dataesr/scientific-paragraphs-categorization huggingface dataset:
Funding: This research was funded by the  EU 's  Horizon 2020 research and innovation program  under grant agreements # 234880  ( EDC-MixRisk ) and # 825759  (ENDpoiNTs), and by the  US National Institutes of Health  # T32ES0007334  and # R01ES015276. Institutional Review Board Statement : Not applicable as the NHANES data are publicly available. Informed Consent Statement: NHANES data are publicly available, and consent statements are handled by  CDC NHANES-Informed Consent  (cdc. gov).
Methods We developed automated reports and presentations with Rmarkdown (R packages knitr, version 1. 39 and rmarkdown, version 2. 14), a technology implemented with R 1 Corresponding Author, Antoine Lamer, F2RSM Psy, Lille University, 2 place de Verdun, F-59000, Lille, France; E-mail: antoine. lamer@f2rsmpsy. fr. (version 4. 1. 3). Two reports formats were developed, a national report for presentation to the French Ministry of Health and Prevention and a regional for each calling center. They contain common indicators, such as the number of received calls, answered call and the response rates. The projection of expected activity for the next two months is performed with an ARIMA model (R package forecast, version 8. 20). Reports could also contain specific studies on the impact of an event on the activity of the helpline.
1° latitude × 0. 1° longitude. The coupled hydrodynamic biogeochemical model is driven at the open ocean boundaries by an Earth system model developed at the Max Planck Institute (MPI-ESM-LR;  Giorgetta et al. 2013 ) and run as part of the Coupled Model Intercomparison Project Phase 5 (CMIP5), in combination with downscaled atmospheric forcing data generated by the Swedish Meteorological and Hydrological Institute Rossby Centre Regional Atmospheric Model, also driven by MPI-ESM-LR. We used 2 sets of POLCOMS-ERSEM outputs: the mean annual carbon biomass of zooplankton and benthic secondary producers from 2006 to 2099. In ERSEM, zooplankton was subdivided into 3 size classes of zooplankton categorized as heterotrophic flagellates, microzooplankton and mesozooplankton, while benthic secondary producers included 3 types of benthic fauna: suspension feeders, deposit feeders and meiobenthos  (Butenschön et al.
Study area and fisheries Our study focused on the European continental shelf from the North Sea to the Strait of Gibraltar, divided into 15 ICES divisions (Fig. 1 ), including the North Sea (4a-c), Western Scotland (6a), Irish Sea (7a), Western Ireland (7b), Celtic Sea (7f -h), English Channel (7e,d), Bay of Biscay (8a,b) and Iberian Coast (8c and 9a). We focused on these 15 areas since they are the most productive and exploited areas of the European continental shelf managed or comanaged by the European Union (before Brexit). Moreover, these areas offer the best spatial resolution at which catches are reported by governmental statistical offices, and were spatially covered by the coupled hydrodynamic-ecosystem model POLCOMS-ERSEM. Catch data from 2013 to 2017 were obtained from the ICES data collection (ICES 2020).
The fisheries catch statistics were reported annually by the national offices, and then prepared and published by ICES in the official catch statistics dataset for the Northeast Atlantic. The catch statistics included catch of fish, crustaceans, molluscs and other aquatic organisms, at the spatial resolution of ICES divisions. A low proportion of catch was reported for a pool of 2 or 3 ICES divisions. These catches were distributed among divisions proportionally to the mean allocated catch of the period. For each species, we assigned a trophic pathway (pelagic or bentho-demersal) based on their feeding affinity reported in FishBase (www. fishbase. org; Froese & Pauly 2000) and Sea -LifeBase (www. sealifebase. org; Palomares & Pauly 2020). If information on feeding affinity was not available, we used information on their associated habitat to categorize their trophic pathway.
(20) V act = -ζ 1 + ζ 2 T + ζ 3 T ln(C O ∂ ) + ζ 4 T ln(i) (21) C O 2 = P O 2 5. 08 × 10 6 e 498 T (22) V ohm = i(R m + R c ) Objective function. The sum square error (SSE) between the measured (V data ) and model output data (V data ) will be used as an objective function. The objective function can be constructed as follows: where N represents the data size, and x represents a vector containing seven unknown parameters. The FC data are compared with those generated by the model, and the fitness value is calculated based on the error between them. The model is developed in MATLAB script, and the data are loaded from the Excel sheet file. The identification is an iterative process that updates the candidate solutions at each iteration by sending them to the MATLAB script that includes the FC model and simulates it after that, and then generates the fitness value.
This process repeated until the last iteration. Results. The suggested RTH algorithm will be used to extract the seven unknown characteristics of three PEM fuel cells: the NedStack PS6, the BCS 500W, and the SR-12 500W. Table  15   87  provided the accurate values of the parameters, testing operating conditions, and measurement data for the tested PEMFC types. The upper and lower limits of the empirical parameters are presented in Table  16. The results are compared to those published for the same FC types. Table  17  shows the comparative findings for the BCS 500 W type, Table  18  for the NedStack PS6, and Table  19  for the SR-12 PEM 500 W. The comparison findings are primarily based on sum square error (SSE). Based on the findings reported in Table  17 , the suggested method-based RTH performed the best of all the reported techniques in this comparison to extract the parameters of the BCS 500W.
Methods and analysis We plan to carry out the living systematic review with metaanalysis in the second half of the year 2023. The methods of this systematic review with meta-analysis were registered in the International Prospective Register of Systematic Reviews database (PROSPERO) on the 24th of April 2023 (registration number CRD42023416996). Prior to starting this project, we searched PubMed, PROSPERO, and Cochrane Central Register of Controlled Trials (CENTRAL) to confirm that no systematic reviews or meta-analyses with the same research questions had recently been published or were currently being conducted. The protocol of this systematic review and meta-analysis is in accordance with the Preferred Reporting Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) guidelines  (Shamseer et al.
Information sources The authors [Wouter A. J. Vints and Ioanna Zorba (Zormpa)information specialist] will search in PubMed, EMBASE (through Elsevier), PsycINFO (through EBSCO), all databases of Web of Science (excluding MEDLINE), SportDiscus (through EBSCO), LILACS (accessed through Portal Regional da BVS), IBECS (accessed through Portal Regional da BVS), CINAHL (through EBSCO), SCOPUS (Elsevier), International Clinical Trials Registry Platform (ICTRP) accessed through CENTRAL, and ClinicalTrials. gov (CT. gov) accessed through CENTRAL. None of the databases will be restricted by date. The searches will be re-run prior to the final analysis. 10. 3389/fnagi. 2023. 1213057.
Search details Literature search strategies are developed using free text words and index terms related to: middle or older age AND physical exercise AND cognition AND myokines. Supplementary Appendix A includes a transcript of the free terms used in the search strategy and the index terms per database where applicable. The search strategy was translated for each of the used databases in a way that they remained as equal as possible, using the same free text terms, and searching for the most similar index terms. The search strategy was developed by Wouter A. J. Vints, who has expertise in the topic of the review with the help of Ioanna Zorba (Zormpa) who works as an information specialist, and was approved by all collaborating authors. Details of the used limitations and filters are provided in Table  1.
Data extraction Following the selection process, pairs of two authors will independently extract the following information: -The name of the first author -Year of publication  -Acute effect in trained/untrained individuals, or chronic effect (how long after the last exercise bout was the cognitive outcome measured and the blood collection performed) -Sample size in treatment and control group -Standardized mean differences (SMDs) between control and treatment group on myokines (or the necessary statistics to calculate SMDs) -SMDs between control and treatment group on cognitive functioning (or the necessary statistics to calculate SMDs) -Bivariate correlations between myokines and cognitive functioning (preferably in the total sample, or else per condition) -Bivariate correlations between different types of myokines (preferably in the total sample, or else per condition) -Bivariate correlations between different types of cognitive functioning (preferably in the total sample, or else per condition).
Meta-analysis with MASEM If data is appropriate for synthesis, we will conduct a metaanalysis using random effects meta-analyses. We will assess the effect of exercise on each of the myokines and each of the cognitive functioning outcomes that are included in at least three or more included randomized controlled trials. A path model (see Figure  1 ) will be evaluated using one-stage meta-analytic structural equation modeling (MASEM). One-stage MASEM is essentially a random-effects multivariate meta-analysis on correlation coefficients, in which the average correlations are restricted to follow the structure of the hypothesized path model. In its simplest form, the random-effects multivariate meta-analytic model decomposes the vector r k of correlation coefficients for a study k in three parts: r k = ρ R + u k + ε k , (1) where ρ R indicates the vector of means of the correlation coefficients over all studies, u k is a vector of deviations of study k's population correlation coefficients from ρ R , and ε k is a vector with the sampling deviations of study k.
(2021). This process will be led by co-author Suzanne Jak. The analyses will be conducted using the metaSEM package in R  (Cheung, 2015). Since one-stage MASEM uses correlation coefficients as input, the SMDs on myokines and cognitive functioning will be transformed to point-biserial correlations with a target base-rate of 0. 50 (see  McGrath and Meyer, 2006). The MASEM will lead to estimates of each of the direct effects in the path model, as well as estimates of the indirect effects of exercise on cognitive functioning through the different myokines. Statistical significance of direct effects will be evaluated using Wald-tests with a significance level of 5%, and statistical significance of mediating (indirect) effects with 95% likelihood-based confidence intervals  (Neale and Miller, 1997; Cheung, 2022).
If new studies are found with likely effects on the effect estimates or the certainty of evidence, the date of the last search will be updated, the details of the new evidence will be added and data will be extracted, quality will be assessed and synthesized and the studies will immediately be incorporated in the paper. Once this process is completed, the updated living systematic review and meta-analysis will be submitted for re-publication in an open access international peer-reviewed journal as soon as possible, preferably a journal that has the resources to support a living systematic review. A summary is presented in Table  2.
ABSTRACT Introduction Friedreich ataxia (FA) is the most common hereditary ataxia in Europe, characterised by progressively worsening movement and speech impairments with a typical onset before the age of 25 years. The symptoms affect the patients' health-related quality of life (HRQoL) and psychosocial health. FA leads to an increasing need for care, associated with an economic burden. Little is known about the impact of FA on daily lives and HRQoL. To fill that gap, we will assess patient-reported, psychosocial and economic outcomes using momentary data assessment via a mobile health application (app).
Insights into the app's usability could be used for future studies using momentary data assessments to measure outcomes of patients with FA. Ethics and dissemination Ethical approval has been obtained from the Ethics Committee of the University Medicine of Greifswald, (BB096/22a, 26 October 2022) and from all local ethics committees of the participating study sites. Findings of the study will be published in peerreviewed journals, presented at relevant international/ national congresses and disseminated to German and French Patient Advocacy Organizations. Trial registration number ClinicalTrials. gov Registry (NCT05943002); Pre-results.
In addition, previous studies were based on small sample sizes, annual assessments and retrospective questionnaires, which are likely affected by recall bias, and unable to capture in-depth insights into patients' everyday life and health fluctuations. As a prerequisite for generating this evidence, momentary data collection, known as the experience sampling method, or daily diary method, is an intensive longitudinal research methodology that assesses patients' data on multiple occasions over time. This data collection method can offer more detailed insights in real time and a more comprehensive understanding of the impact of FA on the patients' and families' everyday life. To obtain a comprehensive picture of the impact of FA on patients' daily life and the healthcare system, the PROFA Study uses an innovative approach through a patient-centric mobile health application (m-health app) and a momentary data collection on a daily to monthly basis over 6 months to assess patient-reported and psychosocial outcomes as well as the economic impact of FA.
METHODS AND ANALYSIS Study design The PROFA Study is a multicentric, prospective, observational study. Eligible patients will be recruited from six study centres in Germany (Aachen, Bonn, Munich and Tübingen), Austria (Innsbruck) and France (Paris), completing a baseline assessment via face-to-face interviews at the six study centres and multiple follow-up remote online momentary data assessments via a m-health app on a daily to monthly basis for 6 months to evaluate the patient-reported, psychosocial and health economic outcomes in FA. The main study design of the PROFA Study is demonstrated in figure  1.
18  There are no standard criteria in sample size calculation for this type of study. Thus, the sample size considerations are based on the literature, reporting that more than 90% of validation studies of patient-reported outcome measures include a minimum of 100 participants. 19  In the previous study EFACTS, the same study centres that are also participating in the PROFA Study have recruited n=200 patients with FA. Based on the recruitment of the EFACTS Study, we assume an initial sample size of 200 patients for six study centres within a 1-year time frame. This number was determined based on original prevalence data and the estimated monthly recruitment deemed feasible by the participating European centres. 18  Patient and public involvement Two Patient Advocacy Organizations (PAOs) from Germany and France participate in the PROFA Study.
The PAOs are involved in (1) the final conceptualisation phase of the study before starting the data assessment to receive added value by confirming the existing and identifying further patient priorities of the PROFA Study and by bringing the patient perspective into the study design; (2) during the study when data assessment is running to evaluate if the study participants are adequately informed about the study and if the assessment procedures are appropriate; (3) after completing the data assessments and analyses to improve the dissemination of the study results using their extensive networks within the FA community and to reach out to policymakers, regulators and other patient organisations. For this purpose, PAOs are members of the executive board of the PROFA Study, attending the annual consortium meetings.
Data assessment procedures Participants will complete baseline assessments via faceto-face interviews in the Austrian, French and German study centres. Subsequently, participants will self-complete multiple follow-up assessments via a study-specific app (Atom5, Aparito). The app is part of the Atom5 platform that enables remote and digital capture of patient-generated data. Atom5 is ISO 27001 Information Security Management System and ISO 13485 Quality Management Systems accredited and available on both iOS and Google Play stores. It is multilingual and disease agnostic, configured as required for each study protocol. The baseline and follow-up assessments include a broad range of measures, capturing patientreported and psychosocial outcomes, clinical parameters and healthcare utilisation indicators.
The participants will complete a test survey over the app under the supervision of a clinician. This is essential to ensure a high-quality data assessment, familiarise the patient with the remote, digital survey and prevent possible handling issues with the app. To improve app usability, a guide for handling the app with information about the completion of tests and surveys, the most common problems and solutions and contact details of the study centre will be handed out to participants. All study centre physicians participating in the study will receive standardised training and a handbook with information about the data collection and  Open access instructions about using the REDCap study centre database and the m-health app assessment. Subsequently, participants will self-complete tests and surveys daily to monthly for 6 months.
Within these focus groups, participants should directly mention the communication difficulties that affect their psychosocial health. A protocol with open-ended questions related to personal, professional and psychosocial aspects will be used to facilitate the discussion during the focus group meetings. The qualitative analysis of the focus groups will be done by three speech therapists who will independently code the transcriptions of the focus groups for the content analysis until data saturation will be reached. A coding tree will be created by identifying minor themes associated with overall central themes. A bank of items will be elaborated and used to build the new COMATAX scale. Cognitive interviews will be conducted to choose the more precise formulation of items.
Specifically, our research on speech and hearing and patients' HRQoL will be highly relevant for designing targeted, quality-controlled, standardised treatment and rehabilitation programmes that aim to improve patients' health. For the first time, the PROFA Study will assess in-depth real-time data in FA by using a remote m-health app. The obtained data on the acceptability and usability of the m-health app can also be used for future studies in FA or other rare diseases using momentary data assessments and interventions that aim to improve outcomes of patients with FA. This underlined the current trend of electronicbased research, reaching now the setting of FA. Patients can state and self-track their health, health service utilisation and specific health events, which could also be beneficial for patients themselves, helping them to monitor and manage all aspects of their health.
express special thanks to the  PAOs (Deutsche Heredo-Ataxie-Gesellschaft  and  Association Française  Funding The  PROFA Study  is funded by the  European Union 's research and innovation program  Horizon  by the  European Joint Programme on rare Diseases  (EJD RD,  COFUND-EJP  no. 825575 ). Under the umbrella of EJP RD, the  PROFA Study  is supported by the following funding agencies:  Federal Ministry of Education and Research, Germany  (grant number  01GM2110 );  Agence Nationale de Recherche/French National Research Agency, France  (grant number  ANR21-RAR4-0003-04 ); and  Canadian Institutes of Health Research-Institute of Genetics. Competing interests None declared. Patient and public involvement Patients and/or the public were involved in the design, or conduct, or reporting, or dissemination plans of this research.
2001; Jordan et al. 2004; Dong et al. 2012; Pegueroles et al. 2013 ). The OdsH duplicate has been proposed to be a new gene in the Sophophora subgenus  (Ting et al. , 2004)  and is associated with speciation in this clade, and we would not expect to see this gene further in Drosophila phylogeny. However, a search in the GenTree database  (Shao et al. 2019 ) indicated the presence of OdsH in the ancestral node of the Drosophila genus, highlighting that its origin might be older than previously thought. We have thus asked the following questions: 1) how extensive is the presence of the OdsH duplicate in the phylogeny; 2) did neofunctionalization in testis occur before the divergence of the melanogaster subgroup; and 3) is OdsH associated with speciation in other recent species, beyond the Sophophora subgenus, such as the mojavensis complex (subgenus Drosophila)? We show that 1) the duplication occurred much earlier than previously proposed, dating back to 62 Mya in the Drosophilinae ancestor, 2) OdsH evolved under less intense negative selection than its paralogue unc-4 and has features that allow the proposal of its ancient neofunctionalization in testis in the Drosophila genus, and 3) despite the presence and expression of OdsH in testis of the mojavensis complex, no clear association was established with the observed hybrid sterility in the crosses between species of this group.
Expression of OdsH and unc-4 in D. arizonae, D. m. baja and their Hybrids The analysis of the Drosophila transcriptomes available in public databases (D. pseudoobscura: PRJNA291085; D. grimshawi: PRJNA317989: T. dalmani: PRJNA240197; other species: PRJNA388952) showed that both genes have low expression levels. However, unc-4 seems to be mainly expressed in somatic tissues, whereas OdsH seems to be specific to male reproductive tissues (Supplementary Fig. S8 , Supplementary Material online). This is expected in the cases of neofunctionalization, suggesting that OdsH neofunctionalization occurred rapidly after its origin. To  Notes -blue: DAPI; red: OdsH probes. H: hybrid. To identify whether the expression of OdsH could be quantitatively differentiated in these hybrids, we quantified its expression in the testes of the parental species and their hybrids by RT-qPCR (Supplementary Table  S7 , Supplementary Material online).
5 ). Regarding OdsH, by using public datasets from NCBI, we observed expression exclusively in male reproductive tracts and testes in Drosophila, except for D. pseudoobscura (Supplementary Fig. S8 , Supplementary Material online). We also found that OdsH expression levels were higher (from 169. 5 to 340 normalized read counts) than unc-4 expression levels (less than 50 normalized read counts)  (Banho et al. 2020 ) in transcriptomes of the reproductive tracts from two D. mojavensis subspecies and D. arizonae previously sequenced by our group (BioProject NCBI PRJNA691040). Additionally, the expression levels of both genes in the female reproductive tract were lower than 10 counts  (Banho et al. 2021). In contrast to unc-4, the OdsH sequence was enriched in a greater diversity of TFBSs in its regulatory regions (Fig.
2004 ). Analysis of synteny was performed manually considering the Drosophilidae genomes available in the OrthoDB database  (Zdobnov et al. 2021). For S. lebanonensis and L. varia, which are not available in OrthoDB, BLASTX  (Altschul et al. 1997 ) was used on the D. melanogaster protein database, considering a threshold of 70% or similarity and coverage. In addition, we also looked for unc-4 and possible duplicates in the publicly available genomes of Diptera, which are outgroups of Drosophilidae (Supplementary Table  1 , Supplementary material online). Since we found only a single copy duplication in these taxa, as in Steganinae, we decided to use only Steganinae data as the duplication outgroup for further analysis.