cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3121888.v1
title: Data from: A rank test for bivariate event time outcomes when one event is a surrogate

description: In many clinical settings, improving patient survival is of interest but a practical surrogate, such as time to disease progression, is instead used as a clinical trial's primary endpoint. A time-to-first endpoint (e.g. death or disease progression) is commonly analyzed but may not be adequate to summarize patient outcomes if a subsequent event contains important additional information. We consider a surrogate outcome very generally, as one correlated with the true endpoint of interest. Settings of interest include those where the surrogate indicates a beneficial outcome so that the usual time-to-first endpoint of death or surrogate event is nonsensical. We present a new two-sample test for bivariate, interval-censored time-to-event data, where one endpoint is a surrogate for the second, less frequently observed endpoint of true interest. This test examines whether patient groups have equal clinical severity. If the true endpoint rarely occurs, the proposed test acts like a weighted logrank test on the surrogate; if it occurs for most individuals, then our test acts like a weighted logrank test on the true endpoint. If the surrogate is a useful statistical surrogate, our test can have better power than tests based on the surrogate that naively handle the true endpoint. In settings where the surrogate is not valid (treatment affects the surrogate but not the true endpoint), our test incorporates the information regarding the lack of treatment effect from the observed true endpoints and hence is expected to have a dampened treatment effect compared to tests based on the surrogate alone.
DOI: 10.6084/m9.figshare.3121894.v2
title: EGB-promoted electrochemical synthesis of 6-thioxo-[1,3,5]- triazinane-2,4 dione derivatives

description: A simple method for the synthesis of 6-thioxo-[1,3,5]-triazinane-2,4-dione derivatives was reported. The electrogenerated cyanomethyl base obtained from electroreduction of neat acetonitrile assisted the reaction between thiourea derivatives and alkyl or aryl isocyanate. This protocol had the advantage of giving good yields using mild conditions. The obtained products have been identified by spectroscopic data, mass spectrometry, and high-resolution mass spectra or elemental analysis.
DOI: 10.6084/m9.figshare.3121855
title: Data from: Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials

description: In a randomized controlled clinical trial that assesses treatment efficacy, a common objective is to assess the association of a measured biomarker response endpoint with the primary study endpoint in the active treatment group, using a case-cohort, case-control, or two-phase sampling design. Methods for power and sample size calculations for such biomarker association analyses typically do not account for the level of treatment efficacy, precluding interpretation of the biomarker association results in terms of biomarker effect modification of treatment efficacy, with detriment that the power calculations may tacitly and inadvertently assume that the treatment harms some study participants. We develop power and sample size methods accounting for this issue, and the methods also account for inter-individual variability of the biomarker that is not biologically relevant (e.g., due to technical measurement error). We focus on a binary study endpoint and on a biomarker subject to measurement error that is normally distributed or categorical with two or three levels. We illustrate the methods with preventive HIV vaccine efficacy trials, and include an R package implementing the methods.
DOI: 10.6084/m9.figshare.3121885.v1
title: Selective binding and lateral clustering of α5β1 and αvβ3 integrins: Unraveling the spatial requirements for cell spreading and focal adhesion assembly

description: Coordination of the specific functions of α5β1 and αvβ3 integrins is crucial for the precise regulation of cell adhesion, spreading and migration, yet the contribution of differential integrin-specific crosstalk to these processes remains unclear. To determine the specific functions of αvβ3 and α5β1 integrins, we used nanoarrays of gold particles presenting immobilized, integrin-selective peptidomimetic ligands. Integrin binding to the peptidomimetics is highly selective, and cells can spread on both ligands. However, spreading is faster and the projected cell area is greater on α5β1 ligand; both depend on ligand spacing. Quantitative analysis of adhesion plaques shows that focal adhesion size is increased in cells adhering to αvβ3 ligand at 30 and 60 nm spacings. Analysis of αvβ3 and α5β1 integrin clusters indicates that fibrillar adhesions are more prominent in cells adhering to α5β1 ligand, while clusters are mostly localized at the cell margins in cells adhering to αvβ3 ligand. αvβ3 integrin clusters are more pronounced on αvβ3 ligand, though they can also be detected in cells adhering to α5β1 ligand. Furthermore, α5β1 integrin clusters are present in cells adhering to α5β1 ligand, and often colocalize with αvβ3 clusters. Taken together, these findings indicate that the activation of αvβ3 integrin by ligand binding is dispensable for initial adhesion and spreading, but essential to formation of stable focal adhesions.
DOI: 10.6084/m9.figshare.3121876
title: Differentially methylated genes and androgen receptor re-expression in small cell prostate carcinomas

description: Small cell prostate carcinoma (SCPC) morphology is rare at initial diagnosis but often emerges during prostate cancer progression and portends a dismal prognosis. It does not express androgen receptor (AR) or respond to hormonal therapies. Clinically applicable markers for its early detection and treatment with effective chemotherapy are needed. Our studies in patient tumor–derived xenografts (PDX) revealed that AR–negative SCPC (AR<sup>−</sup>SCPC) expresses neural development genes instead of the prostate luminal epithelial genes characteristic of AR–positive castration-resistant adenocarcinomas (AR<sup>+</sup>ADENO). We hypothesized that the differences in cellular lineage programs are reflected in distinct epigenetic profiles. To address this hypothesis, we compared the DNA methylation profiles of AR<sup>−</sup> and AR<sup>+</sup> PDX using methylated CpG island amplification and microarray (MCAM) analysis and identified a set of differentially methylated promoters, validated in PDX and corresponding donor patient samples. We used the Illumina 450K platform to examine additional regions of the genome and the correlation between the DNA methylation profiles of the PDX and their corresponding patient tumors. Struck by the low frequency of AR promoter methylation in the AR<sup>−</sup>SCPC, we investigated this region's specific histone modification patterns by chromatin immunoprecipitation. We found that the AR promoter was enriched in silencing histone modifications (H3K27me3 and H3K9me2) and that EZH2 inhibition with 3-deazaneplanocin A (DZNep) resulted in AR expression and growth inhibition in AR<sup>−</sup>SCPC cell lines. We conclude that the epigenome of AR<sup>−</sup> is distinct from that of AR<sup>+</sup> castration-resistant prostate carcinomas, and that the AR<sup>−</sup> phenotype can be reversed with epigenetic drugs.
DOI: 10.6084/m9.figshare.3121855.v1
title: Data from: Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials

description: In a randomized controlled clinical trial that assesses treatment efficacy, a common objective is to assess the association of a measured biomarker response endpoint with the primary study endpoint in the active treatment group, using a case-cohort, case-control, or two-phase sampling design. Methods for power and sample size calculations for such biomarker association analyses typically do not account for the level of treatment efficacy, precluding interpretation of the biomarker association results in terms of biomarker effect modification of treatment efficacy, with detriment that the power calculations may tacitly and inadvertently assume that the treatment harms some study participants. We develop power and sample size methods accounting for this issue, and the methods also account for inter-individual variability of the biomarker that is not biologically relevant (e.g., due to technical measurement error). We focus on a binary study endpoint and on a biomarker subject to measurement error that is normally distributed or categorical with two or three levels. We illustrate the methods with preventive HIV vaccine efficacy trials, and include an R package implementing the methods.
DOI: 10.6084/m9.figshare.3121861
title: Ferritinophagy drives uropathogenic <i>Escherichia coli</i> persistence in bladder epithelial cells

description: Autophagy is a cellular recycling pathway, which in many cases, protects host cells from infections by degrading pathogens. However, uropathogenic <i>Escherichia coli</i> (UPEC), the predominant cause of urinary tract infections (UTIs), persist within the urinary tract epithelium (urothelium) by forming reservoirs within autophagosomes. Iron is a critical nutrient for both host and pathogen, and regulation of iron availability is a key host defense against pathogens. Iron homeostasis depends on the shuttling of iron-bound ferritin to the lysosome for recycling, a process termed ferritinophagy (a form of selective autophagy). Here, we demonstrate for the first time that UPEC shuttles with ferritin-bound iron into the autophagosomal and lysosomal compartments within the urothelium. Iron overload in urothelial cells induces ferritinophagy in an NCOA4-dependent manner causing increased iron availability for UPEC, triggering bacterial overproliferation and host cell death. Addition of even moderate levels of iron is sufficient to increase and prolong bacterial burden. Furthermore, we show that lysosomal damage due to iron overload is the specific mechanism causing host cell death. Significantly, we demonstrate that host cell death and bacterial burden can be reversed by inhibition of autophagy or inhibition of iron-regulatory proteins, or chelation of iron. Together, our findings suggest that UPEC persist in host cells by taking advantage of ferritinophagy. Thus, modulation of iron levels in the bladder may provide a therapeutic avenue to controlling UPEC persistence, epithelial cell death, and recurrent UTIs.
DOI: 10.6084/m9.figshare.3121876.v1
title: Differentially methylated genes and androgen receptor re-expression in small cell prostate carcinomas

description: Small cell prostate carcinoma (SCPC) morphology is rare at initial diagnosis but often emerges during prostate cancer progression and portends a dismal prognosis. It does not express androgen receptor (AR) or respond to hormonal therapies. Clinically applicable markers for its early detection and treatment with effective chemotherapy are needed. Our studies in patient tumor–derived xenografts (PDX) revealed that AR–negative SCPC (AR<sup>−</sup>SCPC) expresses neural development genes instead of the prostate luminal epithelial genes characteristic of AR–positive castration-resistant adenocarcinomas (AR<sup>+</sup>ADENO). We hypothesized that the differences in cellular lineage programs are reflected in distinct epigenetic profiles. To address this hypothesis, we compared the DNA methylation profiles of AR<sup>−</sup> and AR<sup>+</sup> PDX using methylated CpG island amplification and microarray (MCAM) analysis and identified a set of differentially methylated promoters, validated in PDX and corresponding donor patient samples. We used the Illumina 450K platform to examine additional regions of the genome and the correlation between the DNA methylation profiles of the PDX and their corresponding patient tumors. Struck by the low frequency of AR promoter methylation in the AR<sup>−</sup>SCPC, we investigated this region's specific histone modification patterns by chromatin immunoprecipitation. We found that the AR promoter was enriched in silencing histone modifications (H3K27me3 and H3K9me2) and that EZH2 inhibition with 3-deazaneplanocin A (DZNep) resulted in AR expression and growth inhibition in AR<sup>−</sup>SCPC cell lines. We conclude that the epigenome of AR<sup>−</sup> is distinct from that of AR<sup>+</sup> castration-resistant prostate carcinomas, and that the AR<sup>−</sup> phenotype can be reversed with epigenetic drugs.
DOI: 10.6084/m9.figshare.3121861.v1
title: Ferritinophagy drives uropathogenic <i>Escherichia coli</i> persistence in bladder epithelial cells

description: Autophagy is a cellular recycling pathway, which in many cases, protects host cells from infections by degrading pathogens. However, uropathogenic <i>Escherichia coli</i> (UPEC), the predominant cause of urinary tract infections (UTIs), persist within the urinary tract epithelium (urothelium) by forming reservoirs within autophagosomes. Iron is a critical nutrient for both host and pathogen, and regulation of iron availability is a key host defense against pathogens. Iron homeostasis depends on the shuttling of iron-bound ferritin to the lysosome for recycling, a process termed ferritinophagy (a form of selective autophagy). Here, we demonstrate for the first time that UPEC shuttles with ferritin-bound iron into the autophagosomal and lysosomal compartments within the urothelium. Iron overload in urothelial cells induces ferritinophagy in an NCOA4-dependent manner causing increased iron availability for UPEC, triggering bacterial overproliferation and host cell death. Addition of even moderate levels of iron is sufficient to increase and prolong bacterial burden. Furthermore, we show that lysosomal damage due to iron overload is the specific mechanism causing host cell death. Significantly, we demonstrate that host cell death and bacterial burden can be reversed by inhibition of autophagy or inhibition of iron-regulatory proteins, or chelation of iron. Together, our findings suggest that UPEC persist in host cells by taking advantage of ferritinophagy. Thus, modulation of iron levels in the bladder may provide a therapeutic avenue to controlling UPEC persistence, epithelial cell death, and recurrent UTIs.
DOI: 10.6084/m9.figshare.3121774
title: Section 7 consultation data

description: The US Endangered Species Act (ESA) directs federal agencies to consult with the US Fish and Wildlife Service (FWS) if an action they carry out, fund, or authorize might affect ESA-listed species. FWS has recorded information about all consultations they have conducted since 2008. The dataset `FWS_S7_clean_30Jul2015.RData` covers 88,290 consultations from 2008 through early 2015. The file `metadata.R` contains metadata for all of the columns in the data. This dataset is also available as part of a web application package at https://github.com/Defenders-ESC/section7_explorer.
DOI: 10.6084/m9.figshare.3121780
title: Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

description: Synthetic oligopeptides containing -conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterise an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into -sheet-like stacks with strongly favorable monomer association free energies of . Aggregation at high-pH produces disordered aggregates destabilised by Coulombic repulsion between negatively charged Asp termini (). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markov process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.
DOI: 10.6084/m9.figshare.3121819
title: finalaspensubphysdataPLOSONE.csv

description: These data are a comprehensive set of both aspen and subalpine fir physiological indicators along with the treatments set for them for our paper entitled: "Stand composition, tree proximity and size have minimal effects on leaf function of coexisting aspen and subalpine fir". The data is in an excel .csv format ready for input into R. The following are descriptions of column title codes: ID was a random marker used to label samples during the analyses. Label is a label code with the location, species, and treatment codes in a single label. Location data are factors with numbers as codes for the location of the treatment. Stand is a factor describing stand composition. Treat is the facilitation (F) versus control (C) treatment. Size class are set for increasing diameters at breast height. P is phosphorus, N is Nitrogen, Tan is condensed tannins, PG is phenolic gycosides, WP is water potential. Starch, glucose and sucrose are the nonstructural carbohydrates considered. simple sugars are glucose+sucrose and NSC are all non structural carbohydrates together. Each of these are in % of foliar dry mass excepting WP which is measured in megaPascals.
DOI: 10.6084/m9.figshare.3121780.v1
title: Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

description: Synthetic oligopeptides containing -conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterise an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into -sheet-like stacks with strongly favorable monomer association free energies of . Aggregation at high-pH produces disordered aggregates destabilised by Coulombic repulsion between negatively charged Asp termini (). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markov process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.
DOI: 10.6084/m9.figshare.3121819.v1
title: finalaspensubphysdataPLOSONE.csv

description: These data are a comprehensive set of both aspen and subalpine fir physiological indicators along with the treatments set for them for our paper entitled: "Stand composition, tree proximity and size have minimal effects on leaf function of coexisting aspen and subalpine fir". The data is in an excel .csv format ready for input into R. The following are descriptions of column title codes: ID was a random marker used to label samples during the analyses. Label is a label code with the location, species, and treatment codes in a single label. Location data are factors with numbers as codes for the location of the treatment. Stand is a factor describing stand composition. Treat is the facilitation (F) versus control (C) treatment. Size class are set for increasing diameters at breast height. P is phosphorus, N is Nitrogen, Tan is condensed tannins, PG is phenolic gycosides, WP is water potential. Starch, glucose and sucrose are the nonstructural carbohydrates considered. simple sugars are glucose+sucrose and NSC are all non structural carbohydrates together. Each of these are in % of foliar dry mass excepting WP which is measured in megaPascals.
DOI: 10.6084/m9.figshare.3121678
title: Data-Reproductive Health

description: Under request of PLoS ONE journal and in order to contribute to the transparency and replicability of research, the authors of the study “A performance analysis of public expenditure on maternal health in Mexico”; made the data available. Any other use than exploring or replicating the results of the afore-mentioned paper_inc is not authorized and shall not be used without previous authorization of the researchers. If you are interested in analyzing this database for original research purpose please contact Leticia Avila-Burgos (PI of the original study- leticia.avila@insp.mx) or Gustavo Nigenda (corresponding author- gnigenda@outlook.com)
DOI: 10.6084/m9.figshare.3121651
title: Data of Reproductive Health Subaccounts

description: Under request of PLoS ONE journal and in order to contribute to the transparency and replicability of research, the authors of the study “A performance analysis of public expenditure on maternal health in Mexico”; made the data available. Any other use than exploring or replicating the results of the afore-mentioned paper_inc is not authorized and shall not be used without previous authorization of the researchers. If you are interested in analyzing this database for original research purpose please contact Leticia Avila-Burgos (PI of the original study- leticia.avila@insp.mx) or Hustavo Nigenda (corresponding author- gnigenda@outlook.com)
DOI: 10.6084/m9.figshare.3121651.v1
title: Data of Reproductive Health Subaccounts

description: Under request of PLoS ONE journal and in order to contribute to the transparency and replicability of research, the authors of the study “A performance analysis of public expenditure on maternal health in Mexico”; made the data available. Any other use than exploring or replicating the results of the afore-mentioned paper_inc is not authorized and shall not be used without previous authorization of the researchers. If you are interested in analyzing this database for original research purpose please contact Leticia Avila-Burgos (PI of the original study- leticia.avila@insp.mx) or Hustavo Nigenda (corresponding author- gnigenda@outlook.com)
DOI: 10.6084/m9.figshare.3121582
title: Working Memory Training in Healthy Adults

description: This is a database of healthy adults, aged 30-60, who participated in a study comparing online working memory training to online processing speed training. Participants are English speaking and data was collected at the University of Calgary, Calgary, Alberta, Canada between 2011-2013.Participants completed a demographics questionnaire, a brief measure of intelligence (Wechsler Abbreviated Scale of Intelligence; WASI), and measures of working memory, processing speed, and fluid intelligence. After completing 5-weeks of working memory training or processing speed training, participants again completed measures of working memory, processing speed, and fluid intelligence. Of the 81 participants who consented to participate, 61 (75%) completed baseline and post-training testing. Four participants were removed from analysis due to low training dosage, resulting in 57 participants.The University of Calgary Conjoint Faculties Research Ethics Board approved this study, and all participants provided written informed consent. <br>
DOI: 10.6084/m9.figshare.3121045
title: PSBC and covariates

description: Proportion of successful breeders by cohort and relevant covariates.