cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16633032.v1
title: Additional file 2 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 2: Table S2. List of ZYTLF-targets, PMOP-genes, and ZYTLF-PMOP overlapping genes.
DOI: 10.6084/m9.figshare.16633038
title: Additional file 4 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 4: Table S4. Results of Gene Ontology (GO) terms and pathways.
DOI: 10.6084/m9.figshare.15064861
title: Additional file 3 of Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits

description: Additional file 3: Table S3. Haplotype associations of the haplotype blocks in HTR1B gene with milk fatty acids (LSM ± SE).
DOI: 10.6084/m9.figshare.15064864
title: Additional file 4 of Determination of genetic effects and functional SNPs of bovine HTR1B gene on milk fatty acid traits

description: Additional file 4: Table S4. PCR primers information of HTR1B gene.
DOI: 10.6084/m9.figshare.7725155
title: Table S2 from Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in <i>Brassica rapa</i> L.

description: Ka/Ks analysis for the gene pairs with collinearity relationship.
DOI: 10.6084/m9.figshare.11919555.v1
title: Aberrant hydroxymethylation of <i>ANGPTL4</i> is associated with selective intrauterine growth restriction in monochorionic twin pregnancies

description: Selective intrauterine growth restriction (sIUGR) is a severe complication in monochorionic (MC) twin pregnancies, and it carries increased risks of poor prognosis. Current data suggest that vascular anastomoses and unequal placental sharing may be the key contributor to discordant foetal growth. While MC twins derive from a single zygote and have almost identical genetic information, the precise mechanisms remain unknown. DNA hydroxymethylation is a newly discovered epigenetic feature associated with gene regulation and modification. Here, we investigate discordant hydroxymethylation patterns between two placental shares of sIUGR and analyse the potential role of aberrant hydroxymethylation of angiopoietin-like 4 (<i>ANGPTL4</i>) in placental dysplasia. Hydroxymethylation DNA immunoprecipitation (hMeDIP)-chip and mRNA sequencing were performed to identify hydroxymethylation-associated genes. Real-time qPCR, western blotting, and immunohistochemistry were used to confirm <i>ANGPTL4</i> expression. The mechanisms regulating <i>ANGPTL4</i> were investigated by cell migration assay, invasion assay, viability assay, and apoptotic ratio assays, western blotting and hMeDIP-qPCR. Decreased <i>ANGPTL4</i> was detected in the smaller placental shares of sIUGR. <i>ANGPTL4</i> knockdown suppressed trophoblast invasiveness and migration, which possibly occurred through hypoxia inducible factor 1α (<i>HIF-1α</i>) and <i>HIF-1</i> signalling pathway. Hypoxia leads to aberrant expression of <i>ANGPTL4</i> and <i>HIF-1α</i>, positively correlated with their aberrant hydroxymethylation levels in promoter regions. Aberrant hydroxymethylation of <i>ANGPTL4</i> may contribute to placental impairment by the <i>HIF-1</i> signalling pathway in smaller placental shares of sIUGR.
DOI: 10.7266/n78k773n
title: XBT data from Northern Gulf of Mexico October 27- 28, 2015
DOI: 10.6084/m9.figshare.7724945
title: Identiﬁcation of a novel antisense RNA that regulates growth hormone receptor expression in chickens

description: Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identiﬁed a novel antisense transcript in the chicken, designated <i>GHR-AS-EST</i>, transcribed from the growth hormone receptor (<i>GHR</i>) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. <i>GHR-AS-EST</i> is predominantly expressed in the chicken liver and muscle tissues. <i>GHR-AS-EST</i> sequence conservation among vertebrates is weak. <i>GHR-AS-EST</i> forms an RNA–RNA duplex with <i>GHBP</i> to increase its stability, and regulates the expression of <i>GHR</i> sense transcripts at both the mRNA and protein levels. Further, <i>GHR-AS-EST</i> promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.
DOI: 10.6084/m9.figshare.23978271
title: Extreme Changes in Changes*

description: Policy analysts are often interested in treating the units with extreme outcomes, such as infants with extremely low birth weights. Existing changes-in-changes (CIC) estimators are tailored to middle quantiles and do not work well for such subpopulations. This paper proposes a new CIC estimator to accurately estimate treatment effects at extreme quantiles. With its asymptotic normality, we also propose a method of statistical inference, which is simple to implement. Based on simulation studies, we propose to use our extreme CIC estimator for extreme quantiles, while the conventional CIC estimator should be used for intermediate quantiles. Applying the proposed method, we study the effects of income gains from the 1993 EITC reform on infant birth weights for those in the most critical conditions. This paper is accompanied by a Stata command.
DOI: 10.6084/m9.figshare.18211425.v1
title: Transcriptome analysis revealing molecular mechanisms of enhanced pigment yield by succinic acid and fluconazole

description: This study aimed to elucidate the molecular mechanisms through which succinic acid and fluconazole stimulate <i>Monascus</i> pigment biosynthesis under liquid fermentation conditions. The pigment yield was significantly improved by adding 0.35 g·L<sup>−1</sup> succinic acid or 1.5 g·L<sup>−1</sup> fluconazole. Transcriptome sequencing and RT-qPCR confirmation were performed to reveal transcriptome changes. The results indicated that the addition of succinic acid significantly decreased mRNA expression of genes involved in fatty acid biosynthesis while increasing expression of genes involved in pyruvate metabolism. Fluconazole significantly down-regulated transcripts involved in branched-chain amino acid metabolism, fatty acid metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism, as well as the generation of acetyl-CoA for pigment biosynthesis. On the other hand, nitrogen metabolism and lysine degradation pathways were significantly enriched, which could stimulate the generation of acetyl-CoA. Therefore, the mechanism for enhancing pigment yield may be attributed to the competitive regulation of metabolic pathways toward acetyl-CoA biosynthesis. Additionally, up-regulation of some different key genes in the presence of fluconazole or succinic acid was involved in improving pigment production. This study deepens the theoretical understanding for enhancing pigment biosynthesis and provides a few potential approaches for improving pigment yield.
DOI: 10.6084/m9.figshare.23978271.v1
title: Extreme Changes in Changes*

description: Policy analysts are often interested in treating the units with extreme outcomes, such as infants with extremely low birth weights. Existing changes-in-changes (CIC) estimators are tailored to middle quantiles and do not work well for such subpopulations. This paper proposes a new CIC estimator to accurately estimate treatment effects at extreme quantiles. With its asymptotic normality, we also propose a method of statistical inference, which is simple to implement. Based on simulation studies, we propose to use our extreme CIC estimator for extreme quantiles, while the conventional CIC estimator should be used for intermediate quantiles. Applying the proposed method, we study the effects of income gains from the 1993 EITC reform on infant birth weights for those in the most critical conditions. This paper is accompanied by a Stata command.
DOI: 10.6084/m9.figshare.17162885
title: Additional file 2 of Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

description: Additional file 2: Table S1. Phenotypic evaluation of 234 soybean accessions
DOI: 10.6084/m9.figshare.17162891
title: Additional file 4 of Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

description: Additional file 4: Table S2. Resistance-related SNPs and adjacent SNPs formed two haplotype blocks on chromosomes 5 and 20
DOI: 10.6084/m9.figshare.11919417
title: Additional file 1 of Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age

description: Table S1. Cohort-specific results from epigenome-wide association analyses of gestational age. Table S2. Normalization technique and phenotype definitions used by each cohort. Table S3. Bonferroni-significant CpGs from the meta-analysis on the association between continuous gestational age (no complications model) and offspring DNA methylation at birth adjusted for estimated cell counts. Table S4. Bonferroni-significant CpGs from the meta-analysis on the association between continuous gestational age (all births model) and offspring DNA methylation at birth adjusted for estimated cell counts. Table S5. Gene regions that had at least three consecutive Bonferroni significant CpG sites from the continuous gestational age analyses (no complications model). Table S6. DMRs (n = 2375) for gestational age in relation to newborn methylation (no complication model) identified by using both comb-p (P &lt; 0.01) and DMRcate (FDR &lt; 0.01) methods. Table S7. DNA methylation analyses in fetal lung tissue using the no complication gestational age three or more consecutive CpG list. Table S8. DNA methylation analyses in fetal brain tissue using the no complication gestational age three or more consecutive CpG list. Table S9. Methylation look-up analyses in older children using the no complication gestational age three or more consecutive CpG list. Table S10. Longitudinal analysis of methylation levels in the INMA and ALSPAC studies using the no complication gestational age three or more consecutive CpG list. Table S11. Gene Ontology (GO) term enrichment analyses for bonferroni-significant CpGs from the meta-analysis (no complications model). Table S12. KEGG pathway analyses for bonferroni-significant CpGs from the meta-analysis (no complications model). Table S13. Gene Ontology (GO) term enrichment analyses for three or more CpGs being localized to the same gene. Table S14. KEGG pathway analyses for stable and dynamic CpGs. Table S15. Correlation between methylation and gene expression levels in cord blood (cis-effects). Table S16. The replication of bonferroni-significant CpGs from the meta-analysis (no complications model) in previous publication.
DOI: 10.5281/zenodo.10684655
title: MoMA Collection - Automatic Update

description: Temporary Description
DOI: 10.5281/zenodo.10684656
title: MoMA Collection - Automatic Update

description: Temporary Description
DOI: 10.6084/m9.figshare.14541033.v1
title: Targeting the KRAS α4-α5 allosteric interface inhibits pancreatic cancer tumorigenesis

description: <i>RAS</i> is the most frequently mutated oncogene in human cancer with nearly ~20% of cancer patients possessing mutations in one of three <i>RAS</i> genes (<i>K, N</i> or <i>HRAS</i>). However, <i>KRAS</i> is mutated in nearly 90% of pancreatic ductal carcinomas (PDAC). Although pharmacological inhibition of RAS has been challenging, KRAS(G12C)-specific inhibitors have recently entered the clinic. While KRAS(G12C) is frequently expressed in lung cancers, it is rare in PDAC. Thus, more broadly efficacious RAS inhibitors are needed for treating KRAS mutant-driven cancers such as PDAC. A RAS-specific tool biologic, NS1 Monobody, inhibits HRAS- and KRAS-mediated signalling and oncogenic transformation both <i>in vitro</i> and <i>in vivo</i> by targeting the α4–α5 allosteric site of RAS and blocking RAS self-association. Here, we evaluated the efficacy of targeting the α4-α5 interface of KRAS as an approach to inhibit PDAC development using an immunocompetent orthotopic mouse model. Chemically regulated NS1 expression inhibited ERK and AKT activation in KRAS(G12D) mutant KPC PDAC cells and reduced the formation and progression of pancreatic tumours. NS1-expressing tumours were characterized by increased infiltration of CD4 + T helper cells. These results suggest that targeting the #x3B1;4-#x3B1;5 allosteric site of KRAS may represent a viable therapeutic approach for inhibiting KRAS-mutant pancreatic tumours.
DOI: 10.6084/m9.figshare.7725125.v1
title: Table S1 from Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in <i>Brassica rapa</i> L.

description: 134 RBOH genes identified in the 13 species examined.
DOI: 10.6084/m9.figshare.6152351
title: Experimental study on the self-suspending proppant-laden flow in a single fracture

description: Abstract The flow of proppant-laden fluid (PLF) in the fracture is a typical problem of solid-liquid two phase flow, and the transportation and deposition of proppants are essential to determine the flow conductivity of hydraulic fracturing. The self-suspending proppant with a water soluble surface coating is a newly presented supporting material and has great potential for hydraulic fracturing. The purpose of this paper is to understand the physical process, and investigate the effect of the self-suspending proppant on particle placement and transportation in the fracture. Two experiments of the PLF flow were conducted in a fracture, using the common ceramic proppant and self-suspending proppant, respectively. The fracture was formed by two parallel plexiglass planes, and was 4000 mm in length, 10 mm in width and 600 mm in height. It was found that four different zones developed when proppants were injected into the fracture continuously, which were the proppant bank zone, tumbling zone, suspending zone, and free zone. Compared with the common proppant, the self-suspending proppant changes the particle distribution in the fracture, and increases the thickness of proppant suspending and bank zone. The motion behavior of self-suspending proppants in the fracture is described. The conclusion is that appropriate reduction in the proppant concentration and density is beneficial to the good distribution and transportation of proppants in the fracture, and the self-suspending proppant favors the effective supporting of fracture.
DOI: 10.6084/m9.figshare.7725152
title: Table S3 from Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in <i>Brassica rapa</i> L.

description: qRT-PCR primers used to detect the expression of RBOH genes in A. thaliana and B. rapa.
DOI: 10.6084/m9.figshare.7725152.v1
title: Table S3 from Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in <i>Brassica rapa</i> L.

description: qRT-PCR primers used to detect the expression of RBOH genes in A. thaliana and B. rapa.
DOI: 10.6084/m9.figshare.12968089.v1
title: Dynamic changes of throat swabs RNA and serum antibodies for SARS-CoV-2 and their diagnostic performances in patients with COVID-19

description: Dynamic changes of RNA and antibodies in SARS-CoV-2 infected patients remain largely unknown, and influence factors for antibody production have not been fully clarified. In this study, consecutive throat swabs specimens (<i>n</i> = 1875) from 187 patients were collected to analyse the dynamic changes of RNA. Moreover, 162 serial serum samples from 31 patients were tested for seroconversion of IgM and IgG. Meanwhile, IgM and IgG were also detected in 409 COVID-19 patients and 389 controls. Additionally, the logistic regression analysis was executed to identify the possible influence factors for antibody production. The median positive conversion time for RNA was day 7 (IQR, 3–11), and the positive rate was highest in day 1–5 (74.59 %) and then gradually decreased. The median time of seroconversion for IgM and IgG were both day 12 (IQR, 10–15). The sensitivity and specificity for IgM (or IgG) was 87.04% and 96.92%, respectively. Multivariate logistic regression indicated that reduced lymphocytes and short positive conversion time for SARS-CoV-2 RNA were independent factors for negative results of IgM and IgG. In conclusion, RNA and antibodies should be combined for COVID-19 diagnosis, and delayed seroconversion was influenced by the decreased lymphocytes and short positive conversion time for RNA.
DOI: 10.6084/m9.figshare.17162985
title: Additional file 6 of Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research

description: Additional file 6: Table S4. Gene expression stability calculated by 5 algorithms in all BC tissue and cell line samples.
DOI: 10.6084/m9.figshare.11919555
title: Aberrant hydroxymethylation of <i>ANGPTL4</i> is associated with selective intrauterine growth restriction in monochorionic twin pregnancies

description: Selective intrauterine growth restriction (sIUGR) is a severe complication in monochorionic (MC) twin pregnancies, and it carries increased risks of poor prognosis. Current data suggest that vascular anastomoses and unequal placental sharing may be the key contributor to discordant foetal growth. While MC twins derive from a single zygote and have almost identical genetic information, the precise mechanisms remain unknown. DNA hydroxymethylation is a newly discovered epigenetic feature associated with gene regulation and modification. Here, we investigate discordant hydroxymethylation patterns between two placental shares of sIUGR and analyse the potential role of aberrant hydroxymethylation of angiopoietin-like 4 (<i>ANGPTL4</i>) in placental dysplasia. Hydroxymethylation DNA immunoprecipitation (hMeDIP)-chip and mRNA sequencing were performed to identify hydroxymethylation-associated genes. Real-time qPCR, western blotting, and immunohistochemistry were used to confirm <i>ANGPTL4</i> expression. The mechanisms regulating <i>ANGPTL4</i> were investigated by cell migration assay, invasion assay, viability assay, and apoptotic ratio assays, western blotting and hMeDIP-qPCR. Decreased <i>ANGPTL4</i> was detected in the smaller placental shares of sIUGR. <i>ANGPTL4</i> knockdown suppressed trophoblast invasiveness and migration, which possibly occurred through hypoxia inducible factor 1α (<i>HIF-1α</i>) and <i>HIF-1</i> signalling pathway. Hypoxia leads to aberrant expression of <i>ANGPTL4</i> and <i>HIF-1α</i>, positively correlated with their aberrant hydroxymethylation levels in promoter regions. Aberrant hydroxymethylation of <i>ANGPTL4</i> may contribute to placental impairment by the <i>HIF-1</i> signalling pathway in smaller placental shares of sIUGR.
DOI: 10.6084/m9.figshare.17162894
title: Additional file 5 of Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

description: Additional file 5: Table S3. Functional classification of genes in two haplotype blocks on chromosomes 5 and 20
DOI: 10.6084/m9.figshare.17162900
title: Additional file 7 of Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

description: Additional file 7: Table S5. KEGG pathway analysis of genes in the two haplotype blocks
DOI: 10.6084/m9.figshare.19254598
title: Additional file 2 of Comprehensive analysis of SPAG1 expression as a prognostic and predictive biomarker in acute myeloid leukemia by integrative bioinformatics and clinical validation

description: Additional file 2: Different expressed genes correlated with SPAG1 expression.
DOI: 10.6084/m9.figshare.19254598.v1
title: Additional file 2 of Comprehensive analysis of SPAG1 expression as a prognostic and predictive biomarker in acute myeloid leukemia by integrative bioinformatics and clinical validation

description: Additional file 2: Different expressed genes correlated with SPAG1 expression.
DOI: 10.6084/m9.figshare.17162759.v1
title: Additional file 12 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

description: Additional file 12 Supplementary Datasets (S1-S6) provide the identified F-box protein sequences for C. brenneri, C. briggsae, C. elegans, C. japonica, C. remanei, and P. pacificus, respectively.
DOI: 10.6084/m9.figshare.17162762
title: Additional file 13 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

description: Additional file 13: Supplementary File 1. shows the analysis results of gene structural and functional diversification and selection pressure of closely related paralogs from C.elegans and C.briggsae, respectively.
DOI: 10.6084/m9.figshare.17162762.v1
title: Additional file 13 of Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

description: Additional file 13: Supplementary File 1. shows the analysis results of gene structural and functional diversification and selection pressure of closely related paralogs from C.elegans and C.briggsae, respectively.
DOI: 10.6084/m9.figshare.19254628.v1
title: Additional file 2 of Abundant expression of ferroptosis-related SAT1 is related to unfavorable outcome and immune cell infiltration in low-grade glioma

description: Additional file 2: Table S2. The correlation between SAT1 gene expression levels and immune cell infiltration.
DOI: 10.25402/fon.19260296.v1
title: Supplementary Tables – Androgen receptor expression and its prognostic value in T1N0 Luminal/HER2− breast cancer

description: <b>Supplementary
 Table 1. </b> Androgen receptor
 expression and its prognostic value in T1N0 Luminal/HER2− breast cancer<b></b>
 <i>Effects of ER and
 PR on AR expression across the 20th, 45th, 60th and 80th quantiles of the AR expression distribution.</i>
DOI: 10.6084/m9.figshare.11401506
title: Syntheses, structures and properties of two zinc(II) coordination complexes based on two bis(pyridyl)-bis(amide) ligands and 1,2-phenylenediacetic acid

description: Two new zinc(II) coordination complexes [Zn(pda)(3-bpcd)<sub>0.5</sub>] (<b>1</b>) and [Zn(pda)(3-bpoa)]·H<sub>2</sub>O (<b>2</b>) have been synthesized by self-assembly of 1,2-phenylenediacetic acid (H<sub>2</sub>pda), semi-rigid/or flexible bis(pyridyl)-bis(amide) ligands [3-bpcd = N,N′-bis(pyridin-3-yl)cyclohexane-1,4-dicarboxamide, 3-bpoa = N,N'-bis(3-pyridyl)octandiamide] and zinc nitrate. Complex <b>1</b> is a 2 D layered framework derived from the 1 D [Zn(pda)]<sub>2n</sub> ribbon-like chain and the bidentate 3-bpcd, which is a (3,4)-connected (4<sup>2</sup>·6<sup>3</sup>·8)(4<sup>2</sup>·6) topology, then the adjacent layers are linked by hydrogen bonds to build a 3 D supramolecular network. Complex <b>2</b> displays a 3 D framework based on the 1 D [Zn(pda)]<sub>2n</sub> ribbon-like chains and the 1 D [Zn(3-bpoa)]<sub>n</sub> chains, which represents a (3,5)-connected (4<sup>2</sup>.6<sup>5</sup>.8<sup>3</sup>)(4<sup>2</sup>.6) topology. Two bis(pyridyl)-bis(amide) ligands with different flexibilities play an important role in constructing final topological structures for title complexes. Moreover, the fluorescent properties of two zinc(II) complexes and their fluorescent sensing properties toward small solvent molecules have been studied. Additionally, the photocatalytic properties of complexes <b>1 </b>−<b> 2</b> toward the degradation of dyes have been investigated.