dataesr/scientific-paragraphs-categorization huggingface dataset:
Reference lists of all relevant articles were searched manually for additional articles (Fig  1 ). Focus was placed on patients with acute phase STEMI (two studies with mixed STEMI and NSTEMI population) and revascularization therapy with data on deformation imaging (using Peer-reviewed studies assessing the role of STE (two-dimensional and/or tridimensional (2D/3D) were included regardless of the analyzed direction of myocardial motion (longitudinal, circumferential or radial) and of the type of measured parameter (strain, strain rate, torsion or twist). Studies were selected if they reported correlation or diagnostic value of deformation imaging in predicting cardiac remodeling. Studies assessing myocardial deformation using tissue Doppler imaging were excluded from the analysis. Studies were divided into two groups according to the reported type of LV remodeling: • Adverse remodeling with an increase in LVEDV and/or LVESV by 15 to 20% [1.
Tables A and B in S1 File). Specificity of each study (i. e. , clinical outcomes or use of other imaging strategy) was noted. Duration of follow-up when given, characteristics of the study population, parameters studied, inter-group comparison and outcome along with statistical information (data for hazard ratio, relative risk, incidence and statistical significance) were collected. Reproducibility of global peak longitudinal strain (GLS) was also documented if available. A relationship between deformation and LV remodeling was defined as: i) positive if a variation in deformation parameters was significantly associated with LV remodeling or ii) negative if STE was not significantly associated with LV remodeling. The deformation parameter was considered as an absolute value of the number for all references indicating correlation between remodeling or LV function and strain.
Study limitations A main limitation of the present analysis is that most studies were single-center series with small sample sizes. In addition, various imaging techniques and timing of imaging following MI were used, leading to significant heterogeneity of results. There is currently no large study cohort comparing the various strain components. Measurements of STE parameters were performed offline using dedicated software and after acquisition by a GE Vivid 7 or 9 in most instances  (19/23). A few studies did assess strain components using other systems, including Siemens (1 study), Philips (2 studies) and Toshiba (1 study) systems. Recurrent myocardial ischemia, loading condition and therapy may change cardiac volume and thus influence strain values between the first hours after revascularization and discharge.
Another limitation is that only a major database (Medline) was used for search and study selection. One important limitation of our meta-analysis is the absence of available individual data. Importantly, the studies included in our meta-regression used different cut-offs for adverse remodeling (an increase in LVEDV or /and LVESV by 15 to 20%) and reverse remodeling (improvement in WMSI or increase in LVEF greater than 5% or decrease in LVESV greater than 15%). In addition, the studies included in this meta-analysis used various 2DGLS cutoffs. However, cut-offs values of 2DGLS ranged from -12. 5 and 10. 2, and most studies found an optimal cut-off very close to -11, we would promote -11 as the most evidence-based cut-off so far. However, further larger studies, namely multicenter studies with derivation and validation cohorts, should validate the most appropriate cut-off for both adverse and reverse remodeling after MI as well as the 2DGLS cut-off for both these outcomes.
The cluster density corresponds to the numbers of clusters per perimeter. To analyse the formation of the pattern in the cytokinetic ring in mammalian cells, the intensity profiles were measured with ImageJ and a Fourier Transformation was performed with Matlab. We determined the cluster velocities in fission yeast rings as follows. The rings were transformed to lines (Fig. 3g, h ) by a polar transformation (ImageJ) and represented as kymographs. In these kymographs, the cluster can be traced as lines. If the cluster motion could be followed over at least three successive images, we measured their velocities by taking the slopes of their movement. Cluster lifetime and travelling length was also extracted from the kymographs. For better representation, we smoothed images of mammalian cells with ImageJ.
Acknowledgements We thank  P. Nurse ,  F. Ne  ´delec, M. -F. Carlier,  A. Ott ,  J. Comelles  and the  Riveline Lab  for discussions and help, and we are grateful to  X. Le Goff ,  A. -C. Reymann  and  U. Schwarz  for critical reading of the manuscript. We thank  J. Comelles  for providing the scheme in Figs 4 and6. We acknowledge the technical support from  M. Marchand  (Rockefeller),  B. Rhoades  and  M. Skvarla  ( Cornell Ithaca ),  M. Koch  and  P. Kessler  ( Imaging Platform, IGBMC ). We thank  A. Hyman ,  J. Q. Wu ,  M. Balasubramanian ,  M. Lord ,  J. Moseley ,  P. Perez  and  T. Pollard  for sharing strains. This study was performed in part for D. R. in a sabbatical stay at the  Rockefeller University. It involved work at the  Cornell NanoScale Facility , a member of the  National Nanotechnology Infrastructure Network , which is supported by the  National Science Foundation  (Grant  ECS-0335765 ), and in  Femto (Besanc¸on, France ).
This study with the reference  ANR-10-LABX-0030-INRT  has been also supported by a  French  state fund through the  Agence Nationale de la Recherche  under the frame programme  Investissements d'Avenir labelled   ANR-10-IDEX-0002-02. R. T. is an IGBMC International PhD Programme fellow supported by  LabEx INRT  funds. D. R. acknowledges support from  CNRS (ATIP) ,  ciFRC Strasbourg , the  University of Strasbourg, Labex IGBMC ,  Fondation pour la Recherche Medicale and Foundation Cino del Duca. V. W. acknowledges support from  UFA/DFH. K. K. was supported by  Deutsche Forschungsgemeinschaft  through  SFB 1027.
Results During the study period, a complete dataset was available for 6333 treated primary breast cancers. Cancer types were ductal carcinoma in situ (15. 3%), invasive ductal carcinoma (75. 7%), invasive lobular carcinoma (9. 0%), or others (2. 2%). Of the 6333 cancers, 36. 5% (n = 2312) were detected by mammography alone, 54. 8% (n = 3470) by mammography and cbe, and 8. 7% (n = 551) by physician-performed cbe alone (or 5. 3% if considering ultrasonography). Invasive tumours diagnosed by cbe alone were more often triple-negative, her2-positive, node-positive, and larger than those diagnosed by mammography alone (p < 0. 05). Conclusions A significant number of cancers would have been missed if cbe had not been performed. Compared with cancers detected by mammography alone, those detected by cbe had more aggressive features.
Data Collection The Centre des maladies du sein Deschênes-Fabia maintains a registry of all breast cancer cases diagnosed at the centre since 1965. All histologically confirmed primary breast cancers treated at our centre are prospectively entered into the database by trained clerks. All patients undergo at least bilateral mammography and cbe as part of the routine staging procedure. In the presence of an abnormal cbe finding, bus is performed; however, bus results were added to the database only in 2006, even if the test had previously been performed. All patients were categorized according to the presence of abnormalities observed at cbe or at mammography. A cbe was considered abnormal in the presence of a palpable mass, nipple discharge, skin or nipple retraction, edema, erythema, peau d'orange, or skin ulcers.
In cases of multiple cbes yielding different results in the context of the same work-up that led to the cancer diagnosis, only the worst results (that is, positivity for any of the enumerated symptoms or signs) are recorded in the database. An abnormal mammogram or bus result was based on the interpretation of the radiologist and defined as either indeterminate or highly suggestive of malignancy. Tumour size was based on the pathology report. At our centre during the study period, all cbes were performed by surgeons (n = 5, 5-30 years of experience) and by general practitioners specialized in breast diseases (n = 8, 11-30 years of experience). However, the mammography or bus might have been performed at our tertiary breast centre, at private radiology clinics, or at community hospitals. Patients with an incomplete dataset were excluded (n = 1342).
Included patients (n = 6333) were similar to the patients in the database overall (n = 7675) in terms of age (59. 1 ± 12. 3 years vs. 59. 1 ± 12. 2 years) and cancer type distribution [ductal carcinoma in situ (dcis): 15. 3% vs. 15. 3%; invasive ductal carcinoma (idc): 75. 7% vs. 72. 6%; invasive lobular carcinoma (ilc): 9. 0% vs. 9. 0%]. Patients in the bus subset (n = 3005) were also similar to the patients in the database overall in terms of age (60. 0 ± 12. 5 years vs. 59. 1 ± 12. 3 years) and cancer type distribution (dcis: 14. 1% vs. 15. 3%; idc: 72. 6% vs. 73. 7%; ilc: 9. 0% vs. 9. 0%).
RESULTS From July 1999 to April 2010, 7675 patients with new primary breast cancers were treated at our institution, but 1342 patients were excluded from the study because of an incomplete dataset. Among the 6333 remaining patients, 968 had dcis (15. 3%), 4795 had idc (75. 7%), 570 had ilc (9. 0%), and 123 had other cancer types (2. 2%). All physical and imaging examinations were performed during the same time period and for the same reasons. Median time between cbe and mammography was 22. 5 days (range: 0. 0-357 days; interquartile range: 12-42 days). Median time between cbe and bus was 12 days (range: 0. 0-372 days; interquartile range: 3-33 days). Median time between mammography and bus was 15 days (range: 0. 0-339 days; interquartile range: 3-33 days). Thus, except for some outliers, all examinations were performed within a short time span.
In all patients considered here, cancer was detected (Figure  1 ) by mammography alone in 36. 5% (n = 2312), by mammography and cbe in 54. 8% (n = 3470), and by physician-performed cbe alone in 8. 7% (n = 551). In the patient subset with available bus data that had been systematically entered into the registry (March 2006 to December 2010), cancer was detected by mammography alone in 17. 4% (n = 523); by mammography and cbe in 12. 7% (n = 383); by cbe and bus in 9. 8% (n = 293); by mammography and bus in 16. 1% (n = 483); by cbe, mammography, and bus in 38. 8% (n = 1166); and by cbe alone in 5. 2% (n = 157). For invasive cancers only, pathologic tumour size of cancers diagnosed with cbe alone was 29. 2 ± 27. 1 mm compared with 26. 2 ± 24. 4 mm for cancers diagnosed by cbe and bus (p = 0. 28).
The present study is not without limitations. Indeed, it was a retrospective study in a tertiary breast cancer centre limited to the variables available in our database. Data came from a single centre, introducing the possibility of biases in the performance of the cbe itself or in documenting results. The cbes were performed by various physicians and surgeons with different experience levels in cbe. The study was performed during a period of major changes in imaging techniques. Mammography evolved from analog techniques at the beginning of the study period to computed radiology techniques by the end of the period, which could have led to a higher number of cancers being detected by mammography in the late period of the study  49  ; however, digital radiology systems were acquired just after the period covered by this present study.
Similarly, the bus examinations were performed using different units showing great variety in spatial and contrast resolution. In addition, the bus examinations were performed by radiologists with a wide range of experience in various clinical settings. The bus results were compiled into the database starting only in 2006, but the subset of cancers with bus data available was comparable to the overall study sample. As recommended by many organizations and in many guidelines, a positive cbe should always prompt targeted bus  21, 22. Breast density was not available in the database. Finally, our database records the results of only the physical examination that was part of the work-up that led to the diagnosis of cancer, without taking into account earlier examinations and without differentiating between a woman who presented because she herself found a mass or because the physician found a mass during a routine checkup.
CONCLUSIONS A significant number of the records for the breast cancer patients in our institution's database showed that the tumours were not detected using mammography and would have been missed if a cbe had not been performed. Performed by a trained physician, cbe is important for detecting breast cancers. Clinical breast examination is a very low-cost test that could improve the detection of breast cancer. For patients with breast symptoms, a cbe has to be performed. Furthermore, cbe should be a part of routine periodic examinations, especially for women less than 50 and more than 69 years of age, for moderate-and high-risk women, and for women who have had a breast cancer. When a cbe is positive, bus is mandatory, regardless of the mammography result. We are worried that many guidelines and task forces are removing cbe from their recommendations about routine examinations without distinction for highrisk patients, as already discussed.
The virtual mazes. The virtual mazes were created using Blender 2. 49 and Python 2. 6. 2. The location and orientation of the participants' avatar was tracked and recorded at 20 Hz. The avatar representing the participants was not visible, and they had first-person view of the mazes. That is, the visual input was similar to what they would see if they actually navigated through a maze in the real world. Navigation was accomplished using the arrow keys on a standard laptop keyboard, and the auditory cues were delivered via standard headphones. The participants heard a collision sound whenever their avatar came in contact with a virtual wall. Distances within the environment were set so that each 'virtual meter' corresponds to a realworld meter. Thus, the auditory output from the Virtual-EyeCane at one 'virtual meter' is the same as the output from the real-world EyeCane at a distance of one meter.
Statistical analysis A Cross-Nested Mix Model GLM analysis was performed using IBM SPSS Statistics (Version 23. 0. Armonk, NY: IBM Corp). The fixed-effect factors that were used in the model were the age, the feedback modality and the room rotation, with two levels for each factor. The two-way and three-way interactions among these factors were tested. The random-effect factors were the individual participants, and within the individual participants, the maze types and the repetitions within each maze. The REML method was employed for the analysis. In a case where the random effects were found not to contribute to the model, they were removed, and the model was re-fitted. To comply with the basic assumptions for the analysis, the appropriate transformation was performed for each of the performance metrics.
Path drawing The paths drawn by participants following each trial were analyzed. No statistical analysis of the drawing data was performed. The paths drawn were classified as "correct" if the maze drawn was identical to the actual maze, including cases where the participants drew the correct maze while omitting a "dead end" corridor (e. g. , in the example shown in Fig  9  the last two drawings, representing trials 4 and 5, would be classified as "correct"). Classification of the mazes as "incorrect" included cases where the maze drawn was a mirror image of the correct maze (e. g. , Fig  9 , trials 1-3), and cases where the participants rotated a dead-end corridor (not leading to the exit) by 90°with respect to its actual direction. We termed this phenomenon "false corridor" drawing (see  Fig 10).
Acknowledgments The authors wish to thank  Janna Kaplan  for her help with the experiment's coordination, recruitment & running;  Joel Ventura ,  Avijit Bakshi ,  Lee Picard  and  Lisa Khlestova  for their help with running the experiment;  Yoav Raanan  for his help with analysis of the navigation data;  Tamir Duvdevani ,  Yedidya Silverman  and  Yael Baron  for their help with analysis of the drawing data; The Brandeis-Leir and the  Brandeis-Bronfman  foundations for providing funding for this experiment. The research was partially supported by the  Helmsley Charitable Trust through the Agricultural, Biological and Cognitive Robotics Center of the Ben-Gurion University of the Negev. The support of the  Promobilia Foundation  is gratefully acknowledged.
S2 ). When Cdc25A wild type and Cdc25A-S283A were cotransfected, no differences could be observed between wild-type CDC25A and its nonphosphorylatable S283A mutant form. The distribution of transiently expressed wild-type and S283A mutant forms of cdc25A was also studied by immunofluorescence in Hela cells in which Cdc25A is highly predominantly nuclear. High content analysis of the transfected cells revealed only a mild increase of nuclear accumulation of the mutant Cdc25A relative to its wild-type counterpart (i. e. , 92,1 % vs 87,0%, Fig. S3 ). Finally, no differences in intracellular localization could be evidenced in H1299 cells inducibly expressing HA-tagged wild type or mutant Cdc25A (see below) and synchronized in interphase or during mitosis (data not shown). Altogether these studies indicated that phosphorylation of Ser283 has no major impact on Cdc25A nucleocytoplasmic shuttling.
NanoLC-MS/MS analysis and database searches After SDS-PAGE separation of the immunoprecipitated FLAGtagged Cdc25A, the Coomassie blue-stained corresponding band was in-gel digested with trypsin and analyzed by online nanoLC using an Ultimate 3000 System (Dionex, Amsterdam, The Netherlands) coupled to an LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) for data-dependent HCD fragmentation experiments.
Acknowledgments We are very grateful to  Drs Christian Berens  and  Christina Danke  for providing the pWHE644 tricistronic transregulator expression plasmid. We thank  Sander van den Heuvel ,  Jonathon Pines  and  Robert Weinberg  for the CDK and Cyclin expression plasmids. We are grateful to  Manon Farc  e and  Laetitia Ligat  for assistance with flow cytometry and microscopy, respectively. We thank  Charlotte Cavanihac  and  Julie Poulain  for technical assistance.
Funding This work was supported by the  Institut National de la Sant e et de la Recherche M edicale (INSERM) , the  Centre National de la Recherche Scientifique (CNRS) , the  University Paul Sabatier Toulouse III , the  Ligue Nationale Contre le Cancer , the  Fondation ARC pour la Recherche sur le Cancer  and the  Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN. It was also supported in part by the  R egion Midi-Pyr en ees ,  Toulouse M etropole , and  European funds FEDER  ( Fonds Europ eens de D eveloppement R egional ) for mass spectrometry.
Average farmers' yields of soybean and maize (as the main and second crop) in the Goiás state for the period 1977-2013 were retrieved from the database of the Brazilian National Food Supply Agency (CONAB) (www. conab. gov. br). We assumed an average and constant harvest index of 0. 45 for maize  47  and 0. 50 for soybean  48. A conservative value for the root:shoot ratios -corresponding to the 0-40 cm layer-of maize and soybean was assumed at 0. 35  49. Carbon inputs were then calculated by multiplying the residue biomass values by 43%.
Acknowledgements We wish to thank the farmers from  Rio Verde  and Montividiu for their collaboration. This work was supported by the  French Agency for Development (AFD) , the  French Ministry of Foreign Affairs (MAEE)  and the  French Fund for Global Environment (FFEM)  through the  Rime-Pampa  project n° CZZ 3076. We thank  Juaci Vitoria Malaquias  for helping with the statistical analyses.
Data acquisition The temperature of the system was recorded using a National Instruments, 16-channel DAOPad-6015 A/D convertor and VI-logger data acquisition system, at a sampling rate of 0. 2 Hz. The pump pressure and volume signals were directly obtained in 16 bit digital form from the ISCO 65D Pumps, at a sampling rate of 0. 2 Hz using ISCO 65D Panel software.
Leakage rate calibration Both the gas and water systems were tested for leaks before the experiments, at experimental conditions and with no sample present. The tests took ~1 day (versus ~30 days for the CH 4 runs). The pumps were operated in constant pressure mode and changes in both gas and water volume were recorded versus time. The CH 4 /He volume decreased linearly (R 2 N0. 98) with time when maintaining a constant gas pressure of 10 MPa. The corresponding data yielded a leakage rate for CH 4 of ~12. 3 μl/h and for He of ~52. 6 μl/h. No measureable leakage could be detected using the H 2 O pump at a pressure of 11 MPa.
VI) In addition to the above, two more CH 4 expulsion runs were performed in Exp2 only. These runs were executed directly after the CH 4 expulsion run (i. e. Fig. 6 , stage V), to examine the reversibility of the CH 4 sorption/desorption process. 3. 1. 6. Data processing 3. 1. 6. 1. Initial CH 4 uptake vs. associated swelling strain. The introduction of CH 4 into the sample at 10 MPa at the initial confining pressure of 11 MPa, led to an expansion of the sample measured by the ISCO H 2 O pump. Now, the total amount of CH 4 entering the sample at this point consists of two components: an amount entering the free pore volume of the sample, and the amount taken up by diffusion plus adsorption in the coal matrix. The associated expansion is therefore expected to consist of a rapid poro-elastic expansion plus a time-dependent sorption-induced swelling component.
The amount of CH 4 expelled from the sample was measured by increasing the hydrostatic stress or confining pressure in the range 11-43 MPa, after initial equilibration of the sample with CH 4 at a fixed methane pressure of 10 MPa and at a fixed temperature of 40°C. The true amount of CH 4 desorbed from the sample was obtained by subtracting the poro-elastic gas expulsion determined by means of helium (a non-sorbing gas) control experiments. The results show that about 0. 05 mol/kg coal of CH 4 desorbed from the solid sample when the applied confining pressure increased from 11 MPa to 43 MPa, which corresponds to ~6. 2% of the initial uptake of 0. 808 mol/kg coal. 3. The present model describes our experimental data well. The results indicate that our model successfully captures the physical process of gas adsorption by coal that supports a stress state applied in excess of the pressure of the sorbing gas species.
A nonsense mutation in the ERCC6L2 gene To firmly exclude an FA molecular defect, we performed WES and initially filtered the results on the 18 known FA-causing genes  (Wang and Smogorzewska, 2015)  and did not identify variants with frequencies <1% in the public and in-house databases for these genes. The patient being born to consanguineous parents, we also undertook whole genome homozygosity mapping (WGHM) from DNA in the family, which highlighted 14 compatible chromosomal regions (Fig. 3 A ). These regions were subsequently used to filter nonsynonymous variants (NSVs) identified through WES performed on the patient's DNA after an initial filtering on homozygous variants with frequencies <1% in single nucleotide polymorphism and in-house databases (Fig. 3 B ). A nonsense NSV in the ERCC6L2 gene (Chr9 [GRCh37]:g.