dataesr/scientific-paragraphs-categorization huggingface dataset:
Results The National HIV Registry Database developed by the CAC displays a total of 61174 people living with HIV, from which 34076 have AIDS  [12, 20]. Additionally, the National Cancer Registry Database contains a total of 172879 patients with cancer  [19, 23]. By merging these two databases, we found that 736 patients were diagnosed with Cancer and HIV between 1983 and 2015. From the 736 matches, 25 patients were diagnosed with HIV stage I, 103 patients were in stage II, 603 in stage III (AIDS) and five patients were in the process of being classified. 450 matches had no valid dates in both databases and 44 patients were in non-AIDS stage or were in date out of range. The 238 patients included in the analysis developed Cancer up to 60 months before the diagnosis of AIDS, and the last case reported occurred 84 months after the diagnosis of AIDS.
Discussion In this paper, we assessed the association between AIDS and neoplasms in the Colombian population. Our data come from the national administrative cancer and HIV registries  [19, 20] , gathered from all types of insurance within the Colombian health care system. We describe the results of matched data of cancer and HIV national administrative registries, making subsets of interest pathologies for analysis. In Colombia, one prior study published on Kaposi's Sarcoma in patients diagnosed with HIV/AIDS  [6]. However, our paper is the first study to evaluate the incidence and association of AIDS and cancer in Colombia. As expected, this article shows that Kaposi's sarcoma and non-Hodgkin's Lymphoma represent the vast majority of cases within the matched database. We also showed elevated SIR in men for non-AIDS-defining cancers such as those of the anal canal, eye and related types of cancer, Hodgkin's Lymphoma, and connective tissue neoplasms.
These results are relevant in our context, as anal cancer that could be effectively prevented trough HPV vaccination of men in Colombia, challenging the current programs, which only provide vaccine to girls in school age  [24]. Interestingly, data for women was scarce in the matched database, suggesting that there is a lower incidence of cancer in women with AIDS in Colombia. However, the SIR for non-AIDS-defining cancers was elevated for neoplasms of the vagina and vulva as well as for cervical cancer in situ. These findings provide evidence to the Colombian Health Care System that we should promote routine HIV screening in women with any findings suggestive of vulvar and vaginal cancer or in situ carcinoma in cervicovaginal cytology  [24].
Cell attachment assay Ninety-six-microwell plates were coated overnight at 4 °C with fibronectin, collagen IV, collagen I or poly-L-Lysine (10 μg/ml; BD Biosciences,). The cells were detached after over-night serum starvation and seeded on wells previously blocked with 1% bovine serum albumin at 6 × 10 4 cells/well density for 30min at 37°C. Additional experiments were accomplished after a pre-incubation of 30min with saturating concentrations of function-blocking anti-β1-integrin, control antibodies, pharmacological inhibitors, in presence or absence of 1mM Mn 2+. After staining with DAPI, images of the total well surface area were acquired using Zeiss Axiovert 200 microscope and a Coolsnap HQ2 camera with a 10x objective. The total number of adherent cells per well was counted using NIH Image J software.
Phospho-kinase array The relative site-specific phosphorylation of 46 kinases was analyzed using the Human Phospho-Kinase Array Kit from R&D Systems according to the protocol provided by the manufacturer. Briefly, 48h after transfection of T1C3 cells with control or Tspan8 siRNA, cells were serum-starved for 12h, seeded on collagen IV-coated flask for 2h and lysed with the recommended lysis buffer. The chemiluminescence signal intensity of individual spot was analyzed using Quantity One 1-D Analysis Software (BIO-RAD, Marnes-la-Coquette, France).
ACKNOWLEDGMENTS The authors gratefully acknowledge the support and encouragement of  Pr. Jérôme Lamartine  ( Institut de Biologie et Chimie des Protéines ,  UMR5305-LBTICNRS , Lyon). We thank  Elise Malandain  and  Cyril Py  ( Centre Léon Bérard, Lyon, France ) for immunohistochemical stainings of human tissues,  Janine Papon  for experiments on mice,  Donia Amrouni  for immunohistochemical processing of mice tissues,  Alain Géloën  for adhesion assistance,  Béatrice Burdin  ( Center technologic Microstructures, Université Claude Bernard Lyon 1 ) and  Denis Ressnikoff  ( Faculté de médecine Lyon-Est, Université Claude Bernard Lyon 1 ) for microscopy assistance. We gratefully acknowledge  Drs Patrick Verrando  ( INRA-PACA, Sophia-Antipolis, France ) for his helpful critical comments on the manuscript.
profundus 500-1 and report the complete sequence here. Genome sequencing was performed mixing Illumina technology and Oxford Nanopore technology (ONT). First, a multiplexed overlapping paired-end library, with 546-bp insert size, was constructed and loaded on an Illumina MiSeq instrument (2 ϫ 300 bp). In parallel, genomic DNA was tagmented to create an ONT library following the manufacturer's recommendations. This library was loaded on MinION R9. 4 SpotON flow cells. The Illumina and ONT data, around 270-and 20-fold coverage, respectively, were assembled using SPAdes version 3. 6. 0 (http://cab. spbu. ru/software/spades/). An optical map of the D. profundus 500-1 genome was produced using an Argus system (OpGen). The annotation was performed using the Microscope platform  (5). The whole genome consists of a 4,168,905-bp chromosome and 2 circular plasmids of 42,836 bp and 6,167 bp.
The average GϩC contents for the DNA are 52. 83%, 50. 34%, and 45. 86%, respectively. A total of 4,008 coding DNA sequences (CDSs) were predicted for the chromosome, as well as 8 pseudogenes, 11 miscellaneous RNAs (misc-RNA), 3 rRNA operons, and 57 tRNA genes. A total of 43 CDSs and 1 misc-RNA were predicted for the largest plasmid, and 7 CDSs were predicted for the second plasmid. Among the NCBI Genomic Reference sequences, the top genome homologous to D. profundus 500-1 is that of D. piezophilus (GenBank accession no. FO203427  [6] ). Reciprocal best BLAST analysis indicated that D. profundus shares 2,823 orthologous proteins with D. piezophilus. Interestingly, repeated regions account for 10. 64% of the genome. By comparison, they represent only 2% in the genome of D. piezophilus. The 43 CDSs of the largest plasmid were all classified as unknown, but some of them presented similarities to transposases encoding genes.
Among the 7 CDSs of the smallest plasmid, 6 were classified as unknown and 1 as a putative 3-demethylubiquinol 3-O-methyltransferase. To our knowledge, the genome of D. profundus possesses the largest numbers of CDSs, plasmids, and repeated genomic regions reported for a marine Desulfovibrio species to date. It will be of interest to determine the part played by the genomic recombination events in the pressure adaptation capacities of D. profundus. Accession number(s). The final annotated genome of D. profundus is available in GenBank/EMBL under the accession no. LT907975 to LT907977 for the chromosome and the plasmids, respectively.
ACKNOWLEDGMENTS This work was supported by the  France Génomique National Infrastructure , funded as part of the  "Investissements d'Avenir" program  managed by the  Agence Nationale pour la Recherche  (contract  ANR-10-INBS-09 ). The  LABGeM (CEA, Institut de biologie François-Jacob-Genoscope & Université d'Evry & CNRS UMR8030 & Université Paris-Saclay)  is acknowledged for support within the MicroScope annotation platform.
Davies, Albert Einstein College of Medicine, Bronx, NY), phospho-tau S199 (PS199, 1 μg/ml, Invitrogen, Burlington, ON), phosphotau S202-T205 (AT8, 0. 8 μg/ml, Thermo-Fisher Scientific, Waltham, MA), MC-1 (1:100, gift of P. Davies), ALZ-50 (1:100, gift of P. Davies), or β-actin (0. 5 μg/ml, Sigma-Aldrich, Oakville, ON). Membranes were washed and incubated in peroxidase-linked donkey anti-mouse or donkey anti-rabbit antibodies (0. 5 μg/ml, GE Healthcare, Mississauga, ON). Blots were developed with a chemiluminescence reagent (ECL, Amersham Biosciences, Arlington Heights, IL) and exposed to X-OMAT imaging film (Eastman Kodak, Rochester, NY). Densitometry was performed on scanned autoradiographic films using the ImageJ software (http://imagej. nih. gov/ij/). Films were obtained from at least three independent western blots each carried out using retinal samples from different groups.
Interacting social and ecological processes shape productivity and sustainability of island small-scale fisheries (SSF). Understanding limits to productivity through historical catches help frame future expectations and management strategies, but SSF are dispersed and unaccounted, so long-term standardized data are largely absent for such analyses. We analysed 40 years of trade statistics of a SSF product that enter international markets (sea cucumber) from 14 Pacific Island Countries and Territories (PICT) against response variables to test predictors of fishery production: (i) scale, (ii) productivity and (iii) socio-economics. Combined production in PICT peaked over 20 years ago, driven by exploitation trends in Melanesia that accounted for 90% of all production since 1971. The size of island fisheries (as measured by total exports), and the duration and magnitude of fishery booms were most influenced by ungovernable environmental variables, in particular land area.
| Data sources and treatment Trade data from 14 PICT (Figure  1 ) were compiled from published sources, national fisheries and trade agencies, and from records collated by staff of the Pacific Community (SPC) (Table  S1 ). National records and management plans were used to determine when closures were in place and these records were supplemented with information from interviews with national fisheries officials, as appropriate. The data comprised total annual exports of beche-de-mer (dried sea cucumbers) for the period 1971-2013. Unless otherwise specified, all measures of weight in this study refer to dry weight in tonnes (t). For some countries, adjustments of data were necessary due to varying product types and presence of a domestic market. For example, French Polynesia exports both dry and frozen products.
| National sea cucumber production profiles Total exports (t dry weight) were used to create national profiles of production. From these profiles, metrics were derived to characterize national fisheries for further analyses (Table  1 ). Given the erratic production history of sea cucumber fisheries  (Anderson et al. , 2011) , we were particularly interested in volatility in catches (booms and busts in production). First, sums of country exports were accumulated as a measure of fishery size ("Exports"). Then, the coefficient of variance ("CV") for export data was calculated as a measure of overall variability in trade for each country. The upper confidence limit (Mean + 1. 96 × Standard Error) of national export data was calculated as a fishery-specific reference point to create further metrics from the export profiles.
cities database in world. maps package in R and great circle distance for each capital city to the equator calculated using the fossil package in R, as a measure of temperature and irradiance influencing productivity. All GIS data processing and area calculations were carried out using the ESRI ArcGIS Desktop version 10. 0. The SeaWiFS shallow bathymetry data initially in pgm format (http://netpbm. sourceforge. net/doc/ pgm. html; accessed 4 May 2017) were converted and rescaled into a table with "latitude," "longitude" and "depth" values and then interpolated using the "Point to Raster" function in the ArcGIS Geoprocessing Toolbox.
| Model development We adopted a "full subsets model selection" approach, in which models were compared using Akaike information criterion for small sample sizes (AICc), and AICc weight (ω i ) values  (Burnham & Anderson, 2002). To ensure the resulting models remained ecologically interpretable and to avoid overfitting with our relatively small sample size (14 PICT), we only fitted models with up to two predictor variables in a single model. Collinear models (predictors correlated by >|0. 30|, following  Graham, 2003)  were not included in the model set. All models were fitted using generalized additive models (GAM), via the gam function from the mgcv package in R  (Wood, 2006). GAM was adopted rather than linear or nonlinear parametric multiple regression to allow for possible nonlinear effects of predictors on the Fishery-specific reference point for elevated levels of trade within variation descriptor described as "normal" Upper limit of average trade within "normal" variation of trade data set.
The total population of each country was divided by the shallow water area as a measure of population pressure on available fishing grounds. For PNG, which has a high inland population compared to other PICT, the coastal population within a 5-km inland swathe was used; 2. The average Human Development Index (HDI) for available years between 1980 and 2013 was calculated from UNDP (2014), as a measure of national standard of living. For French Polynesia, Kiribati, Marshall Islands, Tuvalu and Wallis and Futuna, which were not included in UNDP (2014), single measurements of HDI were taken from Hastings (2009); 3. The per capita fish consumption was taken from the SPC National Minimum Development Indicator Database v2. 0 (www. spc. int/ nmdi/; accessed 4 May 2017) as a surrogate measure of reliance on coastal fisheries.
ACKNOWLEDGEMENTS Special thanks and recognition goes to the  Heads of Fisheries of SPC 's member countries that provided the data used in the analysis. We thank  Jason Benedict  for GIS work and  Shaun Wilson  for input on the manuscript. This study was undertaken as part of the  CGIAR Research Program on Fish Agrifood Systems (FISH)  and was funded by the  Australian Centre for International Agricultural Research (ACIAR)  project  FIS 2012-074  " Improving Community-based Fisheries Management in Pacific Island Countries ," and the  CGIAR Research Program on Aquatic Agricultural Systems.
1. The total population of each country was divided by the shallow water area as a measure of population pressure on available fishing grounds. For PNG, which has a high inland population compared to other PICT, the coastal population within a 5-km inland swathe was used; 2. The average Human Development Index (HDI) for available years between 1980 and 2013 was calculated from UNDP (2014), as a measure of national standard of living. For French Polynesia, Kiribati, Marshall Islands, Tuvalu and Wallis and Futuna, which were not included in UNDP (2014), single measurements of HDI were taken from Hastings (2009); 3. The per capita fish consumption was taken from the SPC National Minimum Development Indicator Database v2. 0 (www. spc. int/ nmdi/; accessed 4 May 2017) as a surrogate measure of reliance on coastal fisheries.
The following sample size and power considerations are made for an assumed noninferiority situation. Sample size calculations were performed with East 5 software package (Cytel; http://www. cytel. com/) comparing two groups. Assumed study duration timelines are under the alternative hypothesis, that is, treatment effects as specified in each sample size determination section below. • Assume a median PFS time of 11. 0 months for the control arm and an HR of 0. 88 or 13. 64% improvement in median PFS time to 12. 5 months for each of the experimental arms. • Assume a minimum median PFS as the noninferiority margin of 9. 35 months (15% decrease or HR, 1. 1765 or d = 0. 1765). • Assume a recruitment time of approximately 21 months (with ramp-up in the first 6 months) and a study duration time of 35.
Sample Size Determination for PFS Superiority (experimental arm comparisons: single agent T-DM1 v T-DM1 plus pertuzumab) The following sample size and power considerations are made for an assumed superiority situation. Sample size calculations were performed with East 5 software package (Cytel) comparing two groups: • Assume a median PFS time of 14. 7 months for single-agent T-DM1 and an HR of 0. 73 or 36. 99% improvement in median PFS time to 20. 1 months for T-DM1 plus pertuzumab. • Assume a recruitment time of approximately 21 months (with ramp-up in the first 6 months) and a study duration time of 33. 5 months to the required number of events under the alternative hypothesis. • Define 1. 25% one-sided (2. 5% two-sided) as the a level and require a power of 80%. • Request 2 3 364 = 728 patients with 392 PFS events (215 events expected for single-agent T-DM1 and 177 events for T-DM1 plus pertuzuab).
DFT Studies The density functional theory (DFT) computations were carried out using the B3LYP exchangecorrelation functional  [29, 30] , together with the 6-311++G(d,p)  [31]  basis set for all atoms except for iodine in which case the LanL2DZ ECP basis set was used  [32] [33] [34]. All computations were performed using the Gaussian 09 software suite  [35]  running on Gridchem  [36, 37]. The geometrical optimizations were performed in the gas phase as well as in dimethyl sulfoxide (DMSO). The solvent effect was taken into consideration based on the Polarizable Continuum Model (PCM)  [38, 39]. The tight criteria was used for the optimization and the frequency calculation was carried out to confirm the nature of the stationary points. In addition, the optimized structures in DMSO were used for computing chemical shifts with the Gauge-Including Atomic Orbital (GIAO) method  [40]  using shieldings of TMS computed at the same theoretical level and basis set.
Single X-ray Data Collection and Processing X-ray intensity data were determined on a Bruker Venture D8 Photon CMOS diffractometer (Bruker AXS, Madison, WI, USA) with graphite-monochromated MoKα1 (λ = 71073 Å) radiation at 173 K using an Oxford Cryostream 600 cooler. Data reduction was carried out using the program SAINT+, version 6. 02  [46]  and face-indexed  [47]  absorption corrections were made using the program XPREP  [47]. Space group assignments was made using XPREP  [47]. The structure was solved in the WinGX  [47]  suite of programs, using direct methods through using SHELXS-97  [48]  and refined using full-matrix least-squares/difference Fourier techniques on F 2 using SHELXL-97  [48]. Thereafter, the hydrogen atoms attached to the N atoms were located in the difference Fourier map and the coordinates and isotropic parameter refined freely.
Single X-ray Data Collection and Processing X-ray intensity data were determined on a Bruker Venture D8 Photon CMOS diffractometer (Bruker AXS, Madison, WI, USA) with graphite-monochromated MoKα 1 (λ = 71073 Å) radiation at 173 K using an Oxford Cryostream 600 cooler. Data reduction was carried out using the program SAINT+, version 6. 02  [46]  and face-indexed  [47]  absorption corrections were made using the program XPREP  [47]. Space group assignments was made using XPREP  [47]. The structure was solved in the WinGX  [47]  suite of programs, using direct methods through using SHELXS-97  [48]  and refined using full-matrix least-squares/difference Fourier techniques on F 2 using SHELXL-97  [48]. Thereafter, the hydrogen atoms attached to the N atoms were located in the difference Fourier map and the coordinates and isotropic parameter refined freely.
Acknowledgments: The authors are grateful for financial support on this project from the  University of South Africa (Unisa)  and the  National Research Foundation  (SA). DFT calculations used the  Extreme Science and Engineering Discovery Environment (XSEDE) , which is supported by  National Science Foundation  grant number  OCI-1053575. We also thank the  Molecular Sciences Institute of University of the Witwatersrand  for the X-ray data.
The Human Metabolome Database or HMDB (www. hmdb. ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4. 0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60.
INTRODUCTION The Human Metabolome Database (HMDB) is a comprehensive, freely available web resource containing detailed information about the human metabolome. The human metabolome represents the complete collection of small molecules found in the human body including peptides, lipids, amino acids, nucleic acids, carbohydrates, organic acids, biogenic amines, vitamins, minerals, food additives, drugs, cosmetics, contaminants, pollutants, and just about any other chemical that humans ingest, metabolize, catabolize or come into contact with  (1). Critical to the development of metabolomics (i. e. the study of metabolomes) has been the development of metabolomic databases  (2). Just as genomics and proteomics depend on reference sequences in GenBank  (3)  and UniProt (4) to annotate genes and proteins, metabolomics critically depends on having reference compound data and reference spectral data to annotate metabolites.
While many 'metabolism' databases exist, such as KEGG  (5) , Reactome  (6)  and the Cyc databases  (7) , relatively few true 'metabolomics' databases exist. Some of the better-known metabolomics databases include Metlin  (8) , MetaboLights  (9) , the Metabolomics Workbench  (10) , Lipid Maps  (11)  and the HMDB  (12). First released in 2007, the HMDB was one of the first and is currently the world's largest and most comprehensive, organism-specific metabolomic database. Designed to facilitate metabolomics research, the HMDB contains comprehensive, quantitative information about human metabolites along with their chemical structures, biological roles, physiological concentrations, disease associations, chemical reactions, transport mechanisms, metabolic pathways, and reference MS/MS (tandem mass spectrometry), GC-MS (gas chromatography mass spectrometry), and NMR (nuclear magnetic resonance) spectra.
lipid) renderings. Major improvements to the spectral viewing and spectral search tools, spectral data formats (compatible with SPLASH  (21) , mzML  (22)  and nmrML (www. nmrml. org)), chemical taxonomies and chemical ontologies  (23) , and text and structure searching/matching have also been made. Details regarding the HMDB's overall layout, navigation structure, data sources, curation protocols, data management system, and quality assurance criteria have been described previously  (14, 15). This manuscript focuses on the additions and enhancements made to create HMDB 4. 0.
Another major effort taken on by the HMDB curation team has been structure remediation. Structure remediation involves the standardization, correction or re-rendering of stereoisomers, the removal/correction of salt forms, the regularization of how charged group are displayed and the standardization of how certain molecular entities (amines, carboxylates, tertiary amines, aromatic groups, protonation states, etc. ) should be shown. Some of these corrections were done manually (via comparisons to other common rendering methods and other databases such as ChEBI  (31)  and PubChem (32)) while others were done automatically using specially developed in-house programs. For instance, many of the lipid structures in earlier versions of HMDB (esp. HMDB 3. 0) were drawn using commercial software packages that generated lipid structures with a 'squashed bug' appearance (see Figure  1 ).