dataesr/scientific-paragraphs-categorization huggingface dataset:
Both observational studies and randomized controlled trials were included. Random-effect meta-analysis models were used to quantify the effect of BRD on outcomes for which at least 5 studies reported a numeric estimation of the effect of BRD. From an initial pool of 525 references, 27 full-text articles with original data were included in the manuscript. Metaanalysis models were prepared for 4 outcomes: odds of mortality (n = 7 studies), odds of herd removal before first calving (n = 5 studies), average daily gain (n = 10 studies), and milk production during first lactation (n = 5 studies). In these models, heifers diagnosed with BRD during calfhood had 2. 85 times higher odds of dying (95% confidence interval: 1. 22 to 6. 69) and 2. 30 times higher odds of herd removal (i. e. , dead, culled, or sold) before the first calving (95% confidence inter-val: 1.
Systematic Review of the Literature A systematic review of the literature was performed to identify published research articles on the effects of calfhood BRD on health and performance of dairy cattle. To conduct this review, a protocol was designed following Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines and reviewed by all authors to define key words for the search, selection and eligibility of articles (including outcomes of interest), and data to be extracted from each included article. Original articles in English published up to February 3, 2020 (no start date), were searched in CAB (Commonwealth Agricultural Bureau) Abstracts (via EBSCO, https: / / www. ebsco. com/ ) and PubMed/MEDLINE databases (https: / / www. ncbi. nlm. nih. gov/ pubmed/ ).
Both observational studies and randomized controlled trials were included. A flow diagram summarizing inclusions or exclusions of research articles at each step was created (Figure  1 ). The following data were extracted from each included article (where available): basic study characteristics (authors, journal, year of publication, country); study design (prospective or retrospective); number of animals enrolled; age at BRD diagnosis; prevalence of BRD during the study; BRD case definition; person(s) in charge of BRD diagnosis (veterinarian, trained technician, producer or staff); BRD treatment (antimicrobial); outcomes measured; analyses performed (e. g. , type of models used). For mortality and ADG outcomes, the period during which these outcomes have been observed was specified. Data extraction was performed by 1 author (SB) and verified by 2 authors (ET and DA).
Synthesis of Research Findings: Data Extraction Health and performance outcomes were either dichotomous (e. g. , mortality, risk of herd removal before the first calving, and so on) or continuous (e. g. , ADG, milk yield at 305 d, AFC). For dichotomous outcomes, odds ratios (OR) and associated standard errors (SE) of the log OR [ln(OR)] were extracted. When these 2 values were not reported, they were calculated using the following formulas (1, 2): OR = × ( ) × ( ) a d c b , [1] SE OR ln , ( )       = + + +            1 1 1 1 a b c d [2] where a and b are the number of events of interest for BRD positive and BRD negative, respectively, and c and d are the number of nonevents for BRD positive and BRD negative, respectively. When OR and their 95% confidence interval (CI) were derived from logistic regression models, SE were calculated based on the generalized model linear regression assumption using the formula below: 95 1 96 % l n.
Systematic Review of the Literature The flowchart of the literature search is shown (Figure  1 ). The search of PubMed/MEDLINE and CAB Abstracts databases provided a total of 525 references after eliminating duplicates. Of these, 493 were discarded based on titles, abstracts, or both. The full text of the remaining 32 studies was examined in more detail and 4 studies did not meet the inclusion criteria. One additional study  (Rossini, 2004)  was added after searching references of retrieved articles. A few studies (n = 2;  Warnick et al. , 1997; Windeyer et al. , 2014)  were redundant, reporting data set that were already analyzed in studies included in this manuscript  (Warnick et al. , 1995; Windeyer et al. , 2012)  and thus were removed. In total, 27 studies were included in the manuscript (Table  1 ).
ACKNOWLEDGMENTS We gratefully acknowledge  John Kastelic  ( University of Calgary, Calgary, Canada ) for editing the manuscript. This research was supported by  Ceva Santé Animale (Libourne, France). Conflicts of interest:  E. Timsit  is an innovation scientist at Ceva Animal Health and is responsible for early phases of drug discovery and development. D. Achard is an international technical manager and is responsible for the technical support of  Ceva 's antimicrobial range. None of the other authors of this paper has a financial or personal relationship with other people or organizations that could inappropriately influence or bias the content of the paper. This article reflects the views of the authors and should not be construed as representing the views of  Ceva Santé Animale.
Discussion In this 4-year retrospective study, we compared serology and stool examination for the diagnosis of Strongyloides stercoralis infection, in 341 patients tested in our tertiary care hospital. To date, there is no gold standard for strongyloidiasis diagnosis, as serological techniques are reputed sensitive but are prone to cross-reactions with other roundworms, and microscopic examinations lacks sensitivity  [6]. Therefore, our classification of cases considered the results of both analyses. Additional clinical and epidemiological data were also collected to support this classification. As expected, serology had a much higher sensitivity than microscopy (100% versus 45%), meaning that it can be used for screening purposes with a theoretical 100% NPV. However, the PPV of 67% requires us to add other investigations to the workup, such as microscopic examination of stools for ova and parasites and serological tests for other nematodes.
Roe deer data Roe deer of known age are captured annually as part of a long-term monitoring program. Briefly, roe deer were caught using long nets surrounding forest patches and beaters and maintained in wooden boxes until the end of the drive. Details of the capture procedure are available in Gaillard et al. [43]. Fecal samples were collected rectally from immobilized roe deer captured between January Fig. 1  Sampling sites in two regions of France, where roe deer were captured. In Trois Fontaines, habitat is homogeneous with rich coppices, while in Chizé, three sectors with different habitat types and quality are observed (gray color gradient). N corresponds to sampling size within each site and March in 2018 and 2019 under a protocol approved by the Director of Food, Agriculture and Forest (Prefectoral order 2009-14 from Paris) and under authority of the Office Français de la Biodiversité.
We also counted eggs of gastrointestinal nematodes following a modified McMaster protocol  [45] , with a solution of ZnSO 4 (density = 1. 36) and a McMaster slide, providing a theoretical sensitivity of 15 eggs per gram (epg) of feces. We also prepared a "control slide" to improve sensitivity of the technique by fully filling a 14-ml tube with the remaining solution and covering it with a coverslip. After centrifugation (5 min at 1200 rpm), the coverslip was transferred on a microscope slide before microscopical observation. We attributed the value 7. 5 epg for parasite species detected on the control slide but not on the McMaster slide. Coproscopic data were reported only for samples containing enough L3 collected from coproculture and analyzed by metabarcoding.
A conservative approach was used for taxonomic assignment of amplicon sequence variants (ASV) in which three different assignment methods were used (Additional file 1: Table  S1 ): (1) IDTaxa using the default conservative threshold of 60, which corresponds to the confidence at which to truncate the output taxonomic classification  [49] ; (2) assignTaxonomy  [46, 50]  and (3) BLASTn  [51]. The nematode ITS2 rDNA database 1. 1. 0 [52]  containing 9811 complete and non-redundant sequences, with a few additional manual corrections of species assignation corresponding to morphotypes, was used for both IDTaxa and assignTaxonomy. For BLASTn, the three best hits were considered only if they reached a threshold of 90% similarity against NCBI database sequences (2021/04/13). All species-level assignments were ascribed a 'confidence level' (Additional file 1: Table  S1 ): high confidence indicates that all three methods assigned to the same species and moderate confidence indicates that two out of the three methods agree at the species level and also the third method was in agreement but could only be assigned to the genus level.
Taxonomic assignment was limited to the genus level when there was disagreement across any of the three methods at the species level (but consistency at the genus level) or if there was no similar sequence on GenBank with > 98% of similarity and a query cover > 85% with the corresponding ASV. The raw ASV data set was curated following a procedure developed by  Taberlet et al. (2018). ASVs observed only once in the whole data set were considered spurious and were removed  [53]. To delete potential contaminants  [54] , we discarded any ASVs more abundant in the negative controls (maximum 55 reads) than in other samples and reads with < 0. 13% (maximizing the removal of sequences with low abundance in controls) of the total ASV abundance in the entire data set. We only kept ASVs identified as gastrointestinal nematodes at least to the genus level.
Statistical analyses on measures of parasitic community We removed the lungworm Varestrongylus from the data set because the focus of the present study was on gastrointestinal nematodes. To control the representativeness of the data, we drew the accumulation curves for the ASV and taxa with the "exact" method of the function "specaccum" of the package vegan  [60]. Instead of the exact read count per sample and items, we used the relative frequencies of reads. The read relative frequencies in samples were plotted with ggtree  [61]. After controlling for the year, the capture date, the epg and the number of L3 used for DNA extraction, we assessed the effects of age (i. e. young [< 1 year] or adults) and sex (i. e. males or females) on two proxies of diversity of gastrointestinal nematodes community: alpha (measure of community diversity within individual samples) and beta (measure of comparison of dissimilarity between each pair of samples).
contortus and B. trigonocephalum in this population. In Chizé and Trois Fontaines, we noted the presence of T. axei and O. venulosum, at low relative abundance, also considered as generalist species, and T. colubriformis (only in Chizé) and T. circumcincta, which generally infect sheep and goats  [30, 68]. The identifications of H. contortus and T. axei are at a "high confidence level" because these species were well represented in the nemabiome database and the three different methods of assignment provided the same species assignment. For Bunostomum sp. , ASVs were only assigned at the genus level as a result of a relatively low level of identity (92% over 283 bp [query cover of 100%, e-value = 9e -110 ]) to the best BLAST hit in GenBank (Additional file 1: Table  S1 ). To our knowledge, B.
trigonocephalum of sheep and B. phlebotomum of calves are the only Bunostomum species which have been identified in roe deer in Europe (e. g. [36] ). These two species are highly divergent, and considering the low level of intra-specific variation observed within B. trigonocephalum  [69] , it is possible that the Bunostomum sp. identified in Trois Fontaines is a previously unidentified, or cryptic, species closely related to B. trigonocephalum. For some ASVs, the taxonomic identification did not reach the species level, e. g. Trichostrongylus spp. (67% among this genus), Spiculopteragia spp. (6%) or Ostertagia spp. (67%). This may be largely due to the lack of reference sequence available for these species in the nemabiome database and ultimately in GenBank. This issue is accentuated when applying nemabiome metabarcoding to wildlife hosts compared with domestic livestock where parasite communities are better defined.
For example, there is just a single ITS2 reference sequence for Trichostrongylus capricola compared to 299 ITS2 reference sequences for Haemonchus contortus in the nemabiome database (see also  Aivelo and Medlar 2018  for the SILVA database). The potential presence of cryptic species and/ or hybrids of closely related species  [70]  may further complicate accurate species assignation. Consequently, the generation of reference sequences from morphologically validated parasites should continue to be a research priority for the scientific community as a whole. Ashworthius sidemi was not detected in Trois Fontaines, although it has previously been isolated on roe deer carcasses during winter in this study area  [13, 71]. This may be due to the hypobiosis in this species  [72]  or to the fact that during winter females contained only non-embryonated eggs  [73].
Therefore, it appears highly relevant to study roe deer and domestic ungulates living in sympatry in anthropogenic landscapes dominated by farmland to better understand the dynamic of gastrointestinal nematodes among wild and domestic populations and the risk of cross-transmission. This work also illustrated the power and limitations of ITS2 nemabiome metabarcoding for wildlife studies. It allows the screening of large numbers of samples for a large number of parasites, with identification to the species level in many cases. However, some parasites could still only be identified to the genus level emphasizing the need to continue to enrich the DNA sequence databases for more comprehensive identification.
Acknowledgements The authors warmly thank all the professionals from the  Office Français de la Biodiversité  and all the trainees for data collection. This project was founded by  Results Driven Agriculture Research (RDAR ; grant no. 2017R021R ),  University of Calgary , the  Office Français de la Biodiversité , the  NSERC-CREATE (Canada) Host Parasite Interactions (HPI)  graduate training program and  VetAgro Sup-Pôle d'Expertise Vétérinaire et Agronomique des Animaux Sauvages  (EVAAS ; http:// evaas. vetag ro-sup. fr/; DGAL- VetAgro Sup -INRAE funding). G Bourgoin  was supported by the  AgreenSkills+ fellowship program (EU program ;  Marie-Curie   FP7 COFUND People Programme ; grant agreement  n_609398 ).
Each of all possible combinations of one to four of the four different osmolytes selected in the study were tested as explanatory variables, with the actual osmolality as the response variable, using the glmulti package  (Calcagno and de Mainzancourt, 2010). For model comparison, we considered the small number of samples. Therefore, we used the Akaike Information Criteria corrected for small sample sizes (AICC). We selected the model with the lowest AICC as the final model, and the differences of the AICC between models was interpreted according to  Burnham (2002). For better clinical applicability, we simplified the formula to obtain an easy-to-use additive formula without ordinate (we forced intercept to 0). For the same reason, the variable 'Time' was not included as an explanatory variable in this simplified model, as it would be impractical to use it for daily clinical activities.
We additionally ran a similar model with an intercept and with 'Time' as a categorical factor (supplementary data). Afterward, the agreement between the calculated and actual Uosm was assessed thanks to the concordance correlation coefficient (CCC) for repeated measures in the cccrm:ccclon package  (Carasco et al. , 2009; Carasco et al. , 2013). This method relies on a linear mixed modeling approach, the assumptions of the linear model (linearity, homoscedasticity and normality of the residuals) were thus verified graphically prior to the analysis. To account for the lack of independance of the observations and due to the design of the study, an autoregressive correlation structure was chosen for the mixed model. The results of the CCC were interpreted using the scale proposed by  McBride (2005).
The PCR program was as follows: 94˚C for 10 minutes, followed by 40 cycles at 94˚C for 20 seconds, 53˚C for 30 seconds, and 72˚C for 1 minute, with a delay at 72˚C for 7 minutes. After revelation in 2% agarose gel stained with ethidium bromide visualised under an UV illumination (E-gel Imager, Thermo Fisher Scientific, Massachusetts, United States of America), the amplicon was purified using the Sephadex G50 DNA purification kit. Sequencing reactions were processed using a 3500 Genetic Analyzer (Applied Biosystems, Massachusetts, USA), and the sequences obtained were assembled using the CodonCode Aligner software (CodonCode Corporation, Massachusetts, USA). The assembled ITS rRNA gene sequence was queried against the NCBI nucleotide database using the Basic Local Alignment Search Tool (http://www.
blast. ncbi. nlm. nih. gov/ Blast. cgi). The isolate was identified as M. mycetomatis (GenBank: MW131313), showing 99% homology with a known isolate of M. mycetomatis (GenBank: MF980621). The patient was referred to the dermatology ward for treatment. Antibacterial and antifungal therapy, respectively based on amoxicillin-clavulanic acid (1 g/125 mg tid) and terbinafine (500 mg bid), was started. However, the patient could only take the antibacterial treatment for 1 month due to limited financial resources. After 1 month and 15 days, he was discharged from the hospital. We were informed in a telephone follow-up call with his family that the patient had died 1 month after his discharge.
European Registry on Helicobacter pylori Management The European Registry on H. pylori Management (Hp-EuReg) is an international multicenter prospective non-interventional registry with a collection of information on H. pylori infection management since 2013, which was promoted by the European Helicobacter and Microbiota Study Group (www. helicobacter. org, accessed on 1 February 2021)  [33, 34]. The ethics committee of La Princesa University Hospital (Madrid, Spain), which acted as the reference institutional review board, approved the protocol of the Hp-EuReg  [34]. The study protocol conforms to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in a prior approval by the institution's human research committee. The study was classified by the Spanish Drug and Health Product Agency and registered at ClinicalTrials.
gov under the code NCT02328131. Written informed consent was obtained from all participants. Criteria for country selection, national coordinators, and gastroenterologist recruiting investigators, as well as the list of variables and outcomes, are detailed in the published protocol  [33, 34]. Eradication confirmation tests had to be available. Data were recorded in an electronic case report form (e-CRF), collected and managed using the web-based application designed to support data capture for research studies (REDCap)  [35]  and hosted at the Asociación Española de Gastroenterología (AEG; www. aegastro. es, accessed on 1 February 2021), a non-profit scientific and medical society focused on gastroenterology research  [34]. Overall, 31 European countries with over 300 recruiters were selected.
Data Management and Analysis Data extraction was performed in February 2021 and subjected to monitoring (at least 10% of the existing records per country and centre) and a quality check to ensure coherence and data reliability. Primary antibiotic resistance was defined as bacterial resistance to one or more of the antibiotics tested (amoxicillin, clarithromycin, nitroimidazole, levofloxacin, or tetracycline) in H. pylori treatment-naïve patients. Secondary antibiotic resistance was determined in patients who failed eradication (non-naïve individuals). In the latter case, it was defined according to the number of eradication treatments used. Naïve patients were defined as subjects who had never been treated for H. pylori and non-naïve those who had previously undergone treatment (one or more eradication treatment options).
Antimicrobial resistance was determined according to the guidelines and criteria of the European Committee of Antibiotic Susceptibility Testing (EUCAST Clinical Breakpoint Tables V. 9) (http://eucast. org/clincialbreakpoints/, accessed on 1 February 2021). Dual resistance was defined when there was resistance to clarithromycin and metronidazole. Triple resistance was defined when there was resistance to clarithromycin, metronidazole, and levofloxacin. From the countries included in the study, only those with more than 40 cases for which culture testing had been performed were selected for the analysis. Data were stratified by naïve and non-naïve patients as well as by geographic areas. To assess the prevalence of antibiotic resistance in Europe, two regions were established by their geographic location and the number of cultures performed: southern Europe (Italy, Spain, and Greece) and northern Europe (Norway).
Institutional Review Board Statement: This information is included in the text. "The ethics committee of La Princesa University Hospital (Madrid, Spain), which acted as the reference institutional review board, approved the protocol of the Hp-EuReg  [34]. The study protocol conforms to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in a prior approval by the institution's human research committee. The study was classified by the Spanish Drug and Health Product Agency and registered at ClinicalTrials. gov under the code NCT02328131". Informed Consent Statement: This information is included in the text. "Written informed consent was obtained from all participants".
However, data demonstrating how compounds distribute in ZFE after IY delivery is lacking. Moreover, a detailed comparison with results using the same chemicals obtained by the immersion route, and relating the data with their physicochemical characteristics, is missing. In this study, we compared the pharmacokinetics of seven fluorescent compounds with known physicochemical properties that were administered to two-cell stage embryos by immersion or by IY microinjection. Absorption and distribution of the dyes were examined at various timepoints after administration by spatiotemporal fluorescence imaging. Relative exposure levels were first calculated using noncompartmental pharmacokinetic analysis and then related to some physicochemical descriptors of the compounds.
Non-Compartmental Pharmacokinetic Analysis Next, we calculated the relative amount of fluorescent dye present in the embryos from 0. 25 to 72 h post exposure by quantification of the integrated fluorescent intensity in delineated whole-body contours. Of notice, the maximal fluorescence intensity was not recorded immediately after microinjection, probably by temporal formation of aggregates that show no fluorescence during early time points  [14]. These early observations were therefore censored per compound and excluded from the dataset. The semilogarithmic graphs in Figure  3a  show that only in the case of CY3A the immersion and intrayolk microinjection procedure resulted in a similar exposure profile. In addition, as the yolk makes up a significant portion of the zebrafish embryo during the first stages of development and is known to retain small molecules due to its high content of cholesterol and triacylglycerol  [15] , we also assessed the amount of fluorescent dye present in the yolk and in the rest of the body (RoB, i.
1%). Then, using MetaMorph (Microscopy Automation and Image Analysis Software V. 7. 8. 00, Molecular Devices, LLC. , San Jose, CA, USA) and by manual delineation of the whole-body (WB) (up to 120 h) and yolk sac contours (up to 72 h) of the zebrafish embryos the fluorescence in the selected area was quantified as integrated fluorescence intensity (RFU)  [16]. The RFU values of the non-yolk compartment (i. e. , RoB: rest of body) was assessed by subtracting the yolk results from the corresponding integrated fluorescence intensities found in the WB.