Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Bibliometric and performance data of Unisinos' Postgraduate Program in Biology and code to analyze production and impact.

Zip file containing data and R code for running analysis in the MS titled "Productivity and impact of the Unisinos’ Postgraduate Program in Biology and the consequences of its interruption for Brazilian scienceProductivity and impact of the Unisinos’ Postgraduate Program in Biology and the consequences of its interruption for Brazilian science" authored by Piter Kehoma Boll and Lucas Krüger.

opencc-by-4.0Feb 2023View details →

A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology

This data set includes: Luminescence (NeoLuc Luminescence), Fluorescence (eGFP) , NeoLuc/eGFP ratios, Area Under The Curve of NeoLuc/eGFP ratios, Normalized Area Under The Curve of Neoluc/eGFP (FBP-RTAs), Firefly Luciferase luminescence (FLuc), Renilla Luciferase luminescence (RLuc), FLuc/RLuc ratios and Normalized  FLuc/RLuc values of all experiments in this work.

opencc-by-4.0Sep 2022View details →

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas"

Table 1. CCF Specimen, Biological Structure, and Spatial Ontology. For each ontology, we provide all class names, property names, entity Internationalized Resource Identifier (IRI), definition when available, and entity type. Table 2. 3D Reference Objects. The 3rd HRA release features 53 Spatial Entities of type Spatial Object Reference that are linked to anatomical structures in the ASCT+B tables plus 43 Spatial Entities of type Extraction Site. For each entity, we provide the spatial entity name, 3D object file name, ID and version number, organ label, sex, and type. Note that a landmark is a Spatial Entity that has been tagged as an Extraction Set for a specific Extraction Site, see Table 3. Table 3. Registered Tissue Data. This table shows 364 Extraction Site entities that either represent the registration location for Tissue Blocks or Registration Sites. For each, we provide consortium name and entity ID, HuBMAP ID if available, and experimental data donor sex as well as HRA data such as organ name, sex, Uberon ID, and GLB file. The data comes from four consortia. HuBMAP data includes 306 tissue blocks, and many of these have derived tissue sections with one or more associated datasets. The 29 well-defined GTEx extraction set sites link to 5,397 datasets. The 26 SPARC blocks link to one paper while the three KPMP tissue blocks link to two data publications.

opencc-zeroMar 2023View details →

Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modelling framework, which determines the time-dependency of DNA variant-age-at-onset associations, without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the sign of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages, and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age-dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modelling of large-scale biobank data.

opencc-by-4.0Mar 2023View details →

Process controlling iron-manganese regulation of the Southern Ocean biological carbon pump

Netcdf output files at the end of 100-year run Fe-Mn co-limitation model experiments on the ORCA2 grid, as described and discussed in Anugerahanti, et al., in Process controlling iron-manganese regulation of the Southern Ocean biological carbon pump, Philosophical Transactions of the Royal Society A, 2022

A dark side of conservation biology: protected areas fail in representing subterranean biodiversity. Databases.

We obtained distribution data for leiodids by digitizing the information provided by Fresneda and Salgado (2017). This information was updated and expanded with additional data from several sampling campaigns (unpublished data). For subterranean spiders, we included the entirety of the Alps range extending from France in the east westward through Switzerland, Italy, Liechtenstein, Austria, Germany, and Slovenia, by integrating available data in Global Biodiversity Information Facility (GBIF), Spider of Europe), Araneae.it  and other literature sources.

Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer

Spatial transcriptomic data (counts_DSP_afterQC_normalisation.csv) derived using the Nanostring GeoMx digital spatial profiler platform to analyse tumor deposits and lymph node metastases from 10 patients with colorectal cancer. 264 AOIs of cancer transcriptome atlas data.  Normalised using Q3 normalisation, for further information on methods see associated publication.

Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

GenBank accession numbers for nuclear sequence records used to build phylogenetic tree in manuscript entitled "Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study". Nuclear sequences and GenBank accession numbers originally from multigene alignment and supplementary material published in Rabosky et al. (2018; 2019). Rabosky, D.L., Chang, J., Title, P.O. et al. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559, 392–395 (2018). https://doi.org/10.1038/s41586-018-0273-1 Rabosky, Daniel L. et al. (2019), Data from: An inverse latitudinal gradient in speciation rate for marine fishes, Dryad, Dataset, <a href="https://doi.org/10.5061/dryad.fc71cp4">https://doi.org/10.5061/dryad.fc71cp4</a>

Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

These data files are associated with the manuscript entitled: "Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study" by Jacqueline A. May, Zeny Feng, and Sarah J. Adamowicz. This project entailed an evaluation of missing data handling approach on inferences using a molecular evolution case study. A target mixed-type dataset was first imputed using a real data-driven strategy for imputation method selection. Both trait-only (non-phylogenetic) and phylogenetic imputation methods were used to impute the dataset. Phylogenetic generalized least squares (PGLS) analyses were then applied to the complete-case and imputed datasets, specifying the traits as predictors and molecular evolutionary rates as the response variable. Those traits that associate significantly with molecular rates were identified and PGLS models compared to determine how the approach for handling missing data impacts biological inferences and conclusions. The files stored here are the trees built for phylogenetic imputation (RAxML tree and ultrametric tree versions) and the corresponding GenBank accession numbers.

Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial & nuclear biology

This online depository corresponds to manuscript : Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial & nuclear biology. Authors: Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau, Claudia Manzoni Whilst the majority (~90-95%) of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. However, in the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring an increased risk of developing PD across the population.  A recently developed mitophagy screening assay of GWAS candidates, has functionally implicated the non-specific lethal (NSL) complex, a chromatin remodeler, in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. A multi-layered approach has been taken to; i) build the ‘mitochondrial’ NSL interactome, applying PD gene-set enrichment analysis to explore the relevance of the NSL mitochondrial interactome to PD and, ii) build the PD-oriented NSL interactome, using functional enrichment, to uncover biological pathways underpinning the NSL /PD association.

Integrated multi-omics analysis of early lung adenocarcinoma links tumor biological features with predicted indolence or aggressiveness

This is a collection of datasets presented in the manuscript "Multi-omics data analysis identifies correlations between tumor biology features and predicted behaviors in early lung adenocarcinoma". This study provides a comprehensive profiling of LUAD indolence and aggressiveness at the biological bulk and single cell levels, as well as at the clinical and radiomics levels. This hypothesis generating study uncovers several potential future research avenues. It also highlights the importance and power of data integration to improve our systemic understanding of LUAD and to help reduce the gap between basic science research and clinical practice.

opencc-zeroMay 2023View details →

Scaling of biological rates with body size as a backbone in the assembly of metacommunity biodiversity

The dispersal-body mass association has been highlighted as a main determinant of biodiversity patterns in metacommunities. However, less attention has been devoted to other well recognized determinants of metacommunity diversity: the scaling in density and regional richness with body size. Among active dispersers, the increase in movement with body size may enhance local richness and decrease beta diversity. Nevertheless, the reduction of population size and regional richness with body mass may determine a negative diversity-body size association. Consequently, metacommunity assembly probably emerges from a balance between the effect of these scalings. We formalize this hypothesis relating the exponents of size-scaling rules with simulated trends in alpha, beta, and gamma diversity with body size. Our results highlight that the diversity-body size relationship in metacommunities may be driven by the combined effect of different scaling rules. Given their ubiquity in most terrestrial and aquatic biotas, these scaling rules may represent the basic determinants—backbone—of biodiversity, over which other mechanisms operate determining metacommunity assembly. Further studies are needed, aimed at explaining biodiversity patterns from functional relationships between biological rates and body size, as well as their association with environmental conditions and species interactions.

opencc-zeroMay 2023View details →

Fire severity as a key determinant of aboveground and belowground biological community recovery in managed even-aged boreal forests

Changes in fire regime of boreal forests in response to climate warming are expected to impact post-fire recovery. However, quantitative data on how managed forests sustain and recover from recent fire disturbance are limited. Two years after a large wildfire in managed even-aged boreal forests in Sweden, we investigated how recovery of aboveground and belowground communities, i.e., understory vegetation and soil microbial and faunal communities, responded to variation in the severity of soil (i.e., consumption of soil organic matter) and canopy fires (i.e., tree mortality). While fire overall enhanced diversity of understory vegetation through colonization of fire adapted plant species, it reduced the abundance and diversity of soil biota. We observed contrasting effects of tree- and soil-related fire severity on survival and recovery of understory vegetation and soil biological communities. Severe fires that killed overstory Pinus sylvestris promoted a successional stage dominated by the mosses Ceratodon purpureus and Polytrichum juniperum, but reduced regeneration of tree seedlings and disfavoured the ericaceous dwarf-shrub Vaccinium vitis-idaea and the grass Deschampsia flexuosa. Moreover, high tree mortality from fire reduced fungal biomass and changed fungal community composition, in particular that of ectomycorrhizal fungi, and reduced the fungivorous soil Oribatida. In contrast, soil-related fire severity had little impact on vegetation composition, fungal communities and soil animals. Bacterial communities responded to both tree- and soil-related fire severity. Synthesis: Our results two years post-fire suggest that a change in fire regime from a historically low-severity ground-fire regime, with fires that mainly burns into the soil organic layer, to a stand-replacing fire regime with a high degree of tree mortality, as may be expected with climate change, is likely to impact the short-term recovery of stand structure and above- and belowground species composition of even-aged P. sylvestris boreal forests.

openMay 2023View details →

Supplemental Files to "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs"

These are supplemental files to the manuscript, "Mining biodiversity databases establishes a global baseline of cosmopolitan Insecta mOTUs: a case study on Platygastroidea (Hymenoptera) with consequences for biological control programs". Supplements contain excel spreadsheets, DNA alignments, Newick tree files, FigTree files, and csv files.

opencc-zeroMay 2023View details →

Data from: Behaviour-specific spatiotemporal patterns of habitat use by sea turtles revealed using biologging and supervised machine learning

<ol> <li>Conservation of threatened species and anthropogenic threat mitigation commonly rely on spatially managed areas selected according to habitat preference. Since the impact of threats can be behaviour-specific, such information could be incorporated into spatial management to improve conservation outcomes. However, collecting spatially explicit behavioural data is challenging.</li> <li>Using multi-sensor biologging tags containing high-resolution movement sensors (e.g., accelerometer, magnetometer, GPS) and animal-borne video cameras, combined with supervised machine learning, we developed a method to automatically identify and geolocate typically ambiguous behaviours for the poorly understood flatback turtle Natator depressus. Subsequently, we evaluated behaviour-specific spatiotemporal patterns of habitat use.</li> <li>Boosted regression trees successfully identified the presence of foraging and resting in 7074 dives (AUC > 0.9), using dive features representing characteristics of locomotory activity, body posture, and three-dimensional dive paths validated by ancillary video data. Foraging was characterised by dives with longer duration, variable depth, tortuous bottom phases; resting was characterised by dives with decreased locomotory activity and longer duration bottom phases.</li> <li>Foraging and resting showed minimal spatial segregation based on 50% and 95% utilisation distributions. Expected diel patterns of behaviour-specific habitat use were superseded by the extreme tides at the near-shore study site. Turtles rested in areas close to the subtidal and intertidal boundary within larger overlapping foraging areas, allowing efficient access to intertidal food resources upon inundation at high tides when foraging was ~25% more likely.</li> <li> Synthesis and applications: Using supervised machine learning and biologging tools, we show the potential for dynamic spatial management of flatback turtles to mitigate behaviour-specific threats by prioritising protection of important locations at pertinent times. Although results are a species-specific response to a super-tidal environment, our approach can be generalised to a broad range of taxa and study systems, facilitating a conceptual advance in spatial management.</li> </ol>

opencc-by-4.0May 2023View details →

Figure S2. Spearman correlation matrix representing the relationships between the essential trace elements within each biological matrix

Blue represents a positive correlation, while red represents a negative correlation. Color intensity is proportional to the correlation strength. Strikethrough values represent insignificant/negligible associations (p>0.05). Cr, chromium; Cu, copper; Fe, iron; Li, lithium; Mn, manganese; Mo, molybdenum; Se, selenium; Zn, zinc

opencc-by-4.0May 2023View details →

Fig. 1 in Ex-situ conservation of the critically endangered swamp forest crab Parathelphusa reticulata Ng, 1990 (Decapoda: Brachyura: Gecarcinucidae): observations on its reproduction and biology in captivity

Fig. 1. Captive breeding facility in the Singapore Botanic Gardens. Photograph: Daniel J. J. Ng.

opencc-by-4.0Jun 2023View details →

Raw data for Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity

Raw data for growth curves and fluorescence/OD ratio for article "Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity"

opencc-zeroJun 2023View details →

Breeding biology and nesting behaviour of the endemic subspecies of White-eyed Vireo (Vireo griseus bermudianus) on the Bermuda archipelago

See full abstract by searching the title of this article on the Journal of Field Ornithology webpage, ResearchGate, or Google Scholar.