Find research datasets worth reusing

opencc-by-4.0Jun 2017View details →

Fig. 1 in Classificação Digital de Cicadidae com Wavelets e Support Vector Machines

Fig. 1. Ninfa móvel de Quesada gigas

opencc-by-4.0Jun 2017View details →

Fig. 2 in Classificação Digital de Cicadidae com Wavelets e Support Vector Machines

Fig. 2. Cigarras da espécie Quesada gigas, envolvidas nos experimentos

CONSORT flow diagram for The assessment of educational and supportive care to the infertile females undergoes In Vitro Fertilization procedure by clinical pharmacist: a randomized clinical trial

The assessment of educational and supportive care to the infertile females undergoes In Vitro Fertilization procedure by a clinical pharmacist: a randomized clinical trial.

Electronic supporting information for: Evolution of posture in amniotes–diving into the trabecular architecture of the femoral head

Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.

Supporting information for: Accounting for the topology of road networks to better explain human-mediated dispersal in terrestrial landscapes

Human trade and movements are central to biological invasions worldwide. Human activities not only transport species across biogeographical barriers but also accelerate their post-introduction spread in the landscape. Thus, by constraining human movements, the spatial structure of road networks might greatly affect the regional spread of invasive species. However, few invasion models have accounted for the topology of road networks so far, and its importance for explaining the regional distribution of invasive species remains mostly unexplored. To address this issue, we developed a spatially explicit and mechanistic human-mediated dispersal model that accounts and tests for the influence of transport networks on the regional spread of invasive species. Using as a model the spread of the invasive ant Lasius neglectus in the middle Rhône valley (France), we show that accounting for the topology of road networks improves our ability to explain the current distribution of the invasive ant. In contrast, we found that using human population density as a proxy for the frequency of transport events decreases models' performance and might thus not be as appropriate as previously thought. Finally, by differentiating road networks into sub-networks, we show that national and regional roads are more important than smaller roads for explaining spread patterns. Overall, our results demonstrate that the topology of transport networks can strongly bias regional invasion patterns and highlight the importance of better incorporating it into future invasion models. The mechanistic modelling approach developed in this study should help invasion scientists explore how human-mediated dispersal and topography shape invasion dynamics in landscapes. Ultimately, our approach could be combined with demographic, natural dispersal and environmental suitability models to refine spread scenarios and improve invasive species monitoring and management at regional to national scales.

opencc-by-4.0Jun 2023View details →

AlphaFold models and supporting data for the annotation of Vairimorpha necatrix

V_necatrix_alphafold.zip - Contains AlphaFold models and associated files for all V. necatrix proteins.chimerax_annotater_plugin.zip - Contains the ChimeraX plugin we developed and used to annotate the V. necatrix proteome.v_necatrix_annotation_data.zip - Contains all data used in the ChimeraX plugin to annotate the V. necatrix proteome.V_necatrix_proteome.fasta - Protein fasta file containing all protein sequencesV_necatrix_haplotype[1-4].fasta - Nucleotide fasta file for each haplotype

opencc-by-4.0Sep 2022View details →

Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation (GGA) functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.This supporting dataset includes results of PBE0+MBD, PBE+MBD, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at <a href="https://doi.org/10.48550/arXiv.2209.02687">https://doi.org/10.48550/arXiv.2209.02687</a>.

Supplementary data supporting "3D diffusion of water in melt inclusion-bearing olivine phenocrysts"

Supplementary_DataS1Secondary Ion Mass Spectrometry (SIMS) data of water concentrations in olivine crystals from the 1977 Seguam eruption used in this study. Electron probe microanalyser (EPMA) data of major elements and crystal orientations from electron backscatter diffraction (EBSD) are also included.Supplementary_DataS2Model inputs and outputs for the Monte Carlo diffusion modelling used in this study for water loss from a melt inclusion during magma decompression. Spreadsheet includes water loss estimated by 3D, 2D and 1D numerical models in addition to the anisotropic analytical solution. It also includes the inverted decompression rates from the 2D, 1D and analytical models.

opencc-by-4.0Aug 2023View details →

Phlorest phylogeny derived from Sicoli & Holton 2014 'Linguistic phylogenies support back-migration from Beringia to Asia'

Cite the source of the dataset as: <blockquote> Sicoli MA & Holton G (2014) Linguistic phylogenies support back-migration from Beringia to Asia. PLoS One 9(3):e91722. </blockquote>

opencc-by-4.0Jun 2023View details →

Supporting data for Bryłka et al., 2023 Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms.

These are supporting files used in the analysis in Bryłka et al., 2023 "Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms".  All data newly generated from the Alverson lab.

Data and analysis scripts: Evidence supporting an evolutionary trade-off between material properties and architectural design in Anolis lizard long bones

In biology, 'many-to-one mapping' occurs when multiple morphological forms can meet a particular functional demand. Knowledge of this mapping is crucial for understanding how selection on performance shapes the evolution of morphological diversity. Past research has focused primarily on the potential for geometrically alternative morphological designs to produce equivalent performance outcomes. Here we ask whether the material properties of biological tissues hold similar potential. Through phylogenetic comparative study of Anolis lizards, we show that the architectural design and mineral density of the femur trade off in a many-to-one functional system, yielding a morphospace featuring parallel isolines in size-relative bending strength. Anole femur evolution has largely tracked a narrow band of strength isolines over phylogenetic timescales, suggesting that geometry and mineral content shape the course of macroevolution through compensatory effects on performance. Despite this conserved evolutionary relationship, insular and continental species evolve strong bones differently, likely reflecting underlying ecological differences. Mainland anoles, which exhibit fast-paced life histories, typically have femora with lower mineralization and thinner walls than island species, which exhibit the opposite strategy. Together, our results reveal an overlooked dimension in the relationship between form and function, expanding our understanding of how many-to-one mapping can shape patterns of phenotypic diversity.

Supporting Data - The influence of additionality and time-matching requirements on the emissions from grid-connected hydrogen production

This dataset contains all case input and outputs for the analysis done in The influence of additionality and time-matching requirements on the emissions from grid-connected hydrogen production.

Supporting data files for "Binding Sites of Bicarbonate in PEP Carboxylase"

The files in this archive are the supporting data for the article "Binding Sites of Bicarbonate in PEP Carboxylase". The article contains all scripts and input files used to perform and analyse the simulations.

Supporting data for von Fromm et al. (2023) Controls on timescales of soil organic carbon persistence across sub-Saharan Africa

This file contains the supporting data for von Fromm et al. (2024) Controls on timescales of soil organic carbon persistence across sub-Saharan Africa, Global Change Biology, <a href="https://doi.org/10.1111/gcb.17089">https://doi.org/10.1111/gcb.17089</a> We used wet soil chemistry data from Vågen et al., 2021 (<a href="https://doi.org/10.34725/DVN/66BFOB">https://doi.org/10.34725/DVN/66BFOB</a>). In addition, we added newly measured radiocarbon data, extracted global climate data, gross primary productivity and quantified soil mineralogy based on X-ray powder diffraction data. Turnover time for carbon (mean C age) was calculated from Δ14C (&permil;) values by using an one-pool model. For more details about the sampling, calculations, and units see the associated publication. To reproduce all analysis, including calculating the mean C age, please visit the author's github page: <a href="https://github.com/SophievF/AfSIS_14C">https://github.com/SophievF/AfSIS_14C</a>.  The dataset is also part of the International Soil Radiocarbon Database (<a href="https://soilradiocarbon.org/">https://soilradiocarbon.org/</a>).

Wellbeing, resilience and peer support

The idea of Wellbeing can mean many different things, covering elements of mental, emotional, physical, social and societal functions. Whatever your definition, it's worth looking after. So, how can you do that exactly? In todays episode, we hear from  Dr Dianne Wepa, Associate Professor at Charles Darwin University in Australia, and Prof Haaken Strand of the Charles Darwin University Faculty of Health. They discuss what is meant by wellbeing in different cultures, and when facing different challenges, be they personal, professional, or global. Read the original article: <a href="https://doi.org/10.1016/j.ijnsa.2023.100144">https://doi.org/10.1016/j.ijnsa.2023.100144</a>

Data supporting: Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphology. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group. Here we identify an accession of Acacia crassicarpa with high regeneration rates and isolate a clone for genome sequencing. We generate a chromosome-level assembly of this readily transformable clone and using comparative analyses confirm a whole genome duplication unique to Caesalpinoid legumes. This resource will be important for future work examining genome evolution in legumes and the unique developmental genetic mechanisms underlying unifacial morphogenesis in Acacia.

Dataset from publication "Predicting context-sensitive urban green space quality to support urban green infrastructure planning"

Data Description:This dataset presents the spatial outcome of an analysis modelling perceived green space quality across the city of Espoo, Finland. The analysis relies on data gathered through the My Espoo on the Map survey (Mun Espoo kartalla) in the autumn of 2020 as part of the NordForsk-funded research project NORDGREEN. A comprehensive account of the analytical process and potential applications of the dataset is available in the associated publication, "Predicting context-sensitive urban green space quality to support urban green infrastructure planning" (open access: <a href="https://doi.org/10.1016/j.landurbplan.2023.104952">https://doi.org/10.1016/j.landurbplan.2023.104952</a>).Data Processing:This dataset results from an analysis that integrates both primary and secondary sources of geospatial data. The primary data were collected with an online public participation GIS (PPGIS) survey directed for the adult inhabitants of Espoo. The data collection took place in September-October 2020 and was executed in collaboration with Aalto University and the City of Espoo. For a detailed overview of the data collection process, please refer to the related publication.Data characteristics:Format: Shapefile (50m x 50m grid)Geographical area: Espoo, FinlandSpatial reference: EUREF FIN TM35FINNote: Only grid cells intersecting with greenspace have been included in the dataset. For the employed definition of green areas, please consult the related publication.Data attributes and their descriptions:"P_PROB": Probability (P), positive perceived quality"N_PROB": Probability (P), negative perceived qualityFunding: This research was funded by NordForsk, Sustainable Urban Development and Smart Cities Programme, Project Smart Planning for Healthy and Green and Nordic Cities – NORDGREEN, under Grant Number: 95322.

Support information for HiCDiff

The dataset contains all the raw data  and processed data used in HiCDiff, is supplement to GitHub repository: <a href="https://github.com/BioinfoMachineLearning/hicdiff">https://github.com/BioinfoMachineLearning/hicdiff</a>

opencc-by-4.0Dec 2023View details →

Data supporting "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables"

This repository contains the set of data and the code to reproduce the results shown in "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables" published on Journal of Chemical Engineering and Data (DOI: 10.1021/acs.jced.3c00538).