Find research datasets worth reusing

Stronger transgenerational plasticity in clonal compared to sexual offspring of Fragaria vesca: effects of drought, elevated temperature and CO2 conditions

<div>The dataset contains phenotypic data of woodland strawberry (Fragaria vesca) regarding its reproductive strategy, as well as climate and water availability for both parental and offspring generations.</div> <div> </div> <div>F1StatGPT.csv: Table containing Ramet Number at Harvest, Fruit Number at Harvest, Ramet Biomass, Offspring Ramet Biomass, and Total Biomass.</div> <div>StomataStatGPT.csv: Table containing Number of Stomata per mm² and Stomata Size.</div>

Data and Code for "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution"

This repository contains the datasets and data sources, analysis code, and workflow associated with the manuscript "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution". The following resources are provided: <ul> <li> Data Files: <ul> <li><code>time_series_data.csv</code>: A curated time series dataset with dates as rows and NUTS 2 regions as columns. Each column is labeled using a 4-letter abbreviation format "CC.RR", where "CC" represents the country code and "RR" represents the region code. This same abbreviation is also included in the accompanying GeoJSON file.</li> <li><code>geometry_data.geojson</code>: A GeoJSON file representing the spatial boundaries of the NUTS 2 regions, with the same 4-letter abbreviations used in the CSV file. EPSG:4326.</li> <li><code>COVID19_data_sources.xlsx</code>: This Excel file contains important metadata regarding the sources of COVID-19 data used in this study. It includes: <ul> <li>Source of the data for each country</li> <li>Official website(s)</li> <li>The agency responsible for the data</li> <li>Description of the processing steps used to curate the data into the final time series.</li> </ul> </li> </ul> </li> <li> Code: <ul> <li><code>analysis.py</code>: A Python script used to process and analyze the data. This code can be run using Python 3.x. The libraries required to run this script are listed in the first lines of the code. The code is organized in different numbered sections (1), (2), ... and sub-sections (1a), (1b) ... Make sure to run the script one (sub-)section at a time, so that everything stays overviewable and you don't get all the output at once.</li> </ul> </li> <li> Workflow: <ul> <li><code>workflow.png</code> : A detailed workflow according to the Knowledge Discovery in Databases (KDD) process, outlining the steps involved in processing and analyzing the data, including the methods used. This workflow provides a comprehensive guide to reproducing the analysis presented in the paper.</li> </ul> </li> </ul>

opencc-by-4.0Mar 2016View details →

Bark-scratching of storm-felled trees preserves biodiversity at lower economic costs compared to debarking

The abundance data presented here focus on saproxylic beetles collected over two years on trees in a mountain forest ecosystem (analysed and discussed in Thorn et al. <a href="https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecm.1343#ecm1343-bib-0043">2016</a>). The design consists of 12 plots each composed of three experimentally felled trees, resulting in a total of 36 experimental felled trees. In each plot, the bark of one tree was completely removed, the bark of a second tree was only partially removed (i.e., bark-scratched), and the third tree served as a control. The design is thus composed of 12 replications of three different treatments (i.e., control, bark-scratched, and debarked). A total of 120 species of saproxylic beetles were trapped with emergence traps on felled trees (Thorn et al. <a href="https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecm.1343#ecm1343-bib-0043">2016</a>).

The efficacy of hemoglobin spray in wound management: a systematic review and network meta-analysis of comparative studies

Dataset

Data supporting the article: "Comparative analysis of fecal microbiota between adolescents with early-onset psychosis and adults with schizophrenia"

This dataset supports the article titled "Comparative analysis of fecal microbiota between adolescents with early-onset psychosis and adults with schizophrenia.", available at <a href="https://doi.org/10.3390/microorganisms12102071">https://doi.org/10.3390/microorganisms12102071</a>. The dataset includes fecal microbiota sequencing data from adolescent patients with early-onset psychosis, adult patients with schizophrenia, and non-psychotic controls. The data were generated using 16S rRNA gene sequencing and analyzed with QIIME2 and PICRUSt2 to assess microbial diversity and functional pathways. Variables such as age, diagnosis, and medication use are included. The dataset contains: <ul> <li>Processed results from fecal microbiota analysis (OTUs and taxonomic classifications)</li> <li>Metadata associated with each sample (age, diagnosis, medication)</li> <li>Results from diversity analysis (alpha and beta diversity metrics)</li> <li>Functional analysis of microbial pathways (PICRUSt2)</li> </ul> These data are essential for reproducing the findings discussed in the article. Note that the raw sequencing data are available upon request.

Dataset for the manuscript "Assessing the Role of Hydrodynamics in Enhancing HAND-Derived Synthetic Rating Curves: A Comparative Study in the Wu River Basin, Taiwan"

This is the dataset for developing the HAND-hd workflow mentione in the manuscript "Assessing the Role of Hydrodynamics in Enhancing HAND-Derived Synthetic Rating Curves: A Comparative Study in the Wu River Basin, Taiwan". In the manuscript, we used the topographical cross-sectional survey data to generate topographical synthetic rating curves (RCb) to validate the performance of the HAND method based synthetic rating curves (HAND-SRC) produced by the HAND-hd workflow. Due to regulatory restrictions under Taiwanese law, public sharing of 5-meter (or finer) DEM data is prohibited. However, researchers interested in accessing processed HAND raster data for research purposes may contact the corresponding author.

opencc-by-4.0Nov 2024View details →

A Comparative Study of RIPASA and Modified Alvarado Scoring System for the Diagnosis of Acute Appendicitis

This dataset supports the findings of the study titled "Diagnosing Appendicitis with Precision: A Comparative Analysis of Modified Alvarado and RIPASA Scoring Systems in a Northern Divisional Hospital of Bangladesh" and has been de-identified to protect participant confidentiality. The data are accessible on Zenodo but require permission for reuse. Interested researchers are requested to contact the corresponding author to obtain permission before using the dataset in their own work. Please provide details of the intended research purpose when making a request. Terms of Use Data access is granted for research purposes only and requires prior written approval from the corresponding author Dr. Nafisa Naz. By requesting access, researchers agree to comply with ethical and legal guidelines as applicable.

Comparative genomics of Helotiales (Leotiomycetes) and in silico analysis of temperature adaptations of plant-associated genes

Table S1: Genome assembly size and quality for every species in this study;  Table S2: Genome annotation counts for P450, virulence factors, effectors, and CAZy genes and their temperature adaptation.

opencc-zeroDec 2017View details →

Data from: Remarkably conserved plastid genomes of Quercus Group Cerris in China: comparative and phylogenetic analyses

Quercus is one of the most important genera for considering its economic and ecological values, with approximately 500 species worldwide. Quercus group Cerris is endemic to Eurasia (including 11 species), and three species (Quercus acutissima, Quercus chenii and Quercus variabilis) are widely distributed in China. Here, we sequenced the complete plastid genomes of Q. acutissima and Q. chenii by Illumina pair-end sequencing, and obtained an additional plastome of Q. variabilis from GenBank. Although geographically distant sampling, the three plastomes in group Cerris were remarkably conserved with regard to genome size, gene organization, GC content, and IR/SC boundary regions. The phylogenetic analysis showed that group Cerris nested in group Ilex, forming a Cerris-Ilex clade. The current study provided plastid genomic-scale data for the less intensively studied group Cerris, which would be useful for studying speciation processes, geographical structure and phylogeny within the group Cerris in the future.

opencc-zeroApr 2020View details →

Complex ecological phenotypes on phylogenetic trees: a Markov process model for comparative analysis of multivariate count data

The evolutionary dynamics of complex ecological traits – including multistate representations of diet, habitat, and behavior – remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains (CTMC) are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a pre-determined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories.

opencc-zeroMay 2020View details →

Data from: Protection of pepper plants from drought by microbacterium sp. 3J1 by modulation of the plant's glutamine and α-ketoglutarate content: a comparative metabolomics approach

Desiccation-tolerant plants are able to survive for extended periods of time in the absence of water. The molecular understanding of the mechanisms used by these plants to resist droughts can be of great value for improving drought tolerance in crops. This understanding is especially relevant in an environment that tends to increase the number and intensity of droughts. The combination of certain microorganisms with drought-sensitive plants can improve their tolerance to water scarcity. One of these bacteria is Microbacterium sp. 3J1, an actinobacteria able to protect pepper plants from drought. In this study, we supplemented drought-tolerant and drought-sensitive plant rhizospheres with Microbacterium sp. 3J1 and analyzed their proteomes under drought to investigate the plant-microbe interaction. We also compare this root proteome with the proteome found in desiccation-tolerant plants. In addition, we studied the proteome of Microbacterium sp. 3J1 subjected to drought to analyze its contribution to the plant-microbe interaction. We describe those mechanisms shared by desiccation-tolerant plants and sensitive plants protected by microorganisms focusing on protection against oxidative stress, and production of compatible solutes, plant hormones, and other more specific proteins.

opencc-by-4.0Jun 2021View details →

A selective role for receptor activity-modifying protein in sub-chronic action of the amylin selective receptor agonist NN1213 compared to salmon calcitonin on body weight and food intake in male mice

Raw data prism files for the manuscript "A selective role for receptor activity-modifying protein in sub-chronic action of the amylin selective receptor agonist NN1213 compared to salmon calcitonin on body weight and food intake in male mice"

opencc-by-4.0May 2020View details →

Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"

Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"

opencc-zeroSep 2019View details →

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and Cheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e., the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Further, a detailed syntenic comparison of mouse lemurs with mouse (genus Mus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."

opencc-zeroDec 2017View details →

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.

opencc-by-4.0Jul 2021View details →

Data for Publication "Comparing individuals buried in flexed and extended positions at the Greek colony of Chersonesos (Crimea) using cranial metric, dental metric, and dental nonmetric traits"

Data for Publication: H. Rathmann, R. Stoyanov, and R. Posamentir, Comparing individuals buried in flexed and extended positions at the Greek colony of Chersonesos (Crimea) using cranial metric, dental metric, and dental nonmetric traits.

opencc-zeroJan 2020View details →

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity

AbstractCell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.

opencc-zeroJul 2021View details →

Comparing single-species and mixed-species groups in fruit flies: differences in group dynamics but not group formation

Mixed-species groups describe active associations among individuals of two or more species at the same trophic level. Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation; and ignoring the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected. Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species groups form. Further, insects have been almost completely ignored in the study of mixed-species groups, despite their taxonomic importance and relative prominence in the study of single-species groups. Here, we measured group formation processes in Drosophila melanogaster and its sister species Drosophila simulans. Each species was studied alone, and together; and one population of D. melanogaster was also studied both alone and with another, phenotypically-distinct D. melanogaster population, in a nested-factorial design. This approach differs from typical methods of studying mixed-species groups in that we could quantitatively compare group formation between single-population, mixed-population, and mixed-species treatments. Surprisingly, we found no differences between treatments in the number, size, or composition of groups that formed, suggesting that single-species and mixed-species groups form through similar mechanisms of active attraction. However, we found that mixed-species groups showed elevated inter-species male-male interactions, relative to inter-population or inter-genotype interactions in single-species groups. Our findings expand the conceptual and taxonomic study of mixed-species groups while raising new questions about the mechanisms of group formation broadly.

opencc-by-4.0Jul 2021View details →

Comparing and Combining Existing and Emerging Data Collection and Modeling Strategies in Support of Signal Control Optimization and Management (Project M2)

For decades, traffic signal management agencies have used signal timing optimization tools combined with fine-tuning of signal timing based on field observations in their updates of time-of-day signal timing plans.  These traditional signal optimization methods and tools use very limited amount of data and depend on default values in the signal timing optimization/simulation tools to estimate network performance under different signal optimization strategies. In recent years, new data collection technologies are emerging including high resolution controller data, more advanced detection technologies such as video image detection that are based on vehicle tracking and possible integration with microwave detectors, automatic-vehicle based identification technologies, third party crowdsourcing data, connected vehicles, and connected automated vehicles data.  The objective of the proposed study is to propose methods and algorithms to combine data collected from existing and emerging sources with enhanced models and optimization algorithms to optimize and manage signal operations. The results from applying the developed methods and algorithms will be compared with traditional signal timing and optimization methods currently used by transportation agencies.