cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5350450.v1
title: Numerical versus narrative: A comparison between methods to measure medical student performance during clinical clerkships

description: <b>Background:</b> Medical school evaluations typically rely on both language-based narrative descriptions and psychometrically converted numeric scores to convey performance to the grading committee. We evaluated inter-rater reliability and correlation of numeric versus narrative evaluations for students on their Neurology Clerkship. <b>Design/Methods:</b> 50 Neurology Clerkship in-training evaluation reports completed by their residents and faculty members at the University of Rochester School of Medicine were dissected into narrative and numeric components. 5 Clerkship grading committee members retrospectively gave new narrative scores (NNS) while blinded to original numeric scores (ONS). We calculated intra-class correlation coefficients (ICC) and their associated confidence intervals for the ONS and the NNS. In addition, we calculated the correlation between ONS and NNS. <b>Results:</b> The ICC was greater for the NNS (ICC = .88 (95% CI = .70–.94)) than the ONS (ICC = .62 (95% CI = .40–.77)) Pearson correlation coefficient showed that the ONS and NNS were highly correlated (<i>r</i> = .81). <b>Conclusions:</b> Narrative evaluations converted by a small group of experienced graders are at least as reliable as numeric scoring by individual evaluators. We could allow evaluators to focus their efforts on creating richer narrative of greater value to trainees.
DOI: 10.6084/m9.figshare.5350432.v1
title: Geochemistry and zircon Hf isotopes of the Early Mesozoic intrusive rocks in the south Hunchun, Yanbian area, Northeast China: petrogenesis and implications for crustal growth

description: This paper presents major element, trace element, and new zircon Hf isotopic data for the Early Mesozoic intrusive rocks in the south Hunchun, Yanbian area, Northeast China. These data are used to constrain the petrogenesis of these intrusive rocks and their implications for the Phanerozoic continental growth of the Central Asian Orogenic Belt (CAOB). Combining geology, geochronology, and whole-rock geochemistry, we identify three distinct episodes of magmatism as Early–Middle Triassic (249–237 Ma), Late Triassic (224–206 Ma), and Early Jurassic (200–187 Ma). The Early–Middle Triassic (249–237 Ma) adakitic tonalite and granodiorite were produced by the partial melting of subducted oceanic slabs, and the melts were contaminated by mantle peridotite during their ascent, whereas the coeval non-adakitic diorite and monzogranite were most likely derived from partial melting of crustal material. The remarkably high zircon Hf isotopic signature (ε<sub>Hf</sub>(t) = + 9.4 – +18.9), the enrichment in large-ion lithophile element and light rare earth elements, and the depletion in high field strength element suggest that these 224 Ma gabbros were derived from the partial melting of depleted mantle modified by subduction-related fluids. The 212 Ma monzogranite was most likely derived from juvenile material mixed with old crustal material as evidenced by their high SiO<sub>2</sub>, low MgO, and low Cr concentrations and variable ε<sub>Hf</sub>(t) values (–4.6 to +10.0). Except for the 197 Ma tonalites with affinity to the high silica adakites, the overall geochemical evolution of Early Jurassic (200–187 Ma) rocks was consistent with fractional crystallization from quartz diorite, granodiorite, and monzogranite to syenogranite. Both the Early Jurassic syn-subduction lateral continental growth by accretion of arc complexes and the Late Triassic post-collisional vertical continental growth by accretion of mantle-derived material played an important role in the Phanerozoic continental growth of the CAOB.
DOI: 10.6084/m9.figshare.5350447.v1
title: convective_variability_figures_and_meta

description: Zipped directory containing all raw figures and metadata on how to create the figures.<br>
DOI: 10.6084/m9.figshare.5350321
title: An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer

description: These meta-data and codes have been developed and used in our recent publication. <br><b>How to Cite Our Codes/Meta-dataset:<br></b>Lim, S B <i>et al.</i> An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer. <i>Nature Communications</i> 8, 1734, 2017.<br><br><br>
DOI: 10.6084/m9.figshare.5350309
title: Data assessing the reliability and validity of the Sino-Nasal Outcome Test (SNOT-22) Questionnaire

description: This dataset contains a single excel file presenting results of the SNOT-22 questionnaire from 50 Chronic rhinosinusitis (CRS) patients and 30 healthy volunteers.<br>CT scan, Visual Analog Scale (VAS) and SF-36 questionnaire results are also recorded as the basis of validity and reliability tests of the SNOT-22 method in the associated publication.<br>Background:Chronic rhinosinusitis (CRS) is a common health condition that affects the patient's health-related quality of life. This dataset contains results of a Thai-version of Sino-Nasal Outcome Test 22 in chronic rhinosinusitis, translated into English.<br>A total of 80 subjects were recruited into the study and divided into two groups comprising of 50 patients with chronic rhinosinusitis and 30 healthy volunteers. Cronbach's α and Intraclass correlation coefficient were evaluated for its reliability. Validity test was evaluated against VAS score, SF-36 (Thai version) questionnaire and CT scan (based on Lund-Mackay score). Responsiveness was assessed between pre-operative and postoperative scores in 34 patients.<br>All subjects were over 18 year-old and could read and write Thai. Diagnosis of CRS was based on diagnostic criteria of European Position Paper on Rhinosinusitis and Nasal Polyps 2012. The Questionnaire was completed in 3 visits: The first both in CRS and normal group at the first day of enrolment. The second and third visit questionnaire were completed only in the CRS group. The second visit was completed at 2 weeks after first visit. The third vist, which completed only in CRS patients who underwent sinus surgery, 12 weeks after the operation. <br>Pre-operative CT scan of paranasal sinuses and Lund-Mackay scores were recorded in every operated case. Visual analog scale (VAS) of sinonasal symptoms and SF-36 score (Thai version) were recorded in all subjects.
DOI: 10.6084/m9.figshare.5350321.v1
title: A meta-dataset of non-small cell lung cancer for clinical model development

description: These data are pre-publication release. Please refer to our recent publications for detailed methodology and processing techniques.
DOI: 10.6084/m9.figshare.5350321.v2
title: A meta-dataset of non-small cell lung cancer for clinical model development

description: These data are pre-publication release. Please refer to our recent publications for detailed methodology and processing techniques.
DOI: 10.6084/m9.figshare.5350321.v3
title: A meta-dataset of non-small cell lung cancer for clinical model development

description: These data are pre-publication release. Please refer to our recent publications for detailed methodology and processing techniques.
DOI: 10.6084/m9.figshare.5350321.v4
title: A meta-dataset of non-small cell lung cancer for clinical model development

description: These meta-data and codes have been developed and used in our recent publication. <br><b>How to Cite Our Codes/Meta-dataset:<br></b>Lim, S B <i>et al.</i> An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer. <i>Nature Communications</i> 8, 1734, 2017.<br><br><br>
DOI: 10.6084/m9.figshare.5350177
title: Domain hits Pfam

description: Domain hits of human representative fragments identified in <i>S. cerevisiae</i> or <i>P. pastoris</i> SECRiFY screening. 'Common' indicates domains found in both enriched and depleted fragments, 'Unique' domains are found in enriched or depleted fragments exclusively.<br>
DOI: 10.6084/m9.figshare.5350192
title: Complete data for 96 countries

description: Data on 15 variables are provided for 96 countries.<br><br>
DOI: 10.6084/m9.figshare.5350150
title: Inorganic Compounds using Zero-Order Bonds

description: Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.
DOI: 10.6084/m9.figshare.5350147
title: Inorganic Compounds using Zero-Order Bonds

description: Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.
DOI: 10.6084/m9.figshare.5350150.v1
title: Inorganic Compounds using Zero-Order Bonds

description: Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.
DOI: 10.6084/m9.figshare.5350192.v1
title: Complete data for 96 countries

description: Data on 15 variables are provided for 96 countries.<br><br>
DOI: 10.6084/m9.figshare.5350147.v1
title: Inorganic Compounds using Zero-Order Bonds

description: Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.
DOI: 10.6084/m9.figshare.5350177.v2
title: Domain hits Pfam

description: Domain hits of human representative fragments identified in <i>S. cerevisiae</i> or <i>P. pastoris</i> SECRiFY screening. 'Common' indicates domains found in both enriched and depleted fragments, 'Unique' domains are found in enriched or depleted fragments exclusively.<br>
DOI: 10.6084/m9.figshare.5350177.v1
title: Domain hits Pfam

description: Domain hits of human representative fragments identified in <i>S. cerevisiae</i> or <i>P. pastoris</i> SECRiFY screening. 'Common' indicates domains found in both enriched and depleted fragments, 'Unique' domains are found in enriched or depleted fragments exclusively.<br>
DOI: 10.6084/m9.figshare.5350117
title: Duck global expression

description: The supplementary datasets of paper <strong>"</strong>Genomics analyses of wild × domestic segregation population to reveal selected genes associated with body size and plumage color of ducks<strong>".</strong>
DOI: 10.6084/m9.figshare.5350117.v1
title: Duck global expression

description: The supplementary datasets of paper <strong>"</strong>Genomics analyses of wild × domestic segregation population to reveal selected genes associated with body size and plumage color of ducks<strong>".</strong>
DOI: 10.6084/m9.figshare.5350021
title: Contrasting heat budget dynamics during two La Niña marine heat wave events along northwestern Australia

description: Over a three year period, two marine heat waves occurred along the coast of Western Australia (WA) during the alternate austral summer periods of 2010/11 and 2012/13, both linked to the strong La Niña conditions. This led to severe impacts to marine ecosystems over more than 12 degrees of latitude, including unprecedented bleaching of many coral reefs, with sea surface temperature (SST) anomalies reaching up to 5<sup>o</sup> C above climatological averages. However, despite occurring during similar climate (La Niña), the observed warming patterns differed substantially between the two heat waves, with the central coast of WA (south of 22<sup>o</sup> S) experiencing its greatest warming in 2010/11; whereas, the northwestern coast (north of 22<sup>o</sup> S) experiencing higher warming in 2012/13. To investigate how oceanic and atmospheric processes drove these very different spatial patterns, we conducted an ocean heat budget analysis of the region using a combination of remote sensing observation, in situ data, and a high resolution (~1 km) numerical ocean model (Regional Ocean Modeling System). The results revealed a substantial spatial differences in the contributions made by along-shelf heat advection and air-sea heat exchange between the two heat wave events. During 2010/11, anomalous heat advection was present across the entire region, but was much stronger south of 22<sup>o</sup> S where the poleward flowing Leeuwin Current consolidates. During 2012/13, air-sea heat exchange had a much more positive (warming) influence on the SSTs (especially in the northwest), and when combined with the more positive contribution also made by heat advection north of 22<sup>o</sup> S, can explain the regional differences in warming between the two events. Overall, the results highlight how subtle differences in regional oceanic and atmospheric heat fluxes can lead to regional heterogeneity in warming patterns during marine heat waves, even when under the influence of similar large-scale climate drivers.
DOI: 10.6084/m9.figshare.5350021.v1
title: Contrasting heat budget dynamics during two La Niña marine heat wave events along northwestern Australia

description: Over a three year period, two marine heat waves occurred along the coast of Western Australia (WA) during the alternate austral summer periods of 2010/11 and 2012/13, both linked to the strong La Niña conditions. This led to severe impacts to marine ecosystems over more than 12 degrees of latitude, including unprecedented bleaching of many coral reefs, with sea surface temperature (SST) anomalies reaching up to 5<sup>o</sup> C above climatological averages. However, despite occurring during similar climate (La Niña), the observed warming patterns differed substantially between the two heat waves, with the central coast of WA (south of 22<sup>o</sup> S) experiencing its greatest warming in 2010/11; whereas, the northwestern coast (north of 22<sup>o</sup> S) experiencing higher warming in 2012/13. To investigate how oceanic and atmospheric processes drove these very different spatial patterns, we conducted an ocean heat budget analysis of the region using a combination of remote sensing observation, in situ data, and a high resolution (~1 km) numerical ocean model (Regional Ocean Modeling System). The results revealed a substantial spatial differences in the contributions made by along-shelf heat advection and air-sea heat exchange between the two heat wave events. During 2010/11, anomalous heat advection was present across the entire region, but was much stronger south of 22<sup>o</sup> S where the poleward flowing Leeuwin Current consolidates. During 2012/13, air-sea heat exchange had a much more positive (warming) influence on the SSTs (especially in the northwest), and when combined with the more positive contribution also made by heat advection north of 22<sup>o</sup> S, can explain the regional differences in warming between the two events. Overall, the results highlight how subtle differences in regional oceanic and atmospheric heat fluxes can lead to regional heterogeneity in warming patterns during marine heat waves, even when under the influence of similar large-scale climate drivers.
DOI: 10.6084/m9.figshare.5350006
title: Triangular unstructured mesh around Orkney and Shetland Islands for hydrodynamic simulations.

description: Unstructured triangular mesh around Orkney and Shetland Islands for hydrodynamic simulations. Mesh constructed with qmesh (www.qmesh.org), using input files at 10.6084/m9.figshare.4519067.v1 . Also, the mesh is discussed in "Efficient unstructured mesh generation for marine renewable energy applications", Renewable Energy, https://doi.org/10.1016/j.renene.2017.09.058<br>
DOI: 10.6084/m9.figshare.5349967
title: Metabolite BridgeDb ID Mapping Database (20170826)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 154, and Wikidata (26 August 2017) as data sources. Two significant changes: Mappings to the EPA CompTox Dashboard have been added (about 36 thousand) and it is using a newer HMDB 3.6 version with many more compounds. If you experience problems, please report on the project page. See the attached QC for more details on the changes.<br>If you use this data in your research, please cite that data set, and the BridgeDb, ChEBI, and HMDB articles.
DOI: 10.6084/m9.figshare.5350006.v1
title: Unstructured triangular mesh around Orkney and Shetland Islands for hydrodynamic simulations.

description: Unstructured triangular mesh around Orkney and Shetland Islands for hydrodynamic simulations. Mesh constructed with qmesh (www.qmesh.org), using input files at 10.6084/m9.figshare.4519067.v1
DOI: 10.6084/m9.figshare.5349955
title: P. pastoris fragment datasets

description: Results data of two-round SECRiFY screens of human (HEK293) cDNA fragments in P. pastoris (3 replicate screens). Sequencing data was mapped on the human GRCh38 transcriptome assembled using known transcripts from protein-coding genes only.<br>"Pp_resultstable_all.txt" = all in-frame fragments detected in either the unsorted baseline library (merged for 3 replicates), or in all 3 sorted replicate samples. <br>"Pp_resultstable_enriched.txt" = those with log_FC &gt; 1 in all three replicates (10404)<br>"Pp_resultstable_depleted.txt" = those with log_FC &lt; -1 in all three replicates (141357)<br><br>For each fragment, the following information is provided:<br><br># Ensembl_geneID --&gt; Ensembl gene ID<br># Ensembl_txID --&gt; Ensembl transcript ID<br># tx_start --&gt; Transcript start position on human genome GRCh38<br># tx_end --&gt; Transcript end position on human genome GRCh38<br># chr --&gt; chromosome #<br># gene_symbol --&gt; official gene symbol<br># frag_start --&gt; fragment start position on the transcript, 0-based <br># frag_stop --&gt; fragment end position on the transcript, 0-based<br># cDNA --&gt; DNA sequence of the fragment<br># protein --&gt; translated AA sequence of the fragment in frame 1<br># IND_count --&gt; raw count value in the baseline (unsorted) library (merged for 3 replicates), NAs replaced by 0.001<br># SORT(1)_count --&gt; raw count value in the sorted sample replicate (1), NAs replaced by 0.001<br># IND_FPTM --&gt; normalized FPTM value in the baseline (unsorted) library <br># SORT(1)_FPTM --&gt; normalized FPTM value in the sorted sample replicate (1)<br># logFC_(1) --&gt; log2(SORT(1)_FPTM/IND_FPTM)
DOI: 10.6084/m9.figshare.5349964
title: Human transcriptome GRCh38 known protein-coding

description: Fasta file used for mapping of sequenced SECRiFY fragments<br>
DOI: 10.6084/m9.figshare.5349964.v1
title: Human transcriptome GRCh38 known protein-coding

description: Fasta file used for mapping of sequenced SECRiFY fragments<br>
DOI: 10.6084/m9.figshare.5349967.v1
title: Metabolite BridgeDb ID Mapping Database (20170826)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 154, and Wikidata (26 August 2017) as data sources. Two significant changes: Mappings to the EPA CompTox Dashboard have been added (about 36 thousand) and it is using a newer HMDB 3.6 version with many more compounds. If you experience problems, please report on the project page. See the attached QC for more details on the changes.<br>If you use this data in your research, please cite that data set, and the BridgeDb, ChEBI, and HMDB articles.
DOI: 10.6084/m9.figshare.5349955.v2
title: P. pastoris fragment datasets

description: Results data of two-round SECRiFY screens of human (HEK293) cDNA fragments in P. pastoris (3 replicate screens). Sequencing data was mapped on the human GRCh38 transcriptome assembled using known transcripts from protein-coding genes only.<br>"Pp_resultstable_all.txt" = all in-frame fragments detected in either the unsorted baseline library (merged for 3 replicates), or in all 3 sorted replicate samples. <br>"Pp_resultstable_enriched.txt" = those with log_FC &gt; 1 in all three replicates (10404)<br>"Pp_resultstable_depleted.txt" = those with log_FC &lt; -1 in all three replicates (141357)<br><br>For each fragment, the following information is provided:<br><br># Ensembl_geneID --&gt; Ensembl gene ID<br># Ensembl_txID --&gt; Ensembl transcript ID<br># tx_start --&gt; Transcript start position on human genome GRCh38<br># tx_end --&gt; Transcript end position on human genome GRCh38<br># chr --&gt; chromosome #<br># gene_symbol --&gt; official gene symbol<br># frag_start --&gt; fragment start position on the transcript, 0-based <br># frag_stop --&gt; fragment end position on the transcript, 0-based<br># cDNA --&gt; DNA sequence of the fragment<br># protein --&gt; translated AA sequence of the fragment in frame 1<br># IND_count --&gt; raw count value in the baseline (unsorted) library (merged for 3 replicates), NAs replaced by 0.001<br># SORT(1)_count --&gt; raw count value in the sorted sample replicate (1), NAs replaced by 0.001<br># IND_FPTM --&gt; normalized FPTM value in the baseline (unsorted) library <br># SORT(1)_FPTM --&gt; normalized FPTM value in the sorted sample replicate (1)<br># logFC_(1) --&gt; log2(SORT(1)_FPTM/IND_FPTM)