cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4986194
title: Supplementary Material for: Long-Term Neuropathological Changes Associated with Cerebral Palsy in a Nonhuman Primate Model of Hypoxic-Ischemic Encephalopathy

description: <b><i>Background:</i></b> Cerebral palsy (CP) is the most common motor disability in childhood, with a worldwide prevalence of 1.5-4/1,000 live births. Hypoxic-ischemic encephalopathy (HIE) contributes to the burden of CP, but the long-term neuropathological findings of this association remain limited. <b><i>Methodology:</i></b> Thirty-four term <i>Macaca nemestrina</i> macaques were included in this long-term neuropathological study: 9 control animals delivered by cesarean section and 25 animals with perinatal asphyxia delivered by cesarean section after 15-18 min of umbilical cord occlusion (UCO). UCO animals were randomized to saline (<i>n</i> = 11), therapeutic hypothermia (TH; <i>n</i> = 6), or TH + erythropoietin (Epo; <i>n</i> = 8). Epo was given on days 1, 2, 3, and 7. Animals had serial developmental assessments and underwent magnetic resonance imaging with diffusion tensor imaging at 9 months of age followed by necropsy. Histology and immunohistochemical (IHC) staining of brain and brainstem sections were performed. <b><i>Results:</i></b> All UCO animals demonstrated and met the standard diagnostic criteria for human neonates with moderate-to-severe HIE. Four animals developed moderate-to-severe CP (3 UCO and 1 UCO + TH), 9 had mild CP (2 UCO, 3 UCO + TH, 3 UCO + TH + Epo, and 1 control), and 2 UCO animals died. None of the animals treated with TH + Epo died, had moderate-to-severe CP, or demonstrated signs of long-term neuropathological toxicity. Compared to animals grouped together as having no CP (no-CP; controls and mild CP only), animals with CP (moderate and severe) demonstrated decreased fractional anisotropy of multiple white-matter tracts including the corpus callosum and internal capsule, when using Tract-Based Spatial Statistics (TBSS). Animals with CP had decreased staining for cortical neurons and increased brainstem glial scarring compared to animals without CP. The cerebellar cell density of the internal granular layer and white matter was decreased in CP animals compared to that in control animals without CP. <b><i>Conclusions/Significance:</i></b> In this nonhuman primate HIE model, animals treated with TH + Epo had less brain pathology noted on TBSS and IHC staining, which supports the long-term safety of TH + Epo in the setting of HIE. Animals that developed CP showed white-matter changes noted on TBSS, subtle histopathological changes in both the white and gray matter, and brainstem injury that correlated with CP severity. This HIE model may lend itself to further study of the relationship between brainstem injury and CP.
DOI: 10.6084/m9.figshare.4986368.v3
title: Complex alignment dataset on conference organisation

description: This dataset is composed of 3 ontologies of the OAEI conference Track dataset : cmt, conference and edas.<br>The alignments between these ontologies were manually created.<br>The coherence of the alignments was verified by merging the ontologies pair-wise. The merged ontologies are available.<br>The alignments are available in FOL (.txt) and in EDOAL (.edoal), an extension of the Alignment format used in the Alignment API.<br><br><b>Useful links:</b><br>EDOAL : http://alignapi.gforge.inria.fr/edoal.html<br>OAEI : http://oaei.ontologymatching.org/<br>Alignment API : http://alignapi.gforge.inria.fr/<br>Conference Track : http://oaei.ontologymatching.org/2016/conference/index.html<br>
DOI: 10.6084/m9.figshare.4986170
title: Microwave-activated carbons from tucumã (<i>Astrocaryum aculeatum</i>) seed for efficient removal of 2-nitrophenol from aqueous solutions

description: Activated carbons (ACs) prepared from tucumã seed (<i>Astrocaryum aculeatum</i>) were used for 2-nitrophenol removal from aqueous solutions. The ACs were characterized by elemental analysis, FTIR, <i>N</i><sub>2</sub> adsorption/desorption isotherms, TGA, hydrophobicity/hydrophilicity balance, and total of acidic and basic groups. The ACs showed to have hydrophilic surfaces and they presented high specific surface areas (up to 1318 m<sup>2</sup> g<sup>−1</sup>). In batch optimization studies, maximum removal was obtained at pH 7, contact time of 30 min, adsorbent dosage 1.5 gL<sup>−1</sup> and temperature of 50°C. The general-order kinetic model and Liu isotherm model best fit the kinetic and equilibrium adsorption data with a maximum adsorption capacity of 1382 mg g<sup>−1</sup> at 50°C. Effect of temperature and thermodynamic studies revealed that the adsorption processes of 2-nitrophenol onto ACs are dependent on temperature and are exothermic and spontaneous, respectively. About the applicability of the ACs for treating simulated effluents, the tucumã seed-activated carbon showed an excellent outcome in the treatment of simulated effluents, evidencing its high efficiency for phenolic compound adsorption. Tucumã seed-ACs showed to be cost effective and highly efficient adsorbents for efficient removal of 2-nitrophenol from aqueous solutions.
DOI: 10.6084/m9.figshare.4986170.v1
title: Microwave-activated carbons from tucumã (<i>Astrocaryum aculeatum</i>) seed for efficient removal of 2-nitrophenol from aqueous solutions

description: Activated carbons (ACs) prepared from tucumã seed (<i>Astrocaryum aculeatum</i>) were used for 2-nitrophenol removal from aqueous solutions. The ACs were characterized by elemental analysis, FTIR, <i>N</i><sub>2</sub> adsorption/desorption isotherms, TGA, hydrophobicity/hydrophilicity balance, and total of acidic and basic groups. The ACs showed to have hydrophilic surfaces and they presented high specific surface areas (up to 1318 m<sup>2</sup> g<sup>−1</sup>). In batch optimization studies, maximum removal was obtained at pH 7, contact time of 30 min, adsorbent dosage 1.5 gL<sup>−1</sup> and temperature of 50°C. The general-order kinetic model and Liu isotherm model best fit the kinetic and equilibrium adsorption data with a maximum adsorption capacity of 1382 mg g<sup>−1</sup> at 50°C. Effect of temperature and thermodynamic studies revealed that the adsorption processes of 2-nitrophenol onto ACs are dependent on temperature and are exothermic and spontaneous, respectively. About the applicability of the ACs for treating simulated effluents, the tucumã seed-activated carbon showed an excellent outcome in the treatment of simulated effluents, evidencing its high efficiency for phenolic compound adsorption. Tucumã seed-ACs showed to be cost effective and highly efficient adsorbents for efficient removal of 2-nitrophenol from aqueous solutions.
DOI: 10.6084/m9.figshare.4986368.v4
title: Complex alignment dataset on conference organisation

description: This dataset presents exhaustive and coherent (1:n correspondences) alignments between 3 ontologies of the OAEI conference track dataset : cmt, conference and edas.<br><br>The alignments between these ontologies were manually created to ensure their exhaustivity.<br><br>The coherence of the alignments was verified by merging the ontologies pair-wise. The merged ontologies are available.<br><br>The dataset is structured as follow:<br><b><i>- Readme.md</i></b>: Readme file detailing the structure of the files <br><i><b>- Conference_track_ontologies</b></i>: The ontologies of the conference track dataset<br><b><i>- EDOAL_alignments</i></b>: The alignments in EDOAL syntax (an extension of the Alignment Format)<br><i><b>- FOL_alignments:</b></i> The alignments in FOL syntax <br><i><b>- merged_ontologies: </b></i>merging axioms in OWL <br><br><br>
DOI: 10.6084/m9.figshare.4986368.v5
title: Complex alignment dataset on conference organisation

description: This dataset presents exhaustive and coherent (1:n correspondences) alignments between 5 ontologies of the OAEI conference track dataset : cmt, conference, confOf, edas and ekaw.<br><br>The alignments between these ontologies were manually created to ensure their exhaustivity.<br><br>The coherence of the alignments was verified by merging the ontologies pair-wise. The merged ontologies are available.<br><br>The dataset is structured as follow:<br><b><i>- Readme.md</i></b>: Readme file detailing the structure of the files <br><i><b>- Conference_track_ontologies</b></i>: The ontologies of the conference track dataset<br><b><i>- EDOAL_alignments</i></b>: The alignments in EDOAL syntax (an extension of the Alignment Format)<br><i><b>- FOL_alignments:</b></i> The alignments in FOL syntax <br><i><b>- merged_ontologies: </b></i>merging axioms in OWL <br><br><br>
DOI: 10.6084/m9.figshare.4986143
title: Acquired melanocytic naevi in Han Chinese volunteers from Henan, China.

description: Clinical and dermoscopic images of acquired melanocytic naevi in Han Chinese volunteers from Henan, China.<br>
DOI: 10.6084/m9.figshare.4986368.v6
title: Task-oriented complex alignments on conference organisation

description: This archive contains two complex alignment sets between 5 ontologies of the OAEI conference track dataset : cmt, conference, confOf, edas and ekaw. <br><br>One alignment set is designed for <i>ontology merging.<br></i>The other alignment set is designed for <i>query rewriting.</i><br><br>The alignments were manually created tfollowing a methodology.<br><br>The dataset is structured as follow:<br><b><i>- Readme.md</i></b>: Readme file detailing the structure of the files <br><i><b>- Conference_track_ontologies</b></i>: The ontologies of the conference track dataset<br><i>- Ontology_merging_alignments</i>: The alignments created in the purpose of ontology merging in 3 formats: First order logic (FOL), EDOAL and OWL axioms.<br><i>- Query_rewriting_alignments:</i> The alignments created in the purpose of query rewriting in 2 formats: FOL and EDOAL.<br><br><br>
DOI: 10.21421/d2/kdig30
title: Heterotic grouping of sorghum germplasm collection into their specific maturity group

description: Collection of Nigerian Kaura and Fara Fara sorghum land races characterized for grain and seed qualities, height and flowering responses in Nigeria, to assess the germplasm capacity to serve as seed parent for hybrid sorghum development.
DOI: 10.5285/466263b1-06bb-4824-a805-534486be0bfd
title: Santiaguito Volcano 2014-2018 explosion catalogue

description: Seismic waveforms from an explosion catalogue from a seismic network at Santiaguito volcano between November 2014 and December 2018. A network of 6 broadband and 6 short-period stations was used to record explosive volcanic activity. Waveforms from 18,895 explosions have been automatically been detected and extracted.
DOI: 10.6084/m9.figshare.4985567
title: The relationship between species richness and ecosystem variability is shaped by the mechanism of coexistence

description: All code necessary to reproduce Tredennick et al. 2017, Ecology Letters. See ReadMe.html for information on reproducing results.
DOI: 10.6084/m9.figshare.4985561
title: LeafMorphospace

description: This data and code accompany the manuscript "A persistent homology leaf morphospace predicts plant family and region". 182,707 leaf outlines from 141 plant families from 75 sites throughout the world were analyzed using persistent homology, a topological method. Plant family and location can be predicted at a rate higher than chance using this method and persistent homology outperforms traditional shape descriptors in prediction. Figures, tables, and legends for the manuscript are provided ("Figures _and_tables") as well as the data and code used to generate them ("Analysis"). A GitHub repository with code to calculate persistent homology accompanies this manuscript as well (https://github.com/maoli0923/Persistent-Homology-All-Leaf).
DOI: 10.6084/m9.figshare.4985567.v1
title: The relationship between species richness and ecosystem variability is shaped by the mechanism of coexistence

description: All code necessary to reproduce Tredennick et al. 2017, Ecology Letters. See ReadMe.html for information on reproducing results.
DOI: 10.6084/m9.figshare.4985555
title: Morphological characterization of coral reefs by combining LiDAR and MBES data: a case study from Yuanzhi Island, South China Sea

description: The data supplemented here include four datasets and 1 table. The format of the datasets is “Info ASCII Grid”. The format of the table is “Excel”. Table S1. Information about sampling stations (horizontal positions in the dataset 1, coral abundance level, computed SR index values). Data Set S1. The merged bathymetry of Yuanzhi Island. Data Set S 2. The bathymetry of the small area. Data Set S 3. SR index results (without depth calibration). Data Set S 4. SR index results (with depth calibration).
DOI: 10.6084/m9.figshare.4985519.v1
title: Tiime 2- no3- group Eck.docx

description: Data
DOI: 10.6084/m9.figshare.4985510.v1
title: Advocacy -- NORDP table 2.docx

description: Key points from discussion on Advocacy; research institutions
DOI: 10.6084/m9.figshare.4985507.v1
title: How to advocate for scholarly research.pptx

description: How to advocate for scholarly research.pptx
DOI: 10.6084/m9.figshare.4985510.v2
title: Advocacy -- NORDP Table GK.docx

description: Key points from discussion on Advocacy; research institutions
DOI: 10.6084/m9.figshare.4985207
title: Acute impairing effects of morphine related to driving: A systematic review of experimental studies to define blood morphine concentrations related to impairment in opioid-naïve subjects

description: <b>Objective</b>: The objective of this study was to look for dose– and concentration–effect relationships in experimental studies on single-dose administration of morphine on traffic-relevant behavioral tests by a systematic literature review and possibly to see whether a dose/concentration could be defined below which few or no tests would be affected. <b>Methods</b>: Searches for corresponding literature were conducted using MEDLINE, EMBASE, and PsycINFO, throughout March of 2016. The search strategy consisted of words colligated to cognitive and psychomotor functions of relevance to driving, in relation to morphine administration. The tests were arranged in main groups, and tests showing impairment were categorized by doses as well as calculated plasma concentrations. <b>Results</b>: Fifteen studies were included in the review. Impairment after the administration of a single intravenously dose of morphine was found in some of the tests on reaction time, attention, and visual functions. No impairment was observed in tests on psychomotor skills and en-/decoding. Tests on reaction time appeared to be less sensitive to the morphine administration, whereas tests on visual functions and attention appeared to be the most sensitive to the morphine administration. Single-dose administration of morphine with dosages up to 5 mg appeared to cause very few effects on traffic-relevant performance tasks. At higher dosages, impairment was found on various tasks but with no clear dose–effect relationship. Plasma morphine concentrations less than 50 nmol/L are most probably accompanied by few effects on traffic-relevant performance tasks. <b>Conclusions</b>: A plasma morphine concentration of 50 nmol/L (approximately 14.3 ng/mL) could represent an upper level, under which there is little accompanying road traffic risk. A single dose of 5 mg morphine IV and analgetic equivalence doses of fentanyl, hydromorphone, oxycodone, and oxymorphone are presented with the suggestion that few traffic-relevant effects will appear after such doses.
DOI: 10.6084/m9.figshare.4985204
title: <i>Salmonella enterica</i> multilocus sequence typing and its correlation with serotypes

description: <i>Salmonella enterica</i> is a foodborne pathogen of significant public health concern worldwide. In Thailand, <i>S. enterica</i> has also been ranked among the top five most significant bacterial agents of foodborne illnesses by the Ministry of Public Health. Conventionally, biochemical tests and antigen-antibody agglutination have been used to identify and subtype <i>S. enterica</i>, respectively. The objective of this study was to identify the serotypes of 180 <i>S. enterica</i> isolates. Multilocus sequence typing (MLST) was used to deduce the <i>S. enterica</i> serotypes based on sequence type (ST) correlation as shown in the MLST database (http://mlst.warwick.ac.uk/mlst/). Initially, MLST was used to confirm serotypes of 53 previously identified isolates of <i>S</i>. Enteritidis, <i>S</i>. Typhimurium, <i>S</i>. Hadar, <i>S</i>. Virchow, and <i>S</i>. Infantis isolated in Thailand. MLST and serotype correlation confirmed 52 (of 53) known isolates. MLST was performed in 127 <i>S. enterica</i> isolates of unknown serotypes from various sources. Serotypes of all 127 <i>S. enterica</i> isolates were successfully deduced based on STs. With MLST and PCR-based identification, we have shown that the majority of isolates are of monophasic <i>S</i>. Typhimurium (ST34; 43 isolates) and serotype Rissen (ST469; 37 isolates), in agreement with the top serotypes commonly found in Thailand based on the WHO National <i>Salmonella</i> and <i>Shigella</i> Center. We have also confirmed that MLST is a powerful <i>Salmonella</i> subtyping method which could be used not only as a tracking tool for an outbreak investigation at nucleotide level but also as a serotype predictor for making correlations with food safety regulations.
DOI: 10.6084/m9.figshare.4985198
title: Barcode index number, taxonomic rank and modes of speciation: examples from fish

description: Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of <i>Co-1</i>-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (<i>R</i><sup>2</sup> ≈ 0.84–0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.
DOI: 10.6084/m9.figshare.4985204.v1
title: <i>Salmonella enterica</i> multilocus sequence typing and its correlation with serotypes

description: <i>Salmonella enterica</i> is a foodborne pathogen of significant public health concern worldwide. In Thailand, <i>S. enterica</i> has also been ranked among the top five most significant bacterial agents of foodborne illnesses by the Ministry of Public Health. Conventionally, biochemical tests and antigen-antibody agglutination have been used to identify and subtype <i>S. enterica</i>, respectively. The objective of this study was to identify the serotypes of 180 <i>S. enterica</i> isolates. Multilocus sequence typing (MLST) was used to deduce the <i>S. enterica</i> serotypes based on sequence type (ST) correlation as shown in the MLST database (http://mlst.warwick.ac.uk/mlst/). Initially, MLST was used to confirm serotypes of 53 previously identified isolates of <i>S</i>. Enteritidis, <i>S</i>. Typhimurium, <i>S</i>. Hadar, <i>S</i>. Virchow, and <i>S</i>. Infantis isolated in Thailand. MLST and serotype correlation confirmed 52 (of 53) known isolates. MLST was performed in 127 <i>S. enterica</i> isolates of unknown serotypes from various sources. Serotypes of all 127 <i>S. enterica</i> isolates were successfully deduced based on STs. With MLST and PCR-based identification, we have shown that the majority of isolates are of monophasic <i>S</i>. Typhimurium (ST34; 43 isolates) and serotype Rissen (ST469; 37 isolates), in agreement with the top serotypes commonly found in Thailand based on the WHO National <i>Salmonella</i> and <i>Shigella</i> Center. We have also confirmed that MLST is a powerful <i>Salmonella</i> subtyping method which could be used not only as a tracking tool for an outbreak investigation at nucleotide level but also as a serotype predictor for making correlations with food safety regulations.
DOI: 10.6084/m9.figshare.4985207.v2
title: Acute impairing effects of morphine related to driving: A systematic review of experimental studies to define blood morphine concentrations related to impairment in opioid-naïve subjects

description: <b>Objective</b>: The objective of this study was to look for dose– and concentration–effect relationships in experimental studies on single-dose administration of morphine on traffic-relevant behavioral tests by a systematic literature review and possibly to see whether a dose/concentration could be defined below which few or no tests would be affected. <b>Methods</b>: Searches for corresponding literature were conducted using MEDLINE, EMBASE, and PsycINFO, throughout March of 2016. The search strategy consisted of words colligated to cognitive and psychomotor functions of relevance to driving, in relation to morphine administration. The tests were arranged in main groups, and tests showing impairment were categorized by doses as well as calculated plasma concentrations. <b>Results</b>: Fifteen studies were included in the review. Impairment after the administration of a single intravenously dose of morphine was found in some of the tests on reaction time, attention, and visual functions. No impairment was observed in tests on psychomotor skills and en-/decoding. Tests on reaction time appeared to be less sensitive to the morphine administration, whereas tests on visual functions and attention appeared to be the most sensitive to the morphine administration. Single-dose administration of morphine with dosages up to 5 mg appeared to cause very few effects on traffic-relevant performance tasks. At higher dosages, impairment was found on various tasks but with no clear dose–effect relationship. Plasma morphine concentrations less than 50 nmol/L are most probably accompanied by few effects on traffic-relevant performance tasks. <b>Conclusions</b>: A plasma morphine concentration of 50 nmol/L (approximately 14.3 ng/mL) could represent an upper level, under which there is little accompanying road traffic risk. A single dose of 5 mg morphine IV and analgetic equivalence doses of fentanyl, hydromorphone, oxycodone, and oxymorphone are presented with the suggestion that few traffic-relevant effects will appear after such doses.