dataesr/scientific-paragraphs-categorization huggingface dataset:
| Whole exome sequencing, data processing and variant calling After removing duplicate reads, several postprocessing steps have been applied to the raw SBS calls in order to obtain SBSs with confidence. SBSs with coverage less than 10Â were filtered out. SBSs with <10% reads supporting for variant or >1% reads supporting for background control data per site were also removed. Finally, all SBSs that match the common dbSNP version 137 with MAF ≥1% were removed. Annotations of somatic SBS were performed by ANNOVAR and their functional impact was evaluated by the ANNOVAR-embedded SIFT and PolyPhen-2 modules.
To examine the somatic alterations in the tumor RNA, deep whole transcriptome sequencing (RNA-seq) was performed on the UTUC_03, UTUC_18 and UTUC_20 samples used for WES. In the corresponding mRNA samples, we observed the respective counts of 143, 148 and 344 of the WES-identified SBS (Table  S6 ). The SBS type distribution (34% synonymous, 63% nonsynonymous, 2% stopgain, 1% affecting splicing) was consistent across all UTUC RNA samples (data not shown). The number of deleterious mutations detected in both DNA and mRNA was 79 to 170 (range across samples) for any mutation type, and 54 to 117 for A:T>T:As (Figure  3D ). The mutations shared between DNA and RNA are listed in Table  S7. Thus, a large proportion of deleterious DNA mutations in UTUCs are propagated at the mRNA level, and the AA-specific A:T>T:As are likely to have a considerable impact on normal protein function.
DATA AVAILABILITY STATEMENT The mRNA and miRNA profiling data were deposited to the NCBI Gene Expression Omnibus (GEO) public database (www. ncbi. nlm. nih. gov/ gds) under the Series reference ID GSE166912. The WES and RNA-seq data generated in this study were deposited to the European Genome-Phenome Archive (EGA) under the Study ID EGAS00001005363. The list of all somatic SBSs identified by WES and their overlap with the RNA-seq profiling data is available in the Table  S7.
Membranes were incubated overnight at 4 • C with primary antibodies against glucose transporter type 4 (GLUT4) (IF8) (1:1000; Cell signaling, Danvers, MA, USA), and OXPHOS complexes (1:4000; Abcam, Cambridge, MA, USA). After incubation, membranes were washed three times with tris-buffered saline/0. 1% Tween 20 (TTBS) and incubated with the appropriate dilutions of anti-species horseradish peroxidaseconjugated secondary antibodies at room temperature for 1 h. Then, membranes were washed three times in TTBS before addition of the enhanced chemiluminescent solution (Clarity Western ECL; Bio-Rad, Hercules, CA, USA) for 5 min, using the Bio-Rad ChemiDoc system. Band densities were determined using Image Lab V5. 0 (Bio-Rad, USA). The Stain Free ® (Bio-Rad, USA) total protein measurement was used as loading control and for data normalization  [26].
Then, the α-diversity of bacterial communities was assessed by calculating the Shannon's diversity index based on the number of observed operational taxonomic units (OTU). β-diversity was used to analyze the dissimilarity among the group membership and structure. Therefore, at 9103 sequencing depth, based weighted/unweighted UniFrac distances were reported according to the principal coordinate analysis (PCoA). Group differences in α and β-diversity indices were calculated using the Kruskal-Wallis test and permutational multivariate analysis of variance (PERMANOVA), respectively. For taxonomy analysis, features were assigned to OTUs with a 99% threshold of pairwise identity to the Greengenes reference database 13. 8  [31]. Differential taxon abundance among groups was tested with ANCOM  [32].
Statistical Analysis Statistical analyses were performed using the Statistica software (version 12. 0). All data are presented as mean ± standard deviation (SD). Normality was verified using the Kolmogorov-Smirnov's test, and homogeneity of variance was assessed with the Bartlett F-test. In the absence of normal distribution or variance homoscedasticity, data were log-transformed before analysis. One-way-ANOVA with the Newman Keuls's post-hoc test was used to compare the CTRL and HFD groups (effects of obesity induction). Then, one-way ANOVA (with or without repeated measures) followed by the Newman-Keuls post-hoc test was used to determine group effects, and time (T), group (G) and T × G interactions in the four experimental groups (HFD, T63, HIIT and HIIT + T63). Spearman correlations were used to test relationships between variables.
Acknowledgments: We thank the  Installation Experimental de Nutrition (IEN)  for animal care ( INRAE, Theix, France ) and the  Centre Imagerie Cellulaire Santé (CICS) platform (Clermont Auvergne Université, Clermont-Ferrand, France). We also thank  Lucy Garraud ,  Geoffrey Delcros ,  Alice Besson  and. Allison  for their valued technical help during the experiment. Thanks to  Odd-Erik Johansen  ( Nestlé Health Science ) for his scientific assistance and advices in the process of writing this article.
Introduction: To analyse the safety and effectiveness of gliclazide modified release (MR) in adults with type 2 diabetes mellitus participating in Ramadan from three geographically and culturally different regions of the world included in the DIA-RAMADAN study. Methods: DIA-RAMADAN was a real-world, observational, international, non-comparative study. The global study population was divided into three regional subgroups, with data gathered at inclusion 6-8 weeks prior to Ramadan (V0), during Ramadan (4. 5 weeks) and 4-6 weeks after Ramadan (V1). Primary endpoint was the proportion of patients reporting C 1 symptomatic hypoglycaemic events.
DISCUSSION This sub-analysis of the DIA-RAMADAN study analysed the data from the constituent regions in the study-the Indian sub-continent, the Middle East and South-East Asia-representing the diverse cultural and nutritional habits of Muslims worldwide. Overall, the results show that gliclazide MR was safe for patients with type 2 diabetes fasting during Ramadan in the real-world setting. There were relatively few hypoglycaemic events in each region, and none were classed as severe. Effectiveness of gliclazide MR was also similar across regions, with reductions in HbA 1c , FPG and bodyweight in all regions. These results are in line with the previously reported global analysis  [14].
CONCLUSIONS The data from this study indicate that gliclazide MR is safe and effective in maintaining glycaemic control for patients with type 2 diabetes during Ramadan in all three regions studied as part of DIA-RAMADAN, despite cultural and geographical differences among these regions. As anticipated from the primary analysis, no severe hypoglycaemic events or gliclazide MRrelated adverse events were observed in any of the regions during the study  [14]. This subanalysis provides additional real-world evidence to support the safety and tolerability of gliclazide MR in three diverse regions of the world where diabetes is a growing problem due to changing behaviour and dietary habits. contributed to manuscript preparation and approved the final version for WMIWM: acted as national study coordinator; contributed to manuscript preparation and approved the final version for publication.
Three major scientific publication databases were searched from inception until November 3, 2020. Studies included focused on the influence of physiological or psychological parameters throughout at least one phase of the menstrual cycle of elite athletes. Results: A total of 780 search results were yielded and 26 references from a past bibliography were added manually. About 662 papers were reviewed of which 218 studies were assessed for eligibility. Of these, only seven (1%) precisely investigated the influence of a performance or physical parameter during at least one menstrual cycle phase. These seven studies included a total of 314 elite female participants (20. 58 ± 1. 91 years). Three used interviews, questionnaires or prospective analyses of reports. Four conducted several performance tests or included physical measures although only two performed tests during training or before/during competition.
Search Strategy This review focuses on research studies in elite athletes directly investigating the effects of MC phases on performance parameters such as endurance or power resistance, symptoms linked to MC, ligament stiffness, decision making skills, and/or competitiveness (desire to compete and training motivation). To identify eligible papers, a primary search was conducted in the PubMed, Sportdiscus, and Researchgate databases, using a well-defined search strategy that was formulated a priori. The search was conducted using a Boolean strategy following search terms: ("menstrual cycle" OR "menstrual phase" OR "luteal phase" OR "follicular phase") AND ("medal" OR "performance") AND ("elite" OR "athlete" OR "professional" OR "olympic" OR "high-performance"). No restriction was placed upon date of publication.
Data Extraction The following parameters were extracted from the collected studies by the authors (AM, JA, MD): (a) author, (b) country and year of publication, (c) sport, (d) number of athletes included, (e) participant age, (f) type of study (e. g. , questionnaire, physical tests in laboratory conditions or on-field), (g) method of MC phase evaluation, (h) outcomes measures, (i) test performed, (j) results, and (k) statistical significance. Data were extracted from the included studies and collated into a table for further quantitative and qualitative analysis (Supplementary Material).
Study Selection The initial search from the three databases returned 780 results; 26 references from a past bibliography were added manually (Supplementary Material). According to the aforementioned exclusion criteria, 662 papers were reviewed (Figure  2 ) including 218 publications relating to sports and MC phases. Among these, 30 studies on elite athletes were conserved for further investigation. Around 23 papers either focused on MC as a whole, not distinguishing each phase, or examined a non-performance parameter (e. g. , study of hormonal contraception). In total, seven publications investigating different performance parameters in female elite athletes throughout the different phases of the MC were taken forward for full analysis. Collectively, the seven selected studies included 314 female elite athletes aged 20.
58 ± 1. 91 years. According to classification of Sundgot-Borgen and Larsen (1993), sports included are endurance sport (triathlon, swimming), weight-class sports (judo, taekwondo), and ball games (soccer, rugby, netball, handball, and volley-ball). On average, the publications included 28 athletes but only nine who participated in studies involving physical testing and not gathering of information using questionnaires. Study durations varied from 8 weeks to 7 months with an average of 3 months. The only prospective study  (Myklebust et al. , 1998)  used data collected from 1993 to 1996.
, 2020). Information included the distances covered per minute at varying intensities. Two other studies in soccer players included data from field tests of physical performance such as 3 × 30 m sprints to evaluate sprinting capacities, a counter movement jump or a Five-Jump Test to assess lower limb power or the Yo-Yo Intermittent endurance test to measure endurance capacities  (Julian et al. , 2017; Tounsi et al. , 2018). The remaining study employed the Cambridge Gambling Task (CGT) to test decision making  (Statham, 2020). The three other studies relied on questionnaires given to athletes  (Kishali et al. , 2006; Crewther and Cook, 2018)  or prospective analyses in an epidemiological study of anterior cruciate ligament (ACL) injuries  (Myklebust et al. , 1998). Kishali et al. (2006)  asked 21 questions about anthropometric and descriptive data about menstrual cycle including status of participation to training and competition, status of place in competition during menstruation cycle or regularity of the menstruation, presence of dysmenorrhea, and the use of drugs such as pain relieve during menstruation.
Study design and data source We conducted a rapid review to capture case reports of VITT after adenoviral vector-based COVID vaccine administration. We searched PubMed ePubs, Scopus, Embase, and Web of Science databases to include articles published up to April 28, 2021, and related to COVID-19 vaccine-associated CVT after adenoviral vector-based COVID-19 vaccine administration. Case series with more than five cases were considered. We only included cases with CVT documented by clinical and radiologic findings after vaccination with the ChAdOx1 nCoV-19 or Ad26. COV. 2. S vaccine. After reviewing individual abstracts and full texts, we identified 5 case series that met the inclusion criteria for this systematic review  [1] [2] [3] [4] [5]. Laboratory measurements presented were either those obtained at time of admission or peak/nadir values.
Background: Ulcerative colitis (UC) has been the focus of numerous observational studies over the years and a common strategy employed in their design is the use of composite and aggregate outcomes. Objective: This systematic review and meta-analysis aims to identify composite and aggregate outcomes of observational studies in UC and to evaluate how the number and type of variables included and the length of follow-up affect the frequency of patients that achieve these outcomes. Methods: A systematic literature search was carried out using MEDLINE [via PubMed], Scopus, and Web of Science online databases. Observational studies that included UC patients and reported composite or aggregate outcomes were identified. A set of variables considered to be representative of progressive or disabling UC was defined, the proportion of patients attaining the outcomes was determined and a random-effects meta-analysis was performed by dividing the identified studies into subgroups according to different criteria of interest.
Search strategy This study was conducted following the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Guidelines  6  and the Cochrane Collaboration Guidelines for reporting meta-analyses. 7  Literature search was performed from inception to 14 July 2020 using three electronic databases: MED-LINE (via PubMed, https://pubmed. ncbi. nlm. nih. gov), Scopus (https://www. elsevier. com/solutions/scopus) and Web of Science (http://www. isiwebofknowledge). The words or medical subject heading terms used were: "((('aggressive disease') OR ('disabling disease') OR ('disabling outcome') OR ('disabling outcomes') OR ('composite outcome') OR ('composite outcomes') OR ('composite event') OR ('composite events') OR ('composite endpoint') OR ('composite endpoints') OR ('composite') OR (composit*) OR To ensure that all relevant articles were included, the reference lists of the systematic reviews selected from the databases were manually reviewed.
Study selection and data collection process Two reviewers (CA and MS) independently screened the titles and abstracts according to the eligibility criteria and if a particular study failed to meet these criteria, it was excluded. In the second phase, the full text of all the remaining potentially relevant studies was analyzed, and the eligibility criteria were used again to discard non-relevant studies. Disagreement was resolved via consensus between the two reviewers. The following information was collected from the selected studies: authors' names; publication year; country of origin; study design; observation period; number of patients (discriminated between UC and CD, if applicable); UC extent; subgroups (if applicable); outcome name, definition and reported variables (among the ones chosen for analysis).
Statistical analysis The main data analyzed in this meta-analysis were the proportions of patients achieving a composite outcome. The proportion of patients achieving the outcome was calculated and compared according to the predefined variables reported in the study. The following comparisons between subgroups were performed: of study follow-up; [v] number of patients included in the studies. In addition, the entire population of outcomes was divided in subgroups reporting a specific predefined "core" variable, and differences within these subgroups according to the presence or absence of the remaining predefined variables were statistically tested. T A B L E 1 (Continued) Comparisons were not performed when the subgroups defined by the presence or absence of the considered variable were composed by only one or two outcomes.
To perform the meta-analysis, the "metaprop" function from the "meta" package of the R statistical programming language was used and the "PRAW" summary measure was employed for the pooling of studies. A random-effects model was adopted taking into consideration the differences observed across studies. Cochran's Q test and the I 2 statistic were used to assess statistical heterogeneity. 10  In addition, Egger's test was used to detect potential publication bias. 11  A sensitivity analysis was performed to assess the influence of any individual study on the overall results. A Venn diagram and Upset plot were generated using the "UpsetR" and "nVennR" packages included within the R software, to graphically illustrate the distribution of the predefined variables among the individual studies included in the meta-analysis.
Literature search and study selection The selection strategy followed is summarized in Figure  1. The electronic database search yielded 10,250 records (1885 in PubMed, 4323 in Scopus, and 4042 in Web of Science); the manual search identified 14 additional studies. Following the removal of duplicates (n = 4444), 5820 records remained, of which 5582 were excluded on the screening phase. The remaining 238 records were evaluated for eligibility. Following full-text assessment, 205 articles were excluded, and the remaining 33 articles were selected for the qualitative analysis. Twenty of those 33 were included in the meta-analysis (Figure  1 ).
Composite and aggregate outcomes Twenty one composite outcomes  [12] [13] [14] [15] [18] [19] [20] [21] [22] [23] [34] [35] [36] [37] [38] [39] [40] [42] [43] [44]  were included in the meta-analysis. The mean frequency for composite outcomes was 0. 363 [95% confidence interval (CI) 0. 323-0. 403] (Figure  2a ). The funnel plot and sensitivity analysis are depicted in Supplementary Figures  3  and 4. The results of Egger's test on the frequency of composite outcomes were not significant (p = 0. 166), indicating that the dataset was unbiased. This can also be visually appreciated by the symmetry of the corresponding funnel plot in which the standard error was plotted against the outcome frequency. No outliers were detected on the results of the sensitivity analysis, with the mean being unaffected by the sequential exclusion of each individual outcome (Supplementary Figure  4 ).
Nguyen Carvalho F I G U R E 3 (Continued) 66 - UNITED EUROPEAN GASTROENTEROLOGY JOURNAL systematic review and meta-analysis we attempted to assess the prevalence of composite and aggregate outcomes that combine these different methods of quantifying disease progression, focusing specifically on observational studies reported in the literature. As perhaps it is to be expected from a dataset composed of observational studies conducted worldwide in the course of a decade, there was a marked heterogeneity between the studies in terms of number of patients enrolled, total duration of the study and variables included in the outcome. Interestingly, the mean frequency of composite outcomes was unaffected by the total number of variables included in the outcome. Because this result seems counterintuitive, it is possible that the relatively small number of studies that reported four or more variables was simply not enough to show a clear statistical trend, and this may become evident as future or ongoing observational studies are incorporated into the available literature.
However, it was clear from the analysis of the present dataset that the reporting of the variable "Biologics" significantly increased the frequency of composite outcomes. This was evident on the overall analysis of the entire dataset, on the analysis by paired variables in combination with the variable "Surgery," and on three out of seven subgroups defined by the presence of a "core" variable. It should be noticed that this increase in the frequency of composite outcomes was not observed with the inclusion of the other predefined variables considered, indicating that merely reporting additional variables regardless of their specific identity does not necessarily increase the chances of observing a composite outcome. "Biologics" encompasses several different therapeutic agents targeting pro-inflammatory mediators.
This guideline has been initiated by the task force Autoimmune Blistering Diseases of the European Academy of Dermatology and Venereology, including physicians from all relevant disciplines and patient organizations. It is a S3 consensus-based guideline that systematically reviewed the literature on mucous membrane pemphigoid (MMP) in the MEDLINE and EMBASE databases until June 2019, with no limitations on language. While the first part of this guideline addressed methodology, as well as epidemiology, terminology, aetiology, clinical presentation and outcome measures in MMP, the second part presents the diagnostics and management of MMP. MMP should be suspected in cases with predominant mucosal lesions. Direct immunofluorescence microscopy to detect tissue-bound IgG, IgA and/or complement C3, combined with serological testing for circulating autoantibodies are recommended.
Experimental data We investigated a post-stroke patient (female; age, 47 years; height, 1. 60 m; body weight, 63. 8 kg) treated with the ActiGait FES device. The study was approved by the local Ethics Committee at Hannover Medical School (MHH) under reference no. 2489 and the patient provided written and informed consent to participate. All methods were performed in accordance with relevant guidelines and regulations. Overground gait was performed at a self-selected gait speed. Motion capture data were obtained with an optical infrared system consisting of 12 MX cameras controlled by Nexus v1. 8. 5 software (Vicon Motion System, Oxford, UK) at a sampling rate of 200 Hz and with the retroreflective markers attached to the subject in accordance with the plug-in gait model  28. GRF was measured at 1 kHz using two force plates (Type BP400600; AMTI, Watertown, MA, USA).
Optimal control problem formulation Parameter estimation, tracking, and predictive simulation were formulated as an optimal control problem. The frameworks used in this study were developed by Falisse et al. 24, 25. The optimal control problem was transcribed into a nonlinear programming problem using CasADi  30  and the resultant optimization problem was solved using IPOPT  31. Both software were implemented in MATLAB (R2019a). Direct collocation with a third-order Radau collocation scheme was used for transcription  24. The tracking simulation included terms in the objective function that minimized the difference between the optimized variables and ID results. The objective function   was defined as follows: 𝐽 𝑇𝑟𝑎𝑐𝑘 = ∫ ∑ (𝑊 𝑇1 (𝑞 -𝑞 𝑅 ) 2 + 𝑊 𝑇2 (𝑀𝑗 -𝑀𝑗 𝑅 ) 2 + 𝑊 𝑇3 (𝐹𝑟 -𝐹𝑟 𝑅 ) 2 + 𝑊 𝑇4 (𝑀𝑟 -𝑀𝑟 𝑅 ) 2 + 𝑊 𝑇5 𝑎 2 + 𝑡𝑓 𝑡𝑖 𝑊 𝑇6 (𝑞̈2 + 𝑎̇2 + 𝐹𝑚 ̇2)) 𝑑𝑡, (1) where  and  are the initial and final times, respectively;  and  are the joint angle and moment, respectively;  and  are the ground reaction force and moment, respectively; the subscript  represents the experimental data;  and  are the muscle activation and tendon force, respectively; and  1-6 are the weight factors.