cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7648283
title: Additional file 4: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S3. Nucleotide sequences of 47 SWEET genes from B. oleracea and A. thaliana. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8172494.v1
title: Additional file 3: of A new chicken 55K SNP genotyping array

description: The third group of SNPs which related to 861 candidate genes. The information of 861 candidate genes and 118.4â K SNPs selected were provided. (XLSX 6645 kb)
DOI: 10.6084/m9.figshare.7648283.v1
title: Additional file 4: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S3. Nucleotide sequences of 47 SWEET genes from B. oleracea and A. thaliana. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8172506
title: Additional file 4: of A new chicken 55K SNP genotyping array

description: The third group of SNPs which related to serum IgY. The loci and allele information of 0.8â K SNPs related to serum IgY were provided. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.8172566
title: Additional file 3: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S3. The tissue specifically expressed genes (TPMâ â Ľâ 500) in three tissues of ad libitum group. (XLSX 215 kb)
DOI: 10.6084/m9.figshare.7648265
title: Additional file 1: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S1. Primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8172488
title: Additional file 2: of A new chicken 55K SNP genotyping array

description: The second group of SNPs which related to the economic traits. The locus and the p-value of SNPs which related to 15 economic traits were provided. (XLSX 998 kb)
DOI: 10.6084/m9.figshare.8172506.v1
title: Additional file 4: of A new chicken 55K SNP genotyping array

description: The third group of SNPs which related to serum IgY. The loci and allele information of 0.8â K SNPs related to serum IgY were provided. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.8172575
title: Additional file 4: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S4. Gene Ontology (GO) and KEGG pathway of differential expression genes in adipose, ovary and liver between ad libitum and restricted feeding group. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7648418
title: Additional file 2: of Analysis of genetic polymorphisms for age-related macular degeneration (AMD) in Chinese Tujia ethnic minority group

description: Table S2. The distributions of allelic and genotypic frequencies for 39 SNPs were listed in the table. The details of HWE, P value, Pcorrect value, OR and 95%CI were also shown. (XLS 102 kb)
DOI: 10.6084/m9.figshare.12891147
title: Additional file 3 of Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy

description: Additional file 3. Raw data in excel file for all column graphs in figures and additional figures.
DOI: 10.6084/m9.figshare.12891147.v1
title: Additional file 3 of Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy

description: Additional file 3. Raw data in excel file for all column graphs in figures and additional figures.
DOI: 10.6084/m9.figshare.7648271
title: Additional file 2: of Expression profile of microRNAs in porcine alveolar macrophages after Toxoplasma gondii infection

description: Table S2. List of miRNA targets identified by miRanda. (XLSX 1247 kb)
DOI: 10.6084/m9.figshare.8172575.v1
title: Additional file 4: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S4. Gene Ontology (GO) and KEGG pathway of differential expression genes in adipose, ovary and liver between ad libitum and restricted feeding group. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.18134025.v1
title: Caffeine prevents restenosis and inhibits vascular smooth muscle cell proliferation through the induction of autophagy

description: Caffeine is among the most highly consumed substances worldwide, and it has been associated with decreased cardiovascular risk. Although caffeine has been shown to inhibit the proliferation of vascular smooth muscle cells (VSMCs), the mechanism underlying this effect is unknown. Here, we demonstrated that caffeine decreased VSMC proliferation and induced macroautophagy/autophagy in an <i>in vivo</i> vascular injury model of restenosis. Furthermore, we studied the effects of caffeine in primary human and mouse aortic VSMCs and immortalized mouse aortic VSMCs. Caffeine decreased cell proliferation, and induced autophagy flux via inhibition of MTOR signaling in these cells. Genetic deletion of the key autophagy gene <i>Atg5</i>, and the <i>Sqstm1</i>/<i>p62</i> gene encoding a receptor protein, showed that the anti-proliferative effect by caffeine was dependent upon autophagy. Interestingly, caffeine also decreased WNT-signaling and the expression of two WNT target genes, <i>Axin2</i> and <i>Ccnd1</i> (cyclin D1). This effect was mediated by autophagic degradation of a key member of the WNT signaling cascade, DVL2, by caffeine to decrease WNT signaling and cell proliferation. SQSTM1/p62, MAP1LC3B-II and DVL2 were also shown to interact with each other, and the overexpression of DVL2 counteracted the inhibition of cell proliferation by caffeine. Taken together, our <i>in vivo</i> and <i>in vitro</i> findings demonstrated that caffeine reduced VSMC proliferation by inhibiting WNT signaling via stimulation of autophagy, thus reducing the vascular restenosis. Our findings suggest that caffeine and other autophagy-inducing drugs may represent novel cardiovascular therapeutic tools to protect against restenosis after angioplasty and/or stent placement.
DOI: 10.6084/m9.figshare.8172560.v1
title: Additional file 2: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S2. The differentially expressed genes in three tissues between ad libitum and restricted feeding group. (XLSX 3189 kb)
DOI: 10.6084/m9.figshare.12891315.v1
title: Additional file 5 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 5: Table S5. Statistics of DEGs that exhibit different expression patterns.
DOI: 10.6084/m9.figshare.7648319
title: Additional file 8: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S4. Expression of BoSWEET genes in roots of clubroot-resistant and susceptible cabbage lines at different P. brassicae infection stages. (XLSX 18 kb)
DOI: 10.57745/93wwgu
title: phosphax30.txt

description: The data file contain three columns:
“time” date and time UTC
“TP” total phosphorus concentration in mg / l
“TRP” total reactive phosphorus concentration in mg / l
DOI: 10.57745/8yz2xu
title: DataVersePhosphax.pdf

description: :unav
DOI: 10.6084/m9.figshare.19178990
title: Additional file 2 of Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum)

description: Additional file 2: Supplementary tables 1-7. Table S1. Primers used for vectors construction. Table S2. Primers used for positive test. Table S3. Barcode primers for detecting off-target in base editing T0 transgenic plants with deep sequencing for GhPEBE gene. Table S4. Barcode primers for detecting off-target in base editing T0 transgenic plants with deep sequencing for GhCLA gene. Table S5. Summary of genome-wide potential off-targets predictions by Cas-OFFinder tools for target sgRNA1. Table S6. Summary of genome-wide potential off-targets predictions by Cas-OFFinder tools for target sgRNA2. Table S7. Expression levels (TPM) of TadA, nCas9 and dCas9 in GhABE7.10 edited plant.
DOI: 10.6073/pasta/2b006ee5c3712e20fbe22a2c0102682a
title: FCE Redlands 1998 Roads, Miami-Dade County, South Florida

description: Urban growth models have increasingly been used by planners and policy makers to visualize, organize, understand, and predict urban growth. However, these models reveal a wide disparity in their attention to policy factors. Some urban growth models capture few if any specific policy effects (e.g.,as model variables), while others integrate certain policies but not others. Since zoning policies are the most widely used form of land use control in the United States, their conspicuous absence from so many urban growth models is surprising. This research investigated the impacts of zoning on urban growth by calibrating and simulating a cellular automaton urban growth model, SLEUTH, under two conditions in a South Florida location. The first condition integrated restrictive agricultural zoning into SLEUTH, while the other ignored zoning data. Goodness of fit metrics indicate that including the agricultural zoning data improved model performance. The results further suggest that agricultural zoning has been somewhat successful in retarding urban growth in South Florida. Ignoring zoning information is detrimental to SLEUTH performance in particular, and urban growth modeling in general.
DOI: 10.6084/m9.figshare.7648319.v1
title: Additional file 8: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S4. Expression of BoSWEET genes in roots of clubroot-resistant and susceptible cabbage lines at different P. brassicae infection stages. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.14984837.v1
title: Additional file 2 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 2: Table S2. Read number and mapping ratio based on RNA-seq data from S. japonica gametophytes.
DOI: 10.6084/m9.figshare.14984834.v1
title: Additional file 1 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 1: Table S1. List of PCR primers used in this study.
DOI: 10.6084/m9.figshare.14984840
title: Additional file 3 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 3: Table S3. Number of sex-biased genes and sex-specific genes in immature and mature gametophytes.
DOI: 10.6084/m9.figshare.14984837
title: Additional file 2 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 2: Table S2. Read number and mapping ratio based on RNA-seq data from S. japonica gametophytes.
DOI: 10.6084/m9.figshare.14984843
title: Additional file 4 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 4: Table S4. Enriched GO terms of male-biased genes in mature gametophytes.
DOI: 10.6084/m9.figshare.12891321
title: Additional file 7 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 7: Table S7. Cluster analysis of the DEGs.
DOI: 10.6084/m9.figshare.14984840.v1
title: Additional file 3 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 3: Table S3. Number of sex-biased genes and sex-specific genes in immature and mature gametophytes.
DOI: 10.6084/m9.figshare.14984843.v1
title: Additional file 4 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 4: Table S4. Enriched GO terms of male-biased genes in mature gametophytes.
DOI: 10.6084/m9.figshare.14984849
title: Additional file 6 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 6: Table S6. Enriched pathways of sex-biased genes in mature gametophytes.
DOI: 10.6084/m9.figshare.14984849.v1
title: Additional file 6 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 6: Table S6. Enriched pathways of sex-biased genes in mature gametophytes.
DOI: 10.6084/m9.figshare.14984831
title: Additional file 17 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 17. Annotation information of new predicted genes in this study.
DOI: 10.6084/m9.figshare.14984831.v1
title: Additional file 17 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 17. Annotation information of new predicted genes in this study.
DOI: 10.6084/m9.figshare.14984834
title: Additional file 1 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 1: Table S1. List of PCR primers used in this study.
DOI: 10.6084/m9.figshare.14984852
title: Additional file 7 of Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica

description: Additional file 7: Table S7. Sex-specific genes of S. japonica at the different stages.
DOI: 10.6084/m9.figshare.14988433.v1
title: Modeling scale morphogenesis in a Devonian chondrichthyan and scale growth patterns in crown gnathostomes

description: Early chondrichthyans (cartilaginous fishes) possess a rich record of scale fossils that have impacted on taxonomic and phylogenetic studies of early jawed vertebrates, but the significance of these scales remains elusive due to the lack of well-defined characters. <i>Gualepis</i>, a scale-based genus from the Lower Devonian of Yunnan, China, was initially recognized as an early chondrichthyan of uncertain affinity. We investigate new material of <i>Gualepis elegans</i> from the type locality. By combining microtomographic data with morphological and histological examination of specimens at successive growth stages, we have reconstructed the 3D growth pattern of the scales. During growth, <i>Gualepis</i> scales added new odontodes appositionally, which has previously been documented in the dermal skeletons of <i>Seretolepis</i>, <i>Kathemacanthus</i>, <i>Parexus</i>, and other crownward members of the stem chondrichthyans. Phylogenetic analysis resolves <i>Gualepis</i> as a non-acanthodid stem chondrichthyan near the crown chondrichthyan node. Our 3D approach is potentially useful to render more reliable scale-based characters, especially regarding scale growth patterns. This study provides the first 3D virtual growth model of stem chondrichthyan scales with a <i>Seretolepis</i>-type morphogenesis, offering new insights into the early evolution of chondrichthyan dermal skeletons.
DOI: 10.6084/m9.figshare.14988433.v2
title: Modeling scale morphogenesis in a Devonian chondrichthyan and scale growth patterns in crown gnathostomes

description: Early chondrichthyans (cartilaginous fishes) possess a rich record of scale fossils that have impacted on taxonomic and phylogenetic studies of early jawed vertebrates, but the significance of these scales remains elusive due to the lack of well-defined characters. <i>Gualepis</i>, a scale-based genus from the Lower Devonian of Yunnan, China, was initially recognized as an early chondrichthyan of uncertain affinity. We investigate new material of <i>Gualepis elegans</i> from the type locality. By combining microtomographic data with morphological and histological examination of specimens at successive growth stages, we have reconstructed the 3D growth pattern of the scales. During growth, <i>Gualepis</i> scales added new odontodes appositionally, which has previously been documented in the dermal skeletons of <i>Seretolepis</i>, <i>Kathemacanthus</i>, <i>Parexus</i>, and other crownward members of the stem chondrichthyans. Phylogenetic analysis resolves <i>Gualepis</i> as a non-acanthodid stem chondrichthyan near the crown chondrichthyan node. Our 3D approach is potentially useful to render more reliable scale-based characters, especially regarding scale growth patterns. This study provides the first 3D virtual growth model of stem chondrichthyan scales with a <i>Seretolepis</i>-type morphogenesis, offering new insights into the early evolution of chondrichthyan dermal skeletons.
DOI: 10.6084/m9.figshare.7648418.v1
title: Additional file 2: of Analysis of genetic polymorphisms for age-related macular degeneration (AMD) in Chinese Tujia ethnic minority group

description: Table S2. The distributions of allelic and genotypic frequencies for 39 SNPs were listed in the table. The details of HWE, P value, Pcorrect value, OR and 95%CI were also shown. (XLS 102 kb)
DOI: 10.6084/m9.figshare.7648508
title: Additional file 1: of Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy

description: Supplementary tables S1-S7. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7648412.v1
title: Additional file 1: of Analysis of genetic polymorphisms for age-related macular degeneration (AMD) in Chinese Tujia ethnic minority group

description: Table S1. Primer sequences we used to detect the 39 SNPs were listed in the table. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12891303.v1
title: Additional file 1 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 1: Table S1. Summary of the RNA-Seq data collected from the seeds of three wheat varieties (ZM22, BN207 and BN607) under the waterlogging and control treatments.
DOI: 10.6084/m9.figshare.7648412
title: Additional file 1: of Analysis of genetic polymorphisms for age-related macular degeneration (AMD) in Chinese Tujia ethnic minority group

description: Table S1. Primer sequences we used to detect the 39 SNPs were listed in the table. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12891309
title: Additional file 3 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 3: Table S3. Summary of the GO results of the DEGs.
DOI: 10.6084/m9.figshare.12891318
title: Additional file 6 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 6: Table S6. List of primer sequences used for qPCR analysis.
DOI: 10.6084/m9.figshare.12891306.v1
title: Additional file 2 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 2: Table S2. Summary of the genome alignment distribution of the RNA-Seq data.
DOI: 10.6084/m9.figshare.12891321.v1
title: Additional file 7 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 7: Table S7. Cluster analysis of the DEGs.
DOI: 10.57745/ddoizs
title: magatt_test_data.tar.gz

description: Test references and target genome, annotation (GFF) and indexes (bwa,gmap) for the MAGATT pipeline
DOI: 10.6084/m9.figshare.12891312
title: Additional file 4 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 4: Table S4. KEGG enrichment analysis of the DEGs.
DOI: 10.6084/m9.figshare.12891315
title: Additional file 5 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 5: Table S5. Statistics of DEGs that exhibit different expression patterns.
DOI: 10.6084/m9.figshare.12891303
title: Additional file 1 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 1: Table S1. Summary of the RNA-Seq data collected from the seeds of three wheat varieties (ZM22, BN207 and BN607) under the waterlogging and control treatments.
DOI: 10.6084/m9.figshare.12891306
title: Additional file 2 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 2: Table S2. Summary of the genome alignment distribution of the RNA-Seq data.
DOI: 10.6084/m9.figshare.12891387
title: Additional file 1 of The treatment strategy of R0 resection in colorectal cancer with synchronous para-aortic lymph node metastasis

description: Additional file 1.
DOI: 10.6084/m9.figshare.12891309.v1
title: Additional file 3 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 3: Table S3. Summary of the GO results of the DEGs.
DOI: 10.6084/m9.figshare.8172752
title: Additional file 1: of The prognostic value of tumor-infiltrating lymphocytes in colorectal cancer differs by anatomical subsite: a systematic review and meta-analysis

description: Table S1. General characteristics of the studies included in this meta-analysis (XLSX 15 kb)
DOI: 10.6084/m9.figshare.12891318.v1
title: Additional file 6 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 6: Table S6. List of primer sequences used for qPCR analysis.
DOI: 10.6084/m9.figshare.12891312.v1
title: Additional file 4 of Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

description: Additional file 4: Table S4. KEGG enrichment analysis of the DEGs.
DOI: 10.6084/m9.figshare.6599858
title: MOESM3 of Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

description: Additional file 3. Overview of proteins detected in the metasecretome of the wheat straw compost-derived community.
DOI: 10.6084/m9.figshare.6599858.v1
title: MOESM3 of Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

description: Additional file 3. Overview of proteins detected in the metasecretome of the wheat straw compost-derived community.
DOI: 10.6084/m9.figshare.6600041
title: Additional file 2: of Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes

description: Table S2. Nucleotide sequences of twelve elements whose TSD could not be determined. (XLSX 11Â kb)