cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1623209.v2
title: ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing <i>in vivo</i>

description: Adenosine deaminases bind double stranded RNA and convert adenosine to inosine. Editing creates multiple isoforms of neurotransmitter receptors, such as with <i>Gria2</i>. <i>Adar2</i> KO mice die of seizures shortly after birth, but if the <i>Gria2</i> Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on frontal cortices of <i>Adar2</i><sup>-/-</sup> <i>Gria2</i><sup>R/R</sup> mice and littermates. We found 56 editing sites with significantly diminished editing levels in <i>Adar2</i> deficient animals with the majority in coding regions. Only two genes and 3 exons showed statistically significant differences in expression levels. This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has relatively modest effects on gene expression and splicing in the adult mouse frontal cortex.
DOI: 10.6084/m9.figshare.1623210.v2
title: CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

description: Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.
DOI: 10.6084/m9.figshare.1623210.v1
title: CircInteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs

description: ABSTRACTCircular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.
DOI: 10.6084/m9.figshare.1623209.v1
title: ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo

description: Adenosine deaminases bind double stranded RNA and convert adenosine to inosine. Editing creates multiple isoforms of neurotransmitter receptors, such as with <i>Gria2</i>. <i>Adar2</i> KO mice die of seizures shortly after birth, but if the <i>Gria2</i> Q/R editing site is mutated to mimic the edited version then the animals are viable. We performed RNA-Seq on frontal cortices of <i>Adar2</i><sup>−/−</sup><i>Gria2</i><sup>R/R</sup>mice and littermates. We found 56 editing sites with significantly diminished editing levels in <i>Adar2</i> deficient animals with the majority in coding regions. Only two genes and three exons showed statistically significant differences in expression levels. This work illustrates that ADAR2 is important in site-specific changes of protein coding sequences but has relatively modest effects on gene expression and splicing in the adult mouse frontal cortex.
DOI: 10.6084/m9.figshare.1623201.v2
title: Assessment of the convergence of partially self-consistent BSE/<i>GW</i> calculations

description: The most applied <i>ab initio</i> method to determine the transition energies to electronically excited states, namely time-dependent density functional theory (TD-DFT), is now well mastered, but alternative approaches can be necessary to circumvent some of the specific limitations of TD-DFT. In that framework, the Bethe–Salpeter method, following a <i>GW</i> calculation of quasiparticle energies, is certainly an attractive approach with the same scaling with system size as TD-DFT, though its accuracy remains to be completely defined, at least for molecular systems. In the present work, we investigate the performances of a partially self-consistent BSE/<i>GW</i> approach in which the starting DFT eigenvalues (but not eigenvectors) are updated. We particularly focus on the convergence of the calculations, the residual impact of the starting eigenstates and the selection of an adequate atomic basis set. This study provides some guidelines allowing to apply BSE/<i>GW</i> in a computationally efficient way and also highlights some limitations of the non-self-consistent BSE/<i>G</i><sub>0</sub><i>W</i><sub>0</sub> approach.
DOI: 10.6084/m9.figshare.1623201
title: Assessment of the convergence of partially self-consistent BSE/<i>GW</i> calculations

description: The most applied <i>ab initio</i> method to determine the transition energies to electronically excited states, namely time-dependent density functional theory (TD-DFT), is now well mastered, but alternative approaches can be necessary to circumvent some of the specific limitations of TD-DFT. In that framework, the Bethe–Salpeter method, following a <i>GW</i> calculation of quasiparticle energies, is certainly an attractive approach with the same scaling with system size as TD-DFT, though its accuracy remains to be completely defined, at least for molecular systems. In the present work, we investigate the performances of a partially self-consistent BSE/<i>GW</i> approach in which the starting DFT eigenvalues (but not eigenvectors) are updated. We particularly focus on the convergence of the calculations, the residual impact of the starting eigenstates and the selection of an adequate atomic basis set. This study provides some guidelines allowing to apply BSE/<i>GW</i> in a computationally efficient way and also highlights some limitations of the non-self-consistent BSE/<i>G</i><sub>0</sub><i>W</i><sub>0</sub> approach.
DOI: 10.6084/m9.figshare.1623201.v1
title: Assessment of the convergence of partially self-consistent BSE/<i>GW</i> calculations

description: The most applied <i>ab initio</i> method to determine the transition energies to electronically excited states, namely time-dependent density functional theory (TD-DFT), is now well mastered, but alternative approaches can be necessary to circumvent some of the specific limitations of TD-DFT. In that framework, the Bethe–Salpeter method, following a <i>GW</i> calculation of quasiparticle energies, is certainly an attractive approach with the same scaling with system size as TD-DFT, though its accuracy remains to be completely defined, at least for molecular systems. In the present work, we investigate the performances of a partially self-consistent BSE/<i>GW</i> approach in which the starting DFT eigenvalues (but not eigenvectors) are updated. We particularly focus on the convergence of the calculations, the residual impact of the starting eigenstates and the selection of an adequate atomic basis set. This study provides some guidelines allowing to apply BSE/<i>GW</i> in a computationally efficient way and also highlights some limitations of the non-self-consistent BSE/<i>G</i><sub>0</sub><i>W</i><sub>0</sub> approach.
DOI: 10.17632/v2p3th8pb5.1
title: Data for: Failure Analysis of Feed Water Pump Shaft in HRSG of 9F Gas Turbine Generator Unit

description: macrophotograph，fracture morphology，microstructure，mechanical property
DOI: 10.6084/m9.figshare.1623192
title: The allocation of household-based forest protection contracts in Tam Dao National Park, Vietnam: Elite capture as a bureaucratic impulse against community capture

description: ABSTRACTThis article examines the characteristics of households that were allocated paid forest protection contracts in Tam Dao National Park situated in northern Vietnam. Its research indicates that the national park management board systematically favored households with weaker community ties in their contract allocations. Furthermore, the article argues that the national park management board took a defensive stance against buffer zone communes resisting park policy and that they also attempted to manage forest conservation by centralizing the allocation and management of forest protection contracts. These circumstances led to an inequitable distribution of rights and continued land use inside the park, as contract holders were powerless to enforce park regulations.
DOI: 10.6084/m9.figshare.1623192.v1
title: The allocation of household-based forest protection contracts in Tam Dao National Park, Vietnam: Elite capture as a bureaucratic impulse against community capture

description: ABSTRACTThis article examines the characteristics of households that were allocated paid forest protection contracts in Tam Dao National Park situated in northern Vietnam. Its research indicates that the national park management board systematically favored households with weaker community ties in their contract allocations. Furthermore, the article argues that the national park management board took a defensive stance against buffer zone communes resisting park policy and that they also attempted to manage forest conservation by centralizing the allocation and management of forest protection contracts. These circumstances led to an inequitable distribution of rights and continued land use inside the park, as contract holders were powerless to enforce park regulations.
DOI: 10.6084/m9.figshare.1623185
title: Multivariate Seasonal Adjustment, Economic Identities, and Seasonal Taxonomy

description: This article extends the methodology for multivariate seasonal adjustment by exploring the statistical modeling of seasonality jointly across multiple time series, using latent dynamic factor models fitted using maximum likelihood estimation. Signal extraction methods for the series then allow us to calculate a model-based seasonal adjustment. We emphasize several facets of our analysis: (i) we quantify the efficiency gain in multivariate signal extraction versus univariate approaches; (ii) we address the problem of the preservation of economic identities; (iii) we describe a foray into seasonal taxonomy via the device of seasonal co-integration rank. These contributions are developed through two empirical studies of aggregate U.S. retail trade series and U.S. regional housing starts. Our analysis identifies different seasonal subcomponents that are able to capture the transition from prerecession to postrecession seasonal patterns. We also address the topic of indirect seasonal adjustment by analyzing the regional aggregate series. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1623184
title: A Functional Estimate of Covariation

description: The analysis of functional data calls for a bivariate functional covariance function σ(<i>s</i>, <i>t</i>) that may be evaluated at any discrete set of points to define a variance-covariance matrix Σ. This article uses finite element methodology to construct a representation of a functional Choleski factor λ(<i>w</i>, <i>s</i>) to define σ(<i>s</i>, <i>t</i>) = ∫λ(<i>w</i>, <i>s</i>)λ(<i>w</i>, <i>t</i>) <i>dw</i>. An estimate of Σ-1 is especially important for applications and, where the eigenstructure of the covariance permits, this is readily available since the resulting Σ is almost always positive definite. A simulation study compares the performance of estimates of Σ and Σ-1 to those from the classic covariance matrix estimate and an estimate using glasso package in R. The method’s capability of constraining estimates of Σ-1 to be strongly band-structured resulted in superior estimates. The real data application is to the smoothing of the Fels female growth data where σ(<i>s</i>, <i>t</i>) estimates the residual covariance structure in the presence of sampling points varying from one case to another. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.1623185.v1
title: Multivariate Seasonal Adjustment, Economic Identities, and Seasonal Taxonomy

description: This article extends the methodology for multivariate seasonal adjustment by exploring the statistical modeling of seasonality jointly across multiple time series, using latent dynamic factor models fitted using maximum likelihood estimation. Signal extraction methods for the series then allow us to calculate a model-based seasonal adjustment. We emphasize several facets of our analysis: (i) we quantify the efficiency gain in multivariate signal extraction versus univariate approaches; (ii) we address the problem of the preservation of economic identities; (iii) we describe a foray into seasonal taxonomy via the device of seasonal co-integration rank. These contributions are developed through two empirical studies of aggregate U.S. retail trade series and U.S. regional housing starts. Our analysis identifies different seasonal subcomponents that are able to capture the transition from prerecession to postrecession seasonal patterns. We also address the topic of indirect seasonal adjustment by analyzing the regional aggregate series. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1623184.v1
title: A Functional Estimate of Covariation

description: The analysis of functional data calls for a bivariate functional covariance function σ(<i>s</i>, <i>t</i>) that may be evaluated at any discrete set of points to define a variance-covariance matrix Σ. This article uses finite element methodology to construct a representation of a functional Choleski factor λ(<i>w</i>, <i>s</i>) to define σ(<i>s</i>, <i>t</i>) = ∫λ(<i>w</i>, <i>s</i>)λ(<i>w</i>, <i>t</i>) <i>dw</i>. An estimate of Σ-1 is especially important for applications and, where the eigenstructure of the covariance permits, this is readily available since the resulting Σ is almost always positive definite. A simulation study compares the performance of estimates of Σ and Σ-1 to those from the classic covariance matrix estimate and an estimate using glasso package in R. The method’s capability of constraining estimates of Σ-1 to be strongly band-structured resulted in superior estimates. The real data application is to the smoothing of the Fels female growth data where σ(<i>s</i>, <i>t</i>) estimates the residual covariance structure in the presence of sampling points varying from one case to another. Supplementary materials are available online.
DOI: 10.6084/m9.figshare.1623181
title: The Effect of Counseling on Cataract Patient Knowledge, Decisional Conflict, and Satisfaction

description: <i>Purpose</i>: Cataract is the leading cause of non-refractive preventable blindness, and comprehensive strategies to increase cataract surgery rates are imperative, including high-quality supportive patient education. We evaluated the effectiveness of non-physician pre-surgical counselors teaching patients about cataract and cataract surgery in improving patient knowledge, decisional conflict, and satisfaction. <i>Methods</i>: A survey was given before and after 61 newly-diagnosed cataract patients underwent pre-surgical counseling at the Aravind Eye Hospital, Madurai, India. The survey measured change in cataract knowledge and decisional conflict, a measure of anxiety surrounding the decision to undergo surgery, along with patient satisfaction. Multiple regression was used to identify factors that influenced change in knowledge. <i>Results</i>: Both patient knowledge scores and decisional conflict scores improved following counseling (mean difference +2.0, <i>p</i> = 0.004 and +8.4, <i>p</i> p p = 0.04) as important predictors of increased knowledge post-counseling. <i>Conclusion</i>: Counseling both improved knowledge and reduced decisional conflict about cataract surgery, particularly among patients who had traditionally had more limited access to healthcare such as women and illiterate patients. Increased use of high quality counseling might help to further reduce the global burden of cataract and other forms of blindness.
DOI: 10.6084/m9.figshare.1623181.v1
title: The Effect of Counseling on Cataract Patient Knowledge, Decisional Conflict, and Satisfaction

description: <i>Purpose</i>: Cataract is the leading cause of non-refractive preventable blindness, and comprehensive strategies to increase cataract surgery rates are imperative, including high-quality supportive patient education. We evaluated the effectiveness of non-physician pre-surgical counselors teaching patients about cataract and cataract surgery in improving patient knowledge, decisional conflict, and satisfaction. <i>Methods</i>: A survey was given before and after 61 newly-diagnosed cataract patients underwent pre-surgical counseling at the Aravind Eye Hospital, Madurai, India. The survey measured change in cataract knowledge and decisional conflict, a measure of anxiety surrounding the decision to undergo surgery, along with patient satisfaction. Multiple regression was used to identify factors that influenced change in knowledge. <i>Results</i>: Both patient knowledge scores and decisional conflict scores improved following counseling (mean difference +2.0, <i>p</i> = 0.004 and +8.4, <i>p</i> p p = 0.04) as important predictors of increased knowledge post-counseling. <i>Conclusion</i>: Counseling both improved knowledge and reduced decisional conflict about cataract surgery, particularly among patients who had traditionally had more limited access to healthcare such as women and illiterate patients. Increased use of high quality counseling might help to further reduce the global burden of cataract and other forms of blindness.
DOI: 10.6084/m9.figshare.1623178
title: The effect of Invisalign® use on mouth alcohol retention

description: ABSTRACTThree Invisalign®-wearing, alcohol-free subjects were tested for mouth alcohol retention with an Alco-Sensor® IV breath alcohol analyzer (Intoximeters, Inc.). The subjects were given a tolerable amount of beer, wine, or a distilled spirit to swish in their mouths, without swallowing for one minute. The subjects were tested with and without their Invisalign® device in place. In most cases the concentration of alcohol in the mouth was zero 15 minutes post-expectoration in both the controlled and experimental sessions with small to trace amounts of mouth alcohol (≤ 0.016 g/210 L) in several sessions. Based on these findings, Invisalign® use does not significantly affect breath alcohol concentration when a pretest alcohol deprivation period of 15 minutes is performed.
DOI: 10.6084/m9.figshare.1623175
title: The ammonoids from the Late Permian <i>Paratirolites</i> Limestone of Julfa (East Azerbaijan, Iran)

description: The Changhsingian (Late Permian), 4 to 5 m thick <i>Paratirolites</i> Limestone has yielded diverse ammonoid assemblages composed of the genera <i>Neoaganides</i>, <i>Pseudogastrioceras</i>, <i>Dzhulfites</i>, <i>Paratirolites</i>, <i>Julfotirolites</i>, <i>Alibashites</i>, <i>Abichites</i>, <i>Stoyanowites</i> and <i>Arasella</i>. The succession of ammonoid species allows for a subdivision of the rock unit into eight biozones, in ascending order: <i>Dzhulfites zalensis</i> Zone, <i>Paratirolites trapezoidalis</i> Zone, <i>Paratirolites kittli</i> Zone, <i>Stoyanowites dieneri</i> Zone, <i>Alibashites mojsisovicsi</i> Zone, <i>Abichites abichi</i> Zone, <i>Abichites stoyanowi</i> Zone and <i>Arasella minuta</i> Zone. The following 20 new species are described by two of us (DK and AG): <i>Neoaganides ultimus</i> sp. nov., <i>Pseudogastrioceras relicuum</i> sp. nov., <i>Dzhulfites zalensis</i> sp. nov., <i>Dzhulfites hebes</i> sp. nov., <i>Paratirolites coronatus</i> sp. nov., <i>Paratirolites birunii</i> sp. nov., <i>Paratirolites quadratus</i> sp. nov., <i>Paratirolites multiconus</i> sp. nov., <i>Paratirolites serus</i> sp. nov., <i>Julfotirolites kozuri</i> sp. nov., <i>Alibashites ferdowsii</i> sp. nov., <i>Alibashites uncinatus</i> sp. nov., <i>Alibashites stepanovi</i> sp. nov., <i>Abichites subtrapezoidalis</i> sp. nov., <i>Abichites alibashiensis</i> sp. nov., <i>Abichites ariaeii</i> sp. nov., <i>Abichites paucinodus</i> sp. nov., <i>Abichites shahriari</i> sp. nov., <i>Abichites terminalis</i> sp. nov. and <i>Stoyanowites aspinosus</i> sp. nov. After the time-equivalent Chinese occurrences, the material described here is the most diverse assemblage known from the critical interval before the end-Permian mass extinction. http://zoobank.org/urn:lsid:zoobank.org:pub:75D71EE8-27A2-48B1-805B-52E98578A7B8
DOI: 10.6084/m9.figshare.1623176
title: Pre-ovipositional and ovipositional behaviour of <i>Lasioseius ometes</i> (Oudemans) and <i>Hypoaspis kargi</i> Costa (Acari: Dermanyssiae: Ascidae, Laelapidae) with notes on egg protection strategies in Mesostigmata

description: Egg deposition by the soil mites <i>Lasioseius ometes</i> (Oudemans, 1903) and <i>Hypoaspis kargi</i> Costa, 1968 was observed using continuous video-monitoring. The process in both species was found to consist of four distinct phases. In Phase 1, both species engage in pre-ovipositional activity prior to the egg being extruded from the genital opening. In <i>L. ometes</i>, the female often selects a substrate depression for egg laying and examines the depression carefully with the gnathosoma and legs I before oviposition. In <i>H. kargi</i>, egg deposition sites are chosen without regard for substrate depressions. Phase 1 lasted approximately 3 minutes for both species. Phase 2 involved egg extrusion and holding of the egg beneath the gnathosoma. Phase 2 lasted approximately 20 times longer in <i>L. ometes</i> (5 minutes) than in <i>H. kargi</i>. Alteration of the egg surface in the form of thorn-like outgrowths was recorded in <i>L. ometes</i>. Egg deposition occurs in Phase 3, and in <i>L. ometes</i> the egg is generally placed at the deposition site using the chelicerae. <i>Hypoaspis kargi</i> also uses the chelicerae for egg manipulation, but also adjusts orientation of the egg with legs I. The sticky nature of egg surface in <i>H. kargi</i> may provide a means for the female to effectively cover the exposed egg with a protective layer of soil particles. Egg deposition in both species occurred in less than 90 seconds. Phase 4 involves egg covering, but behaviour of the female during this last phase differs markedly between the two species. In <i>L. ometes</i>, the female tends to remain close to the egg, whereas in <i>H. kargi</i> the female moves away from the egg to search for substrate particles appropriate for its covering. The average time for Phase 4 in <i>H. kargi</i> was approximately four times longer (80+ minutes) than in <i>L. ometes</i>.