cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6879713
title: Importance of TFEB acetylation in control of its transcriptional activity and lysosomal function in response to histone deacetylase inhibitors

description: TFEB (transcription factor EB) is a master regulator of lysosomal biogenesis, function and autophagy. The transcriptional activity of TFEB is mainly controlled by its phosphorylation status mediated by the MTOR (mechanistic target of rapamycin [serine/threonine kinase]) complex 1 (MTORC1). At present, little is known whether other forms of posttranslational modifications (PTMs) such as acetylation also affects is transcriptional activity. In this study, we first observed that a well-established histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) activated lysosomal function in human cancer cells, a process independent of the MTORC1 pathway. Second, SAHA treatment activated TFEB transcriptional activity, as evidenced by increased TFEB luciferase activity and expression of its target genes. Third and more importantly, we observed the enhanced TFEB acetylation in SAHA-treated cells, with identification of 4 acetylation sites. Mutation of these 4 sites markedly diminished TFEB transcriptional activity and lysosomal function induced by SAHA. Finally, we found that TFEB acetylation was functionally implicated in SAHA-mediated autophagy and cell death in cancer cells. Taken together, our results demonstrate that TFEB acetylation is a novel form of PTMs in TFEB that plays an important role in determining its transcriptional activity, lysosomal function and autophagy in cancer cells. <b>Abbreviations:</b> ACAT1: acetyl-coenzyme A acetyltransferase 1; AHA: L-azidohomoalanine; AO: acidic orange; ATG: autophagy related; CLEAR: Coordinated Lysosomal Expression and Regulation; CQ: chloroquine; CTSB: cathepsin B; HATs: histone acetyltransferases; HDACIs: HDACs inhibitors; HDACs: histone deacetylases; IP: immunoprecipitation; MEFs: mouse embryonic fibroblasts; MS: mass spectrometry; MTOR: mechanistic target of rapamycin (serine/threonine kinase); MTORC1: mechanistic target of rapamycin (serine/threonine kinase) complex 1; PTMs: posttranslational modifications; SAHA: suberoylanilidehydroxamic acid; TFEB: transcription factor EB
DOI: 10.15131/shef.data.19814737.v1
title: Data for "How foraging honeybees make decisions"

description: When bees navigate for nectar or pollen, they must continually assess the quality of their current observation and the uncertainty about future possibilities under evaluation of the expected reward and the risk of predators and energy cost. They necessitate employing an integrative process of decision-making to accomplish the highest profits. However, the mechanisms underpinning the decision making in animals with miniature brains is still mysterious. Here, we designed a multi-comparison ranking task for honeybees and video analysed their behaviours. Our results reveal honeybees’ choice behaviour is sensitive to both the quality and reliability of evidence. Degrading the evidence and reward likelihood influences time to choose. Importantly, our data suggests that acceptance and rejection are not two sides of the coin. Acceptance is more discriminating and costly for bees and bees spent longer time to accept a flower compared to their fast and less accurate rejections. To investigate the minimally sufficient circuitry required for honeybee foraging choice, we developed a novel model of decision-making. Our neurobiologically plausible model of the insect brain can account for these features by incorporating information about variability and other costs. In this study, we observed a complex autonomous decision making, but with a possibly minimal neural circuitry in bees that is highly applicable in designing the future robots.
DOI: 10.6084/m9.figshare.22084019
title: Extended Data of "Ocean heat uptake and interbasin redistribution driven by anthropogenic aerosols and greenhouse gases"

description: Extended Data of "Ocean heat uptake and interbasin redistribution driven by anthropogenic aerosols and greenhouse gases"
DOI: 10.6084/m9.figshare.16841126
title: Additional file 6 of Light control of catechin accumulation is mediated by photosynthetic capacity in tea plant (Camellia sinensis)

description: Additional file 6: Supplemental data 1. The corresponding indexes of the numbers in the correlation analysis.
DOI: 10.6084/m9.figshare.16841126.v1
title: Additional file 6 of Light control of catechin accumulation is mediated by photosynthetic capacity in tea plant (Camellia sinensis)

description: Additional file 6: Supplemental data 1. The corresponding indexes of the numbers in the correlation analysis.
DOI: 10.25345/c5d50g80b
title: MassIVE MSV000094031 - LC-MS/MS based proteomics analysis of decellularized and non-decellularized mouse kidney tissue samples
title: Two C57Bl6/J male mice were sacrificed by injecting 200 microliters of the lethal anaesthetic Dolethal. Kidneys were perfused with Dulbeccos Phosphate Buffered Saline, dissected, decapsulated and weighted. Kidneys were decellularized using 3 freeze-thaw cycles (freezing at -80C, 30 minute long thawing at 4C) and a 3-day long incubation in 2% SDS at 4C under gentle rotation. Ten to twenty milligram tissue net weight of each sample was homogenised. Protein concentration was determined using Bradford Assay. Ten micrograms of total protein was loaded in SDS-PAGE and migrated for 25min and prepared using the GeLC-MS method (doi: 10.1007/7651_2017_76). For LC-MS/MS analysis a Dionex Ultimate 3000 HPLC nanoflow system was used in combination with a Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer. Samples were reconstituted in 25 microliters mobile phase A (98% water, 2% acetonitrile, 0.1% formic acid) and 10 microliters were loaded onto the LC column configured with a Dionex 0.1 x 20 mm, 5 micrometres, 100 A C18 nano trap column with a 5 microliters/min flow rate. An Acclaim PepMapTM C18 100 nanoViper column 75 micrometres x 50cm, 2 micrometres 100 A was used with a flow rate of 300nL/min. Peptides were eluted under a 250min gradient from 2% mobile phase B (0.1% formic acid in 80% acetonitrile) to 95% mobile phase B. Voltage of the positive ion electrospray ionization was set to 2.1kV. The mass spectrometer parameters were set as follows: 1) full MS: resolution of 70,000, automatic gain control (AGC) target at 1e6, maximum injection time (IT) of 100ms, scan range of 380 - 1,200m/z; 2) dd-MS2: resolution of 17,500, AGC target at 1e5, maximum IT of 50ms, TopN of 20, normalized collision energy of 30; 3) dd settings: intensity threshold 1.6e5, Minimum AGC target 8.00e3, dynamic exclusion for 15s. Raw files were processed with Thermo Proteome Discoverer 2.4 software, utilizing the Sequest search engine and the UniProt Mus musculus fasta database containing only canonical sequences (downloaded on 31/05/2023, including 17,155 reviewed entries). Carbamidomethylation of cysteine was set as a static modification, and oxidation of methionine and oxidation of proline were set as dynamic modifications. Two missed cleavage sites, a precursor mass tolerance of 5ppm, and fragment mass tolerance of 0.05Da were allowed. Feature mapper node was run with default settings.
DOI: 10.6084/m9.figshare.22608340
title: Additional file 1 of Characterization and identification of the powdery mildew resistance gene in wheat breeding line ShiCG15–009

description: Additional file 1: Table S1. The virulence frequency of Blumeria graminis f. sp. tritici (Bgt) isolates E09, E31 and E20.
DOI: 10.6084/m9.figshare.22608398
title: Additional file 8 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 8: Table 6. Age-synchronous and age-inverse regenerative DMRs.
DOI: 10.6084/m9.figshare.22608380
title: Additional file 3 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 3: Table 1. Aging differentially methylated regions (DMRs) identified by comparing between 16-m/o (A16), 8-m/o (A8), and/or 2-m/o (A2) livers (n = 4 for each group). DNA methylation data for individual aging samples are available in GEO (GSE211999).
DOI: 10.6084/m9.figshare.22608380.v1
title: Additional file 3 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 3: Table 1. Aging differentially methylated regions (DMRs) identified by comparing between 16-m/o (A16), 8-m/o (A8), and/or 2-m/o (A2) livers (n = 4 for each group). DNA methylation data for individual aging samples are available in GEO (GSE211999).
DOI: 10.6084/m9.figshare.22608386
title: Additional file 4 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 4: Table 2. Four distinct subsets of aging DMRs based on their changing patterns from 2-to-8 m/o and from 8-to-16 m/o, including those found: (1) only in the 2-to-8-m/o paradigm (early single), (2) only in the 8-16-m/o paradigm (late single), (3) in both 2-to-8-m/o and 8-to-16-m/o paradigms in the same (progressive) direction, and (4) in both paradigms in opposite (inverse) directions. Associated genes were mapped by the DMR locations in their promoter and/or gene body regions.
DOI: 10.21227/39bc-dg24
title: CEMI-GAT

description: This work selects two real datasets, namely Diginetica and Yoochoose. Diginetica is employed in CIKM Cup 2016, which contains user's transaction data. Yoochoose is released in Recsys Challenge 2015 as a public dataset and mainly consists of click data within six months. For better recommendation, we follow previous work and preprocess the real datasets.
DOI: 10.6084/m9.figshare.22608389
title: Additional file 5 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 5: Table 3. Regenerative DMRs by comparing regenerating livers at 1d (R1), 2d (R2), and 4d (R4) after 70% partial hepatectomy (PHx) to pre-surgical livers (R0) (n = 4 for each group). DNA methylation data for individual regeneration samples are available in GEO (GSE211999).
DOI: 10.6084/m9.figshare.22608389.v1
title: Additional file 5 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 5: Table 3. Regenerative DMRs by comparing regenerating livers at 1d (R1), 2d (R2), and 4d (R4) after 70% partial hepatectomy (PHx) to pre-surgical livers (R0) (n = 4 for each group). DNA methylation data for individual regeneration samples are available in GEO (GSE211999).
DOI: 10.6084/m9.figshare.22608395
title: Additional file 7 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 7: Table 5. Mapping of regenerative DMRs to the promoter regions (-7kB to 3kB of transcriptional start site) of differentially expressed genes (DEGs) during PHx-induced liver regeneration. Hypo-DMRs were mapped to up-DEGs and hyper-DMRs were mapped to down-DEGs.
DOI: 10.6084/m9.figshare.22608392
title: Additional file 6 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 6: Table 4. Regenerative DMRs identified at single timepoints (1d, 2d, or 4d) or shared by two or more timepoints during liver regeneration induced by PHx).
DOI: 10.6084/m9.figshare.22608401
title: Additional file 9 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 9: Table 7. Mapping of age-inverse regenerative DMRs to the promoter (TSS7k3k) and gene body (gBody) regions and age-synchronous regenerative DMRs to the promoter regions (TSS7k3k) of genes.
DOI: 10.6084/m9.figshare.16841270.v1
title: Additional file 2 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 2: Table S2. GO enrichment analysis of all differential expression gene in B. cinerea.
DOI: 10.6084/m9.figshare.22608392.v1
title: Additional file 6 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 6: Table 4. Regenerative DMRs identified at single timepoints (1d, 2d, or 4d) or shared by two or more timepoints during liver regeneration induced by PHx).
DOI: 10.6084/m9.figshare.22608395.v1
title: Additional file 7 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 7: Table 5. Mapping of regenerative DMRs to the promoter regions (-7kB to 3kB of transcriptional start site) of differentially expressed genes (DEGs) during PHx-induced liver regeneration. Hypo-DMRs were mapped to up-DEGs and hyper-DMRs were mapped to down-DEGs.
DOI: 10.6084/m9.figshare.22608386.v1
title: Additional file 4 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 4: Table 2. Four distinct subsets of aging DMRs based on their changing patterns from 2-to-8 m/o and from 8-to-16 m/o, including those found: (1) only in the 2-to-8-m/o paradigm (early single), (2) only in the 8-16-m/o paradigm (late single), (3) in both 2-to-8-m/o and 8-to-16-m/o paradigms in the same (progressive) direction, and (4) in both paradigms in opposite (inverse) directions. Associated genes were mapped by the DMR locations in their promoter and/or gene body regions.
DOI: 10.6084/m9.figshare.22608401.v1
title: Additional file 9 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 9: Table 7. Mapping of age-inverse regenerative DMRs to the promoter (TSS7k3k) and gene body (gBody) regions and age-synchronous regenerative DMRs to the promoter regions (TSS7k3k) of genes.
DOI: 10.6084/m9.figshare.16841279.v1
title: Additional file 5 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 5: Table S5. Clustering of all differential expression gene in C. sativus.
DOI: 10.6084/m9.figshare.22608398.v1
title: Additional file 8 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 8: Table 6. Age-synchronous and age-inverse regenerative DMRs.
DOI: 10.6084/m9.figshare.22608404.v1
title: Additional file 10 of Epigenome-wide analysis of aging effects on liver regeneration

description: Additional file 10: Table 8. Mapping of aging DMRs to the promoter regions (TSS7k3k) of regenerative DEGs in both synchronous (hyper-DMRs to down-DEGs; hypo-DMRs to up-DEGs) and inverse (hyper-DMRs to up-DEGs or hypo-DMRs to down-DEGs) patterns.
DOI: 10.6084/m9.figshare.16841267.v1
title: Additional file 1 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 1: Table S1. GO enrichment analysis of all differential expression gene in C. sativus.
DOI: 10.5281/zenodo.10625891
title: Dataset related to article: Case report: SLC6A1 mutations presenting with isolated absence seizures: description of 2 novel cases.

description: Genetic Analysis
DOI: 10.5281/zenodo.10625892
title: Dataset related to article: Case report: SLC6A1 mutations presenting with isolated absence seizures: description of 2 novel cases.

description: Genetic Analysis
DOI: 10.6084/m9.figshare.16841282
title: Additional file 6 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 6: Table S6. Clustering of all differential expression gene in B. cinerea.
DOI: 10.6084/m9.figshare.16841282.v1
title: Additional file 6 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 6: Table S6. Clustering of all differential expression gene in B. cinerea.
DOI: 10.6084/m9.figshare.16841270
title: Additional file 2 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 2: Table S2. GO enrichment analysis of all differential expression gene in B. cinerea.
DOI: 10.6084/m9.figshare.16841279
title: Additional file 5 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 5: Table S5. Clustering of all differential expression gene in C. sativus.
DOI: 10.5066/p13nh4bj
title: Louisiana Outer Coast Restoration Project – 2022 habitat map, Whiskey Island

description: This data release includes 2022 data for the Louisiana Outer Coast Restoration Project for Whiskey Island. Specifically, this data release includes a detailed habitat map, general habitat map, and georeferenced imagery. These habitat maps are developed using the methods and classification scheme from Louisiana Coastal Protection and Restoration Authority’s (CPRA) Barrier Island Comprehensive Monitoring (BICM) program. For more details on BICM habitat classes, see the Entity and Attribute Information section of the metadata. Please consult the accompanying readME.txt file for information and recommendations on the contents of this dataset (that is, dataset and recommended symbology). For more information about BICM habitat mapping, see Enwright and others (2020).

References:
Enwright, N.M., SooHoo, W.M., Dugas, J.L., Conzelmann, C.P., Laurenzano, C., Lee, D.M., Mouton, K., and Stelly, S.J., 2020, Louisiana Barrier Island Comprehensive Monitoring Program—Mapping habitats in beach, dune, and intertidal environments along the Louisiana Gulf of Mexico shoreline, 2008 and 2015–16: U.S. Geological Survey Open-File Report 2020–1030, 57 p., https://doi.org/10.3133/ofr20201030.
DOI: 10.6084/m9.figshare.12122757.v3
title: Molecular investigation of infection sources and transmission chains of brucellosis in Zhejiang, China

description: In the present study, a total of 7793 samples from 5 different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously from 2004 to 2018. A total of 118 <i>Brucella</i> strains containing 4 biotypes were obtained, including <i>Brucella melitensis</i> bv.1 (<i>n</i> = 8) and bv.3 (<i>n</i> = 106), <i>Brucella abortus</i> bv.3 (<i>n</i> = 3) and bv.7 (<i>n</i> = 1). Twenty-one shared MLVA-16 genotypes, each composed of 2 to 19 strains obtained from different hosts, suggest the occurrence of a brucellosis outbreak epidemic with multiple source points and laboratory infection events. Moreover, 30 shared MLVA-16 genotypes were observed among 59.6% (68/114) <i>B. melitensis</i> isolates from Zhejiang and strains from other 21 different provinces, especially northern provinces, China. The analysis highlighted the imported nature of the strains from all over the northern provinces with a dominant part from the developed areas of animal husbandry. These data revealed a potential transmission pattern of brucellosis in this region, due to introduced infected sheep leading to a brucellosis outbreak epidemic, and eventually causing multiple laboratory infection events. It is urgent to strengthen the inspection and quarantine of the introduced animals.
DOI: 10.6084/m9.figshare.12122757
title: Molecular investigation of infection sources and transmission chains of brucellosis in Zhejiang, China

description: In the present study, a total of 7793 samples from 5 different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously from 2004 to 2018. A total of 118 <i>Brucella</i> strains containing 4 biotypes were obtained, including <i>Brucella melitensis</i> bv.1 (<i>n</i> = 8) and bv.3 (<i>n</i> = 106), <i>Brucella abortus</i> bv.3 (<i>n</i> = 3) and bv.7 (<i>n</i> = 1). Twenty-one shared MLVA-16 genotypes, each composed of 2 to 19 strains obtained from different hosts, suggest the occurrence of a brucellosis outbreak epidemic with multiple source points and laboratory infection events. Moreover, 30 shared MLVA-16 genotypes were observed among 59.6% (68/114) <i>B. melitensis</i> isolates from Zhejiang and strains from other 21 different provinces, especially northern provinces, China. The analysis highlighted the imported nature of the strains from all over the northern provinces with a dominant part from the developed areas of animal husbandry. These data revealed a potential transmission pattern of brucellosis in this region, due to introduced infected sheep leading to a brucellosis outbreak epidemic, and eventually causing multiple laboratory infection events. It is urgent to strengthen the inspection and quarantine of the introduced animals.
DOI: 10.6084/m9.figshare.16841267
title: Additional file 1 of Transcriptional differentiation driving Cucumis sativus–Botrytis cinerea interactions based on the Skellam model and Bayesian networks

description: Additional file 1: Table S1. GO enrichment analysis of all differential expression gene in C. sativus.
DOI: 10.6084/m9.figshare.22608391.v1
title: Additional file 7 of Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

description: Additional file 7: Table S3. The GenBank information of the chloroplast genes used in inferring the Eriocaulon phylogeny.
DOI: 10.6084/m9.figshare.12122757.v1
title: Molecular investigation of infection sources and transmission chains of brucellosis in Zhejiang, China

description: In the present study, a total of 7,793 samples from five different types of hosts were collected and tested, with a seroprevalence of 2.4% (184/7,793). Although the seroprevalence of human and animal brucellosis is relatively low, numbers of human brucellosis cases reported have increased continuously from 2004 to 2018. A total of 118 <i>Brucella</i> strains containing four biotypes were obtained, including <i>Brucella melitensis</i> bv.1 (n = 8) and bv.3 (n = 106), <i>Brucella abortus</i> bv.3 (n = 3) and bv.7 (n = 1). Both <i>B. abortus</i> bv.3 and bv.7 were first reported to have been obtained from humans in recent years. <i>B. melitensis</i> was obtained from dogs, sheep blood (food), and laboratory staff members, suggesting that <i>B. melitensis</i> is a crucial threat to the occupational population. Twenty-one shared genotypes, each composed of two to nineteen strains obtained from different hosts, suggest the occurrence of a brucellosis outbreak epidemic with multiple source points and laboratory infection events. Moreover, 30 shared MLVA-16 genotypes were observed among 59.6% (68/114) <i>B. melitensis</i> isolates from Zhejiang and strains from other 21 different provinces, especially northern provinces, China. The analysis highlighted the imported nature of the strains from all over the northern provinces with a dominant part from the developed areas of animal husbandry. These data revealed a potential transmission pattern of brucellosis in this region, due to introduced infected sheep leading to a brucellosis outbreak epidemic, and eventually causing multiple laboratory infection events. It is urgent to strengthen the inspection and quarantine of the introduced animals.
DOI: 10.6084/m9.figshare.22604917
title: Additional file 2 of Molecular and physiological mechanisms of tea (Camellia sinensis (L.) O. Kuntze) leaf and root in response to nitrogen deficiency

description: Additional file 2: Table S2. Up-regulated DEGs in response to N deficiency in tea leaf and root.
DOI: 10.6084/m9.figshare.22604914
title: Additional file 1 of Molecular and physiological mechanisms of tea (Camellia sinensis (L.) O. Kuntze) leaf and root in response to nitrogen deficiency

description: Additional file 1: Table S1. Down-regulated DEGs in response to N deficiency in tea leaf and root.