Find research datasets worth reusing

Genome-wide association summary statistics for sex- and age-specific analysis of chronic back pain

The dataset comprises summary-level statistics for age- and sex-specific genome-wide association study of chronic back pain (cBP) in individuals of European descent from UK Biobank (<a href="https://www.ukbiobank.ac.uk/">https://www.ukbiobank.ac.uk/</a>). The study was carried out under UK Biobank approved project #18219.  The dataset accompanies the paper (please cite if using the dataset): <a href="https://pubmed.ncbi.nlm.nih.gov/33021770/">Freidin, Maxim B.; Tsepilov, Yakov A.; Stanaway, Ian B.; Meng, Weihua; Hayward, Caroline; Smith, Blair H.; Khoury, Samar; Parisien, Marc; Bortsov, Andrey; Diatchenko, Luda; Børte, Sigrid; Winsvold, Bendik S.; Brumpton, Ben M.; Zwart, John-Anker; HUNT All-In Pain; Aulchenko, Yurii S.; Suri, Pradeep; Williams, Frances M.K. Sex- and age-specific genetic analysis of chronic back pain. Pain. 2020. doi:10.1097/j.pain.0000000000002100.</a> The phenotype of cBP was defined as back pain for 3+ months. Linear mixed-effects additive model was fitted adjusting for age, genotyping array type, and 10 genetic PCs provided by UK Biobank. The following filters were applied: minor allele frequency >0.001, genotyping and individual call rates >0.98%, imputation quality score (INFO) >0.7. GWAS were carried out in males and females separately in the whole sample (allages) as well as in groups of younger than 65 years (under65) and 65+ years old (65plus) as detailed in the paper. Accordingly, 6 files are deposited here, corresponding to each group.  Column headers: SNP, SNP rsID  CHR, chromosome BP, genomic position (GRCh37 build) EA, effect allele (coded as "1") OTHER, other allele (coded as "0") A1FREQ, frequency of effect allele INFO, imputation quality BETA, effect size (for effect allele) SE, standard error of effect size PVAL, p-value for association

opencc-zeroOct 2020View details →

dryad40/100

Pathogenic Leptospira isolated from rodents in New Orleans, Louisiana USA, and associated site information

Land use change can elevate disease risk by creating conditions beneficial to species that carry zoonotic pathogens. Observations of concordant global trends in pathogen prevalence and disease incidence have engendered concerns that urbanization could increase transmission risk of some pathogens. Yet host-pathogen relationships underlying transmission risk have not been well characterized within cities, even where contact between humans and species capable of transmitting pathogens of concern occur. We addressed this deficit by testing the hypothesis that areas in cities experiencing greater population loss and infrastructure decline (i.e., counter-urbanization) can support a greater diversity of host species and a larger and more diverse pool of pathogens. We did so by characterizing pathogenic Leptospira infection relative to rodent host richness and abundance across a mosaic of abandonment in post-Katrina New Orleans (Louisiana, USA). We found that Leptospira infection loads were highest in areas that harbored higher rodent species richness. Areas with greater host co-occurrence also harbored a greater number of hosts, including the most competent hosts, indicating that Leptospira infection is amplified by increases in overall and relative host abundance. Evidence of shared infection among rodent hosts indicates that cross-species transmission of Leptospira likely increases infection at sites with greater host syntopy. Additionally, evidence that rodent co-occurrence and abundance and Leptospira infection load parallel abandonment suggests that counter-urbanization can elevate zoonotic disease risk within cities, particularly in underserved communities that are burdened with disproportionate concentrations of derelict properties.

Data for Are Changes in Alcohol Use and Personality Traits associated? A Cohort Study among Young Swiss Men

These are the data and metadata for the article  Are Changes in Alcohol Use and Personality Traits associated? A Cohort Study among Young Swiss Men by  Gerhard Gmel, Simon Marmet, Joseph Studer, and Matthias Wicki to be published in Frontiers of Psychiatry

Observation and modeling of high-7Be events in Northern Europe associated with the instability of the Arctic polar vortex in early 2003

Data repository for paper: "Observation and modeling of high-7Be events in Northern Europe associated with the instability of the Arctic polar vortex in early 2003" Erika Brattich; Hongyu Liu; Bo Zhang; Miguel Angel Hernandez-Ceballos; Jussi Paatero; Darko Sarvan; Vladimir Djurdjevic; Laura Tositti; Jelena Ajtić, submitted to Atmospheric Chemistry and Physics, October 2020 Created by Erika Brattich (erika.brattich@unibo.it), October 2020 -> Data - Pb210_2sites.csv contains daily 210Pb observations at Helsinki and Sodankyla in the period January-March 2003. Dates are in "m/d/yyyy" format and 210Pb measurements are in µBq/m³. Please refer to Mattson et al. (1996) for details. -> Model output - trac_avg.merra2_2x25_RnPbBe.200301-200303-monthly-means.bpch.gz: contains model output of monthly mean 210Pb and 7Be concentrations for January, February, and March 2003. - ts_1h.200301.bpch.tar: hourly model output for January 2003 - ts_1h.200302.bpch.tar: hourly model output for February 2003 - ts_1h.200303.bpch.tar: hourly model output for March 2003 - diaginfo.dat, tracerinfo.dat: information data files needed for the GAMAP package (in IDL) used to read and process the model output. GAMAP is publicly available at: <a href="http://acmg.seas.harvard.edu/gamap/">http://acmg.seas.harvard.edu/gamap/</a>  References: Mattsson, R., Paatero, J., and Hatakka, J.: Automatic Alpha/Beta Analyser for Air Filter Samples - Absolute Determination of Radon Progeny by Pseudo-coincidence Techniques, Radiat. Prot. Dosim., 63, 133-139, doi:10.1093/oxfordjournals.rpd.a031520, 1996.

opencc-by-4.0Nov 2020View details →

Dataset related to the article "Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation"

This record contains raw data related to the article “ Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation”.  Plakophilin-2 (PKP2) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the PKP2 p.S183N mutation was found in a patient affected by Brugada syndrome (BS), an inherited arrhythmic channelopathy most commonly caused by sodium channel gene mutations. We here describe a case of a patient carrier of the same BS-related PKP2 p.S183N mutation but with a clear diagnosis of ACM. Specifically, we report how clinical and molecular investigations can be integrated for diagnostic purposes, distinguishing between ACM and BS, which are increasingly recognized as syndromes with clinical and genetic overlaps. This observation is fundamentally relevant in redefining the role of genetics in the approach to the arrhythmic patient, progressing beyond the concept of "one mutation, one disease", and raising concerns about the most appropriate approach to patients affected by structural/electrical cardiomyopathy. The merging of genetics, electroanatomical mapping, and tissue and cell characterization summarized in our patient seems to be the most complete diagnostic algorithm, favoring a reliable diagnosis.

opencc-by-4.0Sep 2020View details →

Figures 2 in The species of Astymachus Howard (Hymenoptera: Encyrtidae)ı potentially important parasitoids of Aclerdidae (Hemiptera: Coccoidea) associated with grasses (Poaceae)ı with descriptions of three new species

Figures 2. Astymachus saccharum sp. nov.: (a) head (holotype); (b) antenna ♀ (holotype); (c) apex of fore wing venation (paratype); (d) fore wing (paratype). Astymachus felix Singh and Hayat: (e) apex of fore wing venation. Astymachus phainae Sugonjaev: (f) fore wing; (g) apex of fore wing venation. Astymachus lasallei sp. nov. (holotype) (h) antenna ♀; (i) head; (j) fore wing; (k) discal setae below marginal vein, enlarged (differential interference contrast); (l) apex of fore wing venation. Asymachus phragmitis Trjapitzin: (m) head; (n) antenna ♀. (Figures e-g courtesy of Mohammad Hayat).

opencc-by-4.0Sep 2020View details →

Figures 3 in The species of Astymachus Howard (Hymenoptera: Encyrtidae)ı potentially important parasitoids of Aclerdidae (Hemiptera: Coccoidea) associated with grasses (Poaceae)ı with descriptions of three new species

Figures 3. Astymachus phragmitis Trjapitzin: (a) antenna ♂; (b) fore wing; (c) apex of fore wing venation. Astymachus japonicus Howard: (d) head; (e) antenna ♀; (f) antenna ♂; (g) apex of fore wing venation; (h) fore wing. Astymachus srilankae sp. nov. (holotype): (i) head; (j) antenna ♀; (k) antenna ♂; (l) fore wing; (m) apex of fore wing venation.

Data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history''

Eva Bons, Christine Leemann,  Karin J. Metzner, Roland R. Regoes This repository contains all the data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history' See the readme after unpacking the .zip for a description of the files

Data Associated with the paper "Bell correlations between light and vibration"

Data Associated with the <a href="http://doi.org/10.1126/sciadv.abb0260">following paper</a> <blockquote> S. Tarrago Velez, V. Sudhir, N. Sangouard, C. Galland, Bell correlations between light and vibration at ambient conditions. Sci. Adv. 6, eabb0260 (2020). </blockquote> A thorough explanation of the experiment performed is available there.   The file RawData_DelaySweep.zip contains the raw count information as obtained during the experiment. It is organized in different folders, each containing the data associated with one particular position of the delay stage. The file naming convention has the position, followed by the angles in detection (thA corresponds to the Stokes detection arm and thB corresponds to the anti-Stokes detection arm), and the acquisition time. As explained in the Supplementary Information Sec. 2.1, there are multiple measurements for each combination of delay and detection settings. The zip file also contains the file AnalysisBellv3.py, which was used to analyze the data. Running the file produces 'resultsBell.txt' and 'results_g2.txt', which contain the results for the CHSH parameter and the second order cross correlation, respectively.   The file RawData_Visibility.zip contains the raw count information obtained for the visibility curves, as expained in the Supplementary Information Sec. 2.1. The files follow the same naming convention as those in RawData_DelaySweep.zip. It also contains the file AnalysisCounts.py, which analyzes the data to obtain the correlation parameters.   The file BellCorrelations_CompiledData.xlsx is a spreadsheet containing the results of the analysis of the previous two sets of data.

opencc-by-4.0Aug 2020View details →

Non-target screening of organic compounds in offshore produced water by GC×GC-MS (associated data)

Associated data for the manuscript titled "Non-target screening of organic compounds in offshore produced water by GC×GC-MS" Preprint doi://10.26434/chemrxiv.13317938

opencc-by-4.0Dec 2020View details →

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?

This is a dataset containing fragments of internal transcribed spacer 2 (ITS2) extracted from Bistorta vivipara root-associated fungi, sampled from snow fence experiment in Adventdalen, Svalbard.  This dataset was used in Wutkowska et al., 2020, Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? [available at biorXiv.org, DOI: 10.1101/2020.06.20.157099] Now the manuscript is available as a peer-reviewed paper: Wutkowska, Magdalena, Dorothee Ehrich, Sunil Mundra, Anna Vader, and Pernille Bronken Eidesen. 2021. ‘Can Root-Associated Fungi Mediate the Impact of Abiotic Conditions on the Growth of a High Arctic Herb?’ Soil Biology and Biochemistry 159:108284. doi: 10.1016/j.soilbio.2021.108284.   All other corresponding data are available here: https://github.com/magdawutkowska/bistorta

FIG. 5. — Undated female red deer upper left canine from Abri des Autours. A in The worked bone industry and intrusive fauna associated with the prehistoric cave burials of Abri des Autours (Belgium)

FIG. 5. — Undated female red deer upper left canine from Abri des Autours. A, general view; B, detail of perforation; C, detail of the crown with remaining traces of enamel (arrow). Scale bars: A, 10 mm; B, C, 1 mm.

FIG. 7 in The worked bone industry and intrusive fauna associated with the prehistoric cave burials of Abri des Autours (Belgium)

FIG. 7. — Needle made of a suid left fibula, from the Neolithic collective burial at Abri des Autours: A, general view; B, detail of the tip showing a smooth polish associated with fine and short striations; C, detail of the posterior edge near the point, showing fine parallel striations; D, detail of the posterior edge at the midpoint of the tool, showing smooth polish. Scale bars: A, 10 mm; B, C, D, 150 μm.

FIG. 2 in The worked bone industry and intrusive fauna associated with the prehistoric cave burials of Abri des Autours (Belgium)

FIG. 2. — Plan of Abri des Autours: A, circular depression; B, rubble of old (unpublished) excavations; C, crack in the rock; D, pit under low wall (from Polet & Cauwe 2007).

FIG. 6 in The worked bone industry and intrusive fauna associated with the prehistoric cave burials of Abri des Autours (Belgium)

FIG. 6. — Pointed rib of a large bovid, from the Neolithic collective burial at Abri des Autours: A, general view (from left to right: internal, centre and external views); B, detail of the tip (internal view) showing some polish; C, detail of the tip (internal view) showing fine perpendicular striations; D, detail of a lateral edge of the rib devoid of striations. Scale bars: A, 10 mm; B, 500 μm; C, D, 100 μm.

FIG. 3 in The worked bone industry and intrusive fauna associated with the prehistoric cave burials of Abri des Autours (Belgium)

FIG. 3. — Stratigraphy of Abri des Autours, east–west profile (modified from Cauwe 1994): 1a, b, clay, without pebbles; 2, as layer 6, but with more clay; 3a, brown, argillaceous deposit with small, densely dispersed pebbles; 3b, as layer 3a, but less humic. Contains the Neolithic multiple burial; 3c, as layer 3a, but strongly compacted by calcite precipitations; 4, clay with fine pebbles; 5a, b, cryoclastic deposit without humic or clayish fraction; layer 5b corresponds to very fine gravels, while layer 5a includes larger elements. The Mesolithic single burial extends through both of these layers; 6, brown-grey clayey deposit, strongly inclined. Contains the Mesolithic collective burial; 7, cryoclastic layer, included in clayey orange-brown sediment; 8, thin pebble deposit mixed with greyish sediment; 9, low wall constructed of unworked stone blocks.

opencc-by-3.0Dec 2020View details →

Association between meteorological factors and the number of tuberculosis notifications: a time-series study in Hong Kong

Using a 22-year consecutive surveillance data in Hong Kong, including  monthly averages of meteorological factors, air pollution concentrations , total number of TB cases notified, to analyze the association of monthly average temperature and relative humidity with temporal dynamics of monthly total number of TB cases notified.

openother-openDec 2020View details →

Near surface softening and healing in eastern Honshu associated with the 2011 Tohoku-Oki Earthquake: Research data and code

The zip file named 'mainshock.zip' contains the Matlab codes and seismic data for reproducing the results of Figure 2. The Excel file named 'Source Data.xls' contains the raw data of Figures 3 and 4.

opencc-by-4.0Dec 2020View details →

Values and attitudes associated with public support for biodiversity and ecosystem services as goals of ecological restoration

Source data and metadata for "Public support for restoration: Does including ecosystem services as a goal engage a different set of values and attitudes than biodiversity protection alone?", accepted to PLOS One in December 2020.