cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3117757.v1
title: Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations

description: Discovery of cargo carrying cell-penetrating peptides has opened a new gate in the development of peptide-based drugs that can effectively target intracellular enzymes. Success in application and development of cell-penetrating peptides in drug design depends on understanding their translocation mechanisms. In this study, our aim was to examine the bacterial translocation mechanism of the cell-penetrating pVEC peptide (LLIILRRRIRKQAHAHSK) using steered molecular dynamics (SMD) simulations. The significance of specific residues or regions for translocation was studied by performing SMD simulations on the alanine mutants and other variants of pVEC. Residue-based analysis showed that positively charged residues contribute to adsorption to the lipid bilayer and to electrostatic interactions with the lipid bilayer as peptides are translocated. Translocation takes place in three main stages; the insertion of the N-terminus into the bilayer, the inclusion of the whole peptide inside the membrane and the exit of the N-terminus from the bilayer. These three stages mirror the three regions on pVEC; namely, the hydrophobic N-terminus, the cationic midsection, and the hydrophilic C-terminus. The N-terminal truncated pVEC, I3A, L5A, R7A mutants and scramble-pVEC make weaker interactions with the lipids during translocation highlighting the contribution of the N-terminal residues and the sequence of the structural regions to the translocation mechanism. This study provides atomistic detail about the mechanism of pVEC peptide translocation and can guide future peptide-based drug design efforts.
DOI: 10.6084/m9.figshare.3117733
title: Clinicopathological characterization and genomic sequence differences observed in a highly virulent fowl <i>Aviadenovirus</i> serotype 4

description: Highly virulent fowl aviadenoviruses (genus: <i>Aviadenovirus</i>) represent a significant risk in poultry farming that may contribute to increased mortality rates and may adversely affect the growth performance of poultry flocks. In this study, we performed the clinicopathological characterization of a FAdV strain SHP95 isolated from a commercial farm and its whole genome sequencing. The study revealed that the isolated strain is a highly virulent serotype 4 FAdV that can cause 100% mortality in day-old specific pathogen free (SPF) chickens with a dose of 2.5 × 10<sup>5</sup> TCID<sub>50</sub>. At a lower viral dose (1.5 × 10<sup>4</sup> TCID<sub>50</sub>), the infection in day-old SPF chickens caused 40% mortality and lesions characteristic for Hepatitis-hydropericardium syndrome (HHS). The viral strain was detectable by real time PCR in chicken organs, including the lymphoid organs until day 28 after infection. The whole genome assembly of strain SHP95 revealed a size of 45,641 bp, which encodes for 42 viral open reading frame (ORF). The comparative analysis in the genome shows 98.1% similarity between strain SHP95 and other FAdV-4 genomes reported. The major differences in the genome sequence between pathogenic and non-pathogenic fowl Adenovirus were identified in the right arm of the genome.
DOI: 10.6084/m9.figshare.3117733.v1
title: Clinicopathological characterization and genomic sequence differences observed in a highly virulent fowl <i>Aviadenovirus</i> serotype 4

description: Highly virulent fowl aviadenoviruses (genus: <i>Aviadenovirus</i>) represent a significant risk in poultry farming that may contribute to increased mortality rates and may adversely affect the growth performance of poultry flocks. In this study, we performed the clinicopathological characterization of a FAdV strain SHP95 isolated from a commercial farm and its whole genome sequencing. The study revealed that the isolated strain is a highly virulent serotype 4 FAdV that can cause 100% mortality in day-old specific pathogen free (SPF) chickens with a dose of 2.5 × 10<sup>5</sup> TCID<sub>50</sub>. At a lower viral dose (1.5 × 10<sup>4</sup> TCID<sub>50</sub>), the infection in day-old SPF chickens caused 40% mortality and lesions characteristic for Hepatitis-hydropericardium syndrome (HHS). The viral strain was detectable by real time PCR in chicken organs, including the lymphoid organs until day 28 after infection. The whole genome assembly of strain SHP95 revealed a size of 45,641 bp, which encodes for 42 viral open reading frame (ORF). The comparative analysis in the genome shows 98.1% similarity between strain SHP95 and other FAdV-4 genomes reported. The major differences in the genome sequence between pathogenic and non-pathogenic fowl Adenovirus were identified in the right arm of the genome.
DOI: 10.6084/m9.figshare.3117673
title: Swissparam CHARMM parameter file for Pam3CSK4, and CU-T12-9.

description: Swiss param [http://swissparam.ch/] CHARMM parameter files for Pam3CSK4, and CU-T12-9.
DOI: 10.6084/m9.figshare.3117685
title: Models and Advantages of Gratis Open Access

description: This approved BA thesis discusses economically realizable Open Access (OA) publishing models. First, the advantages of and need for OA in scholarly discourse will be addressed. Afterwards, I will discuss the routes to widespread gold (access provided by publishers) and green (access provided by repositories) OA. By drawing from examples in the contemporary landscape of academic publishing, several routes to universal free access to scientific literature (i.e. the green route to gold OA, the hybrid route to gold OA, and gold OA enabled by authors, libraries, institutions and publishers) will be elaborated on and compared.
DOI: 10.6084/m9.figshare.3117685.v1
title: Models and Advantages of Gratis Open Access

description: This approved BA thesis discusses economically realizable Open Access (OA) publishing models. First, the advantages of and need for OA in scholarly discourse will be addressed. Afterwards, I will discuss the routes to widespread gold (access provided by publishers) and green (access provided by repositories) OA. By drawing from examples in the contemporary landscape of academic publishing, several routes to universal free access to scientific literature (i.e. the green route to gold OA, the hybrid route to gold OA, and gold OA enabled by authors, libraries, institutions and publishers) will be elaborated on and compared.
DOI: 10.6084/m9.figshare.3117523
title: TBNA data pone.xlsx

description: TBNA data before and after the introduction of EBUS<br>
DOI: 10.6084/m9.figshare.3117523.v1
title: TBNA data pone.xlsx

description: TBNA data before and after the introduction of EBUS<br>
DOI: 10.4225/03/56ea3afb1705a
title: Supplement 1.docx

description: To date, the evaluation of expanded uncertainty is handled exclusively by Monte Carlo (MC) method. However, there are cases where MC cannot be applied and thus alternative methods are necessary. One typical scenario is when type-A evaluation is required. Currently, the only other mainstream solution is to identify an appropriate distribution based on the information obtained from the high-order moments of the data.<br>On the other hand, there is currently no comprehensive test distributions that exist to standardize the performance evaluation of moment-based distribution fitting techniques. Without such benchmark test distributions, it is not possible to compare the performance of one technique to the other. Therefore, while the fitting techniques can be reliably used for distributions that are close to the previously tested distributions, there is insufficient information on their performance for other distributions.<br>For that reason, the objective of the set of distributions in given here is to establish a benchmark distribution set and a framework for performance comparison between various parametric distribution fitting methods especially for expanded uncertainty estimation. A fitting technique can be assessed easily using the framework shown in the reference article given under <i>References</i>. The Distribution List and Distribution Solution can be obtained from this uploaded supplementary document.
DOI: 10.6084/m9.figshare.3117490
title: DATA

description: BL plots data
DOI: 10.6084/m9.figshare.3117490.v1
title: DATA

description: BL plots data
DOI: 10.6084/m9.figshare.3117430
title: Skinfriction plots Data

description: skin friction plots for various turbulence models
DOI: 10.6084/m9.figshare.3117427
title: Cp Plots data

description: cp plots of various turbulence models<br>
DOI: 10.6084/m9.figshare.3117406
title: Assembly of Biomphalaria glabrata embryonic transcriptome, '100plusbpContigsFasta' file accompanying the Kenny et al 2016 paper

description: Assembly of mixed Biomphalaria glabrata embryonic transcriptome, from schistosome-free individuals. This assembly is linked to the Kenny et al 2016 paper, BMC Infectious Diseases.<br>
DOI: 10.6084/m9.figshare.3117430.v1
title: Skinfriction plots Data

description: skin friction plots for various turbulence models
DOI: 10.6084/m9.figshare.3117397
title: BL plot S-A

description: BL plot
DOI: 10.6084/m9.figshare.3117394
title: BL plot k- omega SSt

description: BL plot
DOI: 10.6084/m9.figshare.3117397.v1
title: BL plot S-A

description: BL plot
DOI: 10.6084/m9.figshare.3117400
title: BL plot Transition SST

description: BL plot
DOI: 10.6084/m9.figshare.3117406.v1
title: Assembly of Biomphalaria glabrata embryonic transcriptome, '100plusbpContigsFasta' file accompanying the Kenny et al 2016 paper

description: Assembly of mixed Biomphalaria glabrata embryonic transcriptome, from schistosome-free individuals. This assembly is linked to the Kenny et al 2016 paper, BMC Infectious Diseases.<br>
DOI: 10.6084/m9.figshare.3117388
title: BL plot gama SST

description: BL plot
DOI: 10.6084/m9.figshare.3117391
title: BL plot K KL omega

description: BL plot
DOI: 10.6084/m9.figshare.3117388.v1
title: BL plot gama SST

description: BL plot
DOI: 10.6084/m9.figshare.3117391.v1
title: BL plot K KL omega

description: BL plot
DOI: 10.6084/m9.figshare.3117394.v1
title: BL plot k- omega SSt

description: BL plot
DOI: 10.6084/m9.figshare.3117400.v1
title: BL plot Transition SST

description: BL plot
DOI: 10.6084/m9.figshare.3117373
title: A Multi-Level Trend-Renewal Process for Modeling Systems With Recurrence Data

description: A repairable system is a system that can be restored to an operational state after a repair event. The system may experience multiple events over time that are called recurrent events. To model the recurrent event data, the renewal process (RP), the nonhomogenous Poisson process (NHPP), and the trend-renewal process (TRP) are often used. Compared to the RP and NHPP, the TRP is more flexible for modeling, because it includes both RP and NHPP as special cases. However, for a multi-level system (e.g., system, subsystem, and component levels), the original TRP model may not be adequate if the repair is effected by a subsystem replacement and if subsystem-level replacement events affect the rate of occurrence of the component-level replacement events. In this article, we propose a general class of models to describe replacement events in a multi-level repairable system by extending the TRP model. We also develop procedures for parameter estimation and the prediction of future events based on historical data. The proposed model and method are validated by simulation studies and are illustrated by an industrial application. This article has online supplementary materials.
DOI: 10.6084/m9.figshare.3117352
title: Variational Approximations for Generalized Linear Latent Variable Models

description: Generalized linear latent variable models (GLLVMs) are a powerful class of models for understanding the relationships among multiple, correlated responses. Estimation, however, presents a major challenge, as the marginal likelihood does not possess a closed form for nonnormal responses. We propose a variational approximation (VA) method for estimating GLLVMs. For the common cases of binary, ordinal, and overdispersed count data, we derive fully closed-form approximations to the marginal log-likelihood function in each case. Compared to other methods such as the expectation-maximization algorithm, estimation using VA is fast and straightforward to implement. Predictions of the latent variables and associated uncertainty estimates are also obtained as part of the estimation process. Simulations show that VA estimation performs similar to or better than some currently available methods, both at predicting the latent variables and estimating their corresponding coefficients. They also show that VA estimation offers dramatic reductions in computation time particularly if the number of correlated responses is large relative to the number of observational units. We apply the variational approach to two datasets, estimating GLLVMs to understanding the patterns of variation in youth gratitude and for constructing ordination plots in bird abundance data. R code for performing VA estimation of GLLVMs is available online. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3117373.v2
title: A Multi-Level Trend-Renewal Process for Modeling Systems With Recurrence Data

description: A repairable system is a system that can be restored to an operational state after a repair event. The system may experience multiple events over time that are called recurrent events. To model the recurrent event data, the renewal process (RP), the nonhomogenous Poisson process (NHPP), and the trend-renewal process (TRP) are often used. Compared to the RP and NHPP, the TRP is more flexible for modeling, because it includes both RP and NHPP as special cases. However, for a multi-level system (e.g., system, subsystem, and component levels), the original TRP model may not be adequate if the repair is effected by a subsystem replacement and if subsystem-level replacement events affect the rate of occurrence of the component-level replacement events. In this article, we propose a general class of models to describe replacement events in a multi-level repairable system by extending the TRP model. We also develop procedures for parameter estimation and the prediction of future events based on historical data. The proposed model and method are validated by simulation studies and are illustrated by an industrial application. This article has online supplementary materials.
DOI: 10.6084/m9.figshare.3117352.v1
title: Variational Approximations for Generalized Linear Latent Variable Models

description: Generalized linear latent variable models (GLLVMs) are a powerful class of models for understanding the relationships among multiple, correlated responses. Estimation, however, presents a major challenge, as the marginal likelihood does not possess a closed form for nonnormal responses. We propose a variational approximation (VA) method for estimating GLLVMs. For the common cases of binary, ordinal, and overdispersed count data, we derive fully closed-form approximations to the marginal log-likelihood function in each case. Compared to other methods such as the expectation-maximization algorithm, estimation using VA is fast and straightforward to implement. Predictions of the latent variables and associated uncertainty estimates are also obtained as part of the estimation process. Simulations show that VA estimation performs similar to or better than some currently available methods, both at predicting the latent variables and estimating their corresponding coefficients. They also show that VA estimation offers dramatic reductions in computation time particularly if the number of correlated responses is large relative to the number of observational units. We apply the variational approach to two datasets, estimating GLLVMs to understanding the patterns of variation in youth gratitude and for constructing ordination plots in bird abundance data. R code for performing VA estimation of GLLVMs is available online. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3117340
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
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.3117373.v1
title: A Multi-level Trend-Renewal Process for Modeling Systems with Recurrence Data

description: A repairable system is a system that can be restored to an operational state after a repair event. The system may experience multiple events over time, which are called recurrent events. To model the recurrent event data, the renewal process (RP), the nonhomogeneous Poisson process (NHPP), and the trend-renewal process (TRP) are often used. Compared to the RP and NHPP, the TRP is more flexible for modeling, because it includes both RP and NHPP as special cases. However, for a multi-level system (e.g., system, subsystem, and component levels), the original TRP model may not be adequate if the repair is effected by a subsystem replacement and if subsystem-level replacement events affect the rate of occurrence of the component-level replacement events. In this paper, we propose a general class of models to describe replacement events in a multi-level repairable system by extending the TRP model. We also develop procedures for parameter estimation and the prediction of future events based on historical data. The proposed model and method are validated by simulation studies and are illustrated by an industrial application. This paper has online supplementary materials.
DOI: 10.6084/m9.figshare.3117313
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.3117316
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.