cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3803037.v1
title: Genome-wide DNA methylation patterns in CD4+ T cells from Chinese Han patients with rheumatoid arthritis

description: <i>Introduction</i>: Rheumatoid arthritis (RA) is an autoimmune disease that causes chronic inflammation of the joints. Recent evidence indicated the epigenetic changes may contribute to the pathogenesis of RA. <i>Method</i>: To understand the extent and nature of dysregulated DNA methylation in RA CD4T cells, we performed a genome-wide DNA methylation study in CD4 + T cells in 12 RA patients compared to 12 matched normal healthy controls. Cytosine methylation status was quantified with Illumina methylation 450K microarray. <i>Result</i>: The DNA methylation profiling showed 383 hyper- and 785 hypo-methylated genes in the CD4 + T cells of the RA patients (<i>p</i> −7). Gene ontology analysis indicated transcript alternative splicing and protein modification mediated by DNA methylation might play an important role in the pathogenesis of RA. In addition, the result showed that human leukocyte antigen (HLA) region including <i>HLA-DRB6</i>, <i>HLA-DQA1</i> and <i>HLA-E</i> was frequently hypomethylated, but <i>HLA-DQB1</i> hypermethylated in CpG island region and hypomethylated in CpG shelf region in RA patients. Outside the MHC region, <i>HDAC4</i>, <i>NXN</i>, <i>TBCD</i> and <i>TMEM61</i> were the most hypermethylated genes, while <i>ITIH3</i>, <i>TCN2</i>, <i>PRDM16</i>, <i>SLC1A5</i> and <i>GALNT9</i> are the most hypomethylated genes. <i>Conclusion</i>: Genome-wide DNA methylation profile revealed significant DNA methylation change in CD4 + T cells from patients with RA.
DOI: 10.6084/m9.figshare.3803025
title: PUPPI simulation files

description: The datasets are the simulated datasets used for type I error and power studies in the paper. Lin PL, Yu YW, Chung RH. Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases. 2016. PLOS ONE. In Press.
DOI: 10.6084/m9.figshare.3803025.v1
title: PUPPI simulation files

description: The datasets are the simulated datasets used for type I error and power studies in the paper. Lin PL, Yu YW, Chung RH. Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases. 2016. PLOS ONE. In Press.
DOI: 10.6084/m9.figshare.3799503
title: Selective Reporting Bias in Neurology. Project date: 06/01/16-07/01/16

description: Working data sheet for entire project. Included are inclusion/exclusion form with criteria. Data extraction sheets from SRDR.
DOI: 10.6084/m9.figshare.3799497
title: SC-Poster.pdf

description: Seismic imaging, used in energy exploration, is arguably the most compute and data intensive application in the private sector. The commonly used methods involve solving the wave equations numerically using finite difference formulations. Writing optimised code for these applications involves multiple man-years of effort that needs to be repeated every time a new development needs to be factored in – for every target platform. <br><br>DeVito is a new tool for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. The application developer needs to provide a differential equation in symbolic form. DeVito performs automated code generation and Just-In-time (JIT) compilation based on this symbolic equation to create and execute highly optimised Finite Difference kernels on multiple computer platforms. DeVito has been designed to be used as part of complex workflows involving data flows across multiple applications over different nodes of a cluster.
DOI: 10.6084/m9.figshare.3799497.v1
title: SC-Poster.pdf

description: Seismic imaging, used in energy exploration, is arguably the most compute and data intensive application in the private sector. The commonly used methods involve solving the wave equations numerically using finite difference formulations. Writing optimised code for these applications involves multiple man-years of effort that needs to be repeated every time a new development needs to be factored in – for every target platform. <br><br>DeVito is a new tool for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. The application developer needs to provide a differential equation in symbolic form. DeVito performs automated code generation and Just-In-time (JIT) compilation based on this symbolic equation to create and execute highly optimised Finite Difference kernels on multiple computer platforms. DeVito has been designed to be used as part of complex workflows involving data flows across multiple applications over different nodes of a cluster.
DOI: 10.6084/m9.figshare.3799494
title: plos_one_data.csv.gz

description: This dataset is a subset of the Audiological and Genetic Database (AudGenDB), a public, de-identified research database derived from electronic health records (EHR). AudGenDB is intended to be a data resource that represents a population enriched for hearing loss research. The complete AudGenDB can be accessed at http://audgendb.chop.edu<br><br>This subset is obtained by applying the following exclusion criteria: (1) Only audiogram tests documenting the specific ear tested (‘left’, ‘right’, or ‘soundfield’) are included; (2) Only <br>bone-conduction tests are included; (3) Tests outside the frequency range of interest (500Hz, 1KHz, 2KHz, and 4KHz) were excluded; (4) Response thresholds recorded as 0 decibels were removed as they typically indicate a failed test attempt; (5) Patients with fewer than 4 tests across all frequencies of interest were also excluded in order to enable <br>a 4-fold cross-validation procedure (described in more detail below); (6) Finally, test results recorded outside the age range of 0 to 21 were also removed in order to focus on a pediatric population. <br><br>This dataset is uploaded for PLOS One publication <i>Latent Patient Cluster Discovery for Robust Future<br>Forecasting and New-patient Generalization</i><br>
DOI: 10.6084/m9.figshare.3799452
title: Changes in Relative Systemic Contentiousness Between Periods 1950-1970 and 1980-2000

description: Author's analysis of data from Banks and Wilson. Relative systemic contentiousness refers to the proportion of all contentious events that are anti-systemic (the number of riots and guerrilla wars as a proportion of riots, guerrilla wars, demonstrations, and strikes).
DOI: 10.6084/m9.figshare.3799452.v1
title: Changes in Relative Systemic Contentiousness Between Periods 1950-1970 and 1980-2000

description: Author's analysis of data from Banks and Wilson. Relative systemic contentiousness refers to the proportion of all contentious events that are anti-systemic (the number of riots and guerrilla wars as a proportion of riots, guerrilla wars, demonstrations, and strikes).
DOI: 10.6084/m9.figshare.3799449
title: Aggregate Support for Revolutionary Change Across Seven European Countries

description: Author's analysis of raw data from the Eurobarometer trend file. The nine countries are France, Italy, Belgium, Netherlands, Germany, Luxembourg, and Netherlands. Countries with shorter time-series were excluded. The United Kingdom and Ireland are excluded because of the conflict over Northern Ireland.
DOI: 10.6084/m9.figshare.3799449.v1
title: Aggregate Support for Revolutionary Change Across Seven European Countries

description: Author's analysis of raw data from the Eurobarometer trend file. The nine countries are France, Italy, Belgium, Netherlands, Germany, Luxembourg, and Netherlands. Countries with shorter time-series were excluded. The United Kingdom and Ireland are excluded because of the conflict over Northern Ireland.
DOI: 10.6084/m9.figshare.3799422
title: 27f/1392r sheared soil amplicons for EMIRGE

description: We extracted DNA from 6 soils and used the 27f/1392r primer pair to amplify near full-length 16S rRNA genes. The amplicons were sheared using the Covaris M220 (Covaris, Woburn, MA) and gene libraries were prepared using TruSeq DNA LT library preparation kits (Illumina, San Diego, CA). Samples were pooled and sequenced on an Illumina MiSeq (2x300bp) at the University of Colorado Next Generation Sequencing Facility.<br>We used these raw sequences to re-assemble the near full length 16S rRNA amplicon using EMIRGE.
DOI: 10.6084/m9.figshare.3799305.v1
title: "The Daily Exchange Quotations" - An Address Delivered by C.S. Addiss before the Foreign Y.M.C.A at Shanghai on Feb. 4th, 1903. Courtesy of the Toyo Bunko 東洋文庫, http://www.toyo-bunko.or.jp/

description: This concerns an Address Delivered by C.S. Addiss before the Foreign Y.M.C.A at Shanghai on Feb. 4th, 1903. Addiss discusses, in vernacular terms, a host of issues related to the foreign exchange business: the mint par of gold, the theory of exchange, ...
DOI: 10.6084/m9.figshare.3799305.v2
title: "The Daily Exchange Quotations" - An Address Delivered by C.S. Addis before the Foreign Y.M.C.A at Shanghai on Feb. 4th, 1903. Courtesy of the Toyo Bunko 東洋文庫, http://www.toyo-bunko.or.jp/

description: This concerns an Address Delivered by C.S. Addiss before the Foreign Y.M.C.A at Shanghai on Feb. 4th, 1903. Addiss discusses, in vernacular terms, a host of issues related to the foreign exchange business: the mint par of gold, the theory of exchange, ...
DOI: 10.6084/m9.figshare.3799251
title: Mozilla Science Lab Mid-Year Report (2016)

description: Mozilla Science Lab's 2016 mid-year report.<br>
DOI: 10.6084/m9.figshare.3799251.v1
title: Mozilla Science Lab Mid-Year Report (2016)

description: Mozilla Science Lab's 2016 mid-year report.<br>
DOI: 10.6084/m9.figshare.3799182
title: Using Demographic Analyses to Evaluate the Impact of Man-made Disasters on Imperiled Species: Piping Plovers and the Deepwater Horizon Oil Spill

description: Even in the presence of environmental safeguards, catastrophic accidents related to anthropogenic activities occur that can result in both immediate and chronic impacts on local biota. However, due to the unplanned nature of catastrophes, studies aimed to identify the effects of these accidents on an ecosystem and its inhabitants often have imperfect study designs that are reactive rather than proactive, resulting in methodological and analytical challenges. On 20 April 2010, following an explosion on the Deepwater Horizon, a well blowout occurred on the seafloor approximately 80 km off the Louisiana coast in the Gulf of Mexico. This blowout resulted in the largest marine oil spill in United States history, which impacted critical migratory stopover and overwintering habitat for many seabird and shorebird species, including species of high conservation concern such as the piping plover (<i>Charadrius melodus</i>). Here, we assessed the potential short-term and carry-over demographic impacts of the Deepwater Horizon oil spill on piping plovers in a capture-mark-recapture framework. We examined whether a series of demographic processes, including probabilities of remaining at a specific wintering site, over-winter and annual apparent survival, winter stopover duration, and abundance varied among oiled and unoiled habitats. We found that the perceived amount of oiling on land, in water, and on individual birds, as well as numerous demographic processes, were spatially or temporally variable. However, we found no support that piping plover demography was negatively influenced by the magnitude of oil observed at an impacted area, or that demographic rates substantially varied between reference and oil impacted areas. Nor did we find that piping plovers that were observed to be oiled had lower survival probabilities following the DWH oil spill relative to non-oiled individuals from the same winter population. Although we did not find that the Deepwater Horizon oil spill substantially influenced piping plovers, our methods provide an analytical framework to more appropriately address both the short or long-term impacts of an anthropogenic disturbance on a species.<b>Data from:</b><b>Gibson, D</b>., D.H. Catlin, K.L. Hunt, J. D. Fraser, S. Karpanty, M.J. Friedrich, M.K. Bimbi, J. B. Cohen, and S.B. Maddock (in review). Using Demographic Analyses to Evaluate the Impact of Man-made Disasters on Imperiled Species: Piping Plovers and the Deepwater Horizon Oil Spill
DOI: 10.6084/m9.figshare.3799182.v1
title: Using Demographic Analyses to Evaluate the Impact of Man-made Disasters on Imperiled Species: Piping Plovers and the Deepwater Horizon Oil Spill

description: Even in the presence of environmental safeguards, catastrophic accidents related to anthropogenic activities occur that can result in both immediate and chronic impacts on local biota. However, due to the unplanned nature of catastrophes, studies aimed to identify the effects of these accidents on an ecosystem and its inhabitants often have imperfect study designs that are reactive rather than proactive, resulting in methodological and analytical challenges. On 20 April 2010, following an explosion on the Deepwater Horizon, a well blowout occurred on the seafloor approximately 80 km off the Louisiana coast in the Gulf of Mexico. This blowout resulted in the largest marine oil spill in United States history, which impacted critical migratory stopover and overwintering habitat for many seabird and shorebird species, including species of high conservation concern such as the piping plover (<i>Charadrius melodus</i>). Here, we assessed the potential short-term and carry-over demographic impacts of the Deepwater Horizon oil spill on piping plovers in a capture-mark-recapture framework. We examined whether a series of demographic processes, including probabilities of remaining at a specific wintering site, over-winter and annual apparent survival, winter stopover duration, and abundance varied among oiled and unoiled habitats. We found that the perceived amount of oiling on land, in water, and on individual birds, as well as numerous demographic processes, were spatially or temporally variable. However, we found no support that piping plover demography was negatively influenced by the magnitude of oil observed at an impacted area, or that demographic rates substantially varied between reference and oil impacted areas. Nor did we find that piping plovers that were observed to be oiled had lower survival probabilities following the DWH oil spill relative to non-oiled individuals from the same winter population. Although we did not find that the Deepwater Horizon oil spill substantially influenced piping plovers, our methods provide an analytical framework to more appropriately address both the short or long-term impacts of an anthropogenic disturbance on a species.<b>Data from:</b><b>Gibson, D</b>., D.H. Catlin, K.L. Hunt, J. D. Fraser, S. Karpanty, M.J. Friedrich, M.K. Bimbi, J. B. Cohen, and S.B. Maddock (in review). Using Demographic Analyses to Evaluate the Impact of Man-made Disasters on Imperiled Species: Piping Plovers and the Deepwater Horizon Oil Spill
DOI: 10.6084/m9.figshare.3798861
title: Phylogenetic Dataset Scrobicularia plana

description: Alignment used for phylogenetic reconstruction: Scrobicularia plana<br>
DOI: 10.6084/m9.figshare.3798861.v1
title: Phylogenetic Dataset Scrobicularia plana

description: Alignment used for phylogenetic reconstruction: Scrobicularia plana<br>
DOI: 10.6084/m9.figshare.3798858
title: Phylogenetic Dataset Yoldia hyperborea

description: Alignment used for phylogenetic reconstruction: Yoldia hyperborea<br>
DOI: 10.6084/m9.figshare.3798858.v1
title: Phylogenetic Dataset Yoldia hyperborea

description: Alignment used for phylogenetic reconstruction: Yoldia hyperborea<br>
DOI: 10.6084/m9.figshare.3798822
title: Phylogenetic Dataset Amino acid

description: Amino acid alignment used to produce phylogenies<br>
DOI: 10.6084/m9.figshare.3798822.v2
title: Phylogenetic Dataset Amino acid

description: Amino acid alignment used to produce phylogenies<br>
DOI: 10.6084/m9.figshare.3798822.v1
title: Phylogenetic data set 2

description: Amino acid alignment used to produce phylogenies<br>
DOI: 10.6084/m9.figshare.3798789
title: Phylogenetic Dataset Nucleotide.fas

description: Nucleotide alignment used to produce phylogenies<br>
DOI: 10.6084/m9.figshare.3798789.v1
title: Phylogenetic Dataset Nucleotide.fas

description: Nucleotide alignment used to produce phylogenies<br>
DOI: 10.15156/bio/sh122694.07fu
title: SH122694.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh122695.07fu
title: SH122695.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh122696.07fu
title: SH122696.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh122697.07fu
title: SH122697.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh122698.07fu
title: SH122698.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh122699.07fu
title: SH122699.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.