cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10295996
title: Biological roles of filamin a in prostate cancer cells

description: ABSTRACT Objective This study aims to investigate the association of filamin A with the function and morphology of prostate cancer (PCa) cells, and explore the role of filamin A in the development of PCa, in order to analyze its significance in the evolvement of PCa. Materials and Methods A stably transfected cell line, in which filamin A expression was suppressed by RNA interference, was first established. Then, the effects of the suppression of filamin A gene expression on the biological characteristics of human PCa LNCaP cells were observed through cell morphology, in vitro cell growth curve, soft agar cloning assay, and scratch test. Results A cell line model with a low expression of filamin A was successfully constructed on the basis of LNCaP cells. The morphology of cells transfected with plasmid pSilencer-filamin A was the following: Cells were loosely arranged, had less connection with each other, had fewer tentacles, and presented a fibrous look. The growth rate of LNCap cells was faster than cells transfected with plasmid pSilencer-filamin A (P &lt;0.05). The clones of LNCap cells in the soft agar cloning assay was significantly fewer than that of cells stably transfected with plasmid pSilencer-filamin A (P &lt;0.05). Cells stably transfected with plasmid pSilencer-filamin A presented with a stronger healing and migration ability compared to LNCap cells (healing rate was 32.2% and 12.1%, respectively; P &lt;0.05). Conclusion The expression of the filamin A gene inhibited the malignant development of LNCap cells. Therefore, the filamin A gene may be a tumor suppressor gene.
DOI: 10.6084/m9.figshare.23047547
title: Merged gene expression profiles (TPM)

description: Gene expression profiles (GEPs) of 19 cancer types in TCGA (TPM format).
DOI: 10.6084/m9.figshare.10295996.v1
title: Biological roles of filamin a in prostate cancer cells

description: ABSTRACT Objective This study aims to investigate the association of filamin A with the function and morphology of prostate cancer (PCa) cells, and explore the role of filamin A in the development of PCa, in order to analyze its significance in the evolvement of PCa. Materials and Methods A stably transfected cell line, in which filamin A expression was suppressed by RNA interference, was first established. Then, the effects of the suppression of filamin A gene expression on the biological characteristics of human PCa LNCaP cells were observed through cell morphology, in vitro cell growth curve, soft agar cloning assay, and scratch test. Results A cell line model with a low expression of filamin A was successfully constructed on the basis of LNCaP cells. The morphology of cells transfected with plasmid pSilencer-filamin A was the following: Cells were loosely arranged, had less connection with each other, had fewer tentacles, and presented a fibrous look. The growth rate of LNCap cells was faster than cells transfected with plasmid pSilencer-filamin A (P &lt;0.05). The clones of LNCap cells in the soft agar cloning assay was significantly fewer than that of cells stably transfected with plasmid pSilencer-filamin A (P &lt;0.05). Cells stably transfected with plasmid pSilencer-filamin A presented with a stronger healing and migration ability compared to LNCap cells (healing rate was 32.2% and 12.1%, respectively; P &lt;0.05). Conclusion The expression of the filamin A gene inhibited the malignant development of LNCap cells. Therefore, the filamin A gene may be a tumor suppressor gene.
DOI: 10.6084/m9.figshare.23047547.v1
title: Merged gene expression profiles (TPM)

description: Gene expression profiles (GEPs) of 19 cancer types in TCGA (TPM format).
DOI: 10.15490/fairdomhub.1.datafile.7126.1
title: RawData_figure4_Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation

description: Raw data of Figure 4, main text
DOI: 10.6084/m9.figshare.17110748.v1
title: Additional file 1 of Circulating noncoding RNAs as early predictive biomarkers in preeclampsia: a diagnostic meta-analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.17110751
title: Additional file 2 of Circulating noncoding RNAs as early predictive biomarkers in preeclampsia: a diagnostic meta-analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.17110751.v1
title: Additional file 2 of Circulating noncoding RNAs as early predictive biomarkers in preeclampsia: a diagnostic meta-analysis

description: Additional file 2.
DOI: 10.5519/qd.zx16ffgh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (5 records)
DOI: 10.15490/fairdomhub.1.datafile.7127.1
title: rawData_figure 5_Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation

description: Raw data of Figure 5, main text
DOI: 10.6084/m9.figshare.11945865.v1
title: Additional file 10 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 10: Data Set S3. mRNA TPM result.
DOI: 10.6084/m9.figshare.22877569.v1
title: Additional file 5 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 5: Table S4. Chromatin loops identified in normal and cold-treated plants.
DOI: 10.11583/dtu.22836338
title: Data for "Quantifying Noise Limitations of Neural Network Segmentations in High-Resolution Transmission Electron Microscopy"

description: Data for reproducing the manuscript "Quantifying Noise Limitations of Neural Network Segmentations in High-Resolution Transmission Electron Microscopy" by Matthew Helmi Leth Larsen, William Bang Lomholdt, Cuauhtemoc Nuñez Valencia, Thomas W. Hansen, and Jakob Schiøtz.
<br>
DOI: 10.6084/m9.figshare.22877560
title: Additional file 2 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 2: Table S1. Hi-C data summary.
DOI: 10.6084/m9.figshare.7149677.v2
title: Identification of factors that promote biogenesis of tRNA<sub>CGA</sub><sup>Ser</sup>

description: A wide variety of factors are required for the conversion of pre-tRNA molecules into the mature tRNAs that function in translation. To identify factors influencing tRNA biogenesis, we previously performed a screen for strains carrying mutations that induce lethality when combined with a <i>sup61-T47:2C</i> allele, encoding a mutant form of tRNACGASer. Analyzes of two complementation groups led to the identification of Tan1 as a protein involved in formation of the modified nucleoside <i>N</i><sup>4</sup>-acetylcytidine (ac<sup>4</sup>C) in tRNA and Bud13 as a factor controlling the levels of ac<sup>4</sup>C by promoting <i>TAN1</i> pre-mRNA splicing. Here, we describe the remaining complementation groups and show that they include strains with mutations in genes for known tRNA biogenesis factors that modify (<i>DUS2, MOD5</i> and <i>TRM1</i>), transport (<i>LOS1</i>), or aminoacylate (<i>SES1</i>) tRNACGASer. Other strains carried mutations in genes for factors involved in rRNA/mRNA synthesis (<i>RPA49, RRN3</i> and <i>MOT1</i>) or magnesium uptake (<i>ALR1</i>). We show that mutations in not only <i>DUS2, LOS1</i> and <i>SES1</i> but also in <i>RPA49, RRN3</i> and <i>MOT1</i> cause a reduction in the levels of the altered tRNACGASer. These results indicate that Rpa49, Rrn3 and Mot1 directly or indirectly influence tRNACGASer biogenesis.
DOI: 10.5281/zenodo.7019871
title: Cross-linguistic sample of middle marking languages

description: This database features the cross-linguistic sample of middle marking languages gathered during the project "Towards a diachronic typology of the middle voice" funded by the FWO (Research Foundation Flanders, grant 12T5320N) and hosted by the Department of Linguistics, KU Leuven (2020-2022).The following papers have been based on this sample (I refer to the Appendixes to the individual papers for details on the sample composition and on the annotation):

 

Inglese, Guglielmo. 2022a. Towards a typology of middle voice systems. Linguistic Typology 26(3): 489-531. [published online 29 November 2021]. https://doi.org/10.1515/lingty-2020-0131

Inglese, Guglielmo. 2022b. How do middle voice markers and valency reducing constructions interact? Typological tendencies and diachronic considerations. Folia Linguistica 56(2): 239–271. https://doi.org/10.1515/flin-2022-2019

Inglese, Guglielmo. 2023. The rise of middle voice systems: a study in diachronic typology. Diachronica 40(2): 195–237. https://doi.org/10.1075/dia.20058.ing
DOI: 10.5281/zenodo.7019872
title: Cross-linguistic sample of middle marking languages

description: This database features the cross-linguistic sample of middle marking languages gathered during the project "Towards a diachronic typology of the middle voice" funded by the FWO (Research Foundation Flanders, grant 12T5320N) and hosted by the Department of Linguistics, KU Leuven (2020-2022).The following papers have been based on this sample (I refer to the Appendixes to the individual papers for details on the sample composition and on the annotation):

 

Inglese, Guglielmo. 2022a. Towards a typology of middle voice systems. Linguistic Typology 26(3): 489-531. [published online 29 November 2021]. https://doi.org/10.1515/lingty-2020-0131

Inglese, Guglielmo. 2022b. How do middle voice markers and valency reducing constructions interact? Typological tendencies and diachronic considerations. Folia Linguistica 56(2): 239–271. https://doi.org/10.1515/flin-2022-2019

Inglese, Guglielmo. 2023. The rise of middle voice systems: a study in diachronic typology. Diachronica 40(2): 195–237. https://doi.org/10.1075/dia.20058.ing
DOI: 10.6084/m9.figshare.9771086.v1
title: Additional file 3: of Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae)

description: Table S4. 14 morphometric characters used in the morphospace construction. Including standard length (SL), preanal length (PreanalL), preanus length (PreanusL), prepelvic length (PrepelvicL), caudal peduncle length (CPL), head length (HeadL), prepectoral length (PrepectoralL), snout length (SnoutL), postorbital length (PostorbitalL), interorbital width (InterorbitalW), eye diameter (EyeD), head depth (HeadD), body depth (BodyD), and caudal peduncle depth (CPD). (CSV 15â kb) (CSV 14 kb)
DOI: 10.6084/m9.figshare.12916819
title: Additional file 1 of Characterization of the regulation mechanism of grapevine microRNA172 family members during flower development

description: Additional file 1: Table S1. Sequences of primer and use.
DOI: 10.6084/m9.figshare.11945865
title: Additional file 10 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 10: Data Set S3. mRNA TPM result.
DOI: 10.6084/m9.figshare.22877563
title: Additional file 3 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 3: Table S2. A/B compartments identified at 50 kb resolution.
DOI: 10.6084/m9.figshare.17110847.v1
title: Additional file 3 of CircEAF2 counteracts Epstein-Barr virus-positive diffuse large B-cell lymphoma progression via miR-BART19-3p/APC/β-catenin axis

description: Additional file 3: Table S2. Sequence information of miRNA mimics and circ siRNA.
DOI: 10.6084/m9.figshare.17110850.v1
title: Additional file 4 of CircEAF2 counteracts Epstein-Barr virus-positive diffuse large B-cell lymphoma progression via miR-BART19-3p/APC/β-catenin axis

description: Additional file 4: Table S3. Sequence information of biotinylated probes.
DOI: 10.6084/m9.figshare.19732446.v1
title: Original source data during pyrolysis of YW (a)，QX ((b) and YH (b) LCV coal;Original source data during combustion of YW (a)，QX ((b) and YH (b) LCV coal;Original source data during OFC of YW (a)，QX ((b) and YH (b) LCV coal; Original source data at 700 ℃ (a), 900 ℃(b) and 1100℃(c) during combustion of QX coal from Release characteristics of elemental mercury during low calorific value coal combustion

description: data for Fig.1;data for Fig.2;data for Fig.4;data for Fig.5
DOI: 10.6084/m9.figshare.22877572.v1
title: Additional file 6 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 6: Table S5. Differential loops were identified between normal and cold-treated plants.
DOI: 10.6084/m9.figshare.17110850
title: Additional file 4 of CircEAF2 counteracts Epstein-Barr virus-positive diffuse large B-cell lymphoma progression via miR-BART19-3p/APC/β-catenin axis

description: Additional file 4: Table S3. Sequence information of biotinylated probes.
DOI: 10.6084/m9.figshare.12916760
title: Additional file 1 of Modeling tumor development and metastasis using paired organoids derived from patients with colorectal cancer liver metastases

description: Additional file 1: Supplementary Table S1. Summary of patient-derived CRC organoid lines and corresponding clinical data.
DOI: 10.11583/dtu.22836338.v1
title: Data for "Quantifying Noise Limitations of Neural Network Segmentations in High-Resolution Transmission Electron Microscopy"

description: Data for reproducing the manuscript "Quantifying Noise Limitations of Neural Network Segmentations in High-Resolution Transmission Electron Microscopy" by Matthew Helmi Leth Larsen, William Bang Lomholdt, Cuauhtemoc Nuñez Valencia, Thomas W. Hansen, and Jakob Schiøtz.
<br>
DOI: 10.6084/m9.figshare.22877661
title: Additional file 4 of Dysregulated endothelial cell markers in systemic lupus erythematosus: a systematic review and meta-analysis

description: Additional file 4. Table showing the statistical methods and reported correlations of individual markers selected for meta-analysis, as well as the P-value calculations for overall correlation coefficients.
DOI: 10.6084/m9.figshare.11945874.v1
title: Additional file 11 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 11: Data Set S4. mRNA sequence.
DOI: 10.6084/m9.figshare.12916760.v1
title: Additional file 1 of Modeling tumor development and metastasis using paired organoids derived from patients with colorectal cancer liver metastases

description: Additional file 1: Supplementary Table S1. Summary of patient-derived CRC organoid lines and corresponding clinical data.
DOI: 10.6084/m9.figshare.22877560.v1
title: Additional file 2 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 2: Table S1. Hi-C data summary.
DOI: 10.6084/m9.figshare.12916819.v1
title: Additional file 1 of Characterization of the regulation mechanism of grapevine microRNA172 family members during flower development

description: Additional file 1: Table S1. Sequences of primer and use.
DOI: 10.6084/m9.figshare.22877661.v1
title: Additional file 4 of Dysregulated endothelial cell markers in systemic lupus erythematosus: a systematic review and meta-analysis

description: Additional file 4. Table showing the statistical methods and reported correlations of individual markers selected for meta-analysis, as well as the P-value calculations for overall correlation coefficients.
DOI: 10.6084/m9.figshare.22877569
title: Additional file 5 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 5: Table S4. Chromatin loops identified in normal and cold-treated plants.
DOI: 10.25402/fon.19208301
title: Supplementary Tables – Efficacy and Safety of First-Line Therapies in EGFR-Mutated Advanced Non-Small Cell Lung Cancer: A Network Meta-Analysis

description: Table
 A1. Full search strategy for Embase.
 
 <b>Table A2. Full search
 strategy for MEDLINE.</b>
 <b>Table A3. Full search
 strategy for Cochrane.</b>
 <b>Table A4. Trials identified
 from the SLR (n=57).</b>
 <b>Table A5. PFS evidence for overall
 EGFRm+ NSCLC patient population, by mutation type, and by geographical region.</b>
 <b>Table A6. OS evidence for
 overall EGFRm+ NSCLC patient population.</b>
 <b>Table A7. Base case PFS
 - pairwise comparisons of all interventions and comparators.</b>
 <b> </b>
 <b>Table A8. Base case OS -
 pairwise comparisons of all interventions and comparators.</b>
DOI: 10.6084/m9.figshare.22877658.v1
title: Additional file 3 of Dysregulated endothelial cell markers in systemic lupus erythematosus: a systematic review and meta-analysis

description: Additional file 3. Quality assessment overview.
DOI: 10.25402/fon.19208301.v1
title: Supplementary Tables – Efficacy and Safety of First-Line Therapies in EGFR-Mutated Advanced Non-Small Cell Lung Cancer: A Network Meta-Analysis

description: Table
 A1. Full search strategy for Embase.
 
 <b>Table A2. Full search
 strategy for MEDLINE.</b>
 <b>Table A3. Full search
 strategy for Cochrane.</b>
 <b>Table A4. Trials identified
 from the SLR (n=57).</b>
 <b>Table A5. PFS evidence for overall
 EGFRm+ NSCLC patient population, by mutation type, and by geographical region.</b>
 <b>Table A6. OS evidence for
 overall EGFRm+ NSCLC patient population.</b>
 <b>Table A7. Base case PFS
 - pairwise comparisons of all interventions and comparators.</b>
 <b> </b>
 <b>Table A8. Base case OS -
 pairwise comparisons of all interventions and comparators.</b>
DOI: 10.6084/m9.figshare.7149677.v1
title: Identification of factors that promote biogenesis of tRNA<sup>Ser</sup><sub>CGA</sub>

description: A wide variety of factors are required for the conversion of pre-tRNA molecules into the mature tRNAs that function in translation. To identify factors influencing tRNA biogenesis, we previously performed a screen for strains carrying mutations that induce lethality when combined with a <i>sup61-T47:2C</i> allele, encoding a mutant form of tRNACGASer. Analyses of two complementation groups led to the identification of Tan1 as a protein involved in formation of the modified nucleoside <i>N</i><sup>4</sup>-acetylcytidine (ac<sup>4</sup>C) in tRNA and Bud13 as a factor controlling the levels of ac<sup>4</sup>C by promoting <i>TAN1</i> pre-mRNA splicing. Here, we describe the remaining complementation groups and show that they include strains with mutations in genes for known tRNA biogenesis factors that modify (<i>DUS2, MOD5</i> and <i>TRM1</i>), transport (<i>LOS1</i>), or aminoacylate (<i>SES1</i>) tRNACGASer. Other strains carried mutations in genes for factors involved in rRNA/mRNA synthesis (<i>RPA49, RRN3</i> and <i>MOT1</i>) or magnesium uptake (<i>ALR1</i>). We show that mutations in not only <i>DUS2, LOS1</i> and <i>SES1</i> but also in <i>RPA49, RRN3</i> and <i>MOT1</i> cause a reduction in the levels of the altered tRNACGASer. These results indicate that Rpa49, Rrn3 and Mot1 directly or indirectly influence tRNACGASer biogenesis.
DOI: 10.6084/m9.figshare.21830027
title: DSM-5 posttraumatic stress symptom dimensions and health-related quality of life among Chinese earthquake survivors

description: It has been well-documented that posttraumatic stress symptoms cause impairments in health-related quality of life (HRQoL). Until now we have little data on how DSM-5 PTSD symptom dimensions relate to different aspects of HRQoL. Clarifying this question would be informative to improve the quality of life of PTSD patients. This study aimed to investigate the effects of dimensions of a well-supported seven-factor model of DSM-5 PTSD symptoms on physical and psychosocial HRQoL. A total of 1063 adult survivors of the 2008 Wenchuan earthquake took part in this study nine years after the disaster. PTSD symptoms were measured by the PTSD Checklist for DSM-5 (PCL-5). HRQoL was measured by the Medical Outcomes Survey Short Form-36 (SF-36). The associations between PTSD symptom dimensions and HRQoL were examined using structural equation models. Dysphoric arousal symptoms were found to significantly relate to physical HRQoL. Other symptom dimensions were not associated with HRQoL. Our findings contribute to the relationship between DSM-5 PTSD and HRQoL, and carry implications for further clinical practice and research on trauma-exposed individuals.
DOI: 10.6084/m9.figshare.22877566
title: Additional file 4 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 4: Table S3. TADs identified at 5 kb resolution.
DOI: 10.6084/m9.figshare.22877572
title: Additional file 6 of High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

description: Additional file 6: Table S5. Differential loops were identified between normal and cold-treated plants.
DOI: 10.6084/m9.figshare.17111438.v1
title: Diagnostic accuracy and prognostic significance of osteopontin in liver cirrhosis and hepatocellular carcinoma: a Meta-analysis

description: At present, there is no definite suggestion about effective tumour biomarkers for the diagnostic accuracy and prognostic significance of hepatocellular carcinoma (HCC) and liver cirrhosis (LC). The aim of our research was to determine the value of the tumour biomarker osteopontin (OPN), which is encoded by the Spp1 gene, in the diagnosis, prognosis and development of HCC and LC through meta-analysis. A systematic literature search was performed in the PubMed, Embase, Cochrane Library and China National Knowledge Infrastructure electronic databases up to March 2021. Studies evaluating the diagnostic and/or prognostic value of OPN in HCC and/or LC were included. From the systematic search, 35 studies including 9150 participants were eligible, 25 of which provided data on the diagnostic value of OPN overexpression, while 15 studies provided data on the prognostic value. OPN had high diagnostic accuracy in both HCC and LC patients compared with healthy controls, and the diagnostic efficiency was increased by the biomarker combination OPN + AFP. OPN may be adopted as a promising predictive tumour biomarker for the diagnosis and prognosis of HCC and LC and may be a potential therapeutic target.
DOI: 10.6084/m9.figshare.9771407.v1
title: Additional file 2: of The fungicide azoxystrobin promotes freshwater cyanobacterial dominance through altering competition

description: Dataset 1. Detailed statistics of clean data, sample transcript and FPKM interval from six microcosms. Dataset 2. Taxonomic proportions in each microcosm. Dataset 3. Annotation and relative abundance of KOs in each microcosm. Dataset 4. Comparison in abundances between control and AZ groups at KEGG level 3. Dataset 5. Comparison in abundances between control and AZ groups at KEGG level 4. (XLSX 1138 kb)