dataesr/scientific-paragraphs-categorization huggingface dataset:
As shown in a companion paper  (Mostafa et al. 2019) , sub-regional differences of climate variability can be evidenced in Egypt. Temperature and precipitation extremes are defined as data outside the 10th-90th percentile range of values of the period of study  (Frich et al. 2002) , and their analysis is done using a methodology similar to the one recommended by the WMO and integrated in the CLIMDEX software  (Donat et al. 2013).
Medical data The raw medical data for the 2006-2016 periods were collected from the Information Centre Department of the Egyptian Ministry of Health and Population (MOHP). The yearly population data for each governorate were obtained from the data published in the CAPMUS reports. The yearly diarrhea morbidity rates of each governorate were obtained by dividing the number of cases of diarrhea recorded by MOHP by the total population, and multiplying these results by 100,000 yields the yearly prevalence of diarrhea in 100,000 populations in each governorate. These calculated values of the diarrhea prevalence were verified by comparison with the data published for the whole Egypt in the WHO annual statistical reports.
Statistical analysis The collected data and the calculated morbidity rates were digitalized. Statistical analysis was done through SPSS version 20. Pearson's correlation coefficient was used to quantify the temporal trend of the incidence of diarrhea and the relationships between this incidence and the meteorological parameters. The multiple linear regressions were used to identify the most effective meteorological parameters, in the form of the effects of time in years and the meteorological variables (extreme hot and cold days, unusual rainy winters, extreme rainy days, and cumulative rain), that affect the trend of the morbidity rate of diarrhea in each governorate (Fig. 2 ).
Convergent anti-SARS-CoV-2 clonotypic response in severe COVID-19 patients To characterize the COVID-19 response signature in the circulating B-cell repertoires of our patients, we first searched for the presence of specific anti-SARS-CoV-2 clonotypes (SC for specific clonotype) listed in the CovAbDab database (The Oxford Protein Informatics Group public database: http://opig. stats. ox. ac. uk/webapps/covabdab/) which now documents thousands of published or patented human SARS-CoV-2-specific binding antibodies and nanobodies. 28 As reported in the literature,  29, 30  we also searched and found, convergent clonotypes (CCs) shared by different individuals of our cohorts in response to COVID-19. Although low, the relative representation of such ''public'' COVID-19 clonotypes in DNA and RNA repertoires from blood cells was significantly higher in severe COVID-19 patients than in controls, as a footprint of the public human antiSARS-CoV-2 humoral response on individual repertoires (Figure  6A ).
41 garding VDJ associations and CDR3 assembly, the immune response of patients is marked by a COVID-19 footprint, with increased occurrence of specific VH-JH pairs and of clonotypes abundantly represented within the CovAbDab database of known anti-spike Abs. Such COVID-related clonotypes first associate with IgM expressed at D0, but later associate with class-switched Ig, the latter association being significantly higher in ARDS neg patients. Another striking aspect of the early class-switched response is the specific expansion of a [long CDR-H3] subset of abundantly transcribed clonotypes, which was higher in ARDS pos patients. CDR3 features in fact highlighted two parallel variations of the Ig response in patients. A standard Ag-specific Ig response including SARS-CoV-2-specific and convergent clonotypes with normal CDR3 length develops and is the most durable, persisting after recovery.
Sequencing and data analysis Libraries from DNA or RNA templates were sequenced with an Illumina MiSeq, standard Illumina sequencing primers and MiSeq Reagent Kit v3 (600 cycles). For DNA libraries, paired-end reads were merged using the flash software  47  and concatenating non-overlapping pairs. For RNA libraries, the migec script  44  was used for UMI-demultiplexing, sequence correction and consensus assembly. The IGHV, IGHD, and IGHJ gene segments and the CDR-H3 junctions were identified using the IMGT/HighV-QUEST sequence alignment software. 45 Quality filtering of sequences only kept reads including a productive CDR-H3 region. For cDNA-templated IGH reads, isotypes and subclasses were called by matching to the constant region gene segment. Sequences were finally assembled into clonal groups with the Change-o toolkit  43  based on common IGHV gene, IGHJ gene and junction length and a maximal Hamming distance between junction amino acid sequences.
ACKNOWLEDGMENTS We thank all the donors, the staff in charge of patients care, clinical data collection, biological sample collection and the staff in charge of ethical and administrative issues. We thank  Dr. Mehdi Alizadeh  for help with sequencing. This work was supported by the  Fondation pour la Recherche Medicale (FRM)  and the  Agence Nationale de la Recherche(ANR) , Flash Covid-19 joint grant (HARMONICOV to MC).
Database and Methods The study focuses on the relationship of malaria with climatic and hydrological variability, exploring whether this disease is influenced by precipitation, river oscillation, and Suspended Sediment Concentration (SSC) in rivers, for each municipality analyzed. Historical series from 2005 to 2015 were used from each station, chosen according to the availability of river water level, precipitation, and SSC data. The choice of data also considered years with months of uninterrupted data for all variables studied. Years with more than three consecutive months of data absence were excluded from the analysis. Data on the population of the municipalities were obtained from the Brazilian Institute of Geography and Statistics (IBGE, Portuguese acronym). Monthly river level data, between 2005 and 2013, from the fluviometric stations of Beruri, Coari, Serrinha (in the municipality of Santa Isabel do Rio Negro), and Itaituba, were acquired from the Brazil National Water Agency (ANA, Portuguese acronym) and the database of the Environmental Research Observatory at the HYdro-geochemistry of the AMazonian Basin, currently the ORE/HYBAM Project (http://www.
This dataset combines microwave data from several satellites to produce a single monthly precipitation rate. The 3B43 product has been widely used for precipitation estimates, mainly because of its 3 h temporal resolution and 0. 25 • × 0. 25 • spatial resolution  [29]. The monthly accumulated precipitation data were acquired from the cloud-based platform for geospatial analysis on a planetary scale Google Earth Engine, developed by Google and accessible at https://earthengine. google. com, accesssed on 10 July 2019. Data on malaria case records were obtained from the Malaria Epidemiological Surveillance System (SIVEP-Malaria), available to authorized users at http://www. saude. gov. br/ sivep_malaria, accesssed on 22 December 2020. SIVEP-Malaria is a Brazilian government program that archives all information about malaria cases registered in all health facilities and doctors' offices.
The data were preprocessed, as SIVEP-Malaria has some limitations in the use of its variables, such as the presence of "outliers" and the absence of data in certain places and periods, which, according to  [30] , affect spatial and temporal comparisons. Positive malaria data were filtered and counted by the probable municipality of infection, from which all malaria records in the municipality were considered, regardless of the type of parasite that caused the disease. To be able to compare the frequency of the disease in different populations, the Monthly Parasitic Malaria Incidence (MPI) was calculated employing the following equation: MPI = M P × 1000, (1) in which M is the number of positive tests for malaria in the month, per probable municipality of infection, and P is the total resident population of the municipality, in the year considered.
Acknowledgments: The authors would like to acknowledge  Fundação de Vigilância em Saúde do Amazonas (FVS)  for providing access to the malaria data and the  Ethics Committee of the Universidade Federal do Amazonas  for authorizing the use of the data. We received support from the  Instituto Leônidas e Maria Deane  ( ILMD-Fiocruz Amazônia ), the  Universidade Federal do Amazonas (UFAM) , the  Institut de Recherche pour le Développement (IRD/France) , the  Graduate Program in Climate and Environment  of the  Instituto Nacional de Pesquisas da Amazônia , and the  Universidade Estadual do Amazonas  ( PPGCLIAMB (INPA/UEA) ), the  Graduate Program in Geosciences of the Universidade Federal do Amazonas , the  Graduate Program in Geoquímica of the Universidade Federal Fluminense , the  Fundação de Amparo a Pesquisa do Estado do Amazonas (FAPEAM) , the  CNPq-AmazonGeoSed Project  and  CAPES-PROCAD 2018 Amazonia Program (Projeto Rio Negro TAR ).
Objective adherence is widely reported as a percentage in the literature, hence this approach was taken to improve the interpretability of SPUR scores when compared with these data. Additional items were included to capture sociodemographic information of participants as well as relevant clinical data such as the number of prescribed antiglycaemic agents and the patients' comorbidities, which were either self-reported or recorded with consent from the medical record (secondary-care arm only). These socioclinical data were collected to explore expected relationships such as MA increasing with age and income, while decreasing in patients who reported a higher number of prescribed antiglycaemic medicines, comorbidities or body mass index (BMI).
Sample size Raosoft  22  produced a minimum sample size (5% margin of error, 95% CI) based on the number of patients with diagnosed diabetes in the immediate population for Richmond, Kingston and Sutton (n=25 213 patients). 23 he 1:9 ratio of type 1 to type 2 diagnoses was applied (n=22 692) before entry to Raosoft that produced a final minimum sample of 378 patients. Exploratory factor analysis (EFA) was performed to identify subscales that are represented by grouped questionnaire items. The Kaiser-Meyer-Olkin (KMO) measure of sampling adequacy and Bartlett's test of sphericity were used to determine database eligibility. Visual inspection for an inflection point in scree plots were used to identify initial factors with the addition of Monte Carlo parallel analysis. 24 EFA was conducted to explore the SPUR tool structure in this specific study population using Principle axis factoring with Direct Oblimin rotation, factor loadings >0.
It was expected that individual SPUR factors would produce stronger correlations with their comparative PROM than the other tools. These individual assessments of convergent validity Open access between PROMs individual factors and overall scores were used to provide evidence of construct validity for the SPUR model. 30 Permission and/or licenses were obtained prior to use of the tools within the study. Objective clinical data were obtained during the study to examine concurrent validity of SPUR-45, which included HbA 1c and the medication possession ratio (MPR). The most recent HbA 1c (%, mmol/mol) within the previous 6 months were either self-reported (community arm) or obtained from patients' clinical records (hospital arm). Results of ≤6. 5% (48 mmol/mol) for single agent or ≤7. 0% (53 mmol/mol) for multi-agent or single hypoglycaemic agent were used to determine adherence.
MPR, a crude measure of MA was calculated as a percentage using the formula below: MPR data were derived from the patient medical record by community pharmacists or the summary care record for hospital participants. An MPR ≥80% was the cut-off for determining a participant as adherent. 31 Spearman's rho was used to test for significant correlations (p<0. 05) between PROMs, objective data and SPUR. T-tests were conducted to investigate significant differences in mean adherence scores between PROMs and objective measures. Pearson's correlation analysis was conducted to evaluate the strength and significance of relationships between SPUR and socio-clinical factors to provide evidence of known-group validity. It was hypothesised that MA would significantly increase in tandem with age and income, while decreasing in patients who were prescribed more antiglycaemic agents, reported a greater number of comorbidities or who had higher BMI values.
RESULTS The study recruited 378 participants, 178 (24. 7% response rate before additional exclusion, n=198/799) and 200 (82. 0% response rate before additional exclusion, n=218/266) from the community and secondarycare arms, respectively. Age, education and income were collected as ordinal data and are reported as such. The modal age was 60-69 years (n=96, 25. 4%), education was reported predominantly at GCSE level or equivalent (n=122, 32. 3%) and more than half the respondents indicated that they were retired (n=196, 51. 9%). The majority of participants were white (n=231, 61. 1%). Females represented 40. 2% (n=152) of the sample. Where data were available for BMI (n=351/378, 92. 9%) mean±SD BMI was 29. 35±6. 17, indicating that a significant proportion of participants were above their recommended weight.
DISCUSSION This study aimed to examine the SPUR model as a multifactorial PROM of MA in type 2 diabetes, in addition to exploring relationships between the model and socioclinical factors associated with MA. Factor and reliability analyses were conducted using the original SPUR-45 tool to identify a suitable model for further psychometric analysis. As a result of the analysis, a revised and more concise model referred to as SPUR-27 was identified. The data support encouraging early results for the psychometric properties of the revised SPUR-27 model as well as demonstrating significant relationships with predicted socio-clinical factors. EFA was conducted with the intention of exploring and understanding the structure of the overall SPUR model. SPUR-27 was derived from an iterative approach to model refinement through factor analysis, reliability testing and item-trimming.
Open access Building on both the EFA and reliability analysis, mean total and individual factor scores for SPUR-27 were assessed. Using a ≥80% cut-off as a measure,  31  SPUR-27 reported sample adherence at 44. 7% (n=169/378), closely reflecting HbA 1c adherence at 39. 9% (n=106/266) for those participants where data were available. Further assessment of the sample based on MPR data indicated that 82. 0% of participants were adherent (MPR≥80%, n=310/378). Although not unexpected, given the tendency of MPR to over-estimate adherence,  33  the large variation in adherence outcome based on objective data was surprising. Anecdotally, pharmacists conducting the study reported less contact with patients given that recruitment took place during the COVID-19 pandemic. Medicines were delivered to patients' homes without faceto-face engagement, reducing the capacity for adherence interventions which may have resulted in poorer HbA 1c.
Moreover, social desirability bias and discrepancies in self-reported HbA1c have not been fully considered for this study. Those recruited from the community arm are more likely to report an incorrect HbA1c value based on their memory versus HbA1c data that were extracted directly from the medical records for patients from the hospital arm. Hence, this is a potential limitation to quantifying true correlations between selfreport and objective measures that future work should look to address. Another notable limitation includes the lack of testretest reliability data. Despite integration of re-testing into the original protocols, the pandemic prevented suitable follow-up. The risk to patients returning for follow-up outweighed the potential benefit of re-testing Open access in this sample, therefore the authors recommend that test-retest analysis be conducted in future studies with the SPUR model.
42 Further work is needed across different samples in order to ensure the results are truly meaningful for participants living with type 2 diabetes. The study has several strengths that have supported the primary outcome of providing early evidence of psychometric properties for the SPUR-27 model. First, the inclusion of numerous PROMs to compare against the multifactorial SPUR-27 questionnaire that provided empirical data for construct evaluation. Second, two objective adherence data sets were used to demonstrate concurrent validity with not only the novel PROM, but previously validated tools that provided greater insight into the influence of numerous adherence behaviours on clinical outcomes such as HbA 1c. Finally, EFA and reliability testing produced a more concise tool, SPUR-27, which provided early evidence of psychometric properties for this sample population.
Acknowledgements The authors thank the  Kingston Hospital NHS Foundation Trust research department, Diabetes Specialist Nursing, Dietetics  and Podiatry teams ( Mary Murray ,  Wendy Mbolonzi ,  Joanne Sewell ,  Lillian White ,  Janet Rideout ,  Alison Kelly ,  Juliet Kean  and  Linda Fleming ) as well as  Dr Ye Kyaw  (Consultant in Diabetes and Endocrinology) for their support with this study during the COVID-19 pandemic. The authors also thank the input of  Rosie Walker  ( Successful Diabetes ),  Diabetes UK , and the members of the  Diabetes Specialist Nurse Forum UK  for providing guidance and encouraging participation. The authors extend their gratitude to all participating pharmacies, the wider Observia team ( Léa Kombargi  and  Hanna Rebibo Seror ) and the  Health Education Foundation  team for supporting the delivery of this study.
Background. Treatment of ischemic mitral regurgitation (IMR) is in evolution as percutaneous procedures and complex surgical repair have been recently investigated in randomized clinical trials and matched studies. This study aims to review and compare the current treatment options for IMR. Methods. A comprehensive literature search was conducted using electronic databases. The primary outcome was all-cause long-term mortality. The secondary outcomes were perioperative mortality, unplanned rehospitalization, reoperation, and composite endpoints as defined in the original articles. Results. A total of 12 articles met the inclusion criteria and were included in the final metaanalysis. The MitraClip procedure did not confer a significant benefit in mortality and repeated hospitalization compared to medical therapy alone.
Surgical mitral valve repair refers to restrictive annuloplasty with rings that can be associated with subvalvular procedures (papillary muscle approximation or relocation), while percutaneous MV repair refers to Mitraclip procedure. Comparisons were performed between GDMT alone and combined with either a MitraClip procedure, mitral valve replacement (MVRpl) and mitral valve repair (MVR), restrictive mitral annuloplasty (RMA) and restrictive mitral annuloplasty plus papillary muscle approximation (RMA+PMA), CABG alone and combined to RMA. A literature search was performed through PubMed, Embase, EBSCO, Cochrane database of systematic reviews, and Web of Science from its inception up to April 2, 2019 using the following search keywords (and their MeSH terms when available) in various combinations: "mitral valve", "repair", "replacement", "ischemic mitral regurgitation", "MitraClip", "ischemic mitral disease", "subvalvular", "annular", "coronary artery bypass graft".
Data Extraction and Quality Assessment (Risk of bias) Data extraction was performed independently by 2 investigators (F. N. and A. N) (Supplementary Figure  1 , Supplementary Table  1 , Supplementary Table  2 , Supplementary Table  3 ). The following variables were included: study details (sample size, number of centers, institutions involved, publication year, study period, design and country, length of follow-up), patient demographics (age, sex, diabetes mellitus, and ejection fraction) and procedural (GDMT, Mitraclip, Surgery) and postoperative data. The methodological quality of the selected studies was assessed with the Cochrane risk-of-bias tool for RCTs, and with the Newcastle-Ottawa scale scoring for non-randomized studies. Only RCTs and observational studies of high quality (Newcastle-Ottawa Scale score>6) were included in the final analysis (Supplementary Figure  2 ).
Results of individual studies A total of 2848 patients were included (GDMT plus MitraClip vs GDMT, 918 patients in 2 studies; CABG plus RMA vs CABG, 615 patients in 5 studies; MVRpl vs RMA, 1109 patients in 3 studies and RMA plus PMA vs RMA 206 patients in 2 studies) from 8 RCTs (n=1772) and 4 observational studies(n=1076). Demographic data are shown in Table  1  and Supplementary Table  1.
Acknowledgements: none. Conflict of interest: none. Financial support: none. Newcastle-Ottawa scale for the included propensity-score matched cohorts. Criteria: IA= Representativeness of the exposed cohort, IB= Selection of the non-exposed cohort,  IC: Ascertainment of exposure, ID= Demonstration that outcome of interest was not present at start of study, II= Comparability, IIIA= Assessment of outcome, IIIB= Was  follow-up long enough for outcomes to occur, IIIC= complete follow-up -all subjects accounted for, IIID= subjects lost to follow-up unlikely to introduce bias. Score: asterisk= the study meets the specified criterion; dash= the criterion is not applicable to the study.
A Bruker D8 4-axes diffractometer with a mirror to give a pseudo-parallel beam was used to obtain the φ-scans, the 200, 400 2θ/θ scans without χ-offset and the 111, 220, 222 2θ/θ scans with χ-offset (supplementary note 3) to calculate the ordering parameters. The experimental peak intensities were determined by profile fitting using HighScore+ software. The theoretical intensities were calculated as outlined in supplementary note 3. A Philips X'Pert Pro MPD θ/θ diffractometer was used to obtain the XRR scans. The anomalous XRD (AXRD) measurements were performed at the BL13XU beamline using a six-circle diffractometer at SPring-8. To evaluate the atomic ordering in the Mn 2 FeAl film, the 111 peak intensity (I 111 ) was measured at the Mn and Fe K absorption edges. Simulations of the I 111 were performed from 6.
In this work, 4. 5 and 3. 4 for the number of holes in the 3d band for Fe  [45]  and Mn  [46]  were used respectively. To remove intermixing complications between the Mn L 3 and L 2 edges, a 1. 47 correction factor  [47]  was used to adjust the Mn spin moment. To measure the anisotropic magnetoresistance (AMR), the Mn 2 FeAl film was patterned into Hall-bar devices using photolithography followed by an Ar ion-milling step. A Quantum Design physical properties measurement system (PPMS Dyn-aCool) was used to carry out the AMR measurement. A constant 1 mA DC current was applied and the magnetic field was rotated in the plane of the film. We calculated the density of states (DOS) of ordered and disordered Mn 2 FeAl using density functional theory (DFT) and the Korringa-Kohn-Rostoker (KKR) method  [48, 49] , implemented in the Akai-KKR software package  [50].
Acknowledgments This work was funded by  H2020-MSCA-ITN-2014   SELECTA  (Grant Agreement No. 642642  of the  European Commission) , and  Grants-in-Aid for Scientic Research  (No. 17H06152 ) from the  Japan Society for the Promotion of Science (JSPS) , the  2019 NIMS internship program. G F N thanks the  Royal Commission for the Exhibition of 1851  for support through the award of a Research Fellowship. We thank  Diamond Light Source  and SPring-8 for time on beamlines I06 (proposal SI18932) and  BL13XU  (proposal 2019A0927) respectively. The authors would like to thank  Dr Niklas Teichert ,  Dr Edouard Lesne  and  Dr Martin Gottschalk  for useful discussions and  N Kojima  for technical support.