dataesr/scientific-paragraphs-categorization huggingface dataset:
For thermal analysis (TG/DTG) a Perkin Elmer STA 6000 thermal analyzer with a Pyris data acquisition interface was used to determine solid phase quantities in cementitious mixtures. To arrest hydration, solvent exchange was as described by Zhang and Scherer  [13]. Quantitative X-ray diffraction analyses were carried out on powdered cementitious mixtures at desired ages using a Bruker D8 Advance diffractometer using Cu-Kα (λ = 1. 54 Å) radiation. Care was taken to minimize preferred orientation errors by texturing the sample surface, and using a rotating sample stage. Xray structure information for the relevant anhydrous and hydrated crystalline phases was sourced from standard databases or from the literature  [14, 15]. Rietveld analysis was carried out using the X'Pert HighScorePlus©  [16].
In addition, these genome sequences may give new insight into the pathogen-host interaction. For instance, a comparison of the predicted repertoires of type III effectors with the effector repertoire of the tomato isolate X. vesicatoria ATCC 35937 revealed that both pepper isolates appear to lack xopD, xopE2, and xopJ2. Contrariwise, the pepper isolates possess homologs of avrBs1 and xopH, which were not found in strain ATCC 35937. Both genes are in tandem arrangement and might be located on a plasmid, as in Xanthomonas euvesicatoria strain 85-10 (16). More sequencing and pathotyping are required to assess the importance of these effectors with respect to the host plants. Nucleotide sequence accession numbers. These wholegenome shotgun projects have been deposited at DDBJ/EMBL/ GenBank under the accession numbers JSXZ00000000 (strain 15b) and JSYJ00000000 (strain 53M).
If these defects are the origin of material's fracture then tensile failure is determined by the largest critical defect. 25, 26 n Fig. 8 , the results of the Weibull analysis on the strength of the ceramic SiCN bers are presented. Although it is known that the variation in diameter inuences the volume variation when the tensile strength is measured using the same gauge length (in this work being 25 mm) the single mode Weibull analysis was used and it was assumed that there is no volume variation as the ber diameter changes. The Weibull parameters, modulus m and scale parameter s 0 are presented in Table  2. The Weibull parameters are similar for the two types of bers. In spite of the diameter variation from 30 to 100 mm, the single mode Weibull distribution ts the strength data reasonably well.
Acknowledgments The authors thank  Ute Kuhn  from the  Polymer Engineering Institute and Andre Prette, University of Bayreuth , for the TGA and DSC measurements, and  Fraunhofer Institute HTL, Bayreuth , for mechanical tests of the bers. We also thank  Deutsche Forschungsgemeinscha  ( DFG ) for supporting this work within the project SiMet. RKB acknowledges the Humboldt Research Award which was responsible for initiating this collaboration.
High throughput sequencing (HTS) has the potential to circumvent these limitations by providing a diagnostic tool for genetic diagnosis and by enabling gene discovery to increase the repertoire of disorders for which genetic diagnosis is possible. Analysis of large case collections recruited through consortia of investigators and technologies such as HTS assist discovery of rare BPD genes  [9, 10]. However, gene discovery additionally requires analysis of shared data through systematic phenotype coding to identify similarities between unrelated cases. Phenotype coding also facilitates creation of clinical registries, genotype-phenotype databases and biobanks. Examples of coding systems include the World Health Organization International Classification of Diseases (ICD)  [11] , which provides a post-diagnosis classification of disease organized by organ system that is unsuitable for coding rare genetic diseases particularly those that affect multiple organs.
The BRIDGE-BPD study is approved by a UK Research Ethics Committee (Cambridgeshire 1 Research Ethics Committee 10/H0304/66) and appropriate national ethics authorities for non-UK enrolment centres (Additional file 1). All study procedures were performed after the participants provided informed written consent and were in accordance with the Declaration of Helsinki. Sequence data for cases who provided consent for public access have been deposited at the European Genome-Phenome Archive (EGAS00001001172).
BRIDGE-BPD database Pseudonymised demographic and clinical data were transferred to electronic data capture pages usually as quantitative or categorical variables but with a minority as free text to maintain detail. Bleeding symptoms were recorded as numerical severity scores for the 12 major symptoms within the MCMDM-1 VWD Bleeding Assessment Tool  [21] , or as the terms 'yes' or 'no' for each symptom (Additional file 2). Laboratory test results were recorded as quantitative variables, except for tests such as platelet light transmission aggregation (LTA) and ATP secretion, which were recorded as 'normal' or 'abnormal' according to the interpretation of the enrolling clinician. Platelet morphology determined by light or electron microscopy was recorded as free text.
Development of HPO terminology for BPD In order to ensure accurate annotation of the bleeding and platelet phenotype, 80 terms and associated is-a relationships were added to HPO  [17] , in parallel with development of hpoPlot, a new free software tool that summarises HPO codes of a set of cases, released on the Comprehensive R Archive Network  [22]. The HPO modifications were predominantly within the abnormality of blood and bloodforming tissue leading class and its constituent classes 'abnormality of thrombocytes', 'abnormal bleeding', 'abnormality of coagulation' and 'abnormal thrombosis'. Some terms required creation of a new 'abnormal platelet morphology' class (Additional file 3). Many terms within 'abnormality of blood and blood-forming tissue' overlap with other system-specific HPO leading classes, particularly 'abnormality of the immune system' (Additional file 4).
Clustering of cases using HPO We performed unsupervised clustering of the HPO-encoded phenotype data in order to obtain an undirected characterisation of different subgroups within the heterogeneous BPD collection and assess whether particular sets of HPO terms tended to co-occur among cases in these groups. The 648 unrelated index cases were partitioned into 30 clusters ranging in size from five to 36 cases. Clinically recognisable subgroups included 'Impaired epinephrineinduced platelet aggregation, Impaired ADP-induced platelet aggregation' (Additional file 10, cluster 18 and Figure  5 ) which is a frequently reported pattern of abnormality in  light transmission aggregation results identified previously as a Gi-pathway defect  [33]. A further prominent cluster was ' Autism spectrum disorder, Thrombocytosis, Decreased mean platelet volume' (Additional file 10, cluster 29 and Figure  5 ) illustrating an increasingly recognised association between platelet abnormalities and neurological disorders  [34].
Pertinent and non-pertinent rare variants in MYH9 We also assessed the HTS and data analysis pipelines with the autosomal dominant disorder MYH9-RD. We selected this disorder because previous descriptions of MYH9-RD suggested that cases are usually readily identified clinically and were unlikely to have been recruited. Despite this, we identified nine different MYH9 missense variants in 13 unrelated BPD cases and one pedigree case. These included seven index cases with rare variants classified as PV or LPV and six index cases with VUS. In order to investigate whether HPO annotation and cluster analysis would have enabled detection of these cases as a distinct phenotype group we explored the HPO terms that had been assigned to these cases. The seven index cases with PV or LPV in MYH9 included six cases with terms indicating macrothrombocytes, six with terms indicating thrombocytopenia and one with neutrophil Döhlebodies but none with other recognised features such as renal impairment, sensorineural deafness or cataract (Table  3 ).
Variant identification in the ThromboGenomics gene list The BRIDGE-BPD HTS and data analysis pipelines were tested by evaluating coding variants in the ThromboGenomics list of known genes linked to autosomal recessive or X-linked recessive BPD. Since cases with BPD of known genetic aetiology were excluded from enrolment, we predicted that causal variants in the ThromboGenomics genes would be uncommon. Consistent with this, we identified PV in only two ThromboGenomics genes that completely explained the phenotype of one case with HPS3 and two cases with WAS. Further cases with PV in F9 and in F8 displayed reduced FIX and FVIII activity, respectively, that were explained by the observed PV. However, these cases also displayed abnormal platelet function indicating that the PV only partially explained the phenotype.
Discussion Heritable BPD are individually rare but collectively common diseases that have heterogeneous clinical characteristics. This clinical complexity, genetic heterogeneity and the large number of candidate genes for BPD has previously hampered gene discovery. In this exploratory Stage 1 of the BRIDGE-BPD study, we first enhanced HPO terminology to enable standardized annotation of the phenotypes of BPD cases. After enrolling the largest collection of BPD cases reported to date, we demonstrated that HPO annotation enabled the characterisation of clusters of BPD cases with similar phenotypes, which we hypothesise have causal genetic variants in the same or related genes. The use of HPO to facilitate research within neurogenetics by comparing standard database descriptions of diseases has been described previously  [18].
Furthermore, patient HPO data can be linked to data in online human databases such as OMIM, and to model system databases such as the Mouse Phenotype Ontology. In future, this could be used to prioritise genes based on the similarity of groups of cases to ontological phenotype terms derived from the literature. We assessed index cases harbouring variants in MHY9 who were not considered likely to have MYH9-RD by the enrolling clinicians based on clinical evaluation. In this group, the cases with PV or LPV in MYH9 displayed a high degree of similarity whereas individuals with VUS in MYH9 were not similar. Furthermore, the index cases with PV or LPV in MYH9 were phenotypically different from the index cases with VUS. This illustrates that HPO-based clustering can reveal phenotype and genotype links that cannot be made by enrolling clinicians in isolation but only in combination with powerful methods for distinguishing variants by predicted pathogenicity.
Acknowledgements The following colleagues of the  Centre de Référence des Pathologies Plaquettaires collaboration network  are acknowledged for case enrolment:  Claude Négrier ,  Unité d'Hémostase Clinique, Hôpital Edouard Herriot, Université Lyon 1, Lyon, France; Jean-François Schved, Hopital Saint-Eloi, Département d'Hématologie Biologique, CHU, Montpelier, France ;  Ségolène Claeyssens-Donadel ,  Centre Régional d'Hémophilie, Centre Hospitalo Universitaire, Toulouse, France, Veronique Latger-Cannard, Service d'Hématologie Biologique, Hôpitaux du Brabois, CHU Nancy, Vandoeuvre les Nancy. We thank the SPEED and PID members of the  BRIDGE Consortium  for granting access to 160 and 19 exomes, respectively, for use as controls in this study. The authors wish to acknowledge the following funding bodies: This study makes use of data generated by the  NIHR BioResource -Rare Disease BRIDGE Consortium.
Work in the Laffan laboratory  is supported by the  NIHR Imperial College Biomedical Research Centre. Work in the Mumford laboratory is supported by the  NIHR Bristol Cardiovascular Biomedical Research Unit. CL and SKW are supported by  Medical Research Council  ( MRC) Clinical Training Fellowships  (number  MR/K023489/1 ) and TKB by a  British Society of Haematology/NHS Blood  and Transplant grant. KF and CvG are supported by  FWO-Vlaanderen  through grants  G. 0B17. 13 N, G. 0A23. 14 N  and  OT/14/098  from  BOF KULeuven. SR acknowledges support from the  MRC  and the  Cambridge Biomedical Research Centre. The French cases were collected with support from  Gis-Maladies Rares ,  DIATROC program ,  INSERM  ( ANR-08-GENO-028-03 ). The development of the HPO system by PNR is funded by the  Bundesministerium für Bildung und Forschung ,  Germany  ( BMBF  project number  0313911 ), and by the  European Commission 's  FP7 programme  (Grant Agreement 602300; SYBIL).
4[28];(3)variant not present in other affected pedigree members recruited to BRIDGE-BPD; (4) <3 reads supporting the alternate allele; (5) allele count >1 among 20 in-house whole-genome sequenced controls; (6) overall allele count >20 including exomes from other BRIDGE projects. Assigning causality to rare variants in known BPD genes (PV): a variant present in the Human Genome Mutation Database (HGMD)[32]with a matched phenotype to the BRIDGE-BPD case; (2) Likely pathogenic variant (LPV): a non-HGMD variant in a gene for which previously reported cases have a matched phenotype with the BRIDGE-BPD case; (3) Variant of unknown significance (VUS): all variants that do.
RNA-seq and analysis For 16. 5 dpc, testes were pooled from at least seven mice per genotype. For 10 dpp and 20 dpp, testes were pooled from three mice per genotype. For RNA-seq, RNA libraries were cloned using Illumina TruSeq stranded mRNA LT kit on total RNA isolated by the TRIzol method (Invitrogen) and DNase-treated (Qiagen). RNA-seq was performed in 100-base-pair (bp) singleend or paired-end reads run using Illumina HiSeq 2500. For bioinformatic analyses, RNA-seq libraries were first depleted in silico of reads mapping to rRNA sequences (GenBank identifiers 18S, NR_003278. 3; 28S, NR_003279. 1; 5S, D14832. 1; and 5. 8S, K01367. 1) with Bowtie version 1. 0. 0  (Langmead and Salzberg 2012) , allowing up to three mismatches. The rRNA-depleted libraries were then mapped onto the mouse reference genome (mm9) using the Bowtie software with zero mismatch and a maximum of 10,000 alignments allowed per read; ∼14 million mapped reads were obtained for the 16.
Acknowledgments We are grateful to  Julian Iranzo ,  Julian Lange , and  Corinne Grey  for experimental help;  Max Greenberg  and  Anahi Molla-Herman  for critical reading of the manuscript;  James Turner ,  Norbert Ghyselinck , and  Florian Guillou  for meiotic mutant samples;  Dubravka Pezic  and  Sergei Manakov  for RNA-seq analysis;  Scott Keeney  for the anti-SPO11 antibody;  Sandy Martin  for anti-LINE1 ORF1 antibody;  Alain Nicolas  for the Spo11 mice;  Alexei Aravin  for the Miwi2 mice; the Platform for Cell and  Tissue Imaging  within the  Unit of Genetics and Developmental Biology, Institut Curie ; and the  Flow Cytometry and Animal House Facility of the Institut Curie. High-throughput sequencing was performed by  Jacobs Genetics and Genomics Laboratory at California Institute of Technology  and the  Institut Curie Next-Generation Sequencing platform  (supported by the  ANR-10-EQPX-03  and  ANR10-INBS-09-08  grants and the  Canceropôle Ile-de-France).
D. B. 's laboratory is part of the  Laboratoire d'Excellence (LABEX)  entitled  DEEP  ( 11-LBX-0044 ). This research was supported by grants from the  Fondation Schlumberger pour l'Education et la Recherche ,  Agence Nationale pour la Recherche ("TranspoFertil"  and " ABS4NGS"-ANR-11-BINF-0001 ),  Fondation pour la Recherche Médicale  (post-doctoral fellowship to N. Z. ), and  Allocation Master Ecole Polytechnique (Ph. D. fellowship to M. W. ).
The main subdetectors used in this analysis are the silicon tracker and the muon system, which enable the measurement of muon momenta over the pseudorapidity range |η| < 2. 4. A more detailed description of the CMS detector, together with a definition of the coordinate system used and the relevant kinematic variables, can be found in Ref. [20]. The events were collected using a two-level trigger system. The first level, made of custom hardware processors, uses data from the muon system to select events with two muon candidates. The high-level trigger, adding information from the silicon tracker, reduces the rate of stored events by requiring an opposite-sign muon pair of invariant mass 2. 8 < M < 3. 35 GeV, p T > 9. 9 GeV, and |y| < 1. 25 for the J/ψ trigger, and 3. 35 < M < 4. 05 GeV and p T > 6.
No specific eligibility criteria were used for household selection because all village households had poultry. The 128 randomly selected village households were investigated six times between November 2009 and February 2011, approximately every three months at points in time that marked the end of each of the four seasons in Mali (tilema or post-rainy season, nene waati or dry cold season, funteni waati or dry hot season, samiya or rainy season). When it was not possible to repeat the survey in a previously surveyed household (absence of the household chief), the next-door household was chosen. A questionnaire was designed aimed at the collection of data on characteristics of traditional poultry management. A large number of the variables dealt with the demographics of the flocks including for each species, the number of birds present in each of three age categories (less than one month-old, from one to less than six month-old, six month-old and older); the number of birds introduced to the flock in the last three months by hatching of eggs, purchase or gift; the number of birds eaten, sold, offered, stolen or lost, and dead.
Data analysis Data were stored in an Excel spreadsheet file (Microsoft, Redmond, WA), maps were produced using ArcMap 9. 3 (ESRI, Redlands, California, USA) and descriptive statistical analyses were conducted using the statistical software R (R Core Team, 2010). To assess whether quantitative and categorical variables describing traditional flock characteristics significantly changed depending on the season, statistical tests for repeated data were used (Friedman test to compare ranks for quantitative variables or Cochran's Q test to compare proportions for categorical variables) using only data from households which were investigated during each of the four seasons in 2010. Post-hoc tests for the Friedman and the Cochran's Q test consisted of pairwise comparisons using the Nemenyi post-hoc test (package "PMCMR" of R) and the Wilcoxon sign test (package "RVAideMemoire" of R), respectively.
Survey of commercial poultry farms A total of 282 farms were identified in the study area and data was collected from all of them. Their spatial distribution is shown in Fig. 1. Among the 282 farms, 6 (2. 1%) were located in the district of Bamako, 171 (60. 6%) in the region of  Koulikoro (with 164 (58. 2%)  in the circle -Malian equivalent of a county -of Kati which is the circle surrounding the district of Bamako), 40 (14. 2%) in the region of Sikasso, 33 (11. 7%) in the region of Kayes, 21 (7. 4%) in the region of Segou and 11 (3. 9%) in the region of Mopti. More specifically, 172 (61. 0%) of the farms were located within a 50 km radius from the center of Bamako and 63 (22. 3%) were located within a 50 km radius from the centers of the capitals (Kayes, Koulikoro, Sikasso, Segou and Mopti) of the regions of our study area.
Acknowledgements We thank  Abbas Diarra ,  Souleymane Magassa  and  Issa Traoré  for participating to the field surveys. We thank all the poultry farmers who accepted to take part to the study. This study was part of the  GRIPAVI  project funded by the  French Ministry of Foreign Affairs. The  French Ministry of Foreign Affairs  had no involvement in the study design, in data collection, analysis and interpretation, in the writing of the manuscript and in the decision to submit the article for publication. The authors declare they have no conflict of interest.
Microbiological data CSF characteristics were analyzed. Bacterial identification could also be derived from other samples, such as blood cultures or skin cultures. Antimicrobial susceptibility was tested according to French national guidelines  [20]  and in accordance with the European Committee on Antimicrobial Susceptibility Testing. Thus, minimal inhibitory concentrations (MICs) for Streptococcus pneumoniae were as follows: 1. Penicillin: susceptible, MIC ≤0. 06 mg/ml; intermediate, MIC 0. 1-1 mg/ml; and resistant, MIC >1 mg/ml 2. Amoxicillin: susceptible, MIC ≤0. 5 mg/ml; intermediate, MIC 1-2 mg/ml; and resistant, MIC >2 mg/ml 3. Third-generation cephalosporins (cefotaxime or ceftriaxone): susceptible, MIC ≤0. 5 mg/ml; intermediate, MIC 1-2 mg/ml; and resistant, MIC >2 mg/ml.
Microbiological data Lumbar puncture was contraindicated in four patients owing to coagulation disorders. For 30 of 153 patients, CSF culture was sterile. Seven of those had a positive microscopic result. Microbiological data were also available from blood (n=25) or skin cultures (n=2) or from molecular techniques (PCR on CSF; n=21). Overall, microbiological documentation was available for 136 patients (87 %). The main causative bacteria were S. pneumoniae (56 %) and Neisseria meningitidis (32 %). The results are shown in Additional file 1: Figure S1. Among S. pneumoniae strains, susceptibility to β-lactams was as follows:  (1).
Mortality-associated factors Factors associated with ICU mortality were analyzed for the whole population. The results of the univariate analysis are summarized in Table  3. On the basis of the results of univariate analyzes, we aimed to build different logistic regression models in order to more accurately assess whether treatment with rifampin was associated with outcome. Demographic parameters, data on severity at admission, and treatment data such as antibiotics and corticosteroids were entered into the model. Possible interactions between variables were also tested. The variables were alternately added or removed from the model to test how they acted on this model. Those variables were selected that allowed the highest likelihood ratio. For the final logistic analysis, 11 variables were kept in the model: pulmonary, renal, cardiovascular, and hematologic failure; pneumococcal infection; early antibiotic administration (<2 h) and early treatment with rifampin (<24 h); corticosteroid administration; age (>75 years) and sex; and immunosuppression.
Discussion In this report, we describe a cohort of 157 patients. Meningeal infections are rare conditions. So, in the present study, for five ICUs and during the study period, these infections represented only 1. 2 % of admissions (among more than 20,000 admitted patients). Patients' baseline characteristics are coherent in terms of severity. Some might be surprised by the high Glasgow Coma Scale scores (median 11) or low SAPS II, but these data are consistent with those reported in other series  [2, 4]. We must emphasize that, at admission, 80 % of the patients met criteria for severe sepsis or septic shock and that for nearly half of them mechanical ventilation was required. A previous study included patients with more severe illness. They had exclusively pneumococcal meningitis  [1]. From a microbiological point of view, our results are not surprising.
Acknowledgments The authors thank  A. Pearson  for assisting with preparation of the manuscript. This work was supported by the  Association pour le Développement de la Réanimation (ADR)  and  Nantes University Hospital  ( PROG/10/14 ). This study was presented in part at the 52nd Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) 2012, 9-12 September 2012, San Francisco, CA, USA [49].