dataesr/scientific-paragraphs-categorization huggingface dataset:
Assessment of Cell Populations in the Spleen, and Bone Marrow Cells were recovered from the spleen and the bone marrow and stained with anti-TER119 and anti-CD71 antibodies (BioLegend) to evaluated erythroid populations. After lysing RBCs with the RBC lysing buffer Hybri-MaxH (Sigma Aldrich, Canada), singlecell suspensions of splenocytes were treated with anti CD4-FITC and anti-F4/80-PE antibody (BioLegend) to respectively assess the number of CD4 T cells and macrophages. Cells were further kept for 30 min at 4uC and fluorescence was analyzed on a FACScan flow cytometer (Becton Dickinson, USA). Data provided by 10,000 events were analyzed using the FlowJo software.
Determination of Heme, Hemopexin and Erythropoietin Concentrations in Plasma Plasma was recovered from euthanized mice in a heparinized eppendorf. Total heme levels were measured in the plasma using its elicited luminescence. Briefly, 5 mL of plasma was diluted in 25 mL PBS and was added to an opaque 96-well plate. A luminescence reader (MLX microtiter plate luminometer with the software Revelation MLX, Version 4. 27, Dynex Technologies, Chantilly, VA, USA) was set to dispense simultaneously 100 mL of a 1 mg/mL luminol solution (dissolved in 0. 1 M NaOH and 3 mM EDTA; Sigma Aldrich, Canada) and 100 mL of a 7. 26 mM t-buthylhydroperoxide solution (dissolved in 0. 1 M NaOH and 3 mM EDTA; Sigma Aldrich, Canada). Luminescence output was measured immediately with a 2 s interval. A standard curve was made with the stock solution of heme to express results in mM.
Supporting Information Figure  S1  Mice were injected with PBS (Ctrl) or hemin (HE; 5 mg/kg) 3 times a week for 2 weeks. Hemoglobin concentrations in blood (A) and hemopexin concentrations in plasma (B) were determined 24 h after the last injection. Cells from femoral bone marrow (BM) and splenocytes (SPL) were recovered and stained with anti-F4/80-PE antibody to estimate the number of macrophages (C), and reticulocytes were determined in blood cells with anti-CD71-FITC antibody (D). BFU-E cells were quantified in BM (E) and spleen cell cultures (F), as described in the Material and Methods section. Data represent 6-13.
Functional GO analysis of DE genes in PCV2-infected PAMs The Ingenuity pathway analysis (IPA) program was used to determine the relevance of PAM gene functionalities and gene networks associated with PCV2 infection. While 266 (24 HPI) and 175 (48 HPI) DE genes were imputed into IPA, only 173 and 124 were characterized with specific cellular functions. The 173 DE genes from 24 HPI PAMs were placed into 19 functional groups (Additional file 6: Table  S6  and Additional file 7: Figure  S8 ). The most frequently represented category of gene functionality was Inflammatory Response (Cellular Movement, and Immune Cell Trafficking) with 22 genes, followed by Cell-To-Cell Signaling and Interaction, Cellular Growth and Proliferation, and Cellular Compromise. The 124 DE genes from 48 HPI PAMs were placed into 16 functional groups (Additional file 8: Table  S7  and Additional file 9: Figure  S9 ).
Virus and cells The PCV2-WH strain (GenBank accession number: FJ870967) was isolated from pooled samples of spleen and lymph nodes of a PMWS-affected pig. The virus was amplified by passaging in PCV-free porcine kidney (PK-15) cells and confirmed as PCV2 by nucleotide sequence analysis and reactivity with PCV2 Cap proteinspecific monoclonal antibody  [66]. The titer of the PCV2 inoculum was 1. 0×10 7 TCID 50 /mL, as determined by titration in PCV-free PK-15 cells. All animals' tissue collection procedures were performed according to protocols approved by the Hubei Province PR China for Biological Studies Animal Care and Use Committee. Three 3-week-old Large White piglets were obtained from a herd in Hubei province, which tested negative for both PCV2 and porcine reproductive and respiratory syndrome virus (PRRSV), and were raised in controlled lab conditions.
RNA labeling, microarray hybridization, and data analysis RNA was converted to aminoallyl-RNA with the Amino Allyl II MessageAmp™ aRNA Amplification Kit (Ambion, USA) and labeled with either Cy3 or Cy5 (Reactuve Dye Pack; Amersham, Sweden). Each Cy3-(or Cy5-) coupled PAM sample was then hybridized to its corresponding Cy5-(or Cy3-) coupled reference sample anchored on a pig microarray slide containing 20,400 oligonucleotides (US Pig Genome Coordination Program; http://www. animalgenome. org/pig/resources/array_request. html). Hybridizations and analyses were carried out according to a previously published protocol from CapitalBio Corporation (Beijing, China)  [74]. Raw data was extracted from the TIFF images using LuxScan 3. 0 software (CapitalBio). A spot-exclusion method was adopted to filter out faint spots, with signal intensities in the lowest 50%, and exclude the corresponding genes from further analysis.
All the microarray results from this study were deposited in the NCBI Gene Expression Omnibus database under the following accession numbers: platform, GPL13968; Series, GSE30918; Samples, GSM766444, GSM766445, GSM766446, GSM766447, GS M766448, GSM766449. Functional interpretation of microarray data as well as pathway and network analysis Differentially expressed genes were selected for pathway exploration using the IPA web-based query system (Ingenuity Systems, www. ingenuity. com), this system can generate the functional analysis and networks that are most significant to the data set, IPA compares proteins in the input group and displays a rank-ordered list of pathways and networks, whose activities are most likely affected. Ficher's exact test was used to calculate a p-value determining the probability that each biofunction assigned to that data set is due to chance alone.
Genes from the dataset that met the fold change cut-off of 2. 0 were considered for the analysis. The score is the probability that a collection of proteins equal to or greater than the number in a network could be achieved by chance alone. A score of 3 indicates that there is a 1/1000 chance that the focus proteins are in a network due to random chance, therefore, score of 3 or higher have a 99. 9% confidence of not being generated by random chance alone.
Quantitative RT-PCR Equal amounts of RNA (1 μg) from PAMs was used to generate cDNA with oligo (dT) primers using the SuperScript II RNase H Reverse Transcriptase Kit (Invitrogen, USA). Quantitative RT-PCR reactions were set up in triplicate using reagents from the SYBR Green I PCR Kit (Toyobo) and 10 μM primers (designed by the Beacon Designer 7. 0 program, www. premierbiosoft. com; Table  2 ). The amplification reactions were performed on a LightCycler 480 (Roche) with the following conditions: 30 s at 95°C, 40 cycles of 95°C for 10 s, 60°C for 5 s and 72°C for 10 s. Subsequently, melting curve analysis and quantitative analysis of the data were performed using the Roche LightCycler 480 software version 1. 5. 0. Each sample was run in triplicate. Samples were normalized at each respective time point, using mock-infected PAMs as calibrators and the hypoxantine phosphoribosyltransferase (HPRT-1) and glyceraldehyde-3-phosphatedehydrogenase (GAPDH) as the reference genes.
Public Health Action Neonatal care and mortality in rural Burundi 277 from the centre are not admitted here, but are instead admitted to the district hospital or referred to neonatal units in the capital. Data on these children were not available. CURGO's delivery room and main operating theatre are equipped with a neonatal resuscitation area, where radiant warming and active resuscitation (bag and mask ventilation with or without oxygen, cardiac massage and resuscitation drugs) can be provided. Trained midwives perform immediate care at birth, including drying, warming, cutting the cord and performing resuscitation when necessary. They also assess Apgar scores and the neonate's postnatal condition. Neonates who are delivered without complications receive routine preventive care, including vaccinations, cord care and eye care, and mothers receive breastfeeding counselling.
Data and analysis A Microsoft Excel-based (Palisade Corp, Newfi eld, NY, USA) data monitoring system, implemented by the project in 2011,  12  served as the data source for the study. Data from maternal and child fi les were single-entered into the database by the hospital project data manager, who was also responsible for ensuring the validity of the data by notifying doctors, nurses and hospital supervisors on a weekly basis if data were incomplete or inconsistent. The main neonatal diagnoses, largely based on standard World Oral caffeine (to prevent apnoea of prematurity).
In this centre, symptomatic neonates born to HIV-infected women were classified as 'congenital infections', although these were in fact simply HIV-exposed babies. CURGO = Centre d'Urgences Gynéco-Obstétrique; HIV = human immunodeficiency virus. Health Organization clinical case defi nitions,  14  are provided in Table 2. Sophisticated investigations, such as blood cultures for the diagnosis of neonatal sepsis, or blood gas analysis for birth asphyxia, were not performed. The facility discharge status was defi ned as discharge (to home), in-facility death before 24 h of life, in-facility death after 24 h of life, absconded or referral. Maternal complications are defi ned elsewhere. 12 Data analyses reporting on frequencies and percentages were performed using SPSS 11. 0 (SPSS Inc, Chicago, IL, USA).
30 Clinicians may also have considered the presence of neurological signs to diagnose asphyxia, which would explain why not all neonates with an Apgar score of <7 were admitted to special services. There was no systematic documentation of the severity of hypoxic-ischaemic encephalopathy, an important study limitation, as Apgar scores alone are not very specifi c and are poor predictors of neurological injury and outcome. 30 ost deaths among neonates who were not admitted to special services presumably occurred in those born in such a poor condition that they did not survive long enough to be transferred. However, the location of their death was not recorded in the database and the proportion of missing values was very high for some key variables. Moreover, we cannot explain how eight neonates died after 24 h without having been admitted to special services.
Levamisole Pharmacokinetics A venous blood sample at 0, 4, 6, and 12 hours after levamisole administration was taken for pharmacokinetic assessment. Levamisole concentrations were determined using a highperformance liquid chromatography method adapted from Vandamme et al  [26]. Plasma levamisole pharmacokinetics were characterized with nonlinear mixed-effects modeling using NONMEM version 6 (Icon Development Solutions). A first-order conditional estimation method allowing an interaction term was used for modeling, and basic diagnostics were visualized using Xpose 4. 0  [27]. A one-compartment model with first-order absorption kinetics allowing a lag time has previously been described for levamisole in cancer patients  [28]. This structural model was maintained as only sparse data were available from this study.
Statistical Procedures Statistical analysis was performed using SPSS (version 15. 0) and Stata software (version 10). Data were log-transformed to obtain a normal distribution, where appropriate. Normally distributed data were compared using Student t test, and the Mann-Whitney U test was used for nonpaired nonparametric data. Categorical data were compared by Pearson χ 2 test and Fisher exact test, as appropriate. The Spearman rank test was used to assess correlations between nonnormally distributed data. Kaplan-Meier plots were constructed for time-dependent parameters. For comparison between treatment groups (Wilcoxon-Breslow test), the lactate clearance times in patients who died before clearance or recovery were set as maximum time (rather than censored), as persistent high plasma lactate concentrations are strongly associated with a fatal course of the disease  [30].
Acknowledgments. The authors thank the staff and patients at  Chittagong Medical College Hospital , without whom this study would not have been possible, in particular, the many doctors who helped to collect clinical data;  Md Safiqul Mostafa Choudhury ,  Sanjib Kanti Paul , and  Sumon Sarma  for their invaluable assistance; and  Kasia Stepniewska  and  Jennifer Flegg , who calculated the parasite clearance rates and clearance half-lives. Financial support. This work was supported by the  Wellcome Trust of Great Britain  (grant number  077166 ). Potential conflicts of interest. All authors: No potential conflicts. All authors have submitted the  ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.
All patients had previously undergone at least one upper gastrointestinal endoscopy and colonoscopy. The data were obtained from the patient medical records and were entered into a semi-standardised electronic database. If one DBE route did not yield a diagnosis, the opposite route was used for the second investigation. Complete DBE was confirmed by tattooing the small bowel. The lesions diagnosed by the physician in charge of interpreting CE were classified according to their size, location and imputability according to Saurin et al  [13]  , using the following criteria: P3 (presence of blood), P2 (high imputability), P1 (intermediate imputability) and P0 (low imputability). Capsule video endoscopy was performed with the PillCam™ SB (Given Imaging Ltd, Yoqneam, Israel). All patients were prepared with 2 L of polyethylenglycol (PEG) solution the night before examination.
Hydrological, biogeochemical and particle data Temperature and conductivity were measured from surface to a maximum of 1500 m depth using a Seabird 911 CTD mounted on a Sea-Bird Carousel sampler with 10 Niskin bottles. The following additional sensors were mounted for the measure of water optical properties used as biogeochemical proxies: fluorometer (Wetlab ECO-AFL/FL model), dissolved oxygen sensor (model SBE 43), nitrate sensor (ISUS with a maximum rating depth of 1000 m Satlantic SA) and a Wetlabs C-star transmissometer (660 nm with a 25 cm pathlength). The beam attenuation signal was converted to particulate attenuation coefficient c p by removing influence of deep (< 700 m) signal considered as the instrumental offset. The ISUS sensor was calibrated using nitrate measurements at 10 depths at each station by computing linear regressions between sensor and water measurements.
Velocity outputs of PSY3V3R1 were quality-controlled by MERCATOR Oceans by comparison with surface drifters  (Lellouche et al. , 2013)  and revealed a tendency to underestimate the magnitude of currents (∼ 20 %) while reproducing directions accurately. We thus quantified the sensitivity of results to the velocity underestimation by running additional simulation with velocity increased by 20 %. Daily averages of the velocity fields were linearly interpolated in time and space during particle tracking. The advection of particles was computed using a 4th order Runge-Kutta numerical scheme as implemented in the ICHTHYOP software  (Lett et al. , 2008). ICHTHYOP is a free java lagrangian tool designed at first to study the effects of physical and biological factors on ichthyoplankton dynamics. In addition to the multidimensional model velocity, particles are assumed to have a vertical settling velocity.
We thank Rainer Kiko, Emmanuel Boss and Sergey Piontkovski for fruitful discussion on the subject, Philippe Verley for helping us with the ICHTHYOP model and Dominique Lefevre for his discussion about oxygen data. This study is partly based on data sets gathered by the TARA oceans expeditions 2009-2012 and funded by the ANR/Investissements d'Avenir program by means of the Oceanomics project (grant No. ANR-11-BTBR-0008). We are keen to thank the commitment of the people and the following sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, ANR, agnès b. , the Veolia Environment Foundation, Region Bretagne, World Courier, Cap l'Orient, the Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois and the Tara schooner, crew. Moreover, this integrated sampling strategy could not have been done without the involvement of Ecole Normale Supérieure, Université Pierre et Marie Curie, Stazione Zoologica, University College Dublin, University of Milan-Bicocca, Institute de Ciences del Mar, University of Bremen, Institute de Microbiologie de la Mediterranée, MNHN, MIT, UofA, Bigelow Institute, Universite libre de Bruxelles, University of Hawaii.
Aims: Detrusor after-contractions (DAC) are non-common in adults. Both definition (nothing in ICS reports) and significance (artefact, link with detrusor overactivity (DO) or bladder outlet obstruction (BOO)) remain discussed. Our purpose was to carry out an analysis of the urodynamic parameters during voidings with DAC and, using the VBN model, to simulate pathophysiological conditions able to explain both voiding phase and DAC. Materials and Methods: From large urodynamic database of patients referred for evaluation of lower urinary tract dysfunction, DAC were observed in 60 patients (5. 7%). Criteria for DAC were post-void residual <30mL and increase of detrusor pressure >10cmH 2 O. VBN model was used for analysis of both pressure and flow curves, and simulations of pathophysiological conditions.
Introduction: C-reactive protein (CRP) levels are associated with cardiovascular disease and systemic inflammation. We assessed whether CRP-associated loci were associated with serum CRP and retinal markers of microvascular disease, in Asian populations. Methods: Genome-wide association analysis (GWAS) for serum CRP was performed in East-Asian Chinese (N = 2,434) and Malays (N = 2,542) and South-Asian Indians (N = 2,538) from Singapore. Leveraging on GWAS data, we assessed, in silico, association levels among the Singaporean datasets for 22 recently identified CRP-associated loci. At loci where directional inconsistencies were observed, quantification of inter-ethnic linkage disequilibrium (LD) difference was determined. Next, we assessed association for a variant at CRP and retinal vessel traits [central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE)] in a total of 24,132 subjects of East-Asian, South-Asian and European ancestry.
Results: Serum CRP was associated with SNPs in/near APOE, CRP, HNF1A and LEPR (p-values #4. 7610 28 ) after meta-analysis of Singaporean populations. Using a candidate-SNP approach, we further replicated SNPs at 4 additional loci that had been recently identified to be associated with serum CRP (IL6R, GCKR, IL6 and IL1F10) (p-values #0. 009), in the Singaporean datasets. SNPs from these 8 loci explained 4. 05% of variance in serum CRP. Two SNPs (rs2847281 and rs6901250) were detected to be significant (p-value #0. 036) but with opposite effect directions in the Singaporean populations as compared to original European studies. At these loci we did not detect significant inter-population LD differences. We further did not observe a significant association between CRP variant and CRVE or CRAE levels after meta-analysis of all Singaporean and European datasets (p-value.
In contrast, with respect to microvascular pathology, a recent study identified a CRP gene variant that was associated with CKD  [16]. Nevertheless, data on the link between serum CRP and evidence of microvascular variations is lacking. In this study, we aimed to identify common genetic variants associated with serum CRP levels among Asian populations (East-Asian Chinese and Malays and South-Asian Indian populations) from Singapore, using a genome-wide association study (GWAS) approach. Leveraging on genome-wide data, we next sought to assess, in silico, the relevance of recently identified variants, several of which have been only detected using European populations  [7] , to these Asian subjects. Finally, to clarify the role of serum CRP in the pathogenesis of vascular disease, we determined whether a genetic variant at the CRP gene locus was associated with changes in retinal vessel traits, which have been found to be associated with serum CRP levels, subclinical vascular pathology and clinical cardiovascular outcomes  [17] [18] [19] [20] [21] [22] [23].
Study Samples To assess for association with serum CRP level, data from 3 adult population-based datasets were utilized. Singapore Prospective Study 2 (SP2) is a cross-sectional study of adult Chinese (N = 5,499), Malay (N = 1,405) and Asian-Indian (N = 1,138) samples. Detailed methodology for SP2 has been previously reported  [24]  and GWAS data was only available for adult Chinese samples (N = 3,066) in SP2. Singapore Malay Eye Study (SiMES) is a cross-sectional study of adult Malays (N = 3,280)  [25]. GWAS data was available for 3,072 Malay samples from SiMES. Singapore Indian Eye Study (SINDI) is a cross-sectional study of adult Asian-Indians (N = 3,400) living in Singapore  [26]  and GWAS data was available for 2,953 subjects. For the association between the most strongly associated CRP variant and retinal vessel traits, we used data available in all 3 Singaporean datasets.
Details of quality-control measures for SNPs are provided in Table  S2  in File S1. Briefly, sex-linked and mitochondrial SNPs were removed, together with gross HWE outliers (p-value ,1610 24 ). SNPs that were monomorphic or with a MAF less than 5% and SNPs with low call-rates (,95%) were also excluded. In SP2 where more than one chip was used for genotyping, the Mantel-extension test was carried out and 62 SNPs with extreme discrepancies in allele frequencies from samples genotyped on different arrays were removed from analyses. We imputed for additional genotypes in all datasets with IMPUTE v0. 5. 0. [32] using a posterior probability of at least 0. 90 and a call-rate of at least 95% for all imputed SNPs. Genotype calls were based on HapMap East-Asian samples (CHB and JPT)  [30]  for SP2 Chinese and to better capture local patterns of haplotype variation, all four HapMap reference panels (CEU, YRI and JPT+CHB)  [34]  for the Malay and Asian-Indian samples.
Main Outcome Variables Serum C-reactive protein levels. Clinical measures from the Singaporean datasets used in this study are presented in Table  1. Venous blood was drawn following a 10-hour overnight fast was drawn from SP2 samples and in the non-fasted state from SiMES and SINDI. Serum CRP was measured in all sample collections from frozen plasma stored at 280uC, using a particleenhanced immunoturbidimetric method implemented on a Roche/Integra 400 Analyser (Roche Diagnostics, Rotkreuz, Switzerland). Samples with CRP measures. 10 mg/L (184 samples from SiMES, 44 samples from SP2 and 242 from SINDI) that may indicate acute clinical inflammation were excluded from subsequent analysis, as recommended by the Centers for Disease Control and Prevention and the American Heart Association  [33] [34].
Raw CRP values were normalised by log transformation and used as the dependent variable in GWAS analyses. Retinal markers of microcirculation. Central retinal vein equivalent (CRVE) and central retinal artery equivalent (CRAE) measures were similarly determined in all datasets. Digital fundus photographs were taken using a retinal camera (Canon CRDGi with a 10D SLR back; Canon, Tokyo, Japan) after pupil dilation. Two retinal images were taken, according to the Early Treatment for Diabetic Retinopathy Study (ETDRS) standard field 1 and ETDRS standard field 2, centered on the optic disc and fovea, respectively  [34]. Retinal vascular caliber was measured with computer-assisted software according to standardized protocols  [27, [35] [36] [37]. Figure  S1  in File S1 highlights retinal arteriolar and venular calibers, summarized as CRAE and CRVE equivalent, respectively from retinal fundus photograph that were used in the study.