Find research datasets worth reusing

Figure 6 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution

Figure 6. Comparison of Boardman et al.11 and Tihelka et al.20 meta-analyses with Fig. 2. Ŀe base phylogram is a Maximum Parsimony analysis calculated as in Fig. 2, with the addition of two problematic sequences mentioned in the text, KY926882 and KY926883, attributed to A. m. syriaca and A. m. intermissa, respectively. Ŀe 17 sequences used by Boardman et al. are marked "B" and the 16 sequences used by Tihelka et al. "T", with the 11 sequences common to both sets "TB". Note the anomalous pairwise placements of two sequences attributed to KY026882 and KY926883 with respect to their nominal sister subspecies (* and *, respectively).

Figure 1 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution

Figure 1. Maximum Parsimony analysis of phylogenetic relationships among mtDNA genomes sequences of nine species of Apis honey bees. (a) Ŀe tree is rooted with a bumblebee Bombus ignitus as outgroup. A. m. mellifera (KY926884) is the basal-most member of that species and the alignment reference. Numbers above branches are inferred numbers of nucleotide substitutions; numbers in bold below branches are percent support in 3000 bootstrap replicates. Identical branching order and substantially similar bootstrap support are given by Maximum Likelihood and Neighbor Joining methods. (b) As above, with removal of Bombus and addition of key subspecies of A. mellifera (cf. Fig. 2).

Figure 4 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution

Figure 4. An mtDNA-based molecular clock for within- and among-subspecies divergences of A. mellifera. Sequences are coded as in Fig. 2: only one representative each of A. m. scutellata and A. m. capensis is included (n = 37). Divergence times are calculated from a linearized ML model with A. m. mellifera sequences as the designated outgroup (cf. Supplementary Fig. S2). Ŀe clock is calibrated from the mean linearized nucleotide subs/site distances to each node (Relative Time) at 0.0115 subs/site/Myr (see text for sample calculation). See Supplementary Fig. S4 for the clock of A. mellifera within Apis, with Bombus as the designated outgroup.

Figure 3 in Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution

Figure 3. Phylogeographic evolution in context of geographic distribution2 of subspecies of A. mellifera as inferred from mitogenomic data. Numbered symbols indicate five clades described in the text and in Fig. 2. Dark and light green circles indicate respectively subspecies in the Southeast European and Asia Minor clades included within the Eurasian superclade. Blue symbols indicate the Levantine (circles), Nilotic (squares), and Arabian (A. m. jemenitica) (diamonds) clades. Light and dark purple circles indicate independent A. m. simensis and A. m. unicolor lineages, respectively. Light orange symbols indicate subspecies in the Mediterranean clade. Red circles indicate the paraphyletic assemblage of A. m. scutellata and A. m. capensis, including A. m. adansonii (light red) and A. m. monticola (brown). Base map modified from [https://commons. wikimedia.org/wiki/File:BlankMap-World.svg].

opencc-by-4.0Oct 2022View details →

Capacity Building for GIS-based SDG Indicator Analysis with Global High-resolution Land Cover Datasets - training datasets

Sample datasets for the Case Studies section of the Capacity Building for GIS-based SDG Indicator Analysis with Global High-resolution Land Cover Datasets web book (<a href="https://isprs-gis-sdg.readthedocs.io">https://isprs-gis-sdg.readthedocs.io</a>)

opencc-by-4.0Jul 2023View details →

MechRepoNet with DrugCentral Indications Knowledge Graph

Mechanistic Repositioning Network with Indications (MIND) is a knowledge graph incorporating two biomedical resources: MechRepoNet and DrugCentral. MechRepoNet is a knowledge graph comprising of 18 biomedical resources that reflects and expands on important drug mechanism relationships identified from a curated biomedical drug mechanism dataset. MechRepoNet consists of 9,652,116 edges, 250,035 nodes, 9 node types and 22 relations. DrugCentral is a curated, open-access, online resource that integrates structure, bioactivity, regulatory, pharmacologic actions and approved drug indications from the FDA and other regulatory agencies. As of October 2021, DrugCentral has 11,292 indications, consisting of 2,494 unique compounds and 1,459 unique diseases. MIND was created by mapping DrugCentral edges to existing MechRepoNet nodes through the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH). A total of 5,379 indication edges made up of 1,308 unique compounds and 1,030 unique diseases were mapped to MechRepoNet. DrugCentral edges incorporated in MIND are labeled have the relationship indication. The indication edge is differentiated from the treat edge in that the latter represents a weaker link between a drug and a disease as some treat edges are not approved by a regulatory body in contrast to the former. In MIND, when both indication and treat edges exist, indication superseded and replaced treat edges. The MIND training set has a total of 9,651,040 edges.  The indications from DrugCentral were divided into a train set (80%; 4303 triples) and a test/valid set (20%; 1076 triples; test.txt/valid.txt). The DrugCentral train set was merged into MechRepoNet to form the train.txt file.

opencc-by-4.0Nov 2020View details →

Towards an Assessment Rubric for EiPE Tasks in Secondary Education: Identifying Quality Indicators and Descriptors

This study reports on reseach to investigating indicators and descriptors which characterize the quality of students’ code explanations to EiPE (Explain in Plain English) tasks in secondary education.  First, a literature review was carried out to identify quality characteristics and descriptors that differentiate the quality of students’ responses in tertiary education. Then, the quality of upper-secondary students’ responses to a simple EiPE task was analyzed. The results of that analysis were used to refine our quality characteristics and descriptors, which were then translated into a prototypical rubric. In the final phase, the rubric was iteratively tested by two teachers and improved based on their feedback. The final rubric prototype can be used to provide feedback during formative assessment. This repository includes the EiPE comprehension task, the student responses, and the results from coding the responses: - StudentResponses.pdf: task and anonymized solutions provided by students, translated to English - Coding_data.xls: coding by two researchers until they came to an agreement (full set of 34 responses), and coding by Teacher1 on complete set, and coding by Teacher2 on the base-set (with duplicate responses omitted)

opencc-by-4.0Dec 2022View details →

Adopted Ranking Methodology for Emerging National Importance Technical Institutions: A Correlation Analysis and Dominance of Research Performance Indicators

The article presents the research performance of newly established technical institutes in India. It gives an overview of NTU and NIRF ranking methodologies. This research would help institutions to check their performance and identify ways to strengthen their rank by producing more output with high-impact research work. The article provides appropriate input to the technical institutions under the study to set out practical and pedagogical approaches, and cross-institutional as well as international collaboration to achieve their research goals. The article gives rank to the technical institutes under the study based on their research performance using the NTU ranking methodology.

FIG. 4 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 4. — Community weighted mean proportions of functional traits for each vegetation type: A, growth forms; B, substrate; C, reproductive structure types; D, photobionts.

FIG. 3 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 3. — Ordination and clustering of lichen communities from the different vegetation types: A, non-parametric multidimensional scaling (NDMS); B, cluster analysis dendrogram. The sites Cerro el Capulín and Cerro Juan el Grande show different affinities in both analyses (part of the xerophytic shrubland in the NDMS, but more similar to the Quercus L. forest in the dendrogram, labeled as the Xerophytic-Quercus group in the latter).

FIG. 5 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 5. — Non-metric Multidimensional Scaling analysis of lichen community functional traits and environmental variables in three vegetation types. * (p <0.05) and ** (p <0.005) represent the significance of functional traits related to the Xerophytic shrubland (X), Subtropical shrubland (S), and Quercus L. forest (Q).

FIG. 1 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 1. — Amplitude and mean values of alpha diversity (species richness) per vegetation type. Symbols: black dot, outlier; white dots, mean values.

FIG. 6 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 6. — Correlation of lichen community functional traits and environmental variables in three vegetation types.

FIG. 2 in Lichen community assemblages and functional traits as indicators of vegetation types in central Mexico, based on herbarium specimens

FIG. 2. — Beta diversity and shared species per vegetation type: A, pairwise comparisons of the different elements of beta diversity (Xerophytic, xerophytic shrubland; Quercus, Quercus forest; Subtropical, subtropical shrubland); B, Venn diagram showing exclusive and shared species among the vegetation types included in this study.

Dinoflagellate cysts and benthic foraminifera from surface sediments of Svalbard fjords and shelves as paleoenvironmental indicators

Supplementary Table 1. Seasonally averaged sea-ice cover, SST and SSS data used for the multivariate statistical analysis. Supplementary Table 2. Relative abundances of individual dinoflagellate cyst taxa, total cyst concentration [cysts g-1], and relative abundance of auto- and heterotrophic cysts at each station. Supplementary Table 3. Relative abundances of individual benthic foraminifera taxa, total benthic foraminifera concentration [forams g-1], and relative abundance of calcareous and agglutinated benthic foraminifera at each station.

opencc-by-4.0Oct 2022View details →

Developing circularity, renewability and efficiency indicators for sustainable resource management : propanol production as a showcase

The data used for the exergy calculations in the associated article.

dryad40/100

Predator exclosures increase nest success but reduce adult survival and increase dispersal distance of Piping Plovers, indicating exclosures should be used with caution

Diagnosing unsuccessful population outcomes for endangered species requires understanding relationships among vital rates, ecological conditions, and management variables, including unintended consequences of management actions. The federally-threatened Piping Plover (Charadrius melodus) has remained below recovery goals, despite intensive management, including the use of nest exclosures to protect eggs from predation. We studied ecological factors and management actions affecting nest success, survival, site fidelity, and dispersal of the New Jersey, USA population of Piping Plovers over a seven-year period, focused on evaluating the impact of exclosures on demography. While exclosures increased nest success by 62% over a 34-day period, exclosed nests were 4.7 times more likely to be abandoned, which was likely a consequence of adult mortality. Abandoned nests were associated with lower adult survival, particularly for males, but there was evidence that site fidelity was greater for birds whose last nest was exclosed vs. unexclosed. Regardless of exclosure status, females who abandoned their first nesting attempt dispersed 10 times farther between attempts than those whose first nest attempts were lost to other causes. Moreover, females that abandoned their last nesting attempts dispersed farther than females that lost their last nest to predation or flooding. This difference was more substantial for males. Our results corroborate studies documenting adverse impacts of exclosures on survival, and, for the first time, demonstrate that surviving mates (particularly females) emigrate from the breeding site, resulting in a realized loss of a local breeding pair. Further, we used an online population project model (i.e., PiperEx) to demonstrate that exclosures are not expected to improve growth rates in New Jersey. We conclude that there is a tradeoff among increased nest survival, reduced adult survival and increased emigration rates, and we encourage managers to consider whether exclosures are worth the protection of eggs from predators using online decision support tools.

opencc-zeroSep 2023View details →

opencc-by-4.0Jul 2023View details →

Standard heat stress indices may not be appropriate for assessing marathons

Code and data supporting the manuscript "Standard heat stress indices may not be appropriate for assessing marathons". These scripts rely on some of the data being present in a certain location. But to reproduce this based on the included data, you need only run pet_calculations.py as all the data area in comrades.nc The order in which the scripts were run was: 1. get_utci.py - downloads ERA5-HEAT data 2. unzip_era5_heat.sh - unzips that data 3. query.py - subsets ERA5-HEAT data, and ERA5 data from CEDA 4. pet_calculations.py - calculations and analysis pet_calculations.ipynb shows the results of pet_calculations.py in notebook form.

opencc-by-4.0Oct 2021View details →

Høje-Taastrup - Sankey and indicator data for construction sector

This excel sheet was made by the CityLoops course participants for Høje-Taastrup, Denmark and contains the data needed for the Sankey diagram and indicators for the Sector-wide Circularity Assessment for the Biomass and Construction sectors.  "CityLoops - Closing the loop for urban material flows" is a EU Horizon2020 project with <a href="https://cityloops.metabolismofcities.org/partners/">28 partners</a>. (Official project website: <a href="https://cityloops.eu/">https://cityloops.eu/</a>). CityLoops brings together six ambitious European cities to demonstrate a series of innovative tools and urban planning approaches, aimed at closing the loops of urban material flows and increasing their regenerative capacity. (For detailed information please visit: <a href="https://cityloops.metabolismofcities.org/dashboards/bodo/datasets/1004599/">https://cityloops.metabolismofcities.org/library/1009545/</a>)