dataesr/scientific-paragraphs-categorization huggingface dataset:
Therefore, we adjusted the threshold for R significance accordingly, to R > = 0. 67 for 9 samples, R > = 0. 71 for 8 samples and R > = 0. 76 for 7 samples. Due to the small sample size of our cohort, we could not apply a correction for multiple testing, such as Bonferroni's or Benjamini-Hochberg's. Candidate driver genes were further selected when i) being completely included in the genomic alteration (i. e. fully amplified or deleted) and ii) not being included in frequent CNVs in healthy individuals, as defined by the Database of Genomic Variants (DGV, http://dgv. tcag. ca/dgv/app/home, as of 31/05/ 2013). Recurrently broken genes were identified by the existence, in at least 2 tumors, of one or several closely mapping breakpoints defined by amplifications/deletions upstream and downstream, within the relevant gene.
Expressional correlation, protein interactor sharing and transcriptomic neighbors sharing between candidate drivers Hierarchical clustering of the expression levels of broken, amplified or deleted candidate drivers and FOXL2 was performed with the MeV software, using complete linkage and the Pearson correlation coefficient as a measure of similarity. For each candidate driver and FOXL2, two sets of transcriptomic neighbors were defined by a statistically significant correlation of expression in all tumors (R > = 0. 63 or R < = -0. 63). These gene sets were analyzed using the Enrichr tool (http://amp. pharm. mssm. edu/Enrichr [10] ). The extensive sharing of transcriptomic neighbors between the candidate drivers or FOXL2 was displayed using Cytoscape 3. 0. 1 software, keeping only the strongly correlated transcriptional neighbors (R > = 0,90) for clarity.
This correlation filter was essential because a local genomic alteration does not necessarily imply a transcriptomic change. Thus, a meaningful driver, mapping to an amplified/deleted region, should display a reasonable correlation between copy number and mRNA expression. We set the threshold for statistical significance of Pearson's correlation coefficient R to 0. 63, which is the standard cut-off for ten samples. Genomic regions involved in large-scale imbalances such as trisomies or monosomies were analyzed separately by removing data from trisomic or monosomic tumors. For these regions, the threshold for R was adjusted to 0. 67 or 0. 71 in cases when 1 or 2 samples were removed. After excluding genes located within CNVs, we obtained a list of 48 candidates. After manual verification, we retained 13 amplified and 7 deleted genes fully located within the imbalances.
The breakpoint must be within the gene in all the tumors, and not included in frequent CNVs detected in healthy control samples. Candidate driver genes were identified as presenting an expression significantly correlated (correlation coefficient >= 0. 63) with the CGH status, in at least 2 tumors, without being included in CNVs detected in healthy control samples. CNVs were verified in DGV database, that contains the genomic alterations involving segments of DNA that are larger than >50bp identified in healthy control samples (DGV update: 31/05/2013). Tab b -Details of the genomic alterations leading to the identification of broken genes in ovarian GCTs. For each breakpoint are indicated: the tumors displaying an alteration, the genomic coordinates of the alterations, the name of the broken gene, bibliographic data centered on cancer-related processes, and the screenshot of the display in MeV software.
Acknowledgements We gratefully acknowledge financial support from the  Centre National de la Recherche Scientifique ,  La Ligue Nationale contre le Cancer (Comité de Paris) , l' Université Paris Diderot-Paris7, l'Institut Universitaire de France , the  Academy of Finland , and  Helsinki University Central Hospital Research Funds. We thank  A-E. Lehesjoki  for providing the Finnish control DNA pool, and  M. Heikinheimo  for support on the GCT research program in Helsinki.
Tailoring treatment by patient strata based on the risk of disease progression and treatment toxicity might improve outcomes of patients with posttransplant lymphoproliferative disorder (PTLD). We analysed the cohort of 70 patients treated in the international, multicenter phase II PTLD-1 trial (NCT01458548) to identify such factors. Of the previously published scoring systems in PTLD, the international prognostic index (IPI), the PTLD prognostic index and the Ghobrial score were predictive for overall survival. None of the scoring systems had a considerable effect on the risk for disease progression. Age and ECOG performance status were the baseline variables with the highest prognostic impact in the different scoring systems. Baseline variables not included in the scoring systems that had an impact on overall survival and disease progression were the type of transplant and the response to rituximab at interim staging.
Internal model validation was performed using bootstrapping. The procedure allows to report mean calibration errors together with corresponding 0. 9 quantiles  (16, 17). The level of significance was set at p < 0. 05. Statistical tests were performed using IBM SPSS 21 and SAS (version 9. 2, SAS Institute GmbH, Heidelberg, Germany). Model validation was performed with R (18) using the R-package 'rms'  (19). Response to treatment and disease progression were classified according to the World Health Organization criteria. Overall response was complete or partial remission. Time to progression was time from start of treatment to disease progression after interim staging with censoring of patients who died before restaging. Overall survival was time from start of treatment to death from any cause.
Sequences analysis Sequence alignments were performed on SeaView software by inputting our sequences with the sequences obtained by Ghai et al. [18]  (accession numbers: KF250585 -KF250660) and by Krief et al. [17]  (KT592234, KT592235). In addition, we included three Oesophagostomum stephanostomum reference sequences (AF136576, AB821022, AB821031), one O. bifurcum sequence (AF136575) and five outgroups (HQ844232, Y11736, Y11735, Y10790, AJ006149). Phylogenetic trees were established using the maximum likelihood method in MEGA  [51]  and the Hasegawa-Kishino-Yano substitution model with five discrete gamma categories  [52]. To assess the phylogenetic robustness of the tree, 1000 bootstrap replicates were performed.
Acknowledgments Data were collected in the context of a long-term research agreement signed between the  Muséum National d'Histoire Naturelle , the  Uganda Wildlife Authority and Makerere University  (Memorandum of Understanding SJ  445-12 ). We are grateful to the  Uganda Wildlife Authority  and the  Uganda National Council for Science and Technology for permission  to conduct this research at  Sebitoli. We thank the  Projet pour la Conservation des Grands Singes  and the  Sebitoli Chimpanzee Project , particularly its co-director  Jean-Michel Krief  and its field assistants,  Japan Musinguzi ,  Ronald Musinguzi ,  Emmanuel Balinda ,  Christopher Aliganyira ,  Deogratius Kyomuhangi ,  Joseph Alinaitwe  and  Denis Sebugwaho. We also thank  René Chermette  and  Bruno Polack  for permission to access the  EnvA Laboratory of Parasitology ,  Anne-Charlotte Grüner  and  Christian Bories  for laboratory training and  Sarah Bortolamiol  for the map realization.
The Demerara plateau, located offshore French Guiana and Suriname, is part of a passive transform continental margin particularly prone to develop slope instabilities, probably in relation to the presence of a free distal border along its steep continental slope. Slope failure occurred at different periods (Cretaceous to Neogene) and shows an overall retrogressive evolution through time. Upslope these failure headscarp, an enigmatic regional MioPliocene unconformity has been discovered through the interpretation of new academic and industrial datasets. The aim of this work is to describe and understand the origin of this surface. Our analysis shows that this unconformity is made of a series of valleys that cross-cut sedimentary strata. Each one of these valleys has a short lateral extent and is closed along two perpendicular directions, which suggests that it could correspond to a highly meandering system, or to some sub-circular depressions.
In 2003, a nearly complete mapping of the French part of the plateau was performed as part of the program for the extension of the French continental shelf EXTRAPLAC. The analysis of this dataset revealed that the Demerara plateau was a place of huge slope failures trending parallel to its transform edge  (Loncke et al. , 2009). These slope failures initiated during cretaceous times, and regular reactivations or new events were recorded until present day  (Pattier et al. , 2013). Numerous elongated depressions were described on the seabed on top of remobilized deposits. There were interpreted as pockmarks elongated by deep-sea bottom currents  (Loncke et al. , 2009; Pattier et al. , 2013). In order to understand the factors that control slide onset (Fluids ascents? Structure? Currents?), another geophysical cruise was carried out in May 2013  (Loncke et al.
, accepted with revisions). This cruise revealed that the main failure headscarp already defined along the French Demerara plateau was continuing off Surinam, reaching 350 km long. It showed also that deep bottom currents were responsible for contourite deposition and that the elongated pockmarks were no more active  (Loncke et al. , accepted with revisions). Finally, an enigmatic regional unconformity already observed on industrial data was recognized on this new high-resolution data set. This regional unconformity affects Miocene to Pliocene sediments located upslope of the main failure headscarp. The meaning of this unconformity seems particularly important to decipher: is it related to massive slope instabilities pre-dating the last failure? Can it be related to the onset of strong deep bottom currents? Or to other phenomenon? In order to answer to these questions that may have important academic and petroleum issues, we carried out a stratigraphic analysis of available academic and industrial seismic data from the area.
Dataset and methodology The FG02 seismic survey was acquired by FUGRO using the R/V "Professor Polshkov". It surveyed the French Guiana continental shelf, the eastern Demerara plateau and the East Guiana continental slope. A total of 7715 km of multichannel seismic data were collected (Figure  3 ) for industrial purposes. The FG02 data were processed by Robertson Research International in Perth, Australia. The shallower part of this dataset was made available by Total S. A. for this study. The GUYAPLAC cruise was carried out onboard the R/V -L'Atalante‖ in 2003, as a part of the French EXTRAPLAC Program (Ifremer-IFP-SHOM-IPEV). It surveyed the French Guiana margin and the adjacent Demerara Abyssal Plain. The dataset comprises: (1) SIMRAD-EM12 Dual multibeam bathymetry and backscatter imagery, (2) 3.
5 kHz echograms, and (3) 6-channel seismic reflection profiles (Figure  3 ). The IGUANES cruise was carried out onboard the R/V "L'Atalante" in 2013 as part of scientific research led by the University of Perpignan. It surveyed the Demerara plateau. The dataset (Figure  3 ) comprises: (1) SIMRAD-EM122 Dual multibeam bathymetry and backscatter imagery, (2) SBP Chirp (1800-2500 Hz), (3) high-resolution 72-channel seismic reflection profiles (noted Iguanes HR on Figure  3 ), acquired at a speed of 5 knots, and (4) 24-channel seismic reflection profiles (noted Iguanes RS survey on Figure  3 ) acquired at 10 knots. The stratigraphy used to calibrate the seismic data is provided by the correlation with the G2 industrial well site published by  Gouyet (1988)  (Figure  4 , modified from  Basile et al.
This unit is made mainly of clayey chalks and oozes. It was affected by polygonal faulting  (Pattier et al. , 2013) ; -R1 marks the base of Unit A. This unit shows high-amplitude continuous reflectors and corresponds to the youngest shale sediments (late Miocene to Quaternary). This unit was deposited coevally with the onset of the Amazon and Maroni. Reflector A6 corresponds to the base of the middle Pliocene; the base of the Pliocene is situated between R1 and A7. Reflectors A6 to A1 could not be dated precisely, but are useful for conducting a geometrical analysis of Neogene to Quaternary geological features. The studied Unconformity Uc affects Plio-Miocene series. Most of the seismic interpretation was carried out using Total's in-house Sismage software. In order to integrate IGUANES newly acquired data, we later conducted an analysis of the seismic date using Kingdom Suite at University of Perpignan.
The hydrate pockmark hypothesis Finally, several observations can lead to a pockmark interpretation for this depressions field. The depressions are similar to km-scale conical collapse structures recently described in literature as gas hydrate pockmarks that developed off Australia  (Imbert and Ho, 2012). These authors described a field of circular fossil depressions from a 3D seismic dataset. Correlation of seismic reflectors outside and within the depressions showed that the depressions were the locus of large-volume material loss (collapsed or vanishing reflectors within the depressions). They compared these structures to active hydrate pockmarks  (Sultan et al. , 2010; Riboulot, 2011)  and proposed that the loss of material within depressions was related to massive hydrate dissolution.
Considering a compaction rate of 10 to 25 % for fine sediment and neglecting vertical movements, we can consider that the base of the hydrates was to be found an average 290 m under A5 or A6 (beginning of hydrate pockmark emplacement) and corresponded to the reflector R1, where the first depressions root. It is therefore possible that R1 reflection was in the stability zone corresponding to a "paleo-BSR" during MTD 03 initiation and the first onset of depressions. At present, no BSR could be observed on the geophysical dataset. This could be a result of a massive Mio-Pliocene degasing phase that allowed the development of wide hydrate pockmarks and the evacuation of most of the gas initially caught within hydrates. Finally if the hydrate pockmark hypothesis is correct, several observations are not totally resolved: (1) why have depressions migrated in a centripetal way through time? (2) How to explain the geometry of type C depressions and the relationships that seem to exist in between slides (MTD 03) and depression emplacement? (3) Some depressions of the Demerara plateau show a syn-sedimentary collapse suggesting progressive hydrate dissociation whereas the hydrate pockmarks of the Australian example suggest an abrupt post depositional dissociation.
Acknowledgments The authors would like to thank the  French EXTRAPLAC program  for providing access to the GUYAPLAC dataset and Ifremer for financing the Ph. D. work of  France Pattier. The  French Research Program "Actions Marges " is acknowledged for supporting this project. We thank  Total S. A. for granting us access to the Well G2 data and industrial data. We thank  Fugro  for granting us access to the FG02 survey. We thank the  IGUANES team  for an unforgettable cruise and access to high-resolution data. Finally, we deeply thank  Marc De Batist ,  Michele Rebesco  and an anonymous reviewer that greatly helped us to strengthen this paper.
(b). These inductances (denoted by ) must be considered parasitic elements, but their presence is mandatory for an accurate description of the shunt branch through a lumped-element equivalent-circuit model over the regulated UWB band. To demonstrate the validity of the proposed model, we have extracted the parameters of the circuit of Fig. 2(b ) for the topology depicted in Fig. 2 (a). To this end, we have inferred the -parameters of the structure for the differential and common modes through full-wave electromagnetic simulation, using the Agilent Momentum commercial software (see Fig. 3 ). The considered substrate is Rogers RO3010 with dielectric constant and thickness m. From the differential mode -parameters, we have obtained the reactance of the series and shunt branch of the equivalent T-circuit model according to standard formulas  [17].
This work was supported by  Spain-MICIIN  under Contract  TEC2010-17512 , Contract  TEC2013-40600-R , Contract  TEC2013-41913-P , and Contract  CSD2008-00066 , and by the  Catalan Government  under Project  2014SGR-157. The work of P. Vélez was supported by  Spain-MINECO  under Grant  AP2010-0467.
The two datasets were collected at 100K by using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF, Grenoble) on a Pilatus 6M S/ N 60-104 detector at beamline ID 29, λ = 0. 977Å. Diffraction images were processed with iMOSFLM  [52]  and internally scaled with SCALA (CCP4i  [53] ), achieving resolutions of 2. 9Å and 2. 7Å for the CVB3 3D pol -GPC-N114 and CVB3 3D pol -GPC-N143 crystals, respectively. Data collection statistics are given in Table  2. Coordinates have been deposited at the PDB with accession codes 4Y2A and 4Y34 for the complexes CVB3 3D pol -GPC-N114 and CVB3 3D pol -GPC-N143, respectively. Crystals of EMCV 3D pol wt and M300V and I304V, mutants were obtained as previously described  [29]. The data sets were collected at the ALBA-CELLS synchrotron light facility (Barcelona) on a Pilatus 6M Dectris detector at beamline XALOC λ = 0.
977Å. Diffraction images were processed with iMOSFLM and SCALA, achieving resolutions of 2. 2Å and 3. 2Å for the M300V and I304V respectively (Table  2 ). Coordinates have been deposited at the PDB with accession codes 4Y2C and 4Y3C for the structures of EMCV 3D pol -M300V and EMCV 3D pol -I304V, respectively.
Structure determination and refinement The initial electron density maps of the CVB3 3D pol -GPC-N114 and CVB3 3D pol -GPC-N143 complexes were obtained after rigid-body fitting of the coordinates of the 3D pol apoenzymes (PDB id. 3DDK) to the new unit cells (Table  2 ), using the program Refmac5  [54, 55]. In both structures, the weighted 2|Fo|-|Fc| and |Fo|-|Fc| difference map showed the presence of extra densities that permitted the initial positioning of the inhibitor molecules. Inhibitor structure files were generated using "Online SMILES Translator and Structure File Generator" (http:// cactus. nci. nih. gov/translate/) and its respective CIF dictionaries were created by Grade  [56]. Several cycles of automatic refinement, performed with Refmac5, were alternated with manual model rebuilding using Coot  [57].
The refinement statistics are summarized in Table  2. The first electron density maps for both EMCV 3D pol mutants were obtained after rigidbody fitting of the EMCV 3D pol wt coordinates to the new unit cells. The PDB id 4NYZ, of space group I4 1 22, was used as a model for the M300V structure and coordinates 4NZ0, of space group C2, were used as a model for the I304V mutant. Noncrystallographic symmetry (ncs) restraints were initially applied to the six independent molecules present in the asymmetric unit of the C2 crystals using Refmac5. However, the ncs restrained-refinement result was unstable because the presence of different conformations in many polymerase regions, especially in the surface-exposed loops, was affected by crystal packing interactions. Therefore, the variable regions were manually rebuilt using Coot, and the final cycles of automatic refinement with Refmac 5, were performed in absence of ncs restraints.
This work was supported by research grants from the  SILVER Large Scale Collaborative Project  (grant agreement number  260644 ) project of the European Union 7th Framework, the  European Virus Archive (EVA)  project (European  FP7   Capacities  Project number  153 228292 ), the  "Convenant K. U. Leuven-Radboud University ESRF  and  ALBA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Study population The HELENA-CSS aimed to describe the lifestyle and nutritional status of European adolescents. Data collection took place between October 2006 and December 2007 in the following cities: Athens and Heraklion in Greece, Dortmund in Germany, Ghent in Belgium, Lille in France, Pécs in Hungary, Rome in Italy, Stockholm in Sweden, Vienna in Austria, and Zaragoza in Spain. Further information about the study design has been published elsewhere  [10, 11]. Participants were recruited at schools. To ensure that the heterogeneity of social background of the population would be represented, schools were randomly selected after stratification by school zone or district. In cases where the selected schools refused to participate, a second list of substitute schools had already been drawn up.
Up to three classes from two grades were selected per school. A class was considered eligible if the participation rate was at least 70%. The general inclusion criteria for HELENA were age range of 12. 5-17. 5 years, not participating simultaneously in another clinical trial, and free of any acute infection lasting less than 1 week before inclusion  [10]. From a sample of 3528 adolescents who met the HELENA general inclusion criteria, one third of the school classes were randomly selected in each centre for blood collection, resulting in a total of 1089 adolescents. For the purposes of the present study, adolescents with valid data for sedentary behaviour, accelerometry, cardiorespiratory fitness, total cholesterol (TC), high density lipoprotein cholesterol (HDL-c), insulin, glucose, systolic blood pressure and triceps, biceps, subscapular and supra-iliac skinfolds were finally included in the analysis (n = 769,.
Physical examination Waist circumference, height, weight and four skinfold thicknesses (on the left side from biceps, triceps, subscapular, supra-iliac) were measured following a standardized protocol  [15]. The definition of obesity (including overweight) was based on international BMI cutoffs proposed by Cole et al. [15]  from several different countries. Systolic and diastolic blood pressure measurements by the arm blood pressure oscillometric monitor device OMRON M6 (HEM 70001) which has been approved by the British Hypertension Society  [13]. Measurements were taken twice (10 min apart) and the lowest value was retained. These data collection procedures have been described previously  [14].
The  HELENA Study  takes place with the financial support of the  European Community Sixth RTD Framework Programme  (contract  FOOD-CT-2005-007034 ). The writing group takes sole responsibility for the content of this article. This study was also supported by granta from the  Spanish Ministry of Health : Maternal,  Child Health  and  Development Network  (number  RD08/ 0072 ), the  Spanish Ministry of Education  ( EX-2008-0641 ) and the  Swedish Heart-Lung Foundation  ( 20090635 ). in girls). Augusto César F. de Moraes  was given a PhD Student scholarship from the  São Paulo Research Foundation -FAPESP  (proc. 2011/11137-1 and  2011/ 20662-2 ) and a  Post-Doctoral scholarship  from the  Brazilian Government  from the  National Counsel of Technological and Scientific Development -CNPq  (proc.
Before any intervention (medical history, screening tests) all volunteers gave written informed consent and answered correctly a questionnaire aimed to test their understanding of the study. They were requested to give three close contact phone numbers and social security numbers, to be able to search for them in case of missing follow-up visits. The study received approval by the ethics committees of Hospital Clínic and Hospital de la Santa Creu i Sant Pau together with the administrative clearance provided by the Health Department of Generalitat de Catalunya. The study followed the principles of the Declaration of Helsinki in its 6th revision (2008) as well as International Conference on Harmonization-Good Clinical Practice (ICH-GCP) guidelines. The study is registered with ClinicalTrials.