dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis Data were described as the mean plus or minus standard deviation (SD). All statistical analyses were performed with GraphPad Prism (version 8. 0; GraphPad Software, Inc, San Diego, CA). Statistical tests included the nonparametric Mann-Whitney test, the Fisher exact test, and 2-way analysis of variance. The threshold for statistical significance was set to P ,. 05. as the percentage of DLNGFR on day 5 after transduction in WT and scurfy CD4 1 T cells. Transduction efficiency was significantly higher with the LNGFRp-eFOXP3 vector than with the LNGFR. t2a. FOXP3 vector for both WT CD4 1 T cells and scurfy CD4 1 T cells (P 5. 002 and. 007, respectively, in a Mann-Whitney test). In contrast, transduction efficacy with the mock vectors was higher with the T2A construct (P 5.
Acknowledgments The authors are grateful to  Aur élia Dujardin ,  Camila Piat ,  Laura Zapata ,  Jennifer Alonso , and  Emilie Panafieu  from the  Structure F éd érative de Recherche (SFR)  Necker animal facility;  Sophie Berissi ,  No émie Gadessaud , and  Sonita Ing  from the  SFR Necker histology facility ; and  Olivier Pell  é and  Corinne Cordier  from the  SFR Necker cytometry facility. The authors also thank  Gis èle Froment ,  Didier N ègre , and  Caroline Costa  from the lentiviral production facility/ SFR BioSciences Gerland-Lyon Sud  ( UMS3444/US8 ). This work was supported by a  European Research Council  grant (Gene for Cure:  E16145KK ). This project has received State funding from the  French National Research Agency (ANR) Investments for the Future Program (PIA)  under grant agreement  ANR-18-RHUS-0003.
Systematic review The literature search was conducted in March 2017 using a combination of keywords related to (1)"Cryptosporidium" "OR" "cryptosporidiosis", (2) "case-control" "OR" "risk factor" "OR" "cohort" (3) "infection" "OR" "disease", joined by the logical connector "AND". Relevant studies were identified from five bibliographic search engines, Science Direct, PubMed, Scielo, ISI Web of Science and Scopus. No restrictions were defined for the year of the study or type of publication. The search was limited to the languages English, French, Portuguese and Spanish. Each reference record was screened for relevance for inclusion in the meta-analysis study. The methodological quality of the "candidate" studies was assessed using pre-set quality criteria, comprising (1) appropriate selection of the controls; (2) adjustment to correct for confounders, (3) comparability between cases and controls, (4) acceptable responses rates for the exposed and control groups; (5) data analysis appropriate to the study design; (6) provision of odds ratio (OR) with confidence interval or p-value; or provision of sufficient data to calculate ORs; overall quality of the study  (Gonzales-Barron et al.
, 2019). Primary studies that passed the screening for relevance were marked as having a potential for bias if they failed to meet at least one of the methodological quality assessment criteria. Data from primary studies were then extracted using a standardized spreadsheet. Data extracted included the relevant study characteristics (location, period, population, case definition, design, sample size of the groups, type of model, etc. ), the categorized risk factors, the setting, the handling practices and the outcome of the study (ORs). A data categorization scheme was established to hierarchically group the risk factors into travel, host-specific factors and, pathways of exposure (i. e. , person-to-person, animal, environment, and food routes) (see the methodological paper of this issue). In addition to the standard risk factors, the class "Hygiene" (e.
Data synthesis The joint meta-analytical data was first described using basic statistics. Next, data was partitioned into subsets of categories of risk factors. The meta-analytical models were then fitted to each of the data partitions or subsets to estimate pooled OR related to travel, host-specific factors and transmission pathways related to person-to-person contagion, animal contact, environmental exposures, and food vehicles. The meta-analytical models were fitted separately by population type. For some food classes, the effects of food preparation (e. g. , eating raw, undercooked) and setting (i. e. , eating food prepared outside the home) on the pooled OR were assessed by calculating the ratio of the mean OR when food is mishandled to the base OR. The statistical analysis was designed to assess the effect of the geographical region, the study period and the analysis type (univariate/ multivariate) on the final result.
Descriptive statistics From 1985 identified references, the quality assessment stage was passed by 57 primary studies -cohort and case-control studies -focusing on sporadic cryptosporidiosis (Fig. 1 ). These published studies were conducted between 1983 and 2016. Table  1  and Appendix 1 compile the list of the primary studies along with their main features. The eligible studies jointly provided 568 odds-ratios categorized for meta-analysis. Meta-analytical data were obtained from primary studies conducted in 31 countries, although studies from only 5 countries generated ~70% of the ORs retrieved. During methodological quality assessment, potential for selection bias status was assigned to six case-control studies since, in those, the controls were not healthy individuals but people affected by another enteric disease such as giardiasis  (Firdu et al.
Acknowledgments The authors would like to thank  ANSES  staff and the members of the  ANSES Working Group on Source Attribution of Foodborne Diseases :  Moez Sanaa ,  Laurence Watier ,  Jean Christophe Augustin ,  Frédéric Carlin ,  Julie David ,  Philippe Fravalo ,  Laurent Guillier ,  Nathalie Jourdan-Da Silva ,  Alexandre Leclercq ,  Lapo Mughini-Gras ,  Nicole Pavio. Ursula Gonzales-Barron  and  Vasco Cadavez  are grateful to the  Foundation for Food Science and Technology (FCT, Portugal)  and  FEDER  under Programme  PT2020  for financial support to CIMO ( UID/ AGR/00690/2019 ).
Acknowledgements The authors thank the  PRAC Interest Group on Measuring the Impact of Pharmacovigilance Activities  for reviewing the study design and welcoming the results of the case analyses. The authors also thank  Nathalie Bere  and  Viola Macolić Šarinić  at  EMA  for reviewing this manuscript. The views expressed in this article are the authors' personal views and may not be understood or quoted as being made on behalf of, or reflect the position of, the EMA or one of its committees or working parties.
Survey and age group were included as fixed effects. The ratio of pfs25 or pvs25 transcripts per parasite genome was assessed, representing the proportion of gametocytes among all parasites. Infections (Pf: n = 12, Pv: n = 5) with densities at the technical limit of detection of 0. 25 copies/μL blood (i. e. 1 DNA/RNA template per PCR) were excluded from correlation analysis as quantification is imprecise at very low densities, and including them at a set density of 0. 25 copies/μL would artificially increase correlation. All data is available in supplementary file S1 Data.
0001, Table  3 ). The probability to detect gametocytes increased in all surveys with increasing genome density. An interaction analysis did not reveal a significant difference of this increase between surveys (Pf: n = 676, P = 0. 471; Pv: n = 1501, P = 0. 512). Likewise, P. falciparum and P. vivax gametocyte densities were not affected by an interaction between DNA copies and survey (Pf: n = 375, P = 0. 877, Pv: n = 415, P = 0. 132). Hemoglobin measurements and multiplicity of infection data were available from the surveys in PNG and Solomon Islands; neither affected gametocyte positivity or density in multivariate analysis (S2 and S3 Tables).
This work was funded by the  TransEPI Consortium/Bill and Melinda Gates Foundation  (www. gatesfoundation. org,IM,  OPP1034577 ), the  Australian National Health and Medical Research Council  (www. nhmrc. gov. au,IM, 1021544; 1092789), and  NIH  (www. nih. gov,JK, 1U19AI089686; IM,  1U19AI129392 ). This work was made possible through  Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS. CK was supported by a fellowship from the  Swiss National Science Foundation  (# P2BSP3_151880 ). LJR was supported by an  NHMRC   Early Career Fellowship  # 1016443  (www. nhmrc. gov. au). IM is supported by a  NHMRC   Senior Research Fellowship  (www. nhmrc. gov. au). ISGlobal is a member of the  CERCA Programme, Generalitat de Catalunya  (https://cerca. cat/en/).
Background & Aims: The NKG2D system is a potent immunosurveillance mechanism in cancer, wherein the activating NK cell receptor (NKG2D) on immune cells recognises its cognate ligands on tumour cells. Herein, we evaluated the expression of NKG2D ligands in hepatocellular carcinoma (HCC), in both humans and mice, taking the genomic features of HCC tumours into account. Methods: The expression of NKG2D ligands (MICA, MICB, ULBP1 and ULBP2) was analysed in large human HCC datasets by Fluidigm TaqMan and RNA-seq methods, and in 2 mouse models (mRNA and protein levels) reproducing the features of both major groups of human tumours. Results: We provide compelling evidence that expression of the MICA and MICB ligands in human HCC is associated with tumour aggressiveness and poor patient outcome. We also found that the expression of ULBP1 and ULBP2 was associated with poor patient outcome, and was downregulated in CTNNB1-mutated HCCs displaying low levels of inflammation and associated with a better prognosis.
Several studies have highlighted the paradoxical relationship between ligand expression and patient outcome. Briefly, high levels of cell surface ligand expression are associated with better disease-free survival in colorectal,  31  cervical  32  and nasopharyngeal carcinomas,  33  but with poor prognosis in breast,  34  lung  35  and ovarian cancers. 36 The expression of NKG2D ligands in HCC remains insufficiently explored, as conflicting data have been obtained concerning the potentially beneficial or deleterious role of NKG2D in HCC. 13  In this study, we investigated the expression of the NKG2D ligand genes MICA/B and ULBP1/2 in a large human HCC dataset and in 2 mouse models reproducing the features of both types of human tumours.
Quantitative RT-PCR and RNA-sequencing We assessed mRNA levels by quantitative reverse transcription (RT)-PCR on 354 HCC samples. We reverse transcribed 500 ng of total RNA with the High-Capacity Transcription Kit (Life Technologies) and assessed gene expression in predesigned TaqMan assays (MICA: Hs00741286_m1; MICB: Hs00792952_m1; ATM: Hs01112326_m1; ATR: Hs00354807_m1; Life Technologies) on Fluidigm 96 dynamic arrays with the Bio-Mark Real-Time PCR system. Expression levels (Ct values) were assessed with Fluidigm Real-Time PCR Analysis software (4. 1. 3) and gene expression data were expressed by the 2-DDCt method, relative to ribosomal 18S (R18S) and the expression level of the corresponding gene in 5 normal liver samples. Published RNA-seq data for 200 tumours were used to evaluate ULBP1 and ULBP2 expression in HCC patients (see Table  2 ).
Preparation of total RNA and quantitative PCR analysis Total RNA was extracted from mouse liver tissue or cell lines (AML12 and Hepa1. 6) with TRIzol (Invitrogen), and 2 lg was used as a template for cDNA synthesis (MMLV, Life Technologies). Purified RNA was then reverse transcribed with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Real-time PCR was performed with the Fast Start Quantitative PCR (q-PCR) kit with SYBR Luminaris Color HiGreen qPCR master mix (Thermo Fisher Scientific) and specific primers. The reactions were performed in 96-well plates in a LightCycler 480 instrument (Roche) with 40 cycles. We determined the relative amounts of the mRNAs studied by the second-derivative maximum method, with LightCycler 480 analysis software and normalization against 18s rRNA, used as an invariant control for all studies.
TCF4 ChIP-sequencing The ChIP protocol was adapted from a previous study,  48  as previously described. 49 The ChIP-seq data were deposited under accession number GSE35213 in the Gene Expression Omnibus database. b-catenin and TCF-4 binding to the Rae promoter, relative to the immunoglobulin isotype control, was assessed on the basis of SYBR green fluorescence, with the following oligonucleotides: FW-GACTTTCCACAAACGCACAA, Rev-GAAACTGCCCCGTTACCAC designed according to the sequence of the TCF-4 peak identified upstream from the Rae-1 gene.
Statistical analysis Data were visualized and statistical analyses were performed with PRISM software (GraphPad Software, Inc. , La Jolla, CA) and R software version 3. 5. 1 (R Foundation for Statistical Computing, Vienna, Austria. https://www. R-project. org) with the Bioconductor package. Comparisons of continuous variables between > -2 groups were performed with Mann-Whitney tests. Correlations between continuous variables were assessed by Pearson's correlation tests if both variables were normally distributed and the assumptions of linearity and homoscedasticity were respected, or by Spearman's rank correlation tests. All tests were 2-tailed and p values <0. 05 were considered significant.
23 e found a positive correlation between the levels of expression of the MICA/B and ATM/ATR genes (Fig. S2B ). Our data show that MICA/B are more strongly expressed in HCCs with TP53 mutations and chromosomal instability, and that their expression is correlated with that of DNA damage repair-related genes. Expression of ULBP1/2 ligands in human HCCs is weaker in tumours with stable chromosomes than in those displaying chromosomal instability and is associated with CTNNB1 mutation status We extended our analysis to the expression of ULBP ligands, which have been little studied in HCC. We investigated whether the expression of ULBPs had characteristics in common with the expression of MICA/B, by comparing the expression of ULBP1 and 2 according to our previous RNA-seq dataset with the molecular classification of human HCCs.
4C ). Rae-1 ligands were expressed in hepatocytes, except for those surrounding the pericentral vein (constitutive activation of b-catenin signalling), absent from hepatocytes in which Apc was knocked out and in tumour hepatocytes with Ctnnb1 mutations, but expressed in HCCs without mutations affecting b-catenin (DEN-induced HCC). Collectively, these data strongly suggest that b-catenin signalling downregulates the expression of Rae-1 NKG2D ligands in hepatocytes. (Apc-KO, Apc DHep ) and control hepatocytes (GSE35213) (Fig. 5A ). Beta-catenin has no DNA-binding domain. The ChIP-seq experiment was therefore performed with an antibody against the preferred partner of b-catenin in hepatocytes, TCF4. 49 The Chipseq data showed a significant induction of TCF4 binding to the Rae-1 promoter region in hepatocytes displaying b-catenin activation (Apc-KO mouse model, Apc DHep ) than in control hepatocytes (Fig.
Acknowledgements We thank the  Tumour Biobank of Henri Mondor University Hospital  and the  Réseau National Centre de Ressources Biologiques (CRB) Foie  for contributing to the tissue collection. We also thank the core facilities of the  Cochin Institute (Histology, Immunostaining [HistIM], Animal Facility , and the  CHIC (Center for Histology Imaging and Cytometry) facility of the Centre de Recherche des Cordeliers. We thank  Nadia Boussetta  for mouse breeding and genotyping. We also thank  Dr. Saadé Kheir  for critical reading of the manuscript, and  Professor Isabelle Cremer  and  Dr. Jules Russick  for their invaluable assistance with the immunostaining of immune cell populations on human HCC sections.
Background: Contact tracing has been a central control measure for coronavirus disease 2019 (COVID-19) transmission. However, without consideration of the needs of specific populations, public health interventions can exacerbate health inequities. Aim: The purpose of this rapid review was to determine if and how health inequities were included in the design of contact tracing interventions in epidemic settings. Methods: A search of the electronic databases MEDLINE and Web of Science was conducted. The following inclusion criteria were applied for article selection: (1) described the design of contact tracing interventions, (2) published between 2013 and 2020 in English, French, Spanish, Chinese, or Portuguese, (3) and included at least 50% of empiricism, according to the Automated Classifier of Texts on Scientific Studies (ATCER) tool.
Research strategy The research strategy was developed in collaboration with librarians from the Research Institute for Development and the University of Montreal. The searches were conducted in the electronic databases MEDLINE and Web of Science. The following keywords were used to define the queries (Appendix 1): "contact tracing"; "design*", "plan*"; "disease*", "epidemic*", "pandemic*". The references were exported and processed with the Automated Classifier of Texts on Scientific Studies (ATCER)  (ATCER, 2021; Langlois et al. , 2018)  tool to assess their degree of empiricism. The ATCER tool distinguishes empirical studies, based on qualitative, quantitative, and mixed methods, from editorials, literature reviews, or professional guidelines. To be included in this rapid review, articles had to include a description of the design or concept of a contact tracing intervention in the context of an outbreak or epidemic.
This research focused on articles published in peer-reviewed scientific journals. Recent articles published between 2013 and July 2020 were selected. The year 2013 was selected as the beginning of the search in order to identify articles related to the Ebola outbreak in West Africa. Publications were included if they were written in English, French, Spanish, Portuguese, or Chinese. As the objective was to retain scientific articles based on empirical data and to avoid theoretical or methodological scientific articles, the ATCER tool was used to assess the empiricism of each article, and a threshold of 50% was used (which is the cut-off of ATCER to determine if an article is empirical or not). The grey literature and pre-publications were excluded from this research. The initial search was conducted between July 22 and July 31, 2020, with an update conducted on November 11, 2020.
Selection of studies All identified studies were exported into Rayyan QCRI software. Two reviewers (IM, LT) first independently assessed the relevance of the titles and abstracts on the basis of the defined inclusion and exclusion criteria. In the case of disagreement between these two reviewers, a third reviewer (KO) decided. The same two reviewers then independently assessed the relevance of the full text of the previously selected articles. The third reviewer was involved in the case of any disagreement.
Study characteristics, quality assessment, and data extraction The dimensions studied to determine whether or not health inequities were considered in the design of contact tracing interventions in articles were (1) the inclusion of health inequities in the rationale for the intervention, (2) the populations targeted by the intervention, (3) the design of contact tracing, and (4) the presence of health inequities in recommendations for improving the design of future interventions. A first reviewer extracted data from the selected articles and a second reviewer verified the extracted data. The information extracted included details of the article (authors, title, year, country, type of publication, and type of evaluation if applicable), information on contact tracing and equity (level of jurisdiction, diseases, description of contact tracing intervention, participants, reference to equity, and main objectives), the Mixed Methods Assessment Tool (MMAT)  (Hong et al.
Data analysis Every hour from 7 p. m. to 9 a. m, the proportion of malaria vectors collected indoors was determined, as well as the proportion of pregnant women under bed nets at each hour from 7 p. m. to 9 a. m the night preceding the survey. The mosquito collection period was divided into 3 different timeframes (7 p. m. -10 p. m. ; 10 p. m. -6 a. m. ; 6 a. m. -9 a. m. ). The proportion of mosquito collected at each timeframe (aggressiveness) was calculated, as well as the 95% confidence interval. CSP index in malaria vectors Anopheles gambiae s. l. in each village was calculated as the number of positive vector divided by the total tested. Endophagy was calculated as the number of vectors collected indoors divided by the total collected. The 95% confidence interval of the CSP index and endophagy were also estimated.
Limitations This study design is an observational cross-sectional and mosquito collection was carried out in 3 different points only for one night due to logistic reasons. This could be considered as a limitation, and a longitudinal design may have brought a higher level of evidence. However, the data collected is precious because such data; aggressiveness rhythm and human behaviour collected simultaneously in the same setting, are rare. Essentially, it is of crucial importance to monitor these indicators at a high scale and with a higher frequency.
Population and data sources The large French National Health System database (Système National des Données de Santé-SNDS), in which all hospitalizations (in any public hospital and private clinic) are registered, was used. This contains information on patient characteristics, diagnoses and treatments. All data were anonymized at data entry through a specific software making it impossible to retrieve patient identity but allowing information to be linked through anonymized codes. Access to data was legally approved. From this database, all singleton births (deliveries ≥22 weeks of gestation, >500 g of birthweight, or both) that occurred in France over a 6-year period (2013-2018), were selected. Pregnancies resulting from spontaneous conception and from fresh embryo transfer were included, and those resulting from frozen embryo transfer were excluded.
Patient characteristics available in the hospital database were as follows: parity, maternal age, active smoking during pregnancy, obesity, history of diabetes (type 1 or 2) and hypertensive disorders, mode of conception, term, neonatal weight, sex and typology of malformation, if any. The main identified maternal morbidity indicators were as follows: venous thrombosis, gestational diabetes mellitus, hypertensive disorders (pre-eclampsia or gestational hypertensive disorders), placenta previa and placental abruption, identified by specific codes in the hospitalization records during the index pregnancy. The main identified perinatal morbidity indicators were as follows: premature birth (<37 weeks' gestation), SGA (<10th percentile adjusted for gestational age and sex) and major congenital malformations (according to the recommendations of the European register EUROCAT) and recorded at birth or until 2018.
A hypothesis could be that, in the case of endometriosis and adenomyosis, progesterone resistance and altered contractility could lead to deferred implantation, causing miscarriage, recurrent pregnancy loss and placenta previa, and defective placentation, which could play a role in intrauterine growth retardation. Adenomyosis by itself could not be treated in our study as its presence was not distinguishable from that of endometriosis in our database. Alterations in uterine junctional zone and inflammation could also induce a shallow invasion playing a role in the genesis of pre-eclampsia and premature birth. Data on pre-eclampsia, however, are discrepant. It has been suggested that alterations in the inner myometrium in women with endometriosis, such as defective remodelling of myometrial from the onset of decidualization, might induce vascular disorders  (Leone Roberti Maggiore et al.