Find research datasets worth reusing

opencc-by-4.0Dec 2022View details →

Single-cell and spatial transcriptomics of cardiac neural crest reveal a dual role of vinculin in Tgf beta signaling and cell-extracellular matrix interaction during cardiac outflow tract development

single-cell RNA-seq data analysis: all.cncc.combined.EMBO.mapped.Rdata: public CNCC single-cell RNA-seq data integration E13.5_CNCC_merged_updated.Rdata: single-cell RNA-seq data of E13.5 CNCC generated in Elly lab all.seurat.GFP.Rdata: scRNA-seq data with GFP detected visium.merge_AB.control.Rdata: R processed ST data for slice A and B visium.merge_CD.mutant.Rdata: R processed ST data for slice A and B

Supporting Students in Team-Based Software Development Projects: An Exploratory Study - Dataset

Dataset for the paper "Supporting Students in Team-Based Software Development Projects: An Exploratory Study"

opencc-by-4.0Aug 2022View details →

Developers' Visuo-spatial Mental Model and Program Comprehension

Dataset for the paper entitled: "Developers' Visuo-spatial Mental Model and Program Comprehension"

Software tools used in ROMI: a quick look into some of the tools used to develop ROMI

The following video describes ROMI's principles and methods for designing with free and open source software and hardware. Funded by EU Grant 773875. Videos are available in: <ul> <li>Hi-res (1080p Apple ProRes)</li> <li>Mid-res (1080p H265)</li> </ul> Video script: (BARBERAN) ROMI develops open tools for farming communities. But I prefer not to say open tools I prefer to say ‘free’ tools. Free not as in ‘Gratis’, not as in it doesn't have a cost, but as in ‘freedom’ you know because it's not the same. And and I think we all in ROMI project agree that we are more in the side of ‘free’ as in ‘freedom’ than in ‘open’ as in you can see what I do. It's more that I can do this, and you can use it for whatever you want and modify it as you want. Hi, I'm Victor, I'm an industrial designer here at the Fab LaN in Barcelona, and I work mostly work developing hardware and software. So the idea is that using free tools gives you control of what you do, so we try to do all the chain, all the the flow with with open source tools, with free tools. So we use Linux that's a free operative system, that anyone can download and use on their own computers. It's installable in any type of computer in any type of TV, in most watches. Super computers use Linux all over the world on top of Linux we use different tools to do the different tasks. We use ‘Blender’ for example for modelling Blender is a tool that can do a lot of tough animation 3D modelling, 3D sculpting Etc. And here we use it like for a strange thing like designing robots, but it's a really nice tool for even design stuff like this, the cabling then all the mechanical parts etc. Then for doing the in fact the electronic boards we use a ‘kiCAD’ that's a really nice software to design electronic boards we do all the electronic design here and we produce the boards later. We try to keep it in a way that boards can be produced locally but not always easy depending on the type of task that you want to do. We're using ‘Inscape’ like a normal open source and free drawing program that anyone can use. And we replace tools that cost a lot of money, and that you cannot customise to do whatever you want. For a coding we try to also keep using only three tools. So it depends on on it's a personal choice, I use ‘VIM’. We use all the the libraries developed by the Arduino project, that's a free really important free software project. We use platform IO, another set of tools to organise libraries to set up stuff to compile, to upload code to different processors. We use a lot of libraries developed by a lot of people all over the world with different interests. Libraries to control motors, libraries to read sensors, libraries to do whatever kind of things people have faced in their own tasks. The people write the library and share it so we got it, and if we see some problems we improve it, or we change it, and we re-share it again. So people can reuse whatever we are doing you know at the end this kind of projects are public money, and there's one model that's being promoted that is; ‘public money, public code’. You know, so it's a more or less the idea that we try to push. Everything I just showed to you in my computer, you can install it in yours because it's free and you can download all the models and all the code and modify it by yourself to build your own robots, and customise them to your own use. All the process that we do it's important, because at the end there's a lot of knowledge being generated we tested a lot of different motors with a lot of different open source and free controllers, and we document all the process so people can get advantage of that work. Here for example so we we use a remote controller and we try different remote controllers and we test the stability Etc and we document all the tests that we do and how we solve the problem in terms of code in terms of electronics in terms of algorithms etc. In since we are adapting for example we are adapting a mouse sensor to measure the position on top of the cable, then we do a lot of experimentation and if we document that experiment people can get advantage of it. Not of the final product but of the process that we did. Because people learn how to use that Mouse sensors to do different stuff.

Data segmentation and analysis: developing algorithms to virtually dissect plants

The following video describes how biological data analysis and image segmentation is conducted at different scales and informs the ROMI data pipeline. Funded by EU Grant 773875. Videos are available in: <ul> <li>Hi-res (1080p Apple ProRes)</li> <li>Mid-res (1080p H265)</li> </ul> Video script: (LEGRAND) I’m an engineer in a biological data analysis. So what I'm doing is to create tools and create a code helping biologists to go from these images they acquire to this labeled image from which we extract cellular features, and from these features we do statistical analysis. Okay so on this board we describe the pipeline we are trying to set up for this image analysis so we're starting with potentially five dimensional images so you have the XYZ spatial Dimension then you have channels and potentially time. So with these images they go to a reader this reader creates a specific data structure so for example if you have a multiple observation of the same object from different angle what you would like to do is to reconstruct and fuse together this multiple angle and then that gives you one big image that you may want to filter and from from these images you can then perform segmentation. For example nuclei detection or cellular segmentation for example this is a pull out transport pump being able to quantify how many pumps you have gives you an idea of the flow of protein or hormones so from that you will be able to build up models and to try and make a realistic model of flower development or phyllotaxis. If you talk about the flower arrangement around the the stem. So compared to my original work the ROMI project is for me we represent a change in scale so we're moving from the cellular scale or to tissular scale, to where we try to understand how flower or leaves are arranged around the stem to use a macroscopic scale where you see the plant in full. And you're trying to observe and also quantify also how flowers or leaves are arranged around the stem. (HÉTROY-WHEELER) So I'm a bit at the end of the pipeline so as input we take a 3D Point cloud which is a sample of the plant represented in a virtual way so we've got a points which each of them has three 3D coordinates. And only from the set of points we try to infer the geometry of the plant and from this geometry so basically to recover the shape of the plant we try then to segment the plant into its organs so the leaves the stems and in between stems and leaves the petals. So the idea is that only from geometry and maybe some colour information or other information which we try to use as less information as possible we would be able to detect the organs of the plants and then do some computation for example simple computation like computing the number of leaves but also more advanced computation like for example trying to guess what is the area of the leaves or the angles between the different stems and so on things that are useful for a biologist and also for people in Agronomy or agriculture.

opennotspecifiedFeb 2023View details →

FIGURES 8–11. Prosternum with variously developed basal process and canal. 8, M in Two new species of Optatus Pascoe and Macroptatus Heller (Coleoptera, Curculionidae, Baridinae), with a reappraisal of generic characters

FIGURES 8–11. Prosternum with variously developed basal process and canal. 8, M. championi; 9, M. deppens; 10, O. palmaris; 11, O. fasciculosus.

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Data for: Spring emergence and canopy development strategies in miscanthus hybrids in Mediterranean, continental and temperate European climates

Due to its versatility and storability, biomass is an important resource for renewable materials and energy. Miscanthus hybrids combine high yield potential, low input demand, tolerance of certain marginal land types and several ecosystem benefits. To date, miscanthus breeding has focussed on increasing yield potential by maximising radiation interception through: 1) selection for early emergence, 2) increasing the growth rate to reach canopy closure fastest possible, and 3) delayed flowering and senescence. The objective of this paper is to compare early season re-growth in miscanthus hybrids cultivated at across Europe. Determination of differences in early canopy development on end-of-year yield traits are required to provide information for breeding decisions to improve future crop performance. Therefore, a trial was planted with four miscanthus hybrids (two novel seed-based hybrids M. sinensis×sinensis (M sin×sin) and M. sacchariflorus×sinensis (M sac×sin), a novel rhizome-based M sac×sin and a standard Miscanthus×giganteus (M×g) clone) in the UK, Germany, Croatia and Italy and was monitored in the third and fourth growing season. We determined differences in base temperature, frost sensitivity and emergence strategy between the hybrids. M×g and M sac×sin mainly emerged from belowground plant organs, producing fewer but thicker shoots at the beginning of the growing season, but these shoots were susceptible to air frosts (as determined by recording 0°C at 2 m above ground surface). By contrast, M sin×sin emerged 10 days earlier avoiding damage by late spring frosts with a high number of thinner shoots from aboveground shoots. Therefore we recommend cultivating M sac×sin at locations with low risk and M sin×sin at locations with higher risk of late spring frosts. Selecting miscanthus hybrids producing shoots throughout the vegetation period is an effective strategy to limit the risk of late frost damages and avoid a reduction in yield due to a shortened growing season.

opencc-zeroFeb 2023View details →

Estradiol Enhances the Development of Addition-Like Features in a Female Rat Model of Opioid Use Disorder

This dataset indicates that, as with findings with psychostimulants and alcohol, estradiol enhances vulnerability in females to developing opioid addiction-like features and serious opioid-related health complications in a rat model of opioid use disorder.

Framework of virtual platforms for learning and developing competencies

Database used for the SLR of the "Framework of virtual platforms for learning and developing competencies" paper.

opencc-zeroFeb 2023View details →

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Development of microsatellite markers for colony delineation of the invasive Asian subterranean termite in South Florida and Taiwan

Delineating the colony identity of Coptotermes gestroi (Wasmann) is a core issue of colony elimination in the implementation of subterranean termite baiting systems. Invasion history is believed the possible cause of genetic variabilities among colonies. Haplotype network analysis of mitochondrial cytochrome c oxidase subunit II revealed the multiple origins of American C. gestroi from the Philippines and Southeast Asia and the Taiwan population only from the Philippines. We further developed 21 new microsatellite markers for the comparison of genetic variabilities on colony delineation of C. gestroi colonies from South Florida (invaded ~30 years; 3–7 generations) and Taiwan (~110 years; 13–27 generations). The present microsatellite markers with 1–4 alleles per locus have validated the effectiveness of colony delineation for three incipient colonies reared in the laboratory and three field colonies from Taiwan. Genetic admixture of the Floridian C. gestroi probably caused by recent invasion history, multiple invasions, and anthropogenic activities among regions. A possible introduction event likely occurred through human-mediated activities between Fort Lauderdale and Miami. Overall, these new microsatellite markers provide suitable and efficient candidate genetic markers for colony delineation of C. gestroi to consolidate the effectiveness of the colony elimination system in termite management.

Chromatin Remodeling via Retinoic Acid Action During Mu-rine Spermatogonial Development

Spermatogonial differentiation is a process that commits germ cells to the complex process of spermatogenesis. Spermatogonial differentiation is mediated by the action of retinoic acid, which triggers major morphological and transcriptional changes. While these transcriptional changes have been well explored, there has been little effort devoted to epigenetic regulation surrounding spermatogonial development. This study aimed to uncover the timing and dynamics of chromatin organization during spermatogonial development within the context of these transcriptional changes. Using germ cell synchrony and the assay for transposase accessible chromatin and next generation sequencing (ATAC-seq) to isolate subpopulations of developing spermatogonia and identify accessible regions within their genome, we found 50% of accessible regions in undifferentiated spermatogonia were condensed following retinoic acid action within 18 hours. Surprisingly, genes with known functional relevance during spermatogonial development were accessible at all times, indicating that chromatin state does not impact transcription at these sites. While there was an overall decrease in gene accessibility during spermatogonial development, we found that transcriptionally active regions were not predictive of chromatin state.

MOOC: ''The development of new technologies for CO2 capture and conversion''

This MOOC on ''The development of new technologies for CO2 capture and conversion'' is given by international professors. Full playlist: https://youtube.com/playlist?list=PLc88uGJ1RIFWKci0m0opuUSQSUfPylYKU MODULE 1: CCUS Carbon Capture Storage and Utilization approach within CO2MPRISE project, introduction by Gabriele Mulas (UNISS). MODULE 2: Mechanochemical activation of Olivine, introduction by Sebastiano Garroni, senior researcher at University of Sassari (UNISS). MODULE 3: Innovative catalytic materials, introduction by Vasiliki Alexiou, project manager at Monolithos Ltd. MODULE 4: Metal hydrides, by Fabiana Gennari, researcher at Comisión Nacional de Energía Atómca (CNEA) – Argentina. || Chapter 4.1: Material synthesis and processes implementation. MODULE 5: Solid-oxides and graphene based systems for CO2 activation and conversion, by Francisco Gracia, professor at University of Chile. MODULE 6: Diffraction experiments for material characterization, by Stefano Enzo, senior researcher at University of Sassari (Italy).

Global-Local Actions, Network and Territorial Development at Iberoamerica: The UNESCO chair in Creative Economy and Public Policy

Gravação do Painel sobre Ações Globais-Locais, Redes e Desenvolvimento Territorial na Iberoamerica: a Cátedra UNESCO em Economia Criativa e Políticas Públicas - Palestra no EnANPAD 2022 Global-Local Actions, Network and Territorial Development at Iberoamerica: The UNESCO chair in Creative Economy and Public Policy. Atividade da divisão APB no EnANPAD 2022 - <a href="http://www.anpad.org.br">www.anpad.org.br</a> Proponente/Proponent: Magnus Luiz Emmendoerfer - PPG-ADM/UFV Painelistas/Panelists: Mário Vasconcellos Sobrinho - PPAD/UNAMA and PPGEDAM/UFPA Estela Najberg - PPGADM/UFG Kelly Maria Paz e Silva - PROPAD/DCA/CCSA/UFPE Thiago Duarte Pimentel - PPGA/FACC/CMAA/UFJF and PPG/UFJF

opencc-by-4.0Sep 2022View details →

Code for paper named "Effects of fluid pressure development on hydrothermal mineralization via cellular automaton simulation"

Code for paper named "Effects of fluid pressure development on hydrothermal mineralization via cellular automaton simulation"

Resulting Pseudonymized Classification Data for "Automatic Core-Developer Identification on GitHub: A Validation Study"

Resulting pseudonymized classification data of the study "Automatic Core-Developer Identification on GitHub: A Validation Study". The corresponding input data, from which the output data have been derived, can be found here: https://zenodo.org/record/7775078

Pseudonymized Raw Data for "Automatic Core-Developer Identification on GitHub: A Validation Study"

Pseudonymized raw data (i.e., commit data and issue data for 25 GitHub projects) that has been used as input for the study published as "Automatic Core-Developer Identification on GitHub: A Validation Study". The pseudonymized raw data has been extracted via the tools <a href="https://github.com/se-sic/codeface/">Codeface</a>, <a href="https://github.com/se-sic/GitHubWrapper/">GitHubWrapper</a>, <a href="https://github.com/mehdigolzadeh/BoDeGHa">BoDeGHa</a>, and <a href="https://github.com/se-sic/codeface-extraction/">codeface-extraction</a> (and additional manual corrections after sanity checks).

opencc-zeroApr 2023View details →

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Data for: Evaluation of pollination traits important for hybrid wheat development in Great Plains germplasm

Hybrid wheat (Triticum aestivum L.) offers potential yield advantages over conventional inbred cultivars. For hybrid wheat to be a commercial success, the cost to produce the hybrid seed needs to be minimized. Although wheat is naturally self-pollinated, hybrid wheat seed production can be improved by increasing the amount and availability of pollen for cross-pollination. This research examined 19 pollination traits using the Hard Winter Wheat Association Mapping Panel for three years. Anther extrusion, pollen 50 date (date at which a genotype has 50% of spikes pollinating), plant height, and pollination duration (last spike pollen 50 date minus first spike pollen 50 date) were identified as the most important traits for hybrid seed production. Anther extrusion, plant height, and pollen 50 date varied widely among genotypes, while pollination duration had significant genotypic differences in one year of testing. These traits also had significant genotype x year interactions, but better and poorer performers were consistent among years. Anther extrusion was weakly, negatively correlated with plant height, and high anther extrusion semi-dwarf genotypes were identified. Pollination duration was reduced in a high temperature (>30ºC) environment, and genotypic differences in pollination duration were identified only in a milder temperature (24ºC) environment. Hierarchical clustering suggested that excellent pollinator genotypes with high anther extrusion and longer pollination duration tended to pollinate early and were of short to moderate stature. Pollination traits were higher when temperatures were mild, which benefited early genotypes because they pollinated before higher temperatures limited their pollination duration.

opencc-by-4.0Apr 2023View details →

Modifying the expression of cysteine protease gene PCP affects pollen develop-ment, germination and plant drought tolerance in maize

Figure S1: The sequencing results of pollen grains of T2 mutants. Figure S2: The relative expression levels of PCP were analyzed via RT-qPCR in pcp mutant lines. Data represent means ± SD of three replicates. Significant differences were indicated with different letters (P < 0.05, one-way ANOVA). Figure S3: Pictures of pollen germination and growth in vitro between wild type and transgenic lines after 4 h and 6 h incubation. Scale bar: 100 μm; Figure S4: Phenotypic observation of wild-type and transgenic maize at flowering stage. Scale bar: 10 cm. Figure S5. DAB staining detection of ROS in WT, KO and OE plants under drought stress. Table S1: PCR primers used in this study.

opennotspecifiedFeb 2019View details →

Figure 5 in Offspring sex and maternal effects influence the development and natal dispersal of an arboreal marsupial

Figure 5.—The age (a) and weight (b) at which movement and development milestones were reached by brushtail possums (Trichosurus vulpecula), based on sex. ***Indicates significance; ^phase only relevant to males.