cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569221.v4
title: Premature termination of <i>GAT1</i> transcription explains paradoxical negative correlation between nitrogen-responsive mRNA, but constitutive low-level protein production

description: The first step in executing the genetic program of a cell is production of mRNA. In yeast, almost every gene is transcribed as multiple distinct isoforms, differing at their 5′ and/or 3′ termini. However, the implications and functional significance of the transcriptome-wide diversity of mRNA termini remains largely unexplored. In this paper, we show that the <i>GAT1</i> gene, encoding a transcriptional activator of nitrogen-responsive catabolic genes, produces a variety of mRNAs differing in their 5′ and 3′ termini. Alternative transcription initiation leads to the constitutive, low level production of 2 full length proteins differing in their N-termini, whereas premature transcriptional termination generates a short, highly nitrogen catabolite repression- (NCR-) sensitive transcript that, as far as we can determine, is not translated under the growth conditions we used, but rather likely protects the cell from excess Gat1.
DOI: 10.6084/m9.figshare.1569204.v1
title: Development of formulae for estimating amylose content and resistant starch content based on the pasting properties measured by RVA of <i>Japonica</i> polished rice and starch

description: We searched for the easy and simple method to measure the novel indicators which reflect not only AAC, but also (RS) based on pasting properties using RVA. Novel indexes such as SB/Con and Max/Fin (Maximum viscosity/Minimum viscosity) ratios had a very high correlation with proportion of intermediate and long chains of amylopectin; Fb<sub>1+2+3</sub> (DP ≧ 13). In <i>Japonica</i> polished rice, estimation formulae for AAC and RS content were developed using novel indexes based on pasting properties by RVA, and these equations showed determination coefficients of 0.89 and 0.80 for calibration and 0.71 and 0.75 for validation test. We developed the estimation formulae for AAC and RS content for <i>Japonica</i> starch samples. These equations showed determination coefficients of 0.86 and 1.00 for calibration and 0.76 and 0.83 for validation test, which showed that these equations can be applied to the unknown rice samples.
DOI: 10.6084/m9.figshare.1569221.v3
title: Premature termination of <i>GAT1</i> transcription explains paradoxical negative correlation between nitrogen-responsive mRNA, but constitutive low-level protein production

description: The first step in executing the genetic program of a cell is production of mRNA. In yeast, almost every gene is transcribed as multiple distinct isoforms, differing at their 5′ and/or 3′ termini. However, the implications and functional significance of the transcriptome-wide diversity of mRNA termini remains largely unexplored. In this paper, we show that the <i>GAT1</i> gene, encoding a transcriptional activator of nitrogen-responsive catabolic genes, produces a variety of mRNAs differing in their 5′ and 3′ termini. Alternative transcription initiation leads to the constitutive, low level production of 2 full length proteins differing in their N-termini, whereas premature transcriptional termination generates a short, highly nitrogen catabolite repression- (NCR-) sensitive transcript that, as far as we can determine, is not translated under the growth conditions we used, but rather likely protects the cell from excess Gat1.
DOI: 10.6084/m9.figshare.1569205.v1
title: Experimental investigation of the effect of occupant characteristics on contemporary seatbelt payout behavior in frontal impacts

description: Objective: The goal of this study was to investigate the influence of the occupant characteristics on seatbelt force vs. payout behaviour based on experiment data from different configurations in frontal impacts. Methods: The dataset reviewed consists of fifty-eight frontal sled tests using several anthropomorphic test devices (ATDs) and post-mortem human subjects (PMHS), restrained by different belt systems (standard belt, SB; force-limiting belt, FLB) at two impact severities (48 km/h and 29 km/h). The seatbelt behavior was characterized in term of the shoulder belt force vs. belt payout behavior. A univariate linear regression was used to assess the factor significance of the occupant body mass or stature on the peak tension force and gross belt payout. Results: With the SB, the seatbelt behavior obtained by the ATDs exhibited similar force slopes regardless of the occupant size and impact severities, while those obtained by the PMHS were varied. Under the 48 km/h impact, the peak tension force and gross belt payout obtained by ATDs was highly correlated to the occupant stature (<i>p</i> = 0.03, <i>p</i> = 0.02) and body mass (<i>p</i> = 0.05, p = 0.04), while no statistical difference with the stature or body mass were noticed for PMHS (peak force: <i>p</i> = 0.09, <i>p</i> = 0.42; gross payout: <i>p</i> = 0.40, <i>p</i> = 0.48). With the FLB under the 48 km/h impact, highly linear relationships were noticed between the occupant body mass and the peak tension force (<i>R</i><sup>2</sup> = 0.9782) and between the gross payout and the stature (<i>R</i><sup>2</sup> = 0.9232) regardless of the occupant types. Conclusions: The analysis indicated that the PMHS characteristics showed significant influence on the belt response, while the belt response obtained with the ATDs were more reproducible. The potentialcause included the occupant anthropometry, the body mass distribution and the relative motion among body segments specific to the population variance. This study provided a primary data source to understand the biomechanical interaction of the occupant with the restraint system. Further research is necessary to consider these effects in the computational studies and optimized design of the restraint system in a more realistic manner.
DOI: 10.6084/m9.figshare.1569205
title: Experimental investigation of the effect of occupant characteristics on contemporary seat belt payout behavior in frontal impacts

description: <b>Objective:</b> The goal of this study was to investigate the influence of the occupant characteristics on seat belt force vs. payout behavior based on experiment data from different configurations in frontal impacts. <b>Methods:</b> The data set reviewed consists of 58 frontal sled tests using several anthropomorphic test devices (ATDs) and postmortem human subjects (PMHS), restrained by different belt systems (standard belt, SB; force-limiting belt, FLB) at 2 impact severities (48 and 29 km/h). The seat belt behavior was characterized in terms of the shoulder belt force vs. belt payout behavior. A univariate linear regression was used to assess the factor significance of the occupant body mass or stature on the peak tension force and gross belt payout. <b>Results:</b> With the SB, the seat belt behavior obtained by the ATDs exhibited similar force slopes regardless of the occupant size and impact severities, whereas those obtained by the PMHS were varied. Under the 48 km/h impact, the peak tension force and gross belt payout obtained by ATDs was highly correlated to the occupant stature (<i>P</i> =.03, <i>P</i> =.02) and body mass (<i>P</i> =.05, <i>P</i> =.04), though no statistical difference with the stature or body mass were noticed for the PMHS (peak force: <i>P</i> =.09, <i>P</i> =.42; gross payout: <i>P</i> =.40, <i>P</i> =.48). With the FLB under the 48 km/h impact, highly linear relationships were noticed between the occupant body mass and the peak tension force (<i>R</i><sup>2</sup> = 0.9782) and between the gross payout and stature (<i>R</i><sup>2</sup> = 0.9232) regardless of the occupant types. <b>Conclusions:</b> The analysis indicated that the PMHS characteristics showed a significant influence on the belt response, whereas the belt response obtained with the ATDs was more reproducible. The potential cause included the occupant anthropometry, body mass distribution, and relative motion among body segments specific to the population variance. This study provided a primary data source to understand the biomechanical interaction of the occupant with the restraint system. Further research is necessary to consider these effects in the computational studies and optimized design of the restraint system in a more realistic manner.
DOI: 10.6084/m9.figshare.1569205.v3
title: Experimental investigation of the effect of occupant characteristics on contemporary seat belt payout behavior in frontal impacts

description: <b>Objective:</b> The goal of this study was to investigate the influence of the occupant characteristics on seat belt force vs. payout behavior based on experiment data from different configurations in frontal impacts. <b>Methods:</b> The data set reviewed consists of 58 frontal sled tests using several anthropomorphic test devices (ATDs) and postmortem human subjects (PMHS), restrained by different belt systems (standard belt, SB; force-limiting belt, FLB) at 2 impact severities (48 and 29 km/h). The seat belt behavior was characterized in terms of the shoulder belt force vs. belt payout behavior. A univariate linear regression was used to assess the factor significance of the occupant body mass or stature on the peak tension force and gross belt payout. <b>Results:</b> With the SB, the seat belt behavior obtained by the ATDs exhibited similar force slopes regardless of the occupant size and impact severities, whereas those obtained by the PMHS were varied. Under the 48 km/h impact, the peak tension force and gross belt payout obtained by ATDs was highly correlated to the occupant stature (<i>P</i> =.03, <i>P</i> =.02) and body mass (<i>P</i> =.05, <i>P</i> =.04), though no statistical difference with the stature or body mass were noticed for the PMHS (peak force: <i>P</i> =.09, <i>P</i> =.42; gross payout: <i>P</i> =.40, <i>P</i> =.48). With the FLB under the 48 km/h impact, highly linear relationships were noticed between the occupant body mass and the peak tension force (<i>R</i><sup>2</sup> = 0.9782) and between the gross payout and stature (<i>R</i><sup>2</sup> = 0.9232) regardless of the occupant types. <b>Conclusions:</b> The analysis indicated that the PMHS characteristics showed a significant influence on the belt response, whereas the belt response obtained with the ATDs was more reproducible. The potential cause included the occupant anthropometry, body mass distribution, and relative motion among body segments specific to the population variance. This study provided a primary data source to understand the biomechanical interaction of the occupant with the restraint system. Further research is necessary to consider these effects in the computational studies and optimized design of the restraint system in a more realistic manner.
DOI: 10.6084/m9.figshare.1569205.v2
title: Experimental investigation of the effect of occupant characteristics on contemporary seatbelt payout behavior in frontal impacts

description: Objective: The goal of this study was to investigate the influence of the occupant characteristics on seatbelt force vs. payout behaviour based on experiment data from different configurations in frontal impacts. Methods: The dataset reviewed consists of fifty-eight frontal sled tests using several anthropomorphic test devices (ATDs) and post-mortem human subjects (PMHS), restrained by different belt systems (standard belt, SB; force-limiting belt, FLB) at two impact severities (48 km/h and 29 km/h). The seatbelt behavior was characterized in term of the shoulder belt force vs. belt payout behavior. A univariate linear regression was used to assess the factor significance of the occupant body mass or stature on the peak tension force and gross belt payout. Results: With the SB, the seatbelt behavior obtained by the ATDs exhibited similar force slopes regardless of the occupant size and impact severities, while those obtained by the PMHS were varied. Under the 48 km/h impact, the peak tension force and gross belt payout obtained by ATDs was highly correlated to the occupant stature (<i>p</i> = 0.03, <i>p</i> = 0.02) and body mass (<i>p</i> = 0.05, p = 0.04), while no statistical difference with the stature or body mass were noticed for PMHS (peak force: <i>p</i> = 0.09, <i>p</i> = 0.42; gross payout: <i>p</i> = 0.40, <i>p</i> = 0.48). With the FLB under the 48 km/h impact, highly linear relationships were noticed between the occupant body mass and the peak tension force (<i>R</i><sup>2</sup> = 0.9782) and between the gross payout and the stature (<i>R</i><sup>2</sup> = 0.9232) regardless of the occupant types. Conclusions: The analysis indicated that the PMHS characteristics showed significant influence on the belt response, while the belt response obtained with the ATDs were more reproducible. The potentialcause included the occupant anthropometry, the body mass distribution and the relative motion among body segments specific to the population variance. This study provided a primary data source to understand the biomechanical interaction of the occupant with the restraint system. Further research is necessary to consider these effects in the computational studies and optimized design of the restraint system in a more realistic manner.
DOI: 10.6084/m9.figshare.1569191.v1
title: Common γ-chain cytokine signaling is required for macroautophagy induction during CD4<sup>+</sup> T cell activation

description: Macroautophagy is a cellular process that mediates the degradation in the lysosome of cytoplasmic components including proteins and organelles. Previous studies have shown that macroautophagy is induced in activated T cells to regulate organelle homeostasis and the cell's energy metabolism. However, the signaling pathways that initiate and regulate activation-induced macroautophagy in T cells have not been identified. Herein, we show that activation-induced macroautophagy in T cells depends on signaling from common γ-chain cytokines. Consequently, inhibition of signaling through JAK3, induced downstream of cytokine receptors containing the common γ-chain, prevents full induction of macroautophagy in activated T cells. Moreover, we found that common γ-chain cytokines are not only required for macroautophagy upregulation during T cell activation but can themselves induce macroautophagy. Our data also show that macroautophagy induction in T cells is associated with an increase of LC3 expression that is mediated by a post-transcriptional mechanism. Overall, our findings unveiled a new role for common γ-chain cytokines as a molecular link between autophagy-induction and T cell activation.
DOI: 10.6084/m9.figshare.1569191.v2
title: Common γ-chain cytokine signaling is required for macroautophagy induction during CD4<sup>+</sup> T cell activation

description: Macroautophagy is a cellular process that mediates the degradation in the lysosome of cytoplasmic components including proteins and organelles. Previous studies have shown that macroautophagy is induced in activated T cells to regulate organelle homeostasis and the cell's energy metabolism. However, the signaling pathways that initiate and regulate activation-induced macroautophagy in T cells have not been identified. Herein, we show that activation-induced macroautophagy in T cells depends on signaling from common γ-chain cytokines. Consequently, inhibition of signaling through JAK3, induced downstream of cytokine receptors containing the common γ-chain, prevents full induction of macroautophagy in activated T cells. Moreover, we found that common γ-chain cytokines are not only required for macroautophagy upregulation during T cell activation but can themselves induce macroautophagy. Our data also show that macroautophagy induction in T cells is associated with an increase of LC3 expression that is mediated by a post-transcriptional mechanism. Overall, our findings unveiled a new role for common γ-chain cytokines as a molecular link between autophagy-induction and T cell activation.
DOI: 10.6084/m9.figshare.1569191.v3
title: Common γ-chain cytokine signaling is required for macroautophagy induction during CD4<sup>+</sup> T cell activation

description: Macroautophagy is a cellular process that mediates the degradation in the lysosome of cytoplasmic components including proteins and organelles. Previous studies have shown that macroautophagy is induced in activated T cells to regulate organelle homeostasis and the cell's energy metabolism. However, the signaling pathways that initiate and regulate activation-induced macroautophagy in T cells have not been identified. Herein, we show that activation-induced macroautophagy in T cells depends on signaling from common γ-chain cytokines. Consequently, inhibition of signaling through JAK3, induced downstream of cytokine receptors containing the common γ-chain, prevents full induction of macroautophagy in activated T cells. Moreover, we found that common γ-chain cytokines are not only required for macroautophagy upregulation during T cell activation but can themselves induce macroautophagy. Our data also show that macroautophagy induction in T cells is associated with an increase of LC3 expression that is mediated by a post-transcriptional mechanism. Overall, our findings unveiled a new role for common γ-chain cytokines as a molecular link between autophagy-induction and T cell activation.
DOI: 10.6084/m9.figshare.1569175
title: Mitogenome metadata: current trends and proposed standards

description: Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal <i>Mitochondrial DNA</i> between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes’s GenBank record, would increase their research value.
DOI: 10.6084/m9.figshare.1569191.v4
title: Common γ-chain cytokine signaling is required for macroautophagy induction during CD4<sup>+</sup> T-cell activation

description: Macroautophagy is a cellular process that mediates degradation in the lysosome of cytoplasmic components including proteins and organelles. Previous studies have shown that macroautophagy is induced in activated T cells to regulate organelle homeostasis and the cell's energy metabolism. However, the signaling pathways that initiate and regulate activation-induced macroautophagy in T cells have not been identified. Here, we show that activation-induced macroautophagy in T cells depends on signaling from common γ-chain cytokines. Consequently, inhibition of signaling through JAK3, induced downstream of cytokine receptors containing the common γ-chain, prevents full induction of macroautophagy in activated T cells. Moreover, we found that common γ-chain cytokines are not only required for macroautophagy upregulation during T cell activation but can themselves induce macroautophagy. Our data also show that macroautophagy induction in T cells is associated with an increase of LC3 expression that is mediated by a post-transcriptional mechanism. Overall, our findings unveiled a new role for common γ-chain cytokines as a molecular link between autophagy induction and T-cell activation.
DOI: 10.6084/m9.figshare.1569191
title: Common γ-chain cytokine signaling is required for macroautophagy induction during CD4<sup>+</sup> T-cell activation

description: Macroautophagy is a cellular process that mediates degradation in the lysosome of cytoplasmic components including proteins and organelles. Previous studies have shown that macroautophagy is induced in activated T cells to regulate organelle homeostasis and the cell's energy metabolism. However, the signaling pathways that initiate and regulate activation-induced macroautophagy in T cells have not been identified. Here, we show that activation-induced macroautophagy in T cells depends on signaling from common γ-chain cytokines. Consequently, inhibition of signaling through JAK3, induced downstream of cytokine receptors containing the common γ-chain, prevents full induction of macroautophagy in activated T cells. Moreover, we found that common γ-chain cytokines are not only required for macroautophagy upregulation during T cell activation but can themselves induce macroautophagy. Our data also show that macroautophagy induction in T cells is associated with an increase of LC3 expression that is mediated by a post-transcriptional mechanism. Overall, our findings unveiled a new role for common γ-chain cytokines as a molecular link between autophagy induction and T-cell activation.
DOI: 10.6084/m9.figshare.1569175.v2
title: Mitogenome metadata: current trends and proposed standards

description: Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal <i>Mitochondrial DNA</i> between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes’s GenBank record, would increase their research value.