPDCRIB: p < 0.0001; wasA\u0001/GFPWASP versus wasA\u0001/GFP-WASP*CRIB: p < 0.0001.",
            "Dictyostelium wild-type, wasA knockout, and inducible double null cells were grown at 22\u000eC on Petri dishes in HL5 supplemented with vitamins and micro-elements (Formedium)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-eryKP0bHY",
        "claim": "Pulldown assay with Swiss3T3 lysates showed that GST-bound IRSp53 strongly associated with WAVE, but did not precipitate N-WASP.",
        "citekey": "miki2000irsp53",
        "context": [
            "As proline-rich regions are known to be involved in protein\u00b1protein interactions, we carried out a two hybrid screening using the proline-rich region of WAVE1 as `bait', which yielded several positive clones. DNA sequencing analysis revealed that they encode three identified proteins (IRSp53, nArgBP2 and profilin) and two unidentified ones. As IRSp53 gave the strongest positive signal on b-galactosidase assay (data not shown), we analysed it further.",
            "Pull down assay GST\u00b1fusion proteins (10\u00b150 mg) were first immobilized on 20 ml of glutathionesepharose beads and then mixed with 400 ml protein samples such as cell lysates and purified proteins. After 2 h, the beads were washed with lysis buffer five times and 20 mlof SDS sample buffer was added. Samples (5 ml) were separated by SDS\u00b1PAGE, followed by immunoblotting and Coomassie staining. Cell lysates of Swiss3T3, COS7 and NIH3T3 cells were obtained by lysing half-confluent cells in a dish (diameter, 150 mm) with 1 ml lysis buffer. In the case of Sf9 cells infected with baculoviruses, cells were collected by centrifugation and then lysed in 1/20 volume of lysis buffer.",
            "Figure 1 The specific and direct interaction of IRSp53 and WAVE2. ... b, Various GST\u00b1fusion SH3 domain-containing proteins immobilized on beads were mixed with Swiss3T3 cell lysates treated with or without PDGF (WAVE mobility-shift occurs by PDGF-treatment23). The bound proteins were analysed by immunoblotting.",
            "We then examined whether the Src-homology (SH)-3 domain, located at the C terminus of IRSp53, associates with WAVE by a pull-down assay. The SH3 domain in IRSp53 strongly associated with WAVE, but N-WASP was not precipitated (Fig. 1b). This is comparable to Grb2/Ash and Fyn, which associate strongly with N-WASP, but less significantly with WAVE (Fig. 1b)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-YsCMystnc",
        "claim": "CLIC markers CTxB, CD44, and Thy1 concentrated at the leading edge of mouse embryonic fibroblasts during wound healing",
        "citekey": "howes2010clathrinindependent",
        "context": [
            "(A) Confluent monolayers of WT MEFs or NIH3T3s were scratched and cells were allowed to migrate for 8\u201312 h. CTxB-555 and Tf-647 were pulsed into migrating cells for 2 min in the presence of anti-CD44 (WT MEF), anti-GFP (GFP-GPI expressing WT MEF), or anti-Thy-1 (NIH3T3) antibodies or cells were labeled for Cav-1 (WT MEF). Dotted lines indicate leading edges. Arrows show colocalization between anti-CD44 or anti\u2013Thy-1 and CTxB-555 but not Tf-647 at the leading edge. Bar, 20 \u03bcm. (p. 12)",
            "For immunocytochemistry, cells were permeabilized in freshly made 0.1% saponin for 10 min and blocked in 0.2% fish skin gelatin/0.2% BSA in PBS. Coverslips were incubated with primary antibodies for 1 h at room temperature, followed by three times 10-min wash in PBS before incubation with secondary Alexa Fluor\u2013conjugated antibodies at 1:400 for 1 h (p. 14)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-XG3wvRdRY",
        "claim": "Overexpression of a cortactin mutant lacking 3 tyrosine residues reduced CME transferrin uptake by nearly 40%",
        "citekey": "zhu2007receptormediated",
        "context": [
            "overexpression of a cortactin mutant, Cort-F, which lacks three tyrosine residues targeted by Src, reduced clathrin-mediated Tfn uptake by \u000540%.",
            "As shown in Fig. 1C, the cells expressing cortactinGFP internalized Tfn at an efficiency similar to the cells infected with the viral GFP vector, indicating no significant effect of overexpression of wild-type cortactin on endocytosis. However, Tfn uptake in the cells expressing Cort-F-GFP was nearly 40% less than in cells expressing the vector alone (p \u0004 0.05) (Fig. 1C).",
            "To study the role of cortactin tyrosine phosphorylation in receptor-mediated endocytosis, HeLa cells were infected with a retroviral vector, MGIN (39), encoding a murine cortactin construct tagged by GFP at the C terminus (cortactinGFP), a mutant of Y421F/Y466F/Y482F (Cort-F-GFP), and a mutation with deletion of the SH3 domain (Cort\u0003SH3-GFP)",
            "FIGURE 1. Analysis of the activity of wild-type and mutant cortactin proteins for internalization of Tfn and formation of clathrin-coated vesicles. ... C, cells expressing cortactin variants were grown in serum-free medium at 37 \u00b0C for 60 min and incubated with biotin-Tfn for 30 min on ice. Endocytosis was initiated at 37 \u00b0C for 5 min and terminated on ice. The treated cells were subjected to enzyme-linked immunosorbent assay-based biotin-Tfn uptake as described under \u201cExperimental Procedures.\u201d The p value calculated by Student\u2019s t test refers to the difference between PP2- and non-PP2-treated cells.",
            "As shown in Fig. 1C, the cells expressing cortactinGFP internalized Tfn at an efficiency similar to the cells infected with the viral GFP vector, indicating no significant effect of overexpression of wild-type cortactin on endocytosis. However, Tfn uptake in the cells expressing Cort-F-GFP was nearly 40% less than in cells expressing the vector alone (p \u0004 0.05) (Fig. 1C). Similarly, cells overexpressing Cort\u0003SH3GFP showed an impaired Tfn uptake at an efficiency 43% less than the control cells.",
            "Capture Enzyme-linked Immunosorbent Assay\u2014Cells expressing cortactin-GFP or Cort-F-GFP were incubated in serum-free Dulbecco\u2019s modified Eagle\u2019s medium containing 1% bovine serum albumin and 20 mM HEPES at 37 \u00b0C for 30 min and incubated with 10 \u0004g/ml bio-Tfn for 30 min on ice. Endocytosis was initiated by incubating the mixture at 37 \u00b0C for 5 min and terminated by placing on ice. To measure internalization of bio-Tfn, total cell lysates were added to a 96-well ELISA (enzyme-linked immunosorbent assay) plate coated with an anti-Tfn antibody. After 12 h of incubation at 4 \u00b0C, each well was added with streptavidin-horseradish peroxidase and Roche BM blue substrate, respectively. Absorption at 450 nm was determined by a microplate reader (Anthos Labtec) and was plotted as a function of time."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-C8_EKRIsh",
        "claim": "GFP-tagged ARPC3/Arc18 at C terminus did not affect __in vitro__ actin nucleation rates",
        "citekey": "egile2005mechanism",
        "context": [
            "Actin was purified from rabbit muscle and isolated as Ca2\u00fe-ATP-G-actin in G buffer (5 mM Tris-Cl [pH 7.8], 0.1 mM CaCl2, 0.2 mM ATP, and 1 mM DTT) according to Pardee and Spudich [15] and pyrenyl labeled. The yeast Arc40/ARPC1-YFP Arp2/3 complex was isolated from a strain expressing an Arp3-CaMBM-tev-ProtA subunit (RLY1945) as previously described [16]. The unlabeled control complex (Arp3MH, which has a [Myc]5His6 tag on Arp3 [16]) as well as the Arp3-, Arp2-, and Arc18/ARPC3-GFP-His10-labeled complexes were isolated as follows. Yeast cells were grown to mid log phase in YPD medium (OD600 2\u00014) washed in U buffer (50 mM HEPES [pH 7.5], 100 mM KCl, 3 mM MgCl2, and 1 mM EGTA) and stored at \u000180 8C until use. A 50- to 100-g cell pellet was resuspended in five volumes of cold U buffer supplemented with 0.5% Triton X-100, 0.2 mM ATP, 1 mM DTT, and protease inhibitor mix (0.5 lg/ml antipain, leupeptin, pepstatin A, chymostatin, and aprotinin, and 1 mM PMSF) and passed through a microfludizer (Microfluidics, Newton, Massachusetts, United States) until 70% lysis was obtained. The cell extracts were cleared by centrifugation at 100,000 3 g for 1 h and filtered through a 0.45-lm filter. A 60% ammonium sulfate precipitation of cell extracts was performed, and the pellet was dialyzed into NaP buffer (100 mM phosphate [pH 7.8], 100 mM KCl, and 20 mM imidazole). This fraction was cleared by centrifugation and incubated with Ni-NTA agarose beads (Qiagen, Valencia, California, United States). Beads were washed with NaP buffer, NaP buffer plus 0.5 M KCl, and NaP buffer plus 0.5% Triton X-100, and the complex was eluted with 250 mM imidazole. The complex was further purified through a HiTrapS column (Amersham Biosciences, Little Chalfont, United Kingdom) in 50 mM MES (pH 6.5), 25 mM NaCl; a UnoQ1 column (Bio-Rad, Hercules, California, United States) in U buffer; and a Superose 12 gel filtration column (Amersham Biosciences) in U buffer on a BioLogic chromatography system (Bio-Rad). (p 5)",
            "(C) Pyrenyl-actin polymerization kinetics obtained with actin alone (black), control complex (light blue), Arp3-GFP complex (red), Arp2-GFP complex (purple), Arc40/ARPC1-YFP complex (green), and Arc18/ARPC3-GFP complex (dark blue). (p. 3)",
            "(B) Purified yeast Arp2/3 complexes visualized by SDS-PAGE and Coomassie blue staining; unlabeled (control), and GFP- or YFP-labeled Arp3, Arp2, Arc40, or Arc18 complexes. The labeled subunits are marked by arrowheads. The Arc40 subunit in the labeled Arc40/ARPC1-YFP complex ran as 30-kDa and high-molecular-weight species (previously confirmed by immunoblotting and peptide sequencing), owing to an unusual electrophoretic mobility [16]. The Arp3 subunit of the unlabeled complex is denoted by an asterisk, and the Arp3 subunit of labeled Arc40/ARPC1-YFP complex is denoted by two asterisks. (p. 3)",
            "Pyrene-actin polymerization assays were performed at Harvard Medical School and repeated at the Burnham Institute. Typically, G-actin was clarified at 436,000 3 g for 30 min. Reactions were performed by mixing 2 lMMg2\u00fe-ATP-Gactin (10% pyrene labeled) with Arp2/3 complex and the appropriate NPF, and actin polymerization was initiated in 13 KMEI buffer (50 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.2 mM DTT, 0.1 mM ATP, 0.02% azide, and 2 mM imidazole [pH 7.0]). Polymerization was followed using a fluorescence spectrophotometer (Cary Eclipse Varian at Harvard Medical School and an MOS-250 spectrofluorometer [BioLogic, Claix, France] equipped with BioKine 32 software at the Burnham Institute), using 365 nm as the excitation wavelength and 407 nm as the emission wavelength. All of the GFP-labeled complexes were used at 50 to 200 nM concentration with 100 to 200 nM GST-NWASp WA. When the reaction reached the plateau, 2 lM phalloidin was added to stabilize the branches, and the reaction was diluted as required in F buffer (5 mM Tris-Cl [pH 7.8], 50 mM KCl, 1 mM MgCl2, 0.1 mM CaCl2, 0.2 mM ATP, and 1 mM DTT). The slight reduction in the polymerization rate with Arc18/ARPC3-GFP complex was due to frozen storage of the complex. This reduction was not observed with fresh complex (data not shown), which was used to obtain the actin branches studied using EM. (p. 6)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-RniLbP0dj",
        "claim": "Angle between membrane and clathrin pit increased from 0 to 90 (early phase/U-shaped) and 90 to 180(neck construction & scission) -",
        "citekey": "avinoam2015endocytic",
        "context": [
            "We further determined the maximal angle (q) between the adjacent plasma membrane (PM) and the invaginating segment of the membrane (Fig. 2B). Independently of invagination size and which model is correct, q will increase during invagination from 0\u00b0 to 90\u00b0 in a U-shaped invagination before tending to 180\u00b0 at neck constriction and scission (13) (Figs. 1A and 2B and movie S6).",
            "To study clathrin-coated pit (CCP) maturation, we used well-characterized genome-edited human cell lines expressing fluorescently tagged clathrin light chain A at endogenous concentrations (8, 9) (hCLTAEN) (Fig. 1, B and C). To distinguish late stages of CME, we used cells that coexpressed endogenously tagged dynamin-2 (9) (hCLTAEN/hDNM2EN) (Fig. 1B). To label CCPs that recruit cargo, we incubated cells with fluorescently labeled transferrin (TF), a constitutive cargo of CME (hCLTAEN/TF) (Fig. 1C). CME events imaged by total internal reflection fluorescence (TIRF) microscopy showed a buildup of clathrin fluorescence that reached a plateau before a burst of dynamin preceded the site\u2019s disappearance, as previously described (8, 10)(Fig.1,Band C, and movies S1 and S2).",
            "Analysis of Clathrin Coated Pits (CCPs) and Vesicles (CCVs) The membrane and coat profiles of invaginations and vesicles were extracted by clicking points along the cytoplasmic leaflet of the membrane and the outer surface of the",
            "Two alternative models describe the transition from planar membrane to clathrin-coated vesicle (CCV). The first\u2014derived from electron microscopy images showing both relatively flat and invaginated clathrin lattices in cells\u2014suggests that clathrin assembles as a planar lattice that subsequently bends as the membrane invaginates (6) (Fig. 1A). For this to happen, complex rearrangements within the clathrin network must occur during budding. The second model avoids this difficulty by proposing that large, flat clathrin lattices are not precursors of CME and that, at sites of CME, clathrin directly assembles to produce the curved coat as the membrane invaginates (7)(Fig.1A)."
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "akamatsulab-ctop9ejQ4",
        "claim": "Endocytic proteins Clathrin light chain A-RFP and dynamin2-GFP increased in lifetimes as a function of concentration of Arp2/3 complex inhibitor CK666 in SK-MEL-2 cells",
        "citekey": "akamatsu2020principles",
        "context": [
            "Histograms of endocytic lifetime in SK-MEL-2 cells endogenously expressing clathrin light chain CLTAtagRFP-T and dynamin2-eGFP and treated with CK-666. n = 368 tracks from 10 cells. (p. 14)",
            "Cells were imaged on either an Olympus 1X-81 or Nikon Ti-2 inverted microscope fitted with TIRFoptics. The IX-81 microscope used a 60 x 1.49 NA objective (Olympus) and an Orca Flash 4.0sCMOS camera (Hamamatsu). Cells were illuminated with solid-state lasers (Melles Griot) with simul-taneous acquisition by a DV-2 image splitter (MAG Biosystems). The microscope was maintained at37 \u00b0C with a WeatherStation chamber and temperature controller (Precision Control) and imageswere acquired using Metamorph software. The Nikon Ti2 microscope was equipped with a motor-ized stage (Nikon), automated Z focus control, LU-N4 integrated four-wavelength solid state lasersetup, TIRF illuminator (Nikon), quad wavelength filter cube, NI-DAQ triggering acquisition (NationalInstruments), an Orca Flash 4.0 sCMOS camera (Hamamatsu), and triggerable filter wheel (FingerLakes Intstrumentation) with 525/50 and 600/50 wavelength emission filters. Cells were seeded onautoclaved 25 mm #1.5 round coverslips coated with 1 mL matrigel (80 ug/ mL) or recombinantVitronectin-N diluted in PBS (Thermo Fisher). Cells were maintained at 37 \u00b0C with a stage top incuba-tor (OKO Lab) and images were acquired with Nikon Elements. (p. 31)",
            "SK-MEL-2 cells endogenously expressing clathrin light chain CLTA-RFP and dynamin2-eGFP (Doyon et al., 2011) were cultured in DMEM/F12 (Thermo Fisher) supplemented with 10% FBS(HyClone) and Penicillin/Streptomycin (Thermo Fisher). A day before imaging, the cells were seeded on 25 mm diameter glass coverslips (Fisher Scientific). (p. 30)",
            "Time-lapse fluorescence quantification: We made modifications to automated MATLAB-based tracking software (Aguet et al., 2013; Hong et al., 2015) to track and analyze fluorescence-intensity time lapse data of genome-edited cells. The core tracking program (based on the software package m-track) automatically identifies fluorescent spots and connects them as tracks by minimizing the linear assignment problem (Jaqaman et al., 2008). We used stringent tracking parameters with gap size 0 and search radius 0\u20132.3 pixels (248 nm). GFP and RFP tracks with high variability in the intensity/time profile were automatically rejected (Ferguson et al., 2017) as well as tracks \u0014 3 s in duration (Dambournet et al., 2018) and the remaining tracks were associated spatiotemporally according to a cost matrix (Hong et al., 2015). We used two track rejection schemes. In the first, users were presented with fluorescence montages and XY coordinates of the tracks to assess the fidelity of tracking for each event (Hong et al., 2015). In the second, tracks were automatically rejected based signal-to-noise ratio (>1.05) and proximity to neighboring tracks (>525 nm) (Hong et al., 2015). We checked that the manual and automatic track rejection schemes yielded similar results (lifetime distributions and intensity versus time plots) as well as to manual, kymographbased quantification of lifetimes (below). From the above workflow (Dambournet et al., 2018) we increased throughput by connecting all steps into an automated tracking pipeline requiring minimal user input. For SK-MEL-2 cells expressing CLTA-RFP and DNM2-GFP, we tracked regions that were not near the nucleus (which has a concentration of Golgi-derived clathrin budding) and that did not have large, bright, persistent structures containing invariant RFP and GFP signals (\u2018plaques,\u2019 which are likely sites of adhesion). (p. 33)"
        ],
        "dataset": "akamatsulab"
    },
    {
        "id": "megacoglab-3jTc6a_9h",
        "claim": "natural experiment with inventors affected by the 1985 Michigan Antitrust Reform Act showed that patents filed by inventors who was new to the patent's field tended to receive fewer forward citations, but less so when they collaborated with an expert in the new field",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "we select all U.S. inventors who patented in Michigan or in another nonenforcing state before the passing of MARA in 1985, including Alaska, California, Connecticut, Minnesota, Montana, Nevada, North Dakota, Oklahoma, Washington, and West Virginia (Malsberger 1996; Marx et al. 2009, Marx et al. 2015). Inventors who did not patent in a nonenforcing state or only did so after the passing of MARA are excluded to ensure that MARA did not affect sample selection. We track all subsequent patents linked to this set of inventors and assigned to a \ufb01rm and identify each move between \ufb01rms (again, the design relies upon inventors patenting at least twice). Only intrastate moves are taken into account because inventors can emigrate from Michigan to a nonenforcing state to avoid a lawsuit (Marx et al. 2015). Finally, we restrict the analysis to the 1975\u20131995 period, that is, 10 years before and after the passing of MARA. Notice that we collect all patents, both before and after MARA and in and out of Michigan. This results in the full sample of patents by inventors at risk for moving between \ufb01rms both in Michigan and elsewhere before and after MARA. The resulting data set spans 21 years and consists of 29,956 inventors and 162,586 patents of which 13,723 patents represent a move, that is, the \ufb01rst subsequent patent of an inventor after moving to a new \ufb01rm. The \ufb01nal analysis is restricted to these mobile inventors because the pressure to explore new \ufb01elds because of MARA only affects inventors who move between \ufb01rms.",
            "In 1985, MARA was passed with the intention of harmonizing state law with the uniform state antitrust act (Bullard 1985). However, while passing MARA, legislators unintentionally revoked statute 445.761, which prohibited the enforcement of noncompete agreements in Michigan (Alterman 1985). After the passing of MARA, employers in Michigan suddenly obtained the legal means to prevent their ex-employees from working in the same \ufb01eld at a different \ufb01rm (Marx et al. 2009). As such, the Michigan experiment provided an exogenous pressure on inventors to explore new \ufb01elds after they left their former employer.",
            "To estimate the effect of exploring new \ufb01elds on the novelty and value of invention, we use a two-stage least square model (2SLS). Because the endogenous variable is binary, we use the approach suggested by Angrist (2001) and Angrist and Pischke (2008). For a recent application of the approach, see Galasso and Schankerman (2015). First, we estimate the likelihood of exploring new fields with a logit model in a difference-in-differences configuration. We include the interaction between Michigan and postmara as an exogenous variable capturing the effect of the policy reversal. Using logit instead of OLS in the \ufb01rst stage results in a better \ufb01t. Second, we calculate the \ufb01tted probabilities of exploring new fields and use these nonlinear fitted values bound between zero and one as an instrument for exploring new fjelds in the 2SLS models. Using nonlinear fitted values as an instrument is the same as plugging in \ufb01tted values when the first stage is estimated by OLS, but the advantage is a better predictor of exploring new fields in the first stage (Angrist and Pischke 2008). The 2SLS model uses a single instrument, resulting in just-identified estimates. Standard errors are clustered at the inventor level to control for repeated observations. (p. 12)",
            "For each inventor-patent observation, we retrieve the three-digit technology classes of all prior patents of the focal inventor and identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked o all prior patents of the same inventor. We rely on all classes assigned to a patent rather than just the primary class. Exploring new fields is a binary indicator that equals one in the absence of any overlapping class between all prior patents and the focal patent. (p. 6)",
            "For each inventor-patent observation, we identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked to all prior patents of the coinventors on the patent (excluding the focal inventor). Expert team is a binary indicator that equals one if at least one of the coinventors has a prior patent in the same class(es) as the focal patent. The measure is used a moderator to test whether collaboration with experts reduces the negative effect of exploring new fields on value. (p. 6)",
            "To assess patent value, we calculate forward citations (ln) as the logarithmic trans-formation of one plus the number of times a patent is referenced as prior art within 10 years. (p. 6)",
            "Our identi\ufb01cation relies on the fact that only mobile inventors residing in Michigan after the passing of MARA are affected; Michigan inventors before MARA and inventors from other states before and after MARA are not affected by the policy change. Therefore, we can combine differences in exploring new \ufb01elds between inventors from different states (Michigan versus nonMichigan) with differences between cohorts induced by the timing of MARA (pre- versus post-MARA). The interaction between binary indicators for Michigan residence and post-MARA is expected to have a positive signi\ufb01cant effect on the likelihood of exploring new \ufb01elds. Thus, this difference-in-differences (DD) can be used as an instrument for exploring new \ufb01elds (Du\ufb02o 2001). The DD speci\ufb01cation controls for overall time trends in exploring new \ufb01elds (across all states) and for time-invariant unobserved differences between Michigan and non-Michigan inventors (Angrist and Pischke 2008). Furthermore, regression DD allows us to include additional inventor and \ufb01eld characteristics affecting the likelihood of exploring new \ufb01elds as controls. The main assumption is that, in the absence of MARA, the trend in exploring new \ufb01elds would not have been systematically different between Michigan and nonMichigan mobile inventors. (p. 12)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-e5Os8ZONI",
        "claim": "natural experiment with inventors affected by the 1985 Michigan Antitrust Reform Act showed that patents filed by inventors who were new to the patent's field tended to be more novel",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "we select all U.S. inventors who patented in Michigan or in another nonenforcing state before the passing of MARA in 1985, including Alaska, California, Connecticut, Minnesota, Montana, Nevada, North Dakota, Oklahoma, Washington, and West Virginia (Malsberger 1996; Marx et al. 2009, Marx et al. 2015). Inventors who did not patent in a nonenforcing state or only did so after the passing of MARA are excluded to ensure that MARA did not affect sample selection. We track all subsequent patents linked to this set of inventors and assigned to a \ufb01rm and identify each move between \ufb01rms (again, the design relies upon inventors patenting at least twice). Only intrastate moves are taken into account because inventors can emigrate from Michigan to a nonenforcing state to avoid a lawsuit (Marx et al. 2015). Finally, we restrict the analysis to the 1975\u20131995 period, that is, 10 years before and after the passing of MARA. Notice that we collect all patents, both before and after MARA and in and out of Michigan. This results in the full sample of patents by inventors at risk for moving between \ufb01rms both in Michigan and elsewhere before and after MARA. The resulting data set spans 21 years and consists of 29,956 inventors and 162,586 patents of which 13,723 patents represent a move, that is, the \ufb01rst subsequent patent of an inventor after moving to a new \ufb01rm. The \ufb01nal analysis is restricted to these mobile inventors because the pressure to explore new \ufb01elds because of MARA only affects inventors who move between \ufb01rms.",
            "To assess patent novelty, we calculate new combinations (ln) as the logarithmic transformation of one plus the number of pairwise subclass combinations of a patent that appear for the first time in the US. patent database (Fleming et al. 2007, Jung and Jeongsik 2016). To do so, each pairwise combination of subclasses is compared with all pairwise combinations of all prior U.S. patents. (p. 5)",
            "In 1985, MARA was passed with the intention of harmonizing state law with the uniform state antitrust act (Bullard 1985). However, while passing MARA, legislators unintentionally revoked statute 445.761, which prohibited the enforcement of noncompete agreements in Michigan (Alterman 1985). After the passing of MARA, employers in Michigan suddenly obtained the legal means to prevent their ex-employees from working in the same \ufb01eld at a different \ufb01rm (Marx et al. 2009). As such, the Michigan experiment provided an exogenous pressure on inventors to explore new \ufb01elds after they left their former employer.",
            "To estimate the effect of exploring new \ufb01elds on the novelty and value of invention, we use a two-stage least square model (2SLS). Because the endogenous variable is binary, we use the approach suggested by Angrist (2001) and Angrist and Pischke (2008). For a recent application of the approach, see Galasso and Schankerman (2015). First, we estimate the likelihood of exploring new fields with a logit model in a difference-in-differences configuration. We include the interaction between Michigan and postmara as an exogenous variable capturing the effect of the policy reversal. Using logit instead of OLS in the \ufb01rst stage results in a better \ufb01t. Second, we calculate the \ufb01tted probabilities of exploring new fields and use these nonlinear fitted values bound between zero and one as an instrument for exploring new fjelds in the 2SLS models. Using nonlinear fitted values as an instrument is the same as plugging in \ufb01tted values when the first stage is estimated by OLS, but the advantage is a better predictor of exploring new fields in the first stage (Angrist and Pischke 2008). The 2SLS model uses a single instrument, resulting in just-identified estimates. Standard errors are clustered at the inventor level to control for repeated observations. (p. 12)",
            "For each inventor-patent observation, we retrieve the three-digit technology classes of all prior patents of the focal inventor and identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked o all prior patents of the same inventor. We rely on all classes assigned to a patent rather than just the primary class. Exploring new fields is a binary indicator that equals one in the absence of any overlapping class between all prior patents and the focal patent. (p. 6)",
            "Our identi\ufb01cation relies on the fact that only mobile inventors residing in Michigan after the passing of MARA are affected; Michigan inventors before MARA and inventors from other states before and after MARA are not affected by the policy change. Therefore, we can combine differences in exploring new \ufb01elds between inventors from different states (Michigan versus nonMichigan) with differences between cohorts induced by the timing of MARA (pre- versus post-MARA). The interaction between binary indicators for Michigan residence and post-MARA is expected to have a positive signi\ufb01cant effect on the likelihood of exploring new \ufb01elds. Thus, this difference-in-differences (DD) can be used as an instrument for exploring new \ufb01elds (Du\ufb02o 2001). The DD speci\ufb01cation controls for overall time trends in exploring new \ufb01elds (across all states) and for time-invariant unobserved differences between Michigan and non-Michigan inventors (Angrist and Pischke 2008). Furthermore, regression DD allows us to include additional inventor and \ufb01eld characteristics affecting the likelihood of exploring new \ufb01elds as controls. The main assumption is that, in the absence of MARA, the trend in exploring new \ufb01elds would not have been systematically different between Michigan and nonMichigan mobile inventors. (p. 12)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-nSzMQuhLB",
        "claim": "case-based reasoning system loaded with diverse cases increased overall novelty of ad campaign ideas, but only for people with lower creative ability",
        "citekey": "althuizenSupportingCreativeProblem2014",
        "context": [
            "Following Amabile [5], we asked three experts to rate independently all of the campaign proposals. two of the experts were creative directors of renowned Dutch marketing agencies. the other expert was the beer brewery\u2019s senior marketing manager in charge of the original campaign. two of the experts had also served as chairmen of the annual Dutch Sales Promotion Campaign Awards. the experts were blind to the study design. All the proposals were given an identical layout and were sent to the experts in randomized batches of 20 proposals. there were no order or batch effects. It took about four hours to rate all 40 proposals. (pp. 9-10)",
            "Study 2 was identical to Study 1, except for the experimental treatments. Of the CBR system with 100 diverse cases used in Study 1, 50 cases were classified as \u201cclose\u201d and 50 as \u201cremote\u201d based on the product category (see [16]). Campaigns for consumer-packaged goods (cpg), such as beer and soft drinks, are quite different from campaigns for consumer durables or services (non-cpg), such as cars or insurance products. Since beer is a consumer-packaged good, we classified all cpg cases as \u201cclose\u201d and all non-cpg cases as \u201cremote.\u201d To test H2, we devised a between-subjects study in which one group of participants (n = 20) was given a CBR system with remote cases only, while the other group (n = 20) received a CBR system with close cases only. (p. 13)",
            "Forty marketing students from the same university as in Study 1 were randomly assigned to one of the two groups. gender and education level were again found to be proportionally distributed over the two groups (gender: 73 percent male; education level: 70 percent master\u2019s degree, 30 percent bachelor\u2019s degree). (p. 13)",
            "the search structure of the CBR system consisted of the following components: (1) general information about the case; (2) problem situation, including market situation, campaign objectives, and constraints; (3) solution, including campaign design and campaign execution; and (4) outcomes. this search structure contained 60 different variables. users could search for cases by specifying the parameters they deemed relevant given the problem situation. the search values were mostly qualitative in nature, such as \u201cintroduction,\u201d \u201cgrowth,\u201d \u201cmaturity,\u201d and \u201cdecline\u201d for the variable \u201cproduct life cycle phase.\u201d users could also attach importance weights to the search variables (ranging from \u201cvery low\u201d to \u201cvery high\u201d). the importance weights could be inferred from the campaign brief. to prevent information overload, the CBR system displayed only the ten most similar past cases. the similarity between the search query and the cases in the CBR system was calculated using a distance-based measure (ranging from 0 = \u201cno similarity\u201d to 1 = \u201cperfect similarity\u201d). users were free to run multiple search queries. (p. 8)",
            "to measure the creative ability of the participants, we used the Abbreviated torrance test for Adults (ATTA) developed and validated by Goff and Torrance [35] (see also [4]). this test is a brief 15-minute version of the Torrance tests of Creative thinking and measures the following cognitive subskills of creative thinking: fluency (number of ideas), flexibility (diversity of ideas), originality (rarity of ideas), and elaboration (embellishment of ideas with details), together with 15 other creativity indicators, such as \u201crichness and colorfulness of imagery\u201d and \u201chumor: conceptual incongruity.\u201d the ATTA test consists of one verbal and two figural response tasks. two independent, trained raters scored the responses to the tasks. With raters considered in agreement whenever their scores differed no more than one point on a seven-point scale (1 = \u201cminimal\u201d to 7 = \u201csubstantial\u201d) (see [23, 63]), there was agreement in 100 percent of the cases. We also calculated the r wg coefficient as an index of within-group interrater agreement [41]. the mean r wg for the creative ability scores was 0.97 (range: 0.85\u20131.00), indicating strong agreement [52]. 5 hence, we combined the scores of the raters. (p. 9)",
            "For measuring the novelty of the solution, we selected three items (i.e., originality, surprise, and uniqueness) from Besemer and O\u2019Quin\u2019s [9] Creative Product Semantic Scale, which is a well-known instrument for evaluating creative products [60]. (p. 9)",
            "to fill the case-base of the CBR system, we collected descriptions of 100 award-winning campaigns in Europe from the 1980s and the first half of the 1990s. the cases were taken from two books: Scoren [56] and European Sales Promotion: Great Campaigns in Action [75]. Examples of how these cases were stored in the CBR system, which we called LEAPS, 3 are given in Appendix A (close case) and Appendix B (remote case). (p. 8)",
            "A Dutch beer brewery gave permission to use one of their campaign briefs in our study. the participant\u2019s task was to write a proposal for a campaign that had to boost brand loyalty and enhance the image of the brand. the campaign had to be targeted at the \u201cheavy-user\u201d segment with \u201clive music\u201d as the main theme. the brief included a number of practical constraints: (1) the promotion had to apply to crates (containing 30 cl [centiliter] or 45 cl bottles), (2) promotional items should not be attached to the sides of the crates, and (3) the value of the promotional offer should not exceed 5 euros per crate. the campaign proposal had to contain a brief description of (1) the basic idea, (2) the sales promotion technique, (3) supporting activities, and (4) a rough cost estimation. the task thus involved all the phases of the creative process, including a divergent (generating ideas) and a convergent phase (selecting and working out the best idea) [5]. the participants were instructed not to copy one of the brand\u2019s previous campaigns (see [67]). they were also told that experts would rate their campaign proposal on novelty and usefulness (see [10]). (p. 8)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-b8pGDFeTc",
        "claim": "US patents filed by inventors who were new to the patent's field tended to receive fewer forward citations, but less so when they collaborated with an expert in the new field",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "we begin with the full population of inventors and collect all patents assigned to \ufb01rms but, by design, must restrict the sample to inventors who have at least two patents assigned to the same \ufb01rm. The advantage of this panel setup is that we can use inventor\u2013firm fixed effect models to control for unobserved heterogeneity among inventors and firms, which arguably have a strong effect on the novelty and value of creative output. This approach basically uses repeated patents of the same inventor within the same firm to identify whether the inventor creates more or less novel\u2014and more or less valuable\u2014patents when any subsequent patent is categorized in a new \ufb01eld. The sample includes 2,705,431 patent\u2013inventor observations assigned to 396,336 unique inventors and 46,880 unique firms, accounting for 473,419 unique inventor\u2013firm pairs. (p. 5)",
            "For each inventor-patent observation, we retrieve the three-digit technology classes of all prior patents of the focal inventor and identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked o all prior patents of the same inventor. We rely on all classes assigned to a patent rather than just the primary class. Exploring new fields is a binary indicator that equals one in the absence of any overlapping class between all prior patents and the focal patent. (p. 6)",
            "we can use inventor\u2013\ufb01rm \ufb01xed effect models to control for unobserved heterogeneity among inventors and \ufb01rms, which arguably have a strong effect on the novelty and value of creative output (p. 5)",
            "For each inventor-patent observation, we identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked to all prior patents of the coinventors on the patent (excluding the focal inventor). Expert team is a binary indicator that equals one if at least one of the coinventors has a prior patent in the same class(es) as the focal patent. The measure is used a moderator to test whether collaboration with experts reduces the negative effect of exploring new fields on value. (p. 6)",
            "To assess patent value, we calculate forward citations (ln) as the logarithmic trans-formation of one plus the number of times a patent is referenced as prior art within 10 years. (p. 6)",
            "we select the full population of inventors with U.S. patents assigned to \ufb01rms for 1975\u20132002 (p. 3)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-W3sdOb60i",
        "claim": "US patents filed by inventors who were new to the patent's field tended to be more novel",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "To assess patent novelty, we calculate new combinations (ln) as the logarithmic transformation of one plus the number of pairwise subclass combinations of a patent that appear for the first time in the US. patent database (Fleming et al. 2007, Jung and Jeongsik 2016). To do so, each pairwise combination of subclasses is compared with all pairwise combinations of all prior U.S. patents. (p. 5)",
            "we begin with the full population of inventors and collect all patents assigned to \ufb01rms but, by design, must restrict the sample to inventors who have at least two patents assigned to the same \ufb01rm. The advantage of this panel setup is that we can use inventor\u2013firm fixed effect models to control for unobserved heterogeneity among inventors and firms, which arguably have a strong effect on the novelty and value of creative output. This approach basically uses repeated patents of the same inventor within the same firm to identify whether the inventor creates more or less novel\u2014and more or less valuable\u2014patents when any subsequent patent is categorized in a new \ufb01eld. The sample includes 2,705,431 patent\u2013inventor observations assigned to 396,336 unique inventors and 46,880 unique firms, accounting for 473,419 unique inventor\u2013firm pairs. (p. 5)",
            "For each inventor-patent observation, we retrieve the three-digit technology classes of all prior patents of the focal inventor and identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked o all prior patents of the same inventor. We rely on all classes assigned to a patent rather than just the primary class. Exploring new fields is a binary indicator that equals one in the absence of any overlapping class between all prior patents and the focal patent. (p. 6)",
            "we can use inventor\u2013\ufb01rm \ufb01xed effect models to control for unobserved heterogeneity among inventors and \ufb01rms, which arguably have a strong effect on the novelty and value of creative output (p. 5)",
            "we select the full population of inventors with U.S. patents assigned to \ufb01rms for 1975\u20132002 (p. 3)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-6e7Wu6JTF",
        "claim": "overall marginally significant negative effect of analogically distant cases on creativity of campaign ad ideas, mostly for students with high creative ability",
        "citekey": "althuizenSupportingCreativeProblem2014",
        "context": [
            "Following Amabile [5], we asked three experts to rate independently all of the campaign proposals. two of the experts were creative directors of renowned Dutch marketing agencies. the other expert was the beer brewery\u2019s senior marketing manager in charge of the original campaign. two of the experts had also served as chairmen of the annual Dutch Sales Promotion Campaign Awards. the experts were blind to the study design. All the proposals were given an identical layout and were sent to the experts in randomized batches of 20 proposals. there were no order or batch effects. It took about four hours to rate all 40 proposals. (pp. 9-10)",
            "Study 2 was identical to Study 1, except for the experimental treatments. Of the CBR system with 100 diverse cases used in Study 1, 50 cases were classified as \u201cclose\u201d and 50 as \u201cremote\u201d based on the product category (see [16]). Campaigns for consumer-packaged goods (cpg), such as beer and soft drinks, are quite different from campaigns for consumer durables or services (non-cpg), such as cars or insurance products. Since beer is a consumer-packaged good, we classified all cpg cases as \u201cclose\u201d and all non-cpg cases as \u201cremote.\u201d To test H2, we devised a between-subjects study in which one group of participants (n = 20) was given a CBR system with remote cases only, while the other group (n = 20) received a CBR system with close cases only. (p. 13)",
            "Forty marketing students from the same university as in Study 1 were randomly assigned to one of the two groups. gender and education level were again found to be proportionally distributed over the two groups (gender: 73 percent male; education level: 70 percent master\u2019s degree, 30 percent bachelor\u2019s degree). (p. 13)",
            "the search structure of the CBR system consisted of the following components: (1) general information about the case; (2) problem situation, including market situation, campaign objectives, and constraints; (3) solution, including campaign design and campaign execution; and (4) outcomes. this search structure contained 60 different variables. users could search for cases by specifying the parameters they deemed relevant given the problem situation. the search values were mostly qualitative in nature, such as \u201cintroduction,\u201d \u201cgrowth,\u201d \u201cmaturity,\u201d and \u201cdecline\u201d for the variable \u201cproduct life cycle phase.\u201d users could also attach importance weights to the search variables (ranging from \u201cvery low\u201d to \u201cvery high\u201d). the importance weights could be inferred from the campaign brief. to prevent information overload, the CBR system displayed only the ten most similar past cases. the similarity between the search query and the cases in the CBR system was calculated using a distance-based measure (ranging from 0 = \u201cno similarity\u201d to 1 = \u201cperfect similarity\u201d). users were free to run multiple search queries. (p. 8)",
            "to measure the creative ability of the participants, we used the Abbreviated torrance test for Adults (ATTA) developed and validated by Goff and Torrance [35] (see also [4]). this test is a brief 15-minute version of the Torrance tests of Creative thinking and measures the following cognitive subskills of creative thinking: fluency (number of ideas), flexibility (diversity of ideas), originality (rarity of ideas), and elaboration (embellishment of ideas with details), together with 15 other creativity indicators, such as \u201crichness and colorfulness of imagery\u201d and \u201chumor: conceptual incongruity.\u201d the ATTA test consists of one verbal and two figural response tasks. two independent, trained raters scored the responses to the tasks. With raters considered in agreement whenever their scores differed no more than one point on a seven-point scale (1 = \u201cminimal\u201d to 7 = \u201csubstantial\u201d) (see [23, 63]), there was agreement in 100 percent of the cases. We also calculated the r wg coefficient as an index of within-group interrater agreement [41]. the mean r wg for the creative ability scores was 0.97 (range: 0.85\u20131.00), indicating strong agreement [52]. 5 hence, we combined the scores of the raters. (p. 9)",
            "For measuring the novelty of the solution, we selected three items (i.e., originality, surprise, and uniqueness) from Besemer and O\u2019Quin\u2019s [9] Creative Product Semantic Scale, which is a well-known instrument for evaluating creative products [60]. (p. 9)",
            "For measuring usefulness, we selected four items from the same scale. We slightly adapted the items to fit the objectives stated in the campaign brief. the four items were effectiveness for increasing the loyalty of heavy users, fit with the brand values, attractiveness for heavy users, and the overall usefulness of the campaign. All seven items were measured on a scale from 0 (very poor) to 10 (excellent). (p. 9)",
            "to fill the case-base of the CBR system, we collected descriptions of 100 award-winning campaigns in Europe from the 1980s and the first half of the 1990s. the cases were taken from two books: Scoren [56] and European Sales Promotion: Great Campaigns in Action [75]. Examples of how these cases were stored in the CBR system, which we called LEAPS, 3 are given in Appendix A (close case) and Appendix B (remote case). (p. 8)",
            "A Dutch beer brewery gave permission to use one of their campaign briefs in our study. the participant\u2019s task was to write a proposal for a campaign that had to boost brand loyalty and enhance the image of the brand. the campaign had to be targeted at the \u201cheavy-user\u201d segment with \u201clive music\u201d as the main theme. the brief included a number of practical constraints: (1) the promotion had to apply to crates (containing 30 cl [centiliter] or 45 cl bottles), (2) promotional items should not be attached to the sides of the crates, and (3) the value of the promotional offer should not exceed 5 euros per crate. the campaign proposal had to contain a brief description of (1) the basic idea, (2) the sales promotion technique, (3) supporting activities, and (4) a rough cost estimation. the task thus involved all the phases of the creative process, including a divergent (generating ideas) and a convergent phase (selecting and working out the best idea) [5]. the participants were instructed not to copy one of the brand\u2019s previous campaigns (see [67]). they were also told that experts would rate their campaign proposal on novelty and usefulness (see [10]). (p. 8)",
            "the novelty items and the usefulness items showed high internal consistency for all experts (Cronbach \u03b1s > 0.86). thus, we averaged the individual item scores to obtain a single \u201cnovelty\u201d score and a single \u201cusefulness\u201d score per expert. to obtain an \u201coverall creativity\u201d score for each expert, we averaged these novelty and usefulness scores (see [13, 55]). (p. 10)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-jJF_B28kC",
        "claim": "An insurance benefits help desk employee struggled to reuse a database record to assist a caller because it was missing contextual information such as the history of changes and authorship, and some details about the caller's employment",
        "citekey": "ackermanOrganizationalMemoryObjects2004",
        "context": [
            "The \ufb01rst task in a distributed cognition analysis is to identify how a functional system works, good and bad (Rogers, 1992). There are low-level functional systems often embedded in larger functional systems that contribute to the overall activity being observed. Functional operation is decomposed into smaller units of analysis that make sense with respect to the particular system. While appearing in some cases to be straightforward task decomposition, it is more essentially an event driven segmentation. (pp. 9-10)",
            "This study is based on field observations of a telephone hotline group (called HLG here) at a well-established company, CyberCorp, headquartered inSilicon Valley. HLG answers human resource questions for CyberCorp, primarily about benefits and personnel policies for the company\u2019s thousands of employees. In general, telephone hotlines are of interest in the study of organizational memory, largely because they are so information intensive. HLG agents have to start forming their answer within 45-60 s while simultaneously listening to the caller\u2019s elaborations and information. Many answers came directly from the hotline member\u2019s memory; hotline questions tend to be repetitive. There is also a great need for additional information sources: Facts must be double-checked, new questions arise, and answers become obsolete with new conditions. (p. 11)",
            "The \ufb01eld study took place over a period of 18 months. A variety of data collection methods were used, including direct observation, video, semistructured interviews, and social network analyses. (p. 11)",
            "Once analyzed into its component representational states and processes, the analyst uses that information to reconstruct the functioning of the system. This allows an analysis with respect to the context of use within an organization. By extension one can speculate about how changes in technologies might a\ufb00ect future operations. We believe that looking at the phenomena of organizational memory is well supported by taking this essentially cognitive view of a system, and in our interpretation, giving it a certain social twist. (p. 10)",
            "Because of privacy reasons, only one side of the conversations was taped. Joan, however, described each call fully to the camera. (Moreover, we are concerned here with Joan\u2019s actions, rather than the intent of the caller.) (p. 11)",
            "As with other cognitive theories, distributed cognition identi\ufb01es the observed informational inputs entering, as well as those outputs leaving, a system. The functional de\ufb01nition of the unit of analysis helps with this identi\ufb01cation. Stepping down in grain size, inside the system the focus is about how information is represented, and how these representations are transformed, combined, and propagated through that system in order to produce the system\u2019s observable behavior (Simon, 1990). It is the detailing of representational states and processes that helps the analyst to understand much of the system processing as it involves transitions between humans and artifacts. One records the representational state, the material media on which it is instantiated, as well as the processes that transform it. Video recording is particularly helpful here because of the ability to review the record repetitively and glean details that are observable but di\ufb03cult to catch in just \u2018\u2018one-pass\u2019\u2019. (p. 10)",
            "Here we describe and analyze the responses to two calls captured on video. (p. 11)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-x62kMph4u",
        "claim": "healthcare workers struggled to specify contextual details on patient interactions in a healthcare records system, leading to downstream problems reusing those records, such as in administration",
        "citekey": "andersonDataBaseMent2008",
        "context": [
            "Bigcity2 Primary Care Trust (BPCT) has some 7,500 members of staff",
            "At present, PiMS is used for data entry, retrieval, and analysis by a variety of professional groups, each of which constitutes different communities of knowledge and practice and has different interests. PiMS is used to record patient details at registration and after (such demographic details as contact address and phone number, GP address and phone number); referrals of the patient to BPCT, either from external sources (such as GPs, self-referral), or from elsewhere within the Trust (between practitioners); planned/booked patient appointments; details of each contact the patient has with Trust Mental Health practitioners; details of patient assessments carried out by Trust practitioners. Currently, data entry is performed within the Trust\u2019s multi-disciplinary teams largely by secretarial, nursing, and related staff, such as occupational therapists. Very few medical consultants or junior doctors use the system themselves, preferring to handwrite records, and delegating computer data entry to their team secretaries.",
            "The data comprise field notes and transcriptions of interviews with staff about their everyday work, their use of PiMS and other information systems, both manual and computer-based, their training on PiMS, and also their use of the Trust\u2019s previous computer systems. (p. 8)",
            "The veracity of findings was established using a number of techniques. These included triangulation through the collection of data by multiple methods and sources. Verification was performed through discussions of findings with clinical and nonclinical BPCT staff; in feedback sessions with the clinical staff interviewed at their weekly team meetings; and in a Trust-wide workshop for feedback and discussion on the PiMS implementation project. As fieldwork progressed, comparisons were also be drawn between the activities of workers over time and between members of different occupational groups. (p. 8)",
            "Nonclinical settings in which fieldwork was conducted included regular meetings of the PiMS Implementation Group (weekly) and the PiMS User Group (monthly). These involved members of the Project Team responsible for implementing PiMS, and staff from the Information Services (IS) and Clinical Governance (CG) Teams. The latter two groups were users of PiMS data from an administrative perspective, analyzing data from the system in order to compile mental healthcare statistics for decision making within and beyond BPCT. All had an interest in ensuring the completeness, accuracy, and timeliness of data entry, including the use of the Contact Purpose menu.",
            "The investigation reported here is based on 12 months of ethnographic fieldwork carried out in BPCT. Data collection methods included participant observation and semistructured interviews with a range of personnel across a number of sites within the Trust, in both clinical and nonclinical departments or settings. The first round of data collection in BPCT took place between autumn 2001 and spring 2002, after which an initial report of fieldwork findings on the implementation process to date, together with some recommendations for action, were presented to Trust managers (Hardstone 2002) (p. 7).",
            "The sites of clinical practice were chosen in order to compare PiMS implementation in a locality-based General Adult Mental Health Service (SW BigCity) with that in one of the larger specialist services, the Alcohol Problems Service. Both of these services were comprised of more than one team: SW Area having three (Outreach, Day Hospital, and Community Psychiatric Nurses, or CPNs) and Alcohol Problems Service having two (Resource and CPNs). Each team covered a different aspect of its service\u2019s mental health provision and had its own caseloads, and therefore had different work patterns and practices influencing its use of PiMS. While CPN Teams were occupationally homogeneous, others had a broader membership, including consultants, nurses, CPNs, occupational and other therapists, and social workers, as well as medical secretaries. In the context of this paper, each team had a different array of purposes for contact with patients. (p. 7)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-jScHaY6Fl",
        "claim": "estimated semantic networks of animal concepts from montessori-educated children were more interconnected, with shorter paths between concepts and fewer subcommunities, compared to networks from traditional-schooled but comparable children",
        "citekey": "denervaudEducationShapesStructure2021",
        "context": [
            "To assess creative thinking, children completed divergent and convergent creativity tasks from the Evaluation of Potential Creativity. Divergent thinking reflects the ability to think of ideas that differ from one another; convergent thinking reflects the ability to think of a single creative solution. Performance on such creative thinking tasks has been shown to predict both academic*' and creative achievement. In the divergent thinking task, the child was asked to draw as many different drawings as possible from one imposed abstract form (i.e, incomplete shape), within 10 min. The final score was the sum of all valid drawings. In the convergent thinking task, the child had to select three different abstract forms out of eight to create an original drawing that combined them, within 15 min. Three blind judges scored the drawings for originality following the EPoC scoring manual (inter-rater agreement; Krippendorff's alpha = 0.905). Independent t tests were computed on each creativity score (divergent and convergent) to test for between-group differences. Pearson\u2019s correlations were computed between each creativity score and the verbal fluency metrics to test whether creative thinking relates to the quantity and quality of words retrieved from semantic memory. (p. 5)",
            "Children completed verbal fluency task. Category verbal fluency tasks have been widely used to efficiently assess semantic network organization. Consistent with traditional task administration, each child had 60s to name as many animals as he/she could. Based on previous work in children, we targeted the animal category. Children spoke their responses out loud, which were recorded (and later transcribed) by an experimenter. For each child, fluency data was preprocessed using the SemNA pipeline in R. Repetitions or variation on roots were converged and non-category members were excluded from the final analysis. Number of responses per participant were summed (total number of responses). (p. 5)",
            "Finally, using these word association matrices, we applied the triangulated maximally filtered graph TMFGY; to minimize noise and potential spurious associations. The TMFG method filters the word association matrices to capture only the most relevant information (i.e, removal of spurious associations and retaining the largest associations) within the original network. This approach retains the same number of edges between groups (i.e, 3n-6, where n equals the number of responses), which avoids the confound of difference network structures being due to a different number of edges, This resulted in a 68 nodes network with 198 edges for both groups. (p. 5)",
            "Next, we computed a word association matrix for each group using the cosine similarity. The cosine similarity is commonly used in related to Pearson\u2019s correlation, which can be considered as the cosine between two normalized vectors. With the cosine similarity measure, all values are positive ranging from 0 (two responses do not co-occur) to 1 (two responses always co-occur). For both groups, each element in the word association matrix, A;, represents the cosine similarity or the co-occurrence between response i and j. (p. 5)",
            "A total of 67 children participated in the current study (Mage =9.31, SD=2.23, 47.8% girls) through the University Hospital of Lausanne researchpool as part of a broader research project on education and neurocognitive development. Children were compensated with a ~30 USD gift voucher for completion of the study. Inclusion criteria were schoolings ystem (participants had to be enrolled in Montessori or in traditional classes from the early years on, in the case of the youngest children, or for at least 3 years), age (5-14 years of age); exclusion criteria were parental report of learning disabilities or sensory impairment. To account for variability in our measures due to nonverbal intelligence, or socioeconomic background, we controlled for between-group homogeneity in nonverbal intelligence (black and white short version of the Progressive Matrices\u00ae) and family socioeconomic status (both parents\u2019 education levels (score from 1 to 5) and current job (score from 1 to 4); scores were summed and averaged between both parents (max 9), with higher scores denoting higher SES). (p. 4)",
            "The processed data were transferred into a binary response matrix, where columns represent the unique exemplars given by the sample and rows represent participants; the response matrix is filled out by 1 (if an exemplar was generated by that participant) and 0 (if that exemplar was not generated). To control for confounding factors (such as different nodes or edges in both groups), as in previous studies, the binary response matrices only include responses that are given by at least two participants in each group. Then, to avoid the two groups including a different number of nodes, which may bias comparison of network parameters, responses in the binary matrices were equated, so that the networks of both groups in each sample are compared using the same nodes. (p. 5)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-zGQwQiY6L",
        "claim": "natural experiment with inventors affected by the 1985 Michigan Antitrust Reform Act showed that patents filed by inventor teams that included an expert in the patent's field tended to be less novel",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "we select all U.S. inventors who patented in Michigan or in another nonenforcing state before the passing of MARA in 1985, including Alaska, California, Connecticut, Minnesota, Montana, Nevada, North Dakota, Oklahoma, Washington, and West Virginia (Malsberger 1996; Marx et al. 2009, Marx et al. 2015). Inventors who did not patent in a nonenforcing state or only did so after the passing of MARA are excluded to ensure that MARA did not affect sample selection. We track all subsequent patents linked to this set of inventors and assigned to a \ufb01rm and identify each move between \ufb01rms (again, the design relies upon inventors patenting at least twice). Only intrastate moves are taken into account because inventors can emigrate from Michigan to a nonenforcing state to avoid a lawsuit (Marx et al. 2015). Finally, we restrict the analysis to the 1975\u20131995 period, that is, 10 years before and after the passing of MARA. Notice that we collect all patents, both before and after MARA and in and out of Michigan. This results in the full sample of patents by inventors at risk for moving between \ufb01rms both in Michigan and elsewhere before and after MARA. The resulting data set spans 21 years and consists of 29,956 inventors and 162,586 patents of which 13,723 patents represent a move, that is, the \ufb01rst subsequent patent of an inventor after moving to a new \ufb01rm. The \ufb01nal analysis is restricted to these mobile inventors because the pressure to explore new \ufb01elds because of MARA only affects inventors who move between \ufb01rms.",
            "In 1985, MARA was passed with the intention of harmonizing state law with the uniform state antitrust act (Bullard 1985). However, while passing MARA, legislators unintentionally revoked statute 445.761, which prohibited the enforcement of noncompete agreements in Michigan (Alterman 1985). After the passing of MARA, employers in Michigan suddenly obtained the legal means to prevent their ex-employees from working in the same \ufb01eld at a different \ufb01rm (Marx et al. 2009). As such, the Michigan experiment provided an exogenous pressure on inventors to explore new \ufb01elds after they left their former employer.",
            "To estimate the effect of exploring new \ufb01elds on the novelty and value of invention, we use a two-stage least square model (2SLS). Because the endogenous variable is binary, we use the approach suggested by Angrist (2001) and Angrist and Pischke (2008). For a recent application of the approach, see Galasso and Schankerman (2015). First, we estimate the likelihood of exploring new fields with a logit model in a difference-in-differences configuration. We include the interaction between Michigan and postmara as an exogenous variable capturing the effect of the policy reversal. Using logit instead of OLS in the \ufb01rst stage results in a better \ufb01t. Second, we calculate the \ufb01tted probabilities of exploring new fields and use these nonlinear fitted values bound between zero and one as an instrument for exploring new fjelds in the 2SLS models. Using nonlinear fitted values as an instrument is the same as plugging in \ufb01tted values when the first stage is estimated by OLS, but the advantage is a better predictor of exploring new fields in the first stage (Angrist and Pischke 2008). The 2SLS model uses a single instrument, resulting in just-identified estimates. Standard errors are clustered at the inventor level to control for repeated observations. (p. 12)",
            "For each inventor-patent observation, we identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked to all prior patents of the coinventors on the patent (excluding the focal inventor). Expert team is a binary indicator that equals one if at least one of the coinventors has a prior patent in the same class(es) as the focal patent. The measure is used a moderator to test whether collaboration with experts reduces the negative effect of exploring new fields on value. (p. 6)",
            "To assess patent value, we calculate forward citations (ln) as the logarithmic trans-formation of one plus the number of times a patent is referenced as prior art within 10 years. (p. 6)",
            "Our identi\ufb01cation relies on the fact that only mobile inventors residing in Michigan after the passing of MARA are affected; Michigan inventors before MARA and inventors from other states before and after MARA are not affected by the policy change. Therefore, we can combine differences in exploring new \ufb01elds between inventors from different states (Michigan versus nonMichigan) with differences between cohorts induced by the timing of MARA (pre- versus post-MARA). The interaction between binary indicators for Michigan residence and post-MARA is expected to have a positive signi\ufb01cant effect on the likelihood of exploring new \ufb01elds. Thus, this difference-in-differences (DD) can be used as an instrument for exploring new \ufb01elds (Du\ufb02o 2001). The DD speci\ufb01cation controls for overall time trends in exploring new \ufb01elds (across all states) and for time-invariant unobserved differences between Michigan and non-Michigan inventors (Angrist and Pischke 2008). Furthermore, regression DD allows us to include additional inventor and \ufb01eld characteristics affecting the likelihood of exploring new \ufb01elds as controls. The main assumption is that, in the absence of MARA, the trend in exploring new \ufb01elds would not have been systematically different between Michigan and nonMichigan mobile inventors. (p. 12)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-IUA1p7faR",
        "claim": "US patents in the early 90's were more likely to be exapted by inventors who had previous patent experience in the focal and-or citing patent subclasses",
        "citekey": "mastrogiorgioInnovationExaptationIts2016",
        "context": [
            "The ability of inventors to draw inventive analogies and exapt existing technologies across different domains is a function of their stock of knowledge spanning these domains. We introduced a novel measure of inventors\u2019 analogical abilities that quantifies their multi-domain skills: In order to build the measure, we considered the inventor (or team) belonging to the first citing patent. We then extracted, from the Patent Network Dataverse (Lai et al, 2011),the inventor\u2019s previous patents that belong to the 1975-1990 pre-sample window. We then counted the number of previous patents whose OR class was equal to the OR class of either the focal patent or the citing patent. (p. 7)",
            "In order to test our hypotheses, we studied exaptation at the invention level; we identified an invention with a patent and considered a cross-section of U.S. patents. Raw patent data were obtained from the USPTO and/NBER databases (Hall et al., 2001),and the main measures were built after merging these databases to the Patent Network Dataverse (Lai et al, 2011). (p. 5)",
            "a forward citation is cross-class if both the OX and XR classes of the focal patent differ from the OR class of the citing patent (p. 6)",
            "As our dependent variable is a proportion, we adopted the fractional logit estimation procedure proposed by Papke and Wooldridge (1996). (p. 10)",
            "Our empirical framework consisted of the following steps: (1) we considered a random cross-section of US. patents granted between January and June 1991 (both theJanuary-June interval and the year 1991 were chosen randomly); (2) for each patent we used a 1991-1999 window of forward citations to calculate exaptation; (3) for each patent we then considered a 1975-1990 pre-sample window in order to calculate technological complexity, inventor's analogical ability, and other controls. The estimation sample consists of 19076 patents. (p. 5)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-d77x3B_Ui",
        "claim": "case-based reasoning system loaded with diverse cases increased overall usefulness and creativity of ad campaign ideas, especially for people with lower creative ability",
        "citekey": "althuizenSupportingCreativeProblem2014",
        "context": [
            "Participants in the \u201cno CBR system\u201d control condition received only a sales promotion technique inventory on paper. It should be noted that this paper document was also made available to the participants in the CBR system condition. the inventory contained a basic description of sales promotion techniques (such as sampling or organizing a contest) together with the most salient pros and cons of each technique (such as aptitude for inducing trial, implementation times, and predictability of the costs). the descriptions were taken from textbooks and verified by experts (who also verified the CBR system\u2019s search structure).",
            "Following Amabile [5], we asked three experts to rate independently all of the campaign proposals. two of the experts were creative directors of renowned Dutch marketing agencies. the other expert was the beer brewery\u2019s senior marketing manager in charge of the original campaign. two of the experts had also served as chairmen of the annual Dutch Sales Promotion Campaign Awards. the experts were blind to the study design. All the proposals were given an identical layout and were sent to the experts in randomized batches of 20 proposals. there were no order or batch effects. It took about four hours to rate all 40 proposals. (pp. 9-10)",
            "the search structure of the CBR system consisted of the following components: (1) general information about the case; (2) problem situation, including market situation, campaign objectives, and constraints; (3) solution, including campaign design and campaign execution; and (4) outcomes. this search structure contained 60 different variables. users could search for cases by specifying the parameters they deemed relevant given the problem situation. the search values were mostly qualitative in nature, such as \u201cintroduction,\u201d \u201cgrowth,\u201d \u201cmaturity,\u201d and \u201cdecline\u201d for the variable \u201cproduct life cycle phase.\u201d users could also attach importance weights to the search variables (ranging from \u201cvery low\u201d to \u201cvery high\u201d). the importance weights could be inferred from the campaign brief. to prevent information overload, the CBR system displayed only the ten most similar past cases. the similarity between the search query and the cases in the CBR system was calculated using a distance-based measure (ranging from 0 = \u201cno similarity\u201d to 1 = \u201cperfect similarity\u201d). users were free to run multiple search queries. (p. 8)",
            "to measure the creative ability of the participants, we used the Abbreviated torrance test for Adults (ATTA) developed and validated by Goff and Torrance [35] (see also [4]). this test is a brief 15-minute version of the Torrance tests of Creative thinking and measures the following cognitive subskills of creative thinking: fluency (number of ideas), flexibility (diversity of ideas), originality (rarity of ideas), and elaboration (embellishment of ideas with details), together with 15 other creativity indicators, such as \u201crichness and colorfulness of imagery\u201d and \u201chumor: conceptual incongruity.\u201d the ATTA test consists of one verbal and two figural response tasks. two independent, trained raters scored the responses to the tasks. With raters considered in agreement whenever their scores differed no more than one point on a seven-point scale (1 = \u201cminimal\u201d to 7 = \u201csubstantial\u201d) (see [23, 63]), there was agreement in 100 percent of the cases. We also calculated the r wg coefficient as an index of within-group interrater agreement [41]. the mean r wg for the creative ability scores was 0.97 (range: 0.85\u20131.00), indicating strong agreement [52]. 5 hence, we combined the scores of the raters. (p. 9)",
            "To test H1, We devised a between-subjects experiment in which one group of participants (n = 20) was given a CBR system filled with a diverse set of cases, plus a sales promotion technique inventory on paper (more details are given in the treatments subsection). the other group of participants (n = 20) received only the sales promotion technique inventory on paper. (p. 7)",
            "Forty marketing students from a Dutch university participated in this study. 1 the participants were randomly assigned to one of the two groups. gender and education level were found to be proportionally distributed over the two groups (gender: 65 percent male; education level: 70 percent master\u2019s degree and 30 percent bachelor\u2019s degree). (p. 7)",
            "For measuring the novelty of the solution, we selected three items (i.e., originality, surprise, and uniqueness) from Besemer and O\u2019Quin\u2019s [9] Creative Product Semantic Scale, which is a well-known instrument for evaluating creative products [60]. (p. 9)",
            "For measuring usefulness, we selected four items from the same scale. We slightly adapted the items to fit the objectives stated in the campaign brief. the four items were effectiveness for increasing the loyalty of heavy users, fit with the brand values, attractiveness for heavy users, and the overall usefulness of the campaign. All seven items were measured on a scale from 0 (very poor) to 10 (excellent). (p. 9)",
            "to fill the case-base of the CBR system, we collected descriptions of 100 award-winning campaigns in Europe from the 1980s and the first half of the 1990s. the cases were taken from two books: Scoren [56] and European Sales Promotion: Great Campaigns in Action [75]. Examples of how these cases were stored in the CBR system, which we called LEAPS, 3 are given in Appendix A (close case) and Appendix B (remote case). (p. 8)",
            "A Dutch beer brewery gave permission to use one of their campaign briefs in our study. the participant\u2019s task was to write a proposal for a campaign that had to boost brand loyalty and enhance the image of the brand. the campaign had to be targeted at the \u201cheavy-user\u201d segment with \u201clive music\u201d as the main theme. the brief included a number of practical constraints: (1) the promotion had to apply to crates (containing 30 cl [centiliter] or 45 cl bottles), (2) promotional items should not be attached to the sides of the crates, and (3) the value of the promotional offer should not exceed 5 euros per crate. the campaign proposal had to contain a brief description of (1) the basic idea, (2) the sales promotion technique, (3) supporting activities, and (4) a rough cost estimation. the task thus involved all the phases of the creative process, including a divergent (generating ideas) and a convergent phase (selecting and working out the best idea) [5]. the participants were instructed not to copy one of the brand\u2019s previous campaigns (see [67]). they were also told that experts would rate their campaign proposal on novelty and usefulness (see [10]). (p. 8)",
            "the novelty items and the usefulness items showed high internal consistency for all experts (Cronbach \u03b1s > 0.86). thus, we averaged the individual item scores to obtain a single \u201cnovelty\u201d score and a single \u201cusefulness\u201d score per expert. to obtain an \u201coverall creativity\u201d score for each expert, we averaged these novelty and usefulness scores (see [13, 55]). (p. 10)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-5gJjNdjMH",
        "claim": "US patents filed by inventor teams that included an expert in the patent's field tended to be less novel",
        "citekey": "artsParadiseNoveltyLoss2018a",
        "context": [
            "To assess patent novelty, we calculate new combinations (ln) as the logarithmic transformation of one plus the number of pairwise subclass combinations of a patent that appear for the first time in the US. patent database (Fleming et al. 2007, Jung and Jeongsik 2016). To do so, each pairwise combination of subclasses is compared with all pairwise combinations of all prior U.S. patents. (p. 5)",
            "we begin with the full population of inventors and collect all patents assigned to \ufb01rms but, by design, must restrict the sample to inventors who have at least two patents assigned to the same \ufb01rm. The advantage of this panel setup is that we can use inventor\u2013firm fixed effect models to control for unobserved heterogeneity among inventors and firms, which arguably have a strong effect on the novelty and value of creative output. This approach basically uses repeated patents of the same inventor within the same firm to identify whether the inventor creates more or less novel\u2014and more or less valuable\u2014patents when any subsequent patent is categorized in a new \ufb01eld. The sample includes 2,705,431 patent\u2013inventor observations assigned to 396,336 unique inventors and 46,880 unique firms, accounting for 473,419 unique inventor\u2013firm pairs. (p. 5)",
            "we can use inventor\u2013\ufb01rm \ufb01xed effect models to control for unobserved heterogeneity among inventors and \ufb01rms, which arguably have a strong effect on the novelty and value of creative output (p. 5)",
            "For each inventor-patent observation, we identify whether there is any overlap between the three-digit technology classes of the focal patent and the three-digit technology classes linked to all prior patents of the coinventors on the patent (excluding the focal inventor). Expert team is a binary indicator that equals one if at least one of the coinventors has a prior patent in the same class(es) as the focal patent. The measure is used a moderator to test whether collaboration with experts reduces the negative effect of exploring new fields on value. (p. 6)",
            "we select the full population of inventors with U.S. patents assigned to \ufb01rms for 1975\u20132002 (p. 3)"
        ],
        "dataset": "megacoglab"
    },
    {
        "id": "megacoglab-mtKPi-Abu",
        "claim": "no overall effect of analogical distance of cases on novelty or usefulness of campaign ad ideas",
        "citekey": "althuizenSupportingCreativeProblem2014",
        "context": [
            "Following Amabile [5], we asked three experts to rate independently all of the campaign proposals. two of the experts were creative directors of renowned Dutch marketing agencies. the other expert was the beer brewery\u2019s senior marketing manager in charge of the original campaign. two of the experts had also served as chairmen of the annual Dutch Sales Promotion Campaign Awards. the experts were blind to the study design. All the proposals were given an identical layout and were sent to the experts in randomized batches of 20 proposals. there were no order or batch effects. It took about four hours to rate all 40 proposals. (pp. 9-10)",
            "Study 2 was identical to Study 1, except for the experimental treatments. Of the CBR system with 100 diverse cases used in Study 1, 50 cases were classified as \u201cclose\u201d and 50 as \u201cremote\u201d based on the product category (see [16]). Campaigns for consumer-packaged goods (cpg), such as beer and soft drinks, are quite different from campaigns for consumer durables or services (non-cpg), such as cars or insurance products. Since beer is a consumer-packaged good, we classified all cpg cases as \u201cclose\u201d and all non-cpg cases as \u201cremote.\u201d To test H2, we devised a between-subjects study in which one group of participants (n = 20) was given a CBR system with remote cases only, while the other group (n = 20) received a CBR system with close cases only. (p. 13)",
            "Forty marketing students from the same university as in Study 1 were randomly assigned to one of the two groups. gender and education level were again found to be proportionally distributed over the two groups (gender: 73 percent male; education level: 70 percent master\u2019s degree, 30 percent bachelor\u2019s degree). (p. 13)",
            "the search structure of the CBR system consisted of the following components: (1) general information about the case; (2) problem situation, including market situation, campaign objectives, and constraints; (3) solution, including campaign design and campaign execution; and (4) outcomes. this search structure contained 60 different variables. users could search for cases by specifying the parameters they deemed relevant given the problem situation. the search values were mostly qualitative in nature, such as \u201cintroduction,\u201d \u201cgrowth,\u201d \u201cmaturity,\u201d and \u201cdecline\u201d for the variable \u201cproduct life cycle phase.\u201d users could also attach importance weights to the search variables (ranging from \u201cvery low\u201d to \u201cvery high\u201d). the importance weights could be inferred from the campaign brief. to prevent information overload, the CBR system displayed only the ten most similar past cases. the similarity between the search query and the cases in the CBR system was calculated using a distance-based measure (ranging from 0 = \u201cno similarity\u201d to 1 = \u201cperfect similarity\u201d). users were free to run multiple search queries. (p. 8)",
            "to measure the creative ability of the participants, we used the Abbreviated torrance test for Adults (ATTA) developed and validated by Goff and Torrance [35] (see also [4]). this test is a brief 15-minute version of the Torrance tests of Creative thinking and measures the following cognitive subskills of creative thinking: fluency (number of ideas), flexibility (diversity of ideas), originality (rarity of ideas), and elaboration (embellishment of ideas with details), together with 15 other creativity indicators, such as \u201crichness and colorfulness of imagery\u201d and \u201chumor: conceptual incongruity.\u201d the ATTA test consists of one verbal and two figural response tasks. two independent, trained raters scored the responses to the tasks. With raters considered in agreement whenever their scores differed no more than one point on a seven-point scale (1 = \u201cminimal\u201d to 7 = \u201csubstantial\u201d) (see [23, 63]), there was agreement in 100 percent of the cases. We also calculated the r wg coefficient as an index of within-group interrater agreement [41]. the mean r wg for the creative ability scores was 0.97 (range: 0.85\u20131.00), indicating strong agreement [52]. 5 hence, we combined the scores of the raters. (p. 9)",
            "For measuring the novelty of the solution, we selected three items (i.e., originality, surprise, and uniqueness) from Besemer and O\u2019Quin\u2019s [9] Creative Product Semantic Scale, which is a well-known instrument for evaluating creative products [60]. (p. 9)",
            "For measuring usefulness, we selected four items from the same scale. We slightly adapted the items to fit the objectives stated in the campaign brief. the four items were effectiveness for increasing the loyalty of heavy users, fit with the brand values, attractiveness for heavy users, and the overall usefulness of the campaign. All seven items were measured on a scale from 0 (very poor) to 10 (excellent). (p. 9)",
            "to fill the case-base of the CBR system, we collected descriptions of 100 award-winning campaigns in Europe from the 1980s and the first half of the 1990s. the cases were taken from two books: Scoren [56] and European Sales Promotion: Great Campaigns in Action [75]. Examples of how these cases were stored in the CBR system, which we called LEAPS, 3 are given in Appendix A (close case) and Appendix B (remote case). (p. 8)",
            "A Dutch beer brewery gave permission to use one of their campaign briefs in our study. the participant\u2019s task was to write a proposal for a campaign that had to boost brand loyalty and enhance the image of the brand. the campaign had to be targeted at the \u201cheavy-user\u201d segment with \u201clive music\u201d as the main theme. the brief included a number of practical constraints: (1) the promotion had to apply to crates (containing 30 cl [centiliter] or 45 cl bottles), (2) promotional items should not be attached to the sides of the crates, and (3) the value of the promotional offer should not exceed 5 euros per crate. the campaign proposal had to contain a brief description of (1) the basic idea, (2) the sales promotion technique, (3) supporting activities, and (4) a rough cost estimation. the task thus involved all the phases of the creative process, including a divergent (generating ideas) and a convergent phase (selecting and working out the best idea) [5]. the participants were instructed not to copy one of the brand\u2019s previous campaigns (see [67]). they were also told that experts would rate their campaign proposal on novelty and usefulness (see [10]). (p. 8)"
        ],
        "dataset": "megacoglab"
    }
]