cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7705508
title: Additional file 8: of A role for actomyosin contractility in Notch signaling

description: Raw data file. Data analyzed for the main and supplemental figures. (XLSX 245 kb)
DOI: 10.6084/m9.figshare.7705694.v1
title: Additional file 2: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: The sequencing and mapped results obtained from each sample. (XLS 22 kb)
DOI: 10.6084/m9.figshare.7705700
title: Additional file 3: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Identification of known genes and new genes in the transcriptome data for eighteen samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7705763
title: Additional file 12: of Genome changes due to artificial selection in U.S. Holstein cattle

description: Data Set1. SNP and pedigree data of the University of Minnesota Holstein control line unselected since 1964. (ZIP 5309 kb)
DOI: 10.6084/m9.figshare.7705934.v1
title: Additional file 1: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Statistical data of the mapped reads. (XLS 11 kb)
DOI: 10.6084/m9.figshare.7705763.v1
title: Additional file 12: of Genome changes due to artificial selection in U.S. Holstein cattle

description: Data Set1. SNP and pedigree data of the University of Minnesota Holstein control line unselected since 1964. (ZIP 5309 kb)
DOI: 10.6084/m9.figshare.7705946.v1
title: Additional file 3: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The novel lncRNAs predicted in this study. (XLS 105 kb)
DOI: 10.6084/m9.figshare.11900472
title: Preoperative serum total cholesterol is a predictor of prognosis in patients with renal cell carcinoma: a meta-analysis of observational studies

description: ABSTRACT Purpose Several studies have demonstrated the strong correlation between the levels of preoperative serum total cholesterol (TC) and the survival of patients with surgically treated renal cell carcinoma (RCC). However, this association remains controversial. We performed a meta-analysis of published reports to evaluate the prognostic significance of the preoperative serum TC levels for patients with surgically treated RCC. Material and Methods The databases from MEDLINE (via PubMed), Embase, Web of Science and Cochrane Library were systematically searched to identify the eligible studies published before August 2019. Multivariate adjusted hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated through inverse variance by using random-effects models. Results Nine cohort studies comprising 15.609 patients were identified. Low preoperative serum TC levels were associated with poor cancer-specific survival (CSS; HR=0.98, 95% CI: 0.97-0.99; P=0.005; I2=74.2%) and progression-free survival (PFS; HR=0.69, 95% CI: 0.49-0.98; P=0.036; I2=80%) in patients with surgically treated RCC. However, no significant association was observed between low preoperative serum TC levels and shorter overall survival (HR=0.93, 95% CI: 0.87-1.00; P=0.057; I2=86.2%). Sensitivity analyses validated the reliability and rationality of the results. Conclusions Preoperative serum TC level is an independent poor prognostic factor for patients with surgically treated RCC, with lower levels associated with worse CSS and PFS. Hence, this parameter may provide additional guidance in the selection of therapeutic strategies to improve prognosis, considering that cholesterol is a broadly applied routine marker in clinical practice.
DOI: 10.6084/m9.figshare.24118007
title: A national-scale trophic state analysis to prioritize lakes for restoration in Aotearoa New Zealand

description: Pressure on lakes in Aotearoa New Zealand is increasing because of elevated catchment nutrient loads, establishment of non-native species, and climate change. Current government legislation requires that pressures are managed to avoid eutrophication and degradation of lake health. This approach requires information on the state of lakes at regional and national scales, which is challenging because &lt;5% are currently monitored. In this study, we (1) modelled lake trophic status at a national scale using a highly representative dataset and lake characteristics, land use, and environmental parameters as predictor variables; and (2) identified lakes that should be prioritized for protection to prevent further degradation. Six statistical models were evaluated, with extreme boosting producing the highest predictive power and lowest error. This model indicated that for the 3738 lakes in the dataset, 44% were eutrophic or higher trophic state, 22% mesotrophic, and 34% oligotrophic or lower trophic state. These data provide a benchmark to guide management and support the call for more resourcing to restore lakes in Aotearoa New Zealand. To identify lakes to prioritise for protection, we focused on the ∼800 mesotrophic lakes. We used (1) the portion of lake catchment not within conservation estate, and (2) road access as proxies for the likelihood of land-use intensification and the introduction of non-native species, respectively. We identified &gt;170 lakes with limited catchment protection and easy human access. Immediate attention should be given to protecting these waterbodies to prevent the need for costly and resource-intensive remediation in the future.
DOI: 10.6084/m9.figshare.11899983.v1
title: Constrained Varying-coefficient Model for Time-Course Experiments in Soft Tissue Fabrication

description: In the fabrication of artificial soft tissues, novel biomaterials with the required properties are obtained by appropriately adjusting process parameters during material synthesis. One key step in finding the desired material is understanding the relationship between the process parameters and the material properties, and time-course experiments are typically conducted for this purpose. This article proposes a constrained varying-coefficient modeling method for such data in which expert knowledge is properly accommodated in the model estimation to make the modeling practically meaningful. The proposed model has a semi-parametric structure and incorporates expert knowledge in the form of constraints on model coefficients. Estimation algorithms based on a smoothing spline and a weighted smoothing spline are also provided. Finally, the proposed method is compared with existing methods in a case study and a numerical study.
DOI: 10.6084/m9.figshare.7705973.v1
title: Additional file 7: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The differential expressed lncRNAs in this study. (XLS 63 kb)
DOI: 10.6084/m9.figshare.12947837
title: Additional file 8 of Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study

description: Additional file 8. Supplemental Table 7. List of 2958 upstream regulators identified for the 10,053 DEGs between HLC_SM and PHHs.
DOI: 10.6084/m9.figshare.7182047
title: Raw data in text format from Effect of components on the curing of glycidyl azide polymer spherical propellant through rheological method

description: Raw data of four curing system (A: IPDI/GAP Spherical Propellant (pure curing system); B: 0.1Cl-20 curing system; C: 0.1AP curing system; D: 0.1RDX curing system) at 50℃, 55℃, 60℃ and 65℃.
DOI: 10.6084/m9.figshare.7705979.v1
title: Additional file 8: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The precursor analysis of the new lncRNAs. (XLS 23 kb)
DOI: 10.6084/m9.figshare.15568297
title: Additional file 5 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 5.
DOI: 10.6084/m9.figshare.7705541
title: Additional file 1: of Transcriptome and metabolome analyses of two contrasting sesame genotypes reveal the crucial biological pathways involved in rapid adaptive response to salt stress

description: Table S1. Summary of RNA-Seq data. Table S2. Significantly enriched KEGG pathways of the DEGs in ST and SS in response to salt stress (P-Valueâ &lt;â 0.05). Table S3. List of genes that were exclusively up-regulated in ST genotype at all salt stress time points. Table S4. List of the core gene set involved in sesame response to salt stress. Table S5. GO terms enriched amongst the core salt-responsive genes in sesame (top 30 terms only). Table S6. The core metabolites involved in sesame response to salt stress. Table S7. The metabolites increased significantly and exclusively in ST genotype in response to salt stress. Table S8. Primers used in qRT-PCR analysis. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.7706030.v1
title: MOESM3 of Characterization of type I and type II diacylglycerol acyltransferases from the emerging model alga Chlorella zofingiensis reveals their functional complementarity and engineering potential

description: Additional file 3: Data S1. Prediction of possible binding sites of MYB and bZIP at the promoter regions (2.0 kb) of CzDGAT1A and CzDGTT5 using the software PlantPAN 2.0 ( http://plantpan2.itps.ncku.edu.tw/ ).
DOI: 10.6084/m9.figshare.7705964.v1
title: Additional file 2: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S2. Summary of mapping reads of the RNA-Seq (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7705967.v1
title: Additional file 6: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Pathway-enrichment analysis for DEGs. (XLS 68 kb)
DOI: 10.6084/m9.figshare.7705976
title: Additional file 4: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S4. Gene accession numbers and sequences of 520 DEGs (XLSX 478 kb)
DOI: 10.6084/m9.figshare.7706030
title: MOESM3 of Characterization of type I and type II diacylglycerol acyltransferases from the emerging model alga Chlorella zofingiensis reveals their functional complementarity and engineering potential

description: Additional file 3: Data S1. Prediction of possible binding sites of MYB and bZIP at the promoter regions (2.0 kb) of CzDGAT1A and CzDGTT5 using the software PlantPAN 2.0 ( http://plantpan2.itps.ncku.edu.tw/ ).
DOI: 10.6084/m9.figshare.7705586.v1
title: Additional file 2: of Prevalence of human papillomavirus infection of 65,613 women in East China

description: Table S2. The all multiple HPV infection mode in participants. (XLSX 29â kb)
DOI: 10.6084/m9.figshare.7705976.v1
title: Additional file 4: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S4. Gene accession numbers and sequences of 520 DEGs (XLSX 478 kb)
DOI: 10.6084/m9.figshare.7705982.v1
title: Additional file 5: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S5. DEGs at 12 d after low N stress in XZ149 and XZ56 (XLSX 160 kb)
DOI: 10.6084/m9.figshare.7706057.v1
title: Additional file 2: of Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm

description: Supplementary tables. (ZIP 3966 kb)
DOI: 10.6084/m9.figshare.11375616
title: Table S3 from Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3

description: Gata3 is a DNA-binding transcription factor involved in cellular differentiation in a variety of tissues including inner ear, hair follicle, kidney, mammary gland and T-cells. In a previous study in 2009, Maeda <i>et al</i>. (<i>Dev. Dyn.</i> <b>238</b>, 2280–2291; doi:10.1002/dvdy.22035) found that Gata3 mutants could be rescued from midgestational lethality by the expression of a Gata3 transgene in sympathoadrenal neuroendocrine cells. The rescued embryos clearly showed multiple defects in lens fibre cell differentiation. To determine whether these defects were truly due to the loss of Gata3 expression in the lens, we generated a lens-specific Gata3 loss-of-function model. Analogous to the previous findings, our Gata3 null embryos showed abnormal regulation of cell cycle exit during lens fibre cell differentiation, marked by reduction in the expression of the cyclin-dependent kinase inhibitors Cdkn1b/p27 and Cdkn1c/p57, and the retention of nuclei accompanied by downregulation of Dnase IIβ. Comparisons of transcriptomes between control and mutated lenses by RNA-Seq revealed dysregulation of lens-specific crystallin genes and intermediate filament protein Bfsp2. Both Cdkn1b/p27 and Cdkn1c/p57 loci are occupied <i>in vivo</i> by Gata3, as well as Prox1 and c-Jun, in lens chromatin. Collectively, our studies suggest that Gata3 regulates lens differentiation through the direct regulation of the Cdkn1b/p27and Cdkn1c/p57 expression, and the direct/or indirect transcriptional control of Bfsp2 and Dnase IIβ.
DOI: 10.6084/m9.figshare.7705922.v1
title: Additional file 10: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Differential expression lncRNAs cis- and trans-target genes. (XLS 100 kb)
DOI: 10.6084/m9.figshare.7705946
title: Additional file 3: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The novel lncRNAs predicted in this study. (XLS 105 kb)
DOI: 10.6084/m9.figshare.7705646.v1
title: Additional file 10: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: KEGG pathways significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘SJ’ and ‘SX’. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7705649.v1
title: Additional file 11: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Sugar-related DEGs in two longan cultivars during the floral induction process. Red indicates the genes that showed upregulated expression; blue indicates the genes that showed downregulated expression. (XLSX 48 kb)
DOI: 10.5281/zenodo.10683229
title: GPR - AUGMENTED 2
DOI: 10.5281/zenodo.10683298
title: GPR - AUGMENTED 2
DOI: 10.6084/m9.figshare.11899983
title: Constrained Varying-Coefficient Model for Time-Course Experiments in Soft Tissue Fabrication

description: In the fabrication of artificial soft tissues, novel biomaterials with the required properties are obtained by appropriately adjusting process parameters during material synthesis. One key step in finding the desired material is understanding the relationship between the process parameters and the material properties, and time-course experiments are typically conducted for this purpose. This article proposes a constrained varying-coefficient modeling method for such data in which expert knowledge is properly accommodated in the model estimation to make the modeling practically meaningful. The proposed model has a semiparametric structure and incorporates expert knowledge in the form of constraints on model coefficients. Estimation algorithms based on a smoothing spline and a weighted smoothing spline are also provided. Finally, the proposed method is compared with existing methods in a case study and a numerical study.
DOI: 10.6084/m9.figshare.7705685.v1
title: Additional file 1: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: List of primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7705967
title: Additional file 6: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Pathway-enrichment analysis for DEGs. (XLS 68 kb)
DOI: 10.6084/m9.figshare.7705724
title: Additional file 8: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: DEGs in â SXâ during floral induction. (XLS 7771 kb)
DOI: 10.6084/m9.figshare.7705724.v1
title: Additional file 8: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: DEGs in â SXâ during floral induction. (XLS 7771 kb)
DOI: 10.6084/m9.figshare.7705985.v1
title: Additional file 9: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Target miRNAs of the DEKLs and DENLs. (XLS 46 kb)
DOI: 10.6084/m9.figshare.7706048.v1
title: Additional file 1: of Persistent mutant oncogene specific T cells in two patients benefitting from anti-PD-1

description: Table S1. Sequence alterations detected in the primary tumor of LUAD-3001, Table S2. Sequence alterations detected in the primary tumor of CRC-010, Table S3. Specimen characteristics used for genomic and immunologic analyses, Table S4. Putative neoantigens tested in LUAD-3001, Table S5. Putative neoantigens tested in CRC-010, Table S6. Neoantigen-specific T cell clonotypes detected in patients LUAD-3001 and CRC-010 (XLSX 98 kb)
DOI: 10.6084/m9.figshare.7705991.v1
title: Additional file 7: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S6. DEGs consistently expressed at three time points under low N stress in each genotype (XLSX 13 kb)
DOI: 10.5281/zenodo.10509497
title: MIND-small Frames

description: Blinded information for submission. More details will be provided after the review process has concluded.
DOI: 10.5281/zenodo.10509498
title: MIND-small Frames

description: Blinded information for submission. More details will be provided after the review process has concluded.
DOI: 10.6084/m9.figshare.7181891
title: Analysis of genetic structure in a large sample of pomegranate (<i>Punica granatum</i> L.) using fluorescent SSR markers

description: Molecular markers are helpful to efficiently protect the plant breeders’ rights. Fluorescent simple sequence repeats (SSR) based on DNA sequencing is a powerful and automated platform for the detection of genetic polymorphism. Here, we first reported 13 SSRs using a fluorescent SSR panel according to the reference genome information, and detected the genetic diversity and population structure of 136 pomegranate varieties. The average number of alleles per locus was 6.31, gene diversity ranged from 0.16 to 0.37 with an average of 0.28, and polymorphic information content (PIC) varied from 0.14 to 0.29 with a mean value of 0.22. The mean genetic distance (GD) between varieties was 0.32. Population structure analysis divided the varieties into three different subpopulations (Q1, Q2, and Q3). The cultivars in Q1 all came from China, and almost all cultivars came from foreign countries combined with Chinese were grouped into Q2. The only accession originated from Myanmar was grouped to Q3. The results indicated that 13 SSR markers were polymorphic. The varieties originating from the same geographical region were more closely related, and extensive gene flow had taken place between the varieties from different regions. The results may be useful for the efficient selection breeding and variety protection.
DOI: 10.6084/m9.figshare.20288763
title: Log Files for Usage and interaction with Online Video Course Material for an Undergraduate Course

description: Usage logfiles capturing interactions for undergraduate students accessing educational video content for an online course. Log file includes all interactions with 52 individual video files and include timestamped keystroke/button press level access covering play, stop, rewind, fast forward, and volume adjustment.
DOI: 10.6084/m9.figshare.7706060
title: Additional file 3: of Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm

description: DNA methylation data for cord blood. (PHENO 2410 kb)
DOI: 10.6084/m9.figshare.12949349
title: The role of non-axisymmetry of magnetic flux rope in constraining solar eruptions

description: fig1.sav: Data for plotting Figure 1;<br>fig2.sav: Data for plotting Figure 2;fig3.sav: Data for plotting Figure 3;fig4.sav: Data for plotting Figure 4;fig5.sav: Data for plotting Figure 5;fig6.sav: Data for plotting Figure 6;fig7.sav: Data for plotting Figure 7;<br>fig8.sav: Data for plotting Figure 8;<br>sfig1.sav: Data for plotting Supplementary Figure 1;sfig2.sav: Data for plotting Supplementary Figure 2;sfig3.sav: Data for plotting Supplementary Figure 3;sfig4.sav: Data for plotting Supplementary Figure 4;sfig5.sav: Data for plotting Supplementary Figure 5;sfig6.sav: Data for plotting Supplementary Figure 6;sfig7.sav: Data for plotting Supplementary Figure 7;sfig8.sav: Data for plotting Supplementary Figure 8;sfig9.sav: Data for plotting Supplementary Figure 9;All files can be opened in Interactive Data Language (IDL) with command 'restore,filename'.<br>
DOI: 10.6084/m9.figshare.8305133
title: MOESM10 of Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

description: Additional file 10. The amino acid sequence of the candidates assigned to the GH5 family.
DOI: 10.6084/m9.figshare.8305136
title: MOESM11 of Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

description: Additional file 11: Table S8. The primers used in RT-PCR amplification of the selected ORFs assigned to the GH5 family.
DOI: 10.6084/m9.figshare.8305136.v1
title: MOESM11 of Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

description: Additional file 11: Table S8. The primers used in RT-PCR amplification of the selected ORFs assigned to the GH5 family.
DOI: 10.6084/m9.figshare.7705955
title: Additional file 4: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The differential expression genes identified in Prunus mume buds by RNA-Seq. (XLS 391 kb)
DOI: 10.6084/m9.figshare.7705982
title: Additional file 5: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S5. DEGs at 12 d after low N stress in XZ149 and XZ56 (XLSX 160 kb)
DOI: 10.6084/m9.figshare.7705997.v1
title: Additional file 9: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S7. Enzymes and sequences in one KEGG pathway (XLSX 12 kb)
DOI: 10.6084/m9.figshare.15569205
title: Additional file 3 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

description: Additional file 3. Relative abundances of genes differentially expressed in microglia isolated from the spinal cord and cortex of rNLS8 control mice.