cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4975223
title: Dataset for: Semiparametric regression on cumulative incidence function with interval-censored competing risks data

description: Many biomedical and clinical studies with time-to-event outcomes involve competing risks data. These data are frequently subject to interval censoring. This means that the failure time is not precisely observed, but is only known to lie between two observation times such as clinical visits in a cohort study. Not taking into account the interval censoring may result in biased estimation of the cause-specific cumulative incidence function, an important quantity in the competing risk framework, used for evaluating interventions in populations, for studying the prognosis of various diseases and for prediction and implementation science purposes. In this work we consider the class of semiparametric generalized odds-rate transformation models in the context of sieve maximum likelihood estimation based on B-splines. This large class of models includes both the proportional odds and the proportional subdistribution hazard models (i.e., the Fine-Gray model) as special cases. The estimator for the regression parameter is shown to be semiparametrically efficient and asymptotically normal. Simulation studies suggest that the method performs well even with small sample sizes. As an illustration we use the proposed method to analyze data from HIV-infected individuals obtained from a large cohort study in sub-Saharan Africa. We also provide the R function ciregic that implements the proposed method, and present an illustrate example.
DOI: 10.6084/m9.figshare.4975217
title: Dataset for: Resolving NMR signals of short chain fatty acid mixtures using Unsupervised Component Analysis

description: Nuclear Magnetic Resonance (NMR) is a very powerful instrumental technique suited to identify and characterize organic compounds. NMR has been successfully used in the analysis of complex biological and environmental samples, however these applications are still rather limited. In this work we describe Unsupervised Component Analysis (UCA) as a multivariate unsupervised method suited to identify the number of relevant NMR signal contributions and to deconvolute mixed signals into signal individual sources and respective contributions. Using this approach we were able to advance further in the field of quantification of NMR spectra and this methodology will help in the characterization of complex biological samples.
DOI: 10.6084/m9.figshare.4975220
title: Dataset for: Bias and inference from misspecified mixed effect models in stepped wedge trial analysis

description: Many stepped wedge trials (SWTs) are analysed using a mixed-effect model with a random intercept and fixed-effects for intervention and time-periods (referred to here as the standard model). However, it is not known whether this model is robust to misspecification. We simulated SWTs with three groups of clusters and two time-periods; one group received the intervention during the first period, and two groups in the second period. We simulated period and intervention effects that were either common-to-all or varied-between clusters. Data were analysed with the standard model, or with additional random effects for period effect or intervention effect. In a second simulation study, we explored the weight given to within-cluster comparisons by simulating a larger intervention effect in the group of the trial that experienced both the control and intervention conditions and applying the three analysis models described previously. Across 500 simulations we computed bias and confidence interval coverage of the estimated intervention effect. We found up to 50% bias in intervention effect estimates when period or intervention effects varied between clusters and were treated as fixed effects in the analysis. All misspecified models showed under-coverage of 95% confidence intervals, particularly the standard model. A large weight was given to within-cluster comparisons in the standard model. In the SWTs simulated here, mixed effect models were highly sensitive to departures from the model assumptions, which can be explained by the high dependence on within-cluster comparisons. Trialists should consider including a random effect for time-period in their SWT analysis model.
DOI: 10.6084/m9.figshare.4975223.v1
title: Dataset for: Semiparametric regression on cumulative incidence function with interval-censored competing risks data

description: Many biomedical and clinical studies with time-to-event outcomes involve competing risks data. These data are frequently subject to interval censoring. This means that the failure time is not precisely observed, but is only known to lie between two observation times such as clinical visits in a cohort study. Not taking into account the interval censoring may result in biased estimation of the cause-specific cumulative incidence function, an important quantity in the competing risk framework, used for evaluating interventions in populations, for studying the prognosis of various diseases and for prediction and implementation science purposes. In this work we consider the class of semiparametric generalized odds-rate transformation models in the context of sieve maximum likelihood estimation based on B-splines. This large class of models includes both the proportional odds and the proportional subdistribution hazard models (i.e., the Fine-Gray model) as special cases. The estimator for the regression parameter is shown to be semiparametrically efficient and asymptotically normal. Simulation studies suggest that the method performs well even with small sample sizes. As an illustration we use the proposed method to analyze data from HIV-infected individuals obtained from a large cohort study in sub-Saharan Africa. We also provide the R function ciregic that implements the proposed method, and present an illustrate example.
DOI: 10.6084/m9.figshare.4975130
title: Automated Discovery of Process Models: Results of Systematic Literature Search

description: The Excel workbooks in this dataset contain the references retrieved during a Systematic Literature Review (SLR) on automated process discovery from event logs.<br>There is one workbook per query: <br>- Process Learning<br>- Workflow Learning<br>- Process Discovery<br>- Workflow Discovery<br><br>
DOI: 10.6084/m9.figshare.4975217.v1
title: Dataset for: Resolving NMR signals of short chain fatty acid mixtures using Unsupervised Component Analysis

description: Nuclear Magnetic Resonance (NMR) is a very powerful instrumental technique suited to identify and characterize organic compounds. NMR has been successfully used in the analysis of complex biological and environmental samples, however these applications are still rather limited. In this work we describe Unsupervised Component Analysis (UCA) as a multivariate unsupervised method suited to identify the number of relevant NMR signal contributions and to deconvolute mixed signals into signal individual sources and respective contributions. Using this approach we were able to advance further in the field of quantification of NMR spectra and this methodology will help in the characterization of complex biological samples.
DOI: 10.6084/m9.figshare.4975028
title: RecodGait_v1

description: The dataset comprises data from 50 volunteers of walking and non-walking activities. All data was collected using a LG Nexus 5 smartphone. There are two sessions of five minutes split into two different days. More information can found on the README file.
DOI: 10.6084/m9.figshare.4975130.v1
title: Automated Discovery of Process Models: Results of Systematic Literature Search

description: The Excel workbooks in this dataset contain the references retrieved during a Systematic Literature Review (SLR) on automated process discovery from event logs.<br>There is one workbook per query: <br>- Process Learning<br>- Workflow Learning<br>- Process Discovery<br>- Workflow Discovery<br><br>
DOI: 10.6084/m9.figshare.4972607
title: Age Category Prediction Feature Set

description: Feature set developed to support "Predicting Age Groups of Twitter Users Based on Language and Metadata Features" by Morgan-Lopez et al. (2017). The feature set encompasses candidate variables for each of the four models referenced in the paper ("Tweet Language Only","Twitter Handle Metadata Only","Tweet Language Use and Handle Metadata", and "WWBP Words"). Description of target variables listed below -- for further description of features and methodology please reference manuscript.<br><b>Target Variables</b><i>age_cat</i>: User age category {"1" : 13-17, "2" : 18-24, "3" : 25-50} <i>age_cat_sen</i>: User age category used for sensitivity analysis {"1" : 13-17, "2" : 18-29, "3" : 30-50}<i>user_age</i>: User age<br><b>Other</b>rand_id: Random ID assigned to Twitter user
DOI: 10.6084/m9.figshare.4975028.v1
title: RecodGait_v1

description: The dataset comprises data from 50 volunteers of walking and non-walking activities. All data was collected using a LG Nexus 5 smartphone. There are two sessions of five minutes split into two different days. More information can found on the README file.
DOI: 10.6084/m9.figshare.4970900
title: Data for Fecchio, Pigorini et al.

description: Description of datasets is in the README file
DOI: 10.6084/m9.figshare.4975028.v2
title: RecodGait_v1

description: The dataset comprises data from 50 volunteers of walking and non-walking activities. All data was collected using a LG Nexus 5 smartphone. There are two sessions of five minutes split into two different days. More information can found on the README file.
DOI: 10.6084/m9.figshare.4970816
title: Experiment_1.mat

description: description is in the README file
DOI: 10.6084/m9.figshare.4970819
title: Experiment_2.mat

description: Description is in the README file
DOI: 10.6084/m9.figshare.4970762
title: The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae).

description: Supplementary files of the article entitled: "<b>The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae)</b>".<br><br><b>Abstract</b>Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, <i>Ruditapes decussatus</i>, also known as the European clam. <i>R. decussatus</i> is morphologically and ecologically similar to the Manila clam <i>Ruditapes philippinarum</i>, which has been recently introduced for aquaculture in the very same habitats of <i>R. decussatus</i>, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy.In this work we: <i>i)</i> assembled <i>R. decussatus</i> mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing, <i>ii)</i> analyzed and characterized the <i>R. decussatus</i> mitochondrial genome, comparing its features with those of other venerid bivalves; <i>iii)</i> assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples.Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the Doubly Uniparental Inheritance of mitochondria, a phenomenon known in ~100 bivalve species. According to our analyses, <i>R. decussatus</i> is more genetically similar to species of the Genus Paphia than to the congeneric <i>R. philippinarum</i>, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions, LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of <i>R. decussatus</i> is a cause or an effect of the ongoing replacement of <i>R. decussatus</i> with the invasive <i>R. philippinarum</i>, and more analyses, especially on nuclear sequences, are required to assess this point.<br><br><br>
DOI: 10.6084/m9.figshare.4970804
title: Raw data from "A Comparison of Malicious Interdiction Strategies Against Electrical Networks"

description: Simply the raw data this project was based on, in MATLAB format. Poorly labelled in many places I'm afraid, but hopefully if you poke around you can figure it out. Just putting it here for openness. Needless to say, don't hesitate to get in touch if you find anything of interest in this data.<br><br>The paper describing this work is published in IEEE Journal on Emerging and Selected Topics in Circuits and Systems.<br>
DOI: 10.6084/m9.figshare.4970819.v1
title: Experiment_2.mat

description: Description is in the README file
DOI: 10.6084/m9.figshare.4970756
title: Picure Island Upper Petroglyph Panel West

description: This dataset contains solely the output of photogrammetric processing of aerial imagery captured in the Atures Rapids, Amazonas state, Venezuela in 2016. This model is of the western section of the upper panel on Picure Island.<br>A full contextualisation of this data and accompanying discussion is published in Antiquity:<br><br><br>The archive contains a Wavefront Object, which can be viewed in Blender. Alternative formats are available upon request. The input data is available in the archive "Atures Rock Art photography" as part of this collection.<br><br>The data was processed in Agisoft Photoscan Pro 1.3.1 with default settings, except for output texture size, which was set at 8196x2. The resulting model was scaled to benchmark photographs. The model units are in metres. <br><br>
DOI: 10.6084/m9.figshare.4970804.v1
title: Raw data from "A Comparison of Malicious Interdiction Strategies Against Electrical Networks"

description: Simply the raw data this project was based on, in MATLAB format. Poorly labelled in many places I'm afraid, but hopefully if you poke around you can figure it out. Just putting it here for openness. Needless to say, don't hesitate to get in touch if you find anything of interest in this data.<br><br>The paper describing this work is published in IEEE Journal on Emerging and Selected Topics in Circuits and Systems.<br>
DOI: 10.6084/m9.figshare.4970756.v1
title: Picure Island Upper Petroglyph Panel West

description: This dataset contains solely the output of photogrammetric processing of aerial imagery captured in the Atures Rapids, Amazonas state, Venezuela in 2016. This model is of the western section of the upper panel on Picure Island.<br>A full contextualisation of this data and accompanying discussion is published in Antiquity:<br><br><br>The archive contains a Wavefront Object, which can be viewed in Blender. Alternative formats are available upon request. The input data is available in the archive "Atures Rock Art photography" as part of this collection.<br><br>The data was processed in Agisoft Photoscan Pro 1.3.1 with default settings, except for output texture size, which was set at 8196x2. The resulting model was scaled to benchmark photographs. The model units are in metres. <br><br>
DOI: 10.6084/m9.figshare.4970744
title: Picure Island Upper Petroglyph Panel East

description: This dataset contains solely the output of photogrammetric processing of aerial imagery captured in the Atures Rapids, Amazonas state, Venezuela in 2016. This model is of the eastern section of the upper panel on Picure Island.<br>A full contextualisation of this data and accompanying discussion is published in Antiquity:<br><br><br>The archive contains a Wavefront Object, which can be viewed in Blender. Alternative formats are available upon request. The input data is available in the archive "Atures Rock Art photography" as part of this collection.<br><br>The data was processed in Agisoft Photoscan Pro 1.3.1 with default settings, except for output texture size, which was set at 8196x2. The resulting model was scaled to benchmark photographs. The model units are in metres. <br>
DOI: 10.6084/m9.figshare.4970762.v1
title: The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae).

description: Supplementary files of the article entitled: "<b>The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae)</b>".<br><br><b>Abstract</b>Despite a large number of animal complete mitochondrial genomes being available in public databases, the current knowledge about mitochondrial genomics in invertebrates is sketchy. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell,<i> Ruditapes decussatus</i>, also known as European clam. <i>R. decussatus</i> is morphologically and ecologically similar to the Manila clam <i>Ruditapes philippinarum</i>, which has been recently introduced for aquaculture in the very same habitats of<i> R. decussatus</i>, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy.In this work we: i) assembled <i>R. decussatus</i> mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing, ii) analyzed and characterized <i>R. decussatus</i> mitochondrial genome, comparing its features with those of other venerid bivalves; iii) assessed mitochondrial genetic polymorphism, both from a nucleotide (SNPs) and a structural (CNV of tandem repeats) point of view, across 26 samples.Despite using high-throughput approaches we did not find evidence of sex-linked mitochondrial genomes, so it seems that <i>R. decussatus</i> does not have Doubly Uniparental Inheritance of mitochondria, a phenomenon known in ~100 bivalve species. According to our analyses, <i>R. decussatus</i> is more genetically similar to species of the Genus Paphia than to the congeneric <i>R. philippinarum</i>, a finding that bolster the already proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with a very low number of SNPs and a low polymorphism of the hypervariable sequences flanking the control region (Largest Unassigned Regions, LURs). Strikingly, contrasting with the low nucleotide variability along the entire mitochondrial genome, we observed a pretty high polymorphism in LUR length due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of <i>R. decussatus</i> is a cause or an effect of the ongoing replacement of <i>R. decussatus</i> with the invasive <i>R. philippinarum</i>, and more analyses, especially on nuclear sequences, are required to assess this point. <br>
DOI: 10.6084/m9.figshare.4970738
title: Diversity and welfare state legitimacy in Europe. The challenge of intra-EU migration

description: It has convincingly been argued that in the United States, immigration is detrimental to welfare state support. In Europe, on the other hand, there is little evidence for such a negative relationship. This article examines whether a particular type of immigration – rapidly escalating intra-European Union (EU) immigration – reduces public support for the welfare state. We argue that because EU states cannot discriminate against resident EU nationals from other countries in the field of social security, intra-EU immigration will negatively affect attitudes towards welfare spending. To test this expectation, we use data from the European Social Survey of 2008, among other sources. The results of our multilevel analyses document a negative relationship between intra-EU immigration and welfare state support, supporting our hypothesis.
DOI: 10.6084/m9.figshare.4970741
title: Picure Island Lower Petroglyph Panel

description: This dataset contains solely the output of photogrammetric processing of aerial imagery captured in the Atures Rapids, Amazonas state, Venezuela in 2016. This model is of the western section of the upper panel on Picure Island.<br>A full contextualisation of this data and accompanying discussion is published in Antiquity:<br><br><br>The archive contains a Wavefront Object, which can be viewed in Blender. Alternative formats are available upon request. The input data is available in the archive "Atures Rock Art photography" as part of this collection.<br><br>The data was processed in Agisoft Photoscan Pro 1.3.1 with default settings, except for output texture size, which was set at 8196x2. There are no benchmark photographs for this panel, and so the units are arbitrary. The double C-scrolls are approximately 30 x 30 cm, for reference.<br>
DOI: 10.6084/m9.figshare.4975028.v5
title: RecodGait_v1

description: The dataset comprises data from 50 volunteers of walking and non-walking activities. All data was collected using a LG Nexus 5 smartphone. There are two sessions of five minutes split into two different days. More information can found on the README file.
DOI: 10.6084/m9.figshare.4970723
title: A Systematic Review on Harmful Alcohol Use Among Civilian Populations Affected by Armed Conflict in Low- and Middle-Income Countries

description: <i>Background</i>: There are currently over 55 million refugees and internally displaced persons due to armed conflict. In addition, there are around 150 million more conflict-affected residents who remain in their home communities. Armed conflict poses a number of potential risks for harmful alcohol use. <i>Objective</i>: The objective of the study was to systematically examine evidence on harmful alcohol use among conflict-affected populations in low- and middle-income countries. <i>Methods</i>: A systematic review methodology was used following PRISMA guidelines. Quantitative studies were selected with outcomes relating to harmful alcohol use among conflict-affected populations in low- and middle-income countries. Seven bibliographic databases and a range of gray literature sources were searched. Descriptive analysis was applied and a quality assessment conducted using the Newcastle-Ottawa Quality Assessment Scale. <i>Results</i>: The search yielded 10,037 references of which 22 studies met inclusion criteria. Twenty-one of the studies used a cross-sectional design, and 1 used a case series design. Evidence on risk factors for harmful alcohol use was weak overall. Factors associated with harmful alcohol use were male gender, older age, cumulative trauma event exposure, and depression. There were no studies on the effectiveness of interventions for harmful alcohol use. The strength of evidence was also limited by the generally moderate quality of the studies. <i>Conclusions</i>: Substantially more evidence is required to understand the scale of conflict-associated harmful alcohol use, key risk factors, association of alcohol use with physical and mental disorders, and effectiveness of interventions to address harmful alcohol use in conflict-affected populations.