cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5267467.v1
title: Are there autochthonous <i>Ferrissia</i> (Mollusca: Planorbidae) in the Palaearctic? Molecular evidence of a widespread North American invasion of the Old World

description: In the last few decades, findings of freshwater limpets belonging to the genus <i>Ferrissia</i> have been frequent and widely distributed throughout the Palaearctic and beyond. The widespread presence of a Nearctic alien taxon was proved, but no consensus was achieved about the possible existence of autochthonous <i>Ferrissia</i> taxa in the area, an occurrence which would be supported by the presence of gastropod fossils attributed to the genus throughout Eurasia and North Africa. In order to test the hypothesis of a possible persistence of autochthonous <i>Ferrissia</i> taxa in the Palaearctic to the present day, all the published data on the genetic diversity of <i>Ferrissia</i> populations occurring in the area were reviewed, expanding also the currently available dataset through dedicated sampling surveys in Italy, Malta and Spain. Here, based on currently published and novel large ribosomal subunit 16S rRNA (16S) and cytochrome oxidase sub-unit 1 (COI) sequences, the presence of the allochthonous <i>Ferrissia californica</i> in the whole Palaearctic was confirmed. Conversely, no evidence supporting the presence of autochthonous <i>Ferrissia</i> taxa was obtained. <i>Ferrissia californica</i> proved to be a highly invasive taxon (in spite of its extremely low genetic diversity) throughout the invaded regions, which is possibly related to the species’ ability of asexual reproduction. Finally, the need to investigate the possible impact exerted by <i>F. californica</i> on the autochthonous Palaearctic biota is briefly stressed.
DOI: 10.6084/m9.figshare.5267365
title: Assessing the Impact of Roaming Radical Reactions on Combustion Properties of Transportation Fuels

description: Scripts, data, models, and results to generate kinetic models, simulations, and figures for a manuscript assessing the impact of including roaming radical reactions in detailed kinetic models of combustion of transportation-relevant fuels. Source code in the form of Python Jupyter Notebooks, necessary input files, and the resulting figures are all included.
DOI: 10.6084/m9.figshare.5267365.v1
title: Assessing the Impact of Roaming Radical Reactions on Combustion Properties of Transportation Fuels

description: Scripts, data, models, and results to generate kinetic models, simulations, and figures for a manuscript assessing the impact of including roaming radical reactions in detailed kinetic models of combustion of transportation-relevant fuels. Source code in the form of Python Jupyter Notebooks, necessary input files, and the resulting figures are all included.
DOI: 10.6084/m9.figshare.5267371.v1
title: A new analog of pyrrolezanthine from the roots of <i>Reynoutria ciliinervis</i> (Nakai) Moldenke

description: In the present study, <i>a</i> new analogue of pyrrolezanthine (<b>1</b>) was isolated from the roots of <i>Reynoutria ciliinervis</i> (Nakai) Moldenke. Its structure was elucidated mainly by NMR, HR-ESI-MS and the single-crystal X-ray diffraction spectroscopic data. Meanwhile, the antimicrobial activity of compound <b>1</b> was measured, it exhibited potent antifungal activity against <i>Sclerotinia sclerotiorum</i> with MIC value of 31.2 μg/mL.
DOI: 10.6084/m9.figshare.5266543
title: Relative catchability (probability of presence) of broadbill swordfish Xiphias gladius in the California Current System. Hindcast predictions for November 2014 using UC Santa Cruz Regional Ocean Modelling System

description: Model-derived relative probability of swordfish presence, hind-cast on Regional Ocean Model outputs for the period 1st-31st November 2014.
DOI: 10.6084/m9.figshare.5266543.v1
title: Swordish probability of presence, hindcast predictions using Regional Ocean Modelling System

description: Model-derived relative probability of swordfish presence, hind-cast on Regional Ocean Model outputs for the period 1st-31st November 2014.
DOI: 10.6084/m9.figshare.5266537
title: CUF101-selmap

description: Data files for reproducing selection mapping results:<br>----------------------------<br><br>"SNPs_counts-R.txt" - Raw count file (84978 x 576) - 84978 markers - 288 individuals, 2 alleles per individual<br>Format:<br>marker1 ind.1a1count ind.1a2count.....ind.na1count ind.na2count <br>----------------------------<br>- Cluster sequences in fasta format- MockReference sequence in fasta format- both produced using modified GBS-SNP-CROP<br>----------------------------<br><br>"SNPsCADL.bwa.sam"<br>"SNPsMt.bwa.sam"<br>- SAM format (without header) alignment information from aligning clusters to Mt v4.0 and CADL<br><br>----------------------------<br><br>"SNP_clustermap.desc.txt"<br>- Cluster information (i.e. which cluster a marker originates from and coordinates) for every marker<br><br>----------------------------<br><br>"pheno-1-R.txt"<br>phenotype (height) data from field evaluation<br>
DOI: 10.6084/m9.figshare.5266468
title: Bam mutant rtPCR

description: Bam mutant rtPCR notebook page
DOI: 10.6084/m9.figshare.5266537.v2
title: CUF101-selmap

description: Data files for reproducing selection mapping results:<br>----------------------------<br><br>"SNPs_counts-R.txt" - Raw count file (84978 x 576) - 84978 markers - 288 individuals, 2 alleles per individual<br>Format:<br>marker1 ind.1a1count ind.1a2count.....ind.na1count ind.na2count <br>----------------------------<br>- Cluster sequences in fasta format- MockReference sequence in fasta format- both produced using modified GBS-SNP-CROP<br>----------------------------<br><br>"SNPsCADL.bwa.sam"<br>"SNPsMt.bwa.sam"<br>- SAM format (without header) alignment information from aligning clusters to Mt v4.0 and CADL<br><br>----------------------------<br><br>"SNP_clustermap.desc.txt"<br>- Cluster information (i.e. which cluster a marker originates from and coordinates) for every marker<br><br>----------------------------<br><br>"pheno-1-R.txt"<br>phenotype (height) data from field evaluation<br>
DOI: 10.6084/m9.figshare.5266468.v1
title: Bam mutant rtPCR

description: Bam mutant rtPCR notebook page
DOI: 10.6084/m9.figshare.5266453
title: Histology image analysis project

description: Histology image analysis project
DOI: 10.6084/m9.figshare.5266537.v1
title: CUF101-selmap

description: Data files for reproducing selection mapping results:<br>----------------------------<br><br>"SNPs_counts-R.txt" - Raw count file (84978 x 576) - 84978 markers - 288 individuals, 2 alleles per individual<br>Format:<br>marker1 ind.1a1count ind.1a2count.....ind.na1count ind.na2count <br>----------------------------<br>- Cluster sequences in fasta format- MockReference sequence in fasta format- both produced using modified GBS-SNP-CROP<br>----------------------------<br><br>"SNPsCADL.bwa.sam"<br>"SNPsMt.bwa.sam"<br>- SAM format (without header) alignment information from aligning clusters to Mt v4.0 and CADL<br><br>----------------------------<br><br>"SNP_clustermap.desc.txt"<br>- Cluster information (i.e. which cluster a marker originates from and coordinates) for every marker<br><br>
DOI: 10.6084/m9.figshare.5266405
title: Statistically Efficient Thinning of a Markov Chain Sampler

description: It is common to subsample Markov chain output to reduce the storage burden. Geyer shows that discarding <i>k</i> − 1 out of every <i>k</i> observations will not improve statistical efficiency, as quantified through variance in a given computational budget. That observation is often taken to mean that thinning Markov chain Monte Carlo (MCMC) output cannot improve statistical efficiency. Here, we suppose that it costs one unit of time to advance a Markov chain and then θ &gt; 0 units of time to compute a sampled quantity of interest. For a thinned process, that cost θ is incurred less often, so it can be advanced through more stages. Here, we provide examples to show that thinning will improve statistical efficiency if θ is large and the sample autocorrelations decay slowly enough. If the lag ℓ ⩾ 1 autocorrelations of a scalar measurement satisfy ρ<sub>ℓ</sub> &gt; ρ<sub>ℓ + 1</sub> &gt; 0, then there is always a θ &lt; ∞ at which thinning becomes more efficient for averages of that scalar. Many sample autocorrelation functions resemble first order AR(1) processes with ρ<sub>ℓ</sub> = ρ<sup>|ℓ|</sup> for some − 1 &lt; ρ &lt; 1. For an AR(1) process, it is possible to compute the most efficient subsampling frequency <i>k</i>. The optimal <i>k</i> grows rapidly as ρ increases toward 1. The resulting efficiency gain depends primarily on θ, not ρ. Taking <i>k</i> = 1 (no thinning) is optimal when ρ ⩽ 0. For ρ &gt; 0, it is optimal if and only if θ ⩽ (1 − ρ)<sup>2</sup>/(2ρ). This efficiency gain never exceeds 1 + θ. This article also gives efficiency bounds for autocorrelations bounded between those of two AR(1) processes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5266453.v1
title: Histology image analysis project

description: Histology image analysis project
DOI: 10.6084/m9.figshare.5266387
title: replication_data.dta

description: This data comprises HealthCare Cost and Utilization Project FastStats state-by-quarter counts of total hospital discharges for community-residing patients from 42 all-capture state databases for the period 2009-2014, merged with state-by-year ACA Medicaid expansion status, and demographics from the Current Population Survey.
DOI: 10.6084/m9.figshare.5266387.v1
title: replication_data.dta

description: This data comprises HealthCare Cost and Utilization Project FastStats state-by-quarter counts of total hospital discharges for community-residing patients from 42 all-capture state databases for the period 2009-2014, merged with state-by-year ACA Medicaid expansion status, and demographics from the Current Population Survey.
DOI: 10.6084/m9.figshare.5266405.v2
title: Statistically Efficient Thinning of a Markov Chain Sampler

description: It is common to subsample Markov chain output to reduce the storage burden. Geyer shows that discarding <i>k</i> − 1 out of every <i>k</i> observations will not improve statistical efficiency, as quantified through variance in a given computational budget. That observation is often taken to mean that thinning Markov chain Monte Carlo (MCMC) output cannot improve statistical efficiency. Here, we suppose that it costs one unit of time to advance a Markov chain and then θ &gt; 0 units of time to compute a sampled quantity of interest. For a thinned process, that cost θ is incurred less often, so it can be advanced through more stages. Here, we provide examples to show that thinning will improve statistical efficiency if θ is large and the sample autocorrelations decay slowly enough. If the lag ℓ ⩾ 1 autocorrelations of a scalar measurement satisfy ρ<sub>ℓ</sub> &gt; ρ<sub>ℓ + 1</sub> &gt; 0, then there is always a θ &lt; ∞ at which thinning becomes more efficient for averages of that scalar. Many sample autocorrelation functions resemble first order AR(1) processes with ρ<sub>ℓ</sub> = ρ<sup>|ℓ|</sup> for some − 1 &lt; ρ &lt; 1. For an AR(1) process, it is possible to compute the most efficient subsampling frequency <i>k</i>. The optimal <i>k</i> grows rapidly as ρ increases toward 1. The resulting efficiency gain depends primarily on θ, not ρ. Taking <i>k</i> = 1 (no thinning) is optimal when ρ ⩽ 0. For ρ &gt; 0, it is optimal if and only if θ ⩽ (1 − ρ)<sup>2</sup>/(2ρ). This efficiency gain never exceeds 1 + θ. This article also gives efficiency bounds for autocorrelations bounded between those of two AR(1) processes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5266405.v1
title: Statistically Efficient Thinning of a Markov Chain Sampler

description: It is common to subsample Markov chain output to reduce the storage burden. Geyer shows that discarding <i>k</i> − 1 out of every <i>k</i> observations will not improve statistical efficiency, as quantified through variance in a given computational budget. That observation is often taken to mean that thinning Markov chain Monte Carlo (MCMC) output cannot improve statistical efficiency. Here, we suppose that it costs one unit of time to advance a Markov chain and then θ &gt; 0 units of time to compute a sampled quantity of interest. For a thinned process, that cost θ is incurred less often, so it can be advanced through more stages. Here, we provide examples to show that thinning will improve statistical efficiency if θ is large and the sample autocorrelations decay slowly enough. If the lag ℓ ⩾ 1 autocorrelations of a scalar measurement satisfy ρ<sub>ℓ</sub> &gt; ρ<sub>ℓ + 1</sub> &gt; 0, then there is always a θ &lt; ∞ at which thinning becomes more efficient for averages of that scalar. Many sample autocorrelation functions resemble first order AR(1) processes with ρ<sub>ℓ</sub> = ρ<sup>|ℓ|</sup> for some − 1 &lt; ρ &lt; 1. For an AR(1) process, it is possible to compute the most efficient subsampling frequency <i>k</i>. The optimal <i>k</i> grows rapidly as ρ increases toward 1. The resulting efficiency gain depends primarily on θ, not ρ. Taking <i>k</i> = 1 (no thinning) is optimal when ρ ⩽ 0. For ρ &gt; 0, it is optimal if and only if θ ⩽ (1 − ρ)<sup>2</sup>/(2ρ). This efficiency gain never exceeds 1 + θ. This article also gives efficiency bounds for autocorrelations bounded between those of two AR(1) processes. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5264521
title: final_irt_10000.csv

description: simulation for interrater reliability
DOI: 10.6084/m9.figshare.5264266
title: Tridacna noae microsatellite genotypes

description: Tridacna noae genotypes at 6 msat loci across 6 sampling locations accross the Indo-Pacific. Dataset made by Cecile Fauvelot and Daphné Grulois, IRD Noumea (New Caledonia). all details are provided in Fauvelot et al. article entitled Phylogeography of Noah’s giant clam submitted to Marine Biodiversity<br><br>
DOI: 10.6084/m9.figshare.5264263
title: Analysis and data from mechanical testing of three-layer wood composites with densified Argentinian beech for the outer layers

description: This fileset includes files detailing the analyses and data related to a study to examine the mechanical properties the three-layered wood composites with surface layers of varying degrees of densification.<br>The files include an R notebook in .pdf and .Rmd format, and three files containing measured flexure, hardness, and annual ring width measurements for the three-layer wood composites. Data files are in csv format with descriptive headers.<br>See the associated publication for more details (reference coming upon final acceptance and publishing!)
DOI: 10.6084/m9.figshare.5264263.v1
title: Analysis and data from mechanical testing of three-layer wood composites with densified Argentinian beech for the outer layers

description: This fileset includes files detailing the analyses and data related to a study to examine the mechanical properties the three-layered wood composites with surface layers of varying degrees of densification.<br>The files include an R notebook in .pdf and .Rmd format, and three files containing measured flexure, hardness, and annual ring width measurements for the three-layer wood composites. Data files are in csv format with descriptive headers.<br>See the associated publication for more details (reference coming upon final acceptance and publishing!)
DOI: 10.6084/m9.figshare.5264266.v1
title: Tridacna noae microsatellite genotypes

description: Tridacna noae genotypes at 6 msat loci across 6 sampling locations accross the Indo-Pacific. Dataset made by Cecile Fauvelot and Daphné Grulois, IRD Noumea (New Caledonia). all details are provided in Fauvelot et al. article entitled Phylogeography of Noah’s giant clam submitted to Marine Biodiversity<br><br>
DOI: 10.6084/m9.figshare.5264521.v2
title: final_irt_10000.csv

description: simulation for interrater reliability
DOI: 10.6084/m9.figshare.5264521.v1
title: final_irt_10000.csv

description: simulation for interrater reliability
DOI: 10.6084/m9.figshare.5264176
title: Fluorometer data files

description: These files provide supporting information for "Multi-tracer field fluorometry: accounting for temperature and turbidity variability during stream tracer tests" published in Water Resources Research.<br> Field_BTCs.zip This file contains field fluorometer calibrations and measurements of tracer breakthrough curves. Calibrations were carried out in the following order: stream water blank, Uranine, Resazurin, Resorufin. Breakthrough curve measurements are presented as mV readings for three tracer lamps and turbidity, plus temperature measurements from the same instrument.<br> Lab_temperature.zip This file contains data showing the effects of temperature on fluorescent tracer dye measurements at varying concentrations.<br> Lab_turbidity.zip This file contains data showing the effects of turbidity on fluorescent tracer dye measurements at varying concentrations.<b></b>
DOI: 10.6084/m9.figshare.5264146
title: Systematic review of the literature on triclosan and health outcomes in humans

description: The ability of epidemiologic evidence to inform regulatory decisions is largely dependent on the coherence and quality of the published literature. This systematic review examines the quality and consistency of studies assessing health outcomes associated with exposure to triclosan (TCS), an antimicrobial chemical with a short physiologic half-life. We used elements of the Biomonitoring, Environmental Epidemiology, and Short-Lived Chemicals instrument to evaluate aspects of study quality. Each methodological domain – overall design, exposure assessment, and data analysis – was categorized according to three tiers where Tier 1 indicated the highest quality. We also examined consistency of methods, results and reporting as considerations for weight of evidence (WOE) assessment. Studies were considered sufficiently comparable if they addressed the same or similar research questions. Forty-two studies met the criteria for inclusion. Only one randomized cross-over clinical trial of TCS was assigned to Tier 1 for all three domains. Most other studies were assigned to Tier 3 for at least one domain. Although the available literature examined more than 100 different health endpoints and reported hundreds of different measures of association, few studies were considered comparable. For reported measures of association, most were not significantly different from the null; the few statistically significant results represented isolated findings without a discernable across- or within-study pattern. We conclude that the current body of epidemiologic literature does not allow a meaningful WOE assessment due to methodological limitations of individual studies and lack of inter-study consistency. On the other hand, methodologically stronger studies may be used to inform future research.
DOI: 10.6084/m9.figshare.5264143
title: Mass spectra of of two Dendeobium plant extracts by two data acquisition methods

description: <b>Raw mass files of the methanol extracts from two Dendrobium plants using LTQ-Orbitrap XL mass spectrometry.</b>Column 1 denotes the mass file acquired by Orbitrap mass analyzer, and Column 2 denotes the mass file acquired by both Orbitrap and LTQ dynode mass analyzer.FE denotes Dendrobium officinale, and M denotes Dendrobium huoshanense.
DOI: 10.6084/m9.figshare.5264143.v1
title: Mass spectra of of two Dendeobium plant extracts by two data acquisition methods

description: <b>Raw mass files of the methanol extracts from two Dendrobium plants using LTQ-Orbitrap XL mass spectrometry.</b>Column 1 denotes the mass file acquired by Orbitrap mass analyzer, and Column 2 denotes the mass file acquired by both Orbitrap and LTQ dynode mass analyzer.FE denotes Dendrobium officinale, and M denotes Dendrobium huoshanense.
DOI: 10.6084/m9.figshare.5264146.v2
title: Systematic review of the literature on triclosan and health outcomes in humans

description: The ability of epidemiologic evidence to inform regulatory decisions is largely dependent on the coherence and quality of the published literature. This systematic review examines the quality and consistency of studies assessing health outcomes associated with exposure to triclosan (TCS), an antimicrobial chemical with a short physiologic half-life. We used elements of the Biomonitoring, Environmental Epidemiology, and Short-Lived Chemicals instrument to evaluate aspects of study quality. Each methodological domain – overall design, exposure assessment, and data analysis – was categorized according to three tiers where Tier 1 indicated the highest quality. We also examined consistency of methods, results and reporting as considerations for weight of evidence (WOE) assessment. Studies were considered sufficiently comparable if they addressed the same or similar research questions. Forty-two studies met the criteria for inclusion. Only one randomized cross-over clinical trial of TCS was assigned to Tier 1 for all three domains. Most other studies were assigned to Tier 3 for at least one domain. Although the available literature examined more than 100 different health endpoints and reported hundreds of different measures of association, few studies were considered comparable. For reported measures of association, most were not significantly different from the null; the few statistically significant results represented isolated findings without a discernable across- or within-study pattern. We conclude that the current body of epidemiologic literature does not allow a meaningful WOE assessment due to methodological limitations of individual studies and lack of inter-study consistency. On the other hand, methodologically stronger studies may be used to inform future research.
DOI: 10.6084/m9.figshare.5264119
title: Counteracting structural errors in ensemble forecast of influenza outbreaks (data sets)

description: This dataset contains the GFT ILI+ data, absolute humidity data and matlab codes that support the study in S. Pei, J. Shaman, Counteracting structural errors in ensemble forecast of influenza outbreaks. Nature Communications (2017).
DOI: 10.6084/m9.figshare.5264146.v1
title: Systematic review of the literature on triclosan and health outcomes in humans

description: The ability of epidemiologic evidence to inform regulatory decisions is largely dependent on the coherence and quality of the published literature. This systematic review examines the quality and consistency of studies assessing health outcomes associated with exposure to triclosan (TCS), an antimicrobial chemical with a short physiologic half-life. We used elements of the Biomonitoring, Environmental Epidemiology, and Short-Lived Chemicals instrument to evaluate aspects of study quality. Each methodological domain – overall design, exposure assessment, and data analysis – was categorized according to three tiers where Tier 1 indicated the highest quality. We also examined consistency of methods, results and reporting as considerations for weight of evidence (WOE) assessment. Studies were considered sufficiently comparable if they addressed the same or similar research questions. Forty-two studies met the criteria for inclusion. Only one randomized cross-over clinical trial of TCS was assigned to Tier 1 for all three domains. Most other studies were assigned to Tier 3 for at least one domain. Although the available literature examined more than 100 different health endpoints and reported hundreds of different measures of association, few studies were considered comparable. For reported measures of association, most were not significantly different from the null; the few statistically significant results represented isolated findings without a discernable across- or within-study pattern. We conclude that the current body of epidemiologic literature does not allow a meaningful WOE assessment due to methodological limitations of individual studies and lack of inter-study consistency. On the other hand, methodologically stronger studies may be used to inform future research.