dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments miro@urv. cat);Sweden:  Jonas BERQUIST  ( Uppsala University Analytical Chemistry , Husargatan 3, 599, Uppsala; jonas. bergquist@kemi. uu. se), Jonas BLOMBERG  ( Uppsala University, Medical Sciences, Academic Hospital, Uppsala ; jonas. blomberg@medsci. uu. se);United Kingdom:  Eliana LACERDA ,  Luis NACUL  ( London School of Hygiene and Tropical Medicine ,  Keppel Street , London; luis. nacul@lshtm. ac. uk), Derek PHEBY ,  Jonathan EDWARDS  ( University College London, Rayne Institute, University Street , London; jo. edwards@ucl. ac. uk), Xia WANG  ( School of Pharmacy, Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich ; xiasteverding@gmail. com).
Data collection The present analysis was performed for all events reported and analyzed from 2007 to 2013. Data were prospectively collected at each meeting. Each report indicated names and occupations of the participants (physician, nurse, pharmacist, pharmacy technician, pharmacy student, physiologist, research assistant), number and short description of all events, names and work category of the pilot and copilot assigned to the analysis, systematic analysis of the chosen event, and corrective actions. We retrospectively classified the type of event (type of process or product) and the stage in the process (prescription, dispensation, administration, supply chain) for all events, and drug classes (according to the International Classification for Patient Safety and classifications usually used in intensive care studies  3, 13  ) and typology in addition for MEs.
Material and methods We developed a two-arm decision-analytic model using TreeAge Pro Healthcare software (TreeAge Software Inc. , Williamstown, MA, USA) structured to reflect implementation of legal recommendations in France  [11, 12]  as well as French guidelines for maternal and congenital toxoplasmosis diagnosis and treatment  [13]. It was validated by two independent experts (R. Piarroux of Sorbonne University, France and E. Petersen of Aarhus University, Denmark). Each expert assessed the global logic of the tree as well as its consistency with the practices (R. Piarroux for French practices and E. Petersen for Danish screening). The final structure of the tree is detailed in S1 Appendix. The target population was French pregnant women and their children. The consequences of congenital toxoplasmosis were based on the Lyon cohort (Toxo-Ly  [5] ) and considered outcomes until 15 years of age, as few data are available beyond that point.
Epidemiological parameters Screening/diagnostic test performances and probabilities of each clinical event were obtained from a systematic critical review of the available literature, detailed in S3 Appendix. Data from the Toxo-Lyon cohort, which includes all pregnant women monitored at the Croix-Rousse Hospital (Lyon University Hospital, France) since 1987 for primary Toxoplasma infection detected through prenatal screening  [5, 6] , supplemented data from the literature (See S4 Appendix). When data were not available, we relied on the opinion of three experts i. e. : E Petersen, R Piarroux, and M Wallon for defining the central estimate of unknown probabilities as well as their possible range of variation. All probabilities and their sources are presented in Table  1. Main baseline parameters were: 37% prevalence, maternal infection in 0.
Effectiveness The reference and alternative strategies were compared at two endpoints: 1) one year of age, when CT can be accurately confirmed or rejected and the major consequences of the disease as well as of the prenatal management have occurred; 2) 15 years, the latest age at which validated outcome data are available and the main sequelae have been diagnosed. Two types of adverse events were considered: 1) strictly Toxoplasma-related events (STRE) and 2) global events. STRE are cases of congenital infection either recognized or not. Of note, STRE include toxoplasmosis-related fetal losses and neonatal deaths for the short-term assessment, and toxo-related sequelae, including delayed ocular lesions for the long term assessment. Global events (GE) include, in addition to the STRE, fetal loss, termination, neonatal death  that may be due to other fetal diseases or may be induced by the management of toxoplasmosis during pregnancy (i.
Cost data and cost-effectiveness analysis The cost-effectiveness analysis was performed from the perspective of the French Health Insurance System. The prenatal screening strategy was used as the reference strategy. Direct medical costs for pregnant women and children are summarized in Table  2. They include all diagnostic procedures and treatments until age 1 or age 15 respectively, valued using French reimbursements. The French system of care coverage as well as hypotheses underlying the costs calculation is detailed in S5 Appendix. An Incremental Cost-Effectiveness Ratio (ICER) with prenatal screening as the reference was calculated, as: cost of neonatal screening À cost of prenatal screening effectiveness of neonatal screening À effectiveness of prenatal screening : ICER was expressed in terms of cost per additional outcome avoided.
Study population The study cohort consisted of prevalent patients who were treated with haemodialysis between 2010 and 2017, derived from the ERA-EDTA Registry. The ERA-EDTA Registry collects data on renal replacement therapy (RRT) via national and regional renal registries in Europe on an annual basis. The core dataset includes date of birth, sex, primary kidney disease, date of start of RRT, dialysis modality at dialysis initiation and during follow-up and date and cause of death. In addition, several renal registries also provided additional clinical and biochemical data. For this study we included patients !20 years of age at any time during follow-up from the following eight national and regional registries that provided data including haemodialysis session duration and frequency: Austria, Catalonia (Spain), France and Scotland (the UK) (2010-17), the French-speaking part of Belgium, Finland, Norway and Sweden (2010-16).
Variables in the imputation model included age at each record (years), age at the start of dialysis (years), sex, primary renal disease, previous kidney transplantation (yes/ no), dialysis vintage (years), time on RRT (years), time since transplantation (years), indicators of censoring, transplantation and death at each record and at any time during follow-up, indicators of treatment at each record and during follow-up and comorbidities (diabetes, cerebrovascular disease, ischemic heart disease, peripheral vascular disease, congestive heart failure and malignancy). We analysed each of the imputed datasets separately and pooled the results according to Rubin's rules  [24]. As patients from France constituted most of the study population (71% of all patients), we repeated all analyses excluding data from this registry.
The major strength of this study is that by using data from population-based national and regional registries contributing to the ERA-EDTA Registry, our cohort covered all adult patients treated with haemodialysis in the respective countries and regions, thus representing a large, unselected population. We therefore believe our results are generalizable to a broad population of European patients treated with haemodialysis. Also, we used marginal structural models for causal inference, which are sophisticated statistical methods to account for the propensity of healthier patients to survive to transfer to EHD. Nevertheless, our findings should also be viewed within the context of certain limitations. The ERA-EDTA Registry depends on data provided by national and regional registries, which did not include haemodialysis session duration and frequency in many registries.
In addition, we studied prevalent patients treated with haemodialysis, which may have introduced survivor bias. Furthermore, data on reasons for transfer to EHD were not available. This may have included a full-time job or other daily activities that are accompanied by more favourable outcomes, introducing potential indication bias. Other limitations include unavailable data on clinical information, including vascular access type, type of dialysis membrane, ultrafiltration rate, actual amount of delivered haemodialysis and transplantation eligibility. Also, we did not distinguish between haemodialysis and haemodiafiltration, which could have led to lower estimates due to potentially more frequent haemodiafiltration in conventional regimens, which may improve survival  [42]. Nevertheless, every observational study is limited by potentially unmeasured confounders and selection bias.
Arcos, J. Comas and J. Tort) and the other ERA-EDTA Registry Committee members not mentioned Survival with extended-hours haemodialysis above for their advice in the analysis and the drafting of this article: P. Ambu ¨hl, J. De Meester, M. Evans, P. Finne, J. Harambat, L. Mercadal, M. Nordio, S. S. Sørensen and E. Vidal; and M. Pippias and V. S. Stel in the AMC Registry office for data collection and management. The ERA-EDTA Registry is funded by the ERA-EDTA. This article was written by T. Jansz, M. Noordzij, A. Kramer.
Data collection tool Participant observations, together with the semi-structured interviews, were conducted between October 2015 and January 2016. These two main methods of data production were used to provide an ethnographic explanation of the nurse's role in ATB prescribing. 16 A total of approximately 120 hours of participant observations were completed. Observational field notes of informal conversations of health providers,  17  as well as methodological notes on the institutional protocols, daily activities, physicians' schedules, health workers' environment, presence of a pharmacy and drugs in the nurses' office, etc. … were taken by the researchers. The registered nurses were followed up from the moment of suspicion of an infection until the application of the prescribed ATB. Comprehensive observation reports were written within two days after the observation in each NH.
In addition, the study participants were interviewed at their workplace by the first author. The semi-structured interviews were digitally audiorecorded, as well as transcribed verbatim by the first author and were checked for accuracy by an independent transcriber. The major ethical considerations involved in data collection process were respected in this study. The second author negotiated the directors of NHs and gained approval to access them. A written informed consent was obtained from all study participants. The data were collected anonymously to protect privacy and maintain confidentiality. The research was approved by steering committee.
Data analysis The qualitative data collected were analyzed using inductive content analysis method to identify themes or patterns within data. 18 The analysis of verbatim transcripts of the interviews and detailed field notes was performed in several steps. First, each member of the research team carefully read over each transcript and field note to obtain an overall understanding of the participant's points of view. The qualitative analysis of interviews and field notes was supported by NVivo software (version 11). Phrases that portrayed key thoughts or concepts were highlighted, and similar phrases were grouped to identify the units of analysis. These text units were coded using words or phrases related to the aim of this study. The various codes were compared based on the differences and similari ties and then sorted into two categories to facilitate reporting final results.
Findings A total of 21 transcripts were analyzed. The average age of the study participants was 38. 1 years (SD=13. 8), and the majority (76. 2%) were females (Table  1 ). Six prescriptions of ATBs were observed during the process of data collection. This study revealed several interesting findings. Through direct observation and informal interviews, it was noted that nurses at the NHs were very familiar with the elderly residents. They had to be on-site for at least five days a week throughout the year to assess the residents' clinical condition when symptoms arise, and quickly begin their initial treatment. This quality was based on the notion of 'proximity'. The fact that nurses are close to residents in the sense that they take care of them on a daily basis, implies sharing different moments during each day.
Purpose Job control, the combination of skill discretion and decision authority, is considered a central component of the psychosocial working environment. This longitudinal study examines the relation between job control and risk of incident depressive disorder using a life-course approach. Methods We analyze data from The Danish Work Life Course Cohort study, including all Danish individuals aged 15-30 who entered the Danish labor market during 1995-2009 and were free from depressive disorder at entry (955,573 individuals). We measured job control using a job exposure matrix. Depressive disorders were measured using information from nationwide registers of psychiatric in-and outpatient admissions. Using Cox regression models we estimated the prospective association between job control and risk of incident depressive disorders.
Study population The study population was drawn from the register-based open cohort DAWCO. DAWCO comprises all young individuals aged 15-30 who lived in Denmark and had gainful employment as their main source of income according to Danish registers  [40]  for at least 1 year during the years 1995-2009, and who had not previously been registered as mainly gainfully employed (N = 979,257). The present study population consisted of 955,573 individuals excluding those DAWCO individuals who emigrated (n = 13,087), died (n = 71), or received disability pension (n = 361) in their year of entry, has missing data on gender and migrant status (n = 5176), or had a clinical diagnosis of depressive disorder prior to workforce entry (n = 4989). The individuals were followed annually from year of entry to end of follow-up in 2010 yielding a total of 6,991,811 person years.
The relatively high levels of missing parental education data (maternal education 37. 7% and paternal education 47. 2% in year of entry) were related to the age of the cohort members as parental linkage to education could not be obtained prior to 1980, and to migration status of the cohort members' parents as information on parental education achieved outside Denmark could not be obtained prior to migration to Denmark. We retained individuals with missing parental data in the cohort to ensure cohort completeness, but accounted for missing data in the analyses.
The items used to measure job control can be found in Online Resource Table  S1. Weighing each item equally, we calculated a scale value ranging from 1 to 5 as the mean of item scores. To ease interpretation, we reversed the original scale so that higher scores indicate lower job control. Using the survey data, we estimated the predicted level of control as a function of job group, gender, age and year of data collection. Subsequently, these JEM-values for predicted level of control were assigned to the register-based population. Occupational groups were classified according to the Danish version of the ISCO-88 classification (DISCO-88). The intraclass correlation coefficient (ICC) for the JEM was 0. 30 which is satisfactory compared to other JEM-based exposures for psychosocial work environment factors  [47].
Both variables were measured when the cohort member was 15 years old, but in cases of missing information we retrieved data back to birth or up to age 20. Parental data linkage was only available from 1980 and onwards leaving this information unavailable for 9. 8% of individuals for maternal data and 11. 1% for paternal data. In the analysis we adjusted for missing parental data by dummy variables. Variables on adolescence SES were included as time-invariant in the analyses while adult SES were time varying. Life-course risk factors for depressive disorder: parental psychiatric and somatic diagnoses Additionally, we included variables on all parental ICD10 psychiatric diagnoses prior to the cohort member entering the workforce because pre-vious research shows that parental psychiatric disorder is a risk factor for depressive disorder  [63] [64] [65].
Analysis For all analyses, we used the SAS 9. 4 program package. We used Cox proportional hazard models with time-dependent covariates and calendar time as underlying time axis to estimate the association between level of job control and subsequent risk of incident depressive disorder  [71]. We included both past year level of job control at time t and the accumulated level of job control at time t and all previous years concurrently. We analyzed data with a 1-year time lag and related exposure to job control in year t to outcome during year t+1. We followed individuals from their year of workforce entry until the first diagnosis of depressive disorder or any of the absorbing states: death, emigration or award of disability pension, or end of follow-up 31 December 2010, whichever came first.
Methods This article is the result of a qualitative research conducted in Bamako, the capital city of Mali. Four field missions were held in 2008 (12 weeks), 2010 (3 weeks), 2012 (2 weeks), and in 2014 (1 week) respectively. Data was collected by means of semi-structured interviews, non-participant observation, and document collection. Multiple methods were used to decrease the limits and biases of each method and improve findings, analysis, and interpretation accordingly  [51].
Participants/study subjects The four missions were dedicated to the study of public action around diabetes and enabled us to interview 55 actors. 1 Amongst them, 38 actors were active in the fight against diabetes, including caregivers working both at hospital and community facilities and involved in local associations (5); representatives 2 of diabetes patient associations  (8) ; representatives of the Malian public administration (9); as well as representatives of local and international non-governmental organisations (NGO, 16). We also interviewed 17 representatives of bilateral and multilateral donors, first targeting donors supporting the health sector in general, and then donors funding diabetes more specifically [see Additional file 1]. The missions held in 2010 and 2014 were also dedicated to data collection pertaining to the fight against HIV/AIDS.
Data analysis For the purpose of data analysis, we used an inductive and iterative approach wherein collection and analytical strategies were gradually drawn from the data itself. Recorded interviews and hand-written notes were both transcribed. After each field mission, a vertical analysis was performed, and all interviews and notes taken during observation were coded apart; a horizontal analysis was then performed for each theme, wherein we triangulated information related to each disease from different sources, including document reviews. A comparative analysis of transversal themes was finally performed between the two diseases. The analysis was progressively refined with the newly data collected in successive missions  [52]. We stopped data collection when saturation was achieved, that is no new themes and no significant increase in the sophistication of analysis emerged.
Based on theories of public and collective action mentioned in the background section, a historical and cognitive approach was adopted. These theories stress the influence of past events and the importance of collective frameworks. We thus retraced the history of the fight against diabetes and HIV/AIDS and took into account the specific contexts within which patients were engaged and participatory practices were developed. We focused on actors' perceptions and knowledge and performed a content analysis of data to explore how different actors viewed the two diseases, and how they perceived patients, their knowledge and skills, both individually and collectively. We also looked at partnerships, resources, and respective interests as these aspects influence actors' strategies and practices. To increase validity and reliability of our findings, data was triangulated by crossing information collected from different methods and sources at different times.
Acknowledgements We gratefully acknowledge all researchers who participated to the broader programmes from which this article derives, as well as all people who contributed to our work and to the completion of this article. The following researchers participated to the program funded by the  French National  research agency from 2007 to 2009:  Isabelle Gobatto  (coordinator),  Annick Tijou Traoré ,  Mireille Bernard †  ,  Rachel Besson ,  Jessica Martini , and  Audrey Fligg. The following researchers participated to the program funded by the  French association Ensemble Contre le Sida/Sidaction  from  2010  to 2012:  Isabelle Gobatto  and  Annick Tijou Traoré  (coordinators), and  Jessica Martini. We are also grateful to the Malian partners without whom the project could not have been carried out, and we are indebted to all the people in Bamako who accepted to be interviewed.
Funding This paper derives from two broader research programs. The first program was titled "From one knowledge to another. Knowledge of caregivers, patients and their families about diabetes in Bamako,  Mali". It  was funded by the  French National research agency (Agence Nationale de la Recherche -ANR ; grant number  ANR-06-APPR-008-01 ) from 2007 to 2009. The second program was titled "Expert and lay knowledge and know-how about patient's role in caring for chronic disease. The examples of HIV/AIDS and diabetes in Mali". It was funded by the  association Ensemble Contre le Sida/Sidaction  (grant number  B120-3-01651 ) from 2010 to 2012. The corresponding author received support from the  Alice and David Van Buuren Fund  and from the  Jaumotte-Demoulin foundation  to complete her study, which is part of her PhD work.
Respondents were randomly selected from opt-in panels to be representative of the general population of each participating country. Based on European telephone survey response rates and our survey topic of homelessness, we expected response rates of approximately 30%. Therefore, initial sample sizes of 2500 per country were taken. The survey questionnaire was translated into different European languages using standardised best practice  14  and interviews conducted using computer assisted telephone interview software. Respondents (18 years and older) were informed of the purpose of the study, intended data use and were assured of anonymity. Respondents were free to decline to participate. Full details of the survey protocol are available. 15.
Respondents' answers were grouped to provide data for past-year, 5-year and lifetime prevalence estimates. Respondents who reported homelessness were asked a follow-up question to determine the time spent homeless: 'How much time in total have you been homeless over your life? Would you say 'less than a week', 'less than a month', 'less than a year', 'less than 2 years', 'less than 4 years', or 'more than 4 years'?'. Respondents' answers were grouped to provide data for homeless durations of 'less than a week', 'less than a month but more than a week',' less than a year but more than a month' and 'more than a year'. Data on sociodemographic characteristics of respondents were collected, namely: gender, age, educational level, professional status, annual household income, marital status and living area as self-reported by respondents (with the question 'would you say that you live in' followed by the options of urban, semiurban or rural areas).