cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7729910.v1
title: Additional file 14: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The promoter regions of TaGT and BdGT genes in different subfamilies. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7729922
title: Additional file 16: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Paralogous TaGT gene pairs. (XLSX 18 kb)
DOI: 10.25407/jacbts.8254469
title: Figure 7: Cardiac Wavelength

description: <b>(A)</b> The critical cardiac wavelength (λc) in Ctrl (n = 7) and MI/iAL (n = 7) wedges. λc was defined as the cardiac wavelength during hypokalemia at the fastest pacing rate before initiation of re-entrant VT/VF (Supplemental Video 1), loss of 1:1 capture, or at the end of the protocol if neither occurred. <b>(B)</b> Individual values of λc. Abbreviations as in Figures 1 and 2.
DOI: 10.6084/m9.figshare.7729883
title: Additional file 10: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The cis-elements in promoter sequences of Trihelix genes in wheat. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.7729883.v1
title: Additional file 10: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The cis-elements in promoter sequences of Trihelix genes in wheat. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.7729895
title: Additional file 12: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The promoter regions of TaGT and BdGT genes contained plant growth/development - and stress response-related cis-elements. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.7729958.v1
title: Additional file 20: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and O.sativa. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7729931
title: Additional file 17: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Paralogous BdGT gene pairs. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7729988.v1
title: Additional file 23: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and Zea mays. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7730018.v1
title: Additional file 28: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and Zea mays. (XLSX 14 kb)
DOI: 10.7910/dvn/9vakfy/nmdb2g
title: Introduction to China Data Online and China Data Lab.pdf

description: :unav
DOI: 10.6084/m9.figshare.6681443
title: Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data

description: Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.
DOI: 10.6084/m9.figshare.7730039
title: Additional file 31: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Gene-specific primer sequences for qRT-PCR. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7730039.v1
title: Additional file 31: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Gene-specific primer sequences for qRT-PCR. (XLSX 14 kb)
DOI: 10.25407/jacbts.8254235
title: Figure 4: Prolonged PF-1355 Treatment Improves Cardiac Function and Remodeling

description: Infarcted mice were divided into 3 groups: untreated (MI-no Tx, n = 6), treated for 21 days (MI-21 days Tx, n = 5), and treated for first 7 days only and then treatment stopped until day 21 for imaging (MI-7 days Tx, n = 8). <b>(A to C)</b> Representative midventricular magnetic resonance images obtained at day 21 after MI. Videos obtained from the same mice at day 2 and day 21 are shown in the Supplemental Video 1. <b>(D)</b> There is significant improvement in ejection fraction (EF) in the 21-day treatment group as compared with untreated infarcts; however, the 7-day treatment group did not show significant improvement. <b>(E) Bar graphs</b> representing end-diastolic volume (EDV). <b>(F)</b> Left ventricular mass is less in the 21-day treatment group representing decreased remote myocardial hypertrophy and improved remodeling. Data plotted as mean ± SEM. *p &lt; 0.05; ***p &lt; 0.001. MI = myocardial infarction; Tx = treatment.
DOI: 10.6084/m9.figshare.7729958
title: Additional file 20: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and O.sativa. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.20306707
title: Additional file 2 of Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats

description: Additional file 2.
DOI: 10.6084/m9.figshare.7730030
title: Additional file 2: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The detailed information of BdGT genes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7729967.v1
title: Additional file 21: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and Hordeum vulgare. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.11924403.v1
title: Additional file 1 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 1: Table S1. The epicardial adipose tissue (EAT) development was correlated with pathways based on time series-related GSEA.
DOI: 10.6084/m9.figshare.11924421.v1
title: Additional file 4 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 4: Table S4. The immunocyte infiltration detection of the GSE82155 and GSE115799 datasets.
DOI: 10.6084/m9.figshare.11924433
title: Additional file 6 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 6: Table S6.Pearsonâ€™s correlation coefficient values of hub miRNAs and monocyte infiltration level.
DOI: 10.6084/m9.figshare.7729988
title: Additional file 23: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and Zea mays. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.12448871.v2
title: Optimal Sampling for Generalized Linear Models Under Measurement Constraints

description: Under “measurement constraints,” responses are expensive to measure and initially unavailable on most of records in the dataset, but the covariates are available for the entire dataset. Our goal is to sample a relatively small portion of the dataset where the expensive responses will be measured and the resultant sampling estimator is statistically efficient. Measurement constraints require the sampling probabilities can only depend on a very small set of the responses. A sampling procedure that uses responses at most only on a small pilot sample will be called “response-free.” We propose a response-free sampling procedure optimal sampling under measurement constraints (OSUMC) for generalized linear models. Using the A-optimality criterion, that is, the trace of the asymptotic variance, the resultant estimator is statistically efficient within a class of sampling estimators. We establish the unconditional asymptotic distribution of a general class of response-free sampling estimators. This result is novel compared with the existing conditional results obtained by conditioning on both covariates and responses. Under our unconditional framework, the subsamples are no longer independent and new martingale techniques are developed for our asymptotic theory. We further derive the A-optimal response-free sampling distribution. Since this distribution depends on population level quantities, we propose the OSUMC algorithm to approximate the theoretical optimal sampling. Finally, we conduct an intensive empirical study to demonstrate the advantages of OSUMC algorithm over existing methods in both statistical and computational perspectives. We find that OSUMC’s performance is comparable to that of sampling algorithms that use complete responses. This shows that, provided an efficient algorithm such as OSUMC is used, there is little or no loss in accuracy due to the unavailability of responses because of measurement constraints. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7730000
title: Additional file 25: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and O.sativa. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7730069.v1
title: Additional file 7: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Representing number of Trihelix genes present in different plant species. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.11924412.v1
title: Additional file 2 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 2: Table S2. The differentially expressed mRNAs and lncRNAs were identified in multiple comparisons among the EAT samples at different developmental stages.
DOI: 10.6084/m9.figshare.11924418
title: Additional file 3 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 3: Table S3. The Gene Ontology enrichment terms for codifferentially expressed mRNAs among the neonatal, infant and child EAT samples.
DOI: 10.25407/jacbts.8254469.v1
title: Figure 7: Cardiac Wavelength

description: <b>(A)</b> The critical cardiac wavelength (λc) in Ctrl (n = 7) and MI/iAL (n = 7) wedges. λc was defined as the cardiac wavelength during hypokalemia at the fastest pacing rate before initiation of re-entrant VT/VF (Supplemental Video 1), loss of 1:1 capture, or at the end of the protocol if neither occurred. <b>(B)</b> Individual values of λc. Abbreviations as in Figures 1 and 2.
DOI: 10.6084/m9.figshare.11924421
title: Additional file 4 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 4: Table S4. The immunocyte infiltration detection of the GSE82155 and GSE115799 datasets.
DOI: 10.6084/m9.figshare.7730006
title: Additional file 26: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and Hordeum vulgare. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.11924634.v1
title: Additional file 2 of Spatio-temporal variations of licensed doctor distribution in China: measuring and mapping disparities

description: Additional file 2: Table S1. The number of different subtypes of licensed doctors in each provincial unit during 2012–2016.
DOI: 10.6084/m9.figshare.11924646
title: Additional file 3 of Spatio-temporal variations of licensed doctor distribution in China: measuring and mapping disparities

description: Additional file 3: Table S2. The number of population in each provincial unit during 2012–2016.
DOI: 10.6084/m9.figshare.7730012.v1
title: Additional file 27: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and Sorghum bicolor. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.11924433.v1
title: Additional file 6 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 6: Table S6.Pearsonâ€™s correlation coefficient values of hub miRNAs and monocyte infiltration level.
DOI: 10.6084/m9.figshare.11924646.v1
title: Additional file 3 of Spatio-temporal variations of licensed doctor distribution in China: measuring and mapping disparities

description: Additional file 3: Table S2. The number of population in each provincial unit during 2012–2016.
DOI: 10.6084/m9.figshare.7730045
title: Additional file 33: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Raw data (including DNA sequences and amino acids) of TaGT and BdGT genes sequences. (FA 396 kb)
DOI: 10.6084/m9.figshare.11924436.v1
title: Additional file 7 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 7: Table S7. The gene set enrichment analysis after grouping by the monocyte infiltration level, CACNA2D4 and MIR210HG expression value.
DOI: 10.6084/m9.figshare.11924802.v1
title: Additional file 12 of The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants

description: Additional file 12. Data sources.
DOI: 10.34740/kaggle/dsv/7666043
title: Balochi Language to English Translation Dataset
DOI: 10.6084/m9.figshare.5108737
title: Direct Likelihood Evaluation for the Renewal Hawkes Process

description: An interesting extension of the widely applied Hawkes self-exiting point process, the renewal Hawkes (RHawkes) process, was recently proposed by Wheatley, Filimonov, and Sornette, which has the potential to significantly widen the application domains of the self-exciting point processes. However, they claimed that computation of the likelihood of the RHawkes process requires exponential time and therefore is practically impossible. They proposed two expectation–maximization (EM) type algorithms to compute the maximum likelihood estimator (MLE) of the model parameters. Because of the fundamental role of likelihood in statistical inference, a practically feasible method for likelihood evaluation is highly desirable. In this article, we provide an algorithm that evaluates the likelihood of the RHawkes process in quadratic time, a drastic improvement from the exponential time claimed by Wheatley, Filimonov, and Sornette. We demonstrate the superior performance of the resulting MLEs of the model relative to the EM estimators through simulations. We also present a computationally efficient procedure to calculate the Rosenblatt residuals of the process for goodness-of-fit assessment, and a simple yet efficient procedure for future event prediction. The proposed methodologies were applied on real data from seismology and finance. An R package implementing the proposed methodologies is included in the supplementary materials.
DOI: 10.5066/p9rmd98m
title: Vegetation and fuels data collected in 2010 and 2011 from historical emergency stabilization and rehabilitation seedings (1990 - 2003) on BLM lands within the Great Basin

description: Data are contained in a Microsoft Access database consisting of 27 data tables. Tables provided include emergency stabilization and rehabilitation (ESR) projects sampled, study plot characteristics, and sampled vegetation and fuels data. All data are from Bureau of Land Management (BLM) federal lands within the Great Basin region of the intermountain west.
DOI: 10.6084/m9.figshare.11924412
title: Additional file 2 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 2: Table S2. The differentially expressed mRNAs and lncRNAs were identified in multiple comparisons among the EAT samples at different developmental stages.
DOI: 10.6084/m9.figshare.5633299
title: PINK1-PRKN/PARK2 pathway of mitophagy is activated to protect against renal ischemia-reperfusion injury

description: Damaged or dysfunctional mitochondria are toxic to the cell by producing reactive oxygen species and releasing cell death factors. Therefore, timely removal of these organelles is critical to cellular homeostasis and viability. Mitophagy is the mechanism of selective degradation of mitochondria via autophagy. The significance of mitophagy in kidney diseases, including ischemic acute kidney injury (AKI), has yet to be established, and the involved pathway of mitophagy remains poorly understood. Here, we show that mitophagy is induced in renal proximal tubular cells in both in vitro and in vivo models of ischemic AKI. Mitophagy under these conditions is abrogated by <i>Pink1</i> and <i>Park2</i> deficiency, supporting a critical role of the PINK1-PARK2 pathway in tubular cell mitophagy. Moreover, ischemic AKI is aggravated in <i>pink1</i> and<i>park2</i> single- as well as double-knockout mice. Mechanistically, <i>Pink1</i> and <i>Park2</i> deficiency enhances mitochondrial damage, reactive oxygen species production, and inflammatory response. Taken together, these results indicate that PINK1-PARK2-mediated mitophagy plays an important role in mitochondrial quality control, tubular cell survival, and renal function during AKI.
DOI: 10.6084/m9.figshare.11924418.v1
title: Additional file 3 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 3: Table S3. The Gene Ontology enrichment terms for codifferentially expressed mRNAs among the neonatal, infant and child EAT samples.
DOI: 10.6084/m9.figshare.11924427
title: Additional file 5 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 5: Table S5. The competing endogenous RNA (ceRNA) regulatory network construction.
DOI: 10.6084/m9.figshare.11924436
title: Additional file 7 of Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease

description: Additional file 7: Table S7. The gene set enrichment analysis after grouping by the monocyte infiltration level, CACNA2D4 and MIR210HG expression value.
DOI: 10.6084/m9.figshare.11924814
title: Additional file 1 of The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants

description: Additional file 1. Details of 124 gene family members and their encoded proteins.
DOI: 10.6084/m9.figshare.6681662.v1
title: Early Butyrate Induced Acetylation of Histone H4 is Proteoform Specific and Linked to Methylation State

description: Histone posttranslational modifications (PTMs) help regulate DNA templated processes; however, relatively little work has unbiasedly explored the single-molecule combinations of histone PTMs, their dynamics on short timescales, or how these preexisting histone PTMs modulate further histone modifying enzyme activity. We use quantitative top down proteomics to unbiasedly measure histone H4 proteoforms (single-molecule combinations of PTMs) upon butyrate treatment. Our results show that histone proteoforms change in cells within 10 minutes of application of sodium butyrate. Cells recover from treatment within 30 minutes after removal of butyrate. Surprisingly, K20me2 containing proteoforms are the near-exclusive substrate of histone acetyltransferases upon butyrate treatment. Single-molecule hierarchies of progressive PTMs mostly dictate the addition and removal of histone PTMs (K16ac&gt;K12ac≥K8ac&gt;K5ac, and the reverse on recovery). This reveals the underlying single-molecule mechanism that explains the previously reported but indistinct and unexplained patterns of H4 acetylation. Thus, preexisting histone PTMs strongly modulate histone modifying enzyme activity and this suggests that proteoform constrained reaction pathways are crucial mechanisms that enable the long-term stability of the cellular epigenetic state. [<i>Keywords</i>: histone posttranslational modifications; histone proteoforms; dynamics of histone proteoforms; epigenetic inhibitors; top down proteomics]
DOI: 10.6084/m9.figshare.11400219
title: China Meteorological Forcing Dataset - Ancillary Data

description: Ancillary data of the China Meteorological Forcing Dataset, e.g. terrain elevation.
DOI: 10.6084/m9.figshare.11400219.v1
title: China Meteorological Forcing Dataset - Ancillary Data

description: Ancillary data of the China Meteorological Forcing Dataset, e.g. terrain elevation.
DOI: 10.6084/m9.figshare.17161636.v1
title: Additional file 3 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 3: Table S4. Associations of 84 gut bacterial genera with obesity and US exposure after further adjusted for Hispanic background.
DOI: 10.6084/m9.figshare.17161639
title: Additional file 4 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 4: Table S5. Associations of 84 gut bacterial genera with US exposure and all covariates in the multivariable regression model.
DOI: 10.7910/dvn/otyquy/zllzvu
title: An Introduction to the Data Resources for Covid-19 Studies.pdf

description: The first webinar for introducingCOVID-19 research project.
DOI: 10.7910/dvn/otyquy/26h57z
title: Data_Descripton_for COVID-19.pdf

description: An Introduction to research data for COVID-19 study on dataVerse and the Cloud
DOI: 10.7910/dvn/otyquy/8ygsna
title: Introductions to Baidu Mobility Data_EN.pptx

description: Introdutions to Baidu mobility data and priliminary studies
DOI: 10.7910/dvn/otyquy/pfmwsd
title: Introduction to Mobile Population Data

description: This talk introduced the mobile population data from Baidu and migration data from the Census data of China. It also introduced some workflows for mobile population data analysis.