cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21505510
title: Additional file 2 of Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

description: Additional file 2: Table S1. Physicochemical data of the PRE samples. Table S2. Assembly qualities of the scaffolds/contigs. Table S3. Detailed information of the vOTUs identified in the PRE samples. Table S4. Detailed information of virus-host linkages prediction. Table S5. Annotation and abundance of the lytic viral AMGs. Table S6. Annotation and abundance of the temperate viral AMGs. Table S7. Occurred frequencies of viruses containing specific AMG functions in the lytic and temperate viral communities. Table S8. Normalized expression level of lytic viral AMGs in the free-living (FL) and particle-attached (PA) samples. Table S9. Normalized expression level of temperate viral AMGs in the free-living (FL) and particle-attached (PA) samples. Table S10. Enriched AMGs (KOs) among three habitats in the lytic or temperate viral communities. Table S11. Comparisons of the expression level of functional pathways between free-living (FL) and particle-attached (PA) samples in lytic or temperate viruses. Table S12. Number of viruses encoding AMGs that belonged to specific functional pathway in the lytic viruses that could infect the given host order. Table S13. Number of viruses encoding AMGs that belonged to specific functional pathway in the temperate viruses that could infect the given host order. Table S14. Detailed information about the biogeochemical-cycle related viral AMGs in the PRE samples.
DOI: 10.6084/m9.figshare.21505525
title: Additional file 1 of Application of logistic differential equation models for early warning of infectious diseases in Jilin Province

description: Additional file 1. Fitting parameters of HFRS, shigellosis, mumps, HFMD and scarlet fever by the LDE model in Jilin Province. (N is the upper limit of cumulative infectious disease cases; k is the correlation coefficient; c is a constant).
DOI: 10.6084/m9.figshare.21505528.v1
title: Additional file 2 of Application of logistic differential equation models for early warning of infectious diseases in Jilin Province

description: Additional file 2. Fitting parameters of HFRS, shigellosis, mumps, HFMD and scarlet fever by the GLDE model in Jilin Province. (N is the upper limit of cumulative infectious disease cases; k is the correlation coefficient; c is a constant; λ is a shape parameter).
DOI: 10.6084/m9.figshare.21505540.v1
title: Additional file 2 of iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C6+ heavy ion irradiation

description: Additional file 2. Protein identification and quantification of Deinococcus radiodurans.
DOI: 10.6084/m9.figshare.21505528
title: Additional file 2 of Application of logistic differential equation models for early warning of infectious diseases in Jilin Province

description: Additional file 2. Fitting parameters of HFRS, shigellosis, mumps, HFMD and scarlet fever by the GLDE model in Jilin Province. (N is the upper limit of cumulative infectious disease cases; k is the correlation coefficient; c is a constant; λ is a shape parameter).
DOI: 10.6084/m9.figshare.21505540
title: Additional file 2 of iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C6+ heavy ion irradiation

description: Additional file 2. Protein identification and quantification of Deinococcus radiodurans.
DOI: 10.6084/m9.figshare.16786728
title: Additional file 2 of Clipper: p-value-free FDR control on high-throughput data from two conditions

description: Additional file 2 Supplementary table. Biological functions of the DEGs (between classical and non-classical human monocytes) that were identified by Clipper only but missed by both edgeR and DESeq2 from the human monocyte RNA-seq dataset (SRA accession number SRP082682).
DOI: 10.6084/m9.figshare.24127004.v1
title: A randomized pairwise likelihood method for complex statistical inferences

description: Pairwise likelihood methods are commonly used for inference in parametric statistical models in cases where the full likelihood is too complex to be used, such as multivariate count data. Although pairwise likelihood methods represent a useful solution to perform inference for intractable likelihoods, several computational challenges remain. The pairwise likelihood function still requires the computation of a sum over all pairs of variables and all observations, which may be prohibitive in high dimensions. Moreover, it may be difficult to calculate confidence intervals of the resulting estimators, as they involve summing all pairs of pairs and all of the four-dimensional marginals. To alleviate these issues, we consider a randomized pairwise likelihood approach, where only summands randomly sampled across observations and pairs are used for the estimation. In addition to the usual tradeoff between statistical and computational efficiency, it is shown that, under a condition on the sampling parameter, this two-way random sampling mechanism makes the individual bivariate likelihood scores become asymptotically independent, allowing more computationally efficient confidence intervals to be constructed. The proposed approach is illustrated in tandem with copula-based models for multivariate count data in simulations, and in real data from a transcriptome study.
DOI: 10.6084/m9.figshare.13117973
title: miR-122 regulates the JAK-STAT signalling pathway by down-regulating <i>EPO</i> in the mammary gland during <i>Streptococcus agalactiae</i>-induced mastitis

description: MicroRNA (miRNA) are single-stranded non-coding RNA of approximately 22 nucleotides estimated to regulate 60% of human and animal genes some of which are associated with cell differentiation, signal transduction and immune processes. <i>Streptococcus agalactiae</i> (<i>S. agalactiae</i>)-induced bovine mastitis is associated with up-regulation of miR-122 and down-regulation of erythropoietin (<i>EPO</i>) abundance in mammary gland tissue. TargetScan analysis revealed that <i>EPO</i> is a predicted target gene of miR-122 and this regulatory relationship was verified by dual-luciferase reporter assay. Overexpression of miR-122 in primary bovine mammary cells led to down-regulation of <i>EPO</i> and also the JAK-STAT signalling pathway genes <i>EPOR</i>, <i>JAK2</i>, <i>STAT5A</i> and <i>STAT5B</i>. Accordingly, the mRNA abundance of <i>BCL-2</i>, a downstream gene in the JAK-STAT signalling pathway was significantly down-regulated. Under conditions of miR-122 inhibition, <i>EPO</i>, <i>EPOR</i>, <i>JAK2</i>, <i>STAT5A</i> and <i>STAT5B</i> were up-regulated. These results demonstrated that, through its action on <i>EPO</i>, miR-122 may play an important role in <i>S. agalactiae</i>-induced mastitis by regulating the JAK-STAT signalling pathway.HighlightsUnderstanding the relationship among miR-122, <i>EPO</i> and the JAK-STAT pathway would be helpful in developing new strategies for controlling mastitis.
 Understanding the relationship among miR-122, <i>EPO</i> and the JAK-STAT pathway would be helpful in developing new strategies for controlling mastitis.
DOI: 10.6084/m9.figshare.11545143
title: ICE6Gavg_GPS model for GIA_induced changes in Stokes coefficients

description: This is a data set for GIA_induced changes in Stokes coefficients. The data presented here have assimilated ICE6G-D, PUR16 and PUR18 GIA model predictions and 4072 global GPS vertical deformation measurements. More details can be found in the accompanying preprint submitted to Remote Sensing (also in this folder).
DOI: 10.5255/ukda-sn-856883
title: The Economic, Social, and Cultural Impact of the COVID-19 Pandemic on Independent Arts Workers in the United Kingdom: Freelancers in the Dark, 2019-2022

description: These datasets pertain to a research project investigating the social, cultural, and economic consequences of COVID19 on independent arts workers, specifically in the theatre sector, across England, Scotland, Wales, and Northern Ireland. The project recognised the unique vulnerability of this workforce in dealing with the impact of COVID19. Their workplaces closed overnight and their sector transformed as theatres moved to digital delivery, and their employment status (freelance) made them ineligible for the UK government’s Coronavirus Job Retention Scheme. The motivation of the project was to understand: the employment experiences of this workforce during the first 18 months of the pandemic; how the pandemic affected their planning for the future; how the pandemic changed their creative practices and skills; what impact government and sectoral policy had on the workforce; and to find strategies for government and industry to support this precarious workforce. 

This data collection includes survey responses (n=397) to an online survey which ran from 23/11/2020 to 19/03/2021, and a database of policy events covering the period from the onset of the pandemic until 27/5/2022 (n=1353). The survey was run through the JISC surveys platform. It had 34 questions collecting a mixture of qualitative and quantitative data. Freeform text responses were alternated with multiple choice, multi-option and Likert scale. The survey captured data on theatre freelancers employment, emotional, and cultural experiences, the region(s) and setting(s) where they worked, and their age, gender identity, race, occupation(s). The database of policy events marks dates of relevance to the experience of theatre freelancers. This includes government policy announcements (including in the devolved administrations), developments in the theatre sector and important cultural events. Events are labelled according to their place of relevance: UK, England, Wales, Scotland, Northern Ireland or Global.
DOI: 10.6084/m9.figshare.7350929.v1
title: Additional file 1: of MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod

description: Table S1. summary of sRNA sequencing data. Table S2. summary of known miRNAs. Table S3. summary of novel miRNAs. Table S4. expression levels of known miRNAs in cucumber shoot tips grown in four temperature-photoperiod conditions. Table S5. expression levels of novel miRNAs in cucumber shoot tips grown in four temperature-photoperiod conditions. Table S6. targets of known miRNAs predicted by psRobot. Table S7. targets of novel miRNAs predicted by psRobot. Table S8. targets of known miRNAs predicted by TargetFinder. Table S9. targets of novel miRNAs predicted by TargetFinder. Table S10. targets of known miRNAs predicted by both psRobot and TargetFinder (intersection). Table S11. targets of novel miRNAs predicted by both psRobot and TargetFinder (intersection). Table S12. targets identified by degradome sequencing. Table S13. GO term enrichment of targets. Table S14. KEGG classification of miRNA targets. Table S15. statistics of transcriptome sequencing for each sample. Table S16. differentially expressed degradome confirmed targets. Table S17. targets (degradome proven) of the temperature and photoperiod affected miRNAs. Table S18. functional annotations (computer predicted targets) of the temperature and photoperiod affected miRNAs. (XLSX 1042Â kb)
DOI: 10.6084/m9.figshare.10005980
title: MOESM1 of The analgesic efficacy of ultrasound-guided transversus abdominis plane block for retroperitoneoscopic renal surgery: a randomized controlled study

description: Additional file 1. Original data. Dataset supporting the conclusions of this article.
DOI: 10.6084/m9.figshare.10005980.v1
title: MOESM1 of The analgesic efficacy of ultrasound-guided transversus abdominis plane block for retroperitoneoscopic renal surgery: a randomized controlled study

description: Additional file 1. Original data. Dataset supporting the conclusions of this article.
DOI: 10.6084/m9.figshare.7351031
title: Additional file 2 of Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

description: Entire DAVID output with adjusted p value cutoff =0.05 and fold enrichment cutoff =2. (XLSX 92 kb)
DOI: 10.6084/m9.figshare.16786728.v1
title: Additional file 2 of Clipper: p-value-free FDR control on high-throughput data from two conditions

description: Additional file 2 Supplementary table. Biological functions of the DEGs (between classical and non-classical human monocytes) that were identified by Clipper only but missed by both edgeR and DESeq2 from the human monocyte RNA-seq dataset (SRA accession number SRP082682).
DOI: 10.6084/m9.figshare.21505525.v1
title: Additional file 1 of Application of logistic differential equation models for early warning of infectious diseases in Jilin Province

description: Additional file 1. Fitting parameters of HFRS, shigellosis, mumps, HFMD and scarlet fever by the LDE model in Jilin Province. (N is the upper limit of cumulative infectious disease cases; k is the correlation coefficient; c is a constant).
DOI: 10.6084/m9.figshare.16787010.v1
title: Novel circular RNA circATRNL1 accelerates the osteosarcoma aerobic glycolysis through targeting miR-409-3p/LDHA

description: In recent researches, circular RNAs (circRNAs) have been shown to exert critical functions in osteosarcoma biology. Nevertheless, the contribution of circRNAs to osteosarcoma remains largely unclear. Results indicated that expression of circATRNL1 was higher in osteosarcoma tissues and cells. The high-expression of circATRNL1 was significantly correlated with aggressive features and acted as an independent risk factor for osteosarcoma patients’ overall survival. Functionally, our findings demonstrate that circATRNL1 promotes the osteosarcoma aerobic glycolysis in vitro. Mechanistically, circATRNL1 up-regulated the expression level of LDHA, which was also targeted by miR-409-3p. Therefore, circATRNL1 exerted the accelerative roles of osteosarcoma aerobic glycolysis through miR-409-3p/LDHA axis. In conclusion, circATRNL1 promoted osteosarcoma progression by enhancing glycolysis via circATRNL1/miR-409-3p/LDHA axis, which may inspire a novel therapeutic target for osteosarcoma.
DOI: 10.6084/m9.figshare.16787010.v2
title: Novel circular RNA circATRNL1 accelerates the osteosarcoma aerobic glycolysis through targeting miR-409-3p/LDHA

description: In recent researches, circular RNAs (circRNAs) have been shown to exert critical functions in osteosarcoma biology. Nevertheless, the contribution of circRNAs to osteosarcoma remains largely unclear. Results indicated that expression of circATRNL1 was higher in osteosarcoma tissues and cells. The high-expression of circATRNL1 was significantly correlated with aggressive features and acted as an independent risk factor for osteosarcoma patients’ overall survival. Functionally, our findings demonstrate that circATRNL1 promotes the osteosarcoma aerobic glycolysis in vitro. Mechanistically, circATRNL1 up-regulated the expression level of LDHA, which was also targeted by miR-409-3p. Therefore, circATRNL1 exerted the accelerative roles of osteosarcoma aerobic glycolysis through miR-409-3p/LDHA axis. In conclusion, circATRNL1 promoted osteosarcoma progression by enhancing glycolysis via circATRNL1/miR-409-3p/LDHA axis, which may inspire a novel therapeutic target for osteosarcoma.
DOI: 10.6084/m9.figshare.16787011.v2
title: LINC00839/miR-144-3p/WTAP (WT1 Associated protein) axis is involved in regulating hepatocellular carcinoma progression

description: The present work aimed to explore LINC00839 expression level and its function in hepatocellular carcinoma (HCC), and identify the downstream molecular mechanisms. qRT-PCR (Real-Time Quantitative Reverse Transcription PCR) and western blot were employed to detect mRNA and protein levels. Functional investigations were performed by flow cytometric-based apoptosis assay, CCK8 (Cell Counting Kit-8) assay, clone formation assay, Transwell migration and invasion assay. Functional interactions between LINC00839 and miR-144-3p or miR-144-3p and WTAP were validated by dual luciferase reporter assay. siRNA (small interfering RNA) was used for LINC00839 silencing, and microRNA mimic or inhibitor were employed to modulate miR-144-3p activity. LINC00839 was upregulated in HCC cells and tissues. Silencing LINC00839 suppressed the proliferation, invasion, migration of HCC cells and induced apoptosis. Additionally, LINC00839 served as a sponge to negatively impact on miR-144-3p activity, which contributed to the high expression of WTAP (WT1 Associated Protein) and the malignant phenotype of HCC cells. Our study revealed an oncogenic role of LINC00839 in HCC, and identified miR-144-3p/WTAP axis as downstream effectors mediating the oncogenic function of LINC00839. LINC00839 might serve as a potential therapeutic target and prognostic marker for HCC.
DOI: 10.6084/m9.figshare.16787041
title: MicroRNA miR-19b-3p mediated G protein γ subunit 7 (GNG7) loss contributes lung adenocarcinoma progression through activating Hedgehog signaling

description: G protein γ subunit 7 (GNG7) is a subunit of heterotrimeric G protein. It has been demonstrated low expressed GNG7 in various cancers. Nevertheless, the role of GNG7 in lung adenocarcinoma (LUAD) remains unclear. In the present study, GNG7 expression in LUAD tissues and cell lines was analyzed by RT-qPCR, western blot and immunohistochemical. Kaplan–Meier analysis was performed for determining the prognostic value of GNG7 expression. Then, the function of GNG7 in LUAD progression was examined by cell proliferation, invasion and mouse xenograft assays. In addition, the underlying biological mechanisms of GNG7 in LUAD progression were explored via the bioinformatics analysis and experimental validation. We found GNG7 was markedly down-regulated in LUAD tissues and cell lines. Clinically, low expression of GNG7 was associated with the dismal prognosis of LUAD patients. Gain-of-function analysis showed that GNG7 overexpression inhibited proliferation and invasion of LUAD cell <i>in vitro</i>, and compromised tumor formation ability <i>in vivo</i>. Besides, mechanistic study revealed that overexpression of GNG7 affected the progression of LUAD via inhibiting activation of Hedgehog signaling. Moreover, bioinformatics prediction and experimental verification confirmed that GNG7 was targeted by miR-19b-3p, which was elevated expression in LUAD and promoting the progression of LUAD. Furthermore, rescue experiments demonstrated that GNG7 reintroduction weakened miR-19b-3p-mediated aggressive tumor phenotypes of LUAD cells. These findings suggested miR-19b-3p/GNG7 axis contributed to the progression of LUAD through Hedgehog signaling, which might be a potential therapeutic target for LUAD treatment.
DOI: 10.6084/m9.figshare.16787041.v1
title: MicroRNA miR-19b-3p mediated G protein γ subunit 7 (GNG7) loss contributes lung adenocarcinoma progression through activating Hedgehog signaling

description: G protein γ subunit 7 (GNG7) is a subunit of heterotrimeric G protein. It has been demonstrated low expressed GNG7 in various cancers. Nevertheless, the role of GNG7 in lung adenocarcinoma (LUAD) remains unclear. In the present study, GNG7 expression in LUAD tissues and cell lines was analyzed by RT-qPCR, western blot and immunohistochemical. Kaplan–Meier analysis was performed for determining the prognostic value of GNG7 expression. Then, the function of GNG7 in LUAD progression was examined by cell proliferation, invasion and mouse xenograft assays. In addition, the underlying biological mechanisms of GNG7 in LUAD progression were explored via the bioinformatics analysis and experimental validation. We found GNG7 was markedly down-regulated in LUAD tissues and cell lines. Clinically, low expression of GNG7 was associated with the dismal prognosis of LUAD patients. Gain-of-function analysis showed that GNG7 overexpression inhibited proliferation and invasion of LUAD cell <i>in vitro</i>, and compromised tumor formation ability <i>in vivo</i>. Besides, mechanistic study revealed that overexpression of GNG7 affected the progression of LUAD via inhibiting activation of Hedgehog signaling. Moreover, bioinformatics prediction and experimental verification confirmed that GNG7 was targeted by miR-19b-3p, which was elevated expression in LUAD and promoting the progression of LUAD. Furthermore, rescue experiments demonstrated that GNG7 reintroduction weakened miR-19b-3p-mediated aggressive tumor phenotypes of LUAD cells. These findings suggested miR-19b-3p/GNG7 axis contributed to the progression of LUAD through Hedgehog signaling, which might be a potential therapeutic target for LUAD treatment.
DOI: 10.6084/m9.figshare.12592766.v1
title: Additional file 6 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 6: Table S2. The distribution of markers in the parents genetic maps.
DOI: 10.6084/m9.figshare.16787041.v2
title: MicroRNA miR-19b-3p mediated G protein γ subunit 7 (GNG7) loss contributes lung adenocarcinoma progression through activating Hedgehog signaling

description: G protein γ subunit 7 (GNG7) is a subunit of heterotrimeric G protein. It has been demonstrated low expressed GNG7 in various cancers. Nevertheless, the role of GNG7 in lung adenocarcinoma (LUAD) remains unclear. In the present study, GNG7 expression in LUAD tissues and cell lines was analyzed by RT-qPCR, western blot and immunohistochemical. Kaplan–Meier analysis was performed for determining the prognostic value of GNG7 expression. Then, the function of GNG7 in LUAD progression was examined by cell proliferation, invasion and mouse xenograft assays. In addition, the underlying biological mechanisms of GNG7 in LUAD progression were explored via the bioinformatics analysis and experimental validation. We found GNG7 was markedly down-regulated in LUAD tissues and cell lines. Clinically, low expression of GNG7 was associated with the dismal prognosis of LUAD patients. Gain-of-function analysis showed that GNG7 overexpression inhibited proliferation and invasion of LUAD cell <i>in vitro</i>, and compromised tumor formation ability <i>in vivo</i>. Besides, mechanistic study revealed that overexpression of GNG7 affected the progression of LUAD via inhibiting activation of Hedgehog signaling. Moreover, bioinformatics prediction and experimental verification confirmed that GNG7 was targeted by miR-19b-3p, which was elevated expression in LUAD and promoting the progression of LUAD. Furthermore, rescue experiments demonstrated that GNG7 reintroduction weakened miR-19b-3p-mediated aggressive tumor phenotypes of LUAD cells. These findings suggested miR-19b-3p/GNG7 axis contributed to the progression of LUAD through Hedgehog signaling, which might be a potential therapeutic target for LUAD treatment.
DOI: 10.6084/m9.figshare.16786689.v1
title: Additional file 6 of Zinc-mediated activation of CREB pathway in proliferation of pulmonary artery smooth muscle cells in pulmonary hypertension

description: Additional file 5: Table S1. The differentially expressed phosphatases in comparison of MCT-treatment 4 weeks with control.
DOI: 10.6084/m9.figshare.12592766
title: Additional file 6 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 6: Table S2. The distribution of markers in the parents genetic maps.