dataesr/scientific-paragraphs-categorization huggingface dataset:
Cytosolic Calcium Imaging For calcium imaging, 100,000 cells were seeded onto glass coverslips (25 mm dia. ) and incubated in a complete culture medium for 48 h. Single-cell cytosolic calcium imaging was performed, using Fluo2 LR-AM calcium dye as previously described  [66]. Fluorescence intensity changes were normalized to the initial fluorescence value F 0 and expressed as F/F 0 (relative [Ca 2+ ] cyt ). One field was acquired from each coverslip and the data were pooled from six independent coverslips on three different days. Data were processed using OriginPro 7. 5 software (Origin Lab, Northampton, MA, USA). On graphs, data were summarized as the mean ± standard deviation (SD).
One of the most important domains in aquaculture is Macrobrachium, since it represents one of the most cultured crustacean genus worldwide. Description of the authors that study and publish on the subject constitutes a solid contribution to the knowledge of this genus. Indicators of productivity, visibility, relevance, sex and co-authorship of the authors were collected from the Scopus database for the period 1980-2016 to describe the Macrobrachium domain. Conceptual mapping techniques were used to visualize co-author relationships. The greatest amount of contributions to knowledge of the genus Macrobrachium was shown to come from researchers in China, Brazil, USA and India. Only seven women are among the most productive and relevant authors. Multiple co-author networks exist in which the most relevant researchers are the center.
MATERIALS AND METHODS All scientific papers published between 1980 and 2016 that included the term Macrobrachium in the title were selected from the Scopus ® database (Elsevier, Netherlands). The complete records were transferred as a text file and then standardized with the EndNote 10 ® program, using the bibliographic references manager. Then, Bibexcel (Olle Persson, Umeå University, Umeå, Sweden) was used to analyze the data extracted from the Scopus database and Pajek (version 3. 14, Batagelj and Mrvar, University of Ljubljana, Ljubljana, Slovenia) was used to create a mapped representation of the results that corresponded to the frequency of publication and the collaborative relationships between the authors. Data related to the H index (A scientist has index h if h of his or her Np papers have at least h citations each and the other (Np -h) papers have ≤ h citations each)  (Hirsch, 2005) , number of published articles and number of citations were obtained with the Citation Tracker tool from the Author Details page of Scopus.
The objective of the present study was to investigate, for the first time in a marine context, whether the induction of the glyoxylate shunt is indeed directly related to Fe-limitation and whether its induction can affect bacterial growth and respiration rates. Through the use of genetic tools, the role of the glyoxylate shunt under Fe-limitation was elucidated via the construction of both a luminescent bioreporter (icl-luc), a knockout ( icl) and its complement (icl+) of the isocitrate lyase gene in the model organism Photobacterium angustum S14. Isocitrate lyase (icl) was the chosen gene of interest as it is a key enzyme within the glyoxylate shunt. The genome of P. angustum S14 has been sequenced and an extensive physiological data set is already established  (Lauro et al. , 2009) , making it a sound candidate for our experimental setup.
Statistics All statistics were conducted in R-studio (Version 1. 0. 136). Data was analyzed accordingly using a parametric Analysis of Variance (ANOVA) test after having respectfully met the assumptions of normality and homoscedasticity using a Levene and Shapiro-Wilk test. A Tukey analysis was subsequently used as a post hoc analysis. In order to account for a skewed and unbalanced dataset obtained for both growth and respiration measurements (i. e. , unequal numbers of observations for each level of a factor), data were trimmed and log transformed before conducting a type III ANOVA with contrasts of both factors set to "contr. sum" and "contr. poly" (Wilcox, 2012).
Methods LUNG SAFE: patients, study design, and data collection LUNG-SAFE was an international, multicenter, prospective observational cohort study conducted in a 459 ICUs worldwide. During 4 consecutive weeks in the winter of 2014 (February-March 2014 in the Northern Hemisphere and June-August 2014 in the Southern Hemisphere), participating ICUs enrolled patients undergoing IMV or NIV. Participating ICUs obtained ethics committee approval and either patient consent or waiver of consent as per local guidelines. National coordinators, site investigators, and endorsing societies are listed in Additional file 1. Exclusion criteria were age < 16 years or lack of informed consent when required. Patients were screened daily for AHRF, defined as follows: (1) ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO 2 /FiO 2 ) ≤ 300 mmHg while receiving IMV or NIV with positive end-expiratory pressure (PEEP) ≥ 5 cmH 2 O and (2) new radiological pulmonary parenchymal abnormalities.
In patients with AHRF, a more detailed set of data was collected to determine whether they met the Berlin definition criteria for ARDS. Data on comorbidities, etiology of AHRF, and risk factors for ARDS were recorded. Data on arterial blood gases, ventilatory support, use of adjunctive therapies (e. g. , prone positioning, extracorporeal membrane oxygenation, neuromuscular blockade), severity of ARDS, and other organ involvement by modified nonpulmonary Sequential Organ Failure Assessment (SOFA) score  [24]  were collected on selected days. The following clinical endpoints were assessed: ICU and hospital survival, censored at 90 days after enrollment; duration of mechanical ventilation; changes in ARDS severity; and decision to withhold or withdraw life-sustaining therapies. A full description of the methods of the LUNG SAFE study, including the full study protocol, case report form (CRF), sample size, and quality control, can be found in the original study paper  [23].
" To the best of our knowledge, this was the first prospective, multicenter study conducted on a large cohort of immunocompromised patients with a diagnosis of ARDS according to Berlin definition criteria  [25] , whereas previous studies relied on the definition of the American-European Consensus Conference on ARDS  [26]. As expected, ARDS in immunocompromised patients was associated mainly with an infectious cause. Pneumonia, noncardiogenic shock, and pulmonary vasculitis were significantly more frequent in immunocompromised patients, whereas other risk factors for ARDS were more frequently represented in the control group. Immunocompromised subjects had a significantly higher ICU and hospital mortality, despite similar ARDS severity and nonpulmonary SOFA score. Another subanalysis of the same database confirmed that active neoplasm, hematologic malignancies, and immunosuppression are independently associated with increased mortality  [27].
Limitations The present study has several limitations. First, it is a post hoc analysis of a prospective multicenter observational trial, and unknown confounders associated with the subgroup analysis may bias the results. Although the data were prospectively collected from a high number of centers from 50 countries, different approaches to clinical decisions from different centers (e. g. , decisions on withholding or withdrawing of life-sustaining measures) may have influenced the outcomes. Second, the criteria used to define the immunocompromised cohort were quite heterogeneous. It was impossible to stratify the patients according to the prognosis of baseline disease and to the severity of immune deficiency. Indeed, causes of immunosuppression, other than malignancies, were not specified in nearly 40% of the whole cohort of immunocompromised patients.
Moreover, in patients with cancer, no information was available on the type of cancer, its staging, and the nature and timing of anticancer treatments. This lack of information, related to the LUNG SAFE original CRF, should be considered a major limitation because the outcome of immunocompromised patients is strictly dependent on the type of underlying diseases and associated therapeutic approach. All these factors may limit the generalizability of our findings. Third, to limit the burden on investigators, data were collected once daily only, and information on the actual hours of duration of ventilatory treatments was not available. This is particularly relevant for patients treated with NIV because the precise duration of NIV before the eventual intubation might be important to understand the impact of NIV failure on outcome  [24].
Acknowledgements LUNG SAFE investigators and ESICM Trial Group email address: lung-safe@esicm. orgStudy coordination:  Guy M. Francois  ( European Society of Intensive Care Medicine, Brussels, Belgium ). Data revision and management:  Francesca Rabboni  ( University of Milan-Bicocca, Monza, Italy ),  Fabiana Madotto  ( University of Milan-Bicocca, Monza, Italy ),  Sara Conti  ( University of Milan-Bicocca, Monza, Italy ). LUNG SAFE executive and steering committees:  John G. Laffey ,  Giacomo Bellani ,  Tai Pham ,  Eddy Fan ,  Antonio Pesenti ,  Laurent Brochard ,  Andres Esteban ,  Luciano Gattinoni ,  Frank van Haren ,  Anders Larsson ,  Daniel F. McAuley ,  Marco Ranieri ,  Gordon Rubenfeld ,  B. Taylor Thompson ,  Hermann Wrigge ,  Arthur S. Slutsky. National coordinators: Argentina:  Fernando Rios Australia/New Zealand: Frank Van Haren.
8, 9 The third strain, a S. enterica serotype Typhimurium phage-type 1a (later reclassified as definitive phage-type [DT] 2), isolated in 1962 in Brighton, United Kingdom, produced a beta-lactamase with a substrate profile different from that of TEM (Table  1 ). This S. enterica serotype Typhimurium strain was isolated during the first reported outbreak caused by an ampicillin-resistant S. enterica serotype Typhimurium strain. It occurred in the second half of 1962, in the United Kingdom, at a time at which dozens of S. enterica serotype Typhimurium DT2 isolates resistant to ampicillin, streptomycin, sulfonamides and tetracyclines were found in humans and pigs. 10 The plasmid of a representative strain, R 1818 , later renamed R46,  9  was sequenced (GenBank accession no. AY046276) and found to be a ~ 50 kb IncN plasmid carrying the bla OXA-2 gene.
S1 ). Whole-genome sequencing was carried out at the genomics platform of Institut Pasteur on an Illumina HiSeq 2500 platform generating 118 to 146 bp paired-end reads, yielding a mean of 233-fold coverage (minimum 41-fold, maximum 960-fold). Short-read sequence data were submitted to EnteroBase (http://enterobase. warwick. ac. uk/). The oldest ampicillin-resistant S. enterica serotype Typhimurium isolate, ExPB 5-59 was also sequenced by GATC Biotech (Konstanz, Germany), on the PacBIO RS II platform (Pacific Biosciences, CA, USA). PacBio sequencing errors for homopolymers were corrected on the basis of Illumina sequences. The plasmid sequence was annotated with the RAST server (http://rast. nmpdr. org/), with manual inspection and correction. The sequence was deposited in GenBank under the accession code MF428416.
Other studied genomes Two published S. enterica serotype Typhimurium genome sequences, those for DT104,  20  a representative strain of the multidrug-resistant DT104 clone (GenBank accession no. NC_022569), and SO4698-09,  21  a representative strain of the multidrug-resistant European monophasic clone (GenBank accession no. NZ_LN999997), were downloaded from GenBank, and 100 bp overlapping simulated reads were generated. Short-read sequences from the S. enterica serotype Weltevreden 840K strain, used as the outgroup, were downloaded from EnteroBase.
Read alignment and SNP detection Illumina-generated paired-end reads and simulated paired-end reads from publicly available assembled genomes were mapped onto the reference genome of S. enterica serotype Typhimurium strain LT2, including the chromosome (GenBank accession no. AE006468) and plasmid pSLT (GenBank accession no. AE006471), with Bowtie 2 version 2. 1. 0. Singlenucleotide polymorphisms (SNPs) were identified with SAMtools version 0. 1. 19, as previously described. 22 SNPs present in insertion sequences identified by ISfinder (https://www-is. biotoul. fr/) or recombinogenic regions identified by Gubbins were removed, as previously described. 22.
kb IS1-mediated deletion (corresponding to region 41,666-48,543 of GenBank accession number FN432031) encompassing the integron (In2) region of the Tn21-like element. The IncF plasmid of the fifth isolate (STM 366-66) was derived from the NR1/R100 plasmid (lacking Tn21) (GenBank accession no. DQ364638). This isolate did not contain the pSLT virulence plasmid. The 45 kb Tn2-containing IncX1 plasmid pExPB5-59-1 was also sequenced with the PacBio platform. This plasmid was present in a clonal bacterial population (ST19-CT160) isolated in France over a10-year period (1959 to 1969). The non-Tn2 backbone of plasmid pExPB5-59-1 resembled a 42. 2 kb conjugative plasmid (pYU39_IncX; GenBank accession no. CP011431) found in an emerging invasive ST213 S. enterica serotype Typhimurium population from Mexico in the 2000s.
Characteristics of the first S. enterica (and E. coli TEM) isolates with plasmidmediated ampicillin resistance to be reported. , antimicrobial drug susceptibility type; Ap, ampicillin; Str, streptomycin; K, kanamycin; C, chloramphenicol; Sul, sulfonamides; Tmp, trimethoprim; Te, tetracycline; -, unknown; DT, definitive phagetype; available from GenBank under accession nos. AY046276* or KY749247 † or from the Wellcome Trust Sanger Institute # , NC non-conjugative; Ω duplicated gene.
Salmonella. The  French National Reference  Centre for E. coli,  Shigella , and Salmonella is funded by the  Institut Pasteur and Santé Publique France. A. Tran-Dien  was supported by a grant from the  Fondation Le Roch-Les Mousquetaires. The "Unité des Bactéries Pathogènes Entériques" belongs to the "Integrative Biology of Emerging Infectious Diseases" Laboratory of Excellence  funded by the  French Government "Investissement d'Avenir" programme  (grant no. ANR-10-LABX-62-IBEID ). The Genomics Platform is member of the " France Génomique " consortium ( ANR10-INBS-09-08 ).
6. 8 8 kb IS1-mediated deletion (corresponding to region 41,666-48,543 of GenBank accession number FN432031) encompassing the integron (In2) region of the Tn21-like element. The IncF plasmid of the fifth isolate (STM 366-66) was derived from the NR1/R100 plasmid (lacking Tn21) (GenBank accession no. DQ364638). This isolate did not contain the pSLT virulence plasmid. The 45 kb Tn2-containing IncX1 plasmid pExPB5-59-1 was also sequenced with the PacBio platform. This plasmid was present in a clonal bacterial population (ST19-CT160) isolated in France over a10-year period (1959 to 1969). The non-Tn2 backbone of plasmid pExPB5-59-1 resembled a 42. 2 kb conjugative plasmid (pYU39_IncX; GenBank accession no. CP011431) found in an emerging invasive ST213 S. enterica serotype Typhimurium population from Mexico in the 2000s.
Literature Search Strategy The outline of the methodological activities undertaken is presented in Fig. 1. The search terms presented in Table  1  were used to systematically search four electronic databases: MEDLINE, CAB Abstracts, Embase, and the National Health Service Economic Evaluation Database (NHS EED; UK). The final search was performed on June 5, 2014, and the search strategies used for each database are presented in S3-S6. In addition to the electronic search, a search verification was performed through expert elicitation to help with the identification of relevant studies within the gray literature, and by manually searching references in recent reviews on the topic  (Zinsstag et al. 2007; Zinsstag et al. 2011; Ha ¨sler et al. 2012; Min et al. 2013).
Study Inclusion Criteria and Screening The predetermined criteria for a publication to be eligible for inclusion are given in S1, while the screening strategy followed is shown in Fig. 1. A publication was considered eligible for inclusion if it reported primary research on a quantitative outcome when using a OH approach, even if not explicitly defined as such, to address complex global health challenges, and was published after 1910. This date was selected based on the setup of the databases, whereby the earliest publication date available was 1910. Primary research was defined as a study where the author(s) collected and/or analyzed data, and included case reports and case series, qualitative studies, observational studies, and experimental studies. Mathematical models and economic studies were included if they were based on field data collected in the same study or elsewhere.
Qualitative Data Extraction and Analysis Data extracted from the included publications are shown in S7-S12; these included: (1) bibliographic information and study design characteristics, (2) how the reference was identified, (3) the health issue addressed, (4) the intersectoral approach used (i. e. , human-animal vs. human-environment vs. animal-environment vs. human-animalenvironment), (5) the quantitative outcome described, and (6) a quality assessment based on the clarity of the methods. All extracted data were checked for consistency by two of the authors (LCF and MLB), and any disagreements were resolved through discussion between all reviewers. To allow for further exploration and description of the studies, the following parameters were extracted: (1) continent where the study was performed; (2) whether the country was considered developed or developing, and its income status; (3) whether the disease agent was abiotic or biotic and, in case of the latter, whether it was a bacterium, virus, protozoa, helminth, or insect; (4) whether the health issue was considered a neglected tropical disease (NTD) or not; and (5) the type of transmission.
The recently published COHERE checklist for OH studies  (Davis et al. 2017)  should help with such future endeavors by setting a benchmark as to what should be considered a OH approach. The final list of studies only included around 0. 0025% of all screened references. This was expected given the broad search terms used. It was agreed that given the objective to identify those studies that described a OH approach (without necessarily containing the term OH), the sensitivity of the search should be prioritized over the specificity. Despite the broad search terms, a certain publication bias is to be expected based on the selection of literature databases, although they were selected pertinent to the type of studies that were sought in the review. An information specialist who specializes in objective, structured reviews of the literature (DG) was consulted and involved in the process of this review to ensure that the most appropriate databases were searched.
; Pulkki-Bra ¨nnstro ¨m et al. 2012). The WHO recommends only distributing long-lasting ITNs (World Health Organization 2007); the findings in the current study are valuable in identifying those interventions that are superior to others A List of the Search Terms Used in Four Electronic Databases (MEDLINE, Embase, NHS EED, and CAB Abstracts) to Identify References that Describe a Quantitative Outcome when Using a One Health Approach to Address Complex Global Health Challenges. ((animal AND human) OR (animals and human) OR (animal AND humans) OR (animals AND humans) OR (human AND environment) OR (humans AND environment) OR (animal AND environment) OR (animals AND environment) OR ''animal to human''.
ACKNOWLEDGEMENTS Many thanks to  Prof. Jakob Zinsstag  (who helped to sow the idea for the review, and helped with defining the research question, search terms and protocol);  Dr. Barbara Ha ¨sler  (who helped with search terms and search verifica-Quantitative Outcomes of a One Health Approach tion);  Ulrich Sperling  (for his assistance with the preparation of the figures); and the  European of Veterinary Public Health  for allowing us to embark on this project. This work has partially been supported by work from the  COST Action TD1404 (Network for Evaluation of One Health ) and supported by  COST (European Cooperation in Science and Technology).
Part of the National Institute for Health Research Centre for Reviews and Dissemination, UK. g Refworks Ó (ProQuest, LLC, Cambridge Information Group; Betheseda, MD, USA). h Community of Practice in Ecosystem Approaches to Health-Canada. Rushton 2009; Ha ¨sler et al. 2012; Minutes of the Expert Workshop 2013. b Based on a recommendation that three to five databases are considered sufficient (Young et al. 2014). c Texts available between 1980 and 2014. d Texts available between 1946 and 2014. e Texts available between 1910 and 2014. f.
Relative brain volume of neuropils was analyzed with a linear-mixed model with relative volume as the dependent variable, treatment as fixed factor and line as random factor for each of the 11 neuropils with a Benjamini-Hochberg FDR correction over all 11 analyses. A principal component analysis (PCA) was performed using the neuropil volume data on all independent structures (FSB + EB + Calyx + Lobes + MED + LOB + AL), and the values for the first and second PC were extracted for further analysis. Differences in PC values between females from selected lines and control lines were analyzed using a two sample t-test. All analyses were performed in R 3. 4. 4. (R Core Team 2018). The function lmer in the lme4 package was used to fit the linear-mixed models and the function lm in the base package was used to fit the linear models.
Background: The p. Asn215Ser or p. N215S GLA variant has been associated with late-onset cardiac variant of Fabry disease. Methods: To expand on the scarce phenotype data, we analyzed natural history data from 125 p. N215S patients (66 females, 59 males) enrolled in the Fabry Registry (NCT00196742) and compared it with data from 401 patients (237 females, 164 males) harboring mutations associated with classic Fabry disease. We evaluated interventricular septum thickness (IVST), left ventricular posterior wall thickness (LVPWT), estimated glomerular filtration rate and severe clinical events.
| Patients This study includes male and female patients enrolled in the Fabry Registry (age range: 0. 5-72. 5 years at first assessment) diagnosed with Fabry disease and harboring the p. N215S mutation. All patients were from 10 international Fabry Registry sites that had contributed clinical data for a minimum of six p. N215S patients, and had received specialized care supervised by one of the authors (D. P. G. , E. B. , F. C. , S. P. S. /D. A. L. , A. L. , L. M. , K. N. , F. P. , S. P. S. , C. W. , A. J. ).
| Outcomes We analyzed natural history data (i. e. , obtained before initiation of enzyme replacement therapy [ERT], if indicated) including left ventricular posterior wall thickness (LVPWT), interventricular septum thickness (IVST) and estimated glomerular filtration rate (eGFR) (bedside Schwartz equation if <18 years of age, Chronic Kidney Disease Epidemiology Collaboration [CKD-EPI] equation if ≥18 years of age). The first values entered in the Fabry Registry were used for analysis. We also evaluated severe clinical events including: (1) Cardiac events: angina pectoris, arrhythmia, congestive heart failure, myocardial infarction, implantation of cardiac devices, significant cardiac procedure; (2) Renal events: first occurrence of either the initiation of chronic dialysis (>40 days) or renal transplantation; (3) Cerebrovascular events: hemorrhagic or ischemic stroke; and (4) Death.