cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21266744.v1
title: Table S7.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.25549/one-ouc17553188
title: Mattachine Society, International Committee for Sexual Equality (1955-1960)
DOI: 10.25549/one-ouc17553185
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.25549/one-ouc17553189
title: Mattachine Society, National League for Social Understanding (1961-1965)
DOI: 10.25549/one-ouc17553187
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.6084/m9.figshare.7635236.v1
title: Additional file 3 of Use of flexible sensor to characterize biomechanics of canine skin

description: Capacitance data from the SEC for the experiment test. The raw, unfiltered, experimental data collected from the SEC DAQ. (TXT 152 kb)
DOI: 10.25549/one-ouc17553192
title: Mattachine Society, National League for Social Understanding (1961-1965)
DOI: 10.6084/m9.figshare.21266750
title: Table S11.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.6084/m9.figshare.21266753
title: Table S6.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.25549/one-ouc17553193
title: Mattachine Society, Mattachine Society vs. San Francisco Police Department (1973)
DOI: 10.6084/m9.figshare.21266729
title: Table S1.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.6084/m9.figshare.21266756.v1
title: Table S4.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.6084/m9.figshare.21266756
title: Table S4.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.6084/m9.figshare.21266762.v1
title: Table S9.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.6084/m9.figshare.7635266.v1
title: Additional file 4: of A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis

description: Table S5. The raw values for Fig. 3b. (XLS 25 kb)
DOI: 10.6084/m9.figshare.7635245
title: Additional file 1: of Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier

description: Table S1. SVM BRCA1-like status and BRCA1ness-MLPA profiles in 10 breast cancer cell lines. Table S2A. TCGA breast tumors with SVM BRCA1-like status. Table S2B. METABRIC breast tumors with SVM BRCA1-like status. Table S3. Complete subject characteristics of TCGA and METABRIC breast tumors with SVM BRCA1-like status. Table S4. Differentially methylated CpGs in BRCA1-like tumors identified by DMRcate. Table S5A. Hypermethylated DMRs (n = 108) from DMRcate analysis. TableÂ 5SB. Hypomethylated DMRs (n = 94) from DMRcate analysis. Table S6A. GOBP terms associated with 158 unique genes from 108 hypermethylated DMRs. Table S6B. GOBP terms associated with 131 unique genes from 94 hypermethylated DMRs. (XLSX 923 kb)
DOI: 10.25549/one-ouc17553186
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.6084/m9.figshare.21266732.v1
title: Table S5.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.5281/zenodo.6993745
title: Data from: Biotic homogenization and differentiation of plant communities in tropical and subtropical forests

description: The article is published in Conservation Biology and available at: https://doi.org/10.1111/cobi.14025

Here we developed a framework to assess the current 'state of the art' of biotic homogenization and differentiation processes in tropical and subtropical plant communities globally, using a systematic literature review.

Please find below the analysis code and data used in the study.

Descriptions for the files and scripts

The `R` folder contains.

1. *analysis_homogenization-differentiation.R* - script to generate the frequency and explanatory plots used in the manuscript.

The `output` folder contains:

1. figures    1. *Fig.1.tiff* - Figure 1 main text.    2. *Fig.2.tiff* - Figure 2 main text.    3. *Fig.3.tiff* - Figure 3 main text.    4. *Fig.4.tiff* - Figure 4 main text.    5. *Fig.5.tiff* - Figure 5 main text.    6. *Fig.6.tiff* - Figure 6 main text.    7. *Fig.7.tiff* - Figure 7 main text.

2. supp   1. *appendix_S1-homogenization-differentiation.xlsx* - Supplementary material of the article. The file contains 4 sheets (*data*, *legend*, *scales_size* and *search_keywords*)

The `data` folder contains:

1. processed    1. *data_homogenization_refined.xlsx* - the data used in the analysis. Each analyzed variable was separated by a different sheet.

1. raw    1. *data_homogenization.xlsx* - the raw data used in the analysis.

 

Acknowledgments

This work was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (Finance code 001), through Portal de Periódicos to articles access and scholarship granted to J.M.F.K.
DOI: 10.5281/zenodo.6993746
title: Kramer-et-al-2022-homogenization_differentiation_tropical-forests

description: A framework to assess the current 'state of the art' of biotic homogenization and differentiation processes in tropical and subtropical plant communities globally, using a systematic literature review.
DOI: 10.5281/zenodo.7295262
title: Data from: Biotic homogenization and differentiation of plant communities in tropical and subtropical forests

description: The article is published in Conservation Biology and available at: https://doi.org/10.1111/cobi.14025

Here we developed a framework to assess the current 'state of the art' of biotic homogenization and differentiation processes in tropical and subtropical plant communities globally, using a systematic literature review.

Please find below the analysis code and data used in the study.

Descriptions for the files and scripts

The `R` folder contains.

1. *analysis_homogenization-differentiation.R* - script to generate the frequency and explanatory plots used in the manuscript.

The `output` folder contains:

1. figures    1. *Fig.1.tiff* - Figure 1 main text.    2. *Fig.2.tiff* - Figure 2 main text.    3. *Fig.3.tiff* - Figure 3 main text.    4. *Fig.4.tiff* - Figure 4 main text.    5. *Fig.5.tiff* - Figure 5 main text.    6. *Fig.6.tiff* - Figure 6 main text.    7. *Fig.7.tiff* - Figure 7 main text.

2. supp   1. *appendix_S1-homogenization-differentiation.xlsx* - Supplementary material of the article. The file contains 4 sheets (*data*, *legend*, *scales_size* and *search_keywords*)

The `data` folder contains:

1. processed    1. *data_homogenization_refined.xlsx* - the data used in the analysis. Each analyzed variable was separated by a different sheet.

1. raw    1. *data_homogenization.xlsx* - the raw data used in the analysis.

 

Acknowledgments

This work was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (Finance code 001), through Portal de Periódicos to articles access and scholarship granted to J.M.F.K.
DOI: 10.6084/m9.figshare.14450961.v1
title: Additional file 8 of CircLIFR synergizes with MSH2 to attenuate chemoresistance via MutSα/ATM-p73 axis in bladder cancer

description: Additional file 8: Supplementary Table S3.
DOI: 10.25549/one-ouc17553190
title: Mattachine Society, Janus Society (1963-1966)
DOI: 10.6084/m9.figshare.14450958
title: Additional file 7 of CircLIFR synergizes with MSH2 to attenuate chemoresistance via MutSα/ATM-p73 axis in bladder cancer

description: Additional file 7: Supplementary Table S2.
DOI: 10.6084/m9.figshare.7635245.v1
title: Additional file 1: of Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier

description: Table S1. SVM BRCA1-like status and BRCA1ness-MLPA profiles in 10 breast cancer cell lines. Table S2A. TCGA breast tumors with SVM BRCA1-like status. Table S2B. METABRIC breast tumors with SVM BRCA1-like status. Table S3. Complete subject characteristics of TCGA and METABRIC breast tumors with SVM BRCA1-like status. Table S4. Differentially methylated CpGs in BRCA1-like tumors identified by DMRcate. Table S5A. Hypermethylated DMRs (n = 108) from DMRcate analysis. TableÂ 5SB. Hypomethylated DMRs (n = 94) from DMRcate analysis. Table S6A. GOBP terms associated with 158 unique genes from 108 hypermethylated DMRs. Table S6B. GOBP terms associated with 131 unique genes from 94 hypermethylated DMRs. (XLSX 923 kb)
DOI: 10.25549/one-ouc17553202
title: Mattachine Society, National Planning Conference of Homosexual Organizations (1966-1967)
DOI: 10.6084/m9.figshare.21261616.v1
title: Additional file 1 of Clinical value of fetal facial profile markers during the first trimester

description: Additional file 1.
DOI: 10.6084/m9.figshare.21266747.v1
title: Table S2.xlsx from Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (<i>Setaria italica</i> (L.) P. Beauv.)

description: A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
DOI: 10.25549/one-ouc17553210
title: Mattachine Society, National League for Social Understanding (1961-1965)
DOI: 10.6084/m9.figshare.7635260
title: Additional file 3: of A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis

description: Table S2. The region and mutations of drug-resistant gene. (XLS 32 kb)
DOI: 10.6084/m9.figshare.7635305.v1
title: Additional file 1: of A high-density genetic map of Schima superba based on its chromosomal characteristics

description: Table S1. Number of clean GBS reads per sample (XLSX 12 kb)