cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1456279
title: Matriz presença ausência epífitas vasculares

description: Matriz binária de ausência ou presença das epífitas vasculares em 21 áreas de Floresta Estacional Semidecidual, Mata Atlântica, Brasil
DOI: 10.6084/m9.figshare.1456299.v2
title: Figures

description: Figures
DOI: 10.6084/m9.figshare.1456313.v3
title: us-ALEX smFRET data

description: An example smFRET us-ALEX measurement in Photon-HDF5 format.
DOI: 10.6084/m9.figshare.1456278
title: Lista espécies epífitas vasculares, Botucatu, SP, Brasil

description: Lista das espécies de epífitas vasculares em Botucatu, SP, Brasil
DOI: 10.6084/m9.figshare.1456279.v1
title: Matriz presença ausência epífitas vasculares

description: Matriz binária de ausência ou presença das epífitas vasculares em 21 áreas de Floresta Estacional Semidecidual, Mata Atlântica, Brasil
DOI: 10.6084/m9.figshare.1456313.v2
title: us-ALEX smFRET data

description: An example smFRET us-ALEX measurement in Photon-HDF5 format.
DOI: 10.6084/m9.figshare.1456267
title: new fileset

description: marketing management, retailing, visual merchandiseing
DOI: 10.6084/m9.figshare.1456278.v1
title: Lista espécies epífitas vasculares, Botucatu, SP, Brasil

description: Lista das espécies de epífitas vasculares em Botucatu, SP, Brasil
DOI: 10.6084/m9.figshare.1456362.v2
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456267.v1
title: new fileset

description: marketing management, retailing, visual merchandiseing
DOI: 10.6084/m9.figshare.1456268
title: NetVotes Data

description: This is the data used in the experiment of the paper submited to ENIC 2015
DOI: 10.6084/m9.figshare.1456268.v1
title: NetVotes Data

description: This is the data used in the experiment of the paper submited to ENIC 2015
DOI: 10.6084/m9.figshare.1456244
title: Principal bicorrelation analysis: Unraveling associations between three data sources

description: In this article, we propose a statistical explorative method for data integration. It is developed in the context of early drug development for which it enables the detection of chemical substructures and the identification of genes that mediate their association with the bioactivity (BA). The core of the method is a sparse singular value decomposition for the identification of the gene set and a permutation-based method for the control of the false discovery rate. The method is illustrated using a real dataset, and its properties are empirically evaluated by means of a simulation study. Quantitative Structure Transcriptional Activity Relationship (QSTAR, www.qstar-consortium.org) is a new paradigm in early drug development that extends QSAR by not only considering data on the chemical structure of the compounds and on the compound-induced BA, but by simultaneously using transcriptomics data (gene expression). This approach enables, for example, the detection of chemical substructures that are associated with BA, while at the same time a gene set is correlated with both these substructures and the BA. Although causal associations cannot be formally concluded, these associations may suggest that the compounds act on the BA through a particular genomic pathway.
DOI: 10.6084/m9.figshare.1456362.v3
title: Example smFRET data files in Photon-HDF5 format2

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456244.v2
title: Principal bicorrelation analysis: Unraveling associations between three data sources

description: In this article, we propose a statistical explorative method for data integration. It is developed in the context of early drug development for which it enables the detection of chemical substructures and the identification of genes that mediate their association with the bioactivity (BA). The core of the method is a sparse singular value decomposition for the identification of the gene set and a permutation-based method for the control of the false discovery rate. The method is illustrated using a real dataset, and its properties are empirically evaluated by means of a simulation study. Quantitative Structure Transcriptional Activity Relationship (QSTAR, www.qstar-consortium.org) is a new paradigm in early drug development that extends QSAR by not only considering data on the chemical structure of the compounds and on the compound-induced BA, but by simultaneously using transcriptomics data (gene expression). This approach enables, for example, the detection of chemical substructures that are associated with BA, while at the same time a gene set is correlated with both these substructures and the BA. Although causal associations cannot be formally concluded, these associations may suggest that the compounds act on the BA through a particular genomic pathway.
DOI: 10.6084/m9.figshare.1456265
title: Comparison of asymptotic confidence sets for regression in small samples

description: In case of small samples, asymptotic confidence sets may be inaccurate, with their actual coverage probability far from a nominal confidence level. In a single framework, we consider four popular asymptotic methods of confidence estimation. These methods are based on model linearization, F-test, likelihood ratio test, and nonparametric bootstrapping procedure. Next, we apply each of these methods to derive three types of confidence sets: confidence intervals, confidence regions, and pointwise confidence bands. Finally, to estimate the actual coverage of these confidence sets, we conduct a simulation study on three regression problems. A linear model and nonlinear Hill and Gompertz models are tested in conditions of different sample size and experimental noise. The simulation study comprises calculation of the actual coverage of confidence sets over pseudo-experimental datasets for each model. For confidence intervals, such metrics as width and simultaneous coverage are also considered. Our comparison shows that the F-test and linearization methods are the most suitable for the construction of confidence intervals, the F-test – for confidence regions and the linearization – for pointwise confidence bands.
DOI: 10.6084/m9.figshare.1456265.v2
title: Comparison of asymptotic confidence sets for regression in small samples

description: In case of small samples, asymptotic confidence sets may be inaccurate, with their actual coverage probability far from a nominal confidence level. In a single framework, we consider four popular asymptotic methods of confidence estimation. These methods are based on model linearization, F-test, likelihood ratio test, and nonparametric bootstrapping procedure. Next, we apply each of these methods to derive three types of confidence sets: confidence intervals, confidence regions, and pointwise confidence bands. Finally, to estimate the actual coverage of these confidence sets, we conduct a simulation study on three regression problems. A linear model and nonlinear Hill and Gompertz models are tested in conditions of different sample size and experimental noise. The simulation study comprises calculation of the actual coverage of confidence sets over pseudo-experimental datasets for each model. For confidence intervals, such metrics as width and simultaneous coverage are also considered. Our comparison shows that the F-test and linearization methods are the most suitable for the construction of confidence intervals, the F-test – for confidence regions and the linearization – for pointwise confidence bands.
DOI: 10.6084/m9.figshare.1456362.v4
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456244.v1
title: Principal Bicorrelation Analysis: Unraveling Associations Between Three Data Sources

description: In this paper we propose a statistical explorative method for data integration. It is developed in the context of early drug development for which it enables the detection of chemical substructures and the identification of genes that mediate their association with the bioactivity (BA). The core of the method is a sparse singular value decomposition for the identification of the gene set and a permutation-based method for the control of the false discovery rate. The method is illustrated using a real dataset, and its properties are empirically evaluated by means of a simulation study. Quantitative Structure Transcriptional Activity Relationship (QSTAR, www.qstar-consortium.org) which is a new paradigm in early drug development that extends QSAR by not only considering data on the chemical structure of the compounds and on the compound-induced bioactivity, but by simultaneously using transcriptomics data (gene expression). This approach enables, for example, the detection of chemical substructures that are associated with bioactivity, while at the same time a gene set is correlated with both these substructures and the bioactivity. Although causal associations cannot be formally concluded, these associations may suggest that the compounds act on the bioactivity through a particular genomic pathway.
DOI: 10.6084/m9.figshare.1456265.v1
title: Comparison of Asymptotic Confidence Sets for Regression in Small Samples

description: 1 In case of small samples, asymptotic confidence sets may be inaccurate, with their actual coverage probability far from a nominal confidence level.In a single framework, we consider four popular asymptotic methods of confidence estimation. These methods are based on model linearization, F-test, likelihood ratio test and nonparametric bootstrapping procedure.Next, we apply each of these methods to derive three types of confidence sets: confidence intervals, confidence regions and pointwise confidence bands.Finally, to estimate the actual coverage of these confidence sets, we conduct a simulation study on three regression problems. A linear model and nonlinear Hill and Gompertz models are tested in conditions of different sample size and experimental noise. The simulation study comprises calculation of the actual coverage of confidence sets over pseudo-experimental data sets for each model. For confidence intervals, such metrics as width and simultaneous coverage are also considered.Our comparison shows that the F-test and linearization methods are the most suitable for the construction of confidence intervals, the F-test – for confidence regions and the linearization – for pointwise confidence bands.
DOI: 10.6084/m9.figshare.1456362.v5
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456362.v6
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456362.v7
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456239
title: VSV-EBOV rapidly protects macaques against infection with the 2014/15 Ebola virus outbreak strain

description: This study analyzed how many days between vaccination with VSV-EBOV and lethal EBOV challenge are needed for protection in macaques. Results showed that 7 days as a minimum between vaccination and challenge offered 100% protection. The study is published in Science (Marzi et al., Science August 2015).
DOI: 10.6084/m9.figshare.1456239.v1
title: VSV-EBOV rapidly protects macaques against infection with the 2014/15 Ebola virus outbreak strain

description: This study analyzed how many days between vaccination with VSV-EBOV and lethal EBOV challenge are needed for protection in macaques. Results showed that 7 days as a minimum between vaccination and challenge offered 100% protection. The study is published in Science (Marzi et al., Science August 2015).
DOI: 10.6084/m9.figshare.1456362.v8
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456238
title: Database

description: Under request of PlosONE and in order to contribute to transparency and replicability of research, the authors of the study entitled “Estimating the Impact of Late ART Initiation on HIV Transmission among Men who have Sex with Men in Mexico using a mathematical model”, made the data available. Any other use than exploring or replicating the results of the above-mentioned paper is not authorized and shall not be used without previous authorization of the investigators. If you are interested in analyzing this database for original research purposes please contact Sergio Bautista-Arredondo (PI of the study, sbautista@insp.mx), Yanink Caro (principal author of the study, yaninkc@yahoo.com.mx), or Juan Sierra-Madero (corresponding author jsmadero@yahoo.com).
DOI: 10.6084/m9.figshare.1456362.v9
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456238.v1
title: Database

description: Under request of PlosONE and in order to contribute to transparency and replicability of research, the authors of the study entitled “Estimating the Impact of Late ART Initiation on HIV Transmission among Men who have Sex with Men in Mexico using a mathematical model”, made the data available. Any other use than exploring or replicating the results of the above-mentioned paper is not authorized and shall not be used without previous authorization of the investigators. If you are interested in analyzing this database for original research purposes please contact Sergio Bautista-Arredondo (PI of the study, sbautista@insp.mx), Yanink Caro (principal author of the study, yaninkc@yahoo.com.mx), or Juan Sierra-Madero (corresponding author jsmadero@yahoo.com).
DOI: 10.6084/m9.figshare.1456236
title: Robust Inference in Generalized Linear Models

description: Robust inference on the parameters in generalized linear models is performed using the weighted likelihood method. Two cases are considered: a case with replicated observations and a case with a single observation of the dependent variable for each combination of the explanatory variables. The first case is common in the design of experiments, while the second case arises in observational studies. Theoretical and computational results on real datasets are presented and compared with other existing techniques.
DOI: 10.6084/m9.figshare.1456362.v10
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.17632/9vbgmp5swg.1
title: US Counties dataset for Spatial Outlier Detection

description: This dataset was used in the validation of the information mining process for discovery of spatial outliers
DOI: 10.6084/m9.figshare.1456234
title: <i>Ganguroo robustiter</i>, sp. nov. (Macropodoidea, Marsupialia), a middle to early late Miocene basal macropodid from Riversleigh World Heritage Area, Australia

description: ABSTRACT——Cranial and dental remains of the middle to early late Miocene macropodid kangaroo, <i>Ganguroo robustiter</i>, sp. nov., are described. Postcranial remains of <i>G. robustiter</i> were previously described as referable to <i>G. bilamina</i>. <i>Ganguroo robustiter</i> is more robust (approximately 20% larger) and more derived than <i>G. bilamina</i> and <i>G. bites</i>, in having a larger m4, a well-developed posterolingual ridge and lingual cingulum on P3, a longer P3/p3, and no stylar cusp C on M3–M4. We used previously published data matrices to analyze the phylogenetic relationship of <i>G. robustiter</i>. Both phylogenetic analyses, using craniodental and postcranial characters, place <i>G. robustiter</i> within Macropodidae, as the sister taxon to sthenurines and macropodines. Species of <i>Ganguroo</i> are not found to be monophyletic despite their extreme similarity in character scores. This may be due to the large amount of missing data for <i>G. bilamina</i> and <i>G. bites</i> for which no postcranial remains have been identified. Phylogenetic results are ambiguous, recovering unresolved trees with low bootstrap values, but the generic assignment of these taxa is maintained because they are remarkably similar. Species of <i>Ganguroo</i> may represent a phyletic lineage, with species increasing in size and losing cusp/cuspids on their premolars through time, which appears to coincide with a broader record of changing vegetation and climates through the middle Miocene.http://zoobank.org/urn:lsid:zoobank.org:pub:D0B542BE-C673-4260-8381-8B163A35AC36SUPPLEMENTAL DATA——Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1456236.v1
title: Robust Inference in Generalized Linear Models

description: Robust inference on the parameters in generalized linear models is performed using the weighted likelihood method. Two cases are considered: a case with replicated observations and a case with a single observation of the dependent variable for each combination of the explanatory variables. The first case is common in the design of experiments, while the second case arises in observational studies. Theoretical and computational results on real datasets are presented and compared with other existing techniques.
DOI: 10.6084/m9.figshare.1456233
title: DNA hypomethylation-mediated activation of <i>Cancer/Testis Antigen 45</i> (<i>CT45</i>) genes is associated with disease progression and reduced survival in epithelial ovarian cancer

description: Epithelial ovarian cancer (EOC) is a highly lethal malignancy due to a lack of early detection approaches coupled with poor outcomes for patients with clinically advanced disease. Cancer-testis (CT) or cancer-germline genes encode antigens known to generate spontaneous anti-tumor immunity in cancer patients. CT45 genes are a recently discovered 6-member family of X-linked CT genes with oncogenic function. Here, we determined CT45 expression in EOC and fully defined its epigenetic regulation by DNA methylation. <i>CT45</i> was silent and hypermethylated in normal control tissues, but a large subset of EOC samples showed increased <i>CT45</i> expression in conjunction with promoter DNA hypomethylation. In contrast, copy number status did not correlate with <i>CT45</i> expression in the TCGA database for EOC. <i>CT45</i> promoter methylation inversely correlated with both CT45 mRNA and protein expression, the latter determined using IHC staining of an EOC TMA. <i>CT45</i> expression was increased and <i>CT45</i> promoter methylation was decreased in late-stage and high-grade EOC, and both measures were associated with poor survival. <i>CT45</i> hypomethylation was directly associated with <i>LINE-1</i> hypomethylation, and <i>CT45</i> was frequently co-expressed with other CT antigen genes in EOC. Decitabine treatment induced CT45 mRNA and protein expression in EOC cells, and promoter transgene analyses indicated that DNA methylation directly represses <i>CT45</i> promoter activity. These data verify CT45 expression and promoter hypomethylation as possible prognostic biomarkers, and suggest CT45 as an immunological or therapeutic target in EOC. Treatment with decitabine or other epigenetic modulators could provide a means for more effective immunological targeting of CT45.
DOI: 10.6084/m9.figshare.1456362.v11
title: Example smFRET data files in Photon-HDF5 format

description: A few smFRET example data files in Photon-HDF5 format. <br>This work was partially supported by NIH Grant R01-GM95904.
DOI: 10.6084/m9.figshare.1456232
title: The combined benefits of motorcycle antilock braking systems (ABS) in preventing crashes and reducing crash severity

description: <b>Objective</b>: Several studies have reported the benefits of motorcycle antilock braking systems (ABS) in reducing injury crashes, due to improved stability and braking performance. Both aspects may prevent crashes but may also reduce the crash severity when a collision occurs. However, it is still unknown to what extent the reductions in injury crashes with ABS may be due to a combination of these mechanisms. <b>Methods</b>: Swedish hospital and police reports (2003–2012) were used. The risk for permanent medical impairment (RPMI) was calculated, showing the risk of at least 1 or 10% permanent medical impairment. In total, 165 crashes involving ABS-equipped motorcycles were compared with 500 crashes with similar motorcycles without ABS. The analysis was performed in 3 steps. First, the reduction in emergency care visits with ABS was calculated using an induced exposure approach. Secondly, the injury mitigating effects of ABS were investigated. The mean RPMI 1+ and RPMI 10+ were analyzed for different crash types. The distributions of impairing injuries (PMI 1+) and severely impairing injuries (PMI 10+) were also analyzed. In the third step, the total reduction of PMI 1+ and PMI 10+ injured motorcyclists was calculated by combining the reductions found in the previous steps. An additional analysis of combined braking systems (CBS) together with ABS was also performed. <b>Results</b>: The results showed that emergency care visits were reduced by 47% with ABS. In the second step, it was found that the mean RPMI 1+ and RPMI 10+ with ABS were 15 and 37% lower, respectively. Finally, the third step showed that the total reductions in terms of crash avoidance and mitigation of PMI 1+ and PMI 10+ injured motorcyclists with ABS were 67 and 55%, respectively. However, PMI 1+ and PMI 10+ leg injuries were not reduced by ABS to the same extent. Indications were found suggesting that the benefits of ABS together with CBS may be greater than ABS alone. <b>Conclusions</b>: This article indicated that motorcycle ABS reduced impairing injuries, mostly due to fewer emergency care visits but also due to a reduction in crash severity. This may seem reasonable as the improved stability and braking performance provided by ABS could prevent some crashes but would also decrease crash severity if a collision still occurs. As suggested by previous studies, however, the lower extremities would be more exposed in a crash with ABS. It is recommended that future research should follow up these results with additional data.