cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13240766
title: Differential mitochondrial genome in patients with Rheumatoid Arthritis

description: Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA &gt; ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A &gt; G and 15924 A &gt; G were found to be pathogenic. We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
DOI: 10.6084/m9.figshare.13240766.v1
title: Differential mitochondrial genome in patients with Rheumatoid Arthritis

description: Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA &gt; ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A &gt; G and 15924 A &gt; G were found to be pathogenic. We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
DOI: 10.6084/m9.figshare.13332725
title: Dioscin alleviates hashimoto’s thyroiditis by regulating the SUMOylation of IRF4 to promote CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> treg cell differentiation

description: Dioscin has been used as a treatment for Hashimoto’s thyroiditis (HT) in China. However, the molecular mechanisms governing the modes of action of dioscin have not been elucidated. In this study, flow cytometry and Western blotting were used to identify the proportions of CD4<sup>+</sup>CD25<sup>+</sup> regulatory T (Treg) cells and the expression of forkhead box P3 (Foxp3) and SUMO-specific protease 1 (SENP1) in HT patients’ peripheral blood mononuclear cells (PBMCs). A pTg-induced rat model of HT was established by injection of 100 μg pTg. Then, the model rats were randomly divided into three groups (<i>n</i> = 5): control (NC), model (HT) and dioscin treatment. After oral administration of dioscin each day for two weeks, CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells were analysed by flow cytometry, and the protein expression levels of SENP1, Foxp3, SUMO-1 and SUMO-2/3 were measured by Western blotting. Co-immunoprecipitation (Co-IP) was used to identify the SUMOylation of interferon regulatory factor 4 (IRF4). The results showed that the proportions of CD4<sup>+</sup>CD25<sup>+</sup> Treg cells and the expression of Foxp3 were significantly decreased in HT patients, but the expression of SENP1 was enhanced compared to healthy controls (HCs). However, compared to the pTg-induced HT rat group, the expression of Foxp3, SUMO-1, and SUMO-2/3 and the proportions of CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells were increased, whereas the expression of SENP1 was decreased, in the dioscin-treated group. Furthermore, the SUMOylation of IRF4 was increased after SENP1 was knocked down. The results of our study indicate that dioscin can promote the differentiation of the CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells and subsequently upregulate the SUMOylation of IRF4 by downregulating SENP1 expression.
DOI: 10.6084/m9.figshare.13332725.v1
title: Dioscin alleviates hashimoto’s thyroiditis by regulating the SUMOylation of IRF4 to promote CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> treg cell differentiation

description: Dioscin has been used as a treatment for Hashimoto’s thyroiditis (HT) in China. However, the molecular mechanisms governing the modes of action of dioscin have not been elucidated. In this study, flow cytometry and Western blotting were used to identify the proportions of CD4<sup>+</sup>CD25<sup>+</sup> regulatory T (Treg) cells and the expression of forkhead box P3 (Foxp3) and SUMO-specific protease 1 (SENP1) in HT patients’ peripheral blood mononuclear cells (PBMCs). A pTg-induced rat model of HT was established by injection of 100 μg pTg. Then, the model rats were randomly divided into three groups (<i>n</i> = 5): control (NC), model (HT) and dioscin treatment. After oral administration of dioscin each day for two weeks, CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells were analysed by flow cytometry, and the protein expression levels of SENP1, Foxp3, SUMO-1 and SUMO-2/3 were measured by Western blotting. Co-immunoprecipitation (Co-IP) was used to identify the SUMOylation of interferon regulatory factor 4 (IRF4). The results showed that the proportions of CD4<sup>+</sup>CD25<sup>+</sup> Treg cells and the expression of Foxp3 were significantly decreased in HT patients, but the expression of SENP1 was enhanced compared to healthy controls (HCs). However, compared to the pTg-induced HT rat group, the expression of Foxp3, SUMO-1, and SUMO-2/3 and the proportions of CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells were increased, whereas the expression of SENP1 was decreased, in the dioscin-treated group. Furthermore, the SUMOylation of IRF4 was increased after SENP1 was knocked down. The results of our study indicate that dioscin can promote the differentiation of the CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Treg cells and subsequently upregulate the SUMOylation of IRF4 by downregulating SENP1 expression.
DOI: 10.6084/m9.figshare.12951219.v1
title: Auto-reactivity against gut bacterial peptides in patients with late-onset diabetes

description: The depletion of gut mucosal barrier enables exposure of gut microbes/gut microbial products to the host mucosal immunity which may increase the risk of metabolic/inflammatory disorders. These immune responses can lead to the development of mild autoimmunity to metabolic peptides coming from gut bacteria and may result in metabolic diseases like late-onset diabetes (LOD). In the present study, we identified host sera cross-reactivity with gut bacterial peptides similar to host proteins. The interaction between diabetic sera and gut peptides was detected by enzyme-linked immunosorbent assay (ELISA) and results were confirmed using surface plasmon resonance (SPR). The ELISA assay showed a higher level of serum cross-reactivity in LOD patients as compared to non-diabetic controls against three peptides (P-5, P-9, and P-13). SPR analysis confirmed binding-affinity against P-5 and P-13. Also, a significant correlation was observed between inflammatory markers and P-5. This study demonstrates that gut health is important not only for intestinal diseases but also for several late-onset diseases, like, diabetes.
DOI: 10.6084/m9.figshare.12951219
title: Auto-reactivity against gut bacterial peptides in patients with late-onset diabetes

description: The depletion of gut mucosal barrier enables exposure of gut microbes/gut microbial products to the host mucosal immunity which may increase the risk of metabolic/inflammatory disorders. These immune responses can lead to the development of mild autoimmunity to metabolic peptides coming from gut bacteria and may result in metabolic diseases like late-onset diabetes (LOD). In the present study, we identified host sera cross-reactivity with gut bacterial peptides similar to host proteins. The interaction between diabetic sera and gut peptides was detected by enzyme-linked immunosorbent assay (ELISA) and results were confirmed using surface plasmon resonance (SPR). The ELISA assay showed a higher level of serum cross-reactivity in LOD patients as compared to non-diabetic controls against three peptides (P-5, P-9, and P-13). SPR analysis confirmed binding-affinity against P-5 and P-13. Also, a significant correlation was observed between inflammatory markers and P-5. This study demonstrates that gut health is important not only for intestinal diseases but also for several late-onset diseases, like, diabetes.
DOI: 10.6084/m9.figshare.8159246
title: Oral administration of green tea Epigallocatechin-3-gallate reduces oxidative stress and enhances restoration of cardiac function in diabetic rats receiving autologous transplantation of adipose-derived stem cells

description: Cardio-dysfunction is one of the complications in patients with diabetes mellitus (DM). This paper aimed to investigate if oral administration of green tea Epigallocatechin-3-gallate (EGCG, E) and transplantation of adipose-derived stem cells (ADSC) show cross effects on the treatment of cardiomyopathy in rats with type 1 DM. Wistar male rats were divided into four groups (each group contained 8 animals) including sham, DM (diabetic group), DM + ADSC (DM group with ADSC treatment) and DM + ADSC + E (DM + ADSC group with oral administration of EGCG). Pathological parameters including hypertrophy, inflammation, and fibrosis were activated in DM group. By contrast, all parameters were significantly improved in treatment group (DM + ADSC group). In addition, improvement of pathological parameters in DM + ADSC + E was significantly better than DM + ADSC. We found that EGCG can increase expression of survival marker in ADSC under high glucose environment and reduce serum oxidative stress in DM rats.
DOI: 10.6084/m9.figshare.8159246.v1
title: Oral administration of green tea Epigallocatechin-3-gallate reduces oxidative stress and enhances restoration of cardiac function in diabetic rats receiving autologous transplantation of adipose-derived stem cells

description: Cardio-dysfunction is one of the complications in patients with diabetes mellitus (DM). This paper aimed to investigate if oral administration of green tea Epigallocatechin-3-gallate (EGCG, E) and transplantation of adipose-derived stem cells (ADSC) show cross effects on the treatment of cardiomyopathy in rats with type 1 DM. Wistar male rats were divided into four groups (each group contained 8 animals) including sham, DM (diabetic group), DM + ADSC (DM group with ADSC treatment) and DM + ADSC + E (DM + ADSC group with oral administration of EGCG). Pathological parameters including hypertrophy, inflammation, and fibrosis were activated in DM group. By contrast, all parameters were significantly improved in treatment group (DM + ADSC group). In addition, improvement of pathological parameters in DM + ADSC + E was significantly better than DM + ADSC. We found that EGCG can increase expression of survival marker in ADSC under high glucose environment and reduce serum oxidative stress in DM rats.
DOI: 10.15468/r32ya3
title: Oxynoemacheilus sarus, a new nemacheilid loach from the lower Ceyhan and Seyhan in southern Anatolia (Teleostei: Nemacheilidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Freyhof, Jörg, Yoğurtçuoğlu, Baran, Kaya, Cüneyt (2021): Oxynoemacheilus sarus, a new nemacheilid loach from the lower Ceyhan and Seyhan in southern Anatolia (Teleostei: Nemacheilidae). Zootaxa 4964 (1): 123-139, DOI: https://doi.org/10.11646/zootaxa.4964.1.6
DOI: 10.3886/e139101
title: Data and code for: Longevity Perceptions and Saving Decisions during the COVID-19 Outbreak: An Experimental Investigation

description: We experimentally study individuals’ perceptions about and advice to others regarding retirement savings and annuitization during the pandemic. Many people recommend that others save more for retirement, but those most affected by the pandemic tell others to save and annuitize less. We investigate two possible channels for this result and show that the pandemic does not substantially alter optimism regarding survival probabilities. Hence, we conclude that economic factors are driving our results. Consequently, some financial ramifications of the COVID-19 outbreak are yet to be revealed, as the pandemic is having longer-term effects on peoples’ willingness to save and annuitize.
DOI: 10.3886/e139101v1
title: Data and code for: Longevity Perceptions and Saving Decisions during the COVID-19 Outbreak: An Experimental Investigation

description: We experimentally study individuals’ perceptions about and advice to others regarding retirement savings and annuitization during the pandemic. Many people recommend that others save more for retirement, but those most affected by the pandemic tell others to save and annuitize less. We investigate two possible channels for this result and show that the pandemic does not substantially alter optimism regarding survival probabilities. Hence, we conclude that economic factors are driving our results. Consequently, some financial ramifications of the COVID-19 outbreak are yet to be revealed, as the pandemic is having longer-term effects on peoples’ willingness to save and annuitize.
DOI: 10.3886/e139541
title: Data and Code for: Work-Care Balance Over the Day and the Gender Wage Gap

description: Using the American Time Use Survey (ATUS) we document that women have higher incidence of household care activities between 8 a.m. and 5 p.m. (prime time of the day). These work interruptions are penalized. The penalty is about 9%, declining to 4% when we control for occupations. This result is consistent with occupations oﬀering more ﬂexibility but also a lower wage. We oﬀer suggestive evidence that missing work due to household demands has a larger penalty in occupations with more coordinated work schedules.<br>
DOI: 10.3886/e139541v1
title: Data and Code for: Work-Care Balance Over the Day and the Gender Wage Gap

description: Using the American Time Use Survey (ATUS) we document that women have higher incidence of household care activities between 8 a.m. and 5 p.m. (prime time of the day). These work interruptions are penalized. The penalty is about 9%, declining to 4% when we control for occupations. This result is consistent with occupations oﬀering more ﬂexibility but also a lower wage. We oﬀer suggestive evidence that missing work due to household demands has a larger penalty in occupations with more coordinated work schedules.<br>
DOI: 10.3886/e139241
title: Data and Code for: "Working for Your Bread: The Labor Supply Effects of SNAP"

description: This study explores whether program rules for the Supplemental Nutrition Assistance Program (SNAP) distorts labor supply along the intensive margin. Specifically, we explore whether we observe an excess mass of SNAP recipients at a sharp tax rate change in the eligibility formula where net income equals zero. Using administrative SNAP records from Colorado and Oregon, we document little evidence of intensive labor supply distortions.
description: Universe of SNAP recipients in Oregon and Colorado
description: Every SNAP recipient in Oregon and Colorado.<br>.
DOI: 10.3886/e139241v1
title: Data and Code for: "Working for Your Bread: The Labor Supply Effects of SNAP"

description: This study explores whether program rules for the Supplemental Nutrition Assistance Program (SNAP) distorts labor supply along the intensive margin. Specifically, we explore whether we observe an excess mass of SNAP recipients at a sharp tax rate change in the eligibility formula where net income equals zero. Using administrative SNAP records from Colorado and Oregon, we document little evidence of intensive labor supply distortions.
description: Universe of SNAP recipients in Oregon and Colorado
description: Every SNAP recipient in Oregon and Colorado.<br>.
DOI: 10.15468/mzaevx
title: A new, enigmatic species of black-eyed gecko (Reptilia: Diplodactylidae Mokopirirakau) from North Otago, New Zealand

description: This dataset contains the digitized treatments in Plazi based on the original journal article Knox, Carey, Hitchmough, Rodney A., Nielsen, Stuart V., Jewell, Tony, Bell, Trent (2021): A new, enigmatic species of black-eyed gecko (Reptilia: Diplodactylidae Mokopirirakau) from North Otago, New Zealand. Zootaxa 4964 (1): 140-156, DOI: https://doi.org/10.11646/zootaxa.4964.1.7
DOI: 10.15468/cvvvnv
title: A new jawfish of the genus Opistognathus (Perciformes: Opistognathidae) from Japan

description: This dataset contains the digitized treatments in Plazi based on the original journal article Shinohara, Gento (2021): A new jawfish of the genus Opistognathus (Perciformes: Opistognathidae) from Japan. Zootaxa 4964 (1): 157-168, DOI: https://doi.org/10.11646/zootaxa.4964.1.8
DOI: 10.6084/m9.figshare.14551008.v1
title: 1864_conserved_genes

description: Information on the 1,864 pan-ecological genes we identified in our 30% gene catalog, including annotations to the Genome Taxonomy Database bac120 genes and functional annotations.
DOI: 10.6084/m9.figshare.14342696.v1
title: Metagenome assembled genomes co_7-Bin_22_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14343032.v1
title: Metagenome assembled genomes co_1-Bin_1_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342693.v1
title: Metagenome assembled genomes co_2-Bin_16_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342693
title: Metagenome assembled genomes co_2-Bin_16_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342699
title: Metagenome assembled genomes co_7-Bin_23_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342696
title: Metagenome assembled genomes co_7-Bin_22_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342702
title: Metagenome assembled genomes co_3-Bin_17_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14343032
title: Metagenome assembled genomes co_1-Bin_1_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.