cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7962884.v1
title: RAB2 regulates the formation of autophagosome and autolysosome in mammalian cells

description: Multiple sources contribute membrane and protein machineries to construct functional macroautophagic/autophagic structures. However, the underlying molecular mechanisms remain elusive. Here, we show that RAB2 connects the Golgi network to autophagy pathway by delivering membrane and by sequentially engaging distinct autophagy machineries. In unstressed cells, RAB2 resides primarily in the Golgi apparatus, as evidenced by its interaction and colocalization with GOLGA2/GM130. Importantly, autophagy stimuli dissociate RAB2 from GOLGA2 to interact with ULK1 complex, which facilitates the recruitment of ULK1 complex to form phagophores. Intriguingly, RAB2 appears to modulate ULK1 kinase activity to propagate signals for autophagosome formation. Subsequently, RAB2 switches to interact with autophagosomal RUBCNL/PACER and STX17 to further specify the recruitment of HOPS complex for autolysosome formation. Together, our study reveals a multivalent pathway in bulk autophagy regulation, and provides mechanistic insights into how the Golgi apparatus contributes to the formation of different autophagic structures. ACTB: actin beta; ATG9: autophagy related 9A; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BCAP31: B cell receptor associated protein 31; BECN1: beclin 1; Ctrl: control; CQ: chloroquine; CTSD: cathepsin D; DMSO: dimethyl sulfoxide; EBSS: Earle’s balanced salt solution; EEA1: early endosome antigen 1; GDI: guanine nucleotide dissociation inhibitor; GFP: green fluorescent protein; GOLGA2: golgin A2; HOPS: homotypic fusion and protein sorting complex; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LC3: microtubule-associated protein 1 light chain 3; OE: overexpression; PtdIns3K: class III phosphatidylinositol 3-kinase; SQSTM1/p62: sequestosome 1; RAB2: RAB2A, member RAS oncogene family; RAB7: RAB7A, member RAS oncogene family; RAB11: RAB11A, member RAS oncogene family; RUBCNL/PACER: rubicon like autophagy enhancer; STX17: syntaxin 17; TBC1D14: TBC1 domain family member 14; TFRC: transferrin receptor; TGOLN2: trans-golgi network protein 2; TUBB: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VPS41: VPS41, HOPS complex subunit; WB: western blot; WT: wild type; YPT1: GTP-binding protein YPT1.
DOI: 10.6084/m9.figshare.11108627
title: Forensic features and genetic structure of the Hotan Uyghur inferred from 27 forensic markers

description: <b>Background:</b> The Uyghur is the fifth largest group in China and also the largest ethnic minority in Xinjiang. <b>Aim:</b> To explore the genetic variations of 27 forensic genetic markers included in the newly developed SureID<sup>®</sup> PanGlobal Human DNA Identification System and analyse the genetic relationship between Xinjiang Uyghur and their neighbours. <b>Subjects and methods:</b> We genotyped 27 markers in 2,189 unrelated Uyghur individuals from the Hotan Prefecture in Southwest Xinjiang. Comprehensive population genetic studies among Chinese populations and worldwide populations were conducted via various statistics. <b>Results:</b> The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the new-generation autosomal STR amplification system in the Hotan Uyghur are 9,9999-E01 and 9,9999-E01, respectively. Population genetic studies indicate that the Hotan Uyghur show a close genetic relationship with geographically different Uyghurs and Kazakhs, while significant genetic differentiation exists between the Hotan Uyghur and some ethnicities from other non-Turkic-speaking populations. The results of population comparisons among the 52 worldwide populations demonstrate that geographically approached intercontinental populations have close genetic relationships. <b>Conclusions:</b> 24 autosomal STRs are highly polymorphic and informative in the Uyghur and this system is suitable for forensic personal identification and paternity testing. Our findings not only reveal that Chinese Uyghur is a homogenous population based on forensic genetic markers, but also indicate that population genetic affinity is closely related to the adjacent populations with common ethnic origin.
DOI: 10.6084/m9.figshare.11108627.v1
title: Forensic features and genetic structure of the Hotan Uyghur inferred from 27 forensic markers

description: <b>Background:</b> The Uyghur is the fifth largest group in China and also the largest ethnic minority in Xinjiang. <b>Aim:</b> To explore the genetic variations of 27 forensic genetic markers included in the newly developed SureID<sup>®</sup> PanGlobal Human DNA Identification System and analyse the genetic relationship between Xinjiang Uyghur and their neighbours. <b>Subjects and methods:</b> We genotyped 27 markers in 2,189 unrelated Uyghur individuals from the Hotan Prefecture in Southwest Xinjiang. Comprehensive population genetic studies among Chinese populations and worldwide populations were conducted via various statistics. <b>Results:</b> The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the new-generation autosomal STR amplification system in the Hotan Uyghur are 9,9999-E01 and 9,9999-E01, respectively. Population genetic studies indicate that the Hotan Uyghur show a close genetic relationship with geographically different Uyghurs and Kazakhs, while significant genetic differentiation exists between the Hotan Uyghur and some ethnicities from other non-Turkic-speaking populations. The results of population comparisons among the 52 worldwide populations demonstrate that geographically approached intercontinental populations have close genetic relationships. <b>Conclusions:</b> 24 autosomal STRs are highly polymorphic and informative in the Uyghur and this system is suitable for forensic personal identification and paternity testing. Our findings not only reveal that Chinese Uyghur is a homogenous population based on forensic genetic markers, but also indicate that population genetic affinity is closely related to the adjacent populations with common ethnic origin.
DOI: 10.25549/usctheses-ouc11364004
title: A comparison of educationally related opinions and perceptions of community organization members with a random sample of voters
DOI: 10.25549/usctheses-ouc11258096
title: 00001.tif
DOI: 10.25549/usctheses-ouc11258107
title: Microsoft Word - MartinsB_Dissertation_Final_2017_FINAL.docx
DOI: 10.5281/zenodo.10635927
title: Macrorhamphosodes_uradoi_FMNH_121213_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10635928
title: Macrorhamphosodes_uradoi_FMNH_121213_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.21065552
title: Transcriptome analysis of strawberry (<i>Fragaria</i> × <i>ananasa</i>) responsive to <i>Colletotrichum gloeosporioides</i> inoculation and mining of resistance genes

description: Strawberry has high nutritional and economic value and is an important horticultural crop widely cultivated worldwide. Strawberry anthracnose is the most harmful disease in strawberry production, which causes huge production losses every year. Mining disease resistance genes and breeding high-quality strawberry varieties are the fundamental way to solve the problem of strawberry anthracnose. In this study, transcriptome analysis and disease resistance-related genes mining were targeted on strawberry anthracnose. The main results are as follows: (1) A total of 100.45 Gb clean reads were obtained, with no less than 6.26 Gb for each sample; (2) The clean reads for each sample were aligned to the reference genome efficiently at 91.30% − 92.27%; (3) 93,042 genes were annotated; (4) 16 anti-anthracnose-related genes were identified, including <i>FaAUX</i>1, <i>FaARF</i>18, <i>FaSAUR</i>50, <i>FaGH</i>3.6, <i>FaAHP</i>1, <i>FaARR</i> (3, 5 and 11), <i>FaPYR</i>1<i>, FaPYL</i>11, <i>FaPP2C</i> (6, 16, 24, 37 and 51) and <i>FaPR</i>1. The above results can provide theoretical guidance for the molecular breeding of disease resistance of strawberry.
DOI: 10.6084/m9.figshare.21065462.v1
title: Identification of <i>Cladosporium fulvum</i> infection responsive genes in tomato through cDNA-AFLP

description: Tomato (<i>Solanum lycopersicum</i>) is one of the highest-value vegetable crops worldwide, but tomato planting can be easily affected by leaf mold. Tomato leaf mold disease is caused by <i>Cladosporium fulvum,</i> and plants carrying the Cf genes have effective resistance to <i>C. fulvum</i>. To identify leaf mold resistant varieties and screen for specific cDNA amplified fragment length polymorphism (cDNA-AFLP) molecular markers, tomato plants harbouring genes <i>Cf-5</i>, <i>Cf-11</i>, <i>Cf-19</i>, and the moneymaker (MM) tomato line (without Cf gene) were used as plant materials. The changes in reactive oxygen species (ROS) levels and antioxidant activities of plant leaves after inoculation of <i>C. fulvum</i> were measured. Ethylene (ETH), abscisic acid (ABA) and salicylic acid (SA) contents were also determined. The results revealed that the ROS levels in <i>Cf-19</i> tomato were the most sensitive to <i>C. fulvum</i> inoculation, while in MM they were the least. The antioxidant enzymes of <i>Cf</i>-carrying plants exhibited different activities as compared to those of MM. In the cDNA-AFLP analysis data, the expression of <i>ERF109</i>, sedoheptulose-1,7-bisphosphatase (SBPase), L-ascorbic acid oxidase (AAO) and Thioredoxin H2 (TRX2) were different between <i>Cf</i>-gene carriers and MM plants. In summary, in the process of leaf–mold interaction, the outbreak of ROS and development of systemic acquired resistance (SAR) are tightly combined with antioxidant enzymes, including thioredoxin. Tomato plants carrying the <i>Cf-19</i> gene appear to have stronger <i>C. fulvum</i> resistance.
DOI: 10.6084/m9.figshare.22631467.v1
title: Additional file 8 of Proteomic profiles and the function of RBP4 in endometrium during embryo implantation phases in pigs

description: Additional file 8.
DOI: 10.6084/m9.figshare.14774249.v1
title: Signatures and Prognostic Values of N6-methyladenosine (m6A) - related Immune Genes in Bladder Cancer

description: In recent years, genes associated with N6-methyladenosine (m6A) modification were found to participate in modulation of multiple tumor biological processes. Concomitantly, the significantly complicated dual effects of tumor microenvironment have been observed on cancer progression. The present study aims to investigate m6A-related immune genes (m6AIGs) for their signatures and prognostic values in bladder cancer (BC). Out of 2856 differentially expressed genes (DEGs) of BC, a total of 85 genes were obtained following intersection of DEGs, immune genes and m6A-related genes. The results of multivariate Cox regression analysis illustrated four genes (BGN, GRK5, IL32, and SREBF1) were significantly associated with the prognosis of BC patients. The BC samples were divided into two types based on the consensus clustering, and the principal component analysis demonstrated a separation between them. It was found that high expression of BGN and GRK5 were linked with advanced T and N stage, and the expression of SREBF1 in early T stage was higher than that in advanced T stage. Subsequently, the nomogram to predict 3- and 5-year survival probability of BC patients was developed and calibrated. GSEA analysis for risk subgroups showed WNT and TGF-beta signaling pathways were involved in regulation of BC progression in high risk level group. In the low risk level group, cytosolic DNA-Sensing cGAS-STING and RIG-I-like receptors signaling pathways were found to be correlated with BC development. These findings provide a novel insight on studies for BC progression.
DOI: 10.25549/usctheses-ouc11258189
title: THESIS TEMPLATE
DOI: 10.6084/m9.figshare.7962998
title: Proteomic Models in Preeclampsia

description: The study aim was to discover
bio-signatures predicting the risk of preeclampsia in two independent cohorts (Stanford
and Detroit) of pregnant women using a highly-multiplexed and aptamer-based
proteomic array (SomaLogic). 



Two spreadsheets contain patient
data listed separately for the two cohorts, namely patient ID (de-identified),
group (preeclampsia or control), age, body mass index, race, gravidity,
and parity. 

Two additional spreadsheets contain
proteomic data listed separately for the two cohorts. Columns A to C list
patient ID (de-identified), group (preeclampsia or control), and
gestational age at the time of sampling. Subsequent columns list relative
plasma concentrations (florescence units) for specific proteins. Rows 1 to 5
indicate SomaLogic ID, full protein name, UniProt ID, Gene ID, and gene symbol
for each protein.
DOI: 10.25549/usctheses-ouc11258197
title: Microsoft Word - Fazio_Victor_EdD_OCL_Dissertation_May2017.docx
DOI: 10.6084/m9.figshare.16871898.v2
title: Synthesis, characterisation, and effects of molecular structure on phase behaviour of 4-chloro-1,3-diazobenzene bent-core liquid crystals with high photosensitivity

description: A series of new compounds were synthesised by adding azo functional groups and chlorine substituent to the central bent-cores to form a 4-chloro-1,3-dizaophenylene bent-core. The structure, mesogenic properties, and photosensitivity of these compounds were characterised. The results show these synthesised compounds exhibit a broad temperature window up to 63.8°C for nematic phase and the rapid rate of <i>trans – cis</i> photoisomerisation. For instance, at 95°C, compound <b>4c</b> in nematic phase became an isotropic liquid under UV-irradiation in 3 s and could be restored to nematic under natural visible light in 5 s. Quantum mechanics calculation confirms that using azos instead of esters as the central linkages can effectively reduce the molecular dipole moment, which appears to promote favourable mesogenic and photonic characteristics. Moreover, varying the carbon number in the terminal alkyl chains can alter molecular dipole moment and polarisability anisotropy, which are strongly correlated with the phase transition temperature and temperature range of the nematic phase. These findings suggest that 1) changing azo group position can effectively alter the intermolecular interactions by varying molecular polarity and polarisability; 2) reducing long-range electrostatic interactions can promote favourable mesogenic and possibly photonic properties of azobenzene bent-core liquid crystal.
DOI: 10.5281/zenodo.10635919
title: PROCEEDINGS OF THE INTERNATIONAL RESEARCH, EDUCATION & TRAINING CENTER
DOI: 10.5281/zenodo.10635920
title: PROCEEDINGS OF THE INTERNATIONAL RESEARCH, EDUCATION & TRAINING CENTER
DOI: 10.5281/zenodo.10635935
title: melanotaenia_affinis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10635936
title: melanotaenia_affinis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22638516
title: Network pharmacology strategy to investigate the pharmacological effects of Suanzaoren Decoction on insomnia

description: Abstract Suanzaoren Decoction (SZRD) is an ancient prescription used in the treatment of insomnia. This study aimed to investigate the components and targets of SZRD in treating insomnia. First, the compounds of five herbs in SZRD were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the putative targets for treating insomnia were obtained from DrugBank to construct the herb-compound-target- disease network. A protein-protein interaction (PPI) network was constructed in the STRING database, and then Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to predict the mechanism of action of intersection target. Finally, 30 mice were divided into five groups: control, model, and quercetin groups (100, 50, 25 mg/kg). The sleep latency and duration of pentobarbital-induced sleeping were measured. The production of interleukin-6 (IL-6) and γ-aminobutyric acid (γ-GABA) was detected by using an enzyme-linked immunosorbent assay kit (ELISA), and Gamma-aminobutyric acid type a receptor subunit alpha1 (GABRA1) was tested by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). A total of 152 active ingredients, including 80 putative targets of SZRD, were obtained. The main active compounds included quercetin and kaempferol, and the key targets involved IL-6 and nitric oxide synthase 3 (NOS3). The results of pathway enrichment analysis indicated that the putative targets of SZRD mainly participated in Neuroactive ligand-receptor interaction. The experiment of P-chlorophenylalanine (PCPA)-induced insomnia model showed that quercetin obviously shortened the sleep latency and prolonged the sleep duration of the insomnia model. The production of IL-6, γ-GABA, and GABRA1 mRNA was significantly increased in mice treated with quercetin. This study predicted the active ingredients and potential targets of SZRD on insomnia on the basis of a systematic network pharmacology approach and illustrated that SZRD might exert hypnotic effects via regulating IL-6, γ-GABA, and GABRA1.
DOI: 10.6084/m9.figshare.22638621
title: Mathematical model for estimating the leaf area of cured dry tobacco using linear measurements

description: ABSTRACT: Leaf area of dried Flue-cured tobacco is a reflection of climate and stage of growth of fresh tobacco in field; it also serves as the foundation for calculating a number of significant physical properties of tobacco. So the purpose of this paper was to establish a model to estimate the leaf area of dried Flue-cured tobacco in China from linear dimensions. Three Hundred eight tobacco leaves from different growing area and stalk position were sampled randomly and separated for model selection among linear, proportional and power model type and external evaluation individually. Results showed that there was a significant and strong correlation between leaf area and length×width , The equation LA = 0.495(L×W), where LA is the leaf area and L×W is the product of leaf length and width, was optimum and adequate for the estimation of leaf area of dried tobacco in China examined by Fisher’s test, Akaike delta information criterion (AIC) and Bayesian information criterion (BIC). Growing area and stalk position had minor effect on the parameter before (L×W). The equation can sufficiently predict the area of leaf for external evaluation.
DOI: 10.6084/m9.figshare.21065462
title: Identification of <i>Cladosporium fulvum</i> infection responsive genes in tomato through cDNA-AFLP

description: Tomato (<i>Solanum lycopersicum</i>) is one of the highest-value vegetable crops worldwide, but tomato planting can be easily affected by leaf mold. Tomato leaf mold disease is caused by <i>Cladosporium fulvum,</i> and plants carrying the Cf genes have effective resistance to <i>C. fulvum</i>. To identify leaf mold resistant varieties and screen for specific cDNA amplified fragment length polymorphism (cDNA-AFLP) molecular markers, tomato plants harbouring genes <i>Cf-5</i>, <i>Cf-11</i>, <i>Cf-19</i>, and the moneymaker (MM) tomato line (without Cf gene) were used as plant materials. The changes in reactive oxygen species (ROS) levels and antioxidant activities of plant leaves after inoculation of <i>C. fulvum</i> were measured. Ethylene (ETH), abscisic acid (ABA) and salicylic acid (SA) contents were also determined. The results revealed that the ROS levels in <i>Cf-19</i> tomato were the most sensitive to <i>C. fulvum</i> inoculation, while in MM they were the least. The antioxidant enzymes of <i>Cf</i>-carrying plants exhibited different activities as compared to those of MM. In the cDNA-AFLP analysis data, the expression of <i>ERF109</i>, sedoheptulose-1,7-bisphosphatase (SBPase), L-ascorbic acid oxidase (AAO) and Thioredoxin H2 (TRX2) were different between <i>Cf</i>-gene carriers and MM plants. In summary, in the process of leaf–mold interaction, the outbreak of ROS and development of systemic acquired resistance (SAR) are tightly combined with antioxidant enzymes, including thioredoxin. Tomato plants carrying the <i>Cf-19</i> gene appear to have stronger <i>C. fulvum</i> resistance.
DOI: 10.6084/m9.figshare.22638516.v1
title: Network pharmacology strategy to investigate the pharmacological effects of Suanzaoren Decoction on insomnia

description: Abstract Suanzaoren Decoction (SZRD) is an ancient prescription used in the treatment of insomnia. This study aimed to investigate the components and targets of SZRD in treating insomnia. First, the compounds of five herbs in SZRD were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the putative targets for treating insomnia were obtained from DrugBank to construct the herb-compound-target- disease network. A protein-protein interaction (PPI) network was constructed in the STRING database, and then Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to predict the mechanism of action of intersection target. Finally, 30 mice were divided into five groups: control, model, and quercetin groups (100, 50, 25 mg/kg). The sleep latency and duration of pentobarbital-induced sleeping were measured. The production of interleukin-6 (IL-6) and γ-aminobutyric acid (γ-GABA) was detected by using an enzyme-linked immunosorbent assay kit (ELISA), and Gamma-aminobutyric acid type a receptor subunit alpha1 (GABRA1) was tested by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). A total of 152 active ingredients, including 80 putative targets of SZRD, were obtained. The main active compounds included quercetin and kaempferol, and the key targets involved IL-6 and nitric oxide synthase 3 (NOS3). The results of pathway enrichment analysis indicated that the putative targets of SZRD mainly participated in Neuroactive ligand-receptor interaction. The experiment of P-chlorophenylalanine (PCPA)-induced insomnia model showed that quercetin obviously shortened the sleep latency and prolonged the sleep duration of the insomnia model. The production of IL-6, γ-GABA, and GABRA1 mRNA was significantly increased in mice treated with quercetin. This study predicted the active ingredients and potential targets of SZRD on insomnia on the basis of a systematic network pharmacology approach and illustrated that SZRD might exert hypnotic effects via regulating IL-6, γ-GABA, and GABRA1.