cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5634913
title: Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress

description: Abstract Alfalfa (Medicago sativa L.) is an important perennial forage, with high nutritional value, which is widely grown in the world. Because of low freezing tolerance, its distribution and production are threatened and limited by winter weather. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed transcriptome sequencing analysis under cold (4 °C) and freezing (-8 °C) stresses. More than 66 million reads were generated, and we identified 5767 transcripts differentially expressed in response to cold and/or freezing stresses. These results showed that these genes were mainly classified as response to stress, transcription regulation, hormone signaling pathway, antioxidant, nodule morphogenesis, etc., implying their important roles in response to cold and freezing stresses. Furthermore, nine CBF transcripts differentially expressed were homologous to CBF genes of Mt-FTQTL6 site, conferring freezing tolerance in M. truncatula, which indicated that a genetic mechanism controlling freezing tolerance was conservative between M. truncatula and M. sativa. In summary, this transcriptome dataset highlighted the gene regulation response to cold and/or freezing stresses in alfalfa, which provides a valuable resource for future identification and functional analysis of candidate genes in determining freezing tolerance.
DOI: 10.6084/m9.figshare.5634913.v1
title: Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress

description: Abstract Alfalfa (Medicago sativa L.) is an important perennial forage, with high nutritional value, which is widely grown in the world. Because of low freezing tolerance, its distribution and production are threatened and limited by winter weather. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed transcriptome sequencing analysis under cold (4 °C) and freezing (-8 °C) stresses. More than 66 million reads were generated, and we identified 5767 transcripts differentially expressed in response to cold and/or freezing stresses. These results showed that these genes were mainly classified as response to stress, transcription regulation, hormone signaling pathway, antioxidant, nodule morphogenesis, etc., implying their important roles in response to cold and freezing stresses. Furthermore, nine CBF transcripts differentially expressed were homologous to CBF genes of Mt-FTQTL6 site, conferring freezing tolerance in M. truncatula, which indicated that a genetic mechanism controlling freezing tolerance was conservative between M. truncatula and M. sativa. In summary, this transcriptome dataset highlighted the gene regulation response to cold and/or freezing stresses in alfalfa, which provides a valuable resource for future identification and functional analysis of candidate genes in determining freezing tolerance.
DOI: 10.6084/m9.figshare.5639575
title: Additional file 2: Table S2. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: Information of 5920 tumor mtDNA base substitutions. (XLSX 488 kb)
DOI: 10.6084/m9.figshare.5639575.v1
title: Additional file 2: Table S2. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: Information of 5920 tumor mtDNA base substitutions. (XLSX 488 kb)
DOI: 10.6084/m9.figshare.5639587
title: Additional file 3: Table S3. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: Phylotree data annotation. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.5639587.v1
title: Additional file 3: Table S3. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: Phylotree data annotation. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.5639614
title: Additional file 4: Table S4. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: All possible base substitution in mRNA coding regions of mtDNA. (XLSX 1519 kb)
DOI: 10.6084/m9.figshare.5639614.v1
title: Additional file 4: Table S4. of Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations

description: All possible base substitution in mRNA coding regions of mtDNA. (XLSX 1519 kb)
DOI: 10.6084/m9.figshare.5639707
title: Additional file 2: of Robust transcriptional signatures for low-input RNA samples based on relative expression orderings

description: The main analyses codes used in this research. (R 4Â kb)
DOI: 10.6084/m9.figshare.5639707.v1
title: Additional file 2: of Robust transcriptional signatures for low-input RNA samples based on relative expression orderings

description: The main analyses codes used in this research. (R 4Â kb)
DOI: 10.6084/m9.figshare.5639740
title: Additional file 1: Figure S1. of Sertad1 antagonizes iASPP function by hindering its entrance into nuclei to interact with P53 in leukemic cells

description: The percentage of cell cycle in G0/G1, S and G2/M in K562-iASPPhi, Sertad1hi and Douhi cells. (ZIP 2313 kb)
DOI: 10.6084/m9.figshare.5639740.v1
title: Additional file 1: Figure S1. of Sertad1 antagonizes iASPP function by hindering its entrance into nuclei to interact with P53 in leukemic cells

description: The percentage of cell cycle in G0/G1, S and G2/M in K562-iASPPhi, Sertad1hi and Douhi cells. (ZIP 2313 kb)
DOI: 10.6084/m9.figshare.5639839
title: Additional file 2: Table S1. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Primers used in this study. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5639839.v1
title: Additional file 2: Table S1. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Primers used in this study. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5639845
title: Additional file 1: S1. of Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

description: Data filtration. S2. Illumina MiSeq sequencing for 16S rRNA genes. S3. Co-occurrence patterns among ARGs. Table S1. Basic information about drinking water samples. Table S2. Information about 16S rRNA gene analysis in drinking water samples. Table S3. The primers (including barcode, pad, and linker) used for 16S rRNA gene amplification. Table S4. Detected ARG types and corresponding abundances in drinking water. Table S5. Detected ARG subtypes and corresponding abundances in drinking water. Table S6. The resistance level in drinking water samples. Table S7. Abundance and frequency of ARG types in drinking water samples. Table S8. Co-occurring ARGs subtypes of network modules. Table S9. Basic information about 56 environmental samples for comparison of ARGs with drinking water samples. Table S10. Occurrence of 9 generalist ARG subtypes that were prevalent in drinking water. Table S11. Assembly statistics for drinking water metagenomic sequencing data. Table S12. Types and subtypes of ARGs carried by ACCs and their occurrence in drinking water. Table S13. Bacterial taxonomy of ARG-carrying contigs in the lowest annotation level and ARGs they carried. Table S14. Bacterial OTUs and their abundances in drinking water. Figure S1. Collection locations of drinking water samples. Figure S2. Cluster analysis of drinking water metagenomes based on abundance of ARG subtypes (Euclidean). Figure S3. Abundance of the top 50 ARG subtypes detected in tap water samples. Figure S4. Correlation-based network statistical analysis reveals co-occurrence patterns among ARG subtypes. Figure S5. Two-dimensional principal coordinate analysis plots show the ARG composition differences among the 81 environmental samples from 8 ecosystems. Figure S6. Two-dimensional principal coordinate analysis plots show the microbial community difference among tap water samples. (ZIP 3889 kb)
DOI: 10.6084/m9.figshare.5639845.v1
title: Additional file 1: S1. of Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

description: Data filtration. S2. Illumina MiSeq sequencing for 16S rRNA genes. S3. Co-occurrence patterns among ARGs. Table S1. Basic information about drinking water samples. Table S2. Information about 16S rRNA gene analysis in drinking water samples. Table S3. The primers (including barcode, pad, and linker) used for 16S rRNA gene amplification. Table S4. Detected ARG types and corresponding abundances in drinking water. Table S5. Detected ARG subtypes and corresponding abundances in drinking water. Table S6. The resistance level in drinking water samples. Table S7. Abundance and frequency of ARG types in drinking water samples. Table S8. Co-occurring ARGs subtypes of network modules. Table S9. Basic information about 56 environmental samples for comparison of ARGs with drinking water samples. Table S10. Occurrence of 9 generalist ARG subtypes that were prevalent in drinking water. Table S11. Assembly statistics for drinking water metagenomic sequencing data. Table S12. Types and subtypes of ARGs carried by ACCs and their occurrence in drinking water. Table S13. Bacterial taxonomy of ARG-carrying contigs in the lowest annotation level and ARGs they carried. Table S14. Bacterial OTUs and their abundances in drinking water. Figure S1. Collection locations of drinking water samples. Figure S2. Cluster analysis of drinking water metagenomes based on abundance of ARG subtypes (Euclidean). Figure S3. Abundance of the top 50 ARG subtypes detected in tap water samples. Figure S4. Correlation-based network statistical analysis reveals co-occurrence patterns among ARG subtypes. Figure S5. Two-dimensional principal coordinate analysis plots show the ARG composition differences among the 81 environmental samples from 8 ecosystems. Figure S6. Two-dimensional principal coordinate analysis plots show the microbial community difference among tap water samples. (ZIP 3889 kb)
DOI: 10.6084/m9.figshare.5639860
title: Additional file 3: Table S2. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Information of sweet potato GST genes identified in this study. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.5639860.v1
title: Additional file 3: Table S2. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Information of sweet potato GST genes identified in this study. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.5639881
title: Additional file 4: Table S3. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Pairwise identity matrix for full-length GST genes in this study. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5639881.v1
title: Additional file 4: Table S3. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Pairwise identity matrix for full-length GST genes in this study. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5639914
title: Additional file 6: Table S4. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Information of GSTs from other species used in this study. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.5639914.v1
title: Additional file 6: Table S4. of Identification and analysis of glutathione S-transferase gene family in sweet potato reveal divergent GST-mediated networks in aboveground and underground tissues in response to abiotic stresses

description: Information of GSTs from other species used in this study. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.5643733
title: Additional file 9: of Smad4 SUMOylation is essential for memory formation through upregulation of the skeletal myopathy gene TPM2

description: Supplementary information. (XLS 62 kb)
DOI: 10.6084/m9.figshare.5643733.v1
title: Additional file 9: of Smad4 SUMOylation is essential for memory formation through upregulation of the skeletal myopathy gene TPM2

description: Supplementary information. (XLS 62 kb)
DOI: 10.6084/m9.figshare.5644897
title: Short-term efficacy and safety of low-intensity extracorporeal shock wave therapy in erectile dysfunction: a systematic review and meta-analysis

description: ABSTRACT Aim: The role of low-intensity extracorporeal shock wave therapy (LI-ESWT) in erectile dysfunction (ED) is not clearly determined. The purpose of this study is to investigate the short-term efficacy and safety of LI-ESWT for ED patients. Materials and Methods: Relevant studies were searched in Medline, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), WANFANG and VIP databases. Effective rate in terms of International Index of Erectile Function-Erectile Function Domain (IIEF-EF) and Erectile Hardness Score (EHS) at about 1XSmonth after LI-ESWT was extracted from eligible studies for meta-analysis to calculate risk ratio (RR) of effective treatment in ED patients treated by LI-ESWT compared to those receiving sham-treatment. Results: Overall fifteen studies were included in the review, of which four randomized controlled trials (RCTs) were for meta-analysis. Effective treatment was 8.31 [95°/o confidence interval (CI): 3.88-17.78] times more effective in the LI-ESWT group (n=176) than in the sham-treatment group (n= 101) at about 1 month after the intervention in terms of EHS, while it was 2.50 (95% CI: 0.74–8.45) times more in the treatment group (n= 121) than in the control group (n=89) in terms of IIEF-EF. Nine-week protocol with energy density of 0.09mJ/mm2 and 1500 pluses seemed to have better therapeutic effect than five-week protocol. No significant adverse event was reported. Conclusion: LI-ESWT, as a noninvasive treatment, has potential short-term therapeutic effect on patients with organic ED irrespective of sensitivity to PDE5is. Owing to the limited number and quality of the studies, more large-scale, well-designed and longterm follow-up time studies are needed to confirm our analysis.
DOI: 10.6084/m9.figshare.5644897.v1
title: Short-term efficacy and safety of low-intensity extracorporeal shock wave therapy in erectile dysfunction: a systematic review and meta-analysis

description: ABSTRACT Aim: The role of low-intensity extracorporeal shock wave therapy (LI-ESWT) in erectile dysfunction (ED) is not clearly determined. The purpose of this study is to investigate the short-term efficacy and safety of LI-ESWT for ED patients. Materials and Methods: Relevant studies were searched in Medline, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), WANFANG and VIP databases. Effective rate in terms of International Index of Erectile Function-Erectile Function Domain (IIEF-EF) and Erectile Hardness Score (EHS) at about 1XSmonth after LI-ESWT was extracted from eligible studies for meta-analysis to calculate risk ratio (RR) of effective treatment in ED patients treated by LI-ESWT compared to those receiving sham-treatment. Results: Overall fifteen studies were included in the review, of which four randomized controlled trials (RCTs) were for meta-analysis. Effective treatment was 8.31 [95°/o confidence interval (CI): 3.88-17.78] times more effective in the LI-ESWT group (n=176) than in the sham-treatment group (n= 101) at about 1 month after the intervention in terms of EHS, while it was 2.50 (95% CI: 0.74–8.45) times more in the treatment group (n= 121) than in the control group (n=89) in terms of IIEF-EF. Nine-week protocol with energy density of 0.09mJ/mm2 and 1500 pluses seemed to have better therapeutic effect than five-week protocol. No significant adverse event was reported. Conclusion: LI-ESWT, as a noninvasive treatment, has potential short-term therapeutic effect on patients with organic ED irrespective of sensitivity to PDE5is. Owing to the limited number and quality of the studies, more large-scale, well-designed and longterm follow-up time studies are needed to confirm our analysis.
DOI: 10.6084/m9.figshare.5645029
title: Partial nephrectomy for T3aN0M0 renal cell carcinoma: shall we step forward?

description: ABSTRACT Objectives: To evaluate the prognosis of non-metastatic T3a renal cell carcinoma (RCC) with partial nephrectomy (PN). Patients and Methods: We retrospectively evaluated 125 patients with non-metastatic T3a RCC. Patients undergoing PN and radical nephrectomy (RN) were strictly matched by clinic-pathologic characteristics. Log-rank test and Cox regression model were used for univariate and multivariate analysis. Results: 18 pair patients were matched and the median follow-up was 35.5 (10-86) months. PN patients had a higher postoperative eGFR than RN patients (P=0.034). Cancer-specific survival (CSS) and recurrence-free survival (RFS) did not differ between two groups (P=0.305 and P=0.524). On multivariate analysis, CSS decreased with positive surgical margin and anemia (both P &lt;0.01) and RFS decreased with Furhman grade, positive surgical margin, and anemia (all P&lt;0.01). Conclusions: For patients with non-metastatic pT3a RCC, PN may be a possible option for similar oncology outcomes and better renal function.
DOI: 10.6084/m9.figshare.5645029.v1
title: Partial nephrectomy for T3aN0M0 renal cell carcinoma: shall we step forward?

description: ABSTRACT Objectives: To evaluate the prognosis of non-metastatic T3a renal cell carcinoma (RCC) with partial nephrectomy (PN). Patients and Methods: We retrospectively evaluated 125 patients with non-metastatic T3a RCC. Patients undergoing PN and radical nephrectomy (RN) were strictly matched by clinic-pathologic characteristics. Log-rank test and Cox regression model were used for univariate and multivariate analysis. Results: 18 pair patients were matched and the median follow-up was 35.5 (10-86) months. PN patients had a higher postoperative eGFR than RN patients (P=0.034). Cancer-specific survival (CSS) and recurrence-free survival (RFS) did not differ between two groups (P=0.305 and P=0.524). On multivariate analysis, CSS decreased with positive surgical margin and anemia (both P &lt;0.01) and RFS decreased with Furhman grade, positive surgical margin, and anemia (all P&lt;0.01). Conclusions: For patients with non-metastatic pT3a RCC, PN may be a possible option for similar oncology outcomes and better renal function.
DOI: 10.6084/m9.figshare.5648794
title: MOESM10 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 10: Table S6. Sequences of qRT-PCR primers.
DOI: 10.6084/m9.figshare.5648794.v1
title: MOESM10 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 10: Table S6. Sequences of qRT-PCR primers.
DOI: 10.6084/m9.figshare.5648815
title: MOESM11 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 11: Table S8. The Studentâ s t-tests on the monosaccharide composition and sequential extraction between pairwise samples.
DOI: 10.6084/m9.figshare.5648815.v1
title: MOESM11 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 11: Table S8. The Studentâ s t-tests on the monosaccharide composition and sequential extraction between pairwise samples.
DOI: 10.6084/m9.figshare.5648887
title: MOESM3 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 3: Table S1. List of differentially expressed genes in switchgrass suspension cells using SOM and the linear model.
DOI: 10.6084/m9.figshare.5648887.v1
title: MOESM3 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 3: Table S1. List of differentially expressed genes in switchgrass suspension cells using SOM and the linear model.
DOI: 10.6084/m9.figshare.5648905
title: MOESM4 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 4: Table S2. Functional distribution of differentially expressed genes in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5648905.v1
title: MOESM4 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 4: Table S2. Functional distribution of differentially expressed genes in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5648926
title: MOESM5 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 5: Table S3. Cell wall-related functional groups in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5648926.v1
title: MOESM5 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 5: Table S3. Cell wall-related functional groups in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5648944
title: MOESM6 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 6: Table S4. List of TFs co-expressed with lignin biosynthesis genes in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5648944.v1
title: MOESM6 of Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

description: Additional file 6: Table S4. List of TFs co-expressed with lignin biosynthesis genes in switchgrass suspension cells.
DOI: 10.6084/m9.figshare.5656930
title: Additional file 6: Table S1. of The miR172c-NNC1 module modulates root plastic development in response to salt in soybean

description: Primers used in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5656930.v1
title: Additional file 6: Table S1. of The miR172c-NNC1 module modulates root plastic development in response to salt in soybean

description: Primers used in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5656933
title: Additional file 1: of Evaluation of an accelerated hydrogen peroxide disinfectant to inactivate porcine epidemic diarrhea virus in swine feces on aluminum surfaces under freezing conditions

description: Results of PEDV N-gene RT-qPCR tests on environmental samples from coupons and rectal swabs from pigs used for bioassay. Results from all diagnostic tests conducted for the study are reported for each replicate, one row for each replicate. Test results, Ct value and genomic copies are reported for PCR tests on pre and post treatment environmental samples from coupons. Test result and Ct values are reported for PCR tests on rectal swabs from pigs 3 and 7Â days post inoculation for the bioassay. (XLSX 12Â kb)