dataesr/scientific-paragraphs-categorization huggingface dataset:
Key Suggestions More clinical data are needed on the sex-specific effects of various interventions and sex-specific differences in response to treatment. Post hoc analyses of data from completed randomized controlled trials and pooled databases would provide useful insights into sex-specific Grading (adapted from the GRADE classification system 92 ): A, several high-quality studies with consistent results; B, several well-performed observational studies (dealing appropriately with selection, observation/measurement, and confounding biases); C, fewer well-performed observational studies (some biases, unlikely to compromise the findings in a major way); and D, no study or studies with major flaws. treatment responses. Clear guidance is needed to enable physicians to better recognize and treat comorbidities in women with COPD.
Acknowledgments Author contributions: All authors contributed to the conceptualization of the review and reviewed and contributed to all drafts of the article. Financial/nonfinancial disclosures: The authors have reported to CHEST the following: C. R. J. is a member of national and international advisory boards and steering committees for  AstraZeneca ,  GlaxoSmithKline ,  Boehringer Ingelheim  and  Novartis , and contributes to many educational programs and symposia for government, nongovernment organizations, and the pharmaceutical industry. K. R. C. has consulted (last 3 years) with  AstraZeneca ,  Baxter ,  Boehringer Ingelheim ,  CSL Behring ,  GlaxoSmithKline ,  Grifols ,  Kamada ,  Novartis ,  Nycomed ,  Roche , and  Teva ; has undertaken research funded by  Amgen ,  AstraZeneca ,  Baxter ,  Boehringer Ingelheim ,  CSL Behring ,  Forest Laboratories ,  GlaxoSmithKline ,  Grifols ,  Novartis ,  Roche , and  Takeda ; and has participated in continuing medical education activities sponsored in whole or in part by  AstraZeneca ,  Boehringer Ingelheim ,  GlaxoSmithKline ,  Grifols ,  Merck Frosst ,  Novartis ,  Pfizer , and  Takeda.
He is also participating in research funded by the  Canadian Institutes of Health Research  operating grant (entitled " Canadian Cohort Obstructive Lung Disease [CanCOLD]")  and holds the GSK-CIHR Research Chair in Respiratory Health Care Delivery at the  University Health Network, Toronto, Ontario, Canada. J. D. has served as a consultant, investigator, or Drug and Safety Monitoring Board member for  AstraZeneca ,  Boehringer Ingelheim ,  GlaxoSmithKline ,  Novartis ,  Teva , and  Mylan. N. R. has consulted for 3M Pharmaceuticals,  AstraZeneca ,  Boehringer Ingelheim ,  Chiesi ,  GlaxoSmithKline ,  Mundipharma ,  Novartis ,  Sanofi ,  Sandoz , and  Teva ; has received honoraria for giving presentations in continuing medical education activities sponsored in whole or in part by  Boehringer Ingelheim ,  Chiesi ,  Cipla ,  GlaxoSmithKline ,  Mundipharma ,  Novartis , and  Teva ; participates in therapeutic trials funded by  Boehringer Ingelheim ,  Chiesi , and  GlaxoSmithKline ; and has received research grants from  Boehringer Ingelheim ,  Novartis , and  Pfizer.
Participants also completed country-specific validated food frequency questionnaires [FFQs], which contained a list of approximately 200 foods and nine frequency of intake categories varying from never eating to several times per day. Recordings of foods were converted to nutrient intake using the European Nutrient Database, a method for estimating total dietary fibre intake. 22 Intakes of total daily dietary fibre and fibre from fruits, vegetables and cereals were calculated. Data on total daily energy intake were also derived from the FFQ. To ensure compatibility between the FFQs used in each centre, a calibration study was performed using a computer-assisted 24-h dietary recall in a sub-sample of each population in each centre on stratified random samples of 36 900 subjects. 18, 23 This was used to correct for any systematic over-or under-estimates of the baseline food frequency questionnaires used and ensure the data could be combined.
The cohort was monitored after recruitment until at least June 2004, and in some centres until 2010, to identify those participants who developed incident CD and UC by linkages with either national or regional registries, follow-up questionnaires. and hospital pathological and radiological databases. All potential cases were reviewed by clinicians to confirm the diagnoses and disease extent within the gastrointestinal tract from the medical records. 21 Cases of indeterminate or microscopic colitis were excluded, as were those with prevalent IBD at recruitment and participants diagnosed with IBD < 18 months after recruitment. The latter helped to ensure the dietary data reflected that prior to the development of symptoms, and for a period between the onset of symptoms and diagnosis. 21 Each case was matched with four randomly selected controls matched for gender, age at recruitment [± 6 months], centre and recruitment date [±3 months].
32 The cohort in the UK, administered from Oxford, is composed of members of vegetarian societies and readers of health food magazines, whose inclusion could affect the generalizability of our findings. However, the proportions of the number of all cases diagnosed in this subcohort were low at 3. 8% for CD and 6. 8% for UC, and the median intakes of fibre between these UK individuals and those in the rest of the cohort were similar. Removing these participants from the analyses did not significantly alter any of the effect sizes or statistical significance of any associations. Only one other prospective cohort study, to the best of our knowledge, has investigated dietary fibre and the aetiology of IBD. Here, in the US Nurses' Health Studies [NHS] dietary, data were collected from 170 776 women, aged between 25 and 55 years at recruitment, who were followed up for 26 years.
cohort of men and women aged 45-74 years. Recruited between 1993 and 1997. Cases identified up to June 2004 from follow-up questionnaires, in-patient admission data and histopathology records. of UK vegetarian societies and readers of health food magazines [78% women], aged 20-80 years recruited between 1994 and 1999. Cases identified up to May 2004 by follow-up questionnaires. cohort of men aged 45-65 years and women aged 35-65 years. Recruited between 1994 and 1998. Cases identified up to June 2007 from follow-up questionnaires. cohort, men and women, aged 35-64 years. Recruited between 1994 and 1998. Cases identified up to April 2007 from follow-up questionnaires. cohort, men and women aged 34-64 years. Recruitment between 1993 and 1998. Cases identified from regional database of IBD up to May 2004cohort, men and women aged 34-65 years recruited between 1993 and 1997.
cohort, men and women aged 30-60 years. Recruited between 1992 and 1996. Cases identified up to February 2007 from regional database of cohort, men and women aged 45-69 years. Recruited between 1991 and 1996. Cases identified up to October 2003 from regional database ofIBDcohort of men and women aged 50-64 years. Recruited between 1993 and 1997. Cases identified up to July 2007 from national database of IBD. aged 40-65 years recruited between 1990 and 1993 who are members of a health insurance scheme for school teachers and co-workers. Cases identified up to July 2009 by follow-up questionnaires. and women, aged 20-70 years recruited between 1993 and 1997 from the general population of three cities [Amsterdam, Doetinchem, Masstricht] and also the breast cancer screening programme in Utrecht.
Anthropometry Self-reported height and weight data were collected each year using a web-based questionnaire. Closest available data after the date of completion of the BIS-11 were used. BMI (kg/m 2 ) was calculated as the ratio of weight to squared height. According to WHO reference values  [1] , participants were classified into four different weight statuses following their BMI: underweight (BMI < 18. 5), normal (18. 5 ≤ BMI < 25), overweight (25 ≤ BMI < 30), and obese (BMI ≥ 30). Obese individuals were further classified into three obese categories: obese class I (30 ≤ BMI < 35), obese class II (35 ≤ BMI < 40) and obese class III (BMI ≥ 40).
Two models were tested: a model without adjustment and a model adjusted on covariates. The adjusted model included the following variables: age, education level, smoking status, alcohol intake, physical activity, employment status, monthly income per household unit and matrimonial status. Missing data on covariates were imputed using multiple imputation. The Hochberg method was applied to correct for multiple testing. All tests of statistical significance were 2-sided and significance was set at 5%. Statistical analyses were performed using SAS software (version 9. 3, SAS Institute Inc. , Cary, NC, USA).
Acknowledgments: We thank all the scientists, dietitians, technicians and assistants who helped carry out the  NutriNet-Santé study. We especially thank the computer scientists  Younes Esseddik ,  Yasmina Chelgoum ,  Mohand Ait Oufella ,  Paul Flanzy  and  Thi Hong Van Duong ; the statisticians  Veronique Gourlet ,  Charlie Ménard ,  Fabien Szabo ,  Nathalie Arnault ,  Laurent Bourhis  and  Stephen Besseau. We are grateful to the volunteers of the  NutriNet-Santé study. The  NutriNet-Santé Study  is supported by the  French Ministry of Health (DGS) , the  French Institute for Public Health Surveillance (InVS) , the  French National Institute for Health and Medical Research (INSERM) , the  French National Institute for Agricultural Research (INRA) , the  National Conservatory for Arts and Crafts (CNAM) , the  Medical Research Foundation (FRM) , the  National Institute for Prevention and Health Education (INPES)  and the  University of Paris 13.
Literature and Patient-Reported Outcomes Instrument Review A targeted peer-reviewed literature search was conducted in the PubMed, PsycINFO, and EMBASE databases to identify qualitative research articles outlining patient-reported PEI symptom and impact concepts. Searches were conducted using disease and qualitative research search terms (Table  1 ) yielding 100 abstracts, six of which met inclusion criteria and were reviewed in full. Symptom and impact concepts identified from the articles informed the development of a preliminary PEI conceptual model. A review of 1520 abstracts identified six existing PRO instruments that have been used in PEI for full review: the European Organisation for Research and Treatment of Cancer core questionnaire  [19] , the European Organisation for Research and Treatment of Cancer pancreatic cancer questionnaire  [20] , the Digestive Diseases Questionnaire  [21] , the Functional Assessment of Cancer Therapy Hepatobiliary Symptom Index  [22] , the Gastrointestinal Symptom Rating Scale  [23] , and the Gastrointestinal Quality of Life Index  [24].
All interviews were audio-recorded, transcribed verbatim, and translated into English where relevant. Transcripts were quality checked by the interviewer who conducted the interview to ensure consistency and accuracy in transcription prior to analysis; however, transcripts were not returned to participants for comment because of project time restraints. Qualitative analysis was performed using Atlas. ti software, which involved grouping of quotes into themes using thematic analysis methods  [27]. All themes identified were driven by data rather than a priori assumptions. A coding tree was developed prior to analysis of any interviews to structure how concepts and sub-concepts would be coded. The coding tree was used consistently to guide coding of all the interviews (Fig. 2 ). A team of three experienced qualitative data coders (N.
It is still possible that some of the symptoms identified are due to CP or CF, for example, epigastric pain. This will be further explored in a quantitative validation study that is already underway, and it is possible that some symptom concepts currently included may be deleted based on the findings of that study. Another strength of the study is that patients were recruited from three countries, ensuring findings have cross-cultural relevance. However, the study has some limitations. Data were collected in France, Germany, and the UK only; further study in other countries and outside Europe would provide further confidence in the cross-cultural validity of the PEI-Q. That said, major differences are considered unlikely given that no differences were found across the countries studied. Another study limitation is that some patients' PEI was diagnosed by symptoms reported rather than laboratory-based tests, allowing the possibility that patients may not have been correctly diagnosed with PEI.
This method was chosen to ensure feasibility and practicality of the study and also reflects clinical practice. Moreover, most participants were diagnosed using clinical tests such as the fecal elastase test, and no differences were identified in symptoms reported between patients diagnosed via different methods. However, we do recommend that future studies collect data from patients diagnosed using laboratory-based tests to cross-validate these findings. This paper describes the first phase of development of the PEI-Q using qualitative interviews, ensuring the full patient experience is captured. Work thus far has been qualitative, leading to a list of symptom and impact concepts to document the comprehensive PEI symptom experience and the associated impact on patients' wellbeing. Symptoms and impacts identified have been integrated into the PEI-Q instrument.
Acknowledgements Mathias Schifflers was an employee at Abbott at the time this work was conducted and was involved in all aspects of the research. Chloe Tolley  and  Laura Maguire  were employees at Adelphi Values and were involved in the conduct of interviews and qualitative analysis of the interview data. Caroline Jonquet was employed by Zeste Research and conducted the interviews in France. Sabine Bielfeldt , as an employee of Medical Market Research, conducted the patient interviews in Germany.
Introduction Early infant diagnosis and therapeutic innovations mean that individuals with perinatally acquired human immunodeficiency virus (PHIV) or HIV acquired during early childhood are increasingly surviving into adolescence and adulthood  [1]. The young people affected are still very small in numbers in northern countries. Given the existing databases, we can only estimate the numbers of young people with HIV acquired during the perinatal period or in early childhood. For example, in 2014 in France, 3930 children and adolescents (up to 14 years) benefit from exemption from their care costs for infection with HIV thanks to universal health insurance, they represent less than 4% of HIV population  [2]. In the United States 3121 adolescents (up to 14 years) were living with diagnosed HIV infection in 2013-less than 1% of the diagnosed HIV population  [3].
Participants identified in this primary listing were used as informants in a snowball procedure. They were asked if they had contacts with professionals involved in healthcare transition of young people with PHIV and if they were willing to provide us directly with potential respondents' contact details. All these recommended professionals were invited to participate, and recruitment of participants continued based on diversification until empirical saturation of the data appeared to have been reached. Saturation means that no additional data are being found whereby the researcher can develop the properties of the category. Seeing similar instances over and over again, the researcher becomes empirically confident that a category is saturated  [22]. Our sample was constructed with the aim of providing a comprehensive overview of situations and problems encountered by professionals involved in transition.
Coding and analysis Interviews were transcribed verbatim by a professional transcriber and digitalized notes taken during the interviews were coded. Contents were analyzed with NVivo1 10 software. Codes were generated through a process of inductive identification of themes  [23]. Transcripts were first coded independently by two of the authors (EL, SG) who had formal training in the analysis of qualitative data. Emerging themes and analytical framework were discussed by the researchers after each working session to reach a consensus on coding. An agreed preliminary coding framework was presented to a multidisciplinary group from the "SocieteFrancaise de Lutte contre le SIDA" in a workshop on the theme "HIV-positive teenagers" with teams from France, French overseas departments, and Francophone countries who had experience of transition.
This study was funded by a grant from the  Roche Foundation  to our institution (contract number  2014RDB010 ) and by the  French Ministry of Health  ( PREPS2013 ). The first author was supported by a doctoral contract funded by the  UPMC  UniversiteParis 6 Sorbonne Paris Citefor this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The availability of suitable infrastructures for performing low dose risk research was specifically addressed by DoReMi. Experimental radiation research is highly dependent on the availability of appropriate radiation sources that are reliable, capable of delivering a range of radiations, are robust and accurate. Low dose research also needs access to welldefined epidemiological cohorts, reliable databases and biobanks and as well the appropriate platforms for analysis. After the initial mapping of infrastructures and their availability, DoReMi has provided access to several new infrastructures that will enhance the European capabilities in addressing scientific questions relevant for low dose risk. Prospects for molecular epidemiologic studies in the European scale were addressed by reviews on potential biomarkers for ionizing radiation  (Pernot et al.
An open consultation process via website and the annual workshops is regularly conducted, the results of which are taken into account in the revised SRA report. Prior to calls for research, in addition to the SRA report short statements presenting the top priorities are developed by the radiation protection research platforms and an open consultation process is initiated. With regard to the sustainable data management, databases and procedures were developed throughout the 1990s and early 2000s to address the needs of the scientific community and radiation protection. Radiobiological archives were developed in ERA-PRO and STORE projects  (Schofield et al. 2010). Later on, STORE was adopted in DoReMi to provide a sustainable infrastructure for knowledge management in the area of low dose risk.
In radioecology, extensive radioecological databases such as FREDERICA were developed  (Garnier-Laplace et al. 2008 ). Such developments have been carried on and continued in the infrastructure activities of OPERRA, COMET and CONCERT. To ensure sustainability of infrastructures, MELODI and Radioecology ALLIANCE have established dedicated Working Groups on Infrastructures with the aim of ensuring availability, continuous development and quality assurance of necessary research infrastructures at the European level. These infrastructures include low dose and low dose rate irradiation facilities, databases and biobanks, analytical platforms and radioecological observatories (i. e. contaminated sites for field studies). Educating the next generation of researchers in radiation sciences is one of the major aims of the European radiation protection research community.
Acknowledgements Dr William (Bill) Morgan  closely followed the development of the European radiation research area. During the years, he participated in advisory committees of several EU projects, including NOTE, EpiRadBio and  DoReMi. Bill  was a wonderful advisor, very knowledgeable, critical but encouraging. The first author of this paper ( Dr Salomaa ) met him for the last time at the ICRP meeting in Soeul, Korea, just 3 weeks before he passed away. Bill spoke about his retirement plans and looked forward to the final DoReMi meeting in Budapest in the first week of December. Bill never made it but he was there anyway. In our minds and hearts.
Funding The research leading to these results has received funding from the  European Atomic Energy Community Seventh Framework Programme   FP7/2007-2011  under grant agreement no. 249689  (DoReMi), the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement no. 604984  (OPERRA) and from the  Euratom  research and training programme  2014-2018  under grant agreement no. 662287  ( CONCERT ).
Materials and methods Proteins associated to the multimorbidity of asthma, eczema and rhinitis Data sources. We built a set of disease-associated genes from the following databases: Online Mendelian Inheritance in Man (OMIM)  [17] , ENSEMBL 77 Short Variations  [18]  databases (via BioMart  [19] ) and the Comparative Toxicogenomics Database (CTD)  [20]. OMIM and CTD provide highly reliable gene-disease associations characterized through various experimental procedures and a process of expert curation of the literature. Since CTD contains a hierarchical collection of diseases, we considered genes associated to any of our diseases of interest and their descendants. Furthermore, only genes labeled as marker (i. e. experimentally associated with a disease) in the CTD database were used. Ensembl Variation contains curated information on disease-associated genetic variations from linkage data, genome-wide association studies and other genomic sources.
Because the use of GWAS-derived data as a means for characterization of risk factors is debated  [21] [22] [23] , we wished to evaluate the influence that GWAS-derived data might have on our results. Thus, we repeated our analysis with a set of disease-associated gene set that excludes data derived solely from GWAS studies (S1 Text). Because the aim of our study was to explore the mechanisms of the diseases in the framework of the cellular network of protein interactions, the proteins encoded by the diseaseassociated genes were obtained in UniProt nomenclature  [24]. Thus, only gene products known to exist at protein level (as defined by the UniProt database) were considered. Details on the databases and on the characterization of the gene-disease associations can be found in S1 Table and S2 Text.
In the first one, protein-disease associations were randomized from all proteins in the proteome  (14, 754)  to generate a null distribution  [26, 27]. This model tested whether the fraction of common proteins was higher than random expectation, and will be simply referred to as random model. We generated 10 3 instances of this model, and the statistical significance was assessed by means of a z-test. The second model tested if the observed fraction of common proteins was significantly higher than expected for any pair or trio of randomly chosen diseases belonging to the Immune System Diseases category of the CTD database. We generated 10 3 pairs and trios of these diseases avoiding the grouping of diseases that are subtypes (or descendants, in CTD terminology) of one another. The list of the selected immune system diseases and their associated proteins can be found in S2 Table.
Network connectivity between asthma, eczema and rhinitis Functional Interaction Network. In order to identify interactions between proteins associated to asthma, eczema and rhinitis, we built the functional interaction network (FIN). The FIN was obtained by combining data from: (1) the Reactome Functional Interaction Network (v. 2013), which contains pairwise protein interactions of different nature such as protein-protein interactions, gene expression interaction, metabolic interactions and signal transduction  [29]  (interactions annotated as predicted were discarded, as were those with score 0. 5, as suggested by the authors); (2) the HIPPIE network, which integrates multiple experimental protein-protein interaction datasets  [30]  (only HIPPIE interactions scoring > 0. 73 were considered, as they are accounted as high confidence by the authors); and (3) the innateDB database, which maintains a curated collection of protein-protein interaction data centered on innate immunity proteins  [31].