dataesr/scientific-paragraphs-categorization huggingface dataset:
The imputation method was fully conditional specification with a linear regression for the model for scale variables. Eventually producing output for each 'complete' dataset, plus pooled output. We used these pooled results, which are pooled by Rubin's rules, by taking the average over the parameter estimates from all imputed datasets. All patient, medical history and treatment variables (including outcome variables) were used when creating the multiple imputation data sets. All probability values were two sided and considered significant if <0. 05. Statistical analyses were conducted using SPSS V. 24. 0. 0. 0.
ConClusIons Our study suggests that there is no difference between patients with HFpEF and HFrEF in relative risk prediction of 6-month mortality by absolute discharge NT-proBNP levels or by percentage NT-proBNP changes. To explain the similar long-term mortality in HFpEF as in HFrEF, despite lower NT-proBNP discharge levels in HFpEF, we raise the possibility that the larger burden of prognostic relevant comorbidities in patients with HFpEF with low NT-proBNP levels unfavourably affects their prognosis. Correction notice this article has been corrected since it first published online. the open access licence type has been amended. Contributors Ks, WeK and YMP had the idea for the project, designed the collaborative analysis and undertook searches of published work. Ks and ss collected the individual patient data and prepared for analysis.
8 eV, EB Ag 3d 5/2 = 368. 3 eV. The instrumental resolution, as evaluated by the full-width at half maximum (FWHM) of the Ag 3d 5/2 peak, was 1. 0 eV. The samples were glued to a molybdenum sample holder. The analysis chamber during experiments was evacuated to a vacuum level better than 1 × 10 -9 mbar. Data processing involved background subtraction by means of an "S-type" integral profile and a curve-fitting procedure (a mixed Gaussian-Lorentzian function was employed) based on a least-squares method (software CasaXPS). The experimental errors were estimated to be ±0. 1 eV for the photoelectron peaks of carbon and oxygen. Charging effects were corrected by using the C 1s component ascribed after deconvolution to the aliphatic carbon bindings (component C-C), and set to 285. 0 eV. The reproducibility of the peak position thus obtained was ±0.
Taking into account that evaporation/sublimation of macromolecules is thermodynamically limited, and that the molecular weight cannot exceed some specific value (for PTFE calculated to about 1000 Da according to  [3] ), we assume that the abovementioned structural changes i. e. , VAc transformation to ketone and chain unsaturation take place most likely on the target surface at the beginning of the ablation process, probably in parallel with the main C-C chain scission (as the presence of C=C groups in the EVA copolymer indirectly indicates it  [23] ). Additional chemical composition study of the surfaces of neat EVA, EVA_E and EVA_L films was performed using X-ray Photoelectron Spectroscopy. Only carbon and oxygen atoms were identified on the surface of all samples. The elemental composition of the surface calculated using the XPS data is given in Table  1.
008) and abnormal variations of endothelial nucleus density in response to exercise training in these patients when compared to SHS (p = 0. 042). COPD patients had significantly fewer occurrences of pericyte/endothelium interdigitations, a morphologic marker of capillary maturation, than SHS (p = 0. 014), and significantly higher levels of F 2 -IsoP (p = 0. 048). Last, the changes in pericyte/endothelium interdigitations and F 2 -IsoP levels in response to exercise training were negatively correlated (r = -0. 62, p = 0. 025). This study is the first to show abnormal capillary remodelling and to reveal impairments during the whole process of angiogenesis (capillary creation and maturation) in COPD patients. Trial registration: NCT01183039 & NCT01183052, both registered 7 August 2010 (retrospectively registered).
Study design This study was conducted on skeletal muscle samples from subgroups of both COPD patients and SHS recruited in two previous studies (registration numbers for clinicaltrial. gov: NCT01183039 and NCT01183052). The subjects were recruited at PhyMedExp (INSERM-CNRS-UM), Montpellier University Hospital, Montpellier, France, or the "La Solane" and "La Vallonie" Pulmonary Rehabilitation Centres in Osseja and Lodève, France. These studies were the subject of a previous publication  [Gouzi et al. , 2013] [6]. The present study used TEM to more closely investigate the underlying mechanisms of the blunted angiogenesis in response to exercise training found in the main study. The inclusion criteria are available in the previous study  [6]  and in clinicaltrials. gov/. Briefly, COPD patients were defined by dyspnoea, chronic cough or sputum production and/or a history of exposure to risk factors for the disease, and postbronchodilator forced expiratory volume in 1 s/forced ventilator capacity ratio < 70%  [23].
Statistical analysis Baseline characteristics of the COPD and SHS groups were compared with t-tests or the Mann-Whitney U depending on the normality and homoscedasticity of the data. Normality was assessed with the Kolmogorov-Smirnov (K-S) test and homoscedasticity with the Brown and Forsythe test  [34]. The data are presented as MEAN (SD) or MEDIAN (Q 1 -Q 3 ) according to the K-S test result. Correlations are described using the Pearson coefficient. As the two groups (SHS and COPD) were evaluated twice (before and after exercise training), we analysed the data with a linear mixed-effect model, taking into account the repeated measures and using the subject effect as a random effect. For this model, the fixed effects were the Time and Group effects and the interaction between these factors (Group x Time).
For variables for which a single parametric value was obtained for each capillary, we performed a multilevel linear mixed-effect model, clustering each capillary value according to its subject of origin to avoid the inflation of Type I error  [35]. Linear mixed models were fit using the lme function from the nlme R package  [36]. To further detail our results, we completed the analysis with Fisher's LSD post-hoc test when the Group x Time interaction term was significant. The normality of the residual distribution was assessed by a Q-Q plot after each lme test  [37]. Data were analysed with Statistica 7. 1 (StatSoft, Inc. ) and R 3. 5. 0 software (www. r-project. org). Data were plotted using GraphPad Prism 5 (GraphPad Software). A p-value< 0. 05 was considered significant.
01; Additional file 1: Figure. S1 ). Angiogenesis-related capillary remodelling in response to exercise training. Capillaries from the vastus lateralis muscle biopsies, obtained before and after exercise training in the 9 COPD patients and 7 SHS, were analysed by TEM. The analyses were performed on 392 capillary profiles, which were always composed of at least Lum, EC and BM. Neither total capillary area nor the number of analysed capillaries differed between groups or training times (p > 0. 05; data not shown). As shown in Table  3 , the baseline values of lumen (Lum), endothelium (EC), basement membrane (BM) and pericyte (Pc) relative volume (RV) and thickness (T) did not differ between COPD patients and SHS. Standard transmission electron micrographs of the skeletal muscle capillaries in COPD patients and SHS, before and after exercise training, are shown on Fig.
Materials and methods Consecutive patients with HNSCC referred in our department for a pre-therapeutic FDG PET/CT from January to March 2016 were retrospectively included. Two nuclear medicine physicians separately segmented all tumors using 3 different segmentation methods: a relative standardized uptake value (SUV) threshold (40%SUVmax), a signal-to-noise adaptive SUV threshold (DAISNE) and an image gradient-based method (PET-EDGE). SUV and metabolic tumor volume were recorded. Thirty-one textural indices were calculated using LIFEx software (www. lifexsoft. org). After correlation analysis, selected indices' inter-segmentation method and inter-observer variability were calculated.
In each VOI, standard PET quantitative parameters were measured (SUVmax, MTV) and thirty-one textural indices were calculated using LIFEx software (www. lifexsoft. org) [16]  (Table  1 ). Theses indices were extracted from 4 different matrices which were computed for each VOI: the Gray-Level Cooccurence Matrix (GLCM), the Gray-Level Run Length Matrix, the Neighborhood Gray-Level Dependence Matrix (NGLDM) and the Gray-Level Zone Length Matrix (GLZLM). GLCM characterizes how often pairs of voxels with specific SUV values can be found at a specific distance in a specific direction and was computed using a distance of 1 voxel and 13 directions  [27]. GLRLM gives the size of homogeneous runs for each gray-level and was computed using 13 directions  [28]. NGLDM corresponds to the difference of gray-level between one voxel and its 26 neighbours in 3 directions  [29].
The baseline pore pressure was fixed by a Back Pressure Regulator (BPR) (model SLA5820B) at 10 bar. The gas mass flow meter and the BPR were connected to a Brooks Microprocessor Control & Read Out Unit model 0152, which allows to change set points. To follow pressure measurements, four Keller pressure transducers were used; three absolute transducers Fig. 1. A schematic of foam flow at the pore scale (from reference  [5] ). Flowing bubbles are unshaded, and trapped gas is darkly shaded. The grains are represented by circles. (model PA-33X) and a differential one (model PD-39X). We used home developed software based on Labview to read and record pressures in real time. Pure water is used as a confining liquid, while the confining pressure (between 20 bar and 30 bar) is maintained by pressurized nitrogen reservoir.
The continuous improvement of long-read sequencing technologies along with the development of ad-doc algorithms has launched a new de novo assembly era that promises high-quality genomes. However, it has proven difficult to use only long reads to generate accurate genome assemblies of large, repeat-rich human genomes. To date, most of the human genomes assembled from long error-prone reads add accurate short reads to further polish the consensus quality. Here, we report the development of a novel algorithm for hybrid assembly, WENGAN, and the de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms that exploit the sequence information of short and long reads to tackle assembly contiguity as well as consensus quality.
WENGAN optimizes the 1-2-3 de novo assembly goals To validate WENGAN, we used public Oxford Nanopore reads  [24]  (rel5) and Illumina shortreads (Table  S1 ) of the NA12878 human cell line. In particular, rel5 has a total of 11. 6 million reads (40X) with an N50 of 13. 6kb (that is, 50% of the total sequence data is in reads longer than 13. 6 kb), and 3. 3X of the genome is covered by reads longer than 100kb (Table  S2 ). WENGAN was benchmarked in its three assembly modes, namely WENGANM (MINIA3  [5] ), WENGANA (ABYSS2  [6] ) and WENGAND (DISCOVARDENOVO  [7] ). WENGAN modes reflect the short-read assembler used (Figure  1A1 , Methods section) and are intended to adapt WENGAN to different computational resources. We compared WENGAN to four state-of-the-art assemblers, MASURCA (hybrid short-read-first)  [26] , CANU (long-read only)  [4] , WTDBG2 (long-read only)  [14] , and FLYE (longread only)  [16].
For very long mate-edges (l(e) ≥ 100kb), we stop searching if we find more than 100 long-read-coherent paths. All the selected long-read-coherent paths are stored in a path database for later use. The final SSG graph is created by performing first bundling and then transitive reduction (approximate long-read overlaps) of mate-edges. From now on, we will refer to this simply as the reduced SSG.
All the selected long-read sequences are sorted according to the mate-edges order using an external merge sort algorithm to create a long-read sequence database. Following the long-read database creation, we build a consensus sequence for each mate-edge using the partial order alignment graph  [30]. For each mate-edge, we select the long-read contributing the most synthetic mate-pairs as consensus template, then the remaining long-reads spanning e are aligned to the template using a fast implementation of Myers' bit-vector algorithm  [31]. The long-read alignments are scanned to partition the long-reads into non-overlapping windows of size w (by default 500bp) on the template sequence. The long-read chunks that have an average identity lower than 65% are removed from the corresponding windows.
Assembly validation. Genome assemblies generated by WENGAN and other assemblers were assessed by whole genome alignment to the human reference genome using the MINIMAP2  [38]  program and a procedure similar to the one described recently by Ruan et al. [14]. To determine breakpoints, a maximum of 5% divergence in the alignments was allowed (MINIMAP2 options: -paf-no-hit -cxasm20 -r2k -z1000,500) and then alignments longer than 50kb were scanned by PAFTOOLS (option asmstat -q50000 -d. 1) to collect several assembly metrics (i. e. NG50, NGA50, largest alignment block and others). The consensus quality was determined by computing a more stringent alignment allowing a maximum of 1% divergence (MINIMAP2 options: cxasm10 -cs -r2k), then alignments longer than 50kb were scanned by PAFTOOLS (option call -l50000 -L50000) to call Single Nucleotide Variants, insertions and deletions.
Additionally, we used the 100-mers completeness analysis to assess with an alignment-free method the consensus quality of the genome assemblies using the KMC  [41]  k-mer counter (Version 3. 1. 0). The GRCh37 (hs37d5) reference genome has a total of 2,825,844,566 distinct 100-mers and those were intersected with the 100mers of the genome assemblies using the KMC TOOLS utility (option intersect -ci1 -cx1000). A QUAST  [32]  (Version: 5. 0. 2) analysis was run with the options min-identity 80 and fragmented to validate the NA12878 assemblies (rel5) using hs37d5 as reference and the HG0075, NA243875 and CHM13 assemblies using the GRCh38 reference (autosomes plus X and Y). The gene completeness of the genome assemblies was assessed with the BUSCO  [42]  program (Version 3. 0. 2) using the MAMMALIA ODB9 gene set (4104 BUSCO groups).
The single plus duplicated complete BUSCO gene counts are reported. The consensus quality of the genome assemblies was determined by aligning orthogonal BAC or Fosmid sequences data (Table  S4 ). The statistics were computed considering fully resolved BAC/Fosmid only. The BAC/Fosmid consensus quality analysis was performed using the BACVALIDATION tool (https://github. com/skoren/bacValidation). The amount of Segmental Duplication (SD) resolved by the genome assemblies of CHM13, HG00733 and NA24385 was determined using SEGDUPPLOTS  [33]  (https://github. com/mvollger/segDupPlots).
Results Genetic clustering and uniparentally inherited markers. We report genome-wide data at a targeted set of 1. 2 million single nucleotide polymorphisms (SNPs)  18, 27  for 59 Eneolithic and BA individuals from the Caucasus region. After filtering out 14 individuals that were first-degree relatives or showed evidence of contamination (Supplementary Data 1, Supplementary Note 3) we retained 45 individuals for downstream analyses using a cutoff of 30,000 SNPs. We merged our newly generated samples with previously published ancient and modern data (Supplementary Data 2). We first performed principal component analysis (PCA)  28  and ADMIXTURE  29  analysis to assess the genetic affinities of the ancient individuals qualitatively (Fig. 2 ). Based on PCA and ADMIXTURE plots we observe two distinct genetic clusters: one falls with previously published ancient individuals from the West Eurasian steppe (hence termed 'Steppe'), and the second clusters with present-day southern Caucasian populations and ancient BA individuals from today's Armenia (henceforth called 'Caucasus'), while a few individuals take on intermediate positions between the two.
Thus, the occurrence of Steppe ancestry in the northern foothills likely coincides with the range expansion of Yamnaya pastoralists. However, more time-stamped data from this region will be needed to provide details on the dynamics of this contact zone. An important observation is that Eneolithic Samara and Eneolithic steppe individuals directly north of the Caucasus had initially not received AF gene flow. Instead, the Eneolithic steppe ancestry profile shows an even mixture of EHG-and CHG ancestry, suggesting an effective cultural and genetic border between the contemporaneous Eneolithic populations, notably Steppe and Caucasus. Due to the temporal limitations of our dataset, we currently cannot determine whether this ancestry is stemming from an existing natural genetic gradient running from EHG far to the north to CHG/Iran in the south or whether this is the result of Iranian/CHG-related ancestry reaching the steppe zone independently and prior to a stream of AF ancestry, where they mixed with local hunter-gatherers that carried only EHG ancestry.
6. 1) 59 against human genome reference GRCh37/hg19 (or just the mitochondrial reference sequence), and removing duplicate reads with the same orientation and start and end positions. To avoid an excess of remaining C-to-T and G-to-A transitions at the ends of the reads, we clipped three bases of the ends of each read for each sample using trimBam (https://genome. sph. umich. edu/wiki/BamUtil:_trimBam). We then generated pseudo-haploid calls by selecting a single read randomly for each individual at each of the targeted SNP positions using the genotype caller pileupCaller (https://github. com/stschiff/sequenceTools/tree/master/src-pileupCaller). Quality control. We report, but have not analyzed, data from individuals that had less than 30,000 SNP hits on the 1240K set. We removed individuals with evidence of contamination based on heterozygosity in the mtDNA genome data, a high rate of heterozygosity on the X chromosome despite being male estimated with ANGSD  60  , or an atypical ratio of the reads mapped to X versus Y chromosomes.
Merging new and published ancient and modern population data. We merged our newly generated ancient samples with ancient populations from the publicly available datasets (Supplementary Data 2), as well as genotyping data from worldwide modern populations using Human Origins arrays published in the same publications. We also included newly genotyped populations from the Caucasus and Asia, described in detail in Jeong et al. 61. Principal component analysis. We carried out principal component analysis on Human Origins Dataset using the smartpca program of EIGENSOFT 28 , using default parameters and the lsqproject: YES, numoutlieriter: 0, and shrinkmode: YES options to project ancient individuals onto the first two components. ADMIXTURE analysis. We carried out ADMIXTURE (v1. 23)  29  analysis after pruning for linkage disequilibrium in PLINK 62 with parameters --indep-pairwise 200 25 0.
4, which retained 318,427 SNPs for the Human Origins Dataset. We ran ADMIXTURE with default fivefold cross-validation (--cv = 5), varying the number of ancestral populations between K = 2 and K = 18 in 100 bootstraps with different random seeds. f-statistics. We computed D-statistics and f 4 -statistics using qpDstat program of ADMIXTOOLS 28 with default parameters. We computed the admixture f 3 -statistics using the qp3Pop program of ADMIXTOOLS with the flag inbreed: YES. ADMIXTOOLS computes standard errors using the default block jackknife. Streams of ancestry and inference of mixture proportions. We used qpWave and qpAdm 18 as implemented in ADMIXTOOLS with the option 'allsnps: YES' to test whether a set of test populations is consistent with being related via N streams of ancestry from a set of outgroup populations and estimate mixture proportions for a Test population as a combination of N 'reference' populations by exploiting (but not explicitly modeling) shared genetic drift with a set of outgroup populations: Mbuti.
Acknowledgements We thank  Stephen Clayton  and all members of the  MPI-SHH Archaeogenetics Department  for support,  Michelle O'Reilly  and  Hans Sell  for graphics support, and  Iosif Lazaridis ,  Vagheesh Narasimhan  and  Nick Patterson  for critical discussions. We thank  Susanne Lindauer ,  Ronny Friedrich ,  Robin van Gyseghem  and  Ute Blach  for radiocarbon dating support. This work was funded by the  Max Planck Society , the  German Archaeological Institute (DAI ; grant no. ERA. Net RUS ,  BFDJ16011 ), and the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (grant agreement n°771234 PALEoRIDER). C. -C. W. was funded by  Nanqiang Outstanding Young Talents Program of Xiamen University  ( X2123302 ), the  Fundamental Research Funds for the Central Universities  ( ZK1144 ) and  National Natural Science Foundation of China  ( 31801040 ).
MeThodology: We performed a systematic search of both indexed and non-indexed publications using PubMed, databases of National Institute of Science Communication and Information Resources (NISCAIR), Annotated Bibliography of Indian Medicine (ABIM), Google Scholar, and hand search including cross-references using key terms 'community acquired pneumonia AND India'. All studies, published between January 1990 and January 2017, that evaluated Indian patients aged above 12 years with a confirmed diagnosis of CAP were eligible for inclusion. Our search retrieved a total of 182 studies, of which only 17 and 12 qualified for inclusion in the systematic review of all etiological organisms, and meta-analysis of S. pneumonia, respectively. ReSulTS: A total of 1435 patients met the inclusion criteria.
Search strategy We performed a systematic search on PubMed, using the key terms 'Community-Acquired Pneumonia AND India', 'Community-Acquired Pneumonia AND aetiology', 'Community-Acquired Pneumonia AND Diagnosis', or 'Community-Acquired Pneumonia AND Management'. The search was performed after applying constant filters based on these additional search criteria: Article Types -Randomized Clinical Trials, Meta-Analysis, Systematic Literature Reviews, Literature Reviews, Observational Studies; Language -English; Publication Date -01/01/1990-08/01/2017; Species -Humans; Adult and Adolescent -12+ years. Additional records were identified through other sources (the National Institute of Science Communication and Information Resources [NISCAIR], the Annotated Bibliography of Indian Medicine [ABIM], and Google Scholar) using the search terms: 'Community-Acquired Pneumonia AND 'India'.
Data extraction Data was collected from all the primary studies using a structured sheet in Microsoft Excel. Any discrepancies arising while entering the data were sorted out by discussion among all the contributors. Two reviewers were involved in determining the risk of bias analysis and data extraction. Reviewers resolved any disagreements by discussion between themselves. Study characteristics extracted included authors details, year of publication, title of study, place of study, and type of study. Patient parameters included number of study participants and their mean age, gender, educational level, and marital status. CAP was classified by aetiology.
Results PubMed searches retrieved 164 studies and Google Scholar searches retrieved ten. Eight additional studies were retrieved via hand search. The ABIM and NISCAIR database searches did not retrieve any relevant study. The analysis identified 17 relevant studies (Figure  1 ). All 17 studies  [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26]  were considered for qualitative as well as the quantitative synthesis of aetiological agents. represents the characteristics of the studies included in the analysis.