cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3117340.v1
title: Efficacy and acceptability of a home-based, family-inclusive intervention for veterans with TBI: A randomized controlled trial

description: <i>Objective</i>: Traumatic brain injury (TBI) often undermines community re-integration, impairs functioning and produces other symptoms. This study tested an innovative programme for veterans with TBI, the Veterans’ In-home Programme (VIP), delivered in veterans’ homes, involving a family member and targeting the environment (social and physical) to promote community re-integration, mitigate difficulty with the most troubling TBI symptoms and facilitate daily functioning. <i>Setting</i>: Interviews and intervention sessions were conducted in homes or by telephone. <i>Participants</i>: Eighty-one veterans with TBI at a VA polytrauma programme and a key family member. <i>Design</i>: This was a 2-group randomized controlled trial. Control-group participants received usual-care enhanced by two attention-control telephone calls. Follow-up interviews occurred up to 4 months after baseline interview. <i>Main measures</i>: VIP’s efficacy was evaluated using measures of community re-integration, target outcomes reflecting veterans’ self-identified problems and self-rated functional competence. <i>Results</i>: At follow-up, VIP participants had significantly higher community re-integration scores and less difficulty managing targeted outcomes, compared to controls. Self-rated functional competence did not differ between groups. In addition, VIP’s acceptability was high. <i>Conclusion</i>: A home-based, family-inclusive service for veterans with TBI shows promise for improving meaningful outcomes and warrants further research and clinical application.
DOI: 10.6084/m9.figshare.3117349.v2
title: Circulant Embedding of Approximate Covariances for Inference From Gaussian Data on Large Lattices

description: Recently proposed computationally efficient Markov chain Monte Carlo (MCMC) and Monte Carlo expectation–maximization (EM) methods for estimating covariance parameters from lattice data rely on successive imputations of values on an embedding lattice that is at least two times larger in each dimension. These methods can be considered exact in some sense, but we demonstrate that using such a large number of imputed values leads to slowly converging Markov chains and EM algorithms. We propose instead the use of a discrete spectral approximation to allow for the implementation of these methods on smaller embedding lattices. While our methods are approximate, our examples indicate that the error introduced by this approximation is small compared to the Monte Carlo errors present in long Markov chains or many iterations of Monte Carlo EM algorithms. Our results are demonstrated in simulation studies, as well as in numerical studies that explore both increasing domain and fixed domain asymptotics. We compare the exact methods to our approximate methods on a large satellite dataset, and show that the approximate methods are also faster to compute, especially when the aliased spectral density is modeled directly. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3117316.v1
title: New Occurrences of <i>Oldhamia</i> in Eastern Yukon, Canada: Stratigraphic Context and Implications for Cambrian Deep-Marine Biostratigraphy

description: For over a century, the ichnogenus <i>Oldhamia</i> has been used as an index fossil for Cambrian deep-marine siliciclastic successions. New specimens from the Cambrian of Selwyn Basin, eastern Yukon, Canada, provide an opportunity to constrain the chronostratigraphic range of <i>Oldhamia</i> and test its potential for more detailed biozonation. The upper part of Narchilla Formation (Arrowhead Lake Member) yields <i>O. antiqua, O. curvata, O. flabellata</i>, and <i>O. radiata</i>. The overlying Gull Lake Formation yields a less diverse assemblage of <i>O. antiqua, O. curvata</i>, and <i>O. flabellata</i>. The upward disappearance of <i>O. radiata</i> is consistent with models that infer increasing complexity of <i>Oldhamia</i> ichnospecies through time but may also be a function of limited sampling. Regional stratigraphic correlations suggest <i>Oldhamia</i> appeared in Arrowhead Lake Member during Cambrian Stage 3. Archaeocyathans and trilobites from Gull Lake Formation confirm that <i>Oldhamia</i> was present during Cambrian Stages 3 to 4. A younger age limit on <i>Oldhamia</i> in Selwyn Basin is provided by syn-volcanic detrital zircons recovered from the base of the overlying Old Cabin Formation, which yield an age of 499.89 ± 0.14 Ma (earliest Guzhangian). <i>Oldhamia</i> appears to be a reliable index fossil for Cambrian Series 2 and Series 3 in Selwyn Basin.
DOI: 10.6084/m9.figshare.3117313.v1
title: Hong_Figshare 1.zip

description: The compositional variation of the Formula Diet fed to the experimental mice (Additional table file), Differentially expressed genes by effect of RS, DJ, and DJ526 (Additional table file), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Additional table file), Globally normalized data (Fold change raw data file), Z transformed data (Z-ratio raw data file), and GSEA results (GSEA results data file)
DOI: 10.6084/m9.figshare.3117283
title: Imagine no religion: Heretical disgust, anger and the symbolic purity of mind

description: Immoral actions, including physical/sexual (e.g., incest) and social (e.g., unfairness) taboos, are often described as disgusting. But what about immoral thoughts, more specifically, thoughts that violate religious beliefs? Do heretical thoughts taint the purity of mind? The present research examined <i>heretical disgust</i> using self-report measures and facial electromyography. Religious thought violations consistently elicited both self-reported disgust and anger. Feelings of disgust also predicted harsh moral judgement, independent of anger, and were mediated by feelings of “contamination”. However, religious thought violations were not associated with a disgust facial expression (i.e., levator labii muscle activity) that was elicited by physically disgusting stimuli. We conclude that people (especially more religious people) do feel disgust in response to heretical thoughts that is meaningfully distinct from anger as a moral emotion. However, heretical disgust is not embodied in a physical disgust response. Rather, disgust has a symbolic moral value that marks heretical thoughts as harmful and aversive.
DOI: 10.6084/m9.figshare.3117286
title: A lower bound error for free-run simulation of the polynomial NARMAX

description: A lower bound error for free-run simulation of the polynomial NARMAX (Nonlinear AutoRegressive Moving Average model with eXogenous input) is introduced. The ultimate goal of the polynomial NARMAX is to predict an arbitrary number of steps ahead. Free-run simulation is also used to validate the model. Although free-run simulation of the polynomial NARMAX is essential, little attention has been given to the error propagation to round off in digital computers. Our procedure is based on the comparison of two pseudo-orbits produced from two mathematical equivalent models, but different from the point of view of floating point representation. We apply successfully our technique for three identified models of the systems: sine map, Chua's circuit and Duffing–Ueda oscillator. This technique may be used to reject a simulation, if a required precision is greater than the lower bound error, increasing the numerical reliability in free-run simulation of the polynomial NARMAX.
DOI: 10.6084/m9.figshare.3117349.v1
title: Circulant embedding of approximate covariances for inference from Gaussian data on large lattices

description: Recently proposed computationally efficient Markov chain Monte Carlo (MCMC) and Monte Carlo Expectation-Maximization (EM) methods for estimating covariance parameters from lattice data rely on successive imputations of values on an embedding lattice that is at least two times larger in each dimension. These methods can be considered exact in some sense, but we demonstrate that using such a large number of imputed values leads to slowly converging Markov chains and EM algorithms. We propose instead the use of a discrete spectral approximation to allow for the implementation of these methods on smaller embedding lattices. While our methods are approximate, our examples indicate that the error introduced by this approximation is small compared to the Monte Carlo errors present in long Markov chains or many iterations of Monte Carlo EM algorithms. Our results are demonstrated in simulation studies, as well as in numerical studies that explore both increasing domain and fixed domain asymptotics. We compare the exact methods to our approximate methods on a large satellite dataset, and show that the approximate methods are also faster to compute, especially when the aliased spectral density is modeled directly.
DOI: 10.6084/m9.figshare.3117283.v1
title: Imagine no religion: Heretical disgust, anger and the symbolic purity of mind

description: Immoral actions, including physical/sexual (e.g., incest) and social (e.g., unfairness) taboos, are often described as disgusting. But what about immoral thoughts, more specifically, thoughts that violate religious beliefs? Do heretical thoughts taint the purity of mind? The present research examined <i>heretical disgust</i> using self-report measures and facial electromyography. Religious thought violations consistently elicited both self-reported disgust and anger. Feelings of disgust also predicted harsh moral judgement, independent of anger, and were mediated by feelings of “contamination”. However, religious thought violations were not associated with a disgust facial expression (i.e., levator labii muscle activity) that was elicited by physically disgusting stimuli. We conclude that people (especially more religious people) do feel disgust in response to heretical thoughts that is meaningfully distinct from anger as a moral emotion. However, heretical disgust is not embodied in a physical disgust response. Rather, disgust has a symbolic moral value that marks heretical thoughts as harmful and aversive.
DOI: 10.6084/m9.figshare.3117235
title: Application of SELDI-TOF in <i>N</i>-glycopeptides profiling of the urine from patients with endometrial, ovarian and cervical cancer

description: <i>Purpose</i>: Endometrial (ECa), ovarian (OCa) and cervical (CCa) cancers are among 10 of the most common cancers affecting women worldwide. Cancers are known to cause some proteins to be differentially glycosylated or aberrantly excreted in the urine, which can be used as biomarkers. Since ECa, OCa and CCa are difficult to diagnose at the early stage, the aim of the present study was to identify a panel of new biomarkers for early detection of the cancers using surface-enhanced laser desorption/ionization-time-of-flight (SELDI-TOF) technology. Identification of early biomarkers that are specific and efficient can increase the survival rate of the patients. <i>Experimental design</i>: Digested urinary proteins from patients with ECa, OCa and CCa were incubated on the champedak mannose-binding (CMB) lectin-immobilized PS10 chip. The lectin-captured glycopeptides were detected with SELDI-TOF mass spectrometry and followed by biomarker wizard analysis. <i>Results</i>: Peaks <i>m/z</i> 1201 and 1449 were detected as potential group discriminators. The peak <i>m/z</i> 1201 could distinguish OCa from CCa and ECa and its sensitivity and specificity were 100%. For <i>m/z</i> 1449, it was able to differentiate ECa from the other two types of cancer. <i>Conclusions</i>: The findings of this study suggest urinary glycopeptides <i>m/z</i> 1201 and 1449 may serve as potential biomarkers for the early detection of ECa, OCa and CCa, although this requires further extensive validation on clinically representative populations.
DOI: 10.6084/m9.figshare.3117235.v1
title: Application of SELDI-TOF in <i>N</i>-glycopeptides profiling of the urine from patients with endometrial, ovarian and cervical cancer

description: <i>Purpose</i>: Endometrial (ECa), ovarian (OCa) and cervical (CCa) cancers are among 10 of the most common cancers affecting women worldwide. Cancers are known to cause some proteins to be differentially glycosylated or aberrantly excreted in the urine, which can be used as biomarkers. Since ECa, OCa and CCa are difficult to diagnose at the early stage, the aim of the present study was to identify a panel of new biomarkers for early detection of the cancers using surface-enhanced laser desorption/ionization-time-of-flight (SELDI-TOF) technology. Identification of early biomarkers that are specific and efficient can increase the survival rate of the patients. <i>Experimental design</i>: Digested urinary proteins from patients with ECa, OCa and CCa were incubated on the champedak mannose-binding (CMB) lectin-immobilized PS10 chip. The lectin-captured glycopeptides were detected with SELDI-TOF mass spectrometry and followed by biomarker wizard analysis. <i>Results</i>: Peaks <i>m/z</i> 1201 and 1449 were detected as potential group discriminators. The peak <i>m/z</i> 1201 could distinguish OCa from CCa and ECa and its sensitivity and specificity were 100%. For <i>m/z</i> 1449, it was able to differentiate ECa from the other two types of cancer. <i>Conclusions</i>: The findings of this study suggest urinary glycopeptides <i>m/z</i> 1201 and 1449 may serve as potential biomarkers for the early detection of ECa, OCa and CCa, although this requires further extensive validation on clinically representative populations.
DOI: 10.6084/m9.figshare.3117286.v1
title: A lower-bound error for free-run simulation of the polynomial NARMAX

description: A lower-bound error for free-run simulation of the polynomial NARMAX is introduced. The ultimate goal of the polynomial NARMAX is to predict an arbitrary number of steps ahead. Free-run simulation is also used to validate the model. Although, free-run simulation of the polynomial NARMAX is essential, little attention has been given to the error propagation to round off in digital computers. Our procedure is based on the comparison of two pseudo-orbits produced from two mathematical equivalent models, but different from the point of view of floating point representation. We apply successfully our technique for three identified models of the systems: sine map, Chua's circuit and Duffing-Ueda oscillator. This technique may be used to reject a simulation, if a required precision is greater than the lower-bound error, increasing the numerical reliability in free-run simulation of the polynomial NARMAX. Supplementary material
DOI: 10.6084/m9.figshare.3117205
title: Coffeyetal2016_EEGdata.zip

description: This file contains EEG data and related behavioural variables for the article:<br><br>Coffey et al. Individual differences in the frequency-following response: Relation to pitch perception. PLoS ONE. 2016<br><br><br>
DOI: 10.6084/m9.figshare.3117124
title: Plant communities and environmental factors in the Guayana Highlands: monitoring for conservation under future climate change

description: The Guayana Highlands (GH) constitute a highly diverse, but relatively poorly studied Neotropical biome, comprised of ∼50 flat-topped mountain summits (called tepuis). Previous studies based on warming forecasts for the region suggested that an upward displacement of environmental conditions of 500–700 m could occur by 2100, potentially resulting in the extinction of <i>c</i>. 50% of its endemic flora due to total habitat loss. To assess the ecological responses of the species to climate change, and select the appropriate conservation measures, long-term monitoring of the GH plant communities will be necessary. In this study, the baseline state for future comparisons was established for the best explored tepui in terms of its flora, Roraima-tepui (2810 m), through a floristic characterization of its different vegetation types. We also identified the environmental gradients underlying the major plant communities, and assessed the effects of human activities on the chemistry of soils and water at three field camps. Our results yielded five main community types: three meadows, one shrubland, and one forest, with their corresponding diagnostic species. The herbaceous communities were mainly influenced by the presence of flat sandy soils, with varying flooding capacity. Shrublands and forests were characterized by irregular organic soils with very low pH. Finally, pH values below 3 were measured on an organic soil of a field camp, although further studies will be necessary to attribute this deviation to human activities.
DOI: 10.6084/m9.figshare.3117124.v1
title: Plant communities and environmental factors in the Guayana Highlands: monitoring for conservation under future climate change

description: The Guayana Highlands (GH) constitute a highly diverse, but relatively poorly studied Neotropical biome, comprised of ∼50 flat-topped mountain summits (called tepuis). Previous studies based on warming forecasts for the region suggested that an upward displacement of environmental conditions of 500–700 m could occur by 2100, potentially resulting in the extinction of <i>c</i>. 50% of its endemic flora due to total habitat loss. To assess the ecological responses of the species to climate change, and select the appropriate conservation measures, long-term monitoring of the GH plant communities will be necessary. In this study, the baseline state for future comparisons was established for the best explored tepui in terms of its flora, Roraima-tepui (2810 m), through a floristic characterization of its different vegetation types. We also identified the environmental gradients underlying the major plant communities, and assessed the effects of human activities on the chemistry of soils and water at three field camps. Our results yielded five main community types: three meadows, one shrubland, and one forest, with their corresponding diagnostic species. The herbaceous communities were mainly influenced by the presence of flat sandy soils, with varying flooding capacity. Shrublands and forests were characterized by irregular organic soils with very low pH. Finally, pH values below 3 were measured on an organic soil of a field camp, although further studies will be necessary to attribute this deviation to human activities.
DOI: 10.6084/m9.figshare.3117118
title: Factors affecting the distribution and abundance of orchids in grasslands and herbaceous wetlands

description: Grasslands, wet meadows, fens, bogs, and marshes represent important ecosystems that host many orchid species. However, research on the joint effect of the multi-scalar abiotic drivers on orchid distribution and abundance in these habitats is limited. In this study, we investigated factors associated with the occurrence and abundance of 42 orchid taxa in grasslands and herbaceous wetlands of 29 mountains and the surrounding low altitude areas in western Serbia (eastern Dinaric Alps, southeastern Europe). Niche analysis of orchids was performed using outlying mean index analysis (OMI). In addition, we used similarity profile analysis (SIMPROF) to classify orchid taxa into ecological groups, multi response permutation procedure (MRPP) to analyse the differences in orchid composition between vegetation types, and indicator species analysis (ISA) to detect orchids with an affinity to a certain type of vegetation and geological bedrock. The most important gradients that separate orchids within the sampled environmental conditions were moisture, temperature, altitude and soil pH. Moreover, this study underlines the importance of certain vegetation types and geological bedrocks in determining the distribution and abundance of orchids. In total, eight ecological groups of orchids were distinguished. The results have shown that 11 orchid taxa are indicators of specific vegetation types, whereas 13 orchid taxa are indicators of specific bedrock types. The study area provides suitable conditions for survival of some rare and endemic orchid species that have southern limits of their distribution in this part of southeastern Europe. The study suggests that the joint effect of ecological factors, especially vegetation communities and bedrock types, is important to consider in the planning and management of orchid species conservation.
DOI: 10.6084/m9.figshare.3117118.v1
title: Factors affecting the distribution and abundance of orchids in grasslands and herbaceous wetlands

description: Grasslands, wet meadows, fens, bogs, and marshes represent important ecosystems that host many orchid species. However, research on the joint effect of the multi-scalar abiotic drivers on orchid distribution and abundance in these habitats is limited. In this study, we investigated factors associated with the occurrence and abundance of 42 orchid taxa in grasslands and herbaceous wetlands of 29 mountains and the surrounding low altitude areas in western Serbia (eastern Dinaric Alps, southeastern Europe). Niche analysis of orchids was performed using outlying mean index analysis (OMI). In addition, we used similarity profile analysis (SIMPROF) to classify orchid taxa into ecological groups, multi response permutation procedure (MRPP) to analyse the differences in orchid composition between vegetation types, and indicator species analysis (ISA) to detect orchids with an affinity to a certain type of vegetation and geological bedrock. The most important gradients that separate orchids within the sampled environmental conditions were moisture, temperature, altitude and soil pH. Moreover, this study underlines the importance of certain vegetation types and geological bedrocks in determining the distribution and abundance of orchids. In total, eight ecological groups of orchids were distinguished. The results have shown that 11 orchid taxa are indicators of specific vegetation types, whereas 13 orchid taxa are indicators of specific bedrock types. The study area provides suitable conditions for survival of some rare and endemic orchid species that have southern limits of their distribution in this part of southeastern Europe. The study suggests that the joint effect of ecological factors, especially vegetation communities and bedrock types, is important to consider in the planning and management of orchid species conservation.
DOI: 10.6084/m9.figshare.3117094
title: Simultaneous standardisation of modules and their components: a global economic perspective

description: This paper deals with the problem of simultaneous standardisation of a set of modules and of several sets of components that may be combined in these modules. The aim is to minimise future costs of production and procurement. We introduce a multilevel standardisation that permits to link the level of forecasts used in manufacturing companies with the modules. This formulation determines the composition of the module i.e. their Bill of Material instead of using a predetermined one. The model takes into account coupling restrictions between components and also permits to modelise the possibility of lifting some of them through ‘junction components’. Our model proposes an efficient approach to deal with temporal dimension in the standardisation process. This approach is illustrated with a real case from the automotive industry and some of the related implementation problems are discussed.