cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14511105
title: Deciphering the role of <i>ttrA</i> and <i>pduA</i> genes for <i>Salmonella enterica</i> serovars in a chicken infection model

description: <i>Salmonella enterica</i> serovars use self-induced intestinal inflammation to increase electron acceptor availability and to obtain a growth advantage in the host gut. There is evidence suggesting that the ability of <i>Salmonella</i> to use tetrathionate and 1,2-propanediol provides an advantage in murine infection. Thus, we present here the first study to evaluate both systemic infection and faecal excretion in commercial poultry challenged by <i>Salmonella</i> Enteritidis (SE) and <i>S</i>. Typhimurium (STM) harbouring deletions in <i>ttrA</i> and <i>pduA</i> genes, which are crucial to the metabolism of tetrathionate and 1,2-propanediol, respectively. Mutant strains were excreted at higher rates when compared to the wild-type strains. The highest rates were observed with white egg-layer and brown egg-layer chicks (67.5%), and broiler chicks (56.7%) challenged by SEΔ<i>ttrA</i>Δ<i>pduA</i>, and brown egg-layer chicks (64.8%) challenged by STMΔ<i>ttrA</i>Δ<i>pduA</i>. SEΔ<i>ttr</i>AΔ<i>pdu</i>A presented higher bacterial counts in the liver and spleen of the three chicken lineages and caecal contents from the broiler chickens, whereas STMΔ<i>ttr</i>AΔ<i>pdu</i>A presented higher counts in the liver and spleen of the broiler and brown-egg chickens for 28 days post-infection (<i>P</i> ttrA and <i>pdu</i>A genes do not appear to be major virulence determinants in faecal excretion or invasiveness for SE and STM in chickens. <b>RESEARCH HIGHLIGHTS</b><i>ttr</i>A and <i>pud</i>A do not impair gut colonization or systemic infection in chicks.Mutant strains were present in higher numbers in broilers than in laying chicks.Mutants of SE and STM showed greater pathogenicity in broiler chicks than layers. <i>ttr</i>A and <i>pud</i>A do not impair gut colonization or systemic infection in chicks. Mutant strains were present in higher numbers in broilers than in laying chicks. Mutants of SE and STM showed greater pathogenicity in broiler chicks than layers.
DOI: 10.6084/m9.figshare.14511105.v1
title: Deciphering the role of <i>ttrA</i> and <i>pduA</i> genes for <i>Salmonella enterica</i> serovars in a chicken infection model

description: <i>Salmonella enterica</i> serovars use self-induced intestinal inflammation to increase electron acceptor availability and to obtain a growth advantage in the host gut. There is evidence suggesting that the ability of <i>Salmonella</i> to use tetrathionate and 1,2-propanediol provides an advantage in murine infection. Thus, we present here the first study to evaluate both systemic infection and faecal excretion in commercial poultry challenged by <i>Salmonella</i> Enteritidis (SE) and <i>S</i>. Typhimurium (STM) harbouring deletions in <i>ttrA</i> and <i>pduA</i> genes, which are crucial to the metabolism of tetrathionate and 1,2-propanediol, respectively. Mutant strains were excreted at higher rates when compared to the wild-type strains. The highest rates were observed with white egg-layer and brown egg-layer chicks (67.5%), and broiler chicks (56.7%) challenged by SEΔ<i>ttrA</i>Δ<i>pduA</i>, and brown egg-layer chicks (64.8%) challenged by STMΔ<i>ttrA</i>Δ<i>pduA</i>. SEΔ<i>ttr</i>AΔ<i>pdu</i>A presented higher bacterial counts in the liver and spleen of the three chicken lineages and caecal contents from the broiler chickens, whereas STMΔ<i>ttr</i>AΔ<i>pdu</i>A presented higher counts in the liver and spleen of the broiler and brown-egg chickens for 28 days post-infection (<i>P</i> ttrA and <i>pdu</i>A genes do not appear to be major virulence determinants in faecal excretion or invasiveness for SE and STM in chickens. <b>RESEARCH HIGHLIGHTS</b><i>ttr</i>A and <i>pud</i>A do not impair gut colonization or systemic infection in chicks.Mutant strains were present in higher numbers in broilers than in laying chicks.Mutants of SE and STM showed greater pathogenicity in broiler chicks than layers. <i>ttr</i>A and <i>pud</i>A do not impair gut colonization or systemic infection in chicks. Mutant strains were present in higher numbers in broilers than in laying chicks. Mutants of SE and STM showed greater pathogenicity in broiler chicks than layers.
DOI: 10.26302/sshade/experiment_bs_20181101_001
title: Vis-NIR reflectance spectra of a mix of three PAHs, PAHs mixed with CO2 snow and PAHs mixed with JSC Mars-1 simulant

description: Vis-NIR reflectance spectra of a series of samples with a mix of 3 PAHs (Anthracene, Phenanthrene-d10 and Pyrene), JSC Mars-1 dust, PAHs mixed with CO2 snow with different abundances (0.1%, 0.54%, 0.67%) and 1.5% PAHs mixed with JSC Mars-1 dust
DOI: 10.21942/uva.14680362.v2
title: Dataset belonging to Pouwels et al. (2021). Adolescents’ Social Media Use and Friendship Closeness: A Person-Specific Investigation of the Rich-Get-Richer and Poor-Get-Richer Hypotheses

description: This data set belongs to:<br>Pouwels, J. L., Valkenburg, P. M., Beyens, I., van Driel, I. I., & Keijsers, L. (2021). Adolescents’ Social Media Use and Friendship Closeness: A Person-Specific Investigation of the Rich-Get-Richer and Poor-Get-Richer Hypotheses.<br><br>The preregistration of the design, sampling and analysis plan of the study (https://osf.io/hxf7t), as well as all syntax files and online supplemental materials are available on the Open Science Framework (OSF) at https://osf.io/9ry7j/.<br>The .csv files are used for the analyses in R. The .dat files for the analyses in Mplus. The variable names of the .dat file could be find in the Mplus input file.<br>For more information, please contact the authors at j.l.pouwels@uva.nl or info@project-awesome.nl.<br><br>
DOI: 10.6084/m9.figshare.5903767.v1
title: New model of proliferative vitreoretinopathy in rabbit for drug delivery and pharmacodynamic studies

description: Blinding retinal diseases become more epidemic as the population ages. These diseases, such as diabetic retinopathy and macular edema, are of chronic nature and require protracted drug presence at the disease site. A sustained intravitreal porous silicon delivery system with dexamethasone (pSiO<sub>2</sub>-COO-DEX) was evaluated in a new rabbit model of proliferative vitreoretinopathy (PVR) in a real treatment design. In contrast to the pretreatment design model, pSiO<sub>2</sub>-COO-DEX was intravitreally injected into the eyes with active inflammation. Subretinal injection of vascular endothelial growth factor (VEGF) and Matrigel induced a late-onset vitreoretinal inflammation that gradually developed into PVR. This method mimics the human disease better than PVR induced by either intravitreal cell injection or trauma. The pSiO<sub>2</sub>-COO-DEX intervened eyes had minimal PVR, while balanced saline solution or free dexamethasone intervened eyes had significantly more PVR formation. In addition, adding VEGF to the Matrigel for subretinal injection induced greater inflammation and retinal neovascularization in comparison to only Matrigel injected under the medullary ray. Clinical and pathological examinations, including fundus fluorescein angiography and optical coherence tomography, confirmed these changes. In the current study, neither subretinal injection of Matrigel or subretinal injection of VEGF and Matrigel induced choroidal neovascularization. However, the current PVR model demonstrates a chronic course with moderate severity, which may be useful for drug screening studies.
DOI: 10.15468/rk46aw
title: New Mixaderus species from the Mascarene Islands (Coleoptera: Aderidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gompel, Nicolas (2021): New Mixaderus species from the Mascarene Islands (Coleoptera: Aderidae). Zootaxa 4969 (1): 166-174, DOI: https://doi.org/10.11646/zootaxa.4969.1.9
DOI: 10.6084/m9.figshare.11914380.v1
title: The use of a variable representing compliance improves accuracy of estimation of the effect of treatment allocation regardless of discontinuation in trials with incomplete follow-up

description: In Clinical Trials, not all randomised patients follow the course of treatment they are allocated to. The potential impact of such deviations is increasingly recognised, and it has been one of the reasons for a redefinition of the targets of estimation (“Estimands”) in the ICH E9 draft Addendum. Among others, the effect of treatment assignment, regardless of the adherence, appears a Estimand of practical interest, in line with the intention-to-treat principle. This study aims at evaluating the performance of different estimation techniques in trials with incomplete post-discontinuation follow-up when a 'treatment-policy' strategy is implemented.. In order to achieve that, we have (i) modelled and visualised as directed acyclic diagram a reasonable data-generating model; (ii) investigated which set of variables allows identification and estimation of such effect; (iii) simulated 10000 trials in Major Depressive Disorder, with varying real treatment effects, proportions of patients discontinuing the treatment, and incomplete follow-up. Our results suggest that, at least in a 'missing at random (MAR)' setting, all studied estimation methods increase their performance when a variable representing compliance is used. This effect is more pronounced the higher the proportion of post-discontinuation follow-up is.
DOI: 10.5281/zenodo.4811488
title: Ultraviolet Index measurements in the Indian Ocean

description: The UV-Indian network is designed to study the variability of ultraviolet radiation in the Indian Ocean region, to validate the outputs of numerical models and satellite measurements, and to monitor ultraviolet radiation in this region over the long term. 9 ground stations have been homogeneously deployed in the western Indian Ocean region.<br> Data from four stations are now stored and available under the Creative Commons Attribution 4.0 International (CC-BY-4.0) licence. Here are the stations available: St-Denis, Reunion Island: 1 UV Radiometer, 1 Whole Sky Camera Antananarivo, Madagascar: 1 UV Radiometer, 1 Whole Sky Camera Anse Quitor, Rodrigues: 1 UV Radiometer Mahé, Seychelles : 1 UV Radiometer
DOI: 10.5281/zenodo.4572025
title: Ultraviolet Index measurements in the Indian Ocean

description: The UV-Indian network is designed to study the variability of ultraviolet radiation in the Indian Ocean region, to validate the outputs of numerical models and satellite measurements, and to monitor ultraviolet radiation in this region over the long term. 9 ground stations have been homogeneously deployed in the western Indian Ocean region.<br> Data from four stations are now stored and available under the Creative Commons Attribution 4.0 International (CC-BY-4.0) licence. Here are the stations available: St-Denis, Reunion Island: 1 UV Radiometer, 1 Whole Sky Camera Antananarivo, Madagascar: 1 UV Radiometer, 1 Whole Sky Camera Anse Quitor, Rodrigues: 1 UV Radiometer Mahé, Seychelles : 1 UV Radiometer
DOI: 10.5281/zenodo.4811212
title: Stardist model and training dataset for automated tracking of MDA-MB-231 and BT20 cells

description: <strong>StarDist Model:</strong><br> The StarDist model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). This custom StarDist model was trained for 300 epochs using 46 manually annotated paired images (image dimensions: (1024, 1024)) with a batch size of 2, an augmentation factor of 4 and a mae loss function. The StarDist “Versatile fluorescent nuclei” model was used as a training starting point. Key python packages used include TensorFlow (v 0.1.12), Keras (v 2.3.1), CSBdeep (v 0.6.1), NumPy (v 1.19.5), Cuda (v 11.0.221). The training was accelerated using a Tesla P100GPU.<br> The model weights can be used in the ZeroCostDL4Mic StarDist 2D notebook or in the StarDist Fiji plugin.<br> <br> <strong>StarDist Training dataset:</strong><br> Paired microscopy images (fluorescence) and corresponding masks Microscopy data type: Fluorescence microscopy (SiR-DNA) and masks obtained via manual segmentation (see https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki/Stardist for details about the segmentation) Cells were imaged using a 20x Nikon CFI Plan Apo Lambda objective (NA 0.75) one frame every 10 minutes for 16h. Cell type: MDA-MB-231 cells and BT20 cells File format: .tif (16-bit for fluorescence and 8 and 16-bit for the masks)
DOI: 10.5066/p92asiyq
title: Slow recovery of headwater-stream fishes following a catastrophic poisoning event

description: Fish collection data for surveys made at 5 localities in Flat Creek, Dawson County GA, on 6 dates that spanned a 4 to 18.5-month period following a catastrophic fish kill caused by a chemical spill near the headwater origin on Flat Creek. The data are: locality descriptions, water depth and velocity measurements made during fish sampling, and tabulated numbers and range in body length of individuals observed, by collection date and locality.
DOI: 10.6084/m9.figshare.12141090.v1
title: Building Representative Matched Samples with Multi-valued Treatments in Large Observational Studies*

description: In this paper, we present a new way of matching in observational studies that overcomes three limitations of existing matching approaches. First, it directly balances covariates with multi-valued treatments without explicitly estimating the generalized propensity score. Second, it builds self-weighted matched samples that are representative of a target population by design. Third, it can handle large data sets, with hundreds of thousands of observations, in a couple of minutes. The key insights of this new approach to matching are balancing the treatment groups relative to a target population and positing a linear-sized mixed integer formulation of the matching problem. We formally show that this formulation is more effective than alternative quadratic-sized formulations, as its reduction in size does not affect its strength from the standpoint of its linear programming relaxation. We also show that this formulation can be used for matching with distributional covariate balance in polynomial time under certain assumptions on the covariates and that it can handle large data sets in practice even when the assumptions are not satisfied. This algorithmic characterization is key to handling large data sets. We illustrate this new approach to matching in both a simulation study and an observational study of the impact of an earthquake on educational attainment. With this approach, the results after matching can be visualized with simple and transparent graphical displays: while increasing levels of exposure to the earthquake have a negative impact on school attendance, there is no effect on college admission test scores.
DOI: 10.6084/m9.figshare.11983836.v3
title: High-Dimensional Copula Variational Approximation Through Transformation

description: Variational methods are attractive for computing Bayesian inference when exact inference is impractical. They approximate a target distribution—either the posterior or an augmented posterior—using a simpler distribution that is selected to balance accuracy with computational feasibility. Here, we approximate an element-wise parametric transformation of the target distribution as multivariate Gaussian or skew-normal. Approximations of this kind are implicit copula models for the original parameters, with a Gaussian or skew-normal copula function and flexible parametric margins. A key observation is that their adoption can improve the accuracy of variational inference in high dimensions at limited or no additional computational cost. We consider the Yeo–Johnson and inverse G&H transformations, along with sparse factor structures for the scale matrix of the Gaussian or skew-normal. We also show how to implement efficient reparameterization gradient methods for these copula-based approximations. The efficacy of the approach is illustrated by computing posterior inference for three different models using six real datasets. In each case, we show that our proposed copula model distributions are more accurate variational approximations than Gaussian or skew-normal distributions, but at only a minor or no increase in computational cost. Supplementary materials comprising an online appendix, MATLAB code to implement the method, and the datasets employed, are available online.
DOI: 10.6084/m9.figshare.11973537.v1
title: Bayesian semiparametric analysis of multivariate continuous responses, with variable selection

description: This paper presents an approach to Bayesian semiparametric inference for Gaussian multivariate response regression. We are motivated by various small and medium dimensional problems from the physical and social sciences. The statistical challenges revolve around dealing with the unknown mean and variance functions and in particular, the correlation matrix. To tackle these problems, we have developed priors over the smooth functions and a Markov chain Monte Carlo algorithm for inference and model selection. Specifically: Dirichlet process mixtures of Gaussian distributions is used as the basis for a cluster-inducing prior over the elements of the correlation matrix. The smooth, multidimensional means and variances are represented using radial basis function expansions. The complexity of the model, in terms of variable selection and smoothness, is then controlled by spike-slab priors. A simulation study is presented, demonstrating performance as the response dimension increases. Finally, the model is fit to a number of real world datasets. An R package, scripts for replicating synthetic and real data examples, and a detailed description of the MCMC sampler are available in the supplemental materials online.
DOI: 10.15468/akkf6f
title: A catalog of the Brachystomatidae of Chile (Diptera: Empidoidea)

description: This dataset contains the digitized treatments in Plazi based on the original journal article González, Christian R., Elgueta, Mario, Rafael, José Albertino (2021): A catalog of the Brachystomatidae of Chile (Diptera: Empidoidea). Zootaxa 4969 (1): 149-165, DOI: https://doi.org/10.11646/zootaxa.4969.1.8
DOI: 10.5281/zenodo.3939706
title: IODP Expedition 359, Hole U1470B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 359: Maldives Monsoon and Sea Level
DOI: 10.5281/zenodo.3939705
title: IODP Expedition 359, Hole U1470B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 359: Maldives Monsoon and Sea Level
DOI: 10.6084/m9.figshare.4616155.v1
title: DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines

description: Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
DOI: 10.6084/m9.figshare.4592638.v1
title: Geographic variation in the spotted-wing drosophila, <i>Drosophila suzukii</i> (Diptera: Drosophilidae), based on mitochondrial DNA sequences

description: The spotted-wing drosophila (SWD), <i>Drosophila suzukii</i> (Diptera: Drosophilidae), is an economically damaging pest that feeds on most thin-skinned fruits. It was originally native to a few Asian countries, including Korea, but is now found in North America and Europe. In this study, we sequenced portions of the mitochondrial (mt) <i>COI</i> and <i>ND4</i> genes from a total of 195 individuals collected mainly from Korea. We then combined GenBank-registered <i>COI</i> sequences from all ancestral-range and introduced-range populations with our own <i>COI</i> data to assess the worldwide diversity, divergence, and relatedness of SWD haplotypes. A total of 139 haplotypes were obtained from the concatenated <i>COI</i> and <i>ND4</i> sequences. Most haplotypes were confined to single localities, but 12 of them were found in more than two localities, and one haplotype (SWDCN61) was found from Korea to Canada. A dataset combining GenBank sequences with our own data identified a total of 94 worldwide <i>COI</i> haplotypes with a maximum sequence divergence (MSD) of 5.433% (32 bp). Although most haplotypes were found in only a single country, a few haplotypes were found commonly in China, Korea, and Japan; these occurred at a higher frequency and were often involved in introductions. A rough estimate of genetic diversity in each country showed higher diversity in ancestral distributional ranges, but the invasion over Asian countries seems to have been substantial because haplotype diversity was only 2.35 to 3.97-fold lower in the U.S.A, Canada, and Italy than that in the populations’ ancestral ranges.
DOI: 10.6084/m9.figshare.4592629.v1
title: Back from the dead! Resurrection and revalidation of the Indian endemic snake genus <i>Wallophis</i> Werner, 1929 (Squamata: Colubridae) insights from molecular data

description: The monotypic colubrid snake genus <i>Wallophis</i> is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-<i>mos</i>), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (<i>ND4</i>) and cytochrome b (cyt <i>b</i>) were used to assess phylogenetic relationship. <i>Wallophis brachyura</i> type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to <i>Wallaceophis gujaratensis</i>. <i>Wallophis</i> differs from <i>Wallaceophis</i> in an uncorrected pairwise p-distance of 17% for mitochondrial <i>ND4</i> gene. <i>Wallaceophis gujaratensis</i> was described in three different spellings in the literature hence we here propose <i>Wallaceophis gujaratensis</i> as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.
DOI: 10.5281/zenodo.3939718
title: IODP Expedition 362, Hole U1480G - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 362: Sumatra Seismogenic Zone