dataesr/scientific-paragraphs-categorization huggingface dataset:
Most cases of CMV reactivation were recorded under two ICD-10 codes (B25. 8: other CMV-D [46. 4%] and B25. 9: CMV-D, unspecified [45. 2%]). As asymptomatic CMV infections could have been misreported as CMV-D under these ICD-10 codes, allo-HCT recipients with CMV-D recorded under these codes were only assumed to have true CMV-D if it was the primary cause of admission and if they stayed in the hospital for at least 7 days. Therefore, it is likely that some cases of CMV-D were excluded. As the patients included in this study were allo-HCT recipients who received their transplant between 2008 and 2011, the 2017 French national recommendations for the management of CMV infection were not used  [26]. Additionally, some exposed allo-HCT recipients may have been excluded due to receiving treatment outside of the hospital because the PMSI database only contains inpatient records.
Furthermore, the PMSI database was primarily developed for administrative purposes, which means that some secondary diagnostics may not have been reported if they did not lead to any additional payment to the hospital. Most published estimates of the incidence of CMV-D are based on specific populations (e. g. For writer -CMV-seropositive patients  [9, 27, 28] , pediatric patients  [24, 29] , and those treated using specific treatment strategies  [30] [31] [32]  that are not comparable with this population, which included allo-HCT recipients of all ages, CMV-seronegative donors, and recipients who underwent different treatment strategies. As the objective of this analysis was not to estimate the incidence of CMV-D, but to describe the impact of CMV-D reactivation on clinical and economic outcomes after allo-HCT, the fact that some cases of CMV-D may not have been identified should not be a major limitation.
This study examined this association and did not show any significant increase in the risk of GVHD in allo-HCT recipients who had developed CMV-D. It should be noted that because GVHD may increase the risk of CMV-D, and could be a confounding factor when evaluating the consequences of CMV-D, GVHD diagnoses that were recorded before or around the index date as part of the allo-HCT recipient matching criteria were taken into account in this study. However, this may have underestimated the effect of CMV-D on GVHD because GVHD occurring during the same hospital stay as the diagnosis of CMV-D was not considered to be attributable to CMV-D. This limitation is particularly notable because the number of cases with CMV-D and GVHD during the same hospital stay was relatively high. The key strength of this study is that the data are based on a national patient population and may be more relevant to real-life clinical practice than data from clinical trials or single-center studies.
MicroCT Analysis Analyses of the bone microarchitecture were performed using a Skyscan 1076 in vivo microCT scanner (Skyscan, Kontich, Belgium). Tests were performed after sacrifice on the tibias and heads of each animal. All tibias and heads were scanned using the same parameters (pixel size 9 µm, 50 kV, 0. 5 mm Al filter, 10 minutes of scanning). The reconstructions were analyzed using NRecon and CTan software (Skyscan, Kontich, Belgium). 3D visualizations of the tibias and heads were made using ANT software (Skyscan, Kontich, Belgium).
Screening and data abstraction One author (NK) screened articles and identified those appropriate for full text review. For each article that passed full text review, one author (KB) recorded characteristics of the study and design, the number of antibiotics assessed. All studies at this stage were included in a descriptive analysis of study characteristics. We restricted our MIC summary value abstraction to articles that reported at least 9 antibiotic MIC50 derived from a minimum of 30 C. difficile strains, and our meta-analysis was limited to classes with at least 10 MIC50 measurements.
Outcomes For each antibiotic assessed within a given study, we abstracted the median MIC (MIC50), the 90 th percentile (MIC90), and calculated the ratio of MIC90 to MIC50 (a large dispersion between the MIC90 and MIC50, as measured by the MIC90 to MIC50 ratio, indicates that a given bacteria may readily develop resistance to a given antibiotic)  [11]. When studies did not report MIC50 or MIC90 directly, but instead reported the distribution of strains, we recorded the MIC50 and MIC90 as the lowest concentration where at least 50% or 90% of strains were inhibited. The values of MIC were in mg/L for results reported in this paper. The resulting dataset had a single record for each study antibiotic, and as such, multiple lines per study.
1002/sim. 7336 ). Due to our interest in the emergence of resistance to C. difficile treatment agents, we developed analogous models (N = 3 x 3) for metronidazole, vancomycin and fidaxomicin. Each model included just the intercept term (no random effect for antibiotic was needed since there was only a single antibiotic within each model). Each model included a fixed effect for the intercept and a random effect for antibiotic class, antibiotic, and study. For each MIC50 model (N = 19 + 1 + 3), we explored factors explaining heterogeneity by creating two more models, one with an additional covariate for study year and one with an additional covariate for study continent. Analyses were conducted in R; the lme4 package was used for fitting mixed-effects models and to estimate bootstrapped confidence intervals for parameter estimates  [12].
Studies We identified 366 articles in PUBMED and 1172 articles in EMBASE meeting our database search inclusion criteria, with 240 duplicate items, leaving us with a total 1289 articles after the initial database search (Figure  1 ). Title and abstract screening eliminated 944 articles, leaving 345 articles for the full-text review. Of these, 182 articles met the study inclusion criteria (Figure  1 ). The pace of publication increased through the period, from 12 articles published in the 1980 to 1984 period (2. 4 per year), to 64 articles published in the 2010 to March 2014 period (14. 8 per year). The number of antibiotics investigated per study decreased, from an average of 11. 8 antibiotics per study to an average of 6. 8 antibiotics per study for the periods described above. The number of isolates per study increased from 39.
Funding and Transparency statement This study was funded through the  Veterans Affairs Fellowship Program in Medical Informatics  and a  Canadian Institute for Health Research Doctoral Fellowship. The funders had no role in the design, analysis, writing, or decision to submit this manuscript. No authors have conflicts related to this work. However, several authors have received funding for work not related to this manuscript. AS received speaking fees from  Cubist pharmaceuticals and Merck Canada. KAB received grant funds from  AstraZeneca. NK reports a PhD grant from  Sanofi Pasteur, non -financial support (travel expenses) from  Alere  and  Sanofi Pasteur  and personal fees from Astellas grants. PV reports grants and personal fees from  Sanofi Pasteur ,  Biomérieux ,  GSK ,  Astellas  and  Sanofi MSD.
Acknowledgments: the authors thank the local tumor biobank of  Henri Mondor Hospital  for providing high-quality samples and the  French clinical and biological network of myeloproliferative neoplasms (FIMBANK)  supported by a grant from the  National Institute of Cancer  (INCa BCB 2013). They also thank the  FIM group  and  J. J. Kiladjian  for assistance. Funding: this work was supported by a grant from the  National Institute of Cancer (INCa ,  TRANSLA CTIM3 ). Correspondence: STEPHANE GIRAUDIER stephane. giraudier@aphp. frdoi:10. 3324/haematol. 2018. 197699Information on authorship, contributions, and financial & other disclosures was provided by the authors and is available with the online version of this article at www. haematologica. org.
Identification of CD4 + T cell epitopes based on HLA class II-associated HCV polymorphisms. As a proof of principle to determine if these putative viral adaptations marked true in vivo CD4 + T cell epitopes, peptides spanning nine HLA class II (-DRB1)-restricted CD4 + T cell genotype 1 epitopes (based on the list of associations in Table  2 ) were designed using a web-based HLA-peptide binding prediction program (netMHCII; see methods; Supplementary Table  3 ). Of these targets four had been previously described. Overall, these targets were restricted by six common HLA-DRB1 alleles. To test the peptides we used stored peripheral blood mononuclear cells (PBMCs) from 14 HIV/HCV subjects from a long-term HIV controller cohort based on their HLA alleles (Supplementary Table  5 ). Peptides relevant to the HLA-DRB1 alleles carried by the HCV-infected subjects were tested in peptide pools.
Genotyping of IFNλ3 rs12979860 for the Single source outbreak cohort. Genotyping data of the IFNλ3 rs12979860 SNP was available on 34 subjects of the Irish single source outbreak as described in  1. Statistical Methods. HLA Association with Viral Polymorphism. Associations between HLA alleles and amino acid distribution at each residue of the HCV proteins were assessed via Fisher's exact tests for classification as consensus versus non-consensus amino acid using TIBCO Spotfire S + 8. 2 (Palo Alto, CA). Here, consensus refers to the most common amino acid at a single amino acid site.
This cohort comprised chronic HCV-infected subjects with pre-treatment viral sequence and host genotype of >800,000 SNPs using the Affymetrix UK Biobank array. The four digit host HLA alleles were imputed as reported previously 3. To limit the impact of population structure we limited the cohort to subjects with self-reported White ancestry infected with genotype 3A virus (n = 411). Principle component analysis was performed on the host SNP data and on the virus nucleotide sequence data and the first two viral PCs and the first 3 host PCs were used as covariates to account for possible hidden population structure. The association testing was performed using logistic regression where the response variable was the presence or absence of the indicated amino acid and the explanatory variable was the presence or absence of the HLA allele and the host and viral PCs as covariates.
All the analysis was performed in R (version 3. 2. 2). This analysis was performed on only a select number of positions within the HCV genome and for specific HLA alleles. No correction for multiple testing was performed and p < 0. 05 was considered significant. IFNλ3 associations with HCV polymorphisms. We had previously assessed associations between the presence or absence of the minor allele of rs12979860 of IFNλ3 and consensus or nonconsensus amino acids at each residue of the HCV proteins via Fisher's exact test. Because of the smaller number of subjects with typing available for this part of the analysis, no assessment of false discovery rates was made, and P < 0. 01 was used to indicate significance. Prediction of CD4 + T cell HCV epitopes: selection of peptides. The web-based HLA binding program netMHCII  42  was used to predict HCV-specific HLA class II-restricted T-cell epitopes based on the list of HLA class II-associated HCV polymorphisms obtained for the genotype 1A and 3A component of the study (Supplementary Table  3 ).
5; anti-CD8-PECF594; anti-CD14-V500; anti-CD19-V500; anti-IFNγ-fluorescein isothiocyanate (FITC); anti-TNFα PE-Cy7; anti-IL2-BV451 pacific blue and anti-PD-1-phycoerythrin (PE) (BioLegend). AquaViD (Life Technologies) was used for the exclusion of dead cells. All samples were acquired using a LSR II flow cytometer (BD Biosciences) and analyzed with BD FACSDiva software (BD Bioscience) or FlowJo v10. 2 (FLOWJO). A response was deemed positive if at least three times the background.
Acknowledgements The authors wish to thank  Drs Mark Watson  and  Susan Herrmann  from the  Institute for Immunology and Infectious Diseases at Murdoch University, Australia. We also thank  Professor Timothy Sterling ,  Sally Bebawy ,  Megan Turner ,  Chike Abana ,  Rama Gangula  and  Cindy Hager  from the  Department of Medicine, Division of Infectious Diseases at Vanderbilt University Medical Centre, USA. This study was, in part, funded by the  McCusker Research Foundation ,  Raine Medical Research Foundation ,  Australian Centre for HIV and Hepatitis Virology Research  and the  NIH-funded Tennessee Center for AIDS Research  ( P30 AI110527 ). This study was also partly financed within the framework of the  Swiss HIV Cohort Study , supported by the  Swiss National Science Foundation  (grant # 148522 ), by  SHCS  project # 430  and by the SHCS research foundation.
Participants and design This study is based on data sets additionally recorded from the participant sample described in a previous paper  [2]. Twenty-four healthy, right-handed students (12 men, 12 women), aged 18-33 years (mean = 22. 50, standard deviation (SD) = 3. 61), participated in the study and received financial compensation. Thirty-four volunteers fulfilled the inclusion criteria and participated in the study, however, 10 had to be excluded either because they did not complete the four sessions of the experiment having decided to drop out (N = 4) or due to technical problems with the psychophysiological recordings (N = 6). The participants were assessed for mental disorder based on the Structured Clinical Interview for DSM-IV (SCID-I) screening module  [32]. No subject had a current or prior history of acute or chronic pain, chronic somatic diseases, lifetime or current mental disorder or pregnancy and no one used analgesic medication.
Interviews Data collection. After each of the four sessions, identical semi-structured interviews aimed at obtaining qualitative descriptions of the participants' pain Intensity, Unpleasantness and Suffering were conducted in English. The interviews were identical each time in order to examine whether the participants qualified pain and suffering similarly following the repeated pain measurement with or without the acoustic startle probes. They lasted 20 min in average and were audiotaped, transcribed and analyzed. All participants were Western European students, 6 were English native speakers and all were selected to participate in the study with the requirement of having excellent proficiency in English. The interview comprised six questions devoted to the individual concepts and lived experience of pain and suffering, presented in a randomized order across participants:   2000)  was used for processing the interviews.
5) and low catastrophic thoughts (PRSSs<1. 9) THEN: low pain intensity. In total 58 variables were included for the data processing: 41 descriptors from the interviews, 10 questionnaire subscales from the first set of questionnaires prior to the experiment and 7 questionnaires from the second set completed during the experiment. This pre-selection of only a subset of the total list of variables was due to values of a variable being completely identical, too sparse or missing. The I, U, PS ratings constituted the target attribute variables defined by the investigators according to the study's objectives. These target attributes were operationalized by using the median ratings of each scale across the whole experiment (I, U and PS) as cut-off points to assign each subject to the category of "high" or "low" (median values are indicated in Table  1 ).
For both the high and low psychophysical scores, the classification technique allows to determine the associated psychological attributes or experiential factors and hence to depict the meaning participants attributed to "Intensity", "Unpleasantness" and "Suffering" based on the post-experiment interviews. Two types of trees' models were generated by employing the classification and regression tree technique (CART) as originally introduced by the tree induction algorithm of Breiman et al. [30]. In the present study, data mining trees models were constructed using Decision Trees Classification with IBM DB2 Intelligent Miner for Data version 8. 1 software  [65]. We applied entropy as a measure for splitting and generating the branches inside the decision tree. It was applied to all selected attributes in a 'step by step' manner in order to determine which ones allowed the best differentiation between subjects displaying different target attribute values.
Acknowledgments We want to thank  Dr. Serge Marchand  for valuable comments on the manuscript. We are grateful to  Dr. Immo Curio  for his help with technical aspects of the study. We also wish to thank  Angela Odero  for helping collect the data for this manuscript and to  Dr. Michèle Baumann  for her methodological advice for processing the interviews. This study was supported by the  Fonds National de la Recherche Luxembourg (PASCOM)  and the  Deutsche Forschungsgemeinschaft  ( Fl 156/34-1 ).
Patients and methods We conducted a retrospective, monocenter study, in a single teaching-based, 12-bed medico-surgical ICU, of all UGE performed between January 2007 and December 2012. The Ethics Committee of the French Society of Intensive Care (SRLF) approved the study (n° 12-363). An informed consent was waived due to the retrospective design of the study. All the patients who underwent a gastroscopy were identified through the endoscopy unit's database, in which all UGEs performed in our institution are registered. All the patients who had an UGE performed during their ICU stay were included, and their whole medical records were analyzed. Excluded patients were those admitted for a patent upper digestive bleeding or those who underwent a second-look gastroscopy of a known lesion or for a planned interventional procedure (such as a gastric tube or esophageal prosthesis placement).
When a patient underwent several procedures, only the first one was taken into account. Data collected were age, gender, the reason for ICU admission, the Sequential Organ Failure Assessment (SOFA) score  [20]  at ICU admission and the number of organ failures according to the individual organ score of the SOFA score  [20]. We also recorded the symptoms and conditions that motivated the UGE, its findings and the subsequent procedures performed if any. Vital status at ICU discharge was also recorded. UGE was performed by a gastroenterologist (in most cases by a senior physician and in rare instances, by a trainee under a senior's supervision) with standard Fuji video gastroscope. It was performed under general anesthesia with orotracheal intubation or under sedation in patients with no previous intubation.
Background: Lynch syndrome is an autosomal dominant disorder that predisposes individuals affected to certain malignancies. Colon and endometrial cancers are the malignancies most highly associated with Lynch syndrome. However, growing body of evidence links Lynch syndrome to urological cancers. Objective: This review aims to clarify the type of urological malignancies that fall under the Lynch-associated cancer spectrum. Methods: Using PRISMA guidelines, a systematic search between January 1990 to February 2018, was conducted using the MEDLINE database with the application of the following MESH terms: colorectal neoplasms, hereditary nonpolyposis; DNA mismatch repair; urologic neoplasms; kidney pelvis; ureteral neoplasms; urinary bladder; carcinoma, transitional cell; prostatic neoplasms; testicular neoplasms.
EVIDENCE ACQUISITION A systematic search was conducted using the MEDLINE database using PRISMA guidelines. Papers were selected using the time period from January 1990 to February 2018. The following MESH terms were applied: colorectal neoplasms, hereditary nonpolyposis; DNA mismatch repair; urologic neoplasms; kidney pelvis; ureteral neoplasms; urinary bladder; carcinoma, transitional cell; prostatic neoplasms; testicular neoplasms. No language restrictions were imposed. Hand-searching references from articles was used to identify additional relevant studies. Initially, articles were selected using title and abstract. The full manuscript of these articles were then obtained and considered for eligibility. Overall, 18 articles were selected for upper tract urothelial cancer, 14 for bladder cancer, seven for prostate cancer and 11 for testicular cancer.
Acknowledgements Thang  Hoang Quoc  was supported by a research grant from the  France-Vietnam Alain Carpentier Foundation  and by a research grant of the  World Federation of Societies of Anesthesiologists  (2012). Alexandre Nuzzo was supported by a research grant of the  Fondation de L'Avenir, France  and by a research grant of The  French National Society of Gastroenterology.
Chemotherapy-induced dose-limiting toxicities (DLT) and dose-limiting neurotoxicity (DLN) Data were prospectively recorded in medical file at each hospital stay. Chemotherapy-induced DLT (all non-neurological toxicities) were defined as any toxicity leading to dose reduction (temporary or permanent), treatment delays or permanent treatment discontinuation. Chemotherapy-induced DLN was defined as permanent peripheral neuropathy (Levi scale grade 2 or 3) leading to dose reduction or permanent treatment discontinuation. DLN and progressive disease as the cause of treatment termination were not considered as DLT. Pre-therapeutic dose adaptation was defined as an initial dose reduction by individual clinical appreciation taking into account patient profile (age, ECOG Performance Status (PS), organ failure, malnutrition or mGPS).
Neurotoxicity affects 80% of patients and becomes chronic in 15-20% of cases, sometimes irreversibly  [27]. A recent systematic review  [37]  has reported the impact of acute oxaliplatin-induced neuropathy and necessity of a large prospective study to established Small intestine 0 (0)  better preventive guidelines. In 2 cohorts of colorectal cancer patients treated with oxaliplatin, Ali et al. [36]  reported that overall DLT, and specifically oxaliplatin-induced neuropathy, occurred mostly in patients who receive > 3. 09 mg/ oxaliplatin/kg LBM. One study is ongoing to determine whether the oxaliplatin dose normalization based on the LBM index can prevent or reduce neurotoxicity associated with oxaliplatin, for colorectal cancer patients treated in adjuvant with FOLFOX regimen (LEANOX trial NCT03255434).
Factors associated with dose adaptation SD standard deviation; malnutrition was defined as BMI < 21 kg/m 2 in patients aged more than 70 years old and BMI < 18. 5 kg/m 2 in patients aged less than 70 years old for the Protection of Person EST I DIJON, 25 March 2016) and was registered in Clinicaltrials. gov(NCT02797197). Competing interestsDamien Botsen reports personal fees from Pierre Fabre and non-financial support from GlaxoSmithKline, Novartis, Chugai, and Amgen outside the submitted work. Camille Mazza reports personal fees from Pierre Fabre outside the submitted work. Mathilde Brasseur reports personal fees from Bayer and non-financial support from Pierre Fabre, Novartis, Amgen, Roche, and AbbVie outside the submitted work. Olivier Bouche reports grants from Roche, personal fees from Roche, grants from Pierre Fabre, personal fees from Pierre Fabre, personal fees from Amgen, personal fees from Bayer, personal fees from Lilly, personal fees from Merck, personal fees from Novartis, outside the submitted work.
Public datasets Genotypes from the Hoglinger et al. GWAS  [8]  (cases onlyno controls) were obtained from the NIAGADS database. Out-of-sample controls were obtained from dbGAP Authorized Access to match each genotyping platform. In total, for the HumanOmni 2. 5 M platform, we obtained 2364 subjects; for the OmniExpress platform, 870 subjects; and for the HumanQuad 660 W platform, 8756 subjects. For the Illumina HumanQuad 660 W Array (Hoglinger et al. study), we used phs000103. v1. p1 "Genome--Wide Association Studies of Prematurity and Its Complications", phs000289. v1. p1 "National Human Genome Research Institute (NHGRI) GENEVA Genome-Wide Association Study of Venous Thrombosis", phs000188. v1. p1 "Vanderbilt Genome-Electronic Records (VGER) Project: QRS Duration", phs000203. v1. p1 "A Genome-Wide Association Study of Peripheral Arterial Disease", phs000237.