dataesr/scientific-paragraphs-categorization huggingface dataset:
g. , SBML, SBGN and MIRIAM Methods and software tools for biological data visualisation Bioinformatics and statistics Fundamentals of DNA, RNA and protein sequence analysis Integrative bioinformatics-interoperability, ontologies, semantics, databases and standards Genomics of communities, meta-genomics of populations of cells and organisms Molecular evolution, phylogeny and population genetics Complex genotype-phenotype relationships-genome-wide association studies for human diseases and desirable traits in plants, animals and microbes Data analysis-standard algorithms, basics of supervised and unsupervised statistical learning, data integration Statistical inference-use of appropriate statistical tests, reverse engineering Machine learning-clustering; neural networks, random forest Experimental design, measurement, analysis, interpretation and knowledge generation.
Study Design This study is a subset of the prospective SHCS, with continuous enrollment of individuals infected with HIV ≥18 years of age observed in the HIV outpatient clinics of 7 Swiss hospitals (Basel, Bern, Geneva, Lausanne, Lugano, St. Gallen, Zurich) and associated smaller hospitals' and physicians' practices  [16]. Data were prospectively collected at time of patients' enrollment in the study and every 6 months thereafter on standardized data collection forms and include basic sociodemographic characteristics and information about the clinical course of the disease, coinfection with hepatitis B and hepatitis C, psychiatric comorbidity, antiretroviral treatment, comedication, and immunological and virological parameters. The patient's ability to work in the month preceding a follow-up visit was assessed, independent of the patient's current employment status or the patient's own opinion, by the treating physician using a scale of 0% to 100% (0% = total disability; 100% = no disability).
In the instruction materials, there were no details specifying which medicals factors should be calculated in assessing each patient's ability to work. The patient's primary source of income was recorded every 6 months according to 5 main categories ( job, insurance, unemployment benefits, relatives, savings). For the present analysis, we used the SHCS database extract of June 2014. The local ethical committees of all participating study sites (Ethics Committee northwest/central Switzerland; Ethics Committee Bern, Ethics Committee Geneva; Ethics Committee St. Gallen, Ethics Committee Ticino; Ethics Committee Vaud; Ethics Committee Zurich) approved the study, and written informed consent was obtained from all participants.
Study Population Antiretroviral-naive HIV-infected individuals below 60 years who were participating in the SHCS and started cART between January 1, 1998 and December 31, 2012, and for whom data on their ability to work at baseline and after 1 year of treatment were available, were eligible for this study. Similar to Switzerland, the retirement age in our cohort was 65, and we restricted our analysis to patients younger than 60, accounting for a potential follow-up of 5 years.
Study Population Among the more than 18 000 SHCS participants, 6782 antiretroviral-naive patients started cART from January 1, 1998 through December 31, 2012. Of these, we excluded 291 who were more than 60 years old and 691 for whom no data were available with respect to their ability to work at baseline or after the first year of treatment. The final study population comprised 5800 persons. At baseline, 4382 individuals (75. 6%) were fully able to work, 471 (8. 1%) were only able to work part time, and 947 (16. 3%) were unable to work at all. Among 471 patients who were classified as partially able to work, only 12 patients were judged to be unable to work in a proportion of 10% and 6 patients were assessed to be 90% able to work; all other patients were able to work between 20% and 80%.
Changes in Ability to Work and the Main Source of Income Over a 5-Year Period Data on ability to work at 5 years after starting cART were available for 3029 (52. 2%) of the 5800 patients included in the study. Of this group, 2187 (72. 2%) were assessed to be fully able to work, 392 (12. 9%) were able to work part time, and 450 (14. 9%) were unable to work at 5 years. Of the 2264 individuals who were able to work at 1 year, 1980 (87. 5%) were still able to work at 5 years, and only 131 (5. 8%) had developed a new disability that impaired their ability to work. Only 71% of the individuals fully able to work at 5 years reported living on income from their jobs. Among those unable to work at 5 years, 89. 1% reported living from insurance payments. The main reasons of the missing data on the ability to work at 5 years in 2771 patients were the short potential follow-up in 1892 (68.
Acknowledgments M. B. had full access to all the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Financial support. This study was funded in the framework of the  Swiss HIV Cohort Study (SHCS) , supported by the  Swiss National Science Foundation  ( SHCS  project  708 ). The members of the  Swiss HIV Cohort Study  ( J. Barth ,  M. Battegay ,  E. Bernasconi ,  J. Böni ,  H. C. Bucher ,  P. Bürgisser ,  C. Burton-Jeangros ,  A. Calmy ,  M. Cavassini ,  R. Dubs ,  M. Egger ,  L. Elzi ,  J. Fehr ,  M. Fischer ,  M. Flepp ,  H. Furrer  [ Chairman of the Clinical and Laboratory Committee ],  C. A. Fux ,  M. Gorgievski ,  H. Günthard  [President of the SHCS],  B. Hasse ,  H. H. Hirsch ,  B. Hirschel ,  I. Hösli ,  C. Kahlert ,  L. Kaiser ,  O.
Dendritic spine analysis Golgi impregnation was performed in the cerebellum of 3 month-old WT and calpain-1 KO mice according to FD Rapid GolgiStain Kit instructions (FD Neurotechnologies). 100 um sagittal sections of the cerebellum were sliced. Images of dendritic branches of Purkinje cells were acquired using a Zeiss light microscope with a 60× objective. Using the Analyze Skeleton plugin of Image J software, spines densities were analyzed in random selected distal branches between 10 and 20 μm in length. Spine morphology analysis was performed as previously described with some changes  (Miyoshi et al. , 2014)  (See Supplemental Information).
Patients Autosomal recessive families of Tunisian, Bangladesh or European origin were studied (pedigrees shown in Figure  1  Genetic linkage/homozygosity analysis-Family members were genotyped using Illumina CytoSNP12 arrays with 301,232 genome-wide markers and the raw data was processed in GenomeStudio (Illumina, San Diego, US). Genotypes were examined with the use of a multipoint parametric linkage analysis and haplotype reconstruction performed with Simwalk2  (Sobel et al. , 2001). Exome sequencing-Libraries were prepared using the TruSeq DNA sample prep kit (Illumina, San Diego, US) and 1 ug of patient DNA. Fragmentation was performed with the Covaris shearing system using the 300bp with size selection by excision from the area between 300-400bp on an agarose gel. CAPN1 Sanger sequencing-To validate the results of exome sequencing and screen controls, primers were designed using Primer3 to amplify the entire CAPN1 gene (primers available on request).
Acknowledgements This work was supported by grant  P01NS045260-01  from  NINDS  (PI:  Dr. C. M. Gall ), the  Agence Nationale de la Recherche (ANR, France ; to GS), the  Verum Foundation  (to GS and AB), the patient association " Connaitre les Syndromes cérébelleux " (CSC, France; to GS), the  Roger de Spoelberg Foundation  (Swiss, to AB), the  European Union  (Omics call: NEUROMICS, to AB and AD) and benefited from the  program Investissements d'avenir   ANR-10-IAIHU-06  (to the  ICM Institute ). The authors want to thank  Western University of Health Sciences  for the financial support to MB. XB is also supported by funds from the  Daljit and Elaine Sarkaria Chair. MC was the recipient of a fellowship from the  Fond.
Repression of the PhoP regulator was observed in N-15 in presence of RBL67. Further, RBL67 activated virulence genes located on the Salmonella pathogenicity islands 1 and 2. Flagellar genes, however, were repressed by RBL67. Sequential expression of flagellar, SPI 1 and fimbrial genes is essential for Salmonella infection. Our data revealed that RBL67 triggers expression of SPI 1 and fimbrial determinants prematurely, potentially leading to redundant energy expenditure. In the competitive environment of the gut such energy expenditure could lead to enhanced clearing of Salmonella.
RNA-Seq data analysis Illumina raw data reads (100 bp) were separated by barcode and mapped against the genome of RBL67 (GenBank accession no. CP004346) or Salmonella Typhimurium LT2 (GenBank accession no. AE006468) using the CLC Genomics Workbench 6. 5. 1 (CLCbio, Aarhus, Denmark) applying the default settings. Maximum allowance of mismatches was set at 2, minimum length fraction at 0. 9 and minimum similarity fraction at 0. 8. Statistical analysis for differential gene expression of the mono-and co-cultures was done with the statistical software R (http://www. R-project. org) using the GLM method  [31]  included in the Bioconductor EdgeR software package  [32] [33] [34]  based on negative binomial distribution. Genes with low read numbers (sum of reads in all samples <3 counts per million (cpm)) or with high read numbers (number of reads >50,000 cpm in each sample) were filtered out before data normalization.
A false discovery rate (FDR) value <0. 05 and a differential expression of at least 2 fold (1 < log 2 ratio < -1) was used as cut off for significant differentially expressed genes in mono-culture and co-culture  [35]. Proteins of RBL67 and LT2 were assigned to gene ontology categories (GO) using Blast2GO at standard settings  [36]. GO categories enrichment analyses were performed and visualized using the BiNGO plugin  [37]  in Cytoscape (v. 3. 0. 1,  [38] ) applying the hypergeometric test with Benjamini and Hochberg false discovery rate correction option. The significance cutoff for overrepresented gene ontology categories was a corrected p-value of <0. 05. Virulence factors of Salmonella LT2 were identified by genome wide blast against the virulence factor database (VFDB)  [39] , using a cut off E-value of 1 -20.
Significant enrichment of virulence factors was calculated using the Fisher's Exact Test Calculator for 2 × 2 Contingency at www. research. microsoft. com/en-us/ um/redmond/projects/mscompbio/fisherexacttest/. The RNAseq data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus  [40]  and are accessible through GEO Series accession number GSE65716 (http://www. ncbi. nlm. nih. gov/geo/ query/acc. cgi?acc=GSE65716).
Twenty-seven genes were down regulated in cocultures compared to monoculture, of which 12 were classified as hypothetical proteins (Table  2 ). A putative operon encoding glycosyltransferases (ORF D805_0351-D805_0356), three genes involved in amino acid metabolism (D805_0341, D805_0525 and D805_1313), including the glutamate producing enzyme aspartate aminotransferase (EC 2. 6. 1. 1) and two metal transporters (D805_0345 and D805_0885) were higher expressed. Mapping the co-culture reads to the Salmonella Typhimurium LT2 genome resulted in less than 5 million reads mapped (data not shown), indicating that the majority of the RNA isolated form the coculture after 5 h consisted of bifidobacterial RNA. Growth characteristics of N-15 in mono-and co-culture with RBL67 In a next step Salmonella N-15 was grown in a mono-and co-culture with RBL67, the latter being a repetition of the co-culture presented above.
A comparison to the virulence database VFDB revealed 151 genes in LT2 putatively involved in virulence  [39]. Of these 151 genes, one was higher expressed in mono-culture, i. e. phoP encoding the transcriptional regulator PhoP, a member of the two-component system PhoQ-PhoP. The PhoQ encoding gene was also overexpressed in the mono-culture, although not significant (FDR = 0. 063, Additional file 1: Table  S2 ). In the co-culture, 122 virulence genes were higher expressed, a significant enrichment of expressed virulence genes (p = 7 × 10 -39 in Fisher's test). The large majority of genes were involved in secretion systems (N = 66) and fimbrial adherence determinants (N = 51). The pathogeny island 1 (SPI-1) encodes 39 genes  [39]  of which 30 were significantly higher expressed in the co-culture including the complete type III secretion system 1 (TTSS-1) consisting of sipB, sipD, prgIHK, invACBGH, spaSRQPO, and sicAP.
The transcriptome of N-15 mapped to the genome of Salmonella Typhimurium LT2 had a similar efficiency as the mapping of the transcriptome of RBL67 to the RBL67 genome, suggesting that mapping reads to a closely related genome is possible. The pathogenicity islands of Salmonella Typhimurium strains are conserved and difference in virulence factors contents mainly occurs on plasmid  [42]. We could map RNAseq reads against the plasmid of LT-2, indicating that N-15 has a virulence-genes-encoding plasmid similar to that of LT2. Hence, both strains seem highly similar and the RNAseq data presented resemble closely the transcriptome profile of Salmonella Typhimurium strain N-15. Sampling points were chosen when growth speed, cell number and metabolite concentrations were similar in both cultures to allow accurate transcriptomic profiling.
Conclusion Our study provides first insights into the transcriptome response of B. thermophilum RBL67 and S. Typhimurium grown in co-cultures under simplified conditions and reveals possible molecular mechanisms of probioticpathogen interaction. Our data show that RBL67 has a huge impact on the transcriptome of Salmonella and causes in an imbalanced virulence gene expression. This imbalance in the cascade pathway of virulence could represent a novel possible mechanism of how probiotic organisms can protect the host against infections.
Availability of data and materials Data presented in this study are available under NCBI BioProject Record PRJNA274782 accessible through http://www. ncbi. nlm. nih. gov/bioproject/PRJNA274782. Gene expression data are directly accessible through GEO Series accession number GSE65716 (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE65716).
This has not been investigated in women with CPP. QST assesses the response of both un-myelinated C and myelinated A fibres, and with the use of calibrated instruments to determine sensation threshold to a variety of stimuli, aims to provide reproducible results (Table  1 ). The viscerosomatic convergence within the spinal column is reflected in cutaneous sensory changes in those with visceral hypersensitivity. This has been well documented, including within the female pelvis  [20]. The majority of the body of work has been done by the German Research Network on Neuropathic Pain (DNFS) who have established protocols for research and databases for thresholds. QST has previously been used as a gold standard in other trials for diagnosis of NeP, and has also been used specifically in CPP of varying aetiologies  [21].
'Loss or gain of function' (i. e. increased/ decreased sensitivity in the affected area was relative to the control site at the xiphisternum. Demographic data collection. Basic demographics were collected, as well as menstrual phase during assessment, current hormonal treatment, analgesics and neuromodulator use. Following QST, the subjects' clinical notes were reviewed for their attending clinician's impression of aetiology, and findings at laparoscopy. If the participant had previously been reviewed by a pain medicine specialist, their diagnosis was also documented. Data Analysis. Descriptive statistics were used to analyse baseline characteristics. We used a χ 2 test to compare dichotomous data. Statistical analysis was performed using GraphPad PRISM Version 6. All women had their QST results sub-analysed for grouping into either pure loss, or gain of function, or mixed neuropathic disorder compared to control area.
Plasma chemistry Samples of plasma were sent to the West Australian Animal Health Laboratories (South Perth, Western Australia) for plasma enzyme and chemistry assessment. The assays were run on an Olympus AU400 automated chemistry analyser (Olympus Optical Co. Ltd). Each of the assays used ). Trace elements were determined after mixed acid digestion using inductively coupled plasma atomic emission spectrophotometry (ICP-AES). Data are presented in Table  6.
Menstrual cycles range from 25 to 38 days, with 10 patients having a cycle length of 28 days (Supplemental Table  S1 ). Patients were divided into luteal phase from 0-11 days between the surgery time and onset of menses afterwards, and into follicular phase from 17-30 days between both dates avoiding uncertainties during mid cycle (Supplemental Table  S2 ). This dataset is used to calibrate the model parameters during physiological homeostasis. The formalin-fixed and paraffin-embedded breast tissues were cut in sections of 3 μm thickness. Immunohistochemistry was performed to stain for cytotoxic T-lymphocytes (CD8; Dako M7103), regulatory T-cells (CD4; Zytomed Systems 503-3354) and macrophages (CD163; medac diagnostika 163M-16) on an automated instrument (Ventana Benchmark Ultra). Quantification of epithelial and immune cells was performed in about 650 (luteal phase) and 250 (follicular phase) representative breast lobular structures with between 250 and 2500 epithelial cells in whole slide images by means of an automated image analysis workflow.
More precisely, a module for automated detection of single cells and nuclei from the Definiens Tissue Phenomics framework was used, which is based on the Definiens Image Miner and Developer Software  44. The healthy women in our cohort were all adult at the time of the surgical procedure. Thus, we assumed that the adult breast is not growing and the epithelial compartment of mammary gland is only subject to a normal, overall balanced cell turnover/renewal at each menstrual cycle. In the following, the amount of immune cells is provided with respect to the number of epithelial cells and referred to as relative number. Figure  3a-c  shows the resulting epithelial and immune cell quantification in normal breast tissue samples with respect to the follicular and luteal menstrual cycle phases (Supplemental Fig.
S6 ). We further consider a "proof-of-principle" dataset consisting of breast tissue samples obtained during surgical procedures from (i) 7 premenopausal healthy women who underwent reduction mammoplasty (RM) without clinical abnormality nor familial history of breast cancer, ages ranging from 21 to 45 years (median age 32 years), (ii) 21 premenopausal women who underwent prophylactic mastectomy (PM) due to an increased risk of hereditary breast cancer (BRCA1/2 mutations) without clinical or pathological abnormalities, ages ranging from 22 to 53 years (median age 38 years), and (iii) a cohort of 7 premenopausal women with clinically manifest breast cancer, ages ranging from 30 to 43 years (median age 41 years). No details about the menstrual cycle phase were reported in the clinical records as it is not routinely collected.
Acknowledgements The authors gratefully acknowledge the support of the  German Federal Ministry of Education and Research (BMBF)  for the eMED project  SYSIMIT  ( 01ZX1308D ) and the  Center for Information Services and High Performance Computing (ZIH) at TU Dresden  for generous allocations of computer time. We thank  Prof. Dr. M. Stöckelhuber  ( Technical University of Munich, Germany ) and  Prof. Dr. Dr. U. Welsch  ( Ludwig-Maximilians University of Munich, Germany ) for kindly allowing the use of normal breast tissue samples from a previous study [43].
Sample selection We analyze gas and stellar kinematic maps of a representative sample of 1351 nearby galaxies with stellar masses above 10 9 solar mass from MaNGA. Fig. 1  shows an example of a counterrotating blue star forming galaxy. The Sloan Digital Sky Survey (SDSS) false-color image is at left, while the kinematics based on spectroscopic IFU data for stars and gas are mapped in the second and third columns (velocities and velocity dispersions, respectively). To quantify the kinematic misalignment between stars and gas, we measured the difference in the kinematic position angle (PA) between ionized gas and stars as ∆PA = |PA * -PA gas |, where PA * is the PA of stars and PA gas is the PA of ionized gas. The kinematic PA is measured based on established methods  17  , defined as the counter-clockwise angle between north and a line which bisects the velocity field of gas or stars, measured on the receding side.
Sample completeness correction An issue with every data set is the selection of weights to correct for missing galaxies. The MaNGA target sample is selected to lie within a redshift range, z min < z < z max , that depends on absolute i-band magnitude in the case of the Primary and Secondary samples, and absolute i-band magnitude and NUV -r color in the case of the color-enhanced (CE) sample. z min and z max are chosen to yield both the same number density of galaxies and angular size distributions, matched to the IFU sizes, at all absolute i-band magnitudes (or magnitudes and colors for the CE sample). This results in lower, and narrower, redshift ranges for less luminous galaxies and higher and wider redshift ranges for more luminous galaxies. At a given M i (or M i and NUV -r color for the CE sample) the sample is effectively volume limited in that all galaxies within z min (M i ) < z < z max (M i ) are targeted irrespective of their other properties.
We characterize the PDF using the median and the 16%-84% range (equivalent to ±1σ range for Gaussian distributions). In this work, we directly apply this PCA method to the MaNGA data to get the stellar mass for each spaxel. The SFR for each spaxel is derived from the dereddened Hα luminosity (L Hα ) as SFR (M ⊙ yr -1 ) = 7. 9 × 10 -42 L Hα (erg s -1 ). We use Balmer decreasement for dust extinction correction.
Acknowledgements We are very grateful to the anonymous referees for useful comments and suggestions that have strengthened this work. Y. M. C. acknowledges support from  NSFC  grant  11573013 ,  11133001 , the  Natural Science Foundation of Jiangsu Province  grant  BK20131263 , the  Opening Project of Key Laboratory of Computational Astrophysics, National Astronomical Observatories, Chinese Academy of Sciences. Y. S. acknowledges support from  NSFC  grant  11373021 , the  CAS  Pilot-b grant No. XDB09000000  and  Jiangsu Scientific Committee  grant  BK20150014. C. A. T. acknowledges support from  National Science Foundation of the United States  Grant No. 1412287. Funding for the  Sloan Digital Sky Survey IV  has been provided by the  Alfred P. Sloan Foundation , the  U. S. Department of Energy Office of Science , and the Participating Institutions.
Data sources De-identified unit record data on deaths for 2000-2007 were obtained during in-country visits from hospital sources with HS (as death) and MC of death (issued at hospitals), and notices of death submitted with monthly nursing reports from CHF below hospital levelarea health centers, dispensaries, and aid posts. Certification and reporting of deaths in Vanuatu are discussed in detail in On et al. 2009  [10]. Because of de-identification, the two sources of hospital deaths (HS, MC) were not linkable. Deaths with no age (n = 138) and fetal deaths (n = 248) were excluded from all data sources, and hospital deaths (n = 21) were removed from community health facility data (Table  1 ). Only deaths 0-59 years were coded for cause because data quality of CoD data was less for those ≥60 years, LE in Vanuatu is likely to be above 60 years, and this age range includes the demographic adult age bracket 15-59 years.