Find research datasets worth reusing

opencc-by-4.0Dec 2018View details →

Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis

This dataset contains the results of 2 related analyses, described in "Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis" (European Heart Journal Supplements, OUP). Link to the article: https://www.hal.inserm.fr/inserm-02310241 1) In the directory "miRNAs_MARTHA_GWAS" : GWAS summary statistics for 162 circulating miRNAs in 344 VTE patients from the MARTHA cohort. Header for each summary file: Trait: miRNA id chr: Chromosome pos.hg19: Position of the variant in hg19/GRCh37 coordinates SNP: rsid A1: Reference allele on the forward strand A2: Alternate allele on the forward strand freq_A1: Frequency of reference allele rsqr: Imputation quality defined by MACH beta_A1: Estimated effect size (beta regression coefficient) of reference allele se_A1: Estimated standard error of beta p: p-value (significance of estimated beta) z.score: Z-score   2) In the directory "meta_analysis": Random effect meta-analysis combining the results of our GWAS on the MARTHA cohort, and the results from a similar analysis conducted by Nikpay et al. (doi: 10.1093/cvr/cvz030). Summary statistics of 142 microRNAs, common to both datasets, were processed (and combine 1054 samples). Header for each summary file: chr: Chromosome pos.hg19: Position of the variant in hg19/GRCh37 coordinates SNP: rsid A1: Reference allele on the forward strand A2: Alternate allele on the forward strand N: Sample size Q: Cochran's heterogeneity statistic Q.p: p-value of Cochran's Q beta_A1: Estimated effect size (beta regression coefficient) of reference allele se_A1: Estimated standard error of beta p: p-value (significance of estimated beta)

opencc-by-4.0Sep 2017View details →

Fig. 1 in A Bayesian analysis of the parasitic ecology in Jenynsia multidentata (Pisces: Anablepidae)

Fig. 1. Map of the sample sites, Salado Relief Channel (S.R.C.) in Samborombon Bay and the Sauce Chico River in Bahia Blanca estuary (B.B.), Argentina.

opencc-by-4.0Sep 2017View details →

Fig. 2. Mean and the 95 in A Bayesian analysis of the parasitic ecology in Jenynsia multidentata (Pisces: Anablepidae)

Fig. 2. Mean and the 95% credibility range of Weight (W.) in grams (gr), total and standard length (TL and SL) in centimeters of Jenynsia multidentata Jenyns, 1842 in Salado River Channel (S.R.C.) and Low Sauce River of Bahia Blanca (B.B.), Argentina.

Fig 1 in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences

Fig 1. Map of Southeast Asia showing the approximate location of the new (Singapore and Bali) and GenBank sequences included in the study. Numbers correspond to the following locations (haplotype IDs in parentheses): ★, Singapore (Sing1–3); 1, Vietnam (Viet1 & 2); 2, Cambodia (Camb1 & 2); 3, Thailand (Thai1); 4, Thailand (Thai2); 5, Malaysia (Selangor1 & 2); 6, Malaysia (Johor); 7, south Sumatra, Indonesia (Sumatra1 & 2, Java1); 8, Java (Java1); 9, Kalimantan, Borneo (Borneo3); 10, Sarawak, Borneo (Borneo1); 11, Sepilok, Borneo (Borneo2); 12, Bali, Indonesia (Bali1 & 2); 13, Sibuyan, Philippines (Phil1); 14, Bangkok, Thailand (Thai3 & 4); 15, Malaysia (W. Malay); 16, Malaysia (E. Malay2); 17 Malaysia (E. Malay1);18, north Sumatra (Sumatra3–6, 9); 19, west Borneo, Indonesia (Borneo9); 20, west Borneo, Indonesia (Borneo4–7); 21, central Borneo, Indonesia (Borneo4 & 6); 22, Bangka, south Sumatra (Sumatra 7 & 8); 23, Java, Indonesia (Java2 & 3); 24, northeast Borneo, Indonesia (Borneo8); 25, Mindanao, Philippines (Phil2); 26, Timor (Timor). Several Borneo haplotypes appear in multiple locations.

Fig 4. Median-joining haplotype network for M in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences

Fig 4. Median-joining haplotype network for M. fascicularis. The size of the circular nodes representing haplotypes is proportional to the number of sequences comprising the haplotype. Shading of circular nodes corresponds to general geographic groupings including Sundaic islands (white), mainland Indochina (gray), Malay Peninsula and northern Sumatra (dark gray), and Singapore (black). Haplotype identifications are presented in Table 1.

Fig 3 in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences

Fig 3. Phylogenetic tree topology from Bayesian inference of 12S/tRNA-val/16S mtDNA sequences using a Birth-Death speciation tree prior, and HYK+G+I nucleotide substitution model in BEAST v2.1.3. Lettered identifications for clades are presented below the branches at major nodes. Posterior probabilities are displayed above the branches at nodes. Numbers in parentheses appearing with haplotype identifications are presented in Table 1, and correspond to numbered locations presented on the Figure 1 map. The Singapore haplotypes form two phylogenetic subgroupings, one from the Bukit Timah Nature Reserve (Sing1) and the other from the Central Catchment Nature Reserve (Sing2 & Sing3).

Fig 2 in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences

Fig 2. Map of central Singapore showing the sampling locations in the Bukit Timah (BTNR) and Central Catchment (CCNR) Nature Reserves. Map created using ArcGIS® (ESRI® 2015).

opencc-zeroSep 2021View details →

Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record

Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in the late Selandian-Ypresian in Dataset I indicate the onset of an ascophoran-grade radiation. Lineage-through-time plots confirm the macroevolutionary lag preceding the radiation of cheilostomes in the mid-Cretaceous, and their renewed diversification in the late Paleocene and Eocene. A multivariate birth-death model indicates that origination rates are shaped by diversity-dependent dynamics coupled with a positive correlation with sea surface temperature, while extinction rates negatively correlate with sea level. Text-mined data provide broadly similar rate dynamics as manually curated data, although discrepancies could be attributed to the omission of key literature in Dataset II, and the inclusion of new published and unpublished data, and revised ranges in Dataset I. Revision and augmentation of PBDB occurrences were necessary to generate rate profiles akin to those of Datasets I and II and highlight the risks of using unedited occurrence data. Our results support the widely held assumption that diversification dynamics are controlled by both biotic and abiotic factors and pave the way for integrating fossils with molecular phylogenies to study these processes in more detail.

opencc-by-4.0Mar 2021View details →

figure 6 Bayesian 50 in Zebrus pallaoroi sp. nov.: a new species of goby (Actinopterygii: Gobiidae) from the Mediterranean Sea with a DNA-based phylogenetic analysis of the Gobius-lineage

figure 6 Bayesian 50% majority-rule consensus tree estimation of phylogenetic relationships of analysed species from the Gobius-lineage sensu Agorreta et al. (2013) based on the nuclear gene rhodopsin. Numbers on branches are Bayesian posterior probabilities and maximum likelihood bootstrap values, respectively. Only values higher than 0.9 for posterior probability and 70% for bootstrap are shown.

opencc-by-4.0Mar 2021View details →

figure 5 Bayesian 50 in Zebrus pallaoroi sp. nov.: a new species of goby (Actinopterygii: Gobiidae) from the Mediterranean Sea with a DNA-based phylogenetic analysis of the Gobius-lineage

figure 5 Bayesian 50% majority-rule consensus tree estimation of phylogenetic relationships of analysed species from the Gobius-lineage sensu Agorreta et al. (2013) based on the mitochondrial gene cytochrome b. Numbers on branches are Bayesian posterior probabilities and maximum likelihood bootstrap values, respectively. Only values higher than 0.9 for posterior probability and 70% for bootstrap are shown.

publicNov 2021View details →

Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record

Open the record for dataset details and reuse information.

publicOct 2022View details →

Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

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publicJul 2024View details →

Data and scripts for: Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI

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opencc-by-4.0Apr 2020View details →

A Bayesian Phylogenetic Hidden Markov Model for B Cell Receptor Sequence Analysis

simulation and PC64/VRC01 input/output data files

opencc-by-4.0Aug 2020View details →

CO2 Reduction Tafel Dataset for Bayesian Data Analysis

This dataset contains 344 different digitized and tagged Tafel slope datasets from the CO2 reduction literature. We re-analyze this data with a Bayesian data analysis procedure that estimates a Tafel slope and yields distributional uncertainty information about its value. We are releasing this dataset along with our study to facilitate re-analyzing and refitting our data using different models and approaches.

dryad36/100

Bayesian diagnostic meta-analysis dataset of pelvic examination in pelvic inflammatory disease

Pelvic inflammatory disease (PID) is not merely a transient sexually transmitted disease. It can lead to chronic pain, ectopic pregnancy, and infertility. Although the Centers for Disease Control and Prevention have established minimum diagnostic criteria, including pelvic examination, the diagnostic value of pelvic tenderness has recently garnered controversy. Our meta-analysis aimed to confirm whether pelvic examination can help diagnose PID among at-risk women. Design A Bayesian meta-analysis of studies reporting diagnostic data of patients at risk for PID. Setting We searched MEDLINE, EMBASE, CENTRAL, CINAHL, Google, and Google Scholar for eligible articles. Participants Female patients at risk for PID. Main results The literature search produced 5,395 articles. After quality assessment, 16 studies and their 4,083 participants were eligible for synthesis on pelvic tenderness.

opencc-zeroDec 2019View details →

opencc-by-4.0Jan 2021View details →

An Introduction to a Bayesian Analysis of the Laboratory Origin of SARS-CoV-2

An Introduction to a Bayesian Analysis of the Laboratory Origin of SARS-CoV-2

opencc-by-4.0Apr 2021View details →

Informing antenna design for Global 21-cm experiments using a simulated Bayesian data analysis pipeline (supplementary data)

These are the posterior files, foreground simulation data sets and chromaticity factor values used to produce the results for <a href="https://arxiv.org/abs/2106.10193">arXiv:2106.10193</a>. Plots of the fitted signal and residuals for each case are included, as is a plotting function to reproduce key figures. Naming conventions: <ul> <li>f0: Centre frequency of the 21cm signal present in the simulated data</li> <li>A: Amplitude of the simulated 21cm signal present in the simulated data</li> <li>M_sig: Model being fit to the data includes a 21cm signal</li> <li>M_nosig: Model being fit to the data is a foreground only</li> </ul> Software used: <ul> <li><a href="https://github.com/PolyChord/PolyChordLite/tree/839292290a7747dbee82933bb9f7f955ac45c3ca">PolyChord</a></li> </ul>

dryad36/100

River dams and the stability of bird communities: A hierarchical Bayesian analysis in a tropical hydroelectric power plant

<ol> <li>The effects of anthropogenic disturbance upon the stability of wildlife communities depend on the heterogeneity and connectivity of habitat remnants on multiple scales. The number of hydroelectric dams in biodiversity hotspots (Africa, South America and Asia) is growing rapidly. To establish their environmental impact, it is essential to understand the dynamics of wildlife communities before and following the establishment of dams.</li> <li>We evaluated the impacts of the filling of the Serra do Facão hydroelectric reservoir in the São Marcos river, central Brazil, upon the bird community. Using data from 1,145 surveys across 20 sampling sites over eight years, two years before and six years after the filling of the reservoir, we assessed the resistance, i.e., maintenance close to an equilibrium state during the disturbance, and resilience, i.e., ability to return to the original state following the disturbance, of the bird community. We used spatiotemporal hierarchical Bayesian models to assess the effects of reservoir filling on five community parameters: abundance, richness, phylogenetic diversity, functional diversity and species composition.</li> <li>In the period subsequent to reservoir filling, there was (i) a marked reduction in bird abundance, richness, phylogenetic diversity and functional diversity, and (ii) a reduction in the proportion of forest species, coupled with an increase in the proportion of savanna species. Except for bird abundance, none of the other community attributes returned to their original levels, even after six years. Our findings indicate that Cerrado bird communities have both low resistance and low resilience to habitat loss associated with the establishment of hydroelectric reservoirs.</li> <li> Synthesis and applications. The environmental costs of hydroelectric dams are still underestimated or neglected in Brazil. A new paradigm in the assessment of their environmental impacts is warranted, incorporating (i) models of spatiotemporal variations based on long-term monitoring with surveys initiated before disturbances and (ii) measures of functional and phylogenetic diversity, such that society can understand the costs and benefits of the establishment of new hydroelectric dams and make informed decisions. Biodiversity loss could be minimized by ensuring the preservation and connectivity of alluvial habitats, capable of maintaining the supply of resources and the functional and phylogenetic attributes of bird communities associated with such habitats.</li> </ol>

opencc-zeroMar 2020View details →

Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)

Figure 1. - Bayesian phylogeny of Euptychia based on one mitochondrial (COI) and one nuclear (EF1-a) gene. Posterior probabilities are listed above and bootstrap values below branches. A dash denotes bootstrap support lower than 50%. (Euptychiaattenboroughi is not included in the analysis – see text for details.)