cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16577649.v2
title: Sedimentary tectonic pattern of Wufeng and Longmaxi Formations in the northern margin of Sichuan Basin, South China

description: Organic-rich black shales in the Sichuan Basin from the Upper Ordovician and Lower Silurian are considered excellent source rocks and unconventional reservoirs of hydrocarbons in South China. The Wufeng and Longmaxi Formations in the Micangshan – Dabashan areas of the northern margin of Sichuan Basin were taken as the research objects. The purpose of this study is to reconstruct the sedimentary tectonic pattern of the Wufeng and Longmaxi Formations in the study area. First, the stratigraphic framework correlation and sedimentary facies analysis of Wufeng and Longmaxi Formations in the study area were carried out. Then, Mo/TOC and Al-Co[EF]×Mn[EF] geochemical indicators were used to identify the degree of water restricted during the deposition period. It was found that the thickness of black shale was relatively small near the uplift area. However, far away from the uplift area, from west to east, the black shale thickened and the TOC content increased gradually, which were controlled by the upwelling of continental margin and intracontinental depression. The results show that: (1) At the front edge of Micangshan, during the deposition period of Wufeng Formation, Fucheng and Qiaoting profiles were located in the intersection area of upwelling formed by two kinds of monsoon, which led to the long-term influence of upwelling in this area. The sedimentation period of Longmaxi Formation was mainly affected by ‘Xixiang Rise’, which led to the uplift of Wangcang and Nanjiang areas into islands. (2) At the front edge of Dabashan and Western Hubei – Eastern Chongqing areas, the Wufeng Formation presented a tectonic pattern of alternating uplift and depression. Due to the continuous compression of the Cathaysian Block from southeast to northwest, the Shizhu – Wuxi areas continued to subside during the deposition period of Longmaxi Formation, and the black shale was quite thick.
DOI: 10.6084/m9.figshare.16577646
title: A novel pyroptosis-related lncRNA signature for prognostic prediction in patients with lung adenocarcinoma

description: Lung adenocarcinoma (LUAD) has been the major cause of tumor-associated mortality in recent years and has a poor prognosis. Pyroptosis is regulated via the activation of inflammasomes and participates in tumorigenesis. However, the effects of pyroptosis-related lncRNAs (PRlncRNAs) on LUAD have not yet been completely elucidated. Therefore, we attempted to systematically explore patterns of cell pyroptosis to establish a novel signature for predicting LUAD survival. Based on TCGA database, we set up a prognostic model by incorporating PRlncRNAs with differential expression using Cox regression and LASSO regression. Kaplan–Meier analysis was conducted to compare the survival of LUAD patients. We further simplified the risk model and created a nomogram to enhance the prediction of LUAD prognosis. Altogether, 84 PRlncRNAs with differential expression were discovered. Subsequently, a new risk model was constructed based on five PRlncRNAs, GSEC, FAM83A-AS1, AL606489.1, AL034397.3 and AC010980.2. The proposed signature exhibited good performance in prognostic prediction and was related to immunocyte infiltration. The nomogram exactly forecasted the overall survival of patients and had excellent clinical utility. In the present study, the five-lncRNA prognostic risk signature and nomogram are trustworthy and effective indicators for predicting the prognosis of LUAD.
DOI: 10.6084/m9.figshare.16577649.v1
title: Sedimentary tectonic pattern of Wufeng and Longmaxi Formations in the northern margin of Sichuan Basin, South China

description: Organic-rich black shales in the Sichuan Basin from the Upper Ordovician and Lower Silurian are considered excellent source rocks and unconventional reservoirs of hydrocarbons in South China. The Wufeng and Longmaxi Formations in the Micangshan – Dabashan areas of the northern margin of Sichuan Basin were taken as the research objects. The purpose of this study is to reconstruct the sedimentary tectonic pattern of the Wufeng and Longmaxi Formations in the study area. First, the stratigraphic framework correlation and sedimentary facies analysis of Wufeng and Longmaxi Formations in the study area were carried out. Then, Mo/TOC and Al-Co[EF]×Mn[EF] geochemical indicators were used to identify the degree of water restricted during the deposition period. It was found that the thickness of black shale was relatively small near the uplift area. However, far away from the uplift area, from west to east, the black shale thickened and the TOC content increased gradually, which were controlled by the upwelling of continental margin and intracontinental depression. The results show that: (1) At the front edge of Micangshan, during the deposition period of Wufeng Formation, Fucheng and Qiaoting profiles were located in the intersection area of upwelling formed by two kinds of monsoon, which led to the long-term influence of upwelling in this area. The sedimentation period of Longmaxi Formation was mainly affected by ‘Xixiang Rise’, which led to the uplift of Wangcang and Nanjiang areas into islands. (2) At the front edge of Dabashan and Western Hubei – Eastern Chongqing areas, the Wufeng Formation presented a tectonic pattern of alternating uplift and depression. Due to the continuous compression of the Cathaysian Block from southeast to northwest, the Shizhu – Wuxi areas continued to subside during the deposition period of Longmaxi Formation, and the black shale was quite thick.
DOI: 10.6084/m9.figshare.16577646.v2
title: A novel pyroptosis-related lncRNA signature for prognostic prediction in patients with lung adenocarcinoma

description: Lung adenocarcinoma (LUAD) has been the major cause of tumor-associated mortality in recent years and has a poor prognosis. Pyroptosis is regulated via the activation of inflammasomes and participates in tumorigenesis. However, the effects of pyroptosis-related lncRNAs (PRlncRNAs) on LUAD have not yet been completely elucidated. Therefore, we attempted to systematically explore patterns of cell pyroptosis to establish a novel signature for predicting LUAD survival. Based on TCGA database, we set up a prognostic model by incorporating PRlncRNAs with differential expression using Cox regression and LASSO regression. Kaplan–Meier analysis was conducted to compare the survival of LUAD patients. We further simplified the risk model and created a nomogram to enhance the prediction of LUAD prognosis. Altogether, 84 PRlncRNAs with differential expression were discovered. Subsequently, a new risk model was constructed based on five PRlncRNAs, GSEC, FAM83A-AS1, AL606489.1, AL034397.3 and AC010980.2. The proposed signature exhibited good performance in prognostic prediction and was related to immunocyte infiltration. The nomogram exactly forecasted the overall survival of patients and had excellent clinical utility. In the present study, the five-lncRNA prognostic risk signature and nomogram are trustworthy and effective indicators for predicting the prognosis of LUAD.
DOI: 10.6084/m9.figshare.16577646.v1
title: A novel pyroptosis-related lncRNA signature for prognostic prediction in patients with lung adenocarcinoma

description: Lung adenocarcinoma (LUAD) has been the major cause of tumor-associated mortality in recent years and has a poor prognosis. Pyroptosis is regulated via the activation of inflammasomes and participates in tumorigenesis. However, the effects of pyroptosis-related lncRNAs (PRlncRNAs) on LUAD have not yet been completely elucidated. Therefore, we attempted to systematically explore patterns of cell pyroptosis to establish a novel signature for predicting LUAD survival. Based on TCGA database, we set up a prognostic model by incorporating PRlncRNAs with differential expression using Cox regression and LASSO regression. Kaplan–Meier analysis was conducted to compare the survival of LUAD patients. We further simplified the risk model and created a nomogram to enhance the prediction of LUAD prognosis. Altogether, 84 PRlncRNAs with differential expression were discovered. Subsequently, a new risk model was constructed based on five PRlncRNAs, GSEC, FAM83A-AS1, AL606489.1, AL034397.3 and AC010980.2. The proposed signature exhibited good performance in prognostic prediction and was related to immunocyte infiltration. The nomogram exactly forecasted the overall survival of patients and had excellent clinical utility. In the present study, the five-lncRNA prognostic risk signature and nomogram are trustworthy and effective indicators for predicting the prognosis of LUAD.
DOI: 10.6084/m9.figshare.19759535
title: Additional file 3 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 3: Table S2. All tidy data used in the main figures.
DOI: 10.6084/m9.figshare.19759535.v1
title: Additional file 3 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 3: Table S2. All tidy data used in the main figures.
DOI: 10.6084/m9.figshare.16577661
title: Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head

description: Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An immune cell abundance identifier was used to explore immune cell infiltration. Furthermore, hub genes were identified based on maximal clique centrality (MCC) evaluation using cytoHubba application and confirmed by qRT-PCR using clinical samples. Finally, the L1000 platform was used to determine potential drugs for SONFH treatment. The SONFH mouse model was used to determine the therapeutic effects of aspirin. In total, 429 DEGs were identified in SONFH samples. Functional enrichment analysis showed that these DEGs were enriched in myeloid leukocyte activation and osteoclast differentiation processes. A set of nine immune cell types was confirmed to be markedly different between the SONFH and control samples. All 10 hub genes were significantly highly expressed in the serum of SONFH patients, as shown by qRT-PCR. Finally, the therapeutic effect of aspirin on SONFH was examined in animal experiments. Taken together, our data revealed the hub genes and infiltrating immune cells in SONFH, and we also screened potential drugs for use in SONFH treatment.
DOI: 10.25919/vbvj-ga45
title: Parkes observations for project P1162 semester 2023OCTS_08

description: Pulsar timing is a powerful tool in studying pulsar physics. Discovering more exotic pulsar systems or timing pulsars with higher precision is an essential part of pulsar astronomy. As a recently discovered millisecond pulsar, PSR J1402+13 is an interesting source for follow-up timing observations. First, its apparent spin-down rate, as reported in the catalogue, was the highest among known millisecond pulsars, causing a seeming tension with the spin-up theory. Second, its apparent high flux density and small distance seemed to give a high timing precision. We have observed J1402+13 with high cadence in the past 9 months and obtained a phase-coherent solution, which gives a much lower pdot (~ 10^{-20} s/s) thus solves the tension with the spin-up theory. We apply for another 15 hours to observe the pulsar to further extend the timing baseline, which will refine our timing solution and help us clearly evaluate its timing precision and potential to be used for pulsar timing arrays. The observation will also help us study the scintillation effect of the pulsar and measure its steep spectral index. The more comprehensive measurements of the pulsar will also facilitate observations in optical and gamma-ray bands.
DOI: 10.6084/m9.figshare.16577661.v2
title: Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head

description: Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An immune cell abundance identifier was used to explore immune cell infiltration. Furthermore, hub genes were identified based on maximal clique centrality (MCC) evaluation using cytoHubba application and confirmed by qRT-PCR using clinical samples. Finally, the L1000 platform was used to determine potential drugs for SONFH treatment. The SONFH mouse model was used to determine the therapeutic effects of aspirin. In total, 429 DEGs were identified in SONFH samples. Functional enrichment analysis showed that these DEGs were enriched in myeloid leukocyte activation and osteoclast differentiation processes. A set of nine immune cell types was confirmed to be markedly different between the SONFH and control samples. All 10 hub genes were significantly highly expressed in the serum of SONFH patients, as shown by qRT-PCR. Finally, the therapeutic effect of aspirin on SONFH was examined in animal experiments. Taken together, our data revealed the hub genes and infiltrating immune cells in SONFH, and we also screened potential drugs for use in SONFH treatment.
DOI: 10.6084/m9.figshare.16577661.v1
title: Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head

description: Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An immune cell abundance identifier was used to explore immune cell infiltration. Furthermore, hub genes were identified based on maximal clique centrality (MCC) evaluation using cytoHubba application and confirmed by qRT-PCR using clinical samples. Finally, the L1000 platform was used to determine potential drugs for SONFH treatment. The SONFH mouse model was used to determine the therapeutic effects of aspirin. In total, 429 DEGs were identified in SONFH samples. Functional enrichment analysis showed that these DEGs were enriched in myeloid leukocyte activation and osteoclast differentiation processes. A set of nine immune cell types was confirmed to be markedly different between the SONFH and control samples. All 10 hub genes were significantly highly expressed in the serum of SONFH patients, as shown by qRT-PCR. Finally, the therapeutic effect of aspirin on SONFH was examined in animal experiments. Taken together, our data revealed the hub genes and infiltrating immune cells in SONFH, and we also screened potential drugs for use in SONFH treatment.
DOI: 10.6084/m9.figshare.19759538
title: Additional file 4 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 4: Table S3. All raw flow data used in the in the main figures.
DOI: 10.6084/m9.figshare.19759538.v1
title: Additional file 4 of Evaporative flux method of leaf hydraulic conductance estimation: sources of uncertainty and reporting format recommendation

description: Additional file 4: Table S3. All raw flow data used in the in the main figures.
DOI: 10.6084/m9.figshare.16577697
title: Identification of a 3-gene signature based on differentially expressed invasion genes related to cancer molecular subtypes to predict the prognosis of osteosarcoma patients

description: Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257 and GSE39058). Patients were divided into high- and low-risk groups by their signature, and the prognosis of osteosarcoma patients in the high-risk group was poor. Based on the time-independent receiver operating characteristic (ROC) curve, the area under the curve (AUC) for 1-year and 2-year OS were higher than 0.75 in internal and external cohorts. This signature also showed a high accuracy and independence in predicting osteosarcoma prognosis and a higher AUC in predicting 1-year osteosarcoma survival than other four existing models. In a word, a 3 invasive gene-based signature was developed, showing a high performance in predicting osteosarcoma prognosis. This signature could facilitate clinical prognostic analysis of osteosarcoma.
DOI: 10.6084/m9.figshare.16577697.v2
title: Identification of a 3-gene signature based on differentially expressed invasion genes related to cancer molecular subtypes to predict the prognosis of osteosarcoma patients

description: Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257 and GSE39058). Patients were divided into high- and low-risk groups by their signature, and the prognosis of osteosarcoma patients in the high-risk group was poor. Based on the time-independent receiver operating characteristic (ROC) curve, the area under the curve (AUC) for 1-year and 2-year OS were higher than 0.75 in internal and external cohorts. This signature also showed a high accuracy and independence in predicting osteosarcoma prognosis and a higher AUC in predicting 1-year osteosarcoma survival than other four existing models. In a word, a 3 invasive gene-based signature was developed, showing a high performance in predicting osteosarcoma prognosis. This signature could facilitate clinical prognostic analysis of osteosarcoma.
DOI: 10.6084/m9.figshare.16577697.v1
title: Identification of a 3-gene signature based on differentially expressed invasion genes related to cancer molecular subtypes to predict the prognosis of osteosarcoma patients

description: Invasion is a critical pathway leading to tumor metastasis. This study constructed an invasion-related polygenic signature to predict osteosarcoma prognosis. We initially determined two molecular subtypes of osteosarcoma, Cluster1 (C1) and Cluster2 (C2).. A 3 invasive-gene signature was established by univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression analysis of the differentially expressed genes (DEGs) between the two subtypes, and was validated in internal and two external data sets (GSE21257 and GSE39058). Patients were divided into high- and low-risk groups by their signature, and the prognosis of osteosarcoma patients in the high-risk group was poor. Based on the time-independent receiver operating characteristic (ROC) curve, the area under the curve (AUC) for 1-year and 2-year OS were higher than 0.75 in internal and external cohorts. This signature also showed a high accuracy and independence in predicting osteosarcoma prognosis and a higher AUC in predicting 1-year osteosarcoma survival than other four existing models. In a word, a 3 invasive gene-based signature was developed, showing a high performance in predicting osteosarcoma prognosis. This signature could facilitate clinical prognostic analysis of osteosarcoma.
DOI: 10.6084/m9.figshare.7664804
title: Additional file 11: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S6. Primers used for qRT-PCR of expansins in wheat (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7664804.v1
title: Additional file 11: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S6. Primers used for qRT-PCR of expansins in wheat (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6616232
title: Additional file 2: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: DR pathways modulated in trout cell lines after inoculation with VHSV. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6616232.v1
title: Additional file 2: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: DR pathways modulated in trout cell lines after inoculation with VHSV. (XLSX 10 kb)
DOI: 10.5281/zenodo.10677369
title: Synthesis of azo dye by coupling of diazonium salt with α-naphthol, β-naphthol
DOI: 10.5281/zenodo.10677370
title: Synthesis of azo dye by coupling of diazonium salt with α-naphthol, β-naphthol
DOI: 10.6084/m9.figshare.7664819
title: Additional file 2: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S1. Distribution of four subfamily members in expansin gene families from different plant species. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7664819.v1
title: Additional file 2: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S1. Distribution of four subfamily members in expansin gene families from different plant species. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7664828
title: Additional file 3: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S2. The information of expansin gene superfamily in wheat. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.7664828.v1
title: Additional file 3: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S2. The information of expansin gene superfamily in wheat. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6616256
title: Additional file 3: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Description of genes significantly up- or down- regulated by incubation with attenuated VHSV in B57 or A22 cells (adj. p &lt; 0.01, FC &gt; 2,5 or &lt; 0.4). (XLSX 1214 kb)