cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853092
title: Genome-wide identification and expression analysis of the AAAP family in <i>Fragaria vesca</i>

description: The amino acid/auxin permease (AAAP) gene family plays a significant role in the long-distance amino acid transport and is involved in plant stress responses and various developmental processes. The functions of the AAAP family have been extensively discussed in multiple organisms, whereas detailed information of this family in strawberry (<i>Fragaria vesca</i>) has not been reported yet. In this study, we identified 45 AAAP genes in the strawberry genome. Phylogenetic analysis indicated that AAAPs from strawberry and <i>Arabidopsis</i> were clustered into eight groups. Expression analysis of the AAAP family showed that AAAP genes were expressed differentially in different developmental stages of flower and fruit, and were significantly induced after <i>Colletotrichum gloeosporioides</i> infection. Our study provides a comprehensive understanding of the strawberry AAAP family and demonstrates their potential roles in disease resistance, providing more reference for further research.
DOI: 10.6084/m9.figshare.12853092.v1
title: Genome-wide identification and expression analysis of the AAAP family in <i>Fragaria vesca</i>

description: The amino acid/auxin permease (AAAP) gene family plays a significant role in the long-distance amino acid transport and is involved in plant stress responses and various developmental processes. The functions of the AAAP family have been extensively discussed in multiple organisms, whereas detailed information of this family in strawberry (<i>Fragaria vesca</i>) has not been reported yet. In this study, we identified 45 AAAP genes in the strawberry genome. Phylogenetic analysis indicated that AAAPs from strawberry and <i>Arabidopsis</i> were clustered into eight groups. Expression analysis of the AAAP family showed that AAAP genes were expressed differentially in different developmental stages of flower and fruit, and were significantly induced after <i>Colletotrichum gloeosporioides</i> infection. Our study provides a comprehensive understanding of the strawberry AAAP family and demonstrates their potential roles in disease resistance, providing more reference for further research.
DOI: 10.6084/m9.figshare.17047343
title: Additional file 2 of Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

description: Table S1: WRKY information, Table S2: The expression of WRKY in different tissues, Table S3: The expression of WRKY under different treatments, Table S4: The different expression genes under heat treatment, Table S5: The different expression genes under cold, salt and drought treatment, Table S6: the correlation matrix of WRKY to ginsenosides pathway genes, Table S7: the expression of UGTs in P. ginseng, Table S8: The correlation matrix of WRKY to select PgUGTs, Table S9: The annotation of select PgUGTs.
DOI: 10.6084/m9.figshare.17047343.v1
title: Additional file 2 of Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

description: Table S1: WRKY information, Table S2: The expression of WRKY in different tissues, Table S3: The expression of WRKY under different treatments, Table S4: The different expression genes under heat treatment, Table S5: The different expression genes under cold, salt and drought treatment, Table S6: the correlation matrix of WRKY to ginsenosides pathway genes, Table S7: the expression of UGTs in P. ginseng, Table S8: The correlation matrix of WRKY to select PgUGTs, Table S9: The annotation of select PgUGTs.
DOI: 10.6084/m9.figshare.12853224
title: Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2

description: Newly emerged SARS-CoV-2 made recent pandemic situations across the globe is accountable for countless unwanted death and insufferable panic associated with co-morbidities among mass people. The scarcity of appropriate medical treatment and no effective vaccine or medicine against SARS-CoV-2 has turned the situation worst. Therefore, in this study, we made a deep literature review to enlist plant-derived natural compounds and considered their binding mechanism with the main protease of SARS-CoV-2 through combinatorial bioinformatics approaches. Among all, a total of 14 compounds were filtered where Carinol, Albanin, Myricetin were had better binding profile than the rest of the compounds with having binding energy of –8.476, –8.036, –8.439 kcal/mol, respectively. Furthermore, MM-GBSA calculations were also considered in this selection process to support docking studies. Besides, 100 ns molecular dynamics simulation endorsed the rigid nature, less conformational variation and binding stiffness. As this study, represents a perfect model for SARS-CoV-2 main protease inhibition through bioinformatics study, these potential drug candidates may assist the researchers to find a superior and effective solution against COVID-19 after future experiments. Communicated by Ramaswamy Sarma
DOI: 10.6084/m9.figshare.12853224.v1
title: Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2

description: Newly emerged SARS-CoV-2 made recent pandemic situations across the globe is accountable for countless unwanted death and insufferable panic associated with co-morbidities among mass people. The scarcity of appropriate medical treatment and no effective vaccine or medicine against SARS-CoV-2 has turned the situation worst. Therefore, in this study, we made a deep literature review to enlist plant-derived natural compounds and considered their binding mechanism with the main protease of SARS-CoV-2 through combinatorial bioinformatics approaches. Among all, a total of 14 compounds were filtered where Carinol, Albanin, Myricetin were had better binding profile than the rest of the compounds with having binding energy of –8.476, –8.036, –8.439 kcal/mol, respectively. Furthermore, MM-GBSA calculations were also considered in this selection process to support docking studies. Besides, 100 ns molecular dynamics simulation endorsed the rigid nature, less conformational variation and binding stiffness. As this study, represents a perfect model for SARS-CoV-2 main protease inhibition through bioinformatics study, these potential drug candidates may assist the researchers to find a superior and effective solution against COVID-19 after future experiments. Communicated by Ramaswamy Sarma
DOI: 10.6084/m9.figshare.19144683
title: Additional file 2 of Determinants of suboptimal immune recovery among a Chinese Yi ethnicity population with sustained HIV suppression

description: Additional file 2. Checklist for the appropriate reporting statement: STROBE.
DOI: 10.6084/m9.figshare.19144683.v1
title: Additional file 2 of Determinants of suboptimal immune recovery among a Chinese Yi ethnicity population with sustained HIV suppression

description: Additional file 2. Checklist for the appropriate reporting statement: STROBE.
DOI: 10.6084/m9.figshare.19144696
title: Additional file 4 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 4. Supporting data for the individual data values (n&lt;6).
DOI: 10.6084/m9.figshare.19144696.v1
title: Additional file 4 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 4. Supporting data for the individual data values (n&lt;6).
DOI: 10.6084/m9.figshare.19144687
title: Additional file 1 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 1: Figure S1. Histomorphology and H&E sections of different types of muscles after DHA supplementation. (A) The gastrocnemius (GAS), tibialis anterior (TA), soleus (SOL) and extensor digitorum longus (EDL). (B) Hematoxylin and eosin–stained sections of GAS. Scale bar: 500 μm. Figure S2. Effects of different concentrations of DHA on C2C12 differentiation and m6A. (A) The proliferative activity of cells with different concentrations of DHA (compared with DHA 0 μM) (n=3). (B) Myotubule with high concentration DHA (50 or 100 Μm, 4d) treatment in Bright field and H&E staining. (C) Western blotting analysis of MyHC expression, (D) qPCR analysis of key genes, Myod1 and Myog (n=3). (E) Oil Red O staining of DHA-treatment C2C12 after four days of differentiation. (F) Quantification of relative lipid accumulation (n=3). (G) qPCR analysis of genes associated with adipogenesis, including Cebpα, Pparγ, Fabp4 after 48h of DHA treatment (n=3). (H) ORO staining and (I) quantification of relative lipid accumulation in C2C12 treated with low concentration of DHA (5 or 10 μM, 4d) (n=3). (J) qPCR analysis of Myod1 and Myog (n=3). (K) Dot Blot Analysis of m6A. Statistical analysis was performed using one-way ANOVA (Figure S2D-G and I-J) and two-tailed paired Student’s t-tests (Figure S2A). Figure S3. DDIT4 is regulated by FTO mediated m6A. (A) qPCR analysis the expression of Ddit4 in NFD, HFD and HFD+DHA group (n=6). (B) Methylated RNA immunoprecipitation (MeRIP)-qPCR analysis of m6A levels of Ddit4 mRNA in NFD, HFD and HFD+DHA group (n=3). (C) Western blot analysis of DDIT4 expression in CTL, FTO-WT, FTO-MUT transfected C2C12 cells. Statistical analysis was performed using two-tailed paired Student’s t-tests.
DOI: 10.6084/m9.figshare.19144687.v1
title: Additional file 1 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 1: Figure S1. Histomorphology and H&E sections of different types of muscles after DHA supplementation. (A) The gastrocnemius (GAS), tibialis anterior (TA), soleus (SOL) and extensor digitorum longus (EDL). (B) Hematoxylin and eosin–stained sections of GAS. Scale bar: 500 μm. Figure S2. Effects of different concentrations of DHA on C2C12 differentiation and m6A. (A) The proliferative activity of cells with different concentrations of DHA (compared with DHA 0 μM) (n=3). (B) Myotubule with high concentration DHA (50 or 100 Μm, 4d) treatment in Bright field and H&E staining. (C) Western blotting analysis of MyHC expression, (D) qPCR analysis of key genes, Myod1 and Myog (n=3). (E) Oil Red O staining of DHA-treatment C2C12 after four days of differentiation. (F) Quantification of relative lipid accumulation (n=3). (G) qPCR analysis of genes associated with adipogenesis, including Cebpα, Pparγ, Fabp4 after 48h of DHA treatment (n=3). (H) ORO staining and (I) quantification of relative lipid accumulation in C2C12 treated with low concentration of DHA (5 or 10 μM, 4d) (n=3). (J) qPCR analysis of Myod1 and Myog (n=3). (K) Dot Blot Analysis of m6A. Statistical analysis was performed using one-way ANOVA (Figure S2D-G and I-J) and two-tailed paired Student’s t-tests (Figure S2A). Figure S3. DDIT4 is regulated by FTO mediated m6A. (A) qPCR analysis the expression of Ddit4 in NFD, HFD and HFD+DHA group (n=6). (B) Methylated RNA immunoprecipitation (MeRIP)-qPCR analysis of m6A levels of Ddit4 mRNA in NFD, HFD and HFD+DHA group (n=3). (C) Western blot analysis of DDIT4 expression in CTL, FTO-WT, FTO-MUT transfected C2C12 cells. Statistical analysis was performed using two-tailed paired Student’s t-tests.
DOI: 10.6084/m9.figshare.19144690
title: Additional file 2 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 2. The lipid mass spec data of muscle after DHA supplementation.
DOI: 10.6084/m9.figshare.19144690.v1
title: Additional file 2 of DHA alleviates diet-induced skeletal muscle fiber remodeling via FTO/m6A/DDIT4/PGC1α signaling

description: Additional file 2. The lipid mass spec data of muscle after DHA supplementation.
DOI: 10.6084/m9.figshare.22814762
title: Supporting Information.pdf

description:  
Table 1:  Whole-rock B and Mo contents and isotopic compositions for the Yardoi Cenozoic granites.
S1. Supplementary Figures
S2. Supplementary Tables
DOI: 10.6084/m9.figshare.7610420
title: Rapid evaluation of soil fertility in tea plantation based on near-infrared spectroscopy

description: An efficient soil analysis technique was developed to monitor soil fertility and perform precise soil management in tea plantations. In this study, near-infrared spectroscopy combined with chemometric methods was utilized to determine the organic matter and total nitrogen content and evaluate fertility of tea plantation soils. First, photometric precision and subtractive spectroscopy were used as indicators in identifying optimal sample preparation condition. Spectral reproducibility reached an optimum with powder particle size of 100 mesh (0.149 mm). Second, after comparing the combinations of the partial least squares method with three different characteristic wavelength extraction methods, the genetic algorithm and competitive adaptive reweighted sampling quantitative discrimination models were determined to be optimal for organic matter and total nitrogen contents, with prediction correlation coefficients of 0.9102 and 0.8763, respectively. Third, classification models for soil fertility level using linear discriminant analysis, support vector machine, and extreme learning machine were established based on a full spectrum and successive projections algorithm separately. The successive projections algorithm-extreme learning machine model was deemed superior with a correct classification rate of 84.38%. Our findings demonstrate that the proposed near-infrared spectroscopy calibration models successfully achieve the nondestructive and rapid evaluation of organic matter and total nitrogen contents, as well as the classification of soil fertility levels, in tea plantation soils. The results provide a basis for the development of internet-of-things sensors in the construction of a high-yield and high-quality tea plantation.
DOI: 10.6084/m9.figshare.7610420.v1
title: Rapid evaluation of soil fertility in tea plantation based on near-infrared spectroscopy

description: An efficient soil analysis technique was developed to monitor soil fertility and perform precise soil management in tea plantations. In this study, near-infrared spectroscopy combined with chemometric methods was utilized to determine the organic matter and total nitrogen content and evaluate fertility of tea plantation soils. First, photometric precision and subtractive spectroscopy were used as indicators in identifying optimal sample preparation condition. Spectral reproducibility reached an optimum with powder particle size of 100 mesh (0.149 mm). Second, after comparing the combinations of the partial least squares method with three different characteristic wavelength extraction methods, the genetic algorithm and competitive adaptive reweighted sampling quantitative discrimination models were determined to be optimal for organic matter and total nitrogen contents, with prediction correlation coefficients of 0.9102 and 0.8763, respectively. Third, classification models for soil fertility level using linear discriminant analysis, support vector machine, and extreme learning machine were established based on a full spectrum and successive projections algorithm separately. The successive projections algorithm-extreme learning machine model was deemed superior with a correct classification rate of 84.38%. Our findings demonstrate that the proposed near-infrared spectroscopy calibration models successfully achieve the nondestructive and rapid evaluation of organic matter and total nitrogen contents, as well as the classification of soil fertility levels, in tea plantation soils. The results provide a basis for the development of internet-of-things sensors in the construction of a high-yield and high-quality tea plantation.
DOI: 10.6084/m9.figshare.19144792
title: Additional file 1 of Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

description: Additional file 1 Table S1. Changes in the fresh weight of Tamarix hispida seeds during germination. Table S2. Expression of differentially expressed genes and the detailed information of gene annotation in the seeds of Tamarix hispida seeds during germination. Table S3. Results of KEGG enrichment of differentially expressed genes in the seeds of Tamarix hispida during germination. Table S4. KEGG enrichment of differentially expressed genes in flavonoid biosynthesis (Ko00941) during seed germination and post-germination. Table S5. KEGG enrichment of differentially expressed genes in plant hormone signal transduction (ko04075) during seed germination and post-germination. Table S6. Results of GO and KEGG enrichment of differentially expressed genes in modules. Table S7. Differentially accumulated metabolites in stages 3, 4 and 5. Table S8. List of primers used for the relative quantification of gene transcripts.
DOI: 10.6084/m9.figshare.19144792.v1
title: Additional file 1 of Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

description: Additional file 1 Table S1. Changes in the fresh weight of Tamarix hispida seeds during germination. Table S2. Expression of differentially expressed genes and the detailed information of gene annotation in the seeds of Tamarix hispida seeds during germination. Table S3. Results of KEGG enrichment of differentially expressed genes in the seeds of Tamarix hispida during germination. Table S4. KEGG enrichment of differentially expressed genes in flavonoid biosynthesis (Ko00941) during seed germination and post-germination. Table S5. KEGG enrichment of differentially expressed genes in plant hormone signal transduction (ko04075) during seed germination and post-germination. Table S6. Results of GO and KEGG enrichment of differentially expressed genes in modules. Table S7. Differentially accumulated metabolites in stages 3, 4 and 5. Table S8. List of primers used for the relative quantification of gene transcripts.
DOI: 10.6084/m9.figshare.19144746
title: Additional file 4 of H3K27ac chromatin acetylation and gene expression analysis reveal sex- and situs-related differences in developing chicken gonads

description: Additional file 4: Table S4. The detailed list of H3K27ac peak adjacent genes after the removal of duplicates.
DOI: 10.6084/m9.figshare.19144746.v1
title: Additional file 4 of H3K27ac chromatin acetylation and gene expression analysis reveal sex- and situs-related differences in developing chicken gonads

description: Additional file 4: Table S4. The detailed list of H3K27ac peak adjacent genes after the removal of duplicates.
DOI: 10.15468/dl.fp9s8k
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phascolarctos cinereus (Goldfuss, 1817)"
 ]
}

 The dataset's 4 records were derived from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030030-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.namd3j
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Botryosphaeria abrupta Berk. & M.A.Curtis ex Cooke",
 {
 "not" : {
 "Country" : [
 "is United States of America"
 ]
 }
 },
 {
 "not" : {
 "Country" : [
 "is Canada"
 ]
 }
 },
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0101160-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s7pdmq
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron chihsinianum Chun & W.P.Fang"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0383934-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6utzc
title: Occurrence Download

description: A dataset containing 430840 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Prunus avium (L.) L.)"
 ]
}

 The dataset includes 430840 records from 2090 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042502-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive123489.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123490.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123490.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123491.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123491.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123492.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123492.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123493.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123493.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123494.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123494.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123495.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123495.20221219.7.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive123496.20220920.7
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.