cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2066601
title: A Marginal Sampler for σ-Stable Poisson–Kingman Mixture Models

description: We investigate the class of σ-stable Poisson–Kingman random probability measures (RPMs) in the context of Bayesian nonparametric mixture modeling. This is a large class of discrete RPMs, which encompasses most of the popular discrete RPMs used in Bayesian nonparametrics, such as the Dirichlet process, Pitman–Yor process, the normalized inverse Gaussian process, and the normalized generalized Gamma process. We show how certain sampling properties and marginal characterizations of σ-stable Poisson–Kingman RPMs can be usefully exploited for devising a Markov chain Monte Carlo (MCMC) algorithm for performing posterior inference with a Bayesian nonparametric mixture model. Specifically, we introduce a novel and efficient MCMC sampling scheme in an augmented space that has a small number of auxiliary variables per iteration. We apply our sampling scheme to a density estimation and clustering tasks with unidimensional and multidimensional datasets, and compare it against competing MCMC sampling schemes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2066598
title: Estimated Survival of Subadult and Adult Atlantic Sturgeon in Four River Basins in the Southeastern United States

description: Prompted by concerns about the status of Atlantic Sturgeon <i>Acipenser oxyrinchus oxyrinchus</i>, in 2012 the National Oceanic and Atmospheric Administration listed one distinct population segment (DPS) as threatened (Gulf of Maine) and listed the remaining four DPSs as endangered (New York Bight, Chesapeake Bay, Carolina, and South Atlantic). To provide information for recovery planning, we estimated the survival of subadult and adult Atlantic Sturgeon in two river basins within the Carolina DPS (Roanoke and Cape Fear rivers, North Carolina) and two basins within the South Atlantic DPS (Ashepoo–Combahee–Edisto rivers [ACE], South Carolina; Altamaha River, Georgia). Estimated detection probability varied strongly by season but was similar among river basins, likely reflecting a winter migration into marine waters with minimal receiver coverage. Apparent monthly survival was very high and precisely estimated for the Roanoke River (0.985; 95% credible interval [CI] = 0.970–0.995), Cape Fear River (0.979; 95% CI = 0.971–0.986), ACE (0.989; 95% CI = 0.979–0.993), and Altamaha River (0.985; 95% CI = 0.973–0.994) basins. A pooled estimate for 87 adults from all four basins was 0.988 (95% CI = 0.982–0.992). The monthly rates implied annual apparent survival rates of 0.839 (Roanoke River basin), 0.778 (Cape Fear River basin), 0.871 (ACE basin), and 0.842 (Altamaha River basin); the pooled estimate for adults was 0.860. Our estimated survival rates were similar to other recent estimates for Atlantic Sturgeon but lower than recent estimates for several populations of Gulf Sturgeon <i>A. oxyrinchus desotoi</i>. Recovery of Atlantic Sturgeon in these southeastern rivers will occur more quickly if survival can be increased to a level that is consistent with published estimates of true natural mortality (0.03–0.07; annual survival ≥ 0.93). Received March 18, 2015; accepted August 26, 2015
DOI: 10.6084/m9.figshare.2066598.v1
title: Estimated Survival of Subadult and Adult Atlantic Sturgeon in Four River Basins in the Southeastern United States

description: Prompted by concerns about the status of Atlantic Sturgeon <i>Acipenser oxyrinchus oxyrinchus</i>, in 2012 the National Oceanic and Atmospheric Administration listed one distinct population segment (DPS) as threatened (Gulf of Maine) and listed the remaining four DPSs as endangered (New York Bight, Chesapeake Bay, Carolina, and South Atlantic). To provide information for recovery planning, we estimated the survival of subadult and adult Atlantic Sturgeon in two river basins within the Carolina DPS (Roanoke and Cape Fear rivers, North Carolina) and two basins within the South Atlantic DPS (Ashepoo–Combahee–Edisto rivers [ACE], South Carolina; Altamaha River, Georgia). Estimated detection probability varied strongly by season but was similar among river basins, likely reflecting a winter migration into marine waters with minimal receiver coverage. Apparent monthly survival was very high and precisely estimated for the Roanoke River (0.985; 95% credible interval [CI] = 0.970–0.995), Cape Fear River (0.979; 95% CI = 0.971–0.986), ACE (0.989; 95% CI = 0.979–0.993), and Altamaha River (0.985; 95% CI = 0.973–0.994) basins. A pooled estimate for 87 adults from all four basins was 0.988 (95% CI = 0.982–0.992). The monthly rates implied annual apparent survival rates of 0.839 (Roanoke River basin), 0.778 (Cape Fear River basin), 0.871 (ACE basin), and 0.842 (Altamaha River basin); the pooled estimate for adults was 0.860. Our estimated survival rates were similar to other recent estimates for Atlantic Sturgeon but lower than recent estimates for several populations of Gulf Sturgeon <i>A. oxyrinchus desotoi</i>. Recovery of Atlantic Sturgeon in these southeastern rivers will occur more quickly if survival can be increased to a level that is consistent with published estimates of true natural mortality (0.03–0.07; annual survival ≥ 0.93). Received March 18, 2015; accepted August 26, 2015
DOI: 10.6084/m9.figshare.2066601.v2
title: A Marginal Sampler for σ-Stable Poisson–Kingman Mixture Models

description: We investigate the class of σ-stable Poisson–Kingman random probability measures (RPMs) in the context of Bayesian nonparametric mixture modeling. This is a large class of discrete RPMs, which encompasses most of the popular discrete RPMs used in Bayesian nonparametrics, such as the Dirichlet process, Pitman–Yor process, the normalized inverse Gaussian process, and the normalized generalized Gamma process. We show how certain sampling properties and marginal characterizations of σ-stable Poisson–Kingman RPMs can be usefully exploited for devising a Markov chain Monte Carlo (MCMC) algorithm for performing posterior inference with a Bayesian nonparametric mixture model. Specifically, we introduce a novel and efficient MCMC sampling scheme in an augmented space that has a small number of auxiliary variables per iteration. We apply our sampling scheme to a density estimation and clustering tasks with unidimensional and multidimensional datasets, and compare it against competing MCMC sampling schemes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2066577
title: Normative Spectral Domain Optical Coherence Tomography Data in Healthy Turkish Children

description: <i>Purpose</i>: To determine the normative database of macular and retinal nerve fiber layer (RNFL) thickness parameters in healthy Turkish children by OCT. <i>Methods</i>: 318 eyes of 318 children (138 boys, 183 girls) aged between 3 and 17 years were evaluated. The children were scanned by Cirrus HD-OCT (Carl Zeiss Meditec) to measure the macula, RNFL, and optic nerve head parameters. <i>Results</i>: Axial length (AL) (<i>p</i> 2 = 0.08), spherical equivalent (SE) (<i>p</i> 2 = 0.12), and rim area (<i>p</i> 2 = 0.15) were the strongest predictors of RNFL thickness. All of the macular measurements were significantly related to age (<i>p</i> 2 &gt; 5%). Average macular thickness (<i>p</i> p = 0.002) showed significant relationship with the AL and SE. <i>Conclusion</i>: This study ensures an age-adjusted pediatric normative database using OCT to diagnose and monitor macular diseases, optic nerve diseases, and glaucoma in children.
DOI: 10.6084/m9.figshare.2066583
title: A PTEN inhibitor displays preclinical activity against hepatocarcinoma cells

description: <i>Phosphatase and tensin homolog</i> (P<i>TEN</i>) gene is considered a tumor suppressor gene. However, PTEN mutations rarely occur in hepatocellular carcinoma (HCC), whereas heterozygosity of PTEN, resulting in reduced PTEN expression, has been observed in 32–44% of HCC patients. In the present study, we investigated the effects of the small molecule PTEN inhibitor VO-OHpic in HCC cells. VO-OHpic inhibited cell viability, cell proliferation and colony formation, and induced senescence-associated β-galactosidase activity in Hep3B (low PTEN expression) and to a lesser extent in PLC/PRF/5 (high PTEN expression) cells, but not in PTEN-negative SNU475 cells. VO-OHpic synergistically inhibited cell viability when combined with PI3K/mTOR and RAF/MEK/ERK pathway inhibitors, but only in Hep3B cells, and significantly inhibited tumor growth in nude mice bearing xenografts of Hep3B cells. Therefore, we demonstrated for the first time that VO-OHpic inhibited cell growth and induced senescence in HCC cells with low PTEN expression, and that the combination of VO-OHpic with PI3K/mTOR and RAF/MEK/ERK inhibitors resulted in a more effective tumor cell kill. Our findings, hence, provide proof-of-principle evidence that pharmacological inhibition of PTEN may represent a promising approach for HCC therapy in a subclass of patients with a low PTEN expression.
DOI: 10.6084/m9.figshare.2066583.v1
title: A PTEN inhibitor displays preclinical activity against hepatocarcinoma cells

description: <i>Phosphatase and tensin homolog</i> (P<i>TEN</i>) gene is considered a tumor suppressor gene. However, PTEN mutations rarely occur in hepatocellular carcinoma (HCC), whereas heterozygosity of PTEN, resulting in reduced PTEN expression, has been observed in 32–44% of HCC patients. In the present study, we investigated the effects of the small molecule PTEN inhibitor VO-OHpic in HCC cells. VO-OHpic inhibited cell viability, cell proliferation and colony formation, and induced senescence-associated β-galactosidase activity in Hep3B (low PTEN expression) and to a lesser extent in PLC/PRF/5 (high PTEN expression) cells, but not in PTEN-negative SNU475 cells. VO-OHpic synergistically inhibited cell viability when combined with PI3K/mTOR and RAF/MEK/ERK pathway inhibitors, but only in Hep3B cells, and significantly inhibited tumor growth in nude mice bearing xenografts of Hep3B cells. Therefore, we demonstrated for the first time that VO-OHpic inhibited cell growth and induced senescence in HCC cells with low PTEN expression, and that the combination of VO-OHpic with PI3K/mTOR and RAF/MEK/ERK inhibitors resulted in a more effective tumor cell kill. Our findings, hence, provide proof-of-principle evidence that pharmacological inhibition of PTEN may represent a promising approach for HCC therapy in a subclass of patients with a low PTEN expression.
DOI: 10.6084/m9.figshare.2066601.v1
title: A marginal sampler for σ-stable Poisson-Kingman mixture models

description: We investigate the class of σ-stable Poisson-Kingman random probability measures (RPMs) in the context of Bayesian nonparametric mixture modeling. This is a large class of discrete RPMs which encompasses most of the popular discrete RPMs used in Bayesian nonparametrics, such as the Dirichlet process, Pitman-Yor process, the normalized inverse Gaussian process and the normalized generalized Gamma process. We show how certain sampling properties and marginal characterisations of σ-stable Poisson-Kingman RPMs can be usefully exploited for devising a Markov chain Monte Carlo (MCMC) algorithm for performing posterior inference with a Bayesian nonparametric mixture model. Specifically, we introduce a novel and efficient MCMC sampling scheme in an augmented space that has a fixed number of auxiliary variables per iteration. We apply our sampling scheme to a density estimation and clustering tasks with unidimensional and multidimensional datasets, and compare it against competing MCMC sampling schemes.
DOI: 10.6084/m9.figshare.2066556
title: Sequence data

description: MBO_mapping_file_impingers_controls_figshare.txt - A tab-delimited text file with sample information. The columns of the text file include a sample identifier ("SampleID"), barcode sequences ("BarcodeSequence"), forward primer sequence ("LinkerPrimerSequence"), date of sample collection ("Sample_date"), sample type (rDNA or rRNA, "Sample_type"), barcode, and sample description (samples versus controls, "Description").<br>seqs_figshare.fastq - Raw 16S sequence data in FASTQ format, produced by a sequencing run using Illumina MiSeq 300 bp single-end sequencing technology.
DOI: 10.6084/m9.figshare.2066568
title: Characterising the zonally asymmetric features of the Southern Hemisphere extratropical circulation and their influence on regional climate variability: supplementary metadata

description: This page contains supplementary material relating to the following PhD thesis:Irving D (2016). Characterising the zonally asymmetric features of the Southern Hemisphere extratropical circulation and their influence on regional climate variability. PhD thesis, University of Melbourne. https://minerva-access.unimelb.edu.au/handle/11343/91740<br>In particular, it contains metadata files (.met) for each of the figures in that thesis, outlining the history of command line entries that were executed from initial data download right up to the generation of the figure. A version controlled (using Git) repository of the code referred to in those .met files is also included (github_DamienIrving_climate-analysis.zip), however readers are encouraged to view that code at the GitHub repository linked to below instead (because then they can view any subsequent improvements to the code and/or submit suggested improvements / pull requests). It should be noted that it is my daily repository, meaning there is code in there that does not directly relate to the paper - the .met files explain which code is relevant.The motivation for this approach to publishing reproducible computational research is outlined in the thesis and also at:Irving D (2016). A minimum standard for publishing computational results in the weather and climate sciences.<em> Bulletin of the American Meteorological Society. </em>97, 1149-1158.<em> </em>doi:10.1175/BAMS-D-15-00010.1.
DOI: 10.6084/m9.figshare.2066541
title: Cobetia_clean.nexml

description: A phylogenetic tree showing the placement of Cobetia sp UCD-24C in relation to the rest of the genus.<br>
DOI: 10.6084/m9.figshare.2066538
title: MAP kinase Hog1 regulates metabolic changes induced by hyperosmotic stress

description: This work represents that MAP kinase Hog1 regulates cellular concentrations of a variety of metabolites during hyperosmotic stress signaling.
DOI: 10.6084/m9.figshare.2066541.v1
title: Cobetia_clean.nexml

description: A phylogenetic tree showing the placement of Cobetia sp UCD-24C in relation to the rest of the genus.<br>
DOI: 10.6084/m9.figshare.2066538.v1
title: MAP kinase Hog1 regulates metabolic changes induced by hyperosmotic stress

description: This work represents that MAP kinase Hog1 regulates cellular concentrations of a variety of metabolites during hyperosmotic stress signaling.
DOI: 10.6084/m9.figshare.2066523
title: Advantages of complex scaling only the most diffuse basis functions in simultaneous description of both resonances and bound states

description: An accurate description of both bound and resonance states is desirable in the study of molecules. However, it is not a trivial task to accomplish, as theoretical and numerical formalisms developed for describing one do not always fit for describing the other. One such formalism, mainly designed to describe resonances, is the complex scaling method, in which the Hamiltonian internal coordinates are scaled by a complex factor of <i>e</i><sup><i>i</i>θ</sup>. As Kaprálová-Žďánská and Šmydke recently showed in their study on helium, in order to well describe both bound and resonance states, one should use quasi-complete basis sets. Yet, the use of large and dense basis sets is ineffective and highly impractical. In addition, the above-mentioned complex scaling method is unsuitable for a molecular analysis. Not long ago, an evidence that a mixed complex-scaled basis set can serve as a solution to the problem was presented by White <i>et al</i>., however, the behaviour of the bound states was not investigated systematically. In this work, we demonstrate systematically that using such a mixed basis set, in which only diffuse functions are scaled, is an appropriate approach for simultaneous description. On the one hand, using this method, complex scaling can be applied on molecular systems in order to find resonance states. On the other hand, in this method, both the bound and the resonance states can be well described even in relatively small basis sets. In addition, we demonstrate the stability of the bound state in relation to the scaling parameter.
DOI: 10.6084/m9.figshare.2066556.v1
title: Sequence data

description: MBO_mapping_file_impingers_controls_figshare.txt - A tab-delimited text file with sample information. The columns of the text file include a sample identifier ("SampleID"), barcode sequences ("BarcodeSequence"), forward primer sequence ("LinkerPrimerSequence"), date of sample collection ("Sample_date"), sample type (rDNA or rRNA, "Sample_type"), barcode, and sample description (samples versus controls, "Description").<br>seqs_figshare.fastq - Raw 16S sequence data in FASTQ format, produced by a sequencing run using Illumina MiSeq 300 bp single-end sequencing technology.
DOI: 10.6084/m9.figshare.2066490
title: Salamander substrate study

description: bacterial community data from salamanders with analysis code
DOI: 10.6084/m9.figshare.2066466
title: The Gold OA Landscape 2011-2014

description: Prepared for <i>The Gold OA Landscape 2011-2014</i>.<br><br>Data on 9,624 journals listed in the <i>Directory of Open Access Journals </i>as of June 8, 2015 that began publishing in 2014 or before, could be analyzed fully (using Google/Chrome translation software as needed), and appear to actually meet normal criteria for open access.<br><br>Data gathered by direct visual analysis of journal sites. Article counts approximate in a few cases.<br><br>See data_key sheet for code explanations.<br><br>This dataset expands and replaces Open Access Journals 2014, DOAJ subset, adding the rest of 2014 and more than to thousand additional journals.<br>
DOI: 10.6084/m9.figshare.2066319
title: Confirmation and Control of Annual Bluegrass with Resistance to Prodiamine and Glyphosate

description: Contains data and analysis files from whole plant greenhouse studies and field experiments confirming glyphosate and prodiamine resistance in annual bluegrass. <br>Additionally, data from laboratory studies documenting shikimate accumulation in resistant and susceptible annual bluegrass biotypes are included.<br>Lastly, data and R-scripts are included from field experiments evaluating alternative herbicide options to control this biotype preemergence<br>Studies conducted by Shane Breeden for his M.S. Thesis at the University of Tennessee-Knoxville
DOI: 10.6084/m9.figshare.2066295
title: CAPTURES_COLONIES_CALONECTRIS_GALICIA_2008-13.xls

description: The Cory’s shearwater (<i>Calonectris diomedea</i>) is a pelagic seabird that has recently established three new colonies in Galicia (NE Atlantic) thus expanding its distribution range 500 km northwards. This is the Dataset of a study aimed to describe the establishment and early progress of the new Galician populations and to determine the genetic and morphometric characteristics of the individuals participating in these foundation events. Using 10 microsatellite loci, we tested the predictions supported by different seabird colonization models.
DOI: 10.6084/m9.figshare.2066262
title: spatial dataset of Xishuangbanna

description: The spatial dataset consists of administrative boundary of Xishuangbanna Prefecture at county level, elevation zones, slopes, layer of net present value of rubber plantations, boundary of nature reserve and shapefiles of rubber plantations of 1988, 2002 and 2010.
DOI: 10.6084/m9.figshare.2066130
title: PubMed history dates and delays for articles published from 1960–2015

description: Data deposition for "The history of publishing delays." While most data files are available from the project GitHub, some large files are exclusively hosted here on figshare.<br>The contents are as follows:<br>1. `esearch_journal-articles_1960-2015.tsv.gz`—a list of 22,499,113 PubMed IDs retrieved from an esearch for `journal article[pt] AND 1960:2015[pdat]`.2. `esummary_journal-articles_1960-2015.xml.bz2`—the combined XML output of esummary queries for the articles from 1. **Generating this file was a time intensive process. Sharing this 2 GB file was the motivation behind this deposition.**3. `history-dates.tsv.bz2`—history dates extracted from the XML from 2.4. `delays.tsv.gz`—acceptance and online publication delays extracted from 3.5. `pubmed-journals.tsv`—a tabular version of the NLM Catalog with the journals in PubMed<br>Refer to the [project GitHub](https://github.com/dhimmel/delays/tree/history-blog-post) for more information.
DOI: 10.6084/m9.figshare.2066319.v1
title: 2015 Data Confirming Glyphosate and Prodiamine Resistance in POAAN

description: Contains data and analysis files from whole plant greenhouse studies and field experiments confirming glyphosate resistance in annual bluegrass. <br>Additionally, data from laboratory studies documenting shikimate accumulation in resistant and susceptible annual bluegrass biotypes are included.<br>Studies conducted by Shane Breeden for his M.S. Thesis at the University of Tennessee-Knoxville
DOI: 10.6084/m9.figshare.2066130.v2
title: PubMed history dates and delays for articles published from 1960–2015

description: Data deposition for "The history of publishing delays." While most data files are available from the project GitHub, some large files are exclusively hosted here on figshare.<br>The contents are as follows:<br>1. `esearch_journal-articles_1960-2015.tsv.gz`—a list of 22,499,113 PubMed IDs retrieved from an esearch for `journal article[pt] AND 1960:2015[pdat]`.2. `esummary_journal-articles_1960-2015.xml.bz2`—the combined XML output of esummary queries for the articles from 1. **Generating this file was a time intensive process. Sharing this 2 GB file was the motivation behind this deposition.**3. `history-dates.tsv.bz2`—history dates extracted from the XML from 2.4. `delays.tsv.gz`—acceptance and online publication delays extracted from 3.5. `pubmed-journals.tsv`—a tabular version of the NLM Catalog with the journals in PubMed<br>Refer to the [project GitHub](https://github.com/dhimmel/delays/tree/history-blog-post) for more information.
DOI: 10.6084/m9.figshare.2066319.v2
title: Confirmation and Control of Annual Bluegrass with Resistance of PRE and POST herbicides

description: Contains data and analysis files from whole plant greenhouse studies and field experiments confirming glyphosate and prodiamine resistance in annual bluegrass. <br>Additionally, data from laboratory studies documenting shikimate accumulation in resistant and susceptible annual bluegrass biotypes are included.<br>Lastly, data and R-scripts are included from field experiments evaluating alternative herbicide options to control this biotype preemergence<br>Studies conducted by Shane Breeden for his M.S. Thesis at the University of Tennessee-Knoxville
DOI: 10.6084/m9.figshare.2066130.v1
title: PubMed History dates for articles published from 1960–2015

description: Data deposition for "The history of publishing delays." While most data files are available from the project GitHub, some large files are exclusively hosted here on figshare.<br>The contents are as follows:<br>1. `esearch_journal-articles_1960-2015.tsv.gz`—a list of 22,499,113 PubMed IDs retrieved from an esearch for `journal article[pt] AND 1960:2015[pdat]`.2. `esummary_journal-articles_1960-2015.xml.bz2`—the combined XML output of esummary queries for the articles from 1. **Generating this file was a time intensive process. Sharing this 2 GB file was the motivation behind this deposition.**3. `history-dates.tsv.bz2`—history dates extracted from the XML from 2.4. `delays.tsv.gz`—acceptance and online publication delays extracted from 3.5. `pubmed-journals.tsv`—a tabular version of the NLM Catalog with the journals in PubMed<br>Refer to the [project GitHub](https://github.com/dhimmel/delays/tree/history-blog-post) for more information.