cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5624824.v2
title: Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells <i>via</i> P53 signaling

description: Rapid development and deployment of engineered nanomaterials, such as amorphous silica nanoparticles (SiNPs) in various commercial and biomedical applications have raised concerns about their potential adverse health effects, especially their chronic effects which have not been well addressed. In this study, human lung epithelial cells, BEAS-2B were continuously exposed to amorphous SiNPs, 5 μg/mL for 40 passages. We demonstrated here that prolonged exposure of BEAS-2B cells to amorphous SiNPs induced malignant transformation as indicated by enhanced cellular proliferation, anchorage-independent cell growth, and increased cell migration. The transformed cells induced tumorigenesis in nude mice. Furthermore, a comprehensive understanding of genome-wide transcriptional analysis was performed to clarify the molecular mechanisms based on microarray and bioinformatics analysis. Microarray data analysis demonstrated that chronic exposure of SiNPs affected expression of 821 genes, including 5 up-regulated and 816 down-regulated genes. Gene ontology and pathway analysis showed that SiNPs caused significant changes in gene expression patterns related to many important functions and pathways, mainly including response to cellular processes, oxidative stress, DNA damage, and cancer. In addition, Signal-net analysis indicated the most prominent significant role of tumor protein p53 in amorphous SiNPs-induced transformation. Further, data confirmed the inactivated p53 and aberrant p53 signaling under chronic amorphous SiNPs exposure. In summary, our data firstly demonstrated chronically low-dose amorphous SiNPs exposure resulted in malignant transformation of human lung epithelial cell <i>via</i> p53 signaling, which provides new <i>in vitro</i> evidence for the carcinogenicity of amorphous SiNPs.
DOI: 10.6084/m9.figshare.5625403
title: Supplementary File 1. Zebrafish Hair Cell RNA-seq Transcriptome

description: Supplementary File 1. Sheet1: RPKM gene expression values of three biological replicates of zebrafish hair cells and nsSCs. Sheet 2: Uniquely (in red fonts) and differentially (in blue fonts) expressed genes in hair cells and nsSCs.<br>
DOI: 10.6084/m9.figshare.5625403.v1
title: Supplementary File 1. Zebrafish Hair Cell RNA-seq Transcriptome

description: Supplementary File 1. Sheet1: RPKM gene expression values of three biological replicates of zebrafish hair cells and nsSCs. Sheet 2: Uniquely (in red fonts) and differentially (in blue fonts) expressed genes in hair cells and nsSCs.<br>
DOI: 10.6084/m9.figshare.5631751
title: Variants drug-related genes Additional File

description: Additional File containing all functional-variants in drug-related genes from the ExAC data set.
DOI: 10.6084/m9.figshare.5631751.v1
title: Variants_drug_related_genes_AddFile.xlsx

description: Additional File containing all functional-variants in drug-related genes from the ExAC data set.
DOI: 10.6084/m9.figshare.5631751.v2
title: Variants drug-related genes Additional File

description: Additional File containing all functional-variants in drug-related genes from the ExAC data set.
DOI: 10.25919/x1hq-aj21
title: Parkes observations for project P456 semester 2023OCTS_11

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We are therefore now attempting to confirm, or deny, this exciting result. With this proposal we aim to maintain our pre-eminent position in the field.

Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.5281/zenodo.10866728
title: Combined RSEI Water Scores and American Community Survey, 2011–2021

description: This dataset was created for a master's thesis in geography at the University of Utah. County-level RSEI scores and county demographics were combined for a spatiotemporal regression analysis. Counties in the contiguous United States and years 2011–2021 are included.

Risk-Screening Environmental Indicators. Annual, county-level RSEI risk scores for surface water were obtained from the EPA RSEI model through the EasyRSEI Dashboard. RSEI scores are defined as the relative potential for health risks, given the estimated exposure calculated by the EPA. A binary risk indicator was created, signifying whether the county had any risk in a given year.

American Community Survey 5-year estimates. County-level population characteristics were collected as five-year estimates from the American Community Survey, with annual estimates for the survey end year applying to each year from 2011–2021. We used the R tidycensus package to collect variables and geometry from the US Census Bureau API. Variables included total population (scaled by 10,000), percent racial composition (American Indian or Alaska Native, or AIAN; Asian; Black or African American; Native Hawaiian or Other Pacific Islander, or NHPI; Some Other Race; Two or More Races; and White), and percent ethnic composition (Hispanic or Latinx). Each census-defined racial category was collected as non-Hispanic or Latinx, such that each group was mutually exclusive.
DOI: 10.6084/m9.figshare.5633830.v1
title: Liver cancer mapping based on actual medical treatment choices

description: The allocation of medical resources is usually inappropriate in China because it is mainly based on the population of each administrative area. In real life, individual patients make choices based on numerous other factors, such as the quality of medical service, the service capacity of certain hospitals and their own income level. This study aims to reveal the differences between theoretical medical resource allocation and the actual medical treatment choices of liver cancer patients in Shenzhen, China, based on case data from 2010 to 2012. Two categories with six group maps are used to illustrate this situation, including independent charts and analytical method-based thematic maps. Meaningful conclusions are then proposed to improve medical resource allocation.
DOI: 10.6084/m9.figshare.5634523
title: Transcriptome analysis for the restrained stem development of the wheat mutant dms

description: ABSTRACT: Wheat (Triticum aestivum L.) stem development significantly affects grain yield. The dwarf plants (D) of wheat mutant dms was less than 30cm. Here, we were to explore the molecular basis for the restrained stem development of the dwarf plants. The results were reached by compare the young spikes and stems transcriptomes of the tall (T) and D plants of mutant dms. We identified 663 genes highly expressed in stem tips. We identified 997 differentially expressed genes (DEGs) in stem tips between T and D, 403 DEGs were significantly related with stem development. Most biological processes in stem tips on dwarf plants were significantly suppressed, such as phytohormone signaling etc. The sequencing analysis results were confirmed by quantitatively analysis the expression profiles of fourteen key DEGs via real-time QRT-PCR. We identified a group genes related to wheat stem development, identified a group DEGs related to the restrained stem development of D plants of dms. The suppressed phytohormone signaling, carbohydrate transport and metabolism were the major causal factors leading to dwarf plants of D. Our dataset provides a useful resource for investigating wheat stem development.
DOI: 10.6084/m9.figshare.5634523.v1
title: Transcriptome analysis for the restrained stem development of the wheat mutant dms

description: ABSTRACT: Wheat (Triticum aestivum L.) stem development significantly affects grain yield. The dwarf plants (D) of wheat mutant dms was less than 30cm. Here, we were to explore the molecular basis for the restrained stem development of the dwarf plants. The results were reached by compare the young spikes and stems transcriptomes of the tall (T) and D plants of mutant dms. We identified 663 genes highly expressed in stem tips. We identified 997 differentially expressed genes (DEGs) in stem tips between T and D, 403 DEGs were significantly related with stem development. Most biological processes in stem tips on dwarf plants were significantly suppressed, such as phytohormone signaling etc. The sequencing analysis results were confirmed by quantitatively analysis the expression profiles of fourteen key DEGs via real-time QRT-PCR. We identified a group genes related to wheat stem development, identified a group DEGs related to the restrained stem development of D plants of dms. The suppressed phytohormone signaling, carbohydrate transport and metabolism were the major causal factors leading to dwarf plants of D. Our dataset provides a useful resource for investigating wheat stem development.
DOI: 10.6084/m9.figshare.5634598
title: Association of polymorphisms in the heparanase gene (HPSE) with hepatocellular carcinoma in Chinese populations

description: Abstract Heparanase activity is involved in cancer growth and development in humans and single nucleotide polymorphisms (SNPs) in the heparanase gene (HPSE) have been shown to be associated with tumors. In this study, we investigated whether SNPs in HPSE were a risk factor for hepatocellular carcinoma (HCC) by undertaking a comprehensive haplotype-tagging, case-control study. For this, six haplotype-tagging SNPs (htSNPs) in HPSE were genotyped in 400 HCC patients and 480 controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A log-additive model revealed significant correlations between the HPSE polymorphisms rs12331678 and rs12503843 and the risk of HCC in the overall samples (p = 0.0046 and p = 0.0055). When the analysis was stratified based on hepatitis B virus (HBV) carrier status, significant interactions between rs12331678 and rs12503843 and HBV were observed. Conditional logistic regression analysis for the independent effect of one significant SNP suggested that rs12331678 or rs12503843 contributed an independent effect to the significant association with the risk of HCC, respectively. Our findings suggest that the SNPs rs12331678 and rs12503843 are HCC risk factors, although the potential functional roles of these two SNPs remain to be fully elucidated.
DOI: 10.6084/m9.figshare.5634598.v1
title: Association of polymorphisms in the heparanase gene (HPSE) with hepatocellular carcinoma in Chinese populations

description: Abstract Heparanase activity is involved in cancer growth and development in humans and single nucleotide polymorphisms (SNPs) in the heparanase gene (HPSE) have been shown to be associated with tumors. In this study, we investigated whether SNPs in HPSE were a risk factor for hepatocellular carcinoma (HCC) by undertaking a comprehensive haplotype-tagging, case-control study. For this, six haplotype-tagging SNPs (htSNPs) in HPSE were genotyped in 400 HCC patients and 480 controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A log-additive model revealed significant correlations between the HPSE polymorphisms rs12331678 and rs12503843 and the risk of HCC in the overall samples (p = 0.0046 and p = 0.0055). When the analysis was stratified based on hepatitis B virus (HBV) carrier status, significant interactions between rs12331678 and rs12503843 and HBV were observed. Conditional logistic regression analysis for the independent effect of one significant SNP suggested that rs12331678 or rs12503843 contributed an independent effect to the significant association with the risk of HCC, respectively. Our findings suggest that the SNPs rs12331678 and rs12503843 are HCC risk factors, although the potential functional roles of these two SNPs remain to be fully elucidated.
DOI: 10.6084/m9.figshare.5634694
title: Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type

description: Abstract The naturally occurring wild barley mutant eibi1/hvabcg31 suffers from severe water loss due to the permeable leaf cuticle. Eibi1/HvABCG31 encodes a full ATP-binding cassette (ABC) transporter, HvABCG31, playing a role in cutin deposition in the elongation zone of growing barley leaves. The eibi1 allele has pleiotropic effects on the appearance of leaves, plant stature, fertility, spike and grain size, and rate of germination. Comparative transcriptome profile of the leaf elongation zone of the eibi1 mutant as well as its isogenic wild type showed that various pathogenesis-related genes were up-regulated in the eibi1 mutant. The known cuticle-related genes that we analyzed did not show significant expression difference between the mutant and wild type. These results suggest that the pleiotropic effects may be a compensatory consequence of the activation of defense genes in the eibi1 mutation. Furthermore, we were able to find the mutation of the eibi1/hvabcg31 allele by comparing transcript sequences, which indicated that the RNA-Seq is useful not only for researches on general molecular mechanism but also for the identification of possible mutant genes.
DOI: 10.6084/m9.figshare.5634694.v1
title: Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type

description: Abstract The naturally occurring wild barley mutant eibi1/hvabcg31 suffers from severe water loss due to the permeable leaf cuticle. Eibi1/HvABCG31 encodes a full ATP-binding cassette (ABC) transporter, HvABCG31, playing a role in cutin deposition in the elongation zone of growing barley leaves. The eibi1 allele has pleiotropic effects on the appearance of leaves, plant stature, fertility, spike and grain size, and rate of germination. Comparative transcriptome profile of the leaf elongation zone of the eibi1 mutant as well as its isogenic wild type showed that various pathogenesis-related genes were up-regulated in the eibi1 mutant. The known cuticle-related genes that we analyzed did not show significant expression difference between the mutant and wild type. These results suggest that the pleiotropic effects may be a compensatory consequence of the activation of defense genes in the eibi1 mutation. Furthermore, we were able to find the mutation of the eibi1/hvabcg31 allele by comparing transcript sequences, which indicated that the RNA-Seq is useful not only for researches on general molecular mechanism but also for the identification of possible mutant genes.
DOI: 10.6084/m9.figshare.5634703
title: Identification of genes related to high royal jelly production in the honey bee (Apis mellifera) using microarray analysis

description: Abstract China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees. A total of 369 DEGs were identified between high and low royal jelly producing bees. Amongst these DEGs, 201 (54.47%) genes were up-regulated, whereas 168 (45.53%) were down-regulated in high royal jelly-yielding bees. Gene ontology (GO) analyses showed that they are mainly involved in four key biological processes, and pathway analyses revealed that they belong to a total of 46 biological pathways. These results provide a genetic basis for further studies on the molecular mechanisms involved in high royal jelly production.
DOI: 10.6084/m9.figshare.5634703.v1
title: Identification of genes related to high royal jelly production in the honey bee (Apis mellifera) using microarray analysis

description: Abstract China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees. A total of 369 DEGs were identified between high and low royal jelly producing bees. Amongst these DEGs, 201 (54.47%) genes were up-regulated, whereas 168 (45.53%) were down-regulated in high royal jelly-yielding bees. Gene ontology (GO) analyses showed that they are mainly involved in four key biological processes, and pathway analyses revealed that they belong to a total of 46 biological pathways. These results provide a genetic basis for further studies on the molecular mechanisms involved in high royal jelly production.
DOI: 10.6084/m9.figshare.5634718
title: The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes

description: Abstract Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome was A+T-biased (74.13%). Group-II introns were found in the nad1, nad5, and cob genes. The most frequently used codon of protein-coding genes was UAU. Isoleucine was identified as the most common amino acid, while proline was the least common amino acid in protein-coding genes. The gene-arrangement order is nearly the same when compared with other Ascomycota mitogenomes. Phylogenetic relationships based on the shared protein-coding genes revealed that E. album is closely related to the Cordycipitaceae family, with a high-confidence support value (100%). The availability of the mitogenome of E. album will shed light on the molecular systematic and genetic differentiation of this species.
DOI: 10.6084/m9.figshare.5634718.v1
title: The complete mitochondrial genome of Engyodontium album and comparative analyses with Ascomycota mitogenomes

description: Abstract Engyodontium album is a widespread pathogen that causes different kinds of dermatoses and respiratory tract diseases in humans and animals. In spite of its perniciousness, the basic genetic and molecular background of this species remains poorly understood. In this study, the mitochondrial genome sequence of E. album was determined using a high-throughput sequencing platform. The circular mitogenome was found to be 28,081 nucleotides in length and comprised of 17 protein-coding genes, 24 tRNA genes, and 2 rRNA genes. The nucleotide composition of the genome was A+T-biased (74.13%). Group-II introns were found in the nad1, nad5, and cob genes. The most frequently used codon of protein-coding genes was UAU. Isoleucine was identified as the most common amino acid, while proline was the least common amino acid in protein-coding genes. The gene-arrangement order is nearly the same when compared with other Ascomycota mitogenomes. Phylogenetic relationships based on the shared protein-coding genes revealed that E. album is closely related to the Cordycipitaceae family, with a high-confidence support value (100%). The availability of the mitogenome of E. album will shed light on the molecular systematic and genetic differentiation of this species.
DOI: 10.6084/m9.figshare.5634739
title: Glycemic control and adipokines after periodontal therapy in patients with Type 2 diabetes and chronic periodontitis

description: Abstract: The mechanism by which chronic periodontitis (CP) affects type 2 diabetes (T2DM) remains unclear. Therefore, the aim of this study is to evaluate the effects of periodontal therapy (PT) on the glycemic control and adipokines of patients with T2DM and CP with the purpose of elucidating the possible mechanisms by which CP influences T2DM. Forty-four patients with T2DM and CP were randomly divided into two groups according to whether they underwent PT. Periodontal status, blood glucose, and the levels of serum tumor necrosis factor α (TNF-α), interleukin-6 (IL-6), adiponectin (APN), and fibroblast growth factor-21 (FGF-21) were measured at baseline and after 3 months. The results revealed that the probing depth (PD) and attachment loss (AL) were significantly improved, the serum levels of TNF-α and IL-6 were significantly decreased, and APN and FGF-21 exhibited substantial increases in the intervention group after 3 months (p &lt; 0.05), whereas no significant changes were observed in the control group. The glycated hemoglobin (HbA1c) levels in both groups decreased significantly after 3 months compared with baseline (p &lt; 0.05), but the intervention group exhibited a significantly greater change (p &lt; 0.05). In conclusion, PT may relieve periodontal inflammation, which causes a reduction of insulin-antagonizing adipokines and an increase in insulin-sensitizing adipokines, thereby eliciting an improvement in glycemic control.
DOI: 10.6084/m9.figshare.5634739.v1
title: Glycemic control and adipokines after periodontal therapy in patients with Type 2 diabetes and chronic periodontitis

description: Abstract: The mechanism by which chronic periodontitis (CP) affects type 2 diabetes (T2DM) remains unclear. Therefore, the aim of this study is to evaluate the effects of periodontal therapy (PT) on the glycemic control and adipokines of patients with T2DM and CP with the purpose of elucidating the possible mechanisms by which CP influences T2DM. Forty-four patients with T2DM and CP were randomly divided into two groups according to whether they underwent PT. Periodontal status, blood glucose, and the levels of serum tumor necrosis factor α (TNF-α), interleukin-6 (IL-6), adiponectin (APN), and fibroblast growth factor-21 (FGF-21) were measured at baseline and after 3 months. The results revealed that the probing depth (PD) and attachment loss (AL) were significantly improved, the serum levels of TNF-α and IL-6 were significantly decreased, and APN and FGF-21 exhibited substantial increases in the intervention group after 3 months (p &lt; 0.05), whereas no significant changes were observed in the control group. The glycated hemoglobin (HbA1c) levels in both groups decreased significantly after 3 months compared with baseline (p &lt; 0.05), but the intervention group exhibited a significantly greater change (p &lt; 0.05). In conclusion, PT may relieve periodontal inflammation, which causes a reduction of insulin-antagonizing adipokines and an increase in insulin-sensitizing adipokines, thereby eliciting an improvement in glycemic control.