cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569191.v6
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.v1
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.v5
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.1569170
title: Autocovariance Function Estimation via Penalized Regression

description: The work revisits the autocovariance function estimation, a fundamental problem in statistical inference for time series. We convert the function estimation problem into constrained penalized regression with a generalized penalty that provides us with flexible and accurate estimation, and study the asymptotic properties of the proposed estimator. In case of a nonzero mean time series, we apply a penalized regression technique to a differenced time series, which does not require a separate detrending procedure. In penalized regression, selection of tuning parameters is critical and we propose four different data-driven criteria to determine them. A simulation study shows effectiveness of the tuning parameter selection and that the proposed approach is superior to three existing methods. We also briefly discuss the extension of the proposed approach to interval-valued time series. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1569170.v1
title: Autocovariance Function Estimation via Penalized Regression

description: The work revisits the autocovariance function estimation, a fundamental problem in statistical inference for time series. We convert the function estimation problem into constrained penalized regression with a generalized penalty that provides us with flexible and accurate estimation, and study the asymptotic properties of the proposed estimator. In case of a nonzero mean time series, we apply a penalized regression technique to a differenced time series, which does not require a separate detrending procedure. In penalized regression, selection of tuning parameters is critical and we propose four different data-driven criteria to determine them. A simulation study shows effectiveness of the tuning parameter selection and that the proposed approach is superior to three existing methods. We also briefly discuss the extension of the proposed approach to interval-valued time series. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1569161
title: RNAi-mediated gene silencing of <i>WsSGTL1</i> in <i>W.somnifera</i> affects growth and glycosylation pattern

description: Sterol glycosyltransferases (SGTs) belong to family 1 of glycosyltransferases (GTs) and are enzymes responsible for synthesis of sterol–glucosides (SGs) in many organisms. <i>WsSGTL1</i> is a SGT of <i>Withania somnifera</i> that has been found associated with plasma membranes. However its biological function in <i>W.somnifera</i> is largely unknown. In the present study, we have demonstrated through RNAi silencing of <i>WsSGTL1</i> gene that it performs glycosylation of withanolides and sterols resulting in glycowithanolides and glycosylated sterols respectively, and affects the growth and development of transgenic <i>W.somnifera</i>. For this, RNAi construct (pFGC1008-<i>WsSGTL1</i>) was made and genetic transformation was done by <i>Agrobacterium tumefaciens</i>. HPLC analysis depicts the reduction of withanoside V (the glycowithanolide of <i>W.somnifera</i>) and a large increase of withanolides (majorly withaferin A) content. Also, a significant decrease in level of glycosylated sterols has been observed. Hence, the obtained data provides an insight into the biological function of <i>WsSGTL1</i> gene in <i>W.somnifera</i>.
DOI: 10.6084/m9.figshare.1569161.v2
title: RNAi-mediated gene silencing of <i>WsSGTL1</i> in <i>W.somnifera</i> affects growth and glycosylation pattern

description: Sterol glycosyltransferases (SGTs) belong to family 1 of glycosyltransferases (GTs) and are enzymes responsible for synthesis of sterol–glucosides (SGs) in many organisms. <i>WsSGTL1</i> is a SGT of <i>Withania somnifera</i> that has been found associated with plasma membranes. However its biological function in <i>W.somnifera</i> is largely unknown. In the present study, we have demonstrated through RNAi silencing of <i>WsSGTL1</i> gene that it performs glycosylation of withanolides and sterols resulting in glycowithanolides and glycosylated sterols respectively, and affects the growth and development of transgenic <i>W.somnifera</i>. For this, RNAi construct (pFGC1008-<i>WsSGTL1</i>) was made and genetic transformation was done by <i>Agrobacterium tumefaciens</i>. HPLC analysis depicts the reduction of withanoside V (the glycowithanolide of <i>W.somnifera</i>) and a large increase of withanolides (majorly withaferin A) content. Also, a significant decrease in level of glycosylated sterols has been observed. Hence, the obtained data provides an insight into the biological function of <i>WsSGTL1</i> gene in <i>W.somnifera</i>.
DOI: 10.6084/m9.figshare.1569161.v1
title: RNAi-mediated gene silencing of <i>WsSGTL1</i> in <i>W.somnifera</i> affects growth and glycosylation pattern

description: Sterol glycosyltransferases (SGTs) belong to family 1 of glycosyltransferases (GTs) are enzymes responsible for synthesis of sterol -glucosides (SGs) in many organism. <i>WsSGTL1</i> is a SGT of <i>Withania somnifera</i> has been found associated with plasma membranes. However its biological function in <i>W.somnifera</i> is largely unknown. In the present study, we have demonstrated through RNAi silencing of <i>WsSGTL1</i> gene that it performs glycosylation of withanolides and sterols resulting in glycowithanolides and glycosylated sterols respectively, affects the growth and development of transgenic <i>W.somnifera</i>. For this RNAi construct (pFGC1008-<i>WsSGTL1</i>) was made and genetic transformation was done by <i>Agrobacterium tumefaciens</i>. HPLC analysis depicts the reduction of withanoside V (the glycowithanolide of <i>W.somnifera</i>) and a large increase of withanolides (majorly withaferin A) content. Also, significant decrease in level of glycosylated sterols have been observed. Hence, the obtained data provides an insights into the biological function of WsSGTL1 gene in W.somnifera.
DOI: 10.6084/m9.figshare.1569145
title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions

description: The relationship between DNA methylation and gene expression is complex and elusive. To further elucidate these relations, we performed an integrative analysis of the methylome and transcriptome of 4 circulating immune cell subsets (B cells, monocytes, CD4<sup>+</sup>, and CD8<sup>+</sup> T cells) from healthy females. Additionally, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male data sets. Immune cell-specific differentially methylated regions (DMRs) were found to be highly similar between sexes, with an average correlation coefficient of 0.82; however, numerous sex-specific DMRs, shared by the cell subsets, were identified, mainly on autosomal chromosomes. This provides a list of highly interesting candidate genes to be studied in disorders with sexual dimorphism, such as autoimmune diseases. Immune cell-specific DMRs were mainly located in the gene body and intergenic region, distant from CpG islands but overlapping with enhancer elements, indicating that distal regulatory elements are important in immune cell specificity. In contrast, sex-specific DMRs were overrepresented in CpG islands, suggesting that the epigenetic regulatory mechanisms of sex and immune cell specificity may differ. Both positive and, more frequently, negative correlations between subset-specific expression and methylation were observed, and cell-specific DMRs of both interactions were associated with similar biological pathways, while sex-specific DMRs were linked to networks of early development or estrogen receptor and immune-related molecules. Our findings of immune cell- and sex-specific methylome and transcriptome profiles provide novel insight on their complex regulatory interactions and may particularly contribute to research of immune-mediated diseases.
DOI: 10.6084/m9.figshare.1569149.v1
title: Adsorption of chromium(VI) from saline wastewater using spent tea-supported magnetite nanoparticle

description: Spent tea-supported magnetite (ST/Mag) nanoparticles were synthesized as an adsorbent for the removal of hexavalent chromium [Cr(VI)] from saline wastewater. Prepared ST/Mag adsorbent was characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. Various factors affecting the uptake behavior such as pH, contact time, initial concentration of metal ions, adsorbent dose, coexisting ions, and desorption behavior were studied using batch tests. The results revealed that adsorption of Cr(VI) was highly pH dependent and the kinetics of the adsorption followed by the Avrami fractional-order and pseudo-second-order kinetic models. The results showed that the adsorption isotherms were more accurately represented by Langmuir and Liu isotherm models with a sorption capacity of 30.0 mg g<sup>−1</sup>. Adsorption experiments with co-ions indicated that the adsorptive removal of Cr(VI) ions was slightly decreased. Desorption studies using alkaline eluents showed maximum recovery of ST/Mag and only 10% decrease occurring in maximum adsorption capacity after five cycles. The ST/Mag nanoparticles proved to be a very prospective adsorbent for Cr(VI) uptake from industrial high-TDS effluents.
DOI: 10.6084/m9.figshare.1569145.v2
title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions

description: The relationship between DNA methylation and gene expression is complex and elusive. To further elucidate these relations, we performed an integrative analysis of the methylome and transcriptome of four circulating immune cell subsets (B cells, monocytes, CD4<sup>+</sup>-, and CD8<sup>+</sup>-T cells) from healthy females. Additionally, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. Immune cell-specific differentially methylated regions (DMRs) were found to be highly similar between sexes, with an average correlation coefficient of 0.82; however, numerous sex-specific DMRs, shared by the cell subsets, were identified, mainly on autosomal chromosomes. This provides a list of highly interesting candidate genes to be studied in disorders with sexual dimorphism, such as autoimmune diseases. Immune cell-specific DMRs were mainly located in the gene body and intergenic region, distant from CpG islands but overlapping with enhancer elements, indicating that distal regulatory elements are important in immune cell specificity. In contrast, sex-specific DMRs were overrepresented in CpG islands, suggesting that the epigenetic regulatory mechanisms of sex and immune cell specificity may differ. Both positive and, more frequently, negative correlations between subset-specific expression and methylation were observed, and cell-specific DMRs of both interactions were associated with similar biological pathways, while sex-specific DMRs were linked to networks of early development or estrogen receptor and immune-related molecules. Our findings of immune cell- and sex-specific methylome and transcriptome profiles provide novel insight on their complex regulatory interactions and may particularly contribute to research of immune-mediated diseases.
DOI: 10.6084/m9.figshare.1569149.v2
title: Adsorption of chromium(VI) from saline wastewater using spent tea-supported magnetite nanoparticle

description: Spent tea-supported magnetite (ST/Mag) nanoparticles were synthesized as an adsorbent for the removal of hexavalent chromium [Cr(VI)] from saline wastewater. Prepared ST/Mag adsorbent was characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. Various factors affecting the uptake behavior such as pH, contact time, initial concentration of metal ions, adsorbent dose, coexisting ions, and desorption behavior were studied using batch tests. The results revealed that adsorption of Cr(VI) was highly pH dependent and the kinetics of the adsorption followed by the Avrami fractional-order and pseudo-second-order kinetic models. The results showed that the adsorption isotherms were more accurately represented by Langmuir and Liu isotherm models with a sorption capacity of 30.0 mg g<sup>−1</sup>. Adsorption experiments with co-ions indicated that the adsorptive removal of Cr(VI) ions was slightly decreased. Desorption studies using alkaline eluents showed maximum recovery of ST/Mag and only 10% decrease occurring in maximum adsorption capacity after five cycles. The ST/Mag nanoparticles proved to be a very prospective adsorbent for Cr(VI) uptake from industrial high-TDS effluents.
DOI: 10.6084/m9.figshare.1569145.v4
title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions

description: The relationship between DNA methylation and gene expression is complex and elusive. To further elucidate these relations, we performed an integrative analysis of the methylome and transcriptome of 4 circulating immune cell subsets (B cells, monocytes, CD4<sup>+</sup>, and CD8<sup>+</sup> T cells) from healthy females. Additionally, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male data sets. Immune cell-specific differentially methylated regions (DMRs) were found to be highly similar between sexes, with an average correlation coefficient of 0.82; however, numerous sex-specific DMRs, shared by the cell subsets, were identified, mainly on autosomal chromosomes. This provides a list of highly interesting candidate genes to be studied in disorders with sexual dimorphism, such as autoimmune diseases. Immune cell-specific DMRs were mainly located in the gene body and intergenic region, distant from CpG islands but overlapping with enhancer elements, indicating that distal regulatory elements are important in immune cell specificity. In contrast, sex-specific DMRs were overrepresented in CpG islands, suggesting that the epigenetic regulatory mechanisms of sex and immune cell specificity may differ. Both positive and, more frequently, negative correlations between subset-specific expression and methylation were observed, and cell-specific DMRs of both interactions were associated with similar biological pathways, while sex-specific DMRs were linked to networks of early development or estrogen receptor and immune-related molecules. Our findings of immune cell- and sex-specific methylome and transcriptome profiles provide novel insight on their complex regulatory interactions and may particularly contribute to research of immune-mediated diseases.
DOI: 10.6084/m9.figshare.1569149
title: Adsorption of chromium(VI) from saline wastewater using spent tea-supported magnetite nanoparticle

description: Spent tea-supported magnetite (ST/Mag) nanoparticles were synthesized as an adsorbent for the removal of hexavalent chromium [Cr(VI)] from saline wastewater. Prepared ST/Mag adsorbent was characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. Various factors affecting the uptake behavior such as pH, contact time, initial concentration of metal ions, adsorbent dose, coexisting ions, and desorption behavior were studied using batch tests. The results revealed that adsorption of Cr(VI) was highly pH dependent and the kinetics of the adsorption followed by the Avrami fractional-order and pseudo-second-order kinetic models. The results showed that the adsorption isotherms were more accurately represented by Langmuir and Liu isotherm models with a sorption capacity of 30.0 mg g<sup>−1</sup>. Adsorption experiments with co-ions indicated that the adsorptive removal of Cr(VI) ions was slightly decreased. Desorption studies using alkaline eluents showed maximum recovery of ST/Mag and only 10% decrease occurring in maximum adsorption capacity after five cycles. The ST/Mag nanoparticles proved to be a very prospective adsorbent for Cr(VI) uptake from industrial high-TDS effluents.
DOI: 10.6084/m9.figshare.1569149.v4
title: Adsorption of chromium(VI) from saline wastewater using spent tea-supported magnetite nanoparticle

description: Spent tea-supported magnetite (ST/Mag) nanoparticles were synthesized as an adsorbent for the removal of hexavalent chromium [Cr(VI)] from saline wastewater. Prepared ST/Mag adsorbent was characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. Various factors affecting the uptake behavior such as pH, contact time, initial concentration of metal ions, adsorbent dose, coexisting ions, and desorption behavior were studied using batch tests. The results revealed that adsorption of Cr(VI) was highly pH dependent and the kinetics of the adsorption followed by the Avrami fractional-order and pseudo-second-order kinetic models. The results showed that the adsorption isotherms were more accurately represented by Langmuir and Liu isotherm models with a sorption capacity of 30.0 mg g<sup>−1</sup>. Adsorption experiments with co-ions indicated that the adsorptive removal of Cr(VI) ions was slightly decreased. Desorption studies using alkaline eluents showed maximum recovery of ST/Mag and only 10% decrease occurring in maximum adsorption capacity after five cycles. The ST/Mag nanoparticles proved to be a very prospective adsorbent for Cr(VI) uptake from industrial high-TDS effluents.
DOI: 10.6084/m9.figshare.1569149.v3
title: Adsorption of chromium(VI) from saline wastewater using spent tea-supported magnetite nanoparticle

description: Spent tea-supported magnetite (ST/Mag) nanoparticles were synthesized as an adsorbent for the removal of hexavalent chromium [Cr(VI)] from saline wastewater. Prepared ST/Mag adsorbent was characterized using X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy. Various factors affecting the uptake behavior such as pH, contact time, initial concentration of metal ions, adsorbent dose, coexisting ions, and desorption behavior were studied using batch tests. The results revealed that adsorption of Cr(VI) was highly pH dependent and the kinetics of the adsorption followed by the Avrami fractional-order and pseudo-second-order kinetic models. The results showed that the adsorption isotherms were more accurately represented by Langmuir and Liu isotherm models with a sorption capacity of 30.0 mg g<sup>−1</sup>. Adsorption experiments with co-ions indicated that the adsorptive removal of Cr(VI) ions was slightly decreased. Desorption studies using alkaline eluents showed maximum recovery of ST/Mag and only 10% decrease occurring in maximum adsorption capacity after five cycles. The ST/Mag nanoparticles proved to be a very prospective adsorbent for Cr(VI) uptake from industrial high-TDS effluents.