cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3206287.v1
title: Sesamin inhibits lipopolysaccharide induced inflammation and extracellular matrix catabolism in rat intervertebral disc

description: Intervertebral disc (IVD) degeneration contributes to most spine degenerative diseases, while treatment retarding IVD degeneration is still in the experiment stage. Sesamin, a bioactive component extracted from sesame, has been reported to exert chondroprotective and anti-inflammatory effects. Here, we analyzed anti-inflammatory and anti-catabolic effects of sesamin on rat intervertebral disc in vitro and ex vivo. Results show that sesamin significantly inhibits the lipopolysaccharide (LPS) induced expression of catabolic enzymes (MMP-1, MMP-3, MMP-13, ADAMTS-4, ADAMTS-5), inflammation factors (IL-1β, TNF-α, iNOS, NO, COX-2, PGE2) in a dose-dependent manner in vitro. It is also proven that migration of macrophage induced by LPS can be inhibited by treatment of sesamin. Organ culture experiments demonstrate that sesamin protects disc from LPS induced depletion of extracellular matrix ex vivo. Moreover, sesamin suppresses LPS induced activation of MAPK pathway through inhibiting phosphorylation of JNK, which may be potential mechanism of the effects of sesamin. In light of our results, sesamin protects intervertebral disc from inflammation and extracellular matrix catabolism, exhibiting broad prospects in treatment of intervertebral disc degenerative diseases.
DOI: 10.5286/isis.e.rb1920547-3
title: Identifying the muon site in fluorine containing compounds

description: Fluorides form model systems with which we can test ideas about muon sites. We therefore propose a series of short experiments on well-defined fluoride systems that will be supported by a programme of DFT+mu; calculations and simulations of the nuclear-dipole coupling Hamiltonian to model the decoherent relaxation. Strongly bound F-mu-F states are favoured in alkali fluorides by the very electronegative nature of fluorine and the small ionic radius of the fluoride ion. But what if F is not in that state? What happens if fluorine happens to be part of a polyatomic anion so that the negative charge is shared between other components of the anion? In that case will the fluorine be a less attractive site for the muon? This experiment is designed to answer these questions by examining a series of carefully chosen compounds in which fluorine is incorporated as part of a more complex anion.
DOI: 10.6084/m9.figshare.3206233.v1
title: Serious Games and the Study of Society

description: The basic notion of a theory of serious games is that culture as an object of study can be described as a set of serious and non-serious games which involve its members in rule-governed and rule creating actions. The notion of “culture as serious game” is not presented as the ultimate explanatory tool, but rather as a description perhaps more apt than “culture as text” or “culture as drama.” Similarly, members of a culture can perhaps be better described as “players,” and “pawns” rather than as “agents” or “actors.” This brings to the fore the performative aspect of culture. The actual serious games that envelope us, the culture we belong to and others we encounter as “strangers,” are not strongly delimited by the theory of serious games. This theory provides the barest of form, a basis upon which any number of serious games, fantastic or not, can be (and have been) fashioned.
DOI: 10.6084/m9.figshare.3206062
title: Biomedical Abstract Meaning Representation as Linked Data

description: This provides the release of an RDF-based linked data translation of the bio-AMR-v0.8 data prepared by the L2K2R2 curation team (acknowledging the original curation work by ISI/USC and SDL, and released at http://amr.isi.edu/download.html).<br><br>This corpus includes annotations of cancer-related PubMed articles, covering 3 full papers (PMID:24651010, PMID:11777939, PMID:15630473) as well as the result sections of 46 additional PubMed papers. The corpus also includes about 1000 sentences each from the BEL BioCreative training corpus and the Chicago Corpus. The Bio AMR corpus is split into dev (500 snt.), training (5,452 snt.), test (500 snt.) sets and is available as RDF translations of core AMR data and automatically-aligned AMR data. <br><br>This release contains training, development and test files with an explanatory README file. We include a written note describing the differences between the Propbank and AMR representations used in this version.<br>UPDATE (10/11/2016). We have corrected some issues with grounding in the following two files:1. amr-bio-v2.grounded.txt<br>2. amr-bio-v2.grounded.rdfIn this, we reconfigured our automatic grounding service to resolve certain typed entities to URLs from UNIPROT, the Gene Ontology and PubChem and linked to the best matching candidate in all cases (rather than presenting the top five). <br>
DOI: 10.6084/m9.figshare.3205975
title: Reproductive Maturation in Geoduck clams (Panopea generosa)

description: This fileset includes a research paper describing reproductive maturation in geoduck clams with 200 images of gonadal histological sections and associated datasheets.<br>Female Staging Pictures* Images of each histology slide of female geoduck tissue samples taken with iPhone 5 camera* Labeling: fG##_s#_##x.jpg * f - female * G## - geoduck number * s# - reproductive maturation stage * ##x - magnification <br><br>Male Staging Pictures* Images of each histology slide of male geoduck tissue samples taken with iPhone 5 camera* Labeling: mG##_s#_##x.jpg * m - male * G## - geoduck number * s# - reproductive maturation stage * ##x - magnification<br>Data Spreadsheets* Female ReproMaturation Staging (.xlsx): lists each female geoduck (labeled Geo_##) under each reproductive maturation stage with the maturation parameters - average oocyte size (µ) and average follicle size (µ)* Male ReproMaturation Staging (.xlsx): lists each male geoduck (labeled Geo_##) under each reproductive maturation stage with the maturation parameters - percent composition of spermatids in acini and percent coverage of tissue sample of acini* Geoduck Data_MASTERSHEET: lists all data collected: sampling date, geoduck label, geoduck gender, reproductive maturation stage, weight prior to dissection (g), shell length (mm), gross examination notes, and whether hemolymph was sampled successfully<br>
DOI: 10.6084/m9.figshare.3205948
title: Fine atmospheric particles emitted by industrial, traffic and urban sources in France: characterization and genotoxicity

description: Health risks associated with inhalation of fine particulate matter of 2.5 µm in diameter or smaller depend on their atmospheric levels and physicochemical properties. The relationships between chemical compositions and genotoxic activities of particles emitted by mineral industries, traffic and urban sources during summer and winter in the region of Provence-Alpes-Côte d'Azur (France) were investigated. The fine particles were separated in respect to water-soluble (13 minerals and metals) and organic-extractable (16 polycyclic aromatic hydrocarbons) components that were quantified. The chromosome damaging properties of the hydrophilic and lipophilic extracts were assessed using the centromeric micronucleus assay on a human lung fibroblast cell line. The composition of the fine particulate matter was variable and depended upon the sources and seasons. Both the hydrophilic and lipophilic extracts induced chromosome damage: (1) in hydrophilic extracts, Ca and Zn affected chromosome losses induction; (2) acenapthylene affected chromosome damage (breakages and losses) induction and naphthalene affected chromosome damage and losses induction in lipophilic extracts without metabolic activation; and (3) benzo[a]pyrene affected chromosome losses induction in lipophilic extracts with metabolic activation. Fine particulate matter arising from coal-fired power station, road traffic, and other urban sources were the most efficient to induce chromosome breakage.
DOI: 10.6084/m9.figshare.3205948.v1
title: Fine atmospheric particles emitted by industrial, traffic and urban sources in France: characterization and genotoxicity

description: Health risks associated with inhalation of fine particulate matter of 2.5 µm in diameter or smaller depend on their atmospheric levels and physicochemical properties. The relationships between chemical compositions and genotoxic activities of particles emitted by mineral industries, traffic and urban sources during summer and winter in the region of Provence-Alpes-Côte d'Azur (France) were investigated. The fine particles were separated in respect to water-soluble (13 minerals and metals) and organic-extractable (16 polycyclic aromatic hydrocarbons) components that were quantified. The chromosome damaging properties of the hydrophilic and lipophilic extracts were assessed using the centromeric micronucleus assay on a human lung fibroblast cell line. The composition of the fine particulate matter was variable and depended upon the sources and seasons. Both the hydrophilic and lipophilic extracts induced chromosome damage: (1) in hydrophilic extracts, Ca and Zn affected chromosome losses induction; (2) acenapthylene affected chromosome damage (breakages and losses) induction and naphthalene affected chromosome damage and losses induction in lipophilic extracts without metabolic activation; and (3) benzo[a]pyrene affected chromosome losses induction in lipophilic extracts with metabolic activation. Fine particulate matter arising from coal-fired power station, road traffic, and other urban sources were the most efficient to induce chromosome breakage.
DOI: 10.6084/m9.figshare.3206062.v1
title: Biomedical Abstract Meaning Representation as Linked Data (v0.8.1)

description: This provides the release of an RDF-based linked data translation of the bio-AMR-v0.8 data prepared by the L2K2R2 curation team (acknowledging the original curation work by ISI/USC and SDL, and released at http://amr.isi.edu/download.html).<br><br>This corpus includes annotations of cancer-related PubMed articles, covering 3 full papers (PMID:24651010, PMID:11777939, PMID:15630473) as well as the result sections of 46 additional PubMed papers. The corpus also includes about 1000 sentences each from the BEL BioCreative training corpus and the Chicago Corpus. The Bio AMR corpus is split into dev (500 snt.), training (5,452 snt.), test (500 snt.) sets and is available as RDF translations of core AMR data and automatically-aligned AMR data. <br><br>This release contains training, development and test files with an explanatory README file. We include a written note describing the differences between the Propbank and AMR representations used in this version.
DOI: 10.6084/m9.figshare.3206062.v3
title: Biomedical Abstract Meaning Representation as Linked Data (v0.8.2)

description: This provides the release of an RDF-based linked data translation of the bio-AMR-v0.8 data prepared by the L2K2R2 curation team (acknowledging the original curation work by ISI/USC and SDL, and released at http://amr.isi.edu/download.html).<br><br>This corpus includes annotations of cancer-related PubMed articles, covering 3 full papers (PMID:24651010, PMID:11777939, PMID:15630473) as well as the result sections of 46 additional PubMed papers. The corpus also includes about 1000 sentences each from the BEL BioCreative training corpus and the Chicago Corpus. The Bio AMR corpus is split into dev (500 snt.), training (5,452 snt.), test (500 snt.) sets and is available as RDF translations of core AMR data and automatically-aligned AMR data. <br><br>This release contains training, development and test files with an explanatory README file. We include a written note describing the differences between the Propbank and AMR representations used in this version.<br>UPDATE (10/11/2016). We have corrected some issues with grounding in the following two files:1. amr-bio-v2.grounded.txt<br>2. amr-bio-v2.grounded.rdfIn this, we reconfigured our automatic grounding service to resolve certain typed entities to URLs from UNIPROT, the Gene Ontology and PubChem and linked to the best matching candidate in all cases (rather than presenting the top five). <br>
DOI: 10.6084/m9.figshare.3205942.v1
title: Dataset_Solid_Bodies_MRI

description: <b>Morphology-based Technique: MRI-only Approach for Joint Kinematics Assessment </b>
DOI: 10.6084/m9.figshare.3206062.v2
title: Biomedical Abstract Meaning Representation as Linked Data (v0.8.1)

description: This provides the release of an RDF-based linked data translation of the bio-AMR-v0.8 data prepared by the L2K2R2 curation team (acknowledging the original curation work by ISI/USC and SDL, and released at http://amr.isi.edu/download.html).<br><br>This corpus includes annotations of cancer-related PubMed articles, covering 3 full papers (PMID:24651010, PMID:11777939, PMID:15630473) as well as the result sections of 46 additional PubMed papers. The corpus also includes about 1000 sentences each from the BEL BioCreative training corpus and the Chicago Corpus. The Bio AMR corpus is split into dev (500 snt.), training (5,452 snt.), test (500 snt.) sets and is available as RDF translations of core AMR data and automatically-aligned AMR data. <br><br>This release contains training, development and test files with an explanatory README file. We include a written note describing the differences between the Propbank and AMR representations used in this version.<br>UPDATE (10/11/2016). We have corrected some issues with grounding in the following two files:1. amr-bio-v2.grounded.txt<br>2. amr-bio-v2.grounded.rdfIn this, we reconfigured our automatic grounding service to resolve certain typed entities to URLs from UNIPROT, the Gene Ontology and PubChem and linked to the best matching candidate in all cases (rather than presenting the top five). <br>
DOI: 10.6084/m9.figshare.3205891
title: My recent Twitter Analytics reports (especially for UC Davis communications group)

description: My Twitter analytics downloads. Posted to save UC Davis some money they are paying to outside groups to watch Twitter.
DOI: 10.6084/m9.figshare.3205891.v1
title: My recent Twitter Analytics reports (especially for UC Davis communications group)

description: My Twitter analytics downloads. Posted to save UC Davis some money they are paying to outside groups to watch Twitter.
DOI: 10.6084/m9.figshare.3205750
title: A genome wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

description: Demultiplexed raw Illumina HISEQ-2500 100 base pair single end reads, barcodes removed leaving 96 base pair including RAD (NDE1) cut site.<br>
DOI: 10.6084/m9.figshare.3205723
title: Additional file (1)_Data.xlsx

description: dataset included demographic characteristics and body indices of study subjects<br>
DOI: 10.6084/m9.figshare.3205684
title: CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences

description: Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often “optimized” as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in <i>Escherichia coli</i>, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education
DOI: 10.6084/m9.figshare.3205723.v2
title: Additional file (1)_Data.xlsx

description: dataset included demographic characteristics and body indices of study subjects<br>
DOI: 10.6084/m9.figshare.3205723.v1
title: Additional file (1)_Data(H.pylori).xlsx

description: dataset included demographic characteristics and body indices of study subjects<br>
DOI: 10.6084/m9.figshare.3205552
title: fMRI to intraneural microstimulation of single mechanoreceptive afferents

description: fMRI raw time series acquired during intranerual microstimulation (INMS) of single mechanoreceptive units (11 datasets, named U1_INMS.nii.gz etc..). fMRI raw time series acquired during vibrotactile stimulation to the corresponding unit's receptive field (U1_vibrotactile.nii.gz etc ...). Structural whole head MRI scans for 4 participants for which fMRI data was acquired. Full description of the type of mechanoreceptive units stimulated during fMRI per subject, paradigm used, etc .. can be found in the following paper: Sanchez Panchuelo RM, Ackerley R, Glover PM, Bowtell RW, Westberg J, Francis ST & McGlone F, "Mapping quantal touch using 7 Tesla functional magnetic resonance imaging and single-unit intraneural microstimulation" eLife, 2016;10.7554/eLife.12812.
DOI: 10.6084/m9.figshare.3205522
title: IGUANA forum

description: Forum: https://groups.google.com/d/forum/iguana-aksw <br>Mailing List: iguana-aksw@googlegroups.com <br>
DOI: 10.6084/m9.figshare.3205507
title: IGUANA website

description: IGUANA is a generic Benchmark execution Framwork for read and write from/to triple stores<br>
DOI: 10.6084/m9.figshare.3205522.v1
title: IGUANA forum

description: Forum: https://groups.google.com/d/forum/iguana-aksw <br>Mailing List: iguana-aksw@googlegroups.com <br>
DOI: 10.6084/m9.figshare.3205486
title: Warmup: SWDF

description: Warmup queries for the SWDF data set<br>
DOI: 10.6084/m9.figshare.3205483
title: Script: Pre and Post script

description: Script to execute pre and post work in IGUANA<br>
DOI: 10.6084/m9.figshare.3205489
title: Warmup: DBpedia

description: Warmup Queries for the DBpedia dataset<br>
DOI: 10.6084/m9.figshare.3205507.v2
title: IGUANA website

description: IGUANA is a generic Benchmark execution Framwork for read and write from/to triple stores<br>
DOI: 10.6084/m9.figshare.3205486.v1
title: Warmup: SWDF

description: Warmup queries for the SWDF data set<br>
DOI: 10.6084/m9.figshare.3205489.v1
title: Warmup: DBpedia

description: Warmup Queries for the DBpedia dataset<br>
DOI: 10.6084/m9.figshare.3205474
title: Queries: SWDF

description: 250 Benchmark queries for the SWDF dataset<br>
DOI: 10.6084/m9.figshare.3205477
title: Queries: DBpedia

description: 250 Benchmark queries for the DBpedia dataset<br>
DOI: 10.6084/m9.figshare.3205483.v1
title: Script: Pre and Post script

description: Script to execute pre and post work in IGUANA<br>
DOI: 10.6084/m9.figshare.3205468
title: Changesets: SWDF

description: Changesets for the SWDF dataset<br>
DOI: 10.6084/m9.figshare.3205465
title: Configuration: DBpedia 100%

description: Configuration file for the DBpedia 100% dataset<br>
DOI: 10.6084/m9.figshare.3205471
title: Changesets: DBpedia

description: Changesets for the DBpedia dataset<br>
DOI: 10.6084/m9.figshare.3205462
title: Configuration: DBpedia 50%

description: Configuration file for the DBpedia 50% dataset
DOI: 10.6084/m9.figshare.3205468.v1
title: Changesets: SWDF

description: Changesets for the SWDF dataset<br>
DOI: 10.6084/m9.figshare.3205459
title: Configuration DBpedia 10%

description: Configuration file for the DBpedia 10% dataset
DOI: 10.6084/m9.figshare.3205465.v1
title: Configuration: DBpedia 100%

description: Configuration file for the DBpedia 100% dataset<br>
DOI: 10.6084/m9.figshare.3205462.v1
title: Configuration: DBpedia 50%

description: Configuration file for the DBpedia 50% dataset
DOI: 10.6084/m9.figshare.3205471.v1
title: Changesets: DBpedia

description: Changesets for the DBpedia dataset<br>
DOI: 10.6084/m9.figshare.3205456
title: Configuration: SWDF

description: Configuration file for the SWDF dataset
DOI: 10.6084/m9.figshare.3205459.v1
title: Configuration DBpedia 10%

description: Configuration file for the DBpedia 10% dataset
DOI: 10.6084/m9.figshare.3205441
title: Benchmark Results: SWDF

description: Results of the IGUANA Benchmark in 2015/16 for the Semantic Web Dog Food (SWDF) dataset<br>
DOI: 10.6084/m9.figshare.3205438
title: Benchmark Results: DBpedia 10%

description: Results of the IGUANA Benchmark in 2015/16 for the truncated DBpedia dataset. The dataset is 10% of the initial 100% dataset.<br>
DOI: 10.6084/m9.figshare.3205435
title: Benchmark Results: DBpedia 50%

description: Results of the IGUANA Benchmark in 2015/16 for the truncated DBpedia dataset. The dataset is 50% of the initial 100% dataset.
DOI: 10.6084/m9.figshare.3205432
title: Benchmark Results: DBpedia 100%

description: Results of the IGUANA Benchmark in 2015/16 for the initial 100% DBpedia dataset.
DOI: 10.6084/m9.figshare.3205438.v1
title: Benchmark Results: DBpedia 10%

description: Results of the IGUANA Benchmark in 2015/16 for the truncated DBpedia dataset. The dataset is 10% of the initial 100% dataset.<br>
DOI: 10.6084/m9.figshare.3205420
title: DICOM files TC study

description: DICOM files of TC study.<br><br>To unzip use 7zip<br>http://7-zip.org/<br>
DOI: 10.6084/m9.figshare.3205432.v1
title: Benchmark Results: DBpedia 100%

description: Results of the IGUANA Benchmark in 2015/16 for the initial 100% DBpedia dataset.
DOI: 10.6084/m9.figshare.3205273
title: In vivo imaging of dendritic pruning in dentate granule cells

description: Data files of the dendritic arbors of all neurons imaged for the following publication:<br>Gonçalves J.T., Bloyd C.W., Shtrahman M, Johnston S.T., Schafer S.T., Parylak S.L., Thanh T., Chang T., Gage F.H., In vivo imaging of dendritic pruning in dentate granule cells, Nature Neurosci.,<i> </i><i>in press, doi:10.1038/nn.4301 </i>(2016)<br><b>Abstract:</b>We longitudinally imaged the developing dendrites of adult-born mouse dentate granule cells (DGCs) in vivo and found that they underwent over-branching and pruning. Exposure to an enriched environment and constraint of dendritic growth by disrupting Wnt signaling led to increased branch addition and accelerated growth, which were, however, counteracted by earlier and more extensive pruning. Our results indicate that pruning is regulated in a homeostatic fashion to oppose excessive branching and promote a similar dendrite structure in DGCs.<br>
DOI: 10.6084/m9.figshare.3205285
title: Shading impacts by coastal infrastructure on biological communities from subtropical rocky shores

description: Dataset refers to André L. Pardal-Souza's master thesis. Those data were used on writing a manuscript which will be published on Journal of Applied Ecology.
DOI: 10.6084/m9.figshare.3205453.v2
title: IGUANA Stresstest overview

description: Overview of the Stresstest implemented in IGUANA<br>
DOI: 10.6084/m9.figshare.3205285.v2
title: Shading impacts by coastal infrastructure on biological communities from subtropical rocky shores

description: Dataset refers to André L. Pardal-Souza's master thesis. Those data were used on writing a manuscript which will be published on Journal of Applied Ecology.
DOI: 10.6084/m9.figshare.3205273.v1
title: In vivo imaging of dendritic pruning in dentate granule cells

description: Data files of the dendritic arbors fof all neurons used in analysis for the following publication:<br>Gonçalves J.T., Bloyd C.W., Shtrahman M, Johnston S.T., Schafer S.T., Parylak S.L., Thanh T., Chang T., Gage F.H., In vivo imaging of dendritic pruning in dentate granule cells, Nature Neurosci.,<i> </i><i>in press, doi:10.1038/nn.4301 </i>(2016)<br><b>Abstract:</b>We longitudinally imaged the developing dendrites of adult-born mouse dentate granule cells (DGCs) in vivo and found that they underwent over-branching and pruning. Exposure to an enriched environment and constraint of dendritic growth by disrupting Wnt signaling led to increased branch addition and accelerated growth, which were, however, counteracted by earlier and more extensive pruning. Our results indicate that pruning is regulated in a homeostatic fashion to oppose excessive branching and promote a similar dendrite structure in DGCs.