dataesr/scientific-paragraphs-categorization huggingface dataset:
Data Collection and Sequence Analysis We analyzed bacterial and fungal communities in 48 skin samples from 11 healthy and 13 dandruff individuals. Scalp and forehead samples were studied to assess variation across two sebaceous body areas and to enable comparison between lesional and nonlesional skin sites in dandruff subjects. In silico analyses were performed to select primer sets for bacteria and fungi considering specificity and coverage. Amplicons containing the V4 hypervariable region of 16S rRNA gene from bacteria and the ITS1 region from fungi were sequenced using Illumina MiSeq platform. We obtained ∼2. 3 million reads for bacteria and 1. 4 million for fungi after quality and size filtering (Supplementary Table  2 ). Approximately 88% of the bacterial sequences were assigned using Greengenes database, and 612 Operational Taxonomic Units (OTUs) were found.
Chloroplast and mitochondria sequences (nearly 8% of the reads) were removed from the analysis. For fungi, only approximately half of the sequences (51. 4%) were assigned using UNITE database. Therefore, we performed a second step of analysis consisting of sequence clustering and assignment using GenBank to allow a larger and more reliable panorama of the fungal communities. This strategy increased the percentage of assigned sequences (>83%). A total of 274 fungal OTUs were found. Moreover, the method allowed the detection of contaminant sequences assigned to nonfungal taxonomic groups (7. 8% of the reads). They correspond to plants and were removed from the analyses. Rarefaction curves were generated to estimate depth of sequence sampling (Supplementary Figures  1, 2 ).
Taxonomic Composition of Microbial Communities Actinobacteria, Firmicutes, and Proteobacteria were the most abundant bacterial phyla. At genus level, Propionibacterium, Staphylococcus, and Corynebacterium were found to be the three most abundant genera in both healthy and dandruff subjects (Figure  1A ). Malassezia sp. comprised the vast majority of fungi in almost all of the samples (∼96% of the reads; Figure  1B ); therefore, we also performed taxonomic assignment at Malassezia species level. Nine Malassezia formally described species were detected (M. restricta, M. globosa, M. sympodialis, M. dermatis, M. japonica, M. obtusa, M. pachydermatis, M. sloofiae, and M. furfur), as well as an uncharacterized phylotype previously described (LCP-2008a-Genbank accession number EU192362). M. restricta was the most abundant species.
, and Staphylococcus sp. (Clavaud et al. , 2013; Wang et al. , 2015). More recently,  Xu et al. (2016)  showed that host factors such as skin sebum and water content are related to dandruff. Analyzing scalp microbiome by NGS, the authors found that dandruff is more closely related to bacteria than to fungi, and reported no significant association with Malassezia at species level, although some OTUs showed positive or negative correlation with dandruff  (Xu et al. , 2016). Our results corroborate the relationship between dandruff and bacteria but not with Malassezia at species level, and showed for the first time increased diversity and dissimilarity among dandruff samples, affecting also asymptomatic skin sites. A bioinformatics strategy based on sequence clustering and OTU assignment using combined databases increased the percentage of fungal assigned sequences, and revealed the presence of uncharacterized Malassezia organisms.
ACKNOWLEDGMENTS We thank the employees and medical team from  Instituto Superior de Medicina e Dermatologia-ISMD, São Paulo, Brazil. We are also grateful to  Suzi Dal Belo  and  Daphine Antonia Clemente  from  L'Oréal Research and Innovation Brazil  for their assistance in the clinical characterization of dandruff,  Daniel H. Littwin  for language revision, and to all volunteers who collaborated with this work. This work was supported by a grant from  L'Oréal. RD, CC, and LB are employees of  L'Oréal Research and Innovation.
We used detailed epidemiologic data from the 2014 vaccination campaigns and the subsequent cholera outbreak in South Sudan to determine how vaccine use may have altered the epidemic course in vaccinated areas. We compared epidemics in 2 areas that included vaccinated and unvaccinated populations: 1) PoC sites (vaccinated) and the community (unvaccinated) in Juba; and 2) Malakal PoC (vaccinated) and Wau Shilluk IDP (unvaccinated), 2 similar camps separated by a river.
Acknowledgments We acknowledge the work of all the public health workers involved in these vaccination campaigns and the larger cholera response, including members of the  South Sudan National Cholera Task Force. The work of A. S. A. , D. A. S. , J. L. , and F. J. L. was supported by the  Bill and Melinda Gates Foundation  ( OPP1089243  and the  DOVE [Delivering Oral Vaccine Effectively ] project,  OPP153556 ). Dr. Azman  is a research associate in the  Epidemiology Department at Johns Hopkins University Bloomberg School of Public Health. His research interests include infectious disease dynamics and vaccine study design, with a particular focus on cholera and hepatitis E.
Population Stratification We assessed population stratification in Cambodian P. vivax with the program STRUCTURE v2. 3. 4  [23]  and the entire haplotype information at the targeted loci using all symptomatic infections determined to be either mono-or biclonal. To increase the discriminating power of our analyses and facilitate the interpretation of the results, we included genotypes at the same loci inferred from whole genome sequencing data generated from parasites collected in Thailand (N = 9)  [24]  and from non-Asian locations (N = 11)  [15, [25] [26] [27]. We assigned the parasites into K = 1 to K = 4 populations using 100,000 burn-ins, 1,000,000 Markov chain Monte Carlo (MCMC) steps and a model of correlated allele frequency with admixture. For each K, we compared the results from five independent runs to verify convergence to a similar solution and recorded the proportions of ancestry of each parasite.
Determinants of the Complexity of Infection in Cambodian P. vivax We then investigated which parameters influenced COI in Cambodian P. vivax infections by i) comparing monoclonal and polyclonal infections (as determined by the genotypes at the 274 SNPs identified in the 100 loci sequenced), and ii) comparing infections with different numbers of clones (inferred statistically from the genotypes at the 100 unlinked SNPs). Using both data sets, we found that COI did not statistically differ between infections from western and eastern Cambodia (Table  1 ). Similarly, we found that COI was not significantly associated with parasitemia or the age or sex of the patient (Table  1 ). We also tested the association between various red blood cell phenotypes and COI but found no influence of hemoglobin level, hemoglobin genotype or G6PD deficiency (Table  1 ).
Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia with a strong genetic component. Molecular pathways involving the homeodomain transcription factor Shox2 control the development and function of the cardiac conduction system in mouse and zebrafish. Here we report the analysis of human SHOX2 as a potential susceptibility gene for early-onset AF. To identify causal variants and define the underlying mechanisms, results from 378 patients with early-onset AF before the age of 60 years were analyzed and compared to 1870 controls or reference datasets. We identified two missense mutations (p. G81E, p. H283Q), that were predicted as damaging. Transactivation studies using SHOX2 targets and phenotypic rescue experiments in zebrafish demonstrated that the p. H283Q mutation severely affects SHOX2 pacemaker function.
H283Q) (Fig. 1B, C ). Both amino acids reside at evolutionary conserved sites with p. G81 being conserved among mammals and p. H283 highly conserved among vertebrates (Fig. 1C ). Different in silico analyses (PolyPhen2, Mutation Taster, PROVEAN, Hansa) predicted that the p. H283Q missense mutation is disease causing (deleterious), while p. G81E is predicted as possibly damaging. Both SHOX2 amino acid variants were absent in the 1000 Genomes dataset (http://www. 1000gen omes. org/) and the Exome Variant Server (http://evs. gs. washingon. edu/EVS/). Thus, both mutations were considered as disease causing and further investigated.
Functional relevance of SHOX2 missense mutations To investigate the functional significance of the two missense mutations, subcellular localization of the SHOX2 mutants was determined in HEK293 and HL-1 cells and compared to wild type. Consistent with its role as transcription factor, wild type as well as p. G81E or p. H283Q SHOX2 mutants localized to the nucleus (data not shown). Next, we performed luciferase reporter assays to determine whether the identified mutations have an impact on the transactivational activity of SHOX2. Wild type SHOX2 activates the promoter of its previously described target genes BMP4 and ISL1  [24, 40]. We could show that SHOX2 harboring the p. G81E mutation has still transactivational activity similar to wild type, while the p. H283Q mutant severely affects the transactivational activity and was not able to activate its targets (Fig.
SHOX2 expression in right atrial appendages of AF patients To investigate SHOX2 expression levels in human tissue specimens, right atrial appendages were obtained during cardiac surgery from patients with AF and patients with sinus rhythm (n = 17 for each group). Expression analysis revealed significantly reduced SHOX2 transcripts in AF patients compared to the control group (p = 0. 0226; Fig. 6A ). Next, we examined ECG recordings from these patients and found significantly longer PR intervals (p = 0. 0157) in AF patients compared to patients with sinus rhythm (Fig. 6B ), whereas other ECG parameters (RR interval, QRS duration, QT interval) were unchanged (data not shown). Together, our data demonstrate for the first time coding and non-coding variants in SHOX2 in patients with atrial fibrillation.
Statistical analysis For the clinical characteristics analysis and miRNA measurements in human plasma, data are presented as mean ± SEM. An unpaired student's t test was used for twogroup comparisons. Categorical variables were analyzed by Fisher's exact test. For the association study a Chi squared (v 2 ) test was used. A p value p \ 0. 05 was considered statistically significant. For luciferase assays and zebrafish injections, data are presented as mean ± SEM from at least 3-4 independent experiments. Comparisons between experimental groups were performed with GraphPad Prism 6 using paired t test or 1-way ANOVA. Differences were considered significant if they showed a p-value of p \ 0. 05.
Acknowledgments We thank  Howard Cooke  and  Beate Niesler  for comments on the manuscript. HL-1 cells were kindly provided by  William C. Claycomb. We thank  Bianca Hildebrand ,  Angelika Bongartz  and  Jelena Sakic  for technical support. This work was funded by the  Deutsche Forschungsgemeinschaft  [ RA 380/14-2 ], by the  People Programme  ( Marie Curie Actions ) of the European Union's  Seventh Framework Programme  (FP7/2007-2013) under REA Grant agreement No. PIOF-GA-2012-328352 ), by the  European Union 's  Horizon 2020 research and innovation programme  under Grant agreement No. 633193  [CATCH ME], by the  DZHK partnersites Heidelberg and Munich (Deutsches Zentrum fu ¨r Herz-Kreislauf-Forschung-German Centre for Cardiovascular Research) , the  BMBF (German Ministry of Education and Research) , the  Fondation Leducq Paris , the  European-North American Atrial Fibrillation Research Alliance  (ENAFRA,  07/CVD/03 ), the  NGFN Plus  and the  LMU Excellence Initiative, Spitzencluster m4 ''Personalisierte Medizin '', by the  Bundesministerium fu ¨r Bildung und Forschung e:Med  ( SYMBOL-HF; 01ZX1407A ).
Material and Methods From an international multicentre database of ASD patients (968 pts), 535 who had completed 1 year follow-up (371 non-surgical -NS), 164 surgical -S), constitute the population of this study. DA was structured in two main steps of: 1) Baseline analysis (Assessing the probabilities of outcomes, Assessing the values of preference -utilities-, Combining information on probability and utility and assigning the quality adjusted life expectancy (QALE) for each treatment) and 2) Sensitivity analysis. Complications were analyzed as life threatening (LT) and non-life threatening (NLT) and their probabilities were calculated from the database as well as a thorough literature review. Outcomes were analyzed as improvement (decrease in ODI > 8pts), no change and deterioration (increase in ODI > 8pts).
Phase Two Dietary choices cards included dietary guidelines set forth by the American Heart Association, the American Dietetic Association, and the American Diabetes Association. These guidelines were then used to develop cards for the number of servings of proteins, fats, dairy, vegetables, and fruit recommended by the United States Department of Agriculture (USDA) based on the daily caloric limit. The food selections for each set of cards were chosen based on nutritional information provided by the Food-A-PediaW application from the USDA. 10 This application allows patients and HCPs to search a database of food items and find a full nutritional description for the given item. Users may also alter the search parameters by setting restrictions, such as limited calories, grams of fat, or milligrams of sodium.
Inclusion criteria and data collection A retrospective single-center observational cohort study (2001 to 2011) was conducted including all consecutive patients managed at our institution receiving teicoplanin as part of S. aureus BJI treatment. Patients diagnosed with staphylococcal BJI were identified by cross-referencing the prospective maintained databases of the regional referral center for BJI and the bacteriology laboratory, which list exhaustively all strains isolated from osteoarticular samples since 2001. Patients with diabetic foot-and decubitus ulcer-related BJI were excluded, as they require a specific management  [9]. If patients presented more than one osteoarticular infected site, they were considered as independent events for cohort description and outcome analysis, but pooled for tolerance and pharmacologic evaluation.
Acknowledgements  Lyon Bone  and  Joint Infection Study Group: Coordinator: Tristan Ferry ;  Infectious Diseases Specialists -Tristan Ferry ,  Florent Valour ,  Thomas Perpoint ,  André Boibieux ,  François Biron ,  Patrick Miailhes ,  Florence Ader ,  Julien Saison ,  Sandrine Roux ,  Claire Philit ,  Fatiha Daoud ,  Johanna Lippman ,  Evelyne Braun ,  Christian Chidiac ,  Yves Gillet ,  Laure Hees ;  Surgeons -Sébastien Lustig ,  Philippe Neyret ,  Olivier Reynaud ,  Adrien Peltier ,  Olivier Cantin ,  Michel-Henry Fessy ,  Anthony Viste ,  Philippe Chaudier ,  Romain Desmarchelier ,  Thibault Vermersch ,  Sébastien Martres ,  Franck Trouillet ,  Cédric Barrey ,  Francesco Signorelli ,  Emmanuel Jouanneau ,  Timothée Jacquesson ,  Ali Mojallal ,  Fabien Boucher ,  Hristo Shipkov ,  Mehdi Ismail ,  Joseph Chateau ;  Microbiologists -Frederic Laurent ,  François Vandenesch ,  Jean-Philippe Rasigade ,  Céline Dupieux ;  Nuclear Medicine -Isabelle Morelec ,  Marc Janier ,  Francesco Giammarile ; PK/PD specialists -Michel Tod,  Marie-Claude Gagnieu ,  Sylvain Goutelle ;  Clinical Research Assistant -Eugénie Mabrut.
Simulations from our model were compared with isolated events extracted from simultaneous (LFP-LD) recordings (Materials and Methods) acquired in the context of epilepsy. More precisely, isolated events called epileptiform discharges occur in LFP signals after bicuculline injection in the cortex. These discharges elicit CBF events visible on LD data, the variations of which are sufficiently large to enable the study of the relationship between the magnitude of the discharges and that of the resulting CBF events. We obtained a good agreement between the model and the data according to the shape of the responses, which indicate that the model is able to reproduce epileptic phenomena. Besides, the sets of parameters found to obtain close simulated and experimental CBF magnitudes suggest that the relationship between neuronal activity and CBF response is nonlinear for epileptiform isolated discharges; and that this nonlinearity is due to the contribution of the astrocytes to CBF magnitude.
Model-data comparison between the CBF part of the model and the LD recording corresponding to the discharges To explore the capacity of the model to represent epileptic phenomena, we decided to manually tune (S2 Fig) the resulting simulations of the total inflow f in to reproduce the isolated laser Doppler recordings, as we assumed f in to be directly related to these recordings (no observation equation). Isolated LD events were extracted together with the isolated discharges from the continuous (LFP-LD) dataset (Materials and Methods, S1 Fig). As the laser Doppler recording was very noisy, we first filtered the isolated events and defined their local baseline in the trough before the principal peak. This allowed us to compare the normalized variable f in with the normalized isolated events.
Discussion We proposed a new computational model developed at the scale of populations corresponding to multimodal acquisitions such as sEEG-fMRI. The model represents the forward signaling chain from neuronal activity to CBF changes, involving neurotransmitter (glutamate and GABA) cycles via the astrocytes. Particular efforts were done to achieve simple equations while describing the main physiological principles found in the literature. We present a comparison of the model with bimodal (simultaneous LFP and laser Doppler) data acquired in the context of epilepsy. This sequential model-data comparison showed a good agreement of the model with the LFP recordings on isolated epileptiform discharges. This was obtained by manually tuning the neuronal parameters to patho-physiological values. We collected from the experimental literature a physiological range for the parameters of the glutamate and GABA cycles.
Extracted isolated events and chosen characteristics used for modeldata comparison The continuous (LFP-LD) data set is composed of isolated interictal-like discharges and burst discharges for LFP recordings, together with the simultaneous LD recordings corresponding to the CBF variations. We decided to compare the nonlinear model with the isolated events extracted from this continuous data set. To this end, we defined an isolated event as an interictal-like discharge on the LFP recording, i. e. an event which was sufficiently apart from the previous and following ones so that the corresponding LD variation had enough time to return to its (local) baseline. Isolated discharges were extracted directly from the continuous dataset (no post-processing) and the magnitudes A peak of their peak (S1 Fig) were collected manually.
Note that the DC component of the LFP recording was hardware-filtered. LD recordings were first filtered with the Matlab 1 (The Mathworks, Inc. ) eegfilt function (1500 points) with a cutoff frequency of 0. 5 Hz in order to obtain a smoothed version of the CBF temporal dynamics (S1 Fig). The CBF characteristics, collected from this smoothed version of the LD recording, were its magnitude F peak and its duration F long relative to the baseline (about 3 mV). We obtained nine isolated events with F long varying from 22. 2 s to 36. 4 s, which were typical durations for the CBF to return to its baseline. We observed decreasing values of A peak as the bicuculline local concentration was washed out over time.
On that basis, this work develops expert consultation to validate the principles and criteria proposed by  Bautista (2016)  in the sustainability assessment framework. The expert consultation has been previously used for the validation of conceptual models and complex issues (van der  Sluijs et al. 2005; Augusiak et al. 2014). Expert consultation was performed through an online survey, which allowed us to collect the data to perform a comprehensive analysis applying methods of descriptive statistics. This paper is structured as follows: in the first section, the hierarchical assessment framework is described. Then, the second section presents the validation method, which includes expert identification, online survey design and application, and the description of the statistical tools applied to survey answers (measures of central tendency, dispersion of data, principal component analysis and hierarchical ascendant classification).
Hierarchical assessment framework The hierarchical assessment framework was defined based on comprehensive analysis of the state of the art. About 400 documents were reviewed, and 103 documents were ultimately selected  (Bautista et al. 2016). The document selection was carried out through a deductive process that includes the identification of the following components: 1) Documents that present at least two of the following concepts: goals, objectives or principles, criteria, and indicators. 2) Document about the traditional dimensions of sustainable development  (social, economic, environmental). 3) Documents presenting research about the sustainability assessment framework. A document is selected if it is part of two or more groups previously described. The information sources employed were academic and research institutions, governmental and non-governmental institutions involved in sustainability assessment of biodiesel, and scientific databases like Web of Science and Scopus, particularly the following journal databases: American Chemical Society ACS, Science Direct, Springer Journal, and Nature.
Methods: We used RT-PCR, in situ hybridisation, and RPPA methods to quantify (i) the full-length (FL) and an alternatively spliced variant (Dsv) of MALAT1, and (ii) a panel of transcripts and proteins involved in MALAT1 pathways, in a large series of breast tumours from patients with known clinical/pathological status and long-term outcome. Results: MALAT1 was overexpressed in 14% (63/446) of the breast tumours. MALAT1-overexpressed tumour epithelial cells showed marked diffuse nuclear signals and numerous huge nuclear speckles. Screening of the dbEST database led to the identification of Dsv-MALAT1, a major alternatively spliced MALAT1 transcript, with a very different expression pattern compared with FL-MALAT1. This alternative Dsv-MALAT1 transcript was mainly underexpressed (18. 8%) in our breast tumour series.
qRT-PCR. Quantitative values were obtained from the cycle number (Ct value) at which the increase in the fluorescence signal associated with exponential growth of PCR products started to be detected by the laser detector of the ABI Prism 7900 sequence detection system (Perkin-Elmer Applied Biosystems, Foster City, CA, USA), using PE biosystems analysis software according to the manufacturer's manuals. The precise amount of total RNA added to each reaction mix (based on optical density) and its quality (i. e. , lack of extensive degradation) are both difficult to assess. Therefore, transcripts of the TBP gene (Genbank accession NM_003194) encoding the TATA box-binding protein (a component of the DNA-binding protein complex TFIID) were also quantified as an endogenous RNA control. Each sample was normalised on the basis of its TBP content.
0 program (National Biosciences, Plymouth, MN, USA; Supplementary Table  2 ). dbEST and nr databases were scanned to confirm the total gene specificity of the nucleotide sequences chosen for the primers and the absence of single-nucleotide polymorphisms. To avoid amplification of contaminating genomic DNA, one of the two primers was placed at the junction between two exons or on two different exons. Agarose gel electrophoresis was used to verify the specificity of PCR amplicons. The conditions of cDNA synthesis and PCR were as previously described  (Bieche et al, 1999). In situ hybridisation. We used Stellaris FISH Probes, Human MALAT1 with Quasar 570 Dye (Biosearch Technologies, Petaluma, CA, USA). First, paraffin-embedded tissue sliced at 4-5 mm thickness were obtained from normal and tumour tissues by using a microtome (Thermo scientific Sandom HE 340 E, Walldorf, Germany).