dataesr/scientific-paragraphs-categorization huggingface dataset:
Study Designs The ANRS CO3 Aquitaine cohort is an open, prospective hospital-based cohort. The proposed research was conceived as an ancillary study to the cohort. This protocol reports on the sequential study design from the prototyping (phase 1a) and usability testing (phase 1b) to piloting (phase 2). Phases 1a and 1b rely on mostly qualitative methods. Perspectives of the patient will be assessed and barriers to and facilitators of implementation identified through usability testing. The second phase of the research will initially be based on a cross-sectional study design with the ultimate aim of collecting these data longitudinally (at least once a year) and systematically via the revised ePRO system.
Platform Design Clinical and laboratory data from medical records have been collected systematically as part of routine care by a team of clinical research associates/technicians from 13 clinics/hospitals throughout the Aquitaine region since the 1980s and via a locally developed information technology (IT) solution, ARPEGE, since 2013. ARPEGE is a secure Web-based data capture and visualization system developed with Microsoft ASP. NET (WebForm). Data are stored within a Microsoft SQL Server 2014-based data management system. A responsive Web-based platform has been designed for patient follow-up within the existing infrastructure of the ANRS CO3 Aquitaine Cohort. This IT solution was originally developed to meet the data collection requirements of the ANRS CO3 Aquitaine Cohort. Unlike the hospital's EMR, which did not allow for data to be visualized nor used for research, ARPEGE provides HIV physicians with patients' medical histories.
Its interoperability with the surrounding health information system infrastructure has evolved to allow laboratory data to be downloaded from the Bordeaux University Hospital's laboratory medicine information system, which includes results of all tests performed as part of hospital-based care. The proposed QuAliV ePRO system expands upon this IT solution by developing a flexible interface for the Web-based collection of ePROs both in a hospital setting and beyond (in the patient's home) with a special focus on the presentation of individual patient's results. The inclusion of administrative data from the Program for Medicalizing Information Systems and clinical data from the hospital's EMR is planned but has not yet been completed.
The study-specific identifier required for participants to create their accounts will then be noted on a detachable part of the patient-oriented brochure for easy reference. This study-specific identifier is required to create an account via ARPEGE. It allows for the patient account and the self-reported data to be linked to the existing clinical data capture and visualization system (ARPEGE). As the patients could be accessing the website from their phones or from their home computers, the section of the brochure for noting the study-specific identifier will be detachable, allowing the study participant to leave the brochure at the hospital for the sake of confidentiality (Multimedia Appendix 1). To monitor study enrollment and ascertain whether the proposed system is acceptable to users, enrollment will be tracked by the centers.
Eligible participants will be directed to the study website where they will be provided with additional details about the research initiative and its aims. The website will provide additional information to "recruited" patients, encouraging them to take a more active role in his or her HIV care and well-being. The patient will be redirected to the account creation page, powered by ARPEGE. To ensure that the participant created his/her account successfully, he/she will be asked to enter his/her email twice together with the unique patient identifier. The patient will then be asked to confirm his/her email address before he/she can access the patient portal. Metadata will be monitored to identify any bottlenecks during the pilot phase.
Acknowledgments The authors would like to thank the patients, investigators, and clinical research assistants involved in the successful implementation of this study. The authors would also like to thank  Alain Volny-Anne  and  Eugenie Destandau  for providing valuable feedback on the design and content and the QuAliV website and ePRO system. The Aquitaine ANRS Cohort is sponsored by the  Bordeaux University Hospital  and funded by the  ANRS (France REcherche Nord&Sud Sida-hiv Hépatites) , the  Bordeaux University Hospital , and the  Inserm U1219 Research Centre.
Metabolic Follow-Up and Graft Assessment Blood samples were collected in heparin tubes from the tail vein before transplantation and at regular times during the study. Blood glucose levels were measured using a blood glucose monitor (AccuCheck, Roche, Basel, Switzerland) and the results are expressed in grams per liter. C-peptide levels were measured using an enzyme-linked immunosorbent assay kit (Mercodia, Uppsala, Sweden) and the results are expressed in picomoles per liter. Data are represented as the mean and minimum/maximum values. After 2 months, the omental grafts were explanted. Omenta were fixed in 4% paraformaldehyde and paraffin embedded. Antibodies against insulin (Ab7842, Abcam, Cambridge, UK) and CD31 (for vessel staining; 555025, BD Biosciences, Franklin Lakes, NJ, USA) were used in combination with Texas Red (TI-7000, Vector Laboratories, Burlingame, CA, USA) and Alexa Fluor 488 (A-11034, Life Technologies, Carlsbad, CA, USA) secondary antibodies on 4-mm-thick sections to assess the morphology and vascularization of transplanted islets.
This anti-COL7-induced gastrointestinal tissue injury is functionally relevant as weight loss or failure to gain weight appropriately gain weight was noted in diseased mice  [24]. Despite several in depth reviews on EBA  [41] [42] [43] , detailed insights into the epidemiological, clinical and immunological characteristics of EBA patients on a larger scale are not available. However, this information would be valuable for coordinating standardized diagnostic and therapeutic interventions as well as planning future clinical trials. Therefore, we collected these data from all EBA cases published from 1971 to 2016 that fulfilled the current diagnostic criteria.
Selection of EBA patients Our search yielded 761 publications. Of these, 410 publications were identified that potentially contained information on EBA patients as determined by reading titles and abstracts. After reading the full text articles, 1159 EBA cases from 224 publications were included in our analysis (Additional file 1: Table  S1 ). Based on the data provided, it is not possible to rule out that some patients were reported in several publications. The remaining cases were excluded if the study did not sufficient provide information on the specific patient(s) or the reported cases failed to meet the current EBA diagnostic criteria. The number of publications as well as the number of reported EBA cases remained relatively constant from 1979 to 2014. An increased number of EBA patients was reported in 1996-1998  [46] [47] [48] , 2011-2012  [17, 21, 49]  and 2016  [50, 51] , which was due to the appearance of new diagnostic tools and thus the publication of large EBA patient collections during these time periods (Fig.
Discussion Our meta-analysis documents the clinical and immunopathological characteristics from EBA patients published Fig. 1  Reported EBA cases and number of publications reporting EBA patients from 1971 to 2016. PubMed was searched using the term "(epidermolysis bullosa acquisita) AND ("1971"[Date -Publication]: "2016"[Date -Publication])". EBA patients fulfilling the current diagnostic criteria were selected from the retrieved records. A total of 1159 EBA cases (data sets) were identified. Over the years, the number of reported cases ranged from 2 to 5 per year with the exception of 1996-99 and 2011-12, when 11-62 patients were reported per year. The graph displays the cumulative number of EBA patients reported between 1971 and 2016. The number of publications on EBA patients remained relatively constant during the time frame assessed; during this time, 2-6 manuscripts per year were typically published.
Method Eligibility criteria Studies written in English were included if (a) they provided original data on subclinical psychosis (schizotypal traits and PLE, isolated hallucinations or delusional symptoms), (b) the study population was adult (aged >16 years) and the study was in a non-clinical setting and (c) they provided data allowing for comparison between a native reference population and migrants (first-and/or second-generation) and/or ethnic minority groups. Studies that used the same database were included if they provided different analysis (different adjustments or different migrant or ethnic groups studied). We excluded studies recruiting only older adults and those set in secondary or tertiary health services, prison or agedcare facilities. Qualitative studies were also excluded.
Search strategy The following search items were entered in several electronic databases (MEDLINE, PubMed, PsycINFO and ScienceDirect): [delusion OR delusional OR hallucination OR hallucinatory OR paranoia OR paranoid OR psychotic OR schizotypy OR schizotypal] AND [migrant OR migration OR ethnicity OR ethnic]. Authors were contacted if full texts or supplement material were not available online. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to conduct our systematic review and meta-analysis 9 (Supplementary material 1 available at https://doi. org/10. 1192/bjo. 2018. 68).
Data extraction After the screening of titles and abstracts, A. T. and B. P. carefully read all the articles retrieved and selected those of interest for our systematic review and meta-analysis, and independently extracted the data needed for the calculations. Authors were contacted for additional data when necessary. We extracted information regarding design (incidence, prevalence), country of study, setting (college students, general population, enlistees, etc. ), age limits, gender, outcome (hallucinations, delusions or both for PLE; scores for schizotypal personality), diagnostic instrument, sample characteristics (ethnicity, migrant status, reference population) and sample size. When available, we used odds ratios and 95% confidence intervals as the main result. To examine the relationship between unadjusted and adjusted odds ratios, we also extracted adjusted odds ratios and their adjustment factors.
Data synthesis and analysis A narrative synthesis was made for all retrieved studies by outcome and migrant status/ethnicity. In the PLE analyses, we also tried to describe the studies according to the assessment period (current or lifetime) and by outcome (delusions, hallucination or any PLE). We then performed a meta-analysis where there was sufficient number of studies (at least two)  13  providing raw data and taking into account the different outcomes in different migrant/ethnic groups. When there was more than one outcome by study (e. g. PLE, delusions or hallucinations), we preferred to include only results on any PLE, to avoid cumulate dependent effect sizes. We estimated pooled odds ratios and corresponding 95% confidence intervals by random effects meta-analysis to investigate the effect of ethnic minority groups on within-and between-study variability.
Association between subclinical psychosis and ethnicity or migration Data from 16 studies regarding PLE and ethnicity were analysed. We found evidence in the narrative review and the meta-analysis for an association between ethnicity and PLE, in line with a previous meta-analysis,  4  although variations were found in contexts and ethnic groups across studies. We extended these outcomes by observing a variation of this risk among different ethnic groups,  Fig. 2  Forest plot of studies on lifetime psychotic-like experiences, by tool and ethnicity, using random effects meta-analysis, crude odds ratios, and 95% confidence intervals. CIDI, Composite International Diagnostic Interview. with a constant trend of higher prevalence of lifetime and current PLE among Black ethnic groups. We did not find clear evidence of an association between PLE and migrant status.
Data collection HA is a notifiable disease in all participating EU/EEA countries. Local public health departments investigated HA cases for demographic, clinical and exposure characteristics, then reported to national surveillance systems. For all countries data from mandatory notifications was used and assumed to be comprehensive at the national level. Reporting practices were similar across countries and had not changed since 2015. For the descriptive study, we asked national focal points for hepatitis A to provide aggregated numbers of all HA cases, by sex and age group, reported from 1 June to 31 March between 2012 and 2017 (used for AR and M:F ratio calculation). National focal points were also asked to complete a line list of all confirmed, probable and possible cases; information on criteria for meeting case definition, onset date, sex, age, travel history, hospitalisation, vaccination, HIV status and MSM status was also requested.
Statistical analysis We calculated country-specific attack rates per 100,000 residents. Population data were extracted from Eurostat  [18]. We also calculated the M:F ratio for HA cases aged 18-45 years. Categorical variables were compared using the chisquared test. Continuous variables were expressed as median with the corresponding interquartile (IQR) range and were compared using the Kruskal-Wallis test. P values of < 0. 05 were considered statistically significant. We developed four logistic regression models to detect associations between exposure variables and specific outbreak strains. Model- Case mapping by country of reporting was done using ArcGIS Desktop software.
Conclusion Our results suggest that a combination of international travel and sexual networks can sustain a large outbreak of HAV, with multiple virus strains, within a susceptible population. Our findings highlight the importance of recording sexual history and HIV status when investigating male HA patients. The inclusion of molecular characterisation in the outbreak case definition enabled the linking of cases occurring at different times and geographical locations; thus demonstrating the added value of utilising molecular epidemiology. Since the joint investigation of the 2013-14 EU/EEA food-borne HA outbreak, the harmonisation of HAV sequencing according to the HAVnet protocol has facilitated data comparison among European laboratories. Typical measures for preventing most STIs (e. g. condom use or personal hygiene instructions) are not sufficient to prevent HA transmission altogether, but are nonetheless an important part of information campaigns for MSM with high-risk sexual behaviour.
Acknowledgements We would like to acknowledge  Caterina Rizzo ,  Maria Elena Tosti ,  Paulo Nogueira  and  Zoran Simonovič  for their contribution in this outbreak investigation. We also would like to acknowledge all the staff at local and national levels, including the personnel working in national health institutes and reference laboratories. We are grateful to  Denis Coulombier  and  Mike Catchpole  for their review of the manuscript. We are also grateful to  Silviu Ionescu  for his support with the case mapping and to  Meghan Hamel  for providing information on Canadian cases.
, 2018). They were followed up at 6, 12, 18 and 24-month visits after surgery, then yearly until 10 years postoperatively. Digestive and urinary outcomes were assessed using the same questionnaires as at baseline. Fertility outcomes were recorded, including pregnancy intention, conception mode, pregnancy outcome, ART management and delivery mode. The event dates considered to analyze time-to conception were the date of surgery or the day when postoperative medical treatment was discontinued, and the day of conception or of last follow-up visit. Statistical analysis was performed using Stata 11. 0 software (Stat Corporation, Lakeway Drive, TX, USA). The population was described using median, first and third quartile (Q1-Q3) if the characteristics had at least ordinal level and were not categorized.
Discussion Our study reveals that skilled surgical management for symptomatic large deep endometriosis nodules infiltrating the rectum in young women is followed by a high pregnancy rate 4 years after surgery. Although a majority of patients had a past history of infertility, most pregnancies resulted from postoperative natural conception. Patients receiving advice from experienced surgeons to attempt natural conception were more likely to conceive faster after the surgery. Our data suggest that experienced surgical teams may safely offer surgical management of endometriosis for patients with deep endometriosis and pregnancy intention, with very good fertility outcomes. Our study has several limitations. Patients were originally enrolled in a randomized trial the main outcome of which was related to postoperative digestive and urinary function.
004). for colorectal endometriosis. In a recent review  (Cohen et al. , 2014)  of series of patients presenting with bowel involvement, exclusively managed by colorectal resection (n = 1320), the postoperative rates of natural conception and overall conception were 28. 6% (95% CI: 25-32. 3) and 46. 9% (95% CI: 42. 9-50. 9), respectively. In a prospective trial  (Meuleman et al. , 2014)  conducted in patients having undergone colorectal resection for deep endometriosis, the postoperative rates of natural conception, overall conception and ART induced conception were 24% (13/54), 50% (27/54) and 26% (14/54). In our database, 65% of patients operated for associated colorectal endometriosis and ovarian endometriomas conceived after surgery and 60% of these pregnancies were natural  (Roman et al.
As the mode of conception in our study was determined after surgical exploration of the pelvic organs, these results regarding mode of conception cannot necessarily be applied to a non-surgical population. On the other hand, the number of women who achieved pregnancy by IVF was too small to draw any meaningful conclusions about the impact of the surgery on IVF outcomes. The original trial randomized the patients on the basis of the surgical technique performed on the rectum, and not on the conception mode or whether colorectal surgery was performed before IVF or not. More consistent data may be provided by a randomized trial assessing the impact of colorectal surgery on IVF performance, which is on going in several French facilities including ours  (Collinet, 2017). Deep endometriosis is known to be related to infertility and is often the cause of severe dyspareunia, which may impede regular sexual intercourse necessary for natural conception.
Data sources and inclusion criteria We invited 57 investigators to contribute IPD for pooled analysis: 52 investigators who had collaborated in a previous systematic review of the association between HIV, ART and cardiometabolic risk factors  [20] , and five investigators identified through personal communication with other collaborators. Briefly, we included studies conducted in SSA that had collected data on HIV/ART status and the relevant cardiometabolic risk factors among black Africans aged 13 years or older. Studies were excluded if they lacked a comparison group, or had too few (<10) or no participants with a risk factor based on a defined cut-off, or had a very small sample size (<10 participants).
Data collation We requested data on cardiometabolic risk factors [blood pressure (BP), lipids, glucose and glycated haemoglobin (HbA1c)], HIV infection and ART status. We also collected additional variables for adjustment (Table  1 ). Data were checked for plausibility and consistency and, when necessary, collaborators were contacted for clarification before analysis. We converted all variables measured on other scales to the SI scale (mmol/L, %, mm Hg or Kg/m 2 ).
Statistical analysis We conducted a two-step IPD pooled analysis, analysing each dataset separately to obtain study-level estimates, before combining them using random-effects models of metaanalysis. We fitted Poisson regression models with robust sandwich estimators of variance for each outcome to obtain study-specific risk ratios (RRs) and prevalence ratios (PRs) for ART use and untreated HIV infection  [27, 28]. RRs and PRs are collectively referred to as RR hereafter. We used multilevel mixed models to adjust for clustering of individuals within households in two cross-sectional studies and to account for correlation in repeated measurements in one longitudinal study included in the analyses. In our primary analysis, we assessed the association between ART and each cardiometabolic risk factor by comparing individuals receiving ART (ART+) with individuals not receiving ART.
Individuals not receiving ART were either untreated HIV-positive individuals (in studies of HIV-positive individuals only) or a combination of untreated HIV-positive individuals and HIV-negative (HIV-) individuals (in studies including both groups). In sensitivity analyses, we also compared associations between individuals receiving ART and HIV-negative individuals, and between individuals receiving ART and untreated HIV-positive individuals. We also compared untreated HIV-positive individuals with HIV-negative individuals to assess the impact of HIV infection on cardiometabolic risk independent of ART use. All models were adjusted for body mass index (BMI), age and sex. In a subgroup of studies where data were available, we also adjusted for alcohol consumption, current smoking status, education level, fruit and vegetable consumption, physical activity and socio-economic position.
Additionally, where data were available for lipid and glucose outcomes, we adjusted for lipid-and glucose-lowering medication, respectively. For BP as an outcome, we adjusted for BPlowering medication where data were available. Further, for each cardiometabolic risk factor studied as an outcome variable, the other cardiometabolic risk factors were additionally adjusted for. To pool the adjusted RRs, we estimated a weighted average of study-specific log (adjusted RR) incorporating between-study heterogeneity according to the method of DerSimonian and Laird  [29]. The I 2 statistic was used to assess the heterogeneity between study-specific estimates  [30]. A predetermined set of study-level characteristics were assessed as potential sources of heterogeneity between studies using meta-regression: study type (population-based, clinic-based), study size, year the study was conducted, location of study (West, East, Central or Southern Africa), sex distribution (proportion of men), mean participant BMI and mean participant age.
Results We received data for 20 studies and included 14 studies conducted between 2003 and 2014 in the current analysis (Fig. 1 ). Overall, the pooled data comprised 21 023 participants aged 13-107 years, with generally fewer men than women but with varying proportions for each cardiometabolic risk factor studied (Table  2 ). The number of individuals and proportion of men and women included in the analyses varied by cardiometabolic risk factors because not all studies had data on all risk factors, and because of missing data within studies. Apart from one all-women study, the proportion of men across all studies ranged between 22% and 49%. In the primary analyses (comparing individuals on ART to individuals not receiving ART), the number of participants included ranged from 6364 with data on glucose to 10 620 with data on TC (Table  2 ).