cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21835201
title: Variations of soil bacterial microbial community and functional structure under different land-uses

description: ABSTRACT To reveal the differences between land-use patterns and the changes in soil properties, the changes in soil bacterial microbial communities and functions driven by land-use patterns were studied by 16SrRNA Gene Fragments and its high-throughput sequencing, relying on the wetland, farmland and forestland soils in the Hongxing National Nature Reserve of Heilongjiang Province. The study area was slightly acidic soil, and the water content, soil organic carbon content, total soil nitrogen and phosphorus contents of wetland soil were higher than farmland and forestland. The suitable C/N of wetland and farmland soil could promote the decomposition of organic matter by microorganisms. The OTUs sequence, Shannon diversity index, ACE index and Chao1 index were significantly higher in wetland than in farmland and forestland. Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria were the dominant bacteria in the tested soil samples. The abundance of Proteobacteria in wetland soil samples was significantly higher than in farmland and forestland. The abundance of Acidobacteria in farmland soil samples was significantly higher than in wetland and forestland. According to FAPROTAX algorithm and BugBase phenotype analysis, land-uses can change the abundance of soil functional microorganisms. The dominant functional genes are mainly Chemoheterotrophy and Aerobic chemoheterotrophy bacteria. Nitrification and Aerobic ammonia oxidation bacteria involved in nitrogen cycle in farmland soil are significantly different from wetland and forestland. Land-use mode leads to significant differences between Mobile elements and Gram negative bacteria. It is mainly related to the changes in soil physical and chemical properties such as soil pH, bulk density, soil organic carbon and total nitrogen contents.
DOI: 10.6084/m9.figshare.7679492.v1
title: Additional file 2: of Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: Table S1. List of cancer cell lines included in the study. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7679504
title: Additional file 3: of Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: Table S2. Mean gene copy-number ratios of cancer associated genes across the cancer cell line panel. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.12921990.v2
title: Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination

description: Tissue-specific alternative splicing (AS) is emerging as one of the most exciting types of mechanisms associated with organ development and disease. In the auditory system, many hearing-related genes undergo AS, and errors in this process result in syndromic or non-syndromic hearing loss. However, little is known about the factors and mechanisms directing AS in the inner ear. In the present study, we identified a novel RNA-binding protein, Rbm24, which was critically involved in regulating inner-ear-specific AS. Rbm24 deletion resulted in hearing loss and defects in motor coordination. Global splicing analysis showed Rbm24 was required for correct splicing of a subset of pre-mRNA transcripts with essential roles in stereocilia integrity and survival of hair cells. Furthermore, we identified that Rbm24 directly regulated the splicing of Cdh23, a known disease gene responsible for human Usher syndrome 1D and non-syndromic autosomal recessive deafness DFNB12. In conclusion, our findings demonstrated that Rbm24 was a critical factor in regulating inner-ear-specific splicing and maintaining the hearing and motor coordination function of the inner ear. Our data not only offer mechanistic insights but also provide functional annotation of Rbm24 splicing targets that contribute to hearing loss.
DOI: 10.6084/m9.figshare.7679507.v1
title: Additional file 2: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S1. Summary of RNA-seq data (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7679507
title: Additional file 2: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S1. Summary of RNA-seq data (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7679519.v1
title: Additional file 4: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S3. List of DEGs up-regulated in Col-0 (XLSX 164 kb)
DOI: 10.6084/m9.figshare.21310488
title: Protective effects of psoralen polymer lipid nanoparticles on doxorubicin - induced myocardial toxicity

description: Abstract Doxorubicin (DOX) induced myocardial toxicity may limit its therapeutic use in clinic. Psoralen (PSO), a major active tricyclic furocoumarin extracted from Psoralea corylifolia, is widely used as an antineoplastic agent in treatment of leukemia and other cancers. This study is aim to find the protective effect of psoralen polymer lipid nanoparticles (PSO-PLN) on doxorubicin-induced myocardial toxicity in mice. The model of myocardial toxicity induced by DOX was established. The experiment was divided into 6 groups: normal saline group, DOX + Sulfotanshinone Sodium, DOX + PSO-PLN (3 mg/kg), DOX + PSO-PLN (6 mg/kg), DOX + PSO-PLN (9 mg/ kg), DOX group. DOX alone treated mice lead to a significant decrease in the body weight, heart weight, and increase in the serum levels of lactate dehydrogenase (LDH), creatine kinase (CK) and malondialdehyde (MDA) markers of cardiotoxicity. However, DOX reduced glutathione (GSH) content and activities of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GPX), were recovered by PSO-PLN. And PSO-PLN also decreased markers of cardiotoxicity in the serum. Western blotting data showed that the protective effects of PSO-PLN might be mediated via regulation of protein kinase A (PKA) and p38. Our study suggest that PSO-PLN possesses antioxidant activities, inactivating PKA and p38 effect, which in turn protect the heart from the DOX-induced cardiotoxicity.
DOI: 10.6084/m9.figshare.21310488.v1
title: Protective effects of psoralen polymer lipid nanoparticles on doxorubicin - induced myocardial toxicity

description: Abstract Doxorubicin (DOX) induced myocardial toxicity may limit its therapeutic use in clinic. Psoralen (PSO), a major active tricyclic furocoumarin extracted from Psoralea corylifolia, is widely used as an antineoplastic agent in treatment of leukemia and other cancers. This study is aim to find the protective effect of psoralen polymer lipid nanoparticles (PSO-PLN) on doxorubicin-induced myocardial toxicity in mice. The model of myocardial toxicity induced by DOX was established. The experiment was divided into 6 groups: normal saline group, DOX + Sulfotanshinone Sodium, DOX + PSO-PLN (3 mg/kg), DOX + PSO-PLN (6 mg/kg), DOX + PSO-PLN (9 mg/ kg), DOX group. DOX alone treated mice lead to a significant decrease in the body weight, heart weight, and increase in the serum levels of lactate dehydrogenase (LDH), creatine kinase (CK) and malondialdehyde (MDA) markers of cardiotoxicity. However, DOX reduced glutathione (GSH) content and activities of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GPX), were recovered by PSO-PLN. And PSO-PLN also decreased markers of cardiotoxicity in the serum. Western blotting data showed that the protective effects of PSO-PLN might be mediated via regulation of protein kinase A (PKA) and p38. Our study suggest that PSO-PLN possesses antioxidant activities, inactivating PKA and p38 effect, which in turn protect the heart from the DOX-induced cardiotoxicity.
DOI: 10.6084/m9.figshare.21835489
title: Systematically analyzed molecular characteristics of lung adenocarcinoma using metabolism-related genes classification

description: Abstract High heterogeneity of lung adenocarcinoma (LUAD) is a major clinical challenge. This study aims to characterize the molecular features of LUAD through classification based on metabolism-related genes. A total of 500 LUAD samples from The Cancer Genome Atlas (TCGA) and 612 from Gene Expression Omnibus (GEO) were integrated with 2,753 metabolism-related genes to determine the molecular classification. Systematic bioinformatics analysis was used to conduct correlation analysis between metabolism-related classification and molecular characteristics of LUAD. LUAD patients were divided into three molecular clusters (C1-C3). Survival analysis revealed that C1 and C2 showed good and poor prognoses, respectively. Associational analysis of classification and molecular characteristics revealed that C1 was associated with low pathological stage, metabolic pathways, high metabolic process, active immune process and checkpoint, sensitive drug response, as well as a low genetic mutation. Nevertheless, C2 was associated with high pathological stage, carcinogenic pathways, low metabolic process, inactive immune signatures, resistant drug response, and frequent genetic mutation. Eventually, a classifier with 60 metabolic genes was constructed, confirming the robustness of molecular classification on LUAD. Our findings promote the understanding of LUAD molecular characteristics, and the research data may be used for providing information be helpful for clinical diagnosis and treatment.
DOI: 10.6084/m9.figshare.7155710
title: Additional file 2: of Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments

description: Figure S1. Structures of PPR proteins and consensus sequence of PPR motif in rice. (A) Typical structures of PPR proteins in rice. The number of motifs in each protein can vary from 2 to 28 in rice. (B) The consensus sequence of 10 PPR motif in rice. The overall height of each stack indicates the conservation of the sequence at that position and the bit score indicates the relative frequency of the corresponding acid. The lengths of the motifs can be estimated using the scale at the bottom. Figure S2. Distribution of PPR genes in rice chromosomes. The 491 PPR genes are widely and unevenly distributed on all 12 chromosomes of rice. Figure S3. Exon/intron structures of the PPR genes in rice. Yellow boxes represent exons, and black lines represent introns. Upstream or downstream regions are indicated by blue boxes. The sizes of exons and introns can be estimated using the scale at the bottom. Figure S4. Phylogenetic relationship of the PLS subgroup genes in rice and other species. Evolutionary relationships of PLS subgroup genes from rice, Arabidopsis, moss, tomato, and foxtail millet. The genes whose IDs start with LOC represent rice gene, AT represents Arabidopsis, Pp represents moss, Solyc represents tomato, and Seita represents foxtail millet. Figure S5. Expression patterns of PPR genes in different rice tissues. The FPKM expression values from RGAP of PPR genes at various developmental stages were log2 transformed, and a heat map was generated using the MeV4.9 software. Samples are indicated at the top of each lane: shoots, leaves-20Â days, pre/post-emergence inflorescence (pre-EI, post-EI), anther, pistil, seed-5 DAP, seed-10 DAP, embryo- 25 DAP and endosperm- 25 DAP. The color scale (representing average log2 signal values) is shown at the top. (ZIP 6622 kb)
DOI: 10.6084/m9.figshare.7679522
title: Additional file 5: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S4. List of DEGs up-regulated in pad4â 1 sid2â 1 (XLSX 98 kb)
DOI: 10.5281/zenodo.10671949
title: Thermal tolerance in salmonids

description: Salmonids are known to be a fish of high commercial value. The global salmon fish market was estimated to be worth USD 14.87 million in 2021 (Grand View Research, 2020). At the same time, their populations are particularly sensitive to climate change, as they need specific temperature ranges for optimal growth, reproduction and survival. Elevated temperatures of streams,  sea surface as well as ocean acidification alongside the fishing industry, puts enormous pressure on their populations (Crozier, et al. 2020).  This dataset synthesises the thermal tolerance values (CTmax - Critical Thermal Maximum) of various salmon species in a wide range of geographical locations, allowing us to compare and determine the most vulnerable species in response to the increasing temperatures. 
description: Literature Search Protocol: 



Literature search was conducted using a variety of literature search engines like: "Web of Science", "Science Direct", "Google Scholar", "Scopus", "Research Gate"

A list of salmon species with their accepted and scientific name was compiled prior to the literature search. 

Keywords and phrases like "thermal tolerance", "CTmax", "Critical thermal tolerance", and "Maximum thermal tolerance" were used during the search process, alongside the specific Latin names of the salmon species  
description: Dataset consists of:



Species scientific name in Latin, for example  Oncorhynchus mykiss

Species accepted name, for example Rainbow Trout 

Location - where was the study conducted, where was the investigated salmon species derived from 

Year of study

CTmin - critical minimum temperature 

CTmax - critical maximum temperature      *n/a - information not available 

Units - degrees Celcius 

Methods - brief description of the way the data was collected 

Paper - the references to the studies used to obtain the data
DOI: 10.5281/zenodo.10671950
title: Thermal tolerance in salmonids

description: Salmonids are known to be a fish of high commercial value. The global salmon fish market was estimated to be worth USD 14.87 million in 2021 (Grand View Research, 2020). At the same time, their populations are particularly sensitive to climate change, as they need specific temperature ranges for optimal growth, reproduction and survival. Elevated temperatures of streams,  sea surface as well as ocean acidification alongside the fishing industry, puts enormous pressure on their populations (Crozier, et al. 2020).  This dataset synthesises the thermal tolerance values (CTmax - Critical Thermal Maximum) of various salmon species in a wide range of geographical locations, allowing us to compare and determine the most vulnerable species in response to the increasing temperatures. 
description: Literature Search Protocol: 



Literature search was conducted using a variety of literature search engines like: "Web of Science", "Science Direct", "Google Scholar", "Scopus", "Research Gate"

A list of salmon species with their accepted and scientific name was compiled prior to the literature search. 

Keywords and phrases like "thermal tolerance", "CTmax", "Critical thermal tolerance", and "Maximum thermal tolerance" were used during the search process, alongside the specific Latin names of the salmon species  
description: Dataset consists of:



Species scientific name in Latin, for example  Oncorhynchus mykiss

Species accepted name, for example Rainbow Trout 

Location - where was the study conducted, where was the investigated salmon species derived from 

Year of study

CTmin - critical minimum temperature 

CTmax - critical maximum temperature      *n/a - information not available 

Units - degrees Celcius 

Methods - brief description of the way the data was collected 

Paper - the references to the studies used to obtain the data
DOI: 10.11583/dtu.23626650
title: 3Shape FDI 16 Meshes from Intraoral Scans

description: Version update 2024-02-16: Changed test data to also be from european scans.<br>The FDI 16 tooth mesh dataset including original meshes and exact data used in the original VF-Net paper. All scans are fully anonymized and donated by 3Shape.<br>The data contains 4844/1465/1423 meshes and point clouds for train/val/test respectively for deep/machine learning. All data stems from clinics based in Europe. The scans were collected using TRIOS scanners, and primarily the TRIOS 3 model. The data serves as a new and highly relevant use case for computer algorithms for 3D objects.<br>Each scan contain:<i>"_mesh.ply"</i> suffix file: A PLY file of the original segmented tooth mesh<i>"_point_cloud.ply": </i>The vertices and facet midpoints of the mesh as a point cloud<i>"_curvature_edgedistance.dat": </i>A binary file including first the curvature of each point in the "_point_cloud.ply" and subsequently the djikstra distance to nearest edge vertex.
DOI: 10.11583/dtu.23626650.v2
title: 3Shape FDI 16 Meshes from Intraoral Scans

description: Version update 2024-02-16: Changed test data to also be from european scans.<br>The FDI 16 tooth mesh dataset including original meshes and exact data used in the original VF-Net paper. All scans are fully anonymized and donated by 3Shape.<br>The data contains 4844/1465/1423 meshes and point clouds for train/val/test respectively for deep/machine learning. All data stems from clinics based in Europe. The scans were collected using TRIOS scanners, and primarily the TRIOS 3 model. The data serves as a new and highly relevant use case for computer algorithms for 3D objects.<br>Each scan contain:<i>"_mesh.ply"</i> suffix file: A PLY file of the original segmented tooth mesh<i>"_point_cloud.ply": </i>The vertices and facet midpoints of the mesh as a point cloud<i>"_curvature_edgedistance.dat": </i>A binary file including first the curvature of each point in the "_point_cloud.ply" and subsequently the djikstra distance to nearest edge vertex.
DOI: 10.11583/dtu.23626650.v1
title: 3Shape FDI 16 Meshes from Intraoral Scans

description: The FDI 16 tooth mesh dataset including original meshes and exact data used in the original VF-Net paper. All scans are fully anonymized and donated by 3Shape.
<br>
The data contains 4844/1465/1423 meshes and point clouds for train/val/test respectively for deep/machine learning. Training and validation data stems from clinics based in Europe, while the test sets is a mix of North American and South American scans. The scans were collected using TRIOS scanners, and primarily the TRIOS 3 model. The data serves as a new and highly relevant use case for computer algorithms for 3D objects. 
<br>
Each scan contain:

 <em>"_mesh.ply"</em> suffix file: A PLY file of the original segmented tooth mesh
 <em>"_point_cloud.ply": </em>The vertices and facet midpoints of the mesh as a point cloud
 <em>"_curvature_edgedistance.dat": </em>A binary file including first the curvature of each point in the "_point_cloud.ply" and subsequently the djikstra distance to nearest edge vertex.
DOI: 10.6084/m9.figshare.6105968.v1
title: Using the device-oriented subjective outcome (DOSO) scale to measure outcomes of different hearing aids

description: <i>Objective</i>: The device-oriented subjective outcome (DOSO) is a device-oriented questionnaire, intended to minimise the influence of personality on self-reported measures. The aim of this study was to provide normative data with 2015-era hearing aid technologies. <i>Design</i>: This retrospective study evaluated data from records of three clinical trials. The DOSO was administered for the participants’ own devices as a part of the intake and after using research devices in the field. <i>Study sample</i>: The DOSO data were collected from 132 experienced bilateral hearing aid wearers who participated in the clinical trials. <i>Results</i>: The DOSO data collected with the participants’ own devices were compared to the interim normative data collected between 2004 and 2005. The DOSO subscale scores from the participants’ own devices were significantly higher than those from the interim norms, except Listening Effort subscale. To demonstrate the utility of the new norms, a separate set of DOSO data collected from the same participants after using research hearing aids were contrasted to the new normative data. After accounting for possible placebo effects, the DOSO data with research devices revealed additional self-reported benefit of technological advancements. <i>Conclusions</i>: Norms for the DOSO are recommended for evaluating hearing aids with more recent technologies.
DOI: 10.6084/m9.figshare.16592937
title: Overexpression of the maize <i>WRKY114</i> gene in transgenic rice reduce plant height by regulating the biosynthesis of GA

description: WRKYs represent an important family of transcription factors that are widely involved in plant development, defense regulation and stress response. Transgenic rice that constitutively expressed <i>ZmWRKY114</i> had shorter plant height and showed less sensitivity to gibberellic acid (GA<sub>3</sub>). Further investigation proved that transgenic rice accumulated lower levels of bioactive GAs than that in wild-type plants. Application of exogenous GA<sub>3</sub> fully rescued the semi-dwarf phenotype of <i>ZmWRKY114</i> transgenic plants. Transcriptome and qRT-PCR analyses indicated that the expression of <i>OsGA2ox4</i>, encoding the repressor of GA biosynthesis, was markedly increased. Electrophoretic mobility shift assay and dual-luciferase reporter assay indicated that ZmWRKY114 directly binds to a W-box motif in the <i>OsGA2ox4</i> promoter. Taken together, these results confirm that <i>ZmWRKY114</i> is a GA-responsive gene and is participated in the regulation of plant height in rice.
DOI: 10.6084/m9.figshare.9777245
title: Exome sequencing of Saudi Arabian patients with ADPKD

description: <b>Purpose:</b> Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive development of kidney cysts and enlargement and dysfunction of the kidneys. The Consortium of Radiologic Imaging Studies of the Polycystic Kidney Disease (CRISP) cohort revealed that 89.1% had either a <i>PKD1</i> or <i>PKD2</i> mutation. Of the CRISP patients with a genetic cause detected, mutations in <i>PKD1</i> accounted for 85%, while mutations in the <i>PKD2</i> accounted for the remaining 15%. Here, we report exome sequencing of 16 Saudi patients diagnosed with ADPKD and 16 ethnically matched controls. <b>Methods:</b> Exome sequencing was performed using combinatorial probe-anchor synthesis and improved DNA Nanoballs technology on BGISEQ-500 sequencers (BGI, China) using the BGI Exome V4 (59 Mb) Kit. Identified variants were validated with Sanger sequencing. <b>Results:</b> With the exception of GC-rich exon 1, we obtained excellent coverage of <i>PKD1</i> (mean read depth = 88) including both duplicated and non-duplicated regions. Of nine patients with typical ADPKD presentations (bilateral symmetrical kidney involvement, positive family history, concordant imaging, and kidney function), four had protein truncating <i>PKD1</i> mutations, one had a <i>PKD1</i> missense mutation, and one had a <i>PKD2</i> mutation. These variants have not been previously observed in the Saudi population. In seven clinically diagnosed ADPKD cases but with atypical features, no <i>PKD1</i> or <i>PKD2</i> mutations were identified, but rare predicted pathogenic heterozygous variants were found in cystogenic candidate genes including <i>PKHD1, PKD1L3, EGF, CFTR</i>, and <i>TSC2</i>. <b>Conclusions:</b> Mutations in PKD1 and PKD2 are the most common cause of ADPKD in Saudi patients with typical ADPKD. <b>Abbreviations:</b> ADPKD: Autosomal dominant polycystic kidney disease; <i>CFTR</i>: Cystic fibrosis transmembrane conductance regulator; <i>EGF</i>: Epidermal growth factor; MCIC: Mayo Clinic Imaging Classification; PKD: Polycystic kidney disease; <i>TSC2</i>: Tuberous sclerosis complex 2