cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9980423
title: MOESM7 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 7. Related to Fig. 4. Complete set of probe-level CGI correlations between DNA methylation and nearby SSV event, according to regression model applied (i.e. what covariates were considered). Results by both genomic region windows method (e.g. 0-100â kb upstream, 0-100â kb downstream, or within the gene body) and distance metric method are included. The top significant mRNAs (FDRâ &lt;â 5% by distance metric method, correcting for cancer type and CNA) and related information are highlighted in a separate Excel tab.
DOI: 10.6084/m9.figshare.9980423.v1
title: MOESM7 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 7. Related to Fig. 4. Complete set of probe-level CGI correlations between DNA methylation and nearby SSV event, according to regression model applied (i.e. what covariates were considered). Results by both genomic region windows method (e.g. 0-100â kb upstream, 0-100â kb downstream, or within the gene body) and distance metric method are included. The top significant mRNAs (FDRâ &lt;â 5% by distance metric method, correcting for cancer type and CNA) and related information are highlighted in a separate Excel tab.
DOI: 10.6084/m9.figshare.9980426
title: MOESM8 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 8. Related to Fig. 5. SSV associations with disruption of TADs. All SSVs involving TAD disruption (i.e. SSVs with breakpoints spanning TAD boundaries), as well as the subset of SSVs with breakpoints located in proximity to a gene (0-100â kb upstream, 0-100â kb downstream, or within the gene body) and associated with altered expression or methylation, are included.
DOI: 10.6084/m9.figshare.9980426.v1
title: MOESM8 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 8. Related to Fig. 5. SSV associations with disruption of TADs. All SSVs involving TAD disruption (i.e. SSVs with breakpoints spanning TAD boundaries), as well as the subset of SSVs with breakpoints located in proximity to a gene (0-100â kb upstream, 0-100â kb downstream, or within the gene body) and associated with altered expression or methylation, are included.
DOI: 10.6084/m9.figshare.9980429
title: MOESM9 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 9. Related to Fig. 5. SSV associations with translocated active in vivo-transcribed enhancers. For the enhancer-related analyses of Fig. 5b, the Andersson et al. tissue- or cell-specific enhancer subsets as applied to each TCGA or ICGC project are listed. Results include the subset of SSV breakpoint associations involving the translocation of an active, in vivo-transcribed enhancer within 0.5â Mb of the gene (where the unaltered gene had no enhancer within 1â Mb), for both the entire set of SSV breakpoint associations occurring 0-500â kb upstream of a gene and with breakpoint mate on the distal side from the gene (for cases with WGS), as well as for the subset of SSV breakpoint associations involving altered gene expression or CGI methylation.
DOI: 10.6084/m9.figshare.9980429.v1
title: MOESM9 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 9. Related to Fig. 5. SSV associations with translocated active in vivo-transcribed enhancers. For the enhancer-related analyses of Fig. 5b, the Andersson et al. tissue- or cell-specific enhancer subsets as applied to each TCGA or ICGC project are listed. Results include the subset of SSV breakpoint associations involving the translocation of an active, in vivo-transcribed enhancer within 0.5â Mb of the gene (where the unaltered gene had no enhancer within 1â Mb), for both the entire set of SSV breakpoint associations occurring 0-500â kb upstream of a gene and with breakpoint mate on the distal side from the gene (for cases with WGS), as well as for the subset of SSV breakpoint associations involving altered gene expression or CGI methylation.
DOI: 10.6084/m9.figshare.24136209
title: Additional file 2 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 2. Table S1. mRNA expression profiling of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.6832403.v1
title: Synthesis, Characterization, and Photocatalytic Properties of Flower-like Mn-doped Ceria

description: Mn-doped CeO2 flower-like microstructures have been synthesized by a facile one-step composite-hydroxide-mediated method. The structure, morphology, optical and the surface properties of Mn doped CeO2 have been investigated by X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), UV-Vis absorption spectroscopy and X-ray photoelectron spectroscopy (XPS). The XRD results confirmed the successful incorporation of Mn into the CeO2 lattice through the formation of face-centered cubic solid solution. The photocatalytic activities of the catalysts were evaluated by measuring the photodegradation efficiency of Rhodamine B (RhB) under ultraviolet light irradiation. With an optimal molar ratio of 1% in Mn/CeO2 the highest rate photodegradation was achieved under the experimental conditions. The enhanced photocatalytic activity can be attributed to the incorporation of multivalent Mn in CeO2 promoted the separation of photogenerated charges, inhibited the recombination of photogenerated carriers, and thus prolonged the charges lifetime to participate in the photocatalytic reaction.
DOI: 10.6084/m9.figshare.24136209.v1
title: Additional file 2 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 2. Table S1. mRNA expression profiling of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.6832442
title: Performance of probe polymerization-conjunction-agarose gel electrophoresis in the rapid detection of KRAS gene mutation

description: Abstract This study aimed to develop a simple and rapid method to detect KRAS gene mutations for conventional clinical applications under laboratory conditions. The genotype of mutation sites was determined based on the occurrence of target bands in the corresponding lanes of the reaction tubes through polymerization-conjunction of the probes, probe purification and amplification, and agarose gel electrophoresis. Circulating DNA samples were obtained from the plasma of 72 patients with lung cancer, which were identified based on six mutation sites (G12S, G12R, G12C, G12D, G12A, and G12V) of codon 12 of the KRAS gene. The detection results were compared with direct sequencing data. The proposed detection method is characterized by simple operation, high specificity, and high sensitivity (2%). This method can detect the mutations of three samples at G12S, G12R, and G12A. In the direct sequencing spectra of these samples, the genotype could not be determined due to the lack of evident sequencing peaks that correspond to the basic group of mutations. In conclusion, a simple and rapid method was established based on probe polymerization-conjunction-agarose gel electrophoresis for detecting KRAS gene mutations. This method can be applied to the conventional mutation detection of inhomogeneous samples.
DOI: 10.6084/m9.figshare.6832493
title: A curcumin derivative J147 ameliorates diabetic peripheral neuropathy in streptozotocin (STZ)-induced DPN rat models through negative regulation AMPK on TRPA1

description: Abstract Purpose: To investigate the specific molecular mechanisms and effects of curcumin derivative J147 on diabetic peripheral neuropathy (DPN). Methods: We constructed streptozotocin (STZ)-induced DPN rat models to detected mechanical withdrawal threshold (MWT) in vivo using Von Frey filaments. In vitro, we measured cell viability and apoptosis, adenosine 5‘-monophosphate-activated protein kinase (AMPK) and transient receptor potential A1 (TRPA1) expression using MTT, flow cytometry, qRT-PCR and western blot. Then, TRPA1 expression level and calcium reaction level were assessed in agonist AICAR treated RSC96cells. Results: The results showed that J147reduced MWT in vivo, increased the mRNA and protein level of AMPK, reduced TRPA1 expression and calcium reaction level in AITCR treated RSC96 cells, and had no obvious effect on cell viability and apoptosis. Besides, AMPK negative regulated TRPA1 expression in RSC96 cells. Conclusions: J147 could ameliorate DPN via negative regulation AMPK on TRPA1 in vivo and in vitro. A curcumin derivative J147might be a new therapeutic potential for the treatment of DPN.
DOI: 10.6084/m9.figshare.9980435
title: Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature

description: Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (<i>Oryza sativa</i> L.). Micro-RNAs are 21–24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.
DOI: 10.6084/m9.figshare.5259718
title: Intervention for children with word-finding difficulties: a parallel group randomised control trial

description: <i>Purpose</i>: The study investigated the outcome of a word-web intervention for children diagnosed with word-finding difficulties (WFDs). <i>Method</i>: Twenty children age 6–8 years with WFDs confirmed by a discrepancy between comprehension and production on the Test of Word Finding-2, were randomly assigned to intervention (<i>n</i> = 11) and waiting control (<i>n</i> = 9) groups. The intervention group had six sessions of intervention which used word-webs and targeted children’s meta-cognitive awareness and word-retrieval. <i>Result</i>: On the treated experimental set <i>(n</i> = 25 items) the intervention group gained on average four times as many items as the waiting control group (<i>d</i> = 2.30). There were also gains on personally chosen items for the intervention group. There was little change on untreated items for either group. <i>Conclusion</i>: The study is the first randomised control trial to demonstrate an effect of word-finding therapy with children with language difficulties in mainstream school. The improvement in word-finding for treated items was obtained following a clinically realistic intervention in terms of approach, intensity and duration.
DOI: 10.6084/m9.figshare.6832493.v1
title: A curcumin derivative J147 ameliorates diabetic peripheral neuropathy in streptozotocin (STZ)-induced DPN rat models through negative regulation AMPK on TRPA1

description: Abstract Purpose: To investigate the specific molecular mechanisms and effects of curcumin derivative J147 on diabetic peripheral neuropathy (DPN). Methods: We constructed streptozotocin (STZ)-induced DPN rat models to detected mechanical withdrawal threshold (MWT) in vivo using Von Frey filaments. In vitro, we measured cell viability and apoptosis, adenosine 5‘-monophosphate-activated protein kinase (AMPK) and transient receptor potential A1 (TRPA1) expression using MTT, flow cytometry, qRT-PCR and western blot. Then, TRPA1 expression level and calcium reaction level were assessed in agonist AICAR treated RSC96cells. Results: The results showed that J147reduced MWT in vivo, increased the mRNA and protein level of AMPK, reduced TRPA1 expression and calcium reaction level in AITCR treated RSC96 cells, and had no obvious effect on cell viability and apoptosis. Besides, AMPK negative regulated TRPA1 expression in RSC96 cells. Conclusions: J147 could ameliorate DPN via negative regulation AMPK on TRPA1 in vivo and in vitro. A curcumin derivative J147might be a new therapeutic potential for the treatment of DPN.
DOI: 10.6084/m9.figshare.6832538.v1
title: Nondestructive ultrasonic testing in rod structure with a novel numerical Laplace based wavelet finite element method

description: Abstract Rod structure has been widely used in aerospace engineering and civil engineering. Nondestructive testing is a very important method applied to detect unseen flaws in structures, ultrasonic wave nondestructive testing has been used in many areas. Finite Element Method is one of the most widely used numerical methods but would have a high cost when doing simulation on ultrasonic wave due to the requirement of small time interval and element size. Wavelet based finite element method could improve the spatial resolution with fewer elements needed but still needs very small time interval. Laplace transform could easily convert the time domain into frequency and then inverse to time domain. This paper presents an innovative method combining Laplace transform and B-spline wavelet on interval (BSWI) finite element method, which could not only decrease the element number but also increase the time integration interval. Moreover, this innovative method is applied to simulate the ultrasonic wave propagation in 1D rod structure as well as used for nondestructive testing of damages in rod structures.
DOI: 10.6084/m9.figshare.9980435.v1
title: Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature

description: Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (<i>Oryza sativa</i> L.). Micro-RNAs are 21–24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.
DOI: 10.25387/g3.7356776.v1
title: Supplemental Material for Meng et al., 2019

description: The complex SV discovered by PacBio targeted sequencing data
DOI: 10.6084/m9.figshare.12599530
title: Additional file 3 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 3: Table S3. Summary of synonymous and nonsynonymous somatic mutations identified in the five CRC patients with LM.
DOI: 10.6084/m9.figshare.12599598.v1
title: Additional file 5 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 5: Table S2. LcMYB4 binding proteins in sheegrass seedling
DOI: 10.6084/m9.figshare.24136212
title: Additional file 3 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 3. Table S2. Protein expression profiling of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.24136212.v1
title: Additional file 3 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 3. Table S2. Protein expression profiling of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.6832715
title: Interleukin-4 protects from chemotherapy-induced peripheral neuropathy in mice modal via the stimulation of IL-4/STAT6 signaling

description: Abstract Purpose: To investigate the possible role of IL-4 signaling pathway in vincristine-induced peripheral neuropathy. Methods: The mouse model of vincristine-induced peripheral neuropathy and interleukin (IL)-4 knockout mice were utilized to investigate the possible role of IL-4 signaling pathway in vincristine-induced peripheral neuropathy. Vincristine induced increased sensitivity to mechanical stimulation was measured by von Frey hair test 7 and 14 days after intraperitoneal administration of 0.1 mg/kg vincristine in mice. Relative expression levels of cytokines were detected by quantitative real-time PCR. STAT6 expression following vincristine treatment was assessed with western blotting. Results: We discovered that IL-4/STAT6 signaling was down-regulated in vincristine-treated mice. Deletion of IL-4 in mice increased the sensitivity to mechanical allodynia. IL-4 knockout mice also produced more pro-inflammatory cytokines, including IL-1β and TNF-α. Notably, co-administration of exogenous recombination IL-4 significantly prevented vincristine-induced mechanical allodynia. Conclusion: Anti-inflammatory cytokine IL-4 protects rodent model from vincristine-induced peripheral neuropathy via the stimulation of IL-4/STAT6 signaling and inhibition of the pro-inflammatory cytokines.
DOI: 10.6084/m9.figshare.23084148.v1
title: Additional file 3 of Extracellular arginine availability modulates eIF2α O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis

description: Additional file 3: Table S4. Proteomic raw data. Table S5. AS pathway
DOI: 10.6084/m9.figshare.24136215
title: Additional file 4 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 4. Table S3. CoIP-MS of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.24136215.v1
title: Additional file 4 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 4. Table S3. CoIP-MS of Nsp6OE, Nsp8OE, or MOE and control hESC-CMs.
DOI: 10.6084/m9.figshare.9980441
title: The annotation of upstream open reading frames and N-terminal extensions in 478 eukaryotes

description: The annotation of putative canonical uORFs and N-terminal extensions in 478 eukaryotes.
DOI: 10.6084/m9.figshare.24136218
title: Additional file 5 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 5. Table S4. Primers for RT-qPCR.
DOI: 10.6084/m9.figshare.24136218.v1
title: Additional file 5 of SARS-CoV-2 viral genes Nsp6, Nsp8, and M compromise cellular ATP levels to impair survival and function of human pluripotent stem cell-derived cardiomyocytes

description: Additional file 5. Table S4. Primers for RT-qPCR.
DOI: 10.6084/m9.figshare.6832715.v1
title: Interleukin-4 protects from chemotherapy-induced peripheral neuropathy in mice modal via the stimulation of IL-4/STAT6 signaling

description: Abstract Purpose: To investigate the possible role of IL-4 signaling pathway in vincristine-induced peripheral neuropathy. Methods: The mouse model of vincristine-induced peripheral neuropathy and interleukin (IL)-4 knockout mice were utilized to investigate the possible role of IL-4 signaling pathway in vincristine-induced peripheral neuropathy. Vincristine induced increased sensitivity to mechanical stimulation was measured by von Frey hair test 7 and 14 days after intraperitoneal administration of 0.1 mg/kg vincristine in mice. Relative expression levels of cytokines were detected by quantitative real-time PCR. STAT6 expression following vincristine treatment was assessed with western blotting. Results: We discovered that IL-4/STAT6 signaling was down-regulated in vincristine-treated mice. Deletion of IL-4 in mice increased the sensitivity to mechanical allodynia. IL-4 knockout mice also produced more pro-inflammatory cytokines, including IL-1β and TNF-α. Notably, co-administration of exogenous recombination IL-4 significantly prevented vincristine-induced mechanical allodynia. Conclusion: Anti-inflammatory cytokine IL-4 protects rodent model from vincristine-induced peripheral neuropathy via the stimulation of IL-4/STAT6 signaling and inhibition of the pro-inflammatory cytokines.
DOI: 10.6084/m9.figshare.25150919.v1
title: The statistics for the factor analysis of the IFRS transition

description: The research is based on the recent IMD statistics (2023). In general, the data studied belong to the period 2020–2023. The sample includes 52 countries for which the values of all indicators are given in the IMD (2023) materials, which is necessary for forming a data array without gaps, which is a prerequisite for regression analysis.
DOI: 10.6084/m9.figshare.6832484.v1
title: Impact of 1,25(OH) 2 D 3 on TG content in liver of rats with type 2 diabetes

description: Abstract Purpose: To evaluate the effects of 1,25 dihydroxy vitamin D3 (1,25(OH)2D3) on the content of triglyceride (TG), as well as on the gene and protein expressions of adiponectin receptor 2 (AdipoR2), p38 mitogen-activated protein kinase (P38MAPK), and lipoprotein lipase (LPL) in the liver of rats with type 2 diabetes mellitus (T2DM) so as to provide theoretical basis for exploring the mechanism by which 1,25(OH)2D3 regulates TG. Methods: Wistar rats were divided into four groups (n=25), with different treatments and detected the gene and protein expressions of AdipoR2, p38MAPK, and LPL in the liver tissue by reverse transcription polymerase chain reaction (RT-PCR) and Western blotting. Meanwhile, the content of TG in the liver tissue was detected by the Enzyme-linked immunosorbent assay. Results: The expression of AdipoR2, p38MAPK, LPL gene and protein in the liver of VitD intervention group was significantly higher than that in T2DM group (P &lt;0.05), while the TG content was significantly lower than that in T2DM group (P &lt;0.05). Conclusion: 1,25(OH)2D3 can decrease the content of TG in the liver, and its mechanism may be achieved by upregulating the expressions of AdipoR2, p38MAPK, and LPL in the liver.