cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5620603
title: The MiAge Calculator: a DNA methylation-based mitotic age calculator of human tissue types

description: Cell division is important in human aging and cancer. The estimation of the number of cell divisions (mitotic age) of a given tissue type in individuals is of great interest as it allows not only the study of biological aging (using a new molecular aging target) but also the stratification of prospective cancer risk. Here, we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions. With the MiAge model, the MiAge Calculator was built using the training data of DNA methylation measures of 4,020 tumor and adjacent normal tissue samples from eight TCGA cancer types and was tested using the testing data of DNA methylation measures of 2,221 tumor and adjacent normal tissue samples of five other TCGA cancer types. We showed that within each of the thirteen cancer types studied, the estimated mitotic age is universally accelerated in tumor tissues compared to adjacent normal tissues. Across the thirteen cancer types, we showed that worse cancer survivals are associated with more accelerated mitotic age in tumor tissues. Importantly, we demonstrated the utility of mitotic age by showing that the integration of mitotic age and clinical information leads to improved survival prediction in six out of the thirteen cancer types studied. The MiAge Calculator is available at http://www.columbia.edu/∼sw2206/softwares.htm.
DOI: 10.17028/rd.lboro.25250599.v1
title: Supplementary information files for A strategy for CO<sub>2</sub> capture and utilization towards methanol production at industrial scale: an integrated highly efficient process based on multi-criteria assessment

description: © the Authors CC-BY 4.0Supplementary files for article A strategy for CO<sub>2</sub> capture and utilization towards methanol production at industrial scale: an integrated highly efficient process based on multi-criteria assessmentCO<sub>2</sub> capture and utilization are an effective solution to the problem of CO<sub>2</sub> emissions, and a combination of ammonia-based CO<sub>2</sub> capture and its use for methanol production is a highly feasible strategy. However, the uses of conventional technologies have resulted in a high demand for energy, with limited use of hydrogen. To address these problems, an innovative strategy is proposed and demonstrated in this study that enhances the conventional design, i.e., to use ammonia-based CO<sub>2</sub> capture with double tower absorption and solvent split, along with wet hydrogen for methanol production at industrial scale. The process is further improved through a multi-criteria assessment that considered the CO<sub>2</sub> capture rate, NH<sub>3</sub> loss rate, CO<sub>2</sub> conversion rate, and energy saving factors, in which the latter is based on two components, namely the reboiler duty and the condenser duty. Moreover, an exergy analysis method is used to optimize the improved process, and a highly efficient integrated process is finally established. It has been found that the use of a double-tower absorption process ensures high rates of CO<sub>2</sub> capture and low rates of NH<sub>3</sub> loss. Additionally, adjusting the molar ratio of H<sub>2</sub> to CO<sub>2</sub> leads to an impressive 8% increase in the CO<sub>2</sub> conversion rate, reaching 25%. In terms of energy savings, the average reboiler duty was reduced from 13.39 to 11.85 MJ/kg<sub>CO2</sub>, i.e., by 11.50%; while the condenser duty was reduced by 11.36%; both contributed to the overall energy savings. In the I-ACCMP process, the total exergy loss is 437.24 kW, of which the exergy loss of the heat exchangers accounts for 16%, and the desorption tower (DES) accounts for 48%. After optimization, the exergy loss of the heat exchangers decreases from 70.02 kW to 40.45 kW, the exergy loss of the DES decreases from 209.29 kW to 180.91 kW, and the reboiler duty is reduced from 10.60 MJ/kg<sub>CO2</sub> to 7.71 MJ/kg<sub>CO2</sub>. The total exergy loss decreases from 437.24 kW to 372.68 kW, which is a reduction by 14.8%.
DOI: 10.6084/m9.figshare.12960432
title: Additional file 1 of Stereotactic body radiotherapy versus conventional/moderate fractionated radiation therapy with androgen deprivation therapy for unfavorable risk prostate cancer

description: Additional file 1 Supplemental Figure. Utilization of standard or moderately hypofractionated radiation (EBRT) versus ultrahypofractionated radiation (SBRT) in men with unfavorable intermediate (a) and high (b) risk prostate cancer receiving androgen deprivation therapy.
DOI: 10.6084/m9.figshare.7717502.v1
title: Additional file 6: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S6. Covariate data, gingival bleeding, and methylation beta values at 247 CpG-sites in blood. (CSV 1595 kb)
DOI: 10.6084/m9.figshare.7193411
title: Additional file 13: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of 56 candidate resistance genes obtained by combining transcription profiling and co-expression network analysis. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7193411.v1
title: Additional file 13: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of 56 candidate resistance genes obtained by combining transcription profiling and co-expression network analysis. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.21228906
title: Additional file 1 of Descriptive study of foodborne disease using disease monitoring data in Zhejiang Province, China, 2016–2020

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.7717505
title: Additional file 7: of Epigenetic findings in periodontitis in UK twins: a cross-sectional study

description: Table S7. Covariate data, tooth mobility, and methylation beta values at 247 CpG sites in blood. (CSV 1486 kb)
DOI: 10.6084/m9.figshare.7717625.v1
title: Additional file 1: of Transperineal versus transrectal prostate biopsy in the diagnosis of prostate cancer: a systematic review and meta-analysis

description: Table S1. Details of excluded studies. Table S2. Sensitivity analysis of RCTs. Table S3. Sensitivity analysis of observational studies. Figure S1. Risk of bias assessment of RCTs. (ZIP 605 kb)
DOI: 10.6084/m9.figshare.7193387
title: Additional file 11: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of differentially expressed genes (DEGs) involved in the ‘Plant-pathogen pathway’ in ‘Yayu889’ and ‘Zhenghong532’. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7717526
title: Additional file 2: of Association of recurrent venous thromboembolism and circulating microRNAs

description: Table S1. Presentation of the 110 miRNAs (ΔCt = Ctglobal mean − CtmiR of interest) in cases and controls. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7717529
title: Additional file 3: of Association of recurrent venous thromboembolism and circulating microRNAs

description: Table S2. Eighty-two KEGG pathway annotation of the miRNA Targets (DAVID 6.8). (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.7193396.v1
title: Additional file 12: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Top GO_BP of three co-expression modules in â Yayu889â . (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7717625
title: Additional file 1: of Transperineal versus transrectal prostate biopsy in the diagnosis of prostate cancer: a systematic review and meta-analysis

description: Table S1. Details of excluded studies. Table S2. Sensitivity analysis of RCTs. Table S3. Sensitivity analysis of observational studies. Figure S1. Risk of bias assessment of RCTs. (ZIP 605 kb)
DOI: 10.6084/m9.figshare.20300788
title: Antimicrobial resistance in <i>Vibrio cholerae</i> O1/O139 clinical isolates: a systematic review and meta-analysis

description: <i>Vibrio cholerae</i> O1/O139 is responsible for cholera epidemics that remains a huge public health menace across the globe. Furthermore, an increasing resistance rate among <i>V. cholerae</i> strains has been reported around the world. Therefore, the objective of this meta-analysis was to evaluate the weighted pooled resistance (WPR) rates in clinical <i>V. cholerae</i> O1/O139 isolates based on different years, areas, antimicrobial susceptibility testing, and resistance rates. We searched the studies in PubMed, Scopus, Embase, and Web of Science (until January 2020). Statistical analyses were conducted using STATA software (ver. 14.0). A total of 139 studies investigating 24,062 <i>V. cholerae</i> O1/O139 isolates were analyzed. The majority of the studies originated in Asia (<i>n</i> = 102). The WPR rates were as follows: azithromycin 1%, erythromycin 36%, ciprofloxacin 3%, cotrimoxazole 79%, doxycycline 7%, and tetracycline 20%. There was increased resistance to cotrimoxazole, ciprofloxacin, and tetracycline during the 1980–2020 years. Temporal changes in antibiotic resistance rate found in this study demonstrated the critical continuous surveillance of antibiotic resistance. Also, ciprofloxacin, azithromycin, gentamicin, cephalexin, imipenem, ofloxacin, and norfloxacin were found to be the best antibiotics against <i>V. cholera</i>, with the highest and the lowest effectiveness resistance rate.
DOI: 10.6084/m9.figshare.7193387.v1
title: Additional file 11: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of differentially expressed genes (DEGs) involved in the ‘Plant-pathogen pathway’ in ‘Yayu889’ and ‘Zhenghong532’. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.19252071
title: MicroRNA-200b-3p restrains gastric cancer cell proliferation, migration, and invasion via C-X-C motif chemokine ligand 12/CXC chemokine receptor 7 axis

description: This study was conducted to investigate the impact of microRNA (miR)-200b-3p on viability, migration, and invasion of gastric cancer (GC) cells and its mechanism. Quantitative real-time PCR (qRT-PCR) was conducted to measure miR-200b-3p expression in GC tissues and cells; besides, the relationship between miR-200b-3p expression and overall survival time (OS) was analyzed with OncomiR database; cell counting kit-8 (CCK-8), colony formation assay, flow cytometry, scratch healing assay, and Transwell assay were performed to detect the proliferation, cell cycle progression, migration, and invasion of GC cells; a lung metastasis model in nude mice was used to examine the effect of miR-200b-3p on the metastasis of GC cells <i>in vivo</i>; the interplay between miR-200b-3p and C-X-C motif chemokine ligand 12 (CXCL12) mRNA 3’ UTR was predicted by bioinformatics and verified with a dual-luciferase reporter gene assay; besides, the expression of CXCL12 and CXC chemokine receptor 7 (CXCR7) was probed by Western blot. It was found that miR-200b-3p expression was down-regulated in GC tissues, which was remarkably associated with the lymph node metastasis and decrease of differentiation of GC; transfection with miR-200b-3p mimics restrained the growth, migration, and invasion of GC cells <i>in vitro</i>, induced cell cycle arrest, and inhibited CXCL12 and CXCR7 expression levels; transfection of miR-200b-3p inhibitors worked oppositely <i>in vitro</i> and promoted lung metastasis <i>in vivo</i>. CXCL12 was confirmed as the downstream target of miR-200b-3p and was negatively modulated by miR-200b-3p. In conclusion, miR-200b-3p inhibited GC progression via regulating CXCL12/CXCR7 axis.
DOI: 10.6084/m9.figshare.7193396
title: Additional file 12: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Top GO_BP of three co-expression modules in â Yayu889â . (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7193429
title: Additional file 1: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of qPCR and PCR primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7193429.v1
title: Additional file 1: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: List of qPCR and PCR primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.19252071.v1
title: MicroRNA-200b-3p restrains gastric cancer cell proliferation, migration, and invasion via C-X-C motif chemokine ligand 12/CXC chemokine receptor 7 axis

description: This study was conducted to investigate the impact of microRNA (miR)-200b-3p on viability, migration, and invasion of gastric cancer (GC) cells and its mechanism. Quantitative real-time PCR (qRT-PCR) was conducted to measure miR-200b-3p expression in GC tissues and cells; besides, the relationship between miR-200b-3p expression and overall survival time (OS) was analyzed with OncomiR database; cell counting kit-8 (CCK-8), colony formation assay, flow cytometry, scratch healing assay, and Transwell assay were performed to detect the proliferation, cell cycle progression, migration, and invasion of GC cells; a lung metastasis model in nude mice was used to examine the effect of miR-200b-3p on the metastasis of GC cells <i>in vivo</i>; the interplay between miR-200b-3p and C-X-C motif chemokine ligand 12 (CXCL12) mRNA 3’ UTR was predicted by bioinformatics and verified with a dual-luciferase reporter gene assay; besides, the expression of CXCL12 and CXC chemokine receptor 7 (CXCR7) was probed by Western blot. It was found that miR-200b-3p expression was down-regulated in GC tissues, which was remarkably associated with the lymph node metastasis and decrease of differentiation of GC; transfection with miR-200b-3p mimics restrained the growth, migration, and invasion of GC cells <i>in vitro</i>, induced cell cycle arrest, and inhibited CXCL12 and CXCR7 expression levels; transfection of miR-200b-3p inhibitors worked oppositely <i>in vitro</i> and promoted lung metastasis <i>in vivo</i>. CXCL12 was confirmed as the downstream target of miR-200b-3p and was negatively modulated by miR-200b-3p. In conclusion, miR-200b-3p inhibited GC progression via regulating CXCL12/CXCR7 axis.
DOI: 10.6084/m9.figshare.7193483.v1
title: Additional file 5: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated chitinases in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7193522
title: Additional file 9: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated WRKY transcription factors in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7193522.v1
title: Additional file 9: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated WRKY transcription factors in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.15057976
title: microRNA-26a shuttled by extracellular vesicles secreted from adipose-derived mesenchymal stem cells reduce neuronal damage through KLF9-mediated regulation of TRAF2/KLF2 axis

description: Extracellular vesicles (EVs) are nano-sized vesicles secreted actively by numeorus cells and have fundamental roles in intercellular communication through shuttling functional RNAs. This study sets out to elucidate the role of microRNA-26a (miR-26a) shuttled by EVs derived from adipose-derived mesenchymal stem cells (ASCs) in neuronal damage. After extraction and identification of ASC-derived EVs (ASC-EVs), mouse cortical neuronal cells were selected to establish an in vivo cerebral ischemia/reperfusion mouse model and an in vitro oxygen glucose deprivation/reperfusion (OGD/RP) cell model. The downstream genes of miR-26a were analyzed. The gain- and loss-of function of miR-26a and KLF9 was performed in mouse and cell models. Neuronal cells were subjected to co-culture with ASC-EVs and biological behaviors were detected by flow cytometry, Motic Images Plus, TTC, TUNEL staining, qRT-PCR and western blot analysis. ASC-EVs protected neuronal cells against neuronal damage following cerebral ischemia/reperfusion, which was related to transfer of miR-26a into neuronal cells. In neuronal cells, miR-26a targeted KLF9. KLF9 could suppress the expression of TRAF2 and KLF2 to facilitate neuronal damage. In vitro and in vivo results showed that miR-26a delivered by ASC-EVs inhibited neuronal damage. In summary, ASC-EVs-derived miR-26a can arrest neuronal damage by disrupting the KLF9-meidated suppression on TRAF2/KLF2 axis.
DOI: 10.6084/m9.figshare.22922080
title: Complete mitochondrial genome of the little-known regional endemic <i>Aporia hastata</i> (Oberthür, 1892) (Lepidoptera: Pieridae)

description: The present study reports the mitochondrial genome of <i>A. hastata</i> (Oberthür, 1892), a little-known <i>Aporia</i> species endemic to the southern margin of the Hengduan Mountains in Yunnan Province. This genome is circular, 15,148 bp in length, and consists of 13 PCGs, 22 tRNAs, and two rRNAs. The Bayesian phylogenetic tree clusters <i>A. hastata</i> with other <i>Aporia</i> taxa inside tribe Pierini Duponchel, [1835]. The findings of this study add valuable new information to the genus <i>Aporia</i> and are beneficial to a better understanding of phylogeography of these butterflies.
DOI: 10.6084/m9.figshare.7193462
title: Additional file 4: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Correlation coefficients between each pair of three biological replicates. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7193462.v1
title: Additional file 4: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Correlation coefficients between each pair of three biological replicates. (XLSX 14 kb)
DOI: 10.17028/rd.lboro.25250599
title: Supplementary information files for A strategy for CO<sub>2</sub> capture and utilization towards methanol production at industrial scale: an integrated highly efficient process based on multi-criteria assessment

description: © the Authors CC-BY 4.0Supplementary files for article A strategy for CO<sub>2</sub> capture and utilization towards methanol production at industrial scale: an integrated highly efficient process based on multi-criteria assessmentCO<sub>2</sub> capture and utilization are an effective solution to the problem of CO<sub>2</sub> emissions, and a combination of ammonia-based CO<sub>2</sub> capture and its use for methanol production is a highly feasible strategy. However, the uses of conventional technologies have resulted in a high demand for energy, with limited use of hydrogen. To address these problems, an innovative strategy is proposed and demonstrated in this study that enhances the conventional design, i.e., to use ammonia-based CO<sub>2</sub> capture with double tower absorption and solvent split, along with wet hydrogen for methanol production at industrial scale. The process is further improved through a multi-criteria assessment that considered the CO<sub>2</sub> capture rate, NH<sub>3</sub> loss rate, CO<sub>2</sub> conversion rate, and energy saving factors, in which the latter is based on two components, namely the reboiler duty and the condenser duty. Moreover, an exergy analysis method is used to optimize the improved process, and a highly efficient integrated process is finally established. It has been found that the use of a double-tower absorption process ensures high rates of CO<sub>2</sub> capture and low rates of NH<sub>3</sub> loss. Additionally, adjusting the molar ratio of H<sub>2</sub> to CO<sub>2</sub> leads to an impressive 8% increase in the CO<sub>2</sub> conversion rate, reaching 25%. In terms of energy savings, the average reboiler duty was reduced from 13.39 to 11.85 MJ/kg<sub>CO2</sub>, i.e., by 11.50%; while the condenser duty was reduced by 11.36%; both contributed to the overall energy savings. In the I-ACCMP process, the total exergy loss is 437.24 kW, of which the exergy loss of the heat exchangers accounts for 16%, and the desorption tower (DES) accounts for 48%. After optimization, the exergy loss of the heat exchangers decreases from 70.02 kW to 40.45 kW, the exergy loss of the DES decreases from 209.29 kW to 180.91 kW, and the reboiler duty is reduced from 10.60 MJ/kg<sub>CO2</sub> to 7.71 MJ/kg<sub>CO2</sub>. The total exergy loss decreases from 437.24 kW to 372.68 kW, which is a reduction by 14.8%.
DOI: 10.6084/m9.figshare.7193669.v1
title: Additional file 6: of The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala

description: Table S5. Relative abundance of 1-d-Larvae and 5-d-Larvae at genus level. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7193483
title: Additional file 5: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated chitinases in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.19769188.v1
title: Additional file 6 of Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils

description: Additional file 6: Material 2. The genome annotation of various putative proteins involved in Se resistance and antibiotic resistance of Pseudomonas putida.
DOI: 10.6084/m9.figshare.11912052
title: Predicting (in)correctly: listeners rapidly use unexpected information to revise their predictions

description: Comprehenders can incorporate rich contextual information to predict upcoming input on the fly, and cues that conflict with their predictions are quickly detected. The present study examined whether and how comprehenders may revise their existing predictions upon encountering a prediction-inconsistent cue. We took advantage of the rich classifier system in Mandarin Chinese and tracked participants’ eye-movements as they listened to sentences in which the final noun is preceded by a classifier which was either compatible with the most expected noun, incompatible with the most expected noun but indicative of another contextually suitable noun, or uninformative. We found that, upon hearing a prediction-inconsistent classifier, listeners quickly directed their eye gaze away from the originally expected object and immediately onto the (initially) unexpected but contextually suitable object. This provides initial evidence that listeners can quickly use prediction-mismatching cues to revise their existing predictions on the fly.
DOI: 10.6084/m9.figshare.14526221
title: Additional file 3 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S3. Sequence alignment of the Jilin ginseng PgbZIP genes to the Korean Ginseng Genome Database.
DOI: 10.6084/m9.figshare.14526209.v1
title: Additional file 11 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S7. Plant materials used for this study.
DOI: 10.6084/m9.figshare.7193510.v1
title: Additional file 8: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated MAP kinases in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 14 kb)