cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13067324.v2
title: De novo Trinity transcript assembly of Atlantic cod

description: The reference is based on a de novo Trinity [1,2] assembly because the official gene models versions did not contain full length sequences for all genes. The assembly consists of sequences from the following RNA-Seq data: <br>Gadus morhua Transcriptome or Gene expressionNCBI project : PRJNA277848https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA277848Developmental stages: 10-dph, 20-dph, 30-dph, 45-dph, 60-dph, 90-dph<br>SRR2045416 brain ,SRR2045417 gills, SRR2045418 heart, SRR2045419 muscle, SRR2045420 liver, SRR2045421 kidney, SRR2045422 bones, SRR2045423 intestine, SRR2045425 embryo, SRR2045415 ovary<br>Three cod liver samples:GEO accession: GSE106968 [3] https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106968Samples: dcod_12_S3, dcod_1_S1, dcod_25_S25<br>Reads were assembled using Trinity through the Agalma pipeline version 0.5.0 [4]. The transcript assemblies from different stages and tissue samples were mapped to both cod genomes (gadMor 1 and 2) [5,6]. Transcripts were mapped to both genomes as each genome is missing some genes.<br>1 Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 2 Haas, B.J. et al. (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 3 Yadetie, F. et al. (2018) RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol. Aquat. Toxicol. 201, 174–186 4 Dunn, C.W. et al. (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14, 330 5 Star, B. et al. (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207–210 6 Tørresen, O.K. et al. (2017) An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 18, 95<br>
DOI: 10.6084/m9.figshare.1560072.v2
title: Lab 02: Dataset 3 - Sampling of adult trees at Danby woodlot.

description: The experiment was conducted on September 24,2015 at Danby woodlot, York university around 2:30-5:20pm. The temperature was around 21° C with bright clear sky. The experiment was done along with Harshvir Hehar, Olivia Kazmierczak and Adilah Ismail. The purpose of the experiment was to identify different plant species and become familiar with collecting data using sampling tools such as the transect. A transect measuring tape was laid out in a straight line from the edge of woodlot to the centre of woodlot. An adult tree that met the criteria i.e. a tree twice as the height of observer was located along the transect. The diameter at breast height of this adult tree (50 inches from the ground) was measured in inches using the tape. A distance from this adult tree to the next closest adult tree along the transect was located and measured in inches using a second transect. The diameter at breast height of the second tree (50 inches from the ground) was also recorded. The condition of the tree was observed simply with our eyes which ranged from a scale of 0-2 with 0 being dead, 1 being living and 2 being a tree with full green canopy. This step was repeated 9 more times to get a total pair of 10 replicates with each replicate pair consisting of two adult trees. Therefore the sample size for this experiment was 20.
DOI: 10.6084/m9.figshare.19314455.v2
title: Integrated evidence-based extent of occurrence for North American bison (Bison bison) since 1500 CE and before: dataset

description: Following the near extinction of bison (<em>Bison bison</em>) from its historic range across North America in late 19<sup>th</sup> century, novel bison conservation efforts in the early 20<sup>th</sup> century catalyzed a popular widespread conservation movement to protect and restore bison among other species and places. Since Allen’s initial delineation (1876) of the historic distribution of North American bison, subsequent attempts have been hampered by knowledge gaps about bison distribution and abundance previous to and following colonial arrival and settlement. For the first time, we apply a multi-disciplinary approach to assemble a comprehensive, integrated geographic database and meta-analysis of bison occurrences over the last 200,000 years BCE, with particular emphasis over the last 450 years before present. We combined paleontology, archaeology, and historical ecology data for our database totaling 6,438 observations. We derived the observations from existing online databases, published literature, and first-hand exploration journal entries. To illustrate the conservative maximum historical extent of occurrence of bison, we created a concave hull using observations occurring over the last 450 years (<em>n </em>= 3,379 observations) which is the broadly accepted historical benchmark at 1500 CE. While this distribution represents a historic extent of occurrence — merely delineating the maximum margins of the near-continental distribution — it does not replace a density-based approach reconstructing potential historical range distributions that identify core and marginal ranges. However, we envision the contained observations of this database will contribute to further research in the increasingly evidence-based disciplines of bison ecology, evolution, rewilding, management, and conservation.
DOI: 10.6084/m9.figshare.22938434.v1
title: Data and R codes from the paper "Landscape heterogeneity and soil biota are central to multi-taxa diversity for landscape restoration"

description: The shared data contains R-scripts and the associated data needed to calculate the partitioning of beta diversity into turnover and nestedness components and to obtain the partial correlation networks for the coarse community (understorey arthropods, soil fungi, soil bacteria, herbaceous plants, trees, and soil fauna) and for the trophic community (pollinator understorey arthropods, parasitic understorey arthropods, predator understorey arthropods, pathotroph fungi, saprotroph fungi, symbiotroph fungi, soil bacteria, herbaceous plants, trees, soil fauna): R-scripts (MT_BD_Coarse.R and MT_BD_Trophic.R) and the data (CoarseCommunity.Rdata; CoarseGroup.Rdata; TrophicCommunity.Rdata; TrophicGroup.Rdata; Soil_variables.Rdata).
DOI: 10.17632/57ct3z6bvv
title: Data for: SNP genotyping and population analysis of five indigenous Kazakh sheep breeds

description: Results of genotyping of 5 sheep breeds from Kazakhstan with Ovine 50K SNP panel. After quality filtering
DOI: 10.17632/6292j9s37h
title: Ethical Implications of Artificial Intelligence in Vaccine Equity: Exploring Vaccine Distribution Planning and Scheduling in Pandemics in Low-Middle-Income-Countries

description: This dataset comprises a witness seminar transcript exploring the effectiveness of AI-based distribution planning and scheduling systems in ensuring equitable vaccine distribution in Low- and Middle-Income Countries (LMICs). The dataset includes discussions from multiple expert participants, including public health professionals, AI researchers, medical practitioners, and ethicists, who shared their perspectives based on their experiences during the COVID-19 vaccine rollout. The research questions focused on identifying systemic inequities in vaccine distribution, the role of AI in scheduling and outreach, and ethical considerations regarding data privacy, bias, and accessibility. Participants discussed how digital platforms such as India’s CoWIN app improved vaccine tracking and administration but also highlighted key challenges, such as limited smartphone access, digital illiteracy, and exclusion of marginalized groups (e.g., transgender individuals, persons with disabilities, and rural communities). Experts noted that AI-based systems require a hybrid approach, combining technological solutions with ground-level outreach by community health workers to ensure equity. The thematic analysis of the transcript reveals recurring themes such as AI's role in optimizing vaccine delivery, ethical concerns regarding data privacy, digital literacy barriers, and challenges in reaching underserved populations. Participants emphasized that while AI can enhance efficiency and tracking, it also risks reinforcing existing inequities if data biases and structural healthcare disparities are not addressed. Discussions further examined the importance of community engagement, transparency, and policy interventions in refining AI-driven vaccine distribution models. This dataset provides rich qualitative insights into the intersection of technology, ethics, and health equity, offering valuable guidance for policymakers, researchers, and global health organizations aiming to improve AI-driven public health interventions in LMICs.
DOI: 10.6084/m9.figshare.26343901.v1
title: IonGen_1M

description: 1 million <i>de novo</i> organic cations and 1 million <i>de novo</i> organic anions generated by a machine learning model IonGen (https://github.com/Mengyang2024/IonGen)
DOI: 10.6084/m9.figshare.5670769.v1
title: Bioprospection and characterization of the amylolytic activity by filamentous fungi from Brazilian Atlantic Forest

description: Abstract Filamentous fungi are widely diverse and ubiquitous organisms. Such biodiversity is barely known, making room for a great potential still to be discovered, especially in tropical environments - which are favorable to growth and species variety. Filamentous fungi are extensively applied to the production of industrial enzymes, such as the amylases. This class of enzymes acts in the hydrolysis of starch to glucose or maltooligosaccharides. In this work twenty-five filamentous fungi were isolated from samples of decomposing material collected in the Brazilian Atlantic Forest. The two best amylase producers were identified as Aspergillus brasiliensis and Rhizopus oryzae. Both are mesophilic, they grow well in organic nitrogen-rich media produce great amounts of glucoamylases. The enzymes of A. brasiliensis and R. oryzae are different, possibly because of their phylogenetical distance. The best amylase production of A. brasiliensis occurred during 120 hours with initial pH of 7.5; it had a better activity in the pH range of 3.5-5.0 and at 60-75°C. Both fungal glucoamylase had wide pH stability (3-8) and were activated by Mn2+. R. oryzae best production occurred in 96 hours and at pH 6.5. Its amylases had a greater activity in the pH range of 4.0-5.5 and temperature at 50-65ºC. The most significant difference between the enzymes produced by both fungi is the resistance to thermal denaturation: A. brasiliensis glucoamylase had a T50 of 60 minutes at 70ºC. The R. oryzae glucoamylase only had a residual activity when incubated at 50°C with a 12 min T50.
DOI: 10.17632/64rvdjgzpy
title: 6MPpregnancyOutcomesRat

description: Dose response data on the pregnancy outomes of rats treated on GD 11 with a broad range of 6-mercaptopurine (6MP) doses : 0, 6, 12 and 24 mg/kg bw sc.
DOI: 10.17632/9swgvr363z
title: Data for: Association between total sleep time and all cancer mortality: Non-linear dose-response meta-analysis of cohort studies

description: This is the detailed information for data extraction.
DOI: 10.17632/hdtpts8t5y
title: Parallel grid library for rapid and flexible simulation development

description: This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We present an easy to use and flexible grid library for developing highly scalable parallel simulations. The distributed cartesian cell-refinable grid (dccrg) supports adaptive mesh refinement and allows an arbitrary C++ class to be used as cell data. The amount of data in grid cells can vary both in space and time allowing dccrg to be used in very different types of simulations, for example in fluid and particle codes. Dccrg transfers the data between neighboring cells on different processes... Title of program: DCCRG Catalogue Id: AEOM_v1_0 Nature of problem Grid library supporting arbitrary data in grid cells, parallel adaptive mesh refinement, transparent remote neighbor data updates and load balancing. Versions of this program held in the CPC repository in Mendeley Data AEOM_v1_0; DCCRG; 10.1016/j.cpc.2012.12.017
DOI: 10.6084/m9.figshare.28375268.v2
title: Underestimated Ecosystem Resilience: Tipping Point Evasion Driven by Adaptive Plant-Pollinator Interactions

description: Global change threatens ecosystem resilience and triggers irreversible critical transitions, especially in ecologically vulnerable coastal wetlands. Previous studies reported that biotic interactions interfered with biophysical feedback process, forcing ecosystem resilience more susceptible. However, dynamic critical threshold of ecosystem resilience lacks quantification, particularly involving adaptive mutualistic interaction. Our study integrates biophysical feedback and plant-pollinator interactions into a spatial vegetation model and generates dynamic thresholds of a saltmarsh ecosystem in the Yellow River Delta, China. Results showed that adaptive plant-pollinator interaction accelerates the biophysical feedback, enabling the ecosystem to evade the tipping point of collapsing and to enhance the tipping point of recovering. This is particularly important at the early stages of vegetation colonization. A comparison with an ecosystem without mutualistic interaction showed that adaptive mutualistic interaction was important in withstanding higher environmental pressures, despite an overall decline in ecosystem resilience under noise-type habitat loss and rate-type escalating salinization. Adaptive plant-pollinator interaction therefore resulted in a more effective and sustainable ecosystem restoration. Our study emphasizes the essential role of plant-pollinator interaction in strengthening ecosystem resilience against external disturbances. Neglecting this adaptive mechanism can underestimate ecosystem resilience. Management that collaborative conservation of plants and pollinators is a prospective approach to deal with climate change challenges and maintain ecosystem sustainability.
DOI: 10.6084/m9.figshare.28935254.v1
title: Supplementary data

description: Detail description of the InVEST model
DOI: 10.6084/m9.figshare.5759517.v1
title: Alignment and partition file of PCGs by MrBayes

description: Alignment and partition file of PCGs by MrBayes
DOI: 10.6084/m9.figshare.8224175.v3
title: Habitat loss does not always entail negative genetic consequences

description: Genotype and sequence data for two plant species: Brasilianthus carajensis (Melastomataceae) and Monogereion carajensis (Asteraceae). For each species we provide geographic coordinates in decimal degrees, genotypes in Variant Call Format and sequences in FASTA format.<br>The data belongs to the following published preprint:<br>Carvalho C da S., Lanes ECM., Silva AR., Caldeira CF., Carvalho-Filho N., Gastauer M., Imperatriz-Fonseca VL., Nascimento W., Oliveira G., Siqueira JO., Viana PL., Jaffe R. 2019. Habitat loss does not always entail negative genetic consequences. bioRxiv:528430. DOI: 10.1101/528430.<br>
DOI: 10.17632/4f63mfn8n4
title: Aircraft observation of fast initiation of mixed phase precipitation in convective cloud over the Tibetan Plateau

description: These data are in service of this paper "Aircraft observation of fast initiation of mixed phase precipitation in convective cloud over the Tibetan Plateau", including vertical distribution of  cloud physical parameters and so on.
DOI: 10.17632/kdh5p39vsc
title: Improvement of Platysma Prominence With OnabotulinumtoxinA: Safety and Efficacy Results From a Randomized, Double-Blinded, Placebo-Controlled Phase 3 Trial

description: These supplementary materials provide additional data supporting the main manuscript (OnabotA for Platysma Prominence Phase 3[309]) on the safety and efficacy of onabotulinumtoxinA for improving platysma prominence. They consist of a plain language summary, tables detailing the number of injections and total doses administered, participant demographics, baseline characteristics, efficacy results in the modified intent-to-treat population, and treatment-related adverse events in the safety population. Diagrams illustrating injection sites and participant flow in the study are also included.
DOI: 10.17632/r8bk2bdw96
title: Effects of Digital Distraction and Time Management Skills on the Math Performance of Aspiring Teachers

description: This study examines the impact of digital distraction and time management skills on the pre-service teachers’ academic performance in mathematics. A total of 121 aspiring educators were selected using simple random selection. They responded to two sets of adopted survey questionnaires that evaluated their digital distraction and time management skills. Moreover, their Mathematics in Modern World (MMW) grade was used as basis for their math performance. Weighted mean was used to assess the levels of the variables and Pearson’s correlation was applied to determine their relationship to the respondents’ math performance. The results show that they had moderate level of digital distraction, high level of skills in managing time, as well as outstanding math performance. Despite exhibiting these levels, the results reveled that digital distraction and time management skills have insignificant impact on the respondents' mathematics performance. These suggest that other underlying factors may play a greater role in influencing student performance. Further research may consider investigating additional variables or employing qualitative methods to gain a better understanding of what truly influences students' academic performance in math.
DOI: 10.17632/xtzgzy997p
title: Risk Factors for Stunting in Toddlers in Developing Countries

description: Introduction; Stunting in toddlers is one of the nutritional problems in the world, especially in developing countries. As many as 21.3% or around 144 million toddlers in the world are stunted, more than half of the world's stunted toddlers are from Asia, and more than two-fifths live in Africa. Stunting is a serious threat to the existence of children as the next generation of a nation.
Purpose; This study analyzed the risk factors associated with the incidence of stunting in toddlers in developing countries using a systematic literature review and meta-analysis.
Method; Literature search using online journal portals namely ProQuest, PubMed, and Garuda. The journal used in this study is a journal with a maximum reputation of Q2 and sinta 2, in the period 2010-2020, with a cross-sectional and case-control study design.
Results; Based on the search results, seven kinds of literature were obtained, and conducted by systematic literature review was.
Conclusion; The results of the meta-analysis of risk factors related to the incidence of stunting in toddlers in developing countries are birth weight and exclusive breastfeeding
DOI: 10.25452/figshare.plus.25199468.v1
title: Multiplex imaging of localized prostate tumors reveals changes in the spatial organization of AR-positive cells in the microenvironment

description: Mapping spatial interactions of cancer, immune and stromal cells present novel opportunities for patient stratification and for advancing immunotherapy. While single-cell studies revealed significant molecular heterogeneity in prostate tumors, there is currently no understanding of how immune cell heterogeneity impacts spatial coordination between tumor and stromal cells in localized tumors. Here, we used cyclic immunofluorescent imaging on whole-tissue sections to uncover novel spatial associations between cancer and stromal cells in low- and high-grade prostate tumors and tumor-adjacent normal tissues. Our results provide a spatial map of 699,461 single-cells that show epigenetic and molecular differences in distinct clinical grades. We report unique populations of mast cells that differentially express CD44, CD90 and Granzyme B (GZMB) and demonstrate GZMB+ mast cells are spatially associated with M2 macrophages in prostate tumors. Finally, we uncover recurrent neighborhoods that are primarily driven by androgen receptor positive (AR+) stromal cells and identify transcriptional networks active in AR+ prostate stroma.Each tissue has 10 Rounds of imaging data; one quenching round of imaging data (R3Q). For each round of imaging consists of 5 tif images from 5 channels (DAPI, M1, M2, M3 and M4).File Name structure: Rx_M1.M2.M3.M4_TissueID_SceneID_ChannelID_ORG.tifRx=Round order (R1-R10); M1=Marker 1; M2=Marker 2; M3=Marker 3; M4=Marker 4; TissueID=Tissue Number; SceneID=Single scene for all images (s001); ChannelID=Channels 0-5; R3Q=Quenching round after R3 imaging.<br>
DOI: 10.4121/12763700.v8
title: A 10-year (2009-2019) surface soil moisture dataset produced based on in situ measurements collected from the Tibet-Obs

description: The Tibet-Obs consists of three regional-scale soil moisture (SM) monitoring networks, i.e. the Maqu, Naqu, and Ngari (including Ali and Shiquanhe) networks. This surface SM dataset includes the original 15-min in situ measurements collected at a depth of 5 cm by multiple SM monitoring sites of the three networks, and the spatially upscaled SM records produced for the Maqu and Shiquanhe networks.
DOI: 10.6084/m9.figshare.16947451.v1
title: Biodiversity promotes ecosystem functioning despite environmental change

description: Online dataset for Fig.2 – 5 in Hong <i>et al. </i>''Biodiversity promotes ecosystem functioning despite environmental change".
DOI: 10.6084/m9.figshare.20063450.v1
title: This flower is our bed: long-term citizen science reveals that hummingbird flies select sleeping places by the shape of the flowers

description: Dataset for the manuscript "This flower is our bed: long-term citizen science reveals that hummingbird flies select sleeping places by the shape of the flowers"
DOI: 10.6084/m9.figshare.26768212.v1
title: Sheep_data

description: Raw data as well as minimal data sets
DOI: 10.6084/m9.figshare.5120497.v1
title: Supplementary Material for: Assessing Genuine Parents-Offspring Trios for Genetic Association Studies

description: <i>Objectives:</i> Family-based association tests such as the transmission disequilibrium test (TDT) are dependent on the successful ascertainment of true nuclear family trios. Relationship misspecification inevitably occurs in a proportion of trios collected for genotyping which undetected can lead to a loss of power and increased Type I error due to biases in over-transmission of common alleles. Here, we introduce a method for evaluating the authenticity of nuclear family trios. <i>Methods:</i> Operating in a Bayesian framework, our approach assesses the extent of pedigree inconsistent genotype configurations in the presence of genotyping errors. Unlike other approaches, our method: (i) utilizes information from three individuals collectively (the whole trio) rather than consider two independent pairwise relationships; (ii) down-weighs SNPs with poor performance; (iii) does not require the user to pre-define a rate of genotyping error, which is often unknown to the user and seldom fixed across the different SNPs considered which available methods unrealistically assumed. <i>Results:</i> Simulation studies and comparisons with a real set of data showed that our approach is more likely to correctly identify the presence of true and misspecified trios compared to available software, accurately infers the extent of relationship misspecification in a trio and accurately estimates the genotyping error rates. <i>Conclusions:</i> Assessing relationship misspecification depends on the fidelity of the genotype data used. Available algorithms are not optimised for genotyping technology with varying rates of errors across the markers. Through our comparison studies, our approach is shown to outperform available methods for assessing relationship misspecifications.