cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4742884
title: Supplementary Material for: Oxidative Balance Score and the Risk of End-Stage Renal Disease and Cardiovascular Disease

description: <b><i>Background:</i></b> Oxidative balance score (OBS) is a composite measure of oxidative stress-related exposures. The aim of this study was to investigate the association between OBS, end-stage renal disease (ESRD), and cardiovascular disease (CVD). <b><i>Methods:</i></b> Using data from the Chronic Renal Insufficiency Cohort, we calculated the main exposure OBS by summing up 12 apriori-defined pro- and antioxidant factors obtained from the diet history questionnaire and lifestyle assessment. We divided OBS into quartiles (Q1-Q4), with Q1 (predominance of pro-oxidants) as the reference. We analyzed OBS quartiles as an ordinal variable. Crude and adjusted hazards ratios (HRs) and 95% CIs were estimated using Cox proportional hazards models for time to ESRD and CVD. <b><i>Results:</i></b> Compared to Q1, Q4 (high antioxidant) was associated with ESRD in the crude model (HR 1.35, 95% CI 1.08-1.69) and adjusting for age, sex, and race (HR 1.36, 95% CI 1.09-1.71) but not in the fully adjusted model (HR 1.12, 95% CI 0.84-1.51). HR of ESRD increased as the OBS quartiles increased in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05) but not in the fully adjusted model (<i>p</i><sub>trend</sub> = 0.30). Compared to Q1, Q4 was associated with CVD in the crude (HR 1.33, 95% CI 1.06-1.68) but not adjusted models. The HR of CVD increased with an increase in OBS quartiles in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05). <b><i>Conclusion:</i></b> The reverse association between OBS and progression to ESRD suggests that perhaps the effect of oxidative balance-related exposure is different in the setting of established chronic kidney disease.
DOI: 10.6084/m9.figshare.4742884.v1
title: Supplementary Material for: Oxidative Balance Score and the Risk of End-Stage Renal Disease and Cardiovascular Disease

description: <b><i>Background:</i></b> Oxidative balance score (OBS) is a composite measure of oxidative stress-related exposures. The aim of this study was to investigate the association between OBS, end-stage renal disease (ESRD), and cardiovascular disease (CVD). <b><i>Methods:</i></b> Using data from the Chronic Renal Insufficiency Cohort, we calculated the main exposure OBS by summing up 12 apriori-defined pro- and antioxidant factors obtained from the diet history questionnaire and lifestyle assessment. We divided OBS into quartiles (Q1-Q4), with Q1 (predominance of pro-oxidants) as the reference. We analyzed OBS quartiles as an ordinal variable. Crude and adjusted hazards ratios (HRs) and 95% CIs were estimated using Cox proportional hazards models for time to ESRD and CVD. <b><i>Results:</i></b> Compared to Q1, Q4 (high antioxidant) was associated with ESRD in the crude model (HR 1.35, 95% CI 1.08-1.69) and adjusting for age, sex, and race (HR 1.36, 95% CI 1.09-1.71) but not in the fully adjusted model (HR 1.12, 95% CI 0.84-1.51). HR of ESRD increased as the OBS quartiles increased in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05) but not in the fully adjusted model (<i>p</i><sub>trend</sub> = 0.30). Compared to Q1, Q4 was associated with CVD in the crude (HR 1.33, 95% CI 1.06-1.68) but not adjusted models. The HR of CVD increased with an increase in OBS quartiles in the crude model (<i>p</i><sub>trend</sub> &lt; 0.05). <b><i>Conclusion:</i></b> The reverse association between OBS and progression to ESRD suggests that perhaps the effect of oxidative balance-related exposure is different in the setting of established chronic kidney disease.
DOI: 10.6084/m9.figshare.4742857
title: ToF-SIMS measurement of Pythium ultimum hyphae and Bacillus subtilis vegetative cells and spores

description: - qualitative analysis of sample composition and yields of secondary ion species<br>- measurements with a ToF-SIMS.5 (ION-TOF GmbH, Münster)<br>- measurement in imaging modeof ToF-SIMS.5 in combination with delayed extraction of negative secondary ions<br>- Mass resolving power above 3000 and lateral resolution of about 130 nm<br>- 30 keV NanoProbe, 0.02 pA of primary Bi3+ cluster ions in 100 ns pulses with 200 µm repetition period<br>- analysis in 400 scans/plains with 5 shots of primary Bi3+ cluster ions per pixel -&gt; distributed randomly in 512 x 512 raster over 56 x 56 µm area on silicon wafer<br><b>Analysis:</b><br>- stacking of scans after lateral drift correction<br>- total stack was analysed for lateral distribution of ion yields using SurfaceLab 6.5 software (ION-TOF GmbH)<br> <br><br>
DOI: 10.6084/m9.figshare.4742857.v1
title: ToF-SIMS measurement of Pythium ultimum hyphae and Bacillus subtilis vegetative cells and spores

description: - qualitative analysis of sample composition and yields of secondary ion species<br>- measurements with a ToF-SIMS.5 (ION-TOF GmbH, Münster)<br>- measurement in imaging modeof ToF-SIMS.5 in combination with delayed extraction of negative secondary ions<br>- Mass resolving power above 3000 and lateral resolution of about 130 nm<br>- 30 keV NanoProbe, 0.02 pA of primary Bi3+ cluster ions in 100 ns pulses with 200 µm repetition period<br>- analysis in 400 scans/plains with 5 shots of primary Bi3+ cluster ions per pixel -&gt; distributed randomly in 512 x 512 raster over 56 x 56 µm area on silicon wafer<br><b>Analysis:</b><br>- stacking of scans after lateral drift correction<br>- total stack was analysed for lateral distribution of ion yields using SurfaceLab 6.5 software (ION-TOF GmbH)<br> <br><br>
DOI: 10.6084/m9.figshare.4742836.v1
title: Rethinking the Effects of Microcredit on Household Welfare in Cambodia

description: This article analyses the effects of microcredit on household welfare in terms of household expenditure per capita in Cambodia, with data from the Cambodia Socio-Economic Survey carried out in 2014. The analysis describes the effects via formal and informal lending sectors, accounting for endogenous selection bias arising from unobserved factors and for structural differences between borrowers and non-borrowers in terms of expenditure functions. The findings suggest that microcredit in both sectors reduces household expenditure.
DOI: 10.6084/m9.figshare.4742272
title: BinLPT: A Workload-Aware Parallel Loop Scheduler for Large-Scale Multicore Platforms (Results)

description: This dataset contains experimental results presented in the paper.<br><br>synthetic-kernel-benchmarking.csv contains the results for synthetic kernel benchmarking.<br><br>application-kernel-benchmarking.csv contains the results for application kernel benchmarking.<br>
DOI: 10.6084/m9.figshare.4742317
title: ESBAM 2012

description: This is the dataset from Wellbeing and Health Survey of Older adults from Peru, that also can be found it in: <br>http://www.midis.gob.pe/dgsye/evaluacion/otros_estudios_pension65.html<br><br>
DOI: 10.6084/m9.figshare.4742317.v1
title: ESBAM 2012

description: This is the dataset from Wellbeing and Health Survey of Older adults from Peru, that also can be found it in: <br>http://www.midis.gob.pe/dgsye/evaluacion/otros_estudios_pension65.html<br><br>
DOI: 10.6084/m9.figshare.4742116
title: High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

description: It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon <i>Pyrococcus abyssi</i>, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of <i>Pab</i>1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in <i>P. abyssi</i>. The large majority of these loci interacted with <i>Pab</i>1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that <i>Pab</i>1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of <i>Pab</i>1020 may facilitate the development of new biotechnological applications <i>e.g.</i> in ligation of preadenylated adaptors to RNA molecules.
DOI: 10.6084/m9.figshare.4742116.v2
title: High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

description: It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon <i>Pyrococcus abyssi</i>, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of <i>Pab</i>1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in <i>P. abyssi</i>. The large majority of these loci interacted with <i>Pab</i>1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that <i>Pab</i>1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of <i>Pab</i>1020 may facilitate the development of new biotechnological applications <i>e.g.</i> in ligation of preadenylated adaptors to RNA molecules.
DOI: 10.6084/m9.figshare.4742116.v1
title: High-Throughput Sequencing Reveals Circular Substrates for an Archaeal RNA ligase

description: It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon <i>Pyrococcus abyssi</i>, has emerged. This led us to investigate the physiological significance of a previously observed weak intramolecular ligation activity of <i>Pab</i>1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in <i>P. abyssi</i>. The large majority of these loci interacted with <i>Pab</i>1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that <i>Pab</i>1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase towards RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of <i>Pab</i>1020 may facilitate the development of new biotechnological applications <i>e.g.</i> in ligation of preadenylated adaptors to RNA molecules.
DOI: 10.6084/m9.figshare.4740331
title: Testing for autocorrelation and random-effects in nonlinear mixed effects models based on <i>M</i>-estimation

description: <i>M</i>-estimation (robust estimation) for the parameters in nonlinear mixed effects models using Fisher scoring method is investigated in the article, which shares some of the features of the existing maximum likelihood estimation: consistency and asymptotic normality. Score tests for autocorrelation and random effects based on <i>M</i>-estimation, together with their asymptotic distribution are also studied. The performance of the test statistics are evaluated via simulations and a real data analysis of plasma concentrations data.
DOI: 10.6084/m9.figshare.4740331.v2
title: Testing for autocorrelation and random-effects in nonlinear mixed effects models based on <i>M</i>-estimation

description: <i>M</i>-estimation (robust estimation) for the parameters in nonlinear mixed effects models using Fisher scoring method is investigated in the article, which shares some of the features of the existing maximum likelihood estimation: consistency and asymptotic normality. Score tests for autocorrelation and random effects based on <i>M</i>-estimation, together with their asymptotic distribution are also studied. The performance of the test statistics are evaluated via simulations and a real data analysis of plasma concentrations data.
DOI: 10.6084/m9.figshare.4740331.v1
title: Testing for Autocorrelation and Random-effects in Nonlinear Mixed Effects Models Based on M-estimation<sup>*</sup>

description: M-estimation (robust estimation) for the parameters in nonlinear mixed effects models using Fisher scoring method is investigated in the paper, which shares some of the features of the existing maximum likelihood estimation: consistency and asymptotic normality. Score tests for autocorrelation and random effects based on M-estimation, together with their asymptotic distribution are also studied. The performance of the test statistics are evaluated via simulations and a real data analysis of plasma concentrations data.
DOI: 10.6084/m9.figshare.4739212
title: Effects of static magnetic fields on the structure, polymerization, and bioelectric of tubulin assemblies

description: Due to widespread exposure of human being to various sources of static magnetic fields (SMF), their effect on the spatial and temporal status of structure, arrangement, and polymerization of tubulin was studied at the molecular level. The intrinsic fluorescence intensity of tubulin was increased by SMF, indicating the repositioning of tryptophan and tyrosine residues. Circular Dichroism spectroscopy revealed variations in the ratios of alpha helix, beta, and random coil structures of tubulin as a result of exposure to SMF at 100, 200, and 300 mT. Transmission Electron microscopy of microtubules showed breaches and curvatures whose risk of occurrence increased as a function of field strength. Dynamic light scattering revealed an increase in the surface potential of tubulin aggregates exposed to SMF. The rate and extent of polymerization increased by 9.8 and 33.8%, at 100 and 300 mT, respectively, but decreased by 36.16% at 200 mT. The conductivity of polymerized tubulin increased in the presence of 100 and 300 mT SMF but remained the same as the control at 200 mT. The analysis of flexible amino acids along the sequence of tubulin revealed higher SMF susceptibility in the helical electron conduction pathway set through histidines rather than the vertical electron conduction pathway formed by tryptophan residues. The results reveal structural and functional effects of SMF on tubulin assemblies and microtubules that can be considered as a potential means to address the safety issues and for manipulation of bioelectrical characteristics of cytosol, intracellular trafficking and thus, the living status of cells, remotely.
DOI: 10.6084/m9.figshare.12696419
title: Targeted metabolic data

description: Targeted metabolomics data of osteoporosis induced by ovarecomy in mice.
DOI: 10.6084/m9.figshare.4739212.v1
title: Effects of static magnetic fields on the structure, polymerization, and bioelectric of tubulin assemblies

description: Due to widespread exposure of human being to various sources of static magnetic fields (SMF), their effect on the spatial and temporal status of structure, arrangement, and polymerization of tubulin was studied at the molecular level. The intrinsic fluorescence intensity of tubulin was increased by SMF, indicating the repositioning of tryptophan and tyrosine residues. Circular Dichroism spectroscopy revealed variations in the ratios of alpha helix, beta, and random coil structures of tubulin as a result of exposure to SMF at 100, 200, and 300 mT. Transmission Electron microscopy of microtubules showed breaches and curvatures whose risk of occurrence increased as a function of field strength. Dynamic light scattering revealed an increase in the surface potential of tubulin aggregates exposed to SMF. The rate and extent of polymerization increased by 9.8 and 33.8%, at 100 and 300 mT, respectively, but decreased by 36.16% at 200 mT. The conductivity of polymerized tubulin increased in the presence of 100 and 300 mT SMF but remained the same as the control at 200 mT. The analysis of flexible amino acids along the sequence of tubulin revealed higher SMF susceptibility in the helical electron conduction pathway set through histidines rather than the vertical electron conduction pathway formed by tryptophan residues. The results reveal structural and functional effects of SMF on tubulin assemblies and microtubules that can be considered as a potential means to address the safety issues and for manipulation of bioelectrical characteristics of cytosol, intracellular trafficking and thus, the living status of cells, remotely.
DOI: 10.6084/m9.figshare.12696419.v4
title: Targeted metabolic data

description: Targeted metabolomics data of osteoporosis induced by ovarecomy in mice.
DOI: 10.6084/m9.figshare.12696419.v3
title: Targeted metabolic data

description: Targeted metabolomics data of osteoporosis induced by ovarecomy in mice.
DOI: 10.6084/m9.figshare.4738594
title: Suppression of the grainyhead transcription factor 2 gene (GRHL2) inhibits the proliferation, migration, invasion and mediates cell cycle arrest of ovarian cancer cells

description: Previously, we have identified the Grainyhead transcription factor 2 gene (GRHL2) as notably hypomethylated in high-grade (HG) serous epithelial ovarian tumors, compared with normal ovarian tissues. GRHL2 is known for its functions in normal tissue development and wound healing. In the context of cancer, the role of GRHL2 is still ambiguous as both tumorigenic and tumor suppressive functions have been reported for this gene, although a role of GRHL2 in maintaining the epithelial status of cancer cells has been suggested. In this study, we report that GRHL2 is strongly overexpressed in both low malignant potential (LMP) and HG serous epithelial ovarian tumors, which probably correlates with its hypomethylated status. Suppression of the GRHL2 expression led to a sharp decrease in cell proliferation, migration and invasion and induced G1 cell cycle arrest in epithelial ovarian cancer (EOC) cells displaying either epithelial (A2780s) or mesenchymal (SKOV3) phenotypes. However, no phenotypic alterations were observed in these EOC cell lines following GRHL2 silencing. Gene expression profiling and consecutive canonical pathway and network analyses confirmed these data, as in both these EOC cell lines, GRHL2 ablation was associated with the downregulation of various genes and pathways implicated in cell growth and proliferation, cell cycle control and cellular metabolism. Taken together, our data are indicative for a strong oncogenic potential of the GRHL2 gene in EOC progression and support recent findings on the role of GRHL2 as one of the major phenotypic stability factors (PSFs) that stabilize the highly aggressive/metastatic hybrid epithelial/mesenchymal (E/M) phenotype of cancer cells.
DOI: 10.6084/m9.figshare.4738600
title: BRCA1 recruitment to damaged DNA sites is dependent on CDK9

description: Double strand break lesions, the most toxic type of DNA damage, are repaired primarily through 2 distinct pathways: homology-directed recombination (HR) and non-homologous end-joining (NHEJ). BRCA1 and 53BP1, 2 proteins containing the BRCT modular domain, play an important role in DNA damage response (DDR) by orchestrating the decision between HR and NHEJ, but the precise mechanisms regarding both pathways are not entirely understood. Previously, our group identified a putative interaction between BRCA1 and BARD1 (BRCA1-associated RING domain 1) and the cyclin-dependent kinase (CDK9). CDK9 is a component of the positive transcription elongation complex and has been implicated in genome integrity maintenance associated with the replication stress response. Here we show that CDK9 interacts with endogenous BRCA1 and BARD1 mediated by their RING finger and BRCT domains, and describe CDK9 ionizing radiation-induced foci (IRIF) formation and its co-localization with BRCA1 in DNA damage sites. Cells lacking CDK9 are characterized by an altered γ−H2AX foci dynamics after DNA damage, a reduced efficiency in HR but not in NHEJ repair, failure to form BRCA1 and RAD51 IRIF and increased sensitivity to genotoxic agents. These data indicate that CDK9 is a player in the DDR and is consistent with its participation in HR pathway by modulating BRCA1 response.
DOI: 10.6084/m9.figshare.4738609.v1
title: Comparative Analyses Identify Molecular Signature of MRI-Classified SVZ-associated Glioblastoma

description: Glioblastoma (GBM) is a highly aggressive brain cancer with limited therapeutic options. While efforts to identify genes responsible for GBM have revealed mutations and aberrant gene expression associated with distinct types of GBM, patients with GBM are often diagnosed and classified based on MRI features. Therefore, we seek to identify molecular representatives in parallel with MRI classification for group I and group II primary GBM associated with the subventricular zone (SVZ). As group I and II GBM contain stem-like signature, we compared gene expression profiles between these two groups of primary GBM and endogenous neural stem progenitor cells to reveal dysregulation of cell cycle, chromatin status, cellular morphogenesis, and signaling pathways in these two types of MRI-classified GBM. In the absence of IDH mutation, several genes associated with metabolism are differentially expressed in these subtypes of primary GBM, implicating metabolic reprogramming occurs in tumor microenvironment. Furthermore, histone lysine methyltransferase EZH2 was up-regulated while histone lysine demethylases KDM2 and KDM4 were down-regulated in both group I and II primary GBM. Lastly, we identified nine common genes across large data sets of gene expression profiles among MRI-classified group I/II GBM, a large cohort of GBM subtypes from TCGA, and glioma stem cells by unsupervised clustering comparison. These commonly upregulated genes have known functions in cell cycle, centromere assembly, chromosome segregation, and mitotic progression. Our findings highlight altered expression of genes important in chromosome integrity across all GBM, suggesting a common mechanism of disrupted fidelity of chromosome structure in GBM.