Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

Analysis of laboratory reporting practices using a quality assessment of a 'virtual patient'. (data)

Dataset for paper Analysis of laboratory reporting practices using a quality assessment of a ‘virtual patient', published in Genetics in Medicine. This dataset consists of the FASTQ, BAM, and VCF for the virtual patients as described in the paper.

opencc-by-4.0Sep 2020View details →

Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis

We provide data and code needed to re-do the analyses and figures presented in our preprint Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ): - data table : data_repetition01.xls, with informations about each column in the file data_repetition_info.pdf - data table : data_individual01.xls, with informations about each column in the file data_indivdual_info.pdf - The R code used to do the analyses : Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R

opencc-by-4.0Sep 2020View details →

data set related to article Brain Network Organization Correlates with Autistic Features in Preschoolers with Autism Spectrum Disorders and in Their Fathers - Preliminary Data from a DWI Analysis

This record contains raw data related to article Brain Network Organization Correlates with Autistic Features in Preschoolers with Autism Spectrum Disorders and in Their Fathers - Preliminary Data from a DWI Analysis

opencc-by-4.0Sep 2020View details →

Synthetic MISE Data for Radiation Robustness Analysis

This dataset contains synthetic observations similar to those that will be produced by the Mapping Imaging Spectrometer for Europa (MISE) instrument. The dataset was created by taking visible Galileo Solid-State Imaging (SSI) experiment observations resized to 300x300 pixels, using pixel intensity as a proxy for albedo, and linearly mixing two 451-channel spectra in proportion to albedo for each pixel. The contents of this directory include the original SSI images and PDS label files, rescaled versions of the images, and the spectral cubes in HDF5 format corresponding to synthetic MISE digital number (DN) measurements. The cube files contain two datasets, "cube" containing the DN values, and "wavelengths," which holds the wavelength in nanometers corresponding to each value in a spectrum. The dataset was created to evaluate the radiation robustness of the Reed-Xiaoli (RX) algorithm used for spectral anomaly detection. For the radiation robustness analysis, only the first 421 channels of the spectra are used. The full dataset size is roughly 781 MB.

Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis

Duplicate of 10.5061/dryad.6hdr7sqxq Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes experience reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, the empirical evidence shows contrasting effects of anthropogenic disturbances on the genetic diversity of species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and more preserved areas (316 paired comparisons) to investigate the genetic responses to different disturbance types. There is a negative effect (effect size: -0.45; 95% CI: -0.61, -0.29) of disturbances on genetic diversity, in which the most detrimental effects are caused by the loss of connectivity and forest cover. The methodological approach can explain part of the heterogeneity among the genetic responses detected by primary studies: (i) studies using the number of effective alleles did not detect genetic erosion, while all other indices, revealed negative responses to disturbances; and (ii) only studies performed with transferred or a combination of transferred and specific microsatellites detected negative responses. The effects on animal populations are more detrimental than in plant populations. Only plant species with shrub life form, self-incompatible reproductive systems, and biotic pollination and seed dispersal, showed negative responses to disturbances. Despite all heterogeneity among studies, there is an overall negative effect of disturbances on the genetic diversity, which indicates that remaining populations inhabiting human-modified landscapes have reduced evolutionary potential and are prone to local extinction.

Data from: The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): characterization and comparative analysis

Characterization of complete mitogenome is a widely used genomics study for species delineation and evolutionary research. However, the sequences and structural motifs contained within the mitogenome have been rarely examined to understand the phylogeny and evolutionary history among Testudines. Hence, the mitogenomic features of several Testudines taxa are still anonymous to the scientific communities. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). The mitogenome contained 19 intergenic spacer and six overlapping regions. Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for cytochrome oxidase subunit 1 with 'GTG' and NADH dehydrogenase subunit 5 with 'ATA'. The termination codons, 'TAA' and 'AGA' were observed in NADH dehydrogenase subunit 4l and NADH dehydrogenase subunit 6 respectively. The Relative Synonymous Codon Usage analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine. The non-synonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for Serine (trnS1) with lack of the conventional DHU arm. The Wobble base pairing was observed in the different stems (DHU, acceptor, and anticodon) of 11 tRNAs. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3´ end of CR. Further, two copies of a unique tandem repeat 'TTCTCTTT' were identified in P. tentoria. The Bayesian and Maximum Likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species, especially for Batagurinae subfamily, are required to improve our understanding their in-depth phylogenetic and evolutionary relationships.

Data from: Multidimensional stable isotope analysis illuminates resource partitioning in a sub-Antarctic island bird community

1. A central theme in community ecology is understanding how similar species co-exist and how their interactions may evolve in the context of climate change. Most studies of resource partitioning among central place foragers, particularly birds, focus on the offspring-rearing period, when they are accessible, but breeding success may be determined earlier and little is known about how such species partition resources at the onset of breeding. 2. We used a non-invasive approach to evaluate resource partitioning in co-existing females at a sub-Antarctic island during their pre-laying periods. 3. Three hypotheses were tested using carbon, nitrogen and oxygen stable isotope ratios measured in shells and membranes of hatched eggs as ecological tracers: 1) resource partitioning by geographic location and trophic level will exist among the 12 bird species and will be enhanced within taxonomic groups; 2) given the absence of strong oxygen gradients in the Southern Ocean we will not detect spatial structuring based on oxygen isotopes, but differences will exist between resident and oceanic species as the former may use meteoric water; 3) capital and income breeder strategies can be differentiated using stable isotopes of egg remains. 4. Two and three dimensional isotopic data showed resource partitioning among species. As predicted, segregation was evident within the four main taxonomic groups: penguins, albatrosses, burrowing petrels and giant petrels. Unexpectedly, oxygen isotopes revealed widespread use of meteoric water among a suite of sub-Antarctic birds. Stable isotopes allowed us to identify females of most species as income breeders at the onset of breeding, with the exception of the two crested penguin females exhibiting a mix of income and capital resources use. 5. Multidimensional isotopic analyses revealed that resource partitioning exists at multiple stages of the annual cycle in ways likely to be important under global change, exhibiting wide potential for ecosystem analysis.

Data from: High frequency of multiple paternity in Eastern red bats, Lasiurus borealis, based on microsatellite analysis

Most species of bats give birth to only one pup each year, although Eastern red bats (Lasiurus borealis) can produce up to five pups per litter. Offspring in a single litter have been documented to be at different stages of development, suggesting that multiple paternity occurs. We tested the null hypothesis of genetic monogamy in red bats using six autosomal microsatellites and one X-linked microsatellite from 31 parent/offspring groups for a total of 128 bats. We sampled both pregnant females and mothers with pups that were obtained from bats submitted to departments of health in Oklahoma and Texas for rabies testing. Multiple paternity was assessed using a maximum-likelihood approach, hypothesis testing, and X-linked locus exclusion. The mean polymorphic information content of our markers was high (0.8819) and combined non-exclusion probability was low (0.00027). Results from the maximum-likelihood approach showed that 22 out of 31 (71%) parent/offspring groups consisted of half siblings, hypothesis testing rejected full sibship in 61% of parent/offspring groups, and X-linked locus exclusion suggested multiple paternity in at least 12 parent/offspring groups, rejecting our hypothesis of genetic monogamy. This frequency of multiple paternity is the highest reported thus far for any bat species. High levels of multiple paternity have the potential to impact interpretations of genetic estimates of effective population size in this species. Further, multiple paternity might be an adaptive strategy to allow for increased genetic variation and large litter size, which would be beneficial to a species threatened by population declines from wind turbines.

opencc-zeroOct 2020View details →

Data from: Parasite infection leads to widespread glucocorticoid hormone increases in vertebrate hosts: a meta-analysis

1. Parasites and pathogens (hereafter parasites) commonly challenge organisms, but the extent to which their infections are physiologically stressful to hosts remains unclear. Importantly, vertebrate hormones, glucocorticoids (GCs), have been reported to increase, decrease, or show no alterations stemming from infections, challenging the generality of parasite-associated GC responses and motivating a search for important moderator variables. 2. We undertook the first meta-analysis of changes in vertebrate GCs following experimental infection with parasites, extracting 146 effect sizes from 42 studies involving 32 host and 32 parasite species to test for general patterns of GC following infection, as well as the influence of moderators. 3. Overall, infection increased GCs relative to preliminary or control levels when the single largest effect sizes from repeated measures studies were examined, suggesting that parasites of vertebrate hosts can be thought of generally as physiological stressors by elevating GCs. 4. When all effect sizes were included along with the moderator of sampling time post-infection (tPI), parasite infection still had a positive effect on host GCs. However, the strength of that effect did not relate consistently to tPI, illustrating temporal differences in GC changes during the course of infection among parasite taxa (e.g., arthropod versus bacterial infections). Other moderator variables examined did not influence GC responses. 5. Studies broadening the range of host and parasite taxa, and sampling during critical time windows, would aid in our understanding of variation in the host stress response and its consequences for fitness of both vertebrate hosts and their parasites. 25-Sep-2019

opencc-by-4.0Oct 2020View details →

Data -SUPPLIMENDARY INFORMATIONS –Growth of D614G Virus – Regression Analysis

Data analysis report for Growth of D614G Virus – Regression Analysis.

opencc-zeroOct 2020View details →

Data from: An analysis of travel reports of the Finnish botanical expeditions to Russian Lapland (Murmansk Region and Northern Karelia) in 1861 and 1863

Finnish botanical expeditions, which were made to Russian Lapland (present-day Murmansk Region and northern Karelia, Russia) in 1861 and 1863, published travel reports with preliminary information, which contained numerous floristic novelties and phytogeographical observations but have been overlooked in present-day studies. Two reports appeared in print, by Gustav Selin on the expedition made in 1861, and by Nils Isak Fellman on the expedition made in 1863. We analysed mentions of vascular plant species published in these travel reports in order to trace and evaluate first records and localities of rare and legally protected species on the basis of herbarium vouchers kept at H. In spite of high self-claims, Selin actually reported 9 species new to present-day Murmansk Region and 1 species new to Republic of Karelia, and 4 species of vascular plants that are currently under legal protection in Murmansk Region, whereas Fellman reported 11 species new to Murmansk Region and 5 species new to Karelia, with 34 species under legal protection in Murmansk Region. First records of alien plants were 7 species from Selin and 4 species from Fellman. These numbers brought the contemporary floristic knowledge in Russian Lapland to 504 species of native plants (50% of the current total) and 54 species of alien plants (11% of the current total). Fellman's report included the first phytogeographical observations from the Kola Peninsula, with the first botanical limits observed, and the first descriptions of key botanical territories which are currently under strict protection. This study contributes to botanical history, plant protection and management of plant invasions in Murmansk Region.

opencc-by-4.0Oct 2020View details →

Dataset: Toothbrushing Data and Analysis of its Potential Use in Human Activity Recognition Applications

This is the dataset that accompanies the paper 'Dataset: Toothbrushing Data and Analysis of its Potential Use in Human Activity Recognition Applications'. In this paper, we describe and analyze a time-series dataset from toothbrushing activity using brush-attached and wearable sensors. The data was collected from 17 participants when they brushed their teeth over one week in 5 different locations. The dataset consists of 62 toothbrushing sessions for each of the brush-attached and wearable sensor approaches, using both electric and manual brushes. The average duration of each session is 2 minutes. One sensor device was attached to the handle of the brush while the other was worn by the participants as a wrist-watch. We collected the data from a 3-axis accelerometer and a 3-axis gyroscope at a 200 Hz sampling rate. Accompanying code can be found at our GitHub repository <a href="https://github.com/icl-mq/toothbrushing-dataset">https://github.com/icl-mq/toothbrushing-dataset</a>. This repository contains example code demonstrating how to process the data along with the file metadata.

opencc-by-4.0Oct 2020View details →

Data and analysis script for channel measurement campaign at POWDER-RENEW using Iris SDRs

This repository contains our raw datasets from channel measurements performed at the University of Utah campus. In addition, we have included a document that explains the setup and methodology used to collect this data, as well as a very brief discussion of results.  File organization: * documentation/ - Contains a .docx with the description of the setup and evaluation. * data/ - HDF5 files containing both metadata and raw IQ samples for each location at which data was collected. Notice we collected data at 14  different client locations. See map in the attached docx (skipped locations 12 and 16). We deployed 5 different receivers at 5 different rooftops. Due to resource constraints, one set of files contains data from 4 different locations whereas another set  contains information from the single remaining location. We have developed a set of python scripts that allow us to parse and analyze the data. Although not included here, they can be found in our public repository: <a href="https://github.com/renew-wireless/RENEWLab">https://github.com/renew-wireless/RENEWLab</a> You can find the top script <a href="https://github.com/renew-wireless/RENEWLab/blob/master/PYTHON/IrisUtils/deployment_tool.py">here</a>. For more information on the POWDER-RENEW project please visit the <a href="https://powderwireless.net/">POWDER website</a>. The RENEW part of the project focuses on the deployment of an open-source massive MIMO system. Please visit our <a href="https://renew-wireless.org/">website </a>for more information.

opencc-by-4.0Nov 2020View details →

Data, analysis scripts, and simulations files for "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"

Measured data and analysis script, as well as, simulated data, and input scripts for our publication "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"

opencc-by-4.0Nov 2020View details →

Data and statistical analysis scripts for manuscript on high-throughput phenotyping of root economics in wheat

This repository contains the root data, GEMMA files, and R code for generating the statistics and figures used in a preprint describing high-throughput phenotyping of root respiration in winter wheat. Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture Haichao Guo, Habtamu Ayalew, Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Xue-Feng Ma, Larry M. York bioRxiv 2020.11.12.380238; doi: <a href="https://doi.org/10.1101/2020.11.12.380238">https://doi.org/10.1101/2020.11.12.380238</a> analysis.R - A script for processing the included 4 CSV files of collected data. It is intended to run directly in RStudio and will automatically set the working directory in that case. The GEMMA folder includes files as output from GEMMA for genetic analysis, as described in the methods section of the preprint. These files are required by the R code for making Manhattan plots and other output. It will automatically create an output folder and the output text and figure files. The protocol for the respiration measurements are available in a separate Zenodo repository: <a href="https://doi.org/10.5281/zenodo.4247873">https://doi.org/10.5281/zenodo.4247873</a> Please cite this repository and the preprint if any data or R code is used in your work.

opencc-by-4.0Nov 2020View details →

Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration

This repository contains a PDF written protocol with figures describing a method for measuring root respiration using an infrared gas analyzer (LI-850) and the R script necessary for processing the text files to derive CO2 flux. Just download the ZIP file, unzip locally, open either the PDF or the .R file. root_respiration_protocol.pdf - The illustrated protocol includes instruments and parts needed. root_respiration_script.R - A script for processing the included 15 .txt files as examples from a LI-850 Gas Analyzer and extract absolute CO2 flux with example code for how to incorporate root mass or length to derive specific root respiration. It is intended to run directly in RStudio and will automatically set the working directory in that case. Please cite this repository if the protocol or R script is used in your work.  Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2020). Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4247873 The first manuscript using and describing this method is available: Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. <a href="https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.17329">New Phytologist. DOI: 10.1111/nph.17329</a>

opencc-zeroNov 2020View details →

Data from Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties

Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. <a name="_Hlk9515878">However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships</a>. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapo-transpiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, e.g., shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.

opencc-by-4.0Dec 2020View details →

Data and code for analysis of ion currents in mass spectrometric profiles using glioblastoma tissue

This upload contains all replication material for "Analysis of ion currents in mass spectrometric profiles using glioblastoma tissue" (forthcoming). Authors: E.S. Zhvansky, A.A. Sorokin, D.S. Zavorotnyuk, V.A. Shurkhay, D.S. Bormotov, A.A. Potapov. Code and data are located within spectra_data_and_code.zip. Code is written in MATLAB R2019b. Please find the readme.txt for code using and the code to replicate the main findings of the paper (figures_replication.m).

opencc-zeroDec 2020View details →

Data from: Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney

The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterise the effects of BP index variants from genome-wide association studies (GWAS) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalisation and Mendelian randomisation analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomisation we uncovered effects of BP on renal outcomes commonly affecting hypertensive patients. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.