cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22621684.v1
title: Additional file 6 of The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses

description: Additional file 6: Table S6. GO analysis of nonoverlapping genes.
DOI: 10.57745/2dvhtu
title: Colletotrichum_destructivum_cd709.TEconsensus.fasta

description: :unav
DOI: 10.57745/qoar4d
title: Colletotrichum_destructivum_Cd709.annotations-TE.xlsx

description: :unav
DOI: 10.57745/5hyyja
title: Readme.txt

description: :unav
DOI: 10.57745/ia3hxo
title: Readme.txt

description: :unav
DOI: 10.57745/rtzgmv
title: Colletotrichum_destructivum_Cd709.TE.gff3

description: :unav
DOI: 10.6084/m9.figshare.22621705
title: Additional file 13 of The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses

description: Additional file 13: Table S7. Genome-wide methylation analysis of linseed seedlings under drought stress.
DOI: 10.6084/m9.figshare.7942088.v1
title: The Influence of Isothermal Holding Times on Microstructural Evolution of X90 Linepipe Steel

description: Microstructural phase of linepipe steels depends on different isothermal conditions. Thermal cycling testing of X90 linepipe steel was conducted using a thermomechanical simulator. The results have shown that with increased holding time, the microstructure constituents change from the martensite and bainitic ferrites to granular bainite and polygonal ferrite. There was the amount of martensite in the microstructure for isothermal holding times of 5 and 10 s at 700ºC. The effects of the martensite strengthening were weak. The changes of the hardness curve are decided by microstructural phase and the precipitation behavior. The interphase precipitation seems to begin for isothermal holding times greater than 30 s. It has a peak value for isothermal holding time of 600 s. Some fcc (Ti, Nb) (N, C) particles which belong to the MX-type precipitates were obtained at this condition. It is a major microstructural contributor to the hardness. The beneficial effects of the precipitates decreased considerably due to coarsening of the precipitates with prolonged holding, which results in the hardness quickly dropping. As a result, the hardness exhibited a low value after isothermal holding for 3600 s because the extent of precipitation strengthening was lessened and a lot of polygonal ferrites were formed.
DOI: 10.6084/m9.figshare.22622030
title: Additional file 1 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22622042
title: Additional file 5 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.22621915.v1
title: Additional file 2 of Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants

description: Additional file 2. Containing a workbook with three sheets of supplementary tables, Table S4-S6. The first sheet, “LoFP_variants”, contains details on unique loss-of-function and known pathogenic variants in the explorative and validation cohorts. The second sheet, “False_negative_variants”, contains details on false negative variants across all unique variants found in the explorative and validation cohorts. The third sheet, “DNA_yield, contains details on DNA extraction yield from Guthrie cards for both cohorts. For all tables; ID is formed by a letter (corresponding to the column batch the patient is in) and a number (corresponding to the row batch the patient is in). For first and second sheet; HGVS, Human Genome Variation Society (variant nomenclature). VAF, variant allele frequency, alt, alternative variant allele number, X, total read depth for locus, and SB, strand bias, are given for whole genome sequencing (WGS), column batch sequencing and row batch sequencing data.
DOI: 10.6084/m9.figshare.22621915
title: Additional file 2 of Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants

description: Additional file 2. Containing a workbook with three sheets of supplementary tables, Table S4-S6. The first sheet, “LoFP_variants”, contains details on unique loss-of-function and known pathogenic variants in the explorative and validation cohorts. The second sheet, “False_negative_variants”, contains details on false negative variants across all unique variants found in the explorative and validation cohorts. The third sheet, “DNA_yield, contains details on DNA extraction yield from Guthrie cards for both cohorts. For all tables; ID is formed by a letter (corresponding to the column batch the patient is in) and a number (corresponding to the row batch the patient is in). For first and second sheet; HGVS, Human Genome Variation Society (variant nomenclature). VAF, variant allele frequency, alt, alternative variant allele number, X, total read depth for locus, and SB, strand bias, are given for whole genome sequencing (WGS), column batch sequencing and row batch sequencing data.
DOI: 10.6084/m9.figshare.20000474
title: Additional file 3 of Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney

description: Additional file 3: Table S2. The proportion of signatures of different scRNA-seq cell types in each ST spot of the 9 and 18 PCW kidney tissues.
DOI: 10.6084/m9.figshare.20000471
title: Additional file 2 of Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney

description: Additional file 2: Table S1. Quality control of ST-seq date from 9 and 18 PCW kidneys.
DOI: 10.5517/ccdc.csd.cc2hfbw5
title: CCDC 2306737: Experimental Crystal Structure Determination

description: Related Article: Corinna Czernetzki, Merle Arrowsmith, Lukas Endres, Ivo Krummenacher, Holger Braunschweig|2024|Inorg.Chem.|63|2670|doi:10.1021/acs.inorgchem.3c04014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hfbx6
title: CCDC 2306738: Experimental Crystal Structure Determination

description: Related Article: Corinna Czernetzki, Merle Arrowsmith, Lukas Endres, Ivo Krummenacher, Holger Braunschweig|2024|Inorg.Chem.|63|2670|doi:10.1021/acs.inorgchem.3c04014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hfby7
title: CCDC 2306739: Experimental Crystal Structure Determination

description: Related Article: Corinna Czernetzki, Merle Arrowsmith, Lukas Endres, Ivo Krummenacher, Holger Braunschweig|2024|Inorg.Chem.|63|2670|doi:10.1021/acs.inorgchem.3c04014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hfbz8
title: CCDC 2306740: Experimental Crystal Structure Determination

description: Related Article: Corinna Czernetzki, Merle Arrowsmith, Lukas Endres, Ivo Krummenacher, Holger Braunschweig|2024|Inorg.Chem.|63|2670|doi:10.1021/acs.inorgchem.3c04014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hfct4
title: CCDC 2306766: Experimental Crystal Structure Determination

description: Related Article: Corinna Czernetzki, Merle Arrowsmith, Lukas Endres, Ivo Krummenacher, Holger Braunschweig|2024|Inorg.Chem.|63|2670|doi:10.1021/acs.inorgchem.3c04014
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.17632/xj4rs77c4j.1
title: OilPalm_Dataset.id

description: All images are from the Palangka Raya oil palm plantation area, Kalimantan Tengah, Indonesia. Data was collected in August 2022. It can be seen 
in the Table, the data is separated into several small sizes, categories, types, and amounts of data.
If you use this data, please cite our journal, available at SSRN: https://ssrn.com/abstract=4596338 or http://dx.doi.org/10.2139/ssrn.4596338
DOI: 10.6084/m9.figshare.22622030.v1
title: Additional file 1 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22622036
title: Additional file 3 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22622036.v1
title: Additional file 3 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22619375
title: Additional file 3 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 3. Supplementary Table 1. Output of EWAS statistical results (p&lt;0.05) arranged in the order from left to the right for the interaction effect, main effect of IC50 and smoking, followed by annotations for each CpGs in the table.
DOI: 10.6084/m9.figshare.22619381.v1
title: Additional file 5 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 5. Supplementary Table 3. Validation of top CpGs showing main effect on IC50 in an multi-omics independent BMD study [33]. Significant q-values are highlighted in bold, while highly significant q-values are also highlighted in red.
DOI: 10.6084/m9.figshare.22619384
title: Additional file 6 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 6. Supplementary Table 4. The number and list of phenotypes in each phenotype group. Each sheet is labelled according to the corresponding “phen#” group.
DOI: 10.6084/m9.figshare.22622042.v1
title: Additional file 5 of Plasma ctDNA increases tissue NGS-based detection of therapeutically targetable mutations in lung cancers

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.20000873
title: Long non-coding RNA MALAT1 aggravated liver ischemia-reperfusion injury via targeting miR-150-5p/AZIN1

description: Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a crucial role in the process of renal ischemia-reperfusion (IR) injury and myocardial IR injury. However, its mechanism in liver IR injury is not clear. IR and hypoxia/reoxygenation (H/R) model were built on C57BL/6 mice. Blood samples were obtained from the inferior vena cava of the model mice. MALAT1 expression was detected in IR model and H/R model. Supported by experimental results, the impacts of MALAT1 on viability, apoptosis, and inflammation of H/R model cells were detected. The correlation between MALAT1 and downstream genes was analyzed by mechanism assays. MALAT1 was detected to be upregulated in IR model and H/R model. MALAT1 knockdown had inhibitory effects on apoptosis and inflammatory reaction while promoting liver cell viability in H/R condition. Meanwhile, MALAT1 targeted miR-150-5p to regulate antizyme inhibitor 1 (AZIN1) in liver cells. Finally, MALAT1 regulated viability, apoptosis, and inflammatory reaction of liver cells by targeting miR-150-5p and AZIN1. To conclude, MALAT1 targeted miR-150-5p/AZIN1 to accelerate liver IR injury, suggesting that MALAT1 might be a novel target for liver IR injury.
DOI: 10.6084/m9.figshare.20000873.v1
title: Long non-coding RNA MALAT1 aggravated liver ischemia-reperfusion injury via targeting miR-150-5p/AZIN1

description: Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays a crucial role in the process of renal ischemia-reperfusion (IR) injury and myocardial IR injury. However, its mechanism in liver IR injury is not clear. IR and hypoxia/reoxygenation (H/R) model were built on C57BL/6 mice. Blood samples were obtained from the inferior vena cava of the model mice. MALAT1 expression was detected in IR model and H/R model. Supported by experimental results, the impacts of MALAT1 on viability, apoptosis, and inflammation of H/R model cells were detected. The correlation between MALAT1 and downstream genes was analyzed by mechanism assays. MALAT1 was detected to be upregulated in IR model and H/R model. MALAT1 knockdown had inhibitory effects on apoptosis and inflammatory reaction while promoting liver cell viability in H/R condition. Meanwhile, MALAT1 targeted miR-150-5p to regulate antizyme inhibitor 1 (AZIN1) in liver cells. Finally, MALAT1 regulated viability, apoptosis, and inflammatory reaction of liver cells by targeting miR-150-5p and AZIN1. To conclude, MALAT1 targeted miR-150-5p/AZIN1 to accelerate liver IR injury, suggesting that MALAT1 might be a novel target for liver IR injury.
DOI: 10.6084/m9.figshare.20000888
title: Long noncoding RNA BBOX1-AS1 promotes the progression of gastric cancer by regulating the miR-361-3p/Mucin 13 signaling axis

description: Gastric cancer (GC) places a heavy burden on global health, and the information on the molecular mechanism of the progression of GC is still inadequate. Long noncoding RNA (LncRNA) has been confirmed to be widely involved in regulating the progression of GC. Our aim in this study was to explore the role and potential regulatory mechanism of lncRNA BBOX1-AS1 in GC. The expression levels of BBOX1-AS1, miR-361-3p, and MUC13 in GC tissues and cells were evaluated using quantitative real-time polymerase chain reaction and western blotting. The silencer of BBOX1 antisense RNA 1 (BBOX1-AS1) and mucin 13 (MUC13), the mimics and inhibitor of miR-361-3p, and their negative controls were used to alter the expression of these genes. Luciferase reporter, pull-down, and RNA immunoprecipitation assays were performed to verify the correlation between miR-361-3p, BBOX1-AS1, and MUC13. GC cell proliferation, invasion, and apoptosis were detected by cell counting kit-8, transwell, and flow cytometry assays, respectively. An <i>in vivo</i> functional experiment was performed to assess the effect of BBOX1-AS1 on GC. The results showed that BBOX1-AS1 was significantly upregulated in GC tissues. Silencing of BBOX1-AS1 inhibited GC cell proliferation and invasion and inhibited tumor growth <i>in vivo</i>, whereas it promoted apoptosis. MiR-361-3p was significantly downregulated in GC and counteracted the inhibitory effects of BBOX1-AS1 on GC progression. MUC13, which is targeted by miR-361-3p, is significantly upregulated in GC. MUC13 silencing inhibited GC progression was aborgated by miR-361-3p inhibitor. Collectively, BBOX1-AS1 silencing inhibits GC progression by regulating the miR-361-3p/MUC13 axis, providing a potential therapeutic biomarker for GC.
DOI: 10.6084/m9.figshare.7942088
title: The Influence of Isothermal Holding Times on Microstructural Evolution of X90 Linepipe Steel

description: Microstructural phase of linepipe steels depends on different isothermal conditions. Thermal cycling testing of X90 linepipe steel was conducted using a thermomechanical simulator. The results have shown that with increased holding time, the microstructure constituents change from the martensite and bainitic ferrites to granular bainite and polygonal ferrite. There was the amount of martensite in the microstructure for isothermal holding times of 5 and 10 s at 700ºC. The effects of the martensite strengthening were weak. The changes of the hardness curve are decided by microstructural phase and the precipitation behavior. The interphase precipitation seems to begin for isothermal holding times greater than 30 s. It has a peak value for isothermal holding time of 600 s. Some fcc (Ti, Nb) (N, C) particles which belong to the MX-type precipitates were obtained at this condition. It is a major microstructural contributor to the hardness. The beneficial effects of the precipitates decreased considerably due to coarsening of the precipitates with prolonged holding, which results in the hardness quickly dropping. As a result, the hardness exhibited a low value after isothermal holding for 3600 s because the extent of precipitation strengthening was lessened and a lot of polygonal ferrites were formed.
DOI: 10.6084/m9.figshare.22619387
title: Additional file 7 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 7. Supplementary Table 5. This table shows the raw data for each CpG and each Phen#, success ratio was calculated as a proportion of #successful SNPs for that CpG to #all SNPs associated with that phenotype group, Phen#. “Success” means that the distance between location of a SNP and location of the CpG is less than the stated max distance. Series of incremental distances from 50,000 bp to 1,000 bp were tested, and then compared across the phenotype groups. The one-tailed Mann-Whitney U test was used to compare differences in success ratios between Phen1 and Phen 2 and “negative control” Phen4 as shown in Table 4.
DOI: 10.6084/m9.figshare.12136383
title: <i>UHRF1</i>, a Regulator of Methylation, as a Diagnostic and Prognostic Marker for Lung Cancer

description: We evaluated the value of <i>UHRF1</i>, a regulator of methylation, as a biomarker for lung cancer. <i>UHRF1</i> is expressed at higher levels in both lung adenocarcinoma (AD) and squamous cell carcinoma (SQ); however, a meta-analysis showed that <i>UHRF1</i> expression is correlated with worse survival in patients with AD but not in those with SQ. <i>UHRF1</i> knockdown suppressed the growth of lung cancer cell lines through G1 cell cycle arrest in some cell lines. These results suggest that <i>UHRF1</i> may server as a diagnostic marker for AD and SQ and as a prognostic marker for AD in lung cancer.
DOI: 10.6084/m9.figshare.12136383.v1
title: <i>UHRF1</i>, a Regulator of Methylation, as a Diagnostic and Prognostic Marker for Lung Cancer

description: We evaluated the value of <i>UHRF1</i>, a regulator of methylation, as a biomarker for lung cancer. <i>UHRF1</i> is expressed at higher levels in both lung adenocarcinoma (AD) and squamous cell carcinoma (SQ); however, a meta-analysis showed that <i>UHRF1</i> expression is correlated with worse survival in patients with AD but not in those with SQ. <i>UHRF1</i> knockdown suppressed the growth of lung cancer cell lines through G1 cell cycle arrest in some cell lines. These results suggest that <i>UHRF1</i> may server as a diagnostic marker for AD and SQ and as a prognostic marker for AD in lung cancer.
DOI: 10.6084/m9.figshare.22619384.v1
title: Additional file 6 of A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

description: Additional file 6. Supplementary Table 4. The number and list of phenotypes in each phenotype group. Each sheet is labelled according to the corresponding “phen#” group.
DOI: 10.6084/m9.figshare.22619479.v1
title: Additional file 2 of Comprehensive analysis of cuproptosis-related long noncoding RNA for predicting prognostic and diagnostic value and immune landscape in colorectal adenocarcinoma

description: Additional file 2: Table S2. The cuproptosis-related lncRNAs
DOI: 10.6084/m9.figshare.20000888.v1
title: Long noncoding RNA BBOX1-AS1 promotes the progression of gastric cancer by regulating the miR-361-3p/Mucin 13 signaling axis

description: Gastric cancer (GC) places a heavy burden on global health, and the information on the molecular mechanism of the progression of GC is still inadequate. Long noncoding RNA (LncRNA) has been confirmed to be widely involved in regulating the progression of GC. Our aim in this study was to explore the role and potential regulatory mechanism of lncRNA BBOX1-AS1 in GC. The expression levels of BBOX1-AS1, miR-361-3p, and MUC13 in GC tissues and cells were evaluated using quantitative real-time polymerase chain reaction and western blotting. The silencer of BBOX1 antisense RNA 1 (BBOX1-AS1) and mucin 13 (MUC13), the mimics and inhibitor of miR-361-3p, and their negative controls were used to alter the expression of these genes. Luciferase reporter, pull-down, and RNA immunoprecipitation assays were performed to verify the correlation between miR-361-3p, BBOX1-AS1, and MUC13. GC cell proliferation, invasion, and apoptosis were detected by cell counting kit-8, transwell, and flow cytometry assays, respectively. An <i>in vivo</i> functional experiment was performed to assess the effect of BBOX1-AS1 on GC. The results showed that BBOX1-AS1 was significantly upregulated in GC tissues. Silencing of BBOX1-AS1 inhibited GC cell proliferation and invasion and inhibited tumor growth <i>in vivo</i>, whereas it promoted apoptosis. MiR-361-3p was significantly downregulated in GC and counteracted the inhibitory effects of BBOX1-AS1 on GC progression. MUC13, which is targeted by miR-361-3p, is significantly upregulated in GC. MUC13 silencing inhibited GC progression was aborgated by miR-361-3p inhibitor. Collectively, BBOX1-AS1 silencing inhibits GC progression by regulating the miR-361-3p/MUC13 axis, providing a potential therapeutic biomarker for GC.
DOI: 10.6084/m9.figshare.12660937
title: Additional file 1 of Reconstruction of monsoon evolution in southernmost Sumatra over the past 35 kyr and its response to northern hemisphere climate changes

description: Additional file 1. Data.
DOI: 10.6084/m9.figshare.25187693
title: Table 2. Research questions based on specific objectives

description: Table 2. Research questions based on specific objectives