dataesr/scientific-paragraphs-categorization huggingface dataset:
The subjects were healthy, malaria-naive, male, Indian adults aged 18-45 years recruited from the volunteer database of healthy subjects available with the study site, Syngene International Limited, Bangalore. Subject recruitment was as per inclusion/exclusion criteria as detailed in the Supplementary Clinical Trial Protocol. All study procedures including screening were conducted after obtaining written Informed Consent from all subjects. The study involved administration of the investigational vaccine candidate, PvDBPII/GLA-SE, in three dose-escalating cohorts corresponding to three dosages of 10, 25 and 50 µg of PvDBPII with a constant dose of adjuvant GLA-SE (5 µg of GLA) as detailed in the Supplementary Clinical Trial Protocol. The vaccine was administered on days 0, 28 and 56 with follow-up till day 180.
Safety analysis Data on AEs were collected throughout the study at regular intervals. The subjects were closely monitored for immediate reactogenicity on the day of each dosing. Other safety data assessed included specified solicited symptoms collected by diary card during Days 0 7; unsolicited AEs collected on Days 0-28 after each dose and serious AEs collected Days 0-180. Laboratory assessments were done on Day 7 post each dose and then at the end-of-study visit by performing predefined laboratory parameter testing as listed in the Supplementary Clinical Trial Protocol. Solicited events, unsolicited events and changes in laboratory parameters are graded as per the standard US FDA Toxicity Grading Scale for Preventive Vaccine Clinical Trials. 24 An independent data safety monitoring committee reviewed 7 days of safety data for each cohort escalation.
Plates were washed and bound antibodies were detected with horseradish peroxidase conjugate anti-human IgG secondary antibody (Sigma). The IgG subclasses IgG1, IgG2, IgG3 and IgG4 in serum samples were detected by biotin conjugated anti-human IgG1, IgG2, IgG3 and IgG4 (Sigma), respectively, followed by Avidin-HRP conjugate (Sigma). The assays were developed with TMB substrate (3,3′,5,5′-tetramethylbenzidine (Sigma)). The reaction was stopped with 2 N H 2 SO 4 and the plates were read at 450 nm using a SpectramaxPlus384 microplate reader (Molecular Devices). Data were collected using Softmax Pro GXP v5. Naive sera from individuals not previously infected with malaria were used as negative control for the assays. Serum samples collected during screening that were reactive to PvDBPII by ELISA assay were pooled and used as reference positive control sera to generate the reference standard curve.
The reference positive control sera pool was assigned 940 ELISA U/mL, which was approximately equivalent to the reciprocal of the dilution that yields an optical density of ~1 at a wavelength of 450 nm (OD 450 ) by ELISA assay. The standard curve was then used to convert absorbance values of individual test sera (diluted to yield absorbance within the linear range of the standard curve) to U/mL using ADAMSEL FLP b040 software (Ed Remarque© 2009, BPRC, The Netherlands). Test samples that did not fall within an acceptable OD 405 range were retested at an alternate dilution. A response for different antibody subclasses in a serum sample was considered positive if an OD value above the cut off (arithmetic mean of negative controls plus 3 standard deviations) was achieved. Anti-PvDBPII IgG antibodies by IFA assay IFA assay was used to test recognition of native PvDBPII antigen in P.
ACKNOWLEDGEMENTS We express our gratitude to the study participants for their participation, kind cooperation and support. We thank  Dr. Suresh Jadhav ,  Serum Institute of India, Pune , for providing GeneVac-B for use as control vaccine, and  Dr. Jean Popovici  and  Dr. Didier Menard ,  Institut Pasteur ,  Phnom Penh ,  Cambodia , for providing slides of P. vivax blood-stage parasites. We thank our  Data Safety Monitoring Board  (DSMB) members  Dr. Anuradha Bose  ( Professor of Paediatrics, Christian Medical College, Vellore ),  Dr. Nithya Gogtay  ( Associate Professor Department of Clinical Pharmacology, Seth GSMC & KEM Hospital, Mumbai ),  Dr R. M. Pandey  ( Professor and Head, Department of Biostatistics, AIIMS, Delhi ),  Dr Ajit Pal Singh  (Director,  Clinical R&D ,  MSD Wellcome Trust Hilleman Laboratories (P) Ltd.
In this respect, our observation benefits from the accuracy of recording two clinically well identified variables: ATG induction and development of colon cancer. The CTS registry has collected data on cancer in transplant recipients since the early 1980s. Because underreporting of tumors was recognized as a potential problem early on, particular emphasis has been placed on the accuracy and completeness of reporting and all centers included in this analysis have confirmed yearly that their cancer data submitted to CTS were complete and accurate. A limitation of our analysis is that the patients included were not tested for Neu5Gc antibodies. Not unusual for large population-based studies, we relied on data by inference from publications showing that ATG treatment of transplant recipients induces a significant and long lasting presence of Neu5Gc antibodies.
In addition, the meat intake was not known. Although the content of Neu5Gc in the diet does not correlate with the level of anti-Neu5Gc  [19] , it might conceivably influence the degree of Neu5Gc deposit on epithelia. Retrospective analyses of data regarding the study of variables possibly involved in cancer etiology  [22, 23]  depend on the accuracy of data collection. In this respect, our observation benefits from the accuracy of recording two clinically well identified variables: ATG induction and development of colon cancer. The CTS registry has collected data on cancer in transplant recipients since the early 1980s. Because underreporting of tumors was recognized as a potential problem early on, particular emphasis has been placed on the accuracy and completeness of reporting and all centers included in this analysis have confirmed yearly that their cancer data submitted to CTS were complete and accurate.
Macrophages express signal regulatory protein α (SIRPα) that interacts with CD47, a ubiquitously expressed protein that mediates a "don't eat me" signal. Cancer cells have evolved to hijack this interaction by upregulating the expression of CD47 on their cell surface, thus counterbalancing prophagocytic signals and increasing the chance of evading innate immune surveillance  (14). Therefore, blockade of the CD47/SIRPα interaction represents a promising strategy to increase the phagocytic clearance of tumor cells from the body. Several mAb and fusion proteins that target this interaction are in early clinical development (clinicaltrials. gov; e. g. NCT02953509, NCT03013218, NCT02367196 and NCT02890368). One limitation of this approach is that CD47, whilst upregulated on tumor cells  (15) , is also ubiquitously expressed on all cells of the body, including relatively high levels on erythrocytes and platelets  (16, 17).
Whole blood binding Human whole blood samples were collected from healthy donors in citrate at the Blood Transfusion Center in Geneva. Samples were mixed with 3 µg/mL of AF488-coupled NI-1701, hB6H12 or isotype control (using the Alexa Fluor 488 Protein Labeling Kit (A10235, Thermo Fisher Scientific)) and surface staining Abs for 30 min at 4°C. More precisely, samples were incubated with PE anti-hCD41a (#555467, BD Biosciences), APC-Cy7 anti-hCD3 (#557757, BD Biosciences) and with BV510 anti-hCD20 (#302311, BioLegend) Abs. Whole blood was then divided in two samples: 5 µL were diluted in PBS for erythrocytes analysis while 150 µL were incubated with erythrocyte lysing solution (#349202, BD Biosciences), and washed for leukocytes and platelets analysis. Samples were then acquired on a CytoFLEX instrument (Beckman Coulter) and analyzed with Flowjo® software.
Control group animals received i. v. bolus injections of vehicle only on days 1, 8, 15 and 22. For both studies, the animals were assessed twice daily for clinical signs and blood samples collected at different time points for hematological and PK analyses. NI-1701 and CD19/CD47 hi biAb serum concentrations were measured by ELISA at Novimmune with inhouse developed assay. IL-6 serum concentrations were measured using MILLIPLEX MAP multiplex immunodetection kits (Millipore) and analysed on the Luminex ® instrument. The evaluation of the PK data was conducted at Novimmune using WinNonlin software (Professional Version 6. 3, Pharsight).
Acknowledgments The authors wish to thank  Dr Alison M Michie  and  Dr Emilio Cosimo  who provided clinical samples used to establish the in vitro ADCP assays;  Dr Stéphanie Hugues  and  Dr Juan Dubrot Armendariz  for video microscopy;  Serge Wolfersperger  and  Emeline Eggimann  for animal husbandry. Financial support. The  R50 award  ( R50CA211466 ;  NCI)  supports  Michael P. Rettig 's research.
After isolation, the viruses were confirmed as APMV-1 by APMV-1-specific polymerase chain reaction (PCR). The cleavage site of the fusion protein gene for 24 representative isolates was sequenced and phylogenetically analysed and compared with representative isolates of the different APMV-1 genotypes in the GenBank database. In total, 711 samples were collected from different regions in the country from which 72 isolates were recovered, giving a prevalence of 10. 1%. Sequence analysis of 24 isolates revealed that the isolates were all lentogenic, with the typical 111 GGRQGR'L 117 avirulent motif. Twenty-two isolates had similar amino acid sequences at the cleavage site, which were different from the LaSota vaccine strain by a silent nucleotide substitution T357C. Two isolates, NDV/waterfowl/Uganda/MU150/2011 and NDV/waterfowl/Uganda/MU186/2011, were different from the rest of the isolates in a single amino acid, with aspartate and alanine at positions 124 and 129, respectively.
Phylogenetic analysis The Basic Local Alignment Search Tool (BLAST) was used to find similar F gene sequences for APMV-1 in the Genbank. Sequences covering the cleavage site of the fusion gene representing all 18 genotypes of APMV-1 recently described by  Diel et al. (2012) , including all the Ugandan and East African sequences, were retrieved. The sequences were aligned together with the Ugandan sequences generated in this study using Clustal W and edited using Bioedit Software version 5. 0. 9  (Hall 1999). Phylogenetic analysis was performed using the MEGA version 5. 05 program  (Tamura et al. 2011)  with the neighbour-joining (NJ) Kimura 2-parameter method and 1000 bootstrap replicates. The amino acids around the fusion protein cleavage site were compared to representative sequences from each of the genotypes.
Pathotypes of Avian paramyxovirus type-1 in Ugandan aquatic birds The deduced amino acid sequences of the F gene cleavage site were used to determine the pathotypes and are shown in Table  2. All 24 isolates sequenced had a lentogenic motif of 111 GGRQGR'L 117 characteristic of the avirulent strains. However, isolates NDV150/waterfowl/Uganda/2011 and NDV186/waterfowl/Uganda/2011 were different from the rest of the 22 isolates in a single amino acid; aspartate and alanine at positions 124 and 129, respectively. The rest of the 22 isolates were identical at all positions. Phylogenetic analysis: To determine the phylogenetic relationships between Ugandan aquatic birds' isolates, other Ugandan strains from poultry and the rest of the world, the sequences of the 201-bp hypervariable region of the F gene were compared to the corresponding region of viruses available in GenBank.
Acknowledgements The sample collection, virus isolation and sequencing of the isolates were supported by the  World Bank Millennium Science Initiative Project  (Grant #  MSI/03/32/2010 ) to  Denis K. Byarugaba  through the  Uganda National Council of Science and Technology. We thank  Mathilde Paul  and  Agnès Waret-Szkuta  ( IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France ) for their help with the cartography.
Availability of data and materials The sequences of the cleavage site of the isolates analysed in this study were deposited in GenBank with accession numbers LT549451, LT549452 and LT549453. These include NDV138/ aquatic birds/Uganda/2011 representing the 22 isolates with identical sequences and NDV150/aquatic birds/Uganda/2011 and NDV186/aquatic birds/Uganda/2011 as indicated in the phylogenetic tree legend in Figure  2.
Search strategy The search strategy was updated on February 10, 2018 in collaboration with personnel from The Cochrane Collaboration. No language or publication restrictions were employed. We searched all databases from the date of their inception to February 10, 2017. All retrieved references were screened for eligibility. The databases searched were the Cochrane Central Register of Controlled Trials (CENTRAL; Issue 1 to February 10, 2017), MEDLINE (1966 to February 10, 2017), and Embase (1980 to February 10, 2017).
Types of studies and participants To be included, RCTs were required to compare antibiotic treatment as a primary outcome in adult patients with acute respiratory infection for whom antibiotic decisions were made by utilizing a PCT treatment algorithm (PCT-guided antibiotic stewardship algorithm) versus standard of care. Paediatric trials and trials that did not use PCT to guide initiation and/or duration of antibiotic treatment were excluded. Data were collected from eligible trials that asthma, or pulmonary fibrosis), sepsis or septic shock, or febrile neutropenia with concomitant respiratory infection.
Data collection and analysis: Two reviewers (YW and RS) independently assessed trial eligibility based on titles, abstracts, full-text reports, and further information obtained from trial investigators as needed. Two additional reviewers (RB and MM) reviewed all PCT algorithms in individual trials. Data were assessed in a consistent manner across all trials with standard definitions and parameters, resulting in slightly different mortality and adverse outcome rates in the meta-analysis than previous reported in the individual studies. In accordance with the Cochrane method, the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE)  14  approach was used to assess risk of selection bias, performance bias, detection bias, attrition bias, reporting bias, and other types of bias  8.
This analysis is listed in the online supplementary material. Summary data on the PCT algorithm including types of protocols, PCT cut-off levels, and predefined overruling criteria were reported and consensus algorithms derived from trial data for the following specific types of respiratory tract infection: CAP, bronchitis, exacerbations of COPD and asthma, sepsis, and post-operative sepsis. To derive consensus algorithms stratified by type of ARI, we studied all protocols and manuscripts included in our analysis with focus on types of patients and PCT cut-offs used in the individual trials, and discussed differences among protocols with all co-authors until A c c e p t e d M a n u s c r i p t consensus was reached. All co-authors agreed to the proposed consensus PCT algorithms presented in this manuscript.
Acknowledgements We thank  Yannick Wirz, MD  and  Ramon Sager, MD  of the  Kantonsspital Aarau, Aarau, Switzerland  for their assistance with the assessment of the trials included in this analysis. We also thank  Prasad Kulkarni, PhD ,  CMPP of Asclepius Medical Communications LLC, Ridgewood, NJ, USA  for editorial assistance, which was funded by bioMérieux.
Detection of Prophages in Bacterial Genomes There is consensus among experts that host strain genome sequencing is an essential initial investigation before starting phage production processes as it allows the identification of prophage genes like integrases, repressors, excisases, recombinases, terminases. Having this sequence available thus makes predictions for prophage properties like virulence factors or for prophage incompleteness possible. Induction ability might be experimentally studied by using Mitomycin C or UV irradiation but these induction methods are not successful enough and require indicator strains that are not always available. Due to the increasing importance of phage applications, entering prophage genomes in databases is necessary when bacterial genomes are analyzed. Algorithms for finding prophages are available like PhiSpy  [55] , PHAST (http://phast.
Prophages in Bacterial Production Strains Temperate phages/prophages present a problem in phage production processes, but are so abundant in all habitats including our own microbiome that we should not blindly demand their elimination from phage production processes. Instead, we broadly advise that an intensive discussion be had on how to deal with situations when no prophage-free production strains are available. We have explained which properties prophages might carry and what their unwanted features are, how abundant they are in opportunistic common ESKAPE bacteria, how genome analyses precisely characterize them and what to calculate if a production strain carries a prophage. We advocate that researchers enter bacterial and (pro)phage genome data into public databases because rich databases will provide the platform that is needed to deal with these particular pressing questions and because phage therapy will be a potent alternative therapy in the global multidrug resistance threat.
Flow cytometry Blood from mice (200 μL) was collected intra-orbitally. Spleen and lymph nodes were also collected and immune cells were filtered through a sterile nylon membrane. Cell suspensions were stained at 4°C in FACS Buffer (PBS, 1% FBS, 2 mM EDTA). The following fluorescent-labelled antibodies were used: anti B220-BV421 (clone RA3-6B2, 1/400), anti CD80-APC (clone16-10A1, 1/2500), anti CD86-FITC (clone GL-1, 1/600), anti CD3-PE (clone 17A2, 1/100) from BioLegend (San Diego, CA, USA). Stained cells were analyzed using a BD-Fortessa SORP flow cytometer (BD Bioscience; US). Results were analyzed using Kaluza Flow Cytometry software 1. 2 (Beckman Coulter; France). was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which this version posted November 24, 2018.
Sequencing of VDJ regions RNA was extracted from total spleen, and one μg was used for sequencing. Immunoglobulin gene transcripts were amplified by 5'RACE PCR as described  (Boice et al. , 2016). Illumina sequencing adapter sequences were added by primer extension, and resulting amplicons were sequenced on an Illumina MiSeq sequencing system using MiSeq kit Reagent V3 600 cycles. Repertoire analysis was done using IMGT/HighV-QUEST tool and R software. Briefly, VH, JH and CDR3 segments were identified using HighV-QUEST. Based on these annotations, reads were grouped in clonotypes that share the same VH and JH gene and high CDR3 homology. The relative abundance of each clonotype was then calculated. was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Acknowledgments: We thank  Dr J Cook Moreau ,  UMR CNRS 7276 ,  Limoges, France , for English editing. The group of  J Feuillard  is supported by grants from the  Ligue Nationale contre le Cancer (Equipe Labellisée Ligue) , the  Institut National contre le Cancer (INCa) , the  Comité Orientation Recherche Cancer (CORC) , the  Limousin Region  and the  Haute Vienne and Corrèze committees of the Ligue Nationale contre le Cancer  and by the  Lyons Club of Corrèze. U Zimber-Strobl  was supported by the  German Research Foundation  ( SFB 1243 ,  TP-A13  and  ZI1382/4-1 ).
Acknowledgements We gratefully acknowledge  Amir Sufi  for his helpful discussions about the cost benefits of point of care. We gratefully acknowledge the support of the  Health Ministry of Morocco , the  American Society for Microbiology (ASM) ,  Roche ,  LDBiO Diagnostics , Somadiag, INH Sciences, and  International Journal Experts. None of these institutions played a role in the analysis or interpretation of data.
Acknowledgements We are indebted to  H. Matheve ,  P. Vantieghem  and  H. De Rycke  for field and lab assistance, to  A. Chaine  for logistic support with the aviary experiments, and to  J. Scheerlinck  for helping with glucocorticoid analysis. The field sampling protocol was approved by the  Ethical Committee of Ghent University. Sparrows were caught under capture and ringing permit n°15038 ( French National Natural History Museum ).
Finally, a multiple logistic regression model was used to identify potential predictors of high FRS (Table 4). A higher FRS was present in SpA patients from Northern showing a similar or lower prevalence of CV risk in AS than PsA patients. The observed discrepancies may be due to the fact that these studies do not compared all clinical phenotypes present in SpA. The present analysis, conducted in the ASAS-COMOSPA database, is the first one that took into account the phenotypes of the disease. Our results demonstrated that axial SpA patients exhibited a lower prevalence of traditional CV risk factors than patients with peripheral and/or mixed phenotypes, and this could be associated to a lower development of CV events. Consistent with our results, previous data showed that predominantly axial SpA is related with a lower frequency of hypertension, dyslipidemia, T2DM and obesity  [14, 30]  than PsA (a mainly peripheral disease).
2%, 31. 4% and 7. 9% respectively) and SpA patients (19. 3%, 34. 7% and 6. 0% respectively). Regarding countries from Mediterranean region, we noted that the estimated prevalence of hypertension, dyslipidemia and T2DM was 42. 6 %, 49. 5 % and 13. 6 % in healthy individual (reference data from Spain)  [39, 40]   This study presents some limitations. First, the study was performed in 2001 of the 3984 patients who form the COMOSPA database, which can hamper the external validity of the study. Secondly, the prevalence of CVD might have been underestimated as a result of the inability of patients to participate or even died at a premature age, preventing them to collaborate in the study. Finally, the prevalence of CV comorbidities in these patients was variable across countries. This finding can be explained by the socioeconomic differences, which has an effect on health systems, and differences in diet, genetic and environment; however, it is possible that this may be also influenced by the selection type used in each country.
Background. Early initiation of combination antiretroviral therapy (cART), at higher CD4 cell counts, prevents disease progression and reduces sexual transmission of human immunodeficiency virus (HIV). We describe the temporal trends in CD4 cell counts at the start of cART in adults from low-income, lower-middle-income, upper-middle-income, and high-income countries (LICs, LMICs, UMICs, and HICs, respectively). Methods. We included HIV-infected individuals aged ≥16 years who started cART between 2002 and 2015 in a clinic participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) or the Collaboration of Observational HIV Epidemiological Research in Europe (COHERE). Missing CD4 cell counts at the start of cART were estimated through multiple imputation. Weighted mixed-effect models were used to smooth trends in median CD4 cell counts.
Weighted Analysis of Temporal Trends We aggregated data by calendar year (3-14 years, depending on the country), country (55 countries), and sex (2 groups), and we calculated the median CD4 cell count at the start of cART for each of the resulting data cells. We assigned a weight to each data cell that consisted of 2 components, which were multiplied. The first component corresponded to the number of observations, divided by the average number of observations in data cells of the same country income group (and was thus normalized by country income group), and captured the precision of the aggregated values in each data cell. The second component corresponded to the ratio of the number of patients who were newly enrolled in that cohort and year to the number of patients starting cART in that country and year, as estimated by UNAIDS  [18]  and was also normalized by country income group.