cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19337498.v1
title: Identification of a five-gene signature deriving from the vacuolar ATPase (V-ATPase) sub-classifies gliomas and decides prognoses and immune microenvironment alterations

description: Aberrant expression of coding genes of the V-ATPase subunits has been reported in glioma patients that can activate oncogenic pathways and result in worse prognosis. However, the predictive effect of a single gene is not specific or sensitive enough. In this study, by using a series of bioinformatics analyses, we identified five coding genes (ATP6V1C2, ATP6V1G2, TCIRG1, ATP6AP1 and ATP6AP2) of the V-ATPase that were related to glioma patient prognosis. Based on the expression of these genes, glioma patients were sub-classified into different prognosis clusters, of which C1 cluster performed better prognosis; however, C2 cluster showed more malignant phenotypes with oncogenic and immune-related pathway activation. The single-cell RNA-seq data revealed that ATP6AP1, ATP6AP2, ATP6V1G2 and TCIRG1 might be cell-type potential markers. Copy number variation and DNA promoter methylation potentially regulate these five gene expressions. A risk score model consisted of these five genes effectively predicted glioma prognosis and was fully validated by six independent datasets. The risk scores also showed a positive correlation with immune checkpoint expression. Importantly, glioma patients with high-risk scores presented resistance to traditional treatment. We also revealed that more inhibitory immune cells infiltration and higher rates of “non-response” to immune checkpoint blockade (ICB) treatment in the high-risk score group. In conclusion, our study identified a five-gene signature from the V-ATPase that could sub-classify gliomas into different phenotypes and their abnormal expression was regulated by distinct mechanisms and accompanied with immune microenvironment alterations potentially act as a biomarker for ICB treatment.
DOI: 10.5281/zenodo.10622193
title: E6AP_16E6_p53_MD_files

description: The MD simulation files for for Wang et al Nat. Commun. 2024 including the initial system configurations, final states, trajectories, simulation parameters, and force field parameters for Supplementary Table 2.
DOI: 10.5281/zenodo.10622192
title: E6AP_16E6_p53_MD_files

description: The MD simulation files for for Wang et al Nat. Commun. 2024 including the initial system configurations, final states, trajectories, simulation parameters, and force field parameters for Supplementary Table 2.
DOI: 10.6084/m9.figshare.8851793
title: The effect of ionizing radiation on the subcellular localization and kinase activity of protein kinase CK2 in human non-small cell lung cancer cells

description: Protein kinase CK2 is a ubiquitously expressed kinase in eukaryotes, which is known to phosphorylate many protein substrates. Because CK2 is involved in the regulation of various signaling pathways, we wondered whether CK2 participated in the regulation of ionizing radiation (IR) induced biological process. In this study, we investigated the effect of IR on the subcellular localization and kinase activity in human non-small cell lung cancer (NSCLC) cells. Immunofluorescent results showed that CK2 subunits shuttle into the nucleus mostly beginning 1 h after IR and lasting more than 6 h. We also conducted in vitro kinase assay and observed an increase in CK2 kinase activity at 6 h after IR. Furthermore, an increase in S phase was observed at 6 h after IR. Colony formation assay results demonstrated that CK2 inhibitor CX-4945 significantly enhanced the effect of irradiation in NSCLC cells. These results indicated that CK2 may be implicated in the regulation of IR-induced biological process.
DOI: 10.6084/m9.figshare.8851793.v1
title: The effect of ionizing radiation on the subcellular localization and kinase activity of protein kinase CK2 in human non-small cell lung cancer cells

description: Protein kinase CK2 is a ubiquitously expressed kinase in eukaryotes, which is known to phosphorylate many protein substrates. Because CK2 is involved in the regulation of various signaling pathways, we wondered whether CK2 participated in the regulation of ionizing radiation (IR) induced biological process. In this study, we investigated the effect of IR on the subcellular localization and kinase activity in human non-small cell lung cancer (NSCLC) cells. Immunofluorescent results showed that CK2 subunits shuttle into the nucleus mostly beginning 1 h after IR and lasting more than 6 h. We also conducted in vitro kinase assay and observed an increase in CK2 kinase activity at 6 h after IR. Furthermore, an increase in S phase was observed at 6 h after IR. Colony formation assay results demonstrated that CK2 inhibitor CX-4945 significantly enhanced the effect of irradiation in NSCLC cells. These results indicated that CK2 may be implicated in the regulation of IR-induced biological process.
DOI: 10.6084/m9.figshare.9900380
title: Methodological description of clinical research data collection through electronic medical records in a center participating in an international multicenter study

description: ABSTRACT Data collection for clinical research can be difficult, and electronic health record systems can facilitate this process. The aim of this study was to describe and evaluate the secondary use of electronic health records in data collection for an observational clinical study. We used Cerner Millennium®, an electronic health record software, following these steps: (1) data crossing between the study’s case report forms and the electronic health record; (2) development of a manual collection method for data not recorded in Cerner Millennium®; (3) development of a study interface for automatic data collection in the electronic health records; (4) employee training; (5) data quality assessment; and (6) filling out the electronic case report form at the end of the study. Three case report forms were consolidated into the electronic case report form at the end of the study. Researchers performed daily qualitative and quantitative analyses of the data. Data were collected from 94 patients. In the first case report form, 76.5% of variables were obtained electronically, in the second, 95.5%, and in the third, 100%. The daily quality assessment of the whole process showed complete and correct data, widespread employee compliance and minimal interference in their practice. The secondary use of electronic health records is safe and effective, reduces manual labor, and provides data reliability. Anesthetic care and data collection may be done by the same professional.
DOI: 10.6084/m9.figshare.9900380.v1
title: Methodological description of clinical research data collection through electronic medical records in a center participating in an international multicenter study

description: ABSTRACT Data collection for clinical research can be difficult, and electronic health record systems can facilitate this process. The aim of this study was to describe and evaluate the secondary use of electronic health records in data collection for an observational clinical study. We used Cerner Millennium®, an electronic health record software, following these steps: (1) data crossing between the study’s case report forms and the electronic health record; (2) development of a manual collection method for data not recorded in Cerner Millennium®; (3) development of a study interface for automatic data collection in the electronic health records; (4) employee training; (5) data quality assessment; and (6) filling out the electronic case report form at the end of the study. Three case report forms were consolidated into the electronic case report form at the end of the study. Researchers performed daily qualitative and quantitative analyses of the data. Data were collected from 94 patients. In the first case report form, 76.5% of variables were obtained electronically, in the second, 95.5%, and in the third, 100%. The daily quality assessment of the whole process showed complete and correct data, widespread employee compliance and minimal interference in their practice. The secondary use of electronic health records is safe and effective, reduces manual labor, and provides data reliability. Anesthetic care and data collection may be done by the same professional.
DOI: 10.6084/m9.figshare.9900389
title: Investigation on Electrical Properties and Microdefects of Nb5+-Doped BaTiO3 Based Ceramics by Positron Annihilation Techniques

description: The influence of the Nb5+-doped content and the doping CaCO3 on the electrical properties and the microdefects of BSTN ceramics by Positron Annihilation Techniques were studied, which were fired at 1350 ºC for 2 hours in air. The PTCR characteristics in the BSTN samples were also investigated. Moreover, the information on microdefects in BSTN ceramics was demonstrated by coincidence Doppler broadening spectrum measurements and positron annihilation lifetime spectra. Meanwhile, the influence of the defects on the electrical properties of the ceramics was also revealed. Furthermore, the critical donor-dopant content was 0.4 mol%, which corresponding room-temperature resistivity and the resistivity jumping ratio was 714.3 Ω·cm and 2.77 × 102, respectively. In addition, the average positrons annihilate lifetime t of the BSTN ceramics was investigated as well.
DOI: 10.5281/zenodo.10724824
title: hepsetus_odoe_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.10724825
title: hepsetus_odoe_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.25308613
title: PINNs Dataset

description: The dataset is extracted from LTPP, USA to develop the prediction models using the novel physics informed neural network approach.
DOI: 10.6084/m9.figshare.25308613.v1
title: PINNs Dataset

description: The dataset is extracted from LTPP, USA to develop the prediction models using the novel physics informed neural network approach.
DOI: 10.6084/m9.figshare.11997588
title: In vivo inhibitory effect of suberoylanilide hydroxamic acid combined with sorafenib on human hepatocellular carcinoma cells

description: The present study aimed to investigate the in vivo inhibitory effect of histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) combined with sorafenib on human hepatocellular carcinoma HCCLM3 cells. The nude mice transplanted with HCCLM3 cells were randomly divided into control, SAHA, sorafenib and SAHA+sorafenib groups. The nude mice in the later 3 groups were intragastrically administrated with SAHA (10 mg·kg-1·day-1), sorafenib (10 mg·kg-1·day-1) and SAHA (10 mg·kg-1·day-1) combined with sorafenib (10 mg·kg-1·day-1), respectively, for successive 20 days. Finally, the inhibition rate of tumor was measured. The expressions of MEK1/2, p-ERK1/2, Cyclin D1, Bcl-2, Bax, p53, MMP-2, MMP-9 and uPA in tumor tissues were determined. Results showed that, compared with SAHA and Sorafenib groups, in SAHA+sorafenib groups the inhibition rate of tumor was significantly increased (P &lt; 0.05), the expression levels of MEK1/2, p-ERK1/2, Cyclin D1, Bcl-2, MMP-2 and MMP-9 and uPA protein in tumor tissues were significantly decreased, respectively (P &lt; 0.05), and the expression levels of Bax and p53 protein were significantly increased, respectively (P &lt; 0.05). In conclusion, compared with single drug, SAHA combined with sorafenib can enhance the inhibitory effects on HCCLM3 xenografts in nude mice.
DOI: 10.6084/m9.figshare.11997588.v1
title: In vivo inhibitory effect of suberoylanilide hydroxamic acid combined with sorafenib on human hepatocellular carcinoma cells

description: The present study aimed to investigate the in vivo inhibitory effect of histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) combined with sorafenib on human hepatocellular carcinoma HCCLM3 cells. The nude mice transplanted with HCCLM3 cells were randomly divided into control, SAHA, sorafenib and SAHA+sorafenib groups. The nude mice in the later 3 groups were intragastrically administrated with SAHA (10 mg·kg-1·day-1), sorafenib (10 mg·kg-1·day-1) and SAHA (10 mg·kg-1·day-1) combined with sorafenib (10 mg·kg-1·day-1), respectively, for successive 20 days. Finally, the inhibition rate of tumor was measured. The expressions of MEK1/2, p-ERK1/2, Cyclin D1, Bcl-2, Bax, p53, MMP-2, MMP-9 and uPA in tumor tissues were determined. Results showed that, compared with SAHA and Sorafenib groups, in SAHA+sorafenib groups the inhibition rate of tumor was significantly increased (P &lt; 0.05), the expression levels of MEK1/2, p-ERK1/2, Cyclin D1, Bcl-2, MMP-2 and MMP-9 and uPA protein in tumor tissues were significantly decreased, respectively (P &lt; 0.05), and the expression levels of Bax and p53 protein were significantly increased, respectively (P &lt; 0.05). In conclusion, compared with single drug, SAHA combined with sorafenib can enhance the inhibitory effects on HCCLM3 xenografts in nude mice.
DOI: 10.6084/m9.figshare.18849216
title: Additional file 5 of Genome-wide association study of the candidate genes for grape berry shape-related traits

description: Additional file 5: Table S1. Experimental material used in this study.
DOI: 10.6084/m9.figshare.23961792
title: The extent of introgression between incipient <i>Clarkia</i> species is determined by temporal environmental variation and mating system

description: This zipped file is a directory containing all of the scripts and data need to reproduce analyses in the paper "The extent of introgression between incipient <i>Clarkia</i> species is determined by temporal environmental variation and mating system." There is a README document in the main directory that contains all information necessary to navigate the file structure, code, and data. There are a suite of folders that have code run in the command line - primarily bioinformatic code. There is an R markdown file (and a rendered html) with all code needed to make figures/tables/analyses in manuscript. There are two subdirectories "R_input_data" and "R_output" that are used with the R markdown file.<br>
DOI: 10.6084/m9.figshare.18849216.v1
title: Additional file 5 of Genome-wide association study of the candidate genes for grape berry shape-related traits

description: Additional file 5: Table S1. Experimental material used in this study.
DOI: 10.15472/ej9dqv
title: Registros de aves capturadas en el marco del proyecto "Estrategias de Aves Urbanas al Aumento de Temperatura en la Ciudad de Cali"

description: Este conjunto de datos contiene la información de aves capturadas durante el desarrollo del Proyecto de Grado "Estrategias de Aves Urbanas al Aumento de Temperatura en la Ciudad de Cali" realizado por Jerlly Daniela Vidal. Los especimenes de este archivo se ubican en el Valle del Cauca, Cali y fueron capturados en el primer semestre del 2021.
DOI: 10.6084/m9.figshare.9900479
title: MOESM1 of The development of an herbal material quality control strategy considering the effects of manufacturing processes

description: Additional file 1: Table S1. Design space and calculated probability.
DOI: 10.6084/m9.figshare.9900479.v1
title: MOESM1 of The development of an herbal material quality control strategy considering the effects of manufacturing processes

description: Additional file 1: Table S1. Design space and calculated probability.
DOI: 10.15472/9och3z
title: Avifauna asociada a la ciénaga de Montaño, Carmen del Darién, 2020

description: Los humedales o ciénagas son ecosistemas que cumplen múltiples funciones a nivel ambiental, biológico y sociocultural, favoreciendo al control de inundaciones, depuración de ríos, soporte y conservación de diversidad ecosistémica y reservorio de especies faunísticas, entre los que se destacan los mamíferos, los cuales son de gran relevancia para el sostenimiento de las comunidades humanas asentadas a su alrededor. Aunque la mayoría de estos ecosistemas cumplen funciones similares, presentan características particularidades, dependiendo de su ubicación, el clima específico de la zona, su tipología en cuanto a la forma de conexión con los sistemas hídricos del que hacen parte y el tipo ambiente en el que se encuentran inmersos. La gran diversidad sustentada por exploraciones realizadas en estos ecosistemas a lo largo y ancho del Chocó biogeográfico, por diferentes investigadores, ponen de manifiesto la necesidad de continuar indagando en el conocimiento y exploración de la alta diversidad biológica presente en esta región. En este sentido, es importante puntualizar que la presente investigación buscó contribuir al conocimiento del estado actual (composición, abundancia, riqueza y estado de conservación) de la avifauna asociadas a la Ciénega de Montaño, evidenciando la influencia que tiene este grupo faunístico en la dinámica y estado de conservación del ecosistema, además de su gran importancia para la alimentación y manufactura de los grupos humanos presentes en la zona. La investigación que concluyó con la elaboración del respectivo documento, proporciona información relevante para la toma de decisiones e implementación de posibles planes de manejos, soportadas en las condiciones reales y de esta manera contribuir en la preservación de la riqueza ecológica, y los bienes y servicios que el ecosistema ofrece a las comunidades humanas asentadas a su alrededor.
DOI: 10.6084/m9.figshare.9900503
title: MOESM3 of Serine hydroxymethyltransferase controls blood-meal digestion in the midgut of Aedes aegypti mosquitoes

description: Additional file 3: Table S2. Digestion enzymes of A. aegypti and their conservative analysis in different species of mosquitoes.
DOI: 10.6084/m9.figshare.9900503.v1
title: MOESM3 of Serine hydroxymethyltransferase controls blood-meal digestion in the midgut of Aedes aegypti mosquitoes

description: Additional file 3: Table S2. Digestion enzymes of A. aegypti and their conservative analysis in different species of mosquitoes.
DOI: 10.6084/m9.figshare.11997681
title: Relationship of gender and age on thyroid hormone parameters in a large Chinese population

description: ABSTRACT Objective This study aimed to present the impact of age and gender on thyroid hormone levels in a large Chinese population with sufficient iodine intake. Subjects and methods A total of 83643 individuals were included and were stratified by age and gender. The median, 2.5th and 97.5th of thyrotropin (TSH), free triiodothyronine (FT3), free thyroxine (FT4) and FT3/FT4 ratio were calculated for both genders for every decade from 18 to over 80 years. TSH, FT3, FT4, FT3/FT4 distribution in each age group was evaluated for females and males using smoothing splines in the generalized additive models (GAM). TSH concentrations were compared in the different age groups in gender. Results In the over 80s age group, the TSH level (median: 2.57 mIU/L, 2.5th-97.5th: 0.86-7.56 mIU/L) was significantly higher than other age groups, irrespective to gender (P&lt;0.001). Females had a higher TSH value than males in all age groups (P&lt;0.001). Results of the smoothing curves showed that TSH increased with age, FT3 concentration was higher in males than in females and the tendency of the FT3/FT4 ratio was basically similar to that of FT3. TSH concentration in the 50s age group (median 2.48 mIU/L for females versus 2.00 mIU/L for males) was significantly higher than that in the 30s age group (median 2.18 mIU/L for females versus median 1.85 mIU/L for males). Conclusions In accord with increasing TSH values during aging, females and older adults have lower FT3 values and lower FT3/FT4 ratios, while the FT4 values remain stable.
DOI: 10.6084/m9.figshare.13046303
title: Species diversity, taxonomy, and phylogeny of <i>Gymnosporangium</i> in China

description: <i>Gymnosporangium</i> is a group of plant fungal pathogens that cause rust diseases on many economically important fruit trees. Most <i>Gymnosporangium</i> are heteroecious and demicyclic, producing four morphologically diverse spore stages on two taxonomically unrelated host plants, the Cupressaceae and Rosaceae. The complex life cycle and heteroecism make it difficult to investigate the species within <i>Gymnosporangium</i>. To determine the taxonomy, phylogeny, and species diversity of <i>Gymnosporangium</i> in China, a large collection of 672 specimens were analyzed using a combination of morphological observations and phylogenetic analyses. In total, 27 <i>Gymnosporangium</i> species from China are documented here, including 22 known species, one new combination, one new record, and three new species. The study also documents a novel aeciospore surface structure with an irregular surface that is described here as “surfy.”
DOI: 10.6084/m9.figshare.13046303.v1
title: Species diversity, taxonomy, and phylogeny of <i>Gymnosporangium</i> in China

description: <i>Gymnosporangium</i> is a group of plant fungal pathogens that cause rust diseases on many economically important fruit trees. Most <i>Gymnosporangium</i> are heteroecious and demicyclic, producing four morphologically diverse spore stages on two taxonomically unrelated host plants, the Cupressaceae and Rosaceae. The complex life cycle and heteroecism make it difficult to investigate the species within <i>Gymnosporangium</i>. To determine the taxonomy, phylogeny, and species diversity of <i>Gymnosporangium</i> in China, a large collection of 672 specimens were analyzed using a combination of morphological observations and phylogenetic analyses. In total, 27 <i>Gymnosporangium</i> species from China are documented here, including 22 known species, one new combination, one new record, and three new species. The study also documents a novel aeciospore surface structure with an irregular surface that is described here as “surfy.”
DOI: 10.6084/m9.figshare.24580651
title: Exosome-delivered circRNA circSYT15 contributes to cisplatin resistance in cervical cancer cells through the miR-503-5p/RSF1 axis

description: The development of chemotherapy resistance is a major obstacle for cervical cancer (CC) patients. Exosome-mediated transfer of circular RNAs (circRNAs) was found to have relevance to the CC. This study is designed to explore the role and mechanism of exosomal circRNA synaptotagmin 15 (circSYT15) on cisplatin (DDP) resistance in CC. Cell proliferation ability and apoptosis rate were detected by Cell Counting Kit-8 (CCK-8), 5-ethynyl-2’-deoxyuridine (EdU), colony formation, and flow cytometry assays. CircSYT15, microRNA-503-5p (miR-503-5p), Remodeling spacing factor 1 (RSF1) levels were detected by real-time quantitative polymerase chain reaction (RT-qPCR). Exosomes were analyzed by a transmission electron microscope and nanoparticle tracking analysis. CD63, CD81, TSC101, Bcl-2, Bax, C-caspase 3, and RSF1 protein levels were examined by western blot assay. The binding between miR-503-5p and circSYT15 or RSF1 was predicted by circBank or Starbase and then verified by a dual-luciferase reporter and RNA Immunoprecipitation (RIP). The biological role of exosomal circSYT15 in DDP resistance of CC in vivo. CircSYT15 was upregulated in the DDP-resistant CC cells and exosomes isolated from DDP-resistant CC cells. CircSYT15 knockdown repressed the proliferation and drug resistance of CC and induced apoptosis in CC cells. Exosomes shuttled circSYT15 act as a sponge to affect RSF1 expression, thereby promoting proliferation and drug resistance and repressing apoptosis of sensitive CC cells. Exosomal circSYT15 boost DDP resistance of cervical cancer in vivo. Exosome-mediated transfer of circSYT15 enhanced DDP resistance in CC partly by targeting the miR-503-5p/RSF1 axis, providing a foundation for future clinical applications of CC drug resistance.