cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4497125.v1
title: Accounting for monogastric livestock as a driver in global land use and cover change assessments

description: Land systems are described based on various characteristics, including land cover composition and agricultural production. However, it is uncertain to what extent livestock, particularly monogastric livestock, determines land systems. We included monogastrics in a land system classification, and statistically analyzed the land cover composition and agricultural production of otherwise similar land systems with and without monogastric livestock. The results indicate that land systems with monogastrics are statistically different from their counterparts in the classification without monogastrics in terms of grassland area and crop yields, but are less different in terms of tree area, crop area, and ruminant livestock production. We then used a land systems map that includes monogastrics in the classification and a similar map that does not include monogastrics to project future changes in a novel manner that integrates livestock as a determinant of land systems. The results show that including monogastrics in otherwise similar projections yields less cropland intensification and more cropland expansion in several world regions, including Northern Africa and the Middle East. Other regions, such as Europe and Australia, were characterized by less decrease or more increase in tree area in the application with monogastrics, mainly due to the occurrence of open forests with monogastrics. This study prompts a call for improved characterization of land systems for land use and cover change (LUCC) assessments in order to better represent LUCC driven by monogastric livestock.
DOI: 10.5281/zenodo.4011972
title: Ontolex-lemon and TIAD versions of Apertium Belarusian-Russian dictionary

description: OntoLex-lemon and TSV conversion of Apertium Bidix. For more details, see https://www.aclweb.org/anthology/2020.lrec-1.401/ Authors of the original data: 2016-2017, Francis M. Tyers 2017, John Lyell 2016, Vladislav Kiryukhin
DOI: 10.6084/m9.figshare.4497218.v1
title: Qualitative codes for the consequences of unhappiness of software developers

description: Qualitative codes for the consequences of unhappiness of software developers
DOI: 10.6084/m9.figshare.4497083
title: Metabolite BridgeDb ID Mapping Database (20161227)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 146, and Wikidata (26 December 2016) as data sources. See the attached QC for more details on the changes.
DOI: 10.6084/m9.figshare.4497074
title: A simplified linear feature matching method using decision tree analysis, weighted linear directional mean, and topological relationships

description: Linear feature matching is one of the crucial components for data conflation that sees its usefulness in updating existing data through the integration of newer data and in evaluating data accuracy. This article presents a simplified linear feature matching method to conflate historical and current road data. To measure the similarity, the shorter line median Hausdorff distance (SMHD), the absolute value of cosine similarity (aCS) of the weighted linear directional mean values, and topological relationships are adopted. The decision tree analysis is employed to derive thresholds for the SMHD and the aCS. To demonstrate the usefulness of the simple linear feature matching method, four models with incremental configurations are designed and tested: (1) Model 1: one-to-one matching based on the SMHD; (2) Model 2: matching with only the SMHD threshold; (3) Model 3: matching with the SMHD and the aCS thresholds; and (4) Model 4: matching with the SMHD, the aCS, and topological relationships. These experiments suggest that Model 2, which considers only distance, does not provide stable results, while Models 3 and 4, which consider direction and topological relationships, produce stable results with levels of accuracy around 90% and 95%, respectively. The results suggest that the proposed method is simple yet robust for linear feature matching.
DOI: 10.6084/m9.figshare.4497074.v1
title: A simplified linear feature matching method using decision tree analysis, weighted linear directional mean, and topological relationships

description: Linear feature matching is one of the crucial components for data conflation that sees its usefulness in updating existing data through the integration of newer data and in evaluating data accuracy. This article presents a simplified linear feature matching method to conflate historical and current road data. To measure the similarity, the shorter line median Hausdorff distance (SMHD), the absolute value of cosine similarity (aCS) of the weighted linear directional mean values, and topological relationships are adopted. The decision tree analysis is employed to derive thresholds for the SMHD and the aCS. To demonstrate the usefulness of the simple linear feature matching method, four models with incremental configurations are designed and tested: (1) Model 1: one-to-one matching based on the SMHD; (2) Model 2: matching with only the SMHD threshold; (3) Model 3: matching with the SMHD and the aCS thresholds; and (4) Model 4: matching with the SMHD, the aCS, and topological relationships. These experiments suggest that Model 2, which considers only distance, does not provide stable results, while Models 3 and 4, which consider direction and topological relationships, produce stable results with levels of accuracy around 90% and 95%, respectively. The results suggest that the proposed method is simple yet robust for linear feature matching.
DOI: 10.6084/m9.figshare.4496924
title: Developing a competency framework for academic physicians

description: <b>Background:</b> There is a mismatch between the requirements of the multifaceted role of academic physicians and their education. Medical institutions use faculty development initiatives to support their junior academic physicians, however, these rarely revolve around academic physician competencies. The aim of this study was to identify these academic physician competencies and develop a competency framework customized to an organizational context. <b>Methods:</b> The authors conducted semi-structured interviews and Critical Incident Technique with 25 academic physicians at a teaching medical center in the Middle East region inquiring about the behaviors of academic physicians in teaching, clinical, research, and administrative roles. <b>Results:</b> Using content analysis, the authors identified 16 competencies: five “Supporting Competencies”, common to all four roles of academic physicians, and 11 “Function-Specific Competencies”, specific to the role being fulfilled. The developed framework shared similarities with frameworks reported in the literature but also had some distinctions. <b>Conclusions:</b> The framework developed represents a step towards closing the gap between the skills medical students are taught and the skills required of academic physicians. The model was customized to the context of the current organization and included a future orientation and addressed the literature calling for increasing focus on the administrative skills of academic physicians.
DOI: 10.6084/m9.figshare.4496924.v1
title: Developing a competency framework for academic physicians

description: <b>Background:</b> There is a mismatch between the requirements of the multifaceted role of academic physicians and their education. Medical institutions use faculty development initiatives to support their junior academic physicians, however, these rarely revolve around academic physician competencies. The aim of this study was to identify these academic physician competencies and develop a competency framework customized to an organizational context. <b>Methods:</b> The authors conducted semi-structured interviews and Critical Incident Technique with 25 academic physicians at a teaching medical center in the Middle East region inquiring about the behaviors of academic physicians in teaching, clinical, research, and administrative roles. <b>Results:</b> Using content analysis, the authors identified 16 competencies: five “Supporting Competencies”, common to all four roles of academic physicians, and 11 “Function-Specific Competencies”, specific to the role being fulfilled. The developed framework shared similarities with frameworks reported in the literature but also had some distinctions. <b>Conclusions:</b> The framework developed represents a step towards closing the gap between the skills medical students are taught and the skills required of academic physicians. The model was customized to the context of the current organization and included a future orientation and addressed the literature calling for increasing focus on the administrative skills of academic physicians.
DOI: 10.6084/m9.figshare.4496906
title: Astroglial transcriptome dysregulation in early disease of an ALS mutant SOD1 mouse model

description: Astroglia are a morphologically diverse and highly abundant cell type in the CNS. Despite these obvious observations, astroglia still remain largely uncharacterized at the cellular and molecular level. In disease contexts such as amyotrophic lateral sclerosis (ALS), it has been widely shown that astroglia downregulate crucial physiological functions, become hypertrophied, reactive, and toxic to motor neurons. However, little is known about the astroglia-specific transcriptomic changes that occur during ALS disease progression, especially early in disease. To address this, we FACS-isolated pure astroglia from early and mid-symptomatic superoxide dismutase 1 (SOD1) G93A spinal cord and performed microarray sequencing, in hopes to uncover markers and pathways driving astroglia dysfunction in ALS. After extensive analyses, we uncovered genes selectively enriched and downregulated in both control and SOD1 astroglia at both disease points. In addition, we were able to identify genes and pathways differentially expressed that may have relevance with other neurodegenerative diseases, such as Parkinson’s and Alzheimer’s disease, suggesting a common theme among astroglial dysfunction in neurodegenerative disease. In aggregate, this study sheds light on the common and unique themes of dysfunction that astroglia undergo during neurodegenerative disease progression and provides candidate targets for therapeutic approaches.
DOI: 10.6084/m9.figshare.4496906.v1
title: Astroglial transcriptome dysregulation in early disease of an ALS mutant SOD1 mouse model

description: Astroglia are a morphologically diverse and highly abundant cell type in the CNS. Despite these obvious observations, astroglia still remain largely uncharacterized at the cellular and molecular level. In disease contexts such as amyotrophic lateral sclerosis (ALS), it has been widely shown that astroglia downregulate crucial physiological functions, become hypertrophied, reactive, and toxic to motor neurons. However, little is known about the astroglia-specific transcriptomic changes that occur during ALS disease progression, especially early in disease. To address this, we FACS-isolated pure astroglia from early and mid-symptomatic superoxide dismutase 1 (SOD1) G93A spinal cord and performed microarray sequencing, in hopes to uncover markers and pathways driving astroglia dysfunction in ALS. After extensive analyses, we uncovered genes selectively enriched and downregulated in both control and SOD1 astroglia at both disease points. In addition, we were able to identify genes and pathways differentially expressed that may have relevance with other neurodegenerative diseases, such as Parkinson’s and Alzheimer’s disease, suggesting a common theme among astroglial dysfunction in neurodegenerative disease. In aggregate, this study sheds light on the common and unique themes of dysfunction that astroglia undergo during neurodegenerative disease progression and provides candidate targets for therapeutic approaches.
DOI: 10.6084/m9.figshare.4496795
title: Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1

description: This is a one microsecond trajectory of the catalytic domain of the human tyrosine protein kinase ABL1 (UNIPROT:ABL1_HUMAN, residues 242-493). The simulation was generated on Folding@home using OpenMM 6.3.1 with the AMBER99SB-ILDN forcefield, TIP3P water, and neutralizing salt. A Langevin integrator with 2 fs timestep, 300 K temperature, and 1/ps collision rate was used. PME with a nonbonded cutoff of 1.0 nm was used with default tolerance of 5.0e-4. A long-range isotropic dispersion correction was used to correct for the truncation of Lennard-Jones interactions at 1.0 nm. A molecular-scaling Monte Carlo barostat was applied using a 1 atm reference pressure, with MC moves attempted every 50 steps. Coordinates were saved every 250ps, and waters and ions stripped. The trajectory file contains 4000 snapshots. Initial models were generated with Ensembler (see References) using the ABL1 structure from chain B of PDB ID: 2GQG as a template.<br>Manifest:* run17-clone3.jpg - image of initial simulation snapshot* run17-clone3.pdb - PDB file of initial simulation snapshot* run17-clone3.h5 - MDTraj HDF5 format trajectory<br>To convert the trajectory, see the MDTraj `mdconvert` command:http://mdtraj.org/latest/mdconvert.html<br>For information on installing MDTraj, see:http://mdtraj.org/
DOI: 10.17608/k6.auckland.4496792
title: create earthquake catalogue with obspy

description: First of three notebooks that form an intro to seismology with python in obspy
DOI: 10.6084/m9.figshare.4496780
title: Dataset

description: "Surgical Teams on GitHub: Modeling Performance of GitHub Project Development Processes" - research dataset<br>
DOI: 10.17608/k6.auckland.4496792.v2
title: create earthquake catalogue with obspy

description: First of three notebooks that form an intro to seismology with python in obspy
DOI: 10.6084/m9.figshare.4496780.v1
title: Dataset

description: "Surgical Teams on GitHub: Modeling Performance of GitHub Project Development Processes" - research dataset<br>
DOI: 10.17608/k6.auckland.4496792.v1
title: obspy for beginners

description: First of three notebooks that form an intro to seismology with python in obspy
DOI: 10.6084/m9.figshare.4496768
title: STNS Dataset

description: This dataset contains tracking small moving targets from a moving platform within heavily cluttered natural environments. Please cite Bagheri Z., Wiederman S., Cazzolato B., Grainger S., & O'Carroll D. (2017) "Performance of an insect-inspired target tracker in natural conditions". Bioinspiration & Biomimetics.
DOI: 10.6084/m9.figshare.4496768.v1
title: STNS Dataset

description: This dataset contains tracking small moving targets from a moving platform within heavily cluttered natural environments. Please cite Bagheri Z., Wiederman S., Cazzolato B., Grainger S., & O'Carroll D. (2017) "Performance of an insect-inspired target tracker in natural conditions". Bioinspiration & Biomimetics.
DOI: 10.6084/m9.figshare.4496747
title: Interleukin-6-174G &gt; C (rs1800795) polymorphism distribution and its association with rheumatoid arthritis: A case-control study and meta-analysis

description: The association of interleukin-6 (IL-6)-174G &gt; C (rs1800795) single nucleotide polymorphism (SNP) with the risk of acquiring rheumatoid arthritis (RA) is a relevant issue because of conflicting and consensus lacking reports published in literature. We investigated IL-6-174G &gt; C promoter polymorphism in 34 RA patients, attending a tertiary care hospital in north India. We also performed a meta-analysis, of the previously published studies reporting this genetic relationship, in overall population, and independently in Asian and Caucasian ethnicities to further elucidate this association. A total of 13 studies, including the current one, involving 3291 RA cases and 3812 controls were analyzed. Out of the 13 studies, 6 were from Asian, 6 from Caucasian and 1 from a mixed population. Our case-control study showed significant association of IL-6-174G &gt; C SNP with increased RA risk: allelic (OR = 3.750, 95% CI = 1.800–7.813, <i>p </i>&lt;<i> </i>0.001); dominant (OR = 2.800, 95% CI = 1.167–6.721, <i>p </i>=<i> </i>0.021); and recessive (OR = 36.72, 95% CI = 2.004–672.7, <i>p </i>=<i> </i>0.015). The meta-analysis revealed the increased RA risk associated with IL-6-174G &gt; C SNP in overall population: allelic (OR = 1.650, 95% CI = 1.169–2.329, <i>p </i>=<i> </i>0.004); homozygous (OR = 1.380, 95% CI = 0.906–2.101, <i>p = </i>0.133); heterozygous (OR = 1.559, 95% CI = 1.001–2.428, <i>p </i>=<i> </i>0.049); dominant (OR = 1.663, 95% CI = 1.078–2.567, <i>p </i>=<i> </i>0.022); and recessive (OR = 1.366, 95% CI = 0.964–1.935, <i>p </i>=<i> </i>0.079). Subgroup analysis also showed this polymorphism to be associated with increased RA risk in Asian population: allelic (OR = 3.724, 95% CI = 1.361–10.190, <i>p </i>=<i> </i>0.010); dominant (OR = 3.823, 95% CI = 1.320–11.074, <i>p </i>=<i> </i>0.013); and recessive (OR = 4.357, 95% CI = 1.634–11.623, <i>p </i>=<i> </i>0.003), but not in Caucasian population. This meta-analysis shows that IL-6-174G &gt; C SNP is significantly associated with increased RA risk in overall, and specifically in Asian population.
DOI: 10.6084/m9.figshare.4496750
title: Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

description: The systematics of Coralliidae has been revised based on molecular phylogenetic analysis and detailed morphological studies. This revision has also revealed the existence of new species. In order to fully accomplish this revision, five new species including <i>Hemicorallium aurantiacum</i> sp. nov., <i>Pleurocorallium bonsaiarborum</i> sp. nov., <i>P. clavatum</i> sp. nov., and <i>P. norfolkicum</i> sp. nov. from New Caledonia, and <i>H. guttatum</i> sp. nov. from the Hawaiian Archipelago are described by integrating the phylogenetic inference and morphological comparisons. Moreover, the type specimens of <i>Corallium tortuosum</i>, <i>H. reginae</i>, <i>H. halmaheirense</i>, <i>P. porcellanum</i> and <i>P. kishinouyei</i> as well as non-type specimens of <i>C. stylasteroides</i> are redescribed. The sclerites of <i>H. reginae</i>, <i>H. halmaheirense</i>, <i>P. porcellanum</i> and <i>C. stylasteroides</i> were first depicted by scanning electron microcopy. A thorough comparison between <i>P. porcellanum</i> and <i>P. kishinouyei</i> indicated that they should be regarded as one species and the former was adopted as the senior synonym<i>.</i> The two new species of <i>Hemicorallium</i> can be separated by morphological features based on the result of multiple factor analysis<i>.</i> A key is proposed for the identification of all existing species of Coralliidae. http://zoobank.org/urn:lsid:zoobank.org:pub:7B772D08-E3D6-4585-AE78-E5A31BE32ECC
DOI: 10.6084/m9.figshare.4496750.v1
title: Taxonomic revision of Coralliidae with descriptions of new species from New Caledonia and the Hawaiian Archipelago

description: The systematics of Coralliidae has been revised based on molecular phylogenetic analysis and detailed morphological studies. This revision has also revealed the existence of new species. In order to fully accomplish this revision, five new species including <i>Hemicorallium aurantiacum</i> sp. nov., <i>Pleurocorallium bonsaiarborum</i> sp. nov., <i>P. clavatum</i> sp. nov., and <i>P. norfolkicum</i> sp. nov. from New Caledonia, and <i>H. guttatum</i> sp. nov. from the Hawaiian Archipelago are described by integrating the phylogenetic inference and morphological comparisons. Moreover, the type specimens of <i>Corallium tortuosum</i>, <i>H. reginae</i>, <i>H. halmaheirense</i>, <i>P. porcellanum</i> and <i>P. kishinouyei</i> as well as non-type specimens of <i>C. stylasteroides</i> are redescribed. The sclerites of <i>H. reginae</i>, <i>H. halmaheirense</i>, <i>P. porcellanum</i> and <i>C. stylasteroides</i> were first depicted by scanning electron microcopy. A thorough comparison between <i>P. porcellanum</i> and <i>P. kishinouyei</i> indicated that they should be regarded as one species and the former was adopted as the senior synonym<i>.</i> The two new species of <i>Hemicorallium</i> can be separated by morphological features based on the result of multiple factor analysis<i>.</i> A key is proposed for the identification of all existing species of Coralliidae. http://zoobank.org/urn:lsid:zoobank.org:pub:7B772D08-E3D6-4585-AE78-E5A31BE32ECC
DOI: 10.6084/m9.figshare.4496747.v1
title: Interleukin-6-174G &gt; C (rs1800795) polymorphism distribution and its association with rheumatoid arthritis: A case-control study and meta-analysis

description: The association of interleukin-6 (IL-6)-174G &gt; C (rs1800795) single nucleotide polymorphism (SNP) with the risk of acquiring rheumatoid arthritis (RA) is a relevant issue because of conflicting and consensus lacking reports published in literature. We investigated IL-6-174G &gt; C promoter polymorphism in 34 RA patients, attending a tertiary care hospital in north India. We also performed a meta-analysis, of the previously published studies reporting this genetic relationship, in overall population, and independently in Asian and Caucasian ethnicities to further elucidate this association. A total of 13 studies, including the current one, involving 3291 RA cases and 3812 controls were analyzed. Out of the 13 studies, 6 were from Asian, 6 from Caucasian and 1 from a mixed population. Our case-control study showed significant association of IL-6-174G &gt; C SNP with increased RA risk: allelic (OR = 3.750, 95% CI = 1.800–7.813, <i>p </i>&lt;<i> </i>0.001); dominant (OR = 2.800, 95% CI = 1.167–6.721, <i>p </i>=<i> </i>0.021); and recessive (OR = 36.72, 95% CI = 2.004–672.7, <i>p </i>=<i> </i>0.015). The meta-analysis revealed the increased RA risk associated with IL-6-174G &gt; C SNP in overall population: allelic (OR = 1.650, 95% CI = 1.169–2.329, <i>p </i>=<i> </i>0.004); homozygous (OR = 1.380, 95% CI = 0.906–2.101, <i>p = </i>0.133); heterozygous (OR = 1.559, 95% CI = 1.001–2.428, <i>p </i>=<i> </i>0.049); dominant (OR = 1.663, 95% CI = 1.078–2.567, <i>p </i>=<i> </i>0.022); and recessive (OR = 1.366, 95% CI = 0.964–1.935, <i>p </i>=<i> </i>0.079). Subgroup analysis also showed this polymorphism to be associated with increased RA risk in Asian population: allelic (OR = 3.724, 95% CI = 1.361–10.190, <i>p </i>=<i> </i>0.010); dominant (OR = 3.823, 95% CI = 1.320–11.074, <i>p </i>=<i> </i>0.013); and recessive (OR = 4.357, 95% CI = 1.634–11.623, <i>p </i>=<i> </i>0.003), but not in Caucasian population. This meta-analysis shows that IL-6-174G &gt; C SNP is significantly associated with increased RA risk in overall, and specifically in Asian population.