dataesr/scientific-paragraphs-categorization huggingface dataset:
A multidimensional pre-inclusion geriatric assessment was performed at baseline. Data concerning the patient's medical charts, nutrition, functionality and an extensive psychocognitive assessment were collected, including comorbities, comedications, body mass index (BMI), serum albumin levels, and functional scores for Activities of Daily Living (ADL), Instrumental ADL (IADL), Geriatric Depression Scale (GDS), Hospital Anxiety and Depression Scale (HADS), and the Mini-Mental Scale (MMS). Patient outcomes of treatment completion rate (defined as receiving six courses of chemotherapy without premature discontinuation for death, treatment toxicity or tumor progression), survival, serious adverse events, unplanned hospital admissions, and grade ≥3 toxicities were recorded. The GVS was calculated for each patient as described previously  [11].
This score is the addition of the following geriatric vulnerability parameters: ADL score <6, IADL score <25, HADS score >14, albuminemia <35 g/L, and lymphopenia <1 x 10 (TRF) chemiluminescence signals were captured using a LAS-3000 Imager (FujiFilm Life Science, France) and images were processed using ImageJ software (http://rsb. info. nih. gov/ij/). The optical densities (OD) versus mean TRF length were calculated according to the formula (Σ ODi/ Σ(ODi/MWi), where ODi is the chemiluminescent signal and MWi is the length of the TRF at position i (  [13]  and Supplementary figure  1 ). Measurements were performed on each sample at least twice in different gels and the mean was used for statistical analyses. Pearson's correlation coefficient for duplicates was 0•74, with an average coefficient of variation for pair sets of 7•3%.
Survival curves were estimated using the Kaplan-Meier method and OS models were adjusted for FIGO stage (IV versus III). Odd ratios (ORs) and hazard ratios (HRs), 95% confidence intervals (CIs), and p values (P) were calculated. Analyses were performed using R statistical package (R Foundation for Statistical Computing, Austria) and Splus, version 6•2 (Insightful Corp. , WA, USA).
ACKNOWLEDGEMENTS The authors would like to acknowledge  Douglas Micheau-Bonnier ,  Nicolas Gane , and  Benedicte Votan  from the GINECO study office and the  Delegation a la Recherche Clinique et a l'Innovation of the Hospices Civils de Lyon. We also thank the following investigators who participated in the trial:  Pr. H. Cure  ( Institut Jean Godinot, Reims ),  Dr J. Salvat  (Hopitaux.
Funding This work was supported by research grants from the  French Ministry of Health (Projet Hospitalier de Recherche Clinique)  and  La Fondation de France  and promoted by the  Hospices Civils de Lyon. EG Lab was supported by  "La Ligue Nationale Contre le Cancer" (Équipe labellisée) , the " Institut National du Cancer" (EG Lab: INCa, TELOFUN program ) and the  "Agence Nationale de la Recherche " ( ANR, TELOREP program ). CF held fellowships from "la  Région Rhônes-Alpes", the "Association de Recherche contre le Cancer " and  Astra-Zeneca.
Multiparameter flow cytometry and TCRγ rearrangement study in circulating CD3 -CD4 + T cells All CD3 -CD4 + L-HES patients followed in the French Eosinophil Network had been diagnosed on the basis of circulating CD3 -CD4 + T-cell aberrant subset detected by flow cytometry, as previously described. 13 For this work, 15 were newly collected (n=13), or re-analyzed (n=2) with Kaluza ® 1. 2 software (Beckman Coulter). Fluorochrome-coupled antibodies (CD45, CD2, CD3, CD4, CD5, CD7, CD8, CD10, CXCL13, and PD1) were purchased from Beckman Coulter ®. A CD3 -CD4 + subset was considered to be positive or negative for a surface marker if more than 95% or less than 5% of the cells expressed or not the marker, respectively. When only a part of the subset expressed the surface marker, the percentages of positive cells were noted.
Mean fluorescence intensities of pan T-cell markers (CD2, CD5, CD7) on CD3 -CD4 + T cells were expressed as "low" or "high" in comparison to CD3 + CD4 + T cells. Study of CD10 expression, which was not done routinely before, was performed on the 14 newly obtained samples. TCRγ rearrangement analysis was also performed in peripheral blood, as previously described. 27 Analysis was carried out with the 3130 Genetic Analyzer ® and the GeneMapper 4. 1 ® software from Applied Biosystems ®.
Many single or overlapping mutations have been recently reported in AITL. TET2, DNMT3A and IDH2 mutations were searched by NGS using the Ion Torrent Proton instrument in samples of our both AITL patients: only one TET2 A1876E mutation was found in Patient P16's skin lesions, in 9% of extracted DNA. There was no detected mutation in Patient P4's skin, bone marrow and lymph node biopsies performed at AITL diagnosis (data not shown). Larger studies are needed to assess the significance of such mutations in CD3 -CD4 + L-HES-related AITL. In conclusion, our study shows that CD3 -CD4 + L-HES can be considered as an indolent T-cell lymphoproliferative disorder with blood, nodal and extra-nodal involvement. CD3 -CD4 + T cells can persist over years without transformation in lymphoma, as demonstrated by repeated biopsies showing persistent clonal T-cell infiltrates.
Acknowledgments We would like to acknowledge all of the persons involved in the  French Eosinophil Network  (alphabetical order):  Abibou Ba ,  Maïté Balden ,  Yamina Benallal ,  Pr Olivier Blétry ,  Pr Jean-Francois Cordier ,  Pr Vincent Cottin ,  Marie Delbeke ,  Virginie Dutoit-Lefèvre ,  Sylvie Fievet ,  Laurence Fofana ,  Solène Gatault ,  Aline Renneville , and  Amandine Verhaeghe. We also want to acknowledge  Dr Clio Baillet  for 18-FDG-PET pictures, and pathologists who allowed us to recover biopsies for centralized review and analysis complement:  Dr Anne Moreau ,  Dr Sif Bendjaballah ,  Dr Marthe Delage-Corre ,  Dr Anne Croué ,  Dr Thierry Lazure ,  Dr Jérôme Chetritt ,  Dr Josette Brière. Mrs Polly Gobin , a medical writer, provided editorial assistance to the authors during preparation of this manuscript.
This hypothesis is currently being investigated in an ongoing study assessing mean arterial level optimization through Doppler-based resistive index (RI) in patients with septic shock (NCT01473498). Ultrasonography (US) is performed routinely to assess renal and collecting system morphology  [4]. B-mode US provides valuable information regarding anatomic features and pathological findings including search for signs suggestive of chronic renal disease, hydronephrosis, calcifications, cysts or solid masses. Renal Doppler US has been used to assess vasculature of either native or transplanted kidneys  [5]. Although renal Doppler is valuable for assessing large arterial or venous abnormalities, this technique has been advocated in evaluating changes in intra-renal perfusion due to kidney diseases  [6, 7].
Acknowledgments AC acknowledges the financial support from  1D-RENOX project  ( Cellule Energie INSIS-CNRS ). J. M. V. -F. also acknowledges  MINECO  for support with a Ph. D. grant of the  FPI program. We thank  David Montero  and  L. Picas  for technical support. We also thank  P. Regreny ,  C. Botella ,  J. B. Goure  for technical assistance on the Nanolyon technological platform. We acknowledge  MICINN  ( MAT2008-01022 MAT2011-28874-c02-01  and  MAT2012-35324 ),  Consolider NANOSELECT  ( CSD2007-00041 ),  Generalitat de Catalunya  ( 2009 SGR 770  and Xarmae), and  EU  (HIPERCHEM,  NMP4-CT2005-516858 ) projects. The HAADF-STEM microscopy work was conducted at the  Center for Nanophase Materials Sciences , which is a  DOE Office of Science User Facility. This research was supported by the  European Research Council  ( ERC StG-2DTHERMS ),  Ministerio de Economía y Competitividad of Spain  ( MAT2013-44673-R ) and  EU funding Project  " TIPS" Thermally Integrated Smart Photonics Systems  Ref: 644453 call  H2020-ICT-2014-1.
Acknowledgements The researchers of the University Carlos Ill of Madrid are indebted to  Ministerio de Ciencia e lnnovaci6n de Espana  (Project DPl /2011 24068 ) for the fi nancial support received which allowed conducting part of this work. The researchers are indebted to lATI Company for PEEK material supplied. The authors express their thanks to  Mr. Sergio Puerta ,  Mr. David Pedroche  and  Ms Penelope Miller  for their technical support.
Covariates at a 0. 10 level of significance in the univariate analysis will be included in the multivariate analysis. In addition, each component of the composite end point treatment response will be analysed separately. Efficacy analyses will be performed for the intentionto-treat (ITT) population. Given that patients will be hospitalised during antibiotic treatment and close follow-up is expected, this population will consist of all randomised participants. To account for dropouts between end-of-therapy and TOC visits, we will explore the various dropout patterns and their impact on response. Appropriate multiple imputation procedures will be employed to account for missing data for treatment response. When analysing survival analysis end points (time to death, time to negative blood culture, time to treatment failure), relevant patients will be censored at the time of withdrawal.
ETHICAL ISSUES The trial will be conducted according to the principles of the Declaration of Helsinki (2008) and current Spanish legislation (Real decreto 223/2004). The principal investigator or collaborator at each site will obtain written informed consent from all patients, or their legal representatives (LRs) if they lack capacity, before enrolment. Patients (or their LRs) are free to withdraw from the trial at any time and this will be explicitly stated on the patient's information sheets (see online supplementary appendix 2). The data collected for the study will be identified by a code and only the study doctor and collaborators will be able to link those data with patients and their clinical history. Consequently, the patient's identity will not be revealed to any other person, except in cases of medical emergency or if required to do so by law.
, 2002)  are especially well suited for this purpose because they can acquire surface reflectances at multiple view angles of the same ground position on one orbit. POLDER is best used at the global scale because of its $6 km nadir resolution and high angular resolution while MISR can be used at both global and regional scales with its 275 m resolution. In turn, Moderate Resolution Imaging Spectroradiometer (MODIS) at 500 m resolution currently provides the finest pseudo multi-angular data for the global land surface  (Schaaf et al. , 2002). In this study we compared the most recent CI products from the respective sensors (POLDER -  Pisek et al. , 2010a; MODIS -He et al. , 2012; MISR -Pisek et al. , 2013). The evaluation of temporal and spatial consistency between the products was assessed by using (a) selection of sites representing the global distribution of biomes, (b) a set of sites with vertical profiles of clumping, and (c) sites with available CI estimates covering a complete seasonal cycle.
Methodology The intercomparison procedure was defined to comply as much as possible with the best practices proposed by the CEOS WGCV LPV subgroup  (Garrigues et al. , 2008; Baret et al. , 2009). It corresponds to Stage 1 validation as defined by the CEOS (Nightingale   et al. , 2011; Weiss et al. , 2014). First we evaluated the consistency of the CI products over selected locations (Section 3. 1. ). Next, individual product accuracy was assessed using a small set (<30) of locations by comparison with reference in situ data (Section 3. 2). We concluded with an assessment of how well the products compare with the temporal changes in clumping over a subset sites with available in situ temporal profiles of CI (Section 3. 2. 2).
Comparing clumping products with in situ measurements The CI products were validated over an additional global validation dataset with measured vertical or temporal profiles of foliage clumping from  Pisek et al. (2013)  that was further expanded with additional sites to represent all the main biomes. Detailed site descriptions are provided in Table  3. The methodology to obtain in situ CI estimates has been previously described in detail in  Pisek et al. (2013). The field data should be optimally integrated with high resolution imagery to allow a real product validation  (Morisette et al. , 2006). Unfortunately, with only one exception of a limited extent high resolution map of clumping index (<1 km 2 ) by  Simic et al. (2010) , no such maps are currently available, allowing only a limited evaluation.
Acknowledgements Jan Pisek  was supported by the funding from the  FP7-Marie Curie Actions programme ,  Estonian Science Foundation  Grant nos. ERMOS32  and  PUT232. Financial support by the Transnational Access to Research Infrastructures activity in the 7th  Framework Programme  of the EC under the  ExpeER  project for conducting the research at Castelporziano and Hesse sites is gratefully acknowledged. The measurements at Wombat, Whroo and Warra in Australia were funded by the  Terrestrial Ecosystem Research Network (TERN) Australian Supersite Network , the  TERN OzFlux Network , and  Australian Research Council (ARC)  Grants  LE0882936  and  DP120101735. Data collection at the Honghe farm was supported by the  National Natural Science Foundation of China  ( 41171333 ). The first author would like to thank  Drs.
To exclude any cell passage effect, the following experiments were performed in MDCK-E1-Cre and MDCK-E1 cells at P0. HDV/HV MOI ratio. To establish optimal conditions to produce HDV (maximum productivity and lowest HV contamination), production assays under different MOI ratios (5 to 1, 5 to 0. 5, and 5 to 0. 1 IP) were performed. MOI ratio of 5 to 5 was initially tested, but critically compromised cell viability and production of either HDV or HV (data not shown). Similar HDV specific productivities of approximately 300 IP/cell were obtained using the different MOI ratios tested (Figure  4A ). Even with a MOI as low as 0. 1, HDV productivity was still maintained. When using MDCK-E1-Cre cells, HV contamination levels were similar in the three co-infections (2-3%) (Figure  4B ). To further understand how Cre recombinase impacts HV propagation in the different MOI ratios, the assays were also performed in MDCK-E1 cells (Figure  4A, B ).
Cells were then pelleted at 300 g during 10 min and resuspended in fresh medium. To evaluate the effect of culture passages, cells were maintained in duplicates, either with or without antibiotic pressure. For antibiotic pressure, 500 mg/mL of Geneticin (G418) (Invivogen, Toulouse, France) was added to culture medium for MDCK-E1 cells maintenance, while for MDCK-E1-Cre cells G418 plus 500 mg/mL of Zeocin (Invivogen) was used. Cells were frozen once adapted to Optipro medium (P0) and after 10 and 20 cell culture passages in CryoStor CS10 (Sigma-Aldrich, St. Louis, MO, USA) using a Mr. Frosty Freezing Container (Thermo-scientific, Rockford, IL, USA). Viral vectors. CAVGFP, JBD5 and HD CAVGFP are vectors derived from CAV-2 strain Toronto A 26/61, GenBank J04368. CAVGFP  13  and HD CAVGFP  16  are E1deleted (DE1) and HD vectors, respectively, and contain an eGFP expression cassette.
Acknowledgments We thank  Sandy Ibanes  and  Aurelie Gennetier  for the initial preparations of CAV-2 vectors. This work was supported by  Fundaça ˜o para a Ciencia e a Tecnologia (FCT) -Portugal , through the project  PTDC/EBB-BIO/118615/2010 , and  European Commission  through  FP7  project  BrainCAV  ( 222992 ). Paulo Fernandes acknowledges  FCT  for his Ph. D. grant ( SFRH/BD/70810/2010 ).
MATERIALS AND METHODS A systematic review of the literature from the data bases of PubMed and MEDLINE from January 1960 to March 2015 was performed. The search algorithm used the following strategy: ("tumour"[All Fields] OR "tumor"[All Fields] OR "submucosal tumor"[All Fields] OR "early gastric cancer" [All Fields] OR "GIST"[All Fields] OR "gastrointestinal stromal tumor"[All Fields] OR "neoplasms"[MeSH Terms] OR "neoplasms"[All Fields]). And [("laparoscopic"[All Fields] or "laparoscopy" [All Fields] OR "laparoscopy"[MeSH Terms]) and ("endoscopic"[All Fields] or "endoscopy"[All Fields] or "endoscopy"[MeSH Terms]) and ("intragastric"[All Fields] or "transgastric"[All Fields] or "cooperative"[All Fields] or "combined"[All Fields] or "rendezvous"[All Fields] or "hybrid"[All Fields])]. And ("stomach"[MeSH Terms] or "stomach"[All Fields] or "gastric"[All Fields] or "upper gastrointestinal" [All Fields] or "Upper Gastrointestinal Tract"[MeSH Terms]).
Data extraction and analysis The included studies were assessed; and the relevant data that was extracted by the reviewers was filled onto a spreadsheet data extraction form. The extracted data for each study focused on: first author's name, year of publication, country involved, study design, number of cases, lesion pathology, its' size and location, operative technique name, endoscopy team and surgical team role, operative time, type of closure of visceral wall defect, any blood loss or complications and length of hospital stay. If a technique has a commonly used acronym this is given in a parenthesis after its name. The investigated outcomes for each technique were: type of technique used, number of cases, lesion size, tumor location, tumor pathology, role of endoscopic and of laparoscopic team, technique of visceral wall closure, operative time duration, adverse events and complications.
Given the different trial designs, an individual-patient approach has the added advantage of pooling data from similar groups of patients, for example by selecting out those anatomically suitable for EVAR from the IMPROVE trial for comparison with patients from the AJAX and ECAR trials. Unfortunately, the data from the Nottingham trial could not be retrieved, so this meta-analysis is based on the data from the AJAX 4 , ECAR  5  and IMPROVE 6 trials only. The purpose was to test the hypotheses that, particularly for patients anatomically suitable for EVAR, endovascular repair offers an improvement in 90-day survival and earlier hospital discharge compared with open repair, as well as identifying whether specific subgroup analyses by age, sex and Hardman index (a validated morbidity score for ruptured aneurysm  8, 9  ) had better 90-day survival with EVAR.
Kaplan-Meier survival plots and cumulative incidence of time to primary hospital discharge were produced by randomized group within each trial separately and accompanied by a log rank test. A Cox proportional hazards model was used to assess whether the randomized groups differed in terms of the cause-specific hazard of primary hospital discharge (competing in-hospital mortality not withstanding). The subgroups age, sex and Hardman index were assessed for differences in the effect of the endovascular and open strategies by including an interaction term between the subgroup and randomized group in a logistic regression model. The reporting of complications and reinterventions was very different in the three trials, but they all reported on the use of occlusion balloons and the incidence of abdominal compartment syndrome and other non-occlusive mesenteric hypoperfusion syndromes  16  ; however, the abdominal compartment syndrome data for the AJAX trial were collected retrospectively.
Results The baseline characteristics of the 836 patients are shown in Table  1. Because the design of the IMPROVE trial was different from that of the other two trials, the number of patients with ruptured aortoiliac aneurysm (core laboratory diagnosis) who were anatomically suitable for EVAR is shown. The one patient in ECAR who did not have direct aneurysm repair underwent axillobifemoral bypass. The demographic details are shown for all 836 patients randomized. The patients in IMPROVE tended to be older, with more women included, and patients had larger aneurysms. The operative details and discharge data for the patients are shown in Table  2. Both AJAX and ECAR used predominantly aortouni-iliac endografts, which restricted completion of the procedure, with femorofemoral cross-over grafts, under local anaesthesia.
Acknowledgements This analysis was funded by the  National Institute for Health Research (NIHR) Health   Technology Assessment programme  (project number  07/37/64 ). The views and opinions expressed herein are those of the authors and do not necessarily reflect those of the  Health Technology Assessment programme, NIHR, National Health Service  or the Department of Health. The AJAX trial was supported by  Netherlands Heart Foundation  project  2002B197. The ECAR trial was supported by the  French Ministry of Health. The IMPROVE trial was supported by  Health Technology Assessment  project  07/37/64  (as above). Disclosure: The authors declare no conflict of interest.
Reduced expression of GALNT9 or CCDC8 is significantly associated with poor relapse-free survival The clinical significance of the expression of BNC1, CCDC8 and GALNT9 was analysed using publically available GEO expression profiles using the prognoscan database  [33]. Prognoscan partitions a patient population into high-expressor and low-expressor group for each gene by choosing a threshold that maximises the statistical significance of difference in outcome. It corrects for multiple testing using the method of Miller and Siegmund  [34]. In two independent datasets, low CCDC8 expression was significantly associated with poor relapse free survival (GSE12276, p = 0. 001; GSE1456-GPL97, p = 0. 004) (Fig. 5a ), and in one data set, low GALNT9 expression was associated with poor relapse free survival, (GSE1379, p = 0.
BA-exposure alters male fertility in the context of metabolic syndrome As BA exposure was previously demonstrated to induce male fertility disorders, we next analyzed male reproductive capacity. Male fertility was assessed by breeding males of each group with C57Bl6J females during 2 weeks (as described in method section). Fertility tests highlight reproductive defaults in HF-CA group compared to HFD group (Fig  2A ). Even if there was no difference in the number of vaginal plugs observed per male between groups (data not shown), data revealed a 4 to 5-fold increase in the number of males unable to give progeny after two weeks of breeding with females; these males were thus qualified as non-efficient males (Fig  2A ). For the males that were still able to give progenies, there was a significant decrease in the number of pups per litter in HF-CA animals (Fig  2B ).
Note that no effect was observed on testis weight (Fig 2C). We then analyzed whether bile acid levels and pool were modified in HF-CA group compared to HFD males. We show a 6-fold increase of BA concentrations in testis of males exposed BAs induce lower germ cell proliferation rate HF-CA diet did not drastically alter histology of testis compared to HFD group (data not shown). No statistical impact of HF-CA-diet was observed on germ cell apoptosis compared to HFD-group (Fig  3A ). However, we confirmed that as previously described HFD induced germ In contrast, a decrease of germ cell proliferation was observed at 4 months in HF-CA group compared to HFD-group as identified by Ki67 staining (Fig  3B ). This decrease in germ cell proliferation was supported by the lower accumulation of the PCNA protein in HF-CA group compared to HFD animals (Fig  3C ).
Background: Selumetinib (AZD6244, ARRY-142886) þ docetaxel increases median overall survival (OS) and significantly improves progression-free survival (PFS) and objective response rate (ORR) compared with docetaxel alone in patients with KRAS mutant, stage IIIB/IV non-small-cell lung cancer (NSCLC; NCT00890825). Methods: Retrospective analysis of OS, PFS, ORR and change in tumour size at week 6 for different sub-populations of KRAS codon mutations. Results: In patients receiving selumetinib þ docetaxel and harbouring KRAS G12C or G12V mutations there were trends towards greater improvement in OS, PFS and ORR compared with other KRAS mutations.