cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14445058.v1
title: Additional file 1 of In vitro anti‐bacterial activity and network pharmacology analysis of Sanguisorba officinalis L. against Helicobacter pylori infection

description: Additional file 1: Table S1. Corresponding targets of 8 active ingredients in S. officinalis. Table S2. GO analysis for potential targets, BP, Biological process, CC, Cellular components, MF, Molecular function. Table S3. KEGG pathway enrichment analysis.
DOI: 10.25549/one-ouc17551624
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.8157452.v1
title: MOESM2 of Predicting the regrowth of clinically non-functioning pituitary adenoma with a statistical model

description: Additional file 2: Table S2. P values of 41 tumour related proteins in differential and Kaplanâ Meier analyses.
DOI: 10.25549/one-ouc17551633
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.7109315
title: MOESM2 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 2: Table S2. Amplicon primers designed for the WGS hotspot mutation (WHM) panel.
DOI: 10.6084/m9.figshare.7109342
title: MOESM4 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 4: Table S4. Amplicon primers designed for the CHM panel.
DOI: 10.6084/m9.figshare.7109357
title: MOESM5 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 5: Table S5. The WHM panel of hotspots identified by whole-genome sequencing (WGS).
DOI: 10.6084/m9.figshare.7109378
title: MOESM6 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 6: Table S6. Definition of case groups and permutation groups.
DOI: 10.6084/m9.figshare.7109342.v1
title: MOESM4 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 4: Table S4. Amplicon primers designed for the CHM panel.
DOI: 10.6084/m9.figshare.8157434.v1
title: Additional file 4: of RNA-seq data reveals a coordinated regulation mechanism of multigenes involved in the high accumulation of palmitoleic acid and oil in sea buckthorn berry pulp

description: Table S4. Differentially expressed genes for each of the 16 pairwise comparison groups. (XLSX 3263 kb)
DOI: 10.6084/m9.figshare.8157452
title: MOESM2 of Predicting the regrowth of clinically non-functioning pituitary adenoma with a statistical model

description: Additional file 2: Table S2. P values of 41 tumour related proteins in differential and Kaplanâ Meier analyses.
DOI: 10.25549/one-ouc17551625
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)
DOI: 10.6084/m9.figshare.7109357.v1
title: MOESM5 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 5: Table S5. The WHM panel of hotspots identified by whole-genome sequencing (WGS).
DOI: 10.6084/m9.figshare.7109408
title: Additional file 3: of Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes

description: This file contains all molybdoprotein sequences analyzed in this study. (TXT 32763 kb)
DOI: 10.6084/m9.figshare.8157416.v1
title: Additional file 2: of RNA-seq data reveals a coordinated regulation mechanism of multigenes involved in the high accumulation of palmitoleic acid and oil in sea buckthorn berry pulp

description: Table S2. FA composition in sea buckthorn berry pulp from lines ‘Za56’ and ‘TF2–36’ at four developmental stages. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7109378.v1
title: MOESM6 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 6: Table S6. Definition of case groups and permutation groups.
DOI: 10.6084/m9.figshare.7109408.v1
title: Additional file 3: of Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes

description: This file contains all molybdoprotein sequences analyzed in this study. (TXT 32763 kb)
DOI: 10.25549/one-ouc17551630
title: Mattachine Society, correspondence, Dale Olson (1954-1956)
DOI: 10.6084/m9.figshare.7109327.v1
title: MOESM3 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 3: Table S3. Targeted genes and mutations in the cancer hotspot mutation (CHM) panel.
DOI: 10.6084/m9.figshare.7109471
title: Additional file 3: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Single copy genes in six phytoplasmas. (XLS 41 kb)
DOI: 10.6084/m9.figshare.7109375
title: Additional file 2: of Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

description: Corroborating GH expression by methanogens through blasting their genome sequences (download from NCBI database) against dbCAN database. (XLSX 378Â kb)
DOI: 10.6084/m9.figshare.7109375.v1
title: Additional file 2: of Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

description: Corroborating GH expression by methanogens through blasting their genome sequences (download from NCBI database) against dbCAN database. (XLSX 378Â kb)
DOI: 10.6084/m9.figshare.7109456
title: Additional file 2: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: The identity of core genes of the six phytoplasmas (XLS 6 kb)
DOI: 10.6084/m9.figshare.7109456.v1
title: Additional file 2: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: The identity of core genes of the six phytoplasmas (XLS 6 kb)
DOI: 10.25549/one-ouc17555588
title: Mattachine Society, Tay-Bush legal defense fund (1961-1962)
DOI: 10.6084/m9.figshare.7109327
title: MOESM3 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 3: Table S3. Targeted genes and mutations in the cancer hotspot mutation (CHM) panel.
DOI: 10.6084/m9.figshare.12872156.v1
title: Additional file 5 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 5 : Table S5 GO enrichment analysis of the DEGs in C7–2 and C7–2t.
DOI: 10.6084/m9.figshare.7109384
title: Additional file 1: of Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes

description: Table S1. Occurrence of theÂ Mo utilization trait in bacteria. Table S2. Occurrence of theÂ Mo utilization trait in archaea. Table S3. Occurrence of theÂ Mo utilization trait in eukaryotes. Table S4. Distribution of Mo transporters in Mo-utilizing bacteria. Table S5. Distribution of Mo transporters in Mo-utilizing archaea. Table S6. Distribution of Mo transporters in Mo-utilizing eukaryotes. Table S7. List of Mo transporters, Moco biosynthesis components and molybdoproteins. (XLSX 488 kb)
DOI: 10.6084/m9.figshare.5012375.v1
title: w09, a novel autophagy enhancer, induces autophagy-dependent cell apoptosis via activation of the EGFR-mediated RAS-RAF1-MAP2K-MAPK1/3 pathway

description: The EGFR (epidermal growth factor receptor) signaling pathway is frequently deregulated in many malignancies. Therefore, targeting the EGFR pathway is regarded as a promising strategy for anticancer drug discovery. Herein, we identified a 2-amino-nicotinonitrile compound (w09) as a novel autophagy enhancer, which potently induced macroautophagy/autophagy and consequent apoptosis in gastric cancer cells. Mechanistic studies revealed that EGFR-mediated activation of the RAS-RAF1-MAP2K-MAPK1/3 signaling pathway played a critical role in w09-induced autophagy and apoptosis of gastric cancer cells. Inhibition of the MAPK1/3 pathway with U0126 or blockade of autophagy by specific chemical inhibitors markedly attenuated the effect of w09-mediated growth inhibition and caspase-dependent apoptosis. Furthermore, these conclusions were supported by knockdown of <i>ATG5</i> or knockout of <i>ATG5</i> and/or <i>ATG7</i>. Notably, w09 increased the expression of SQSTM1 by transcription, and knockout of <i>SQSTM1</i> or deleting the LC3-interaction region domain of SQSTM1, significantly inhibited w09-induced PARP1 cleavage, suggesting the central role played by SQSTM1 in w09-induced apoptosis. In addition, in vivo administration of w09 effectively inhibited tumor growth of SGC-7901 xenografts. Hence, our findings not only suggested that activation of the EGFR-RAS-RAF1-MAP2K-MAPK1/3 signaling pathway may play a critical role in w09-induced autophagy and apoptosis, but also imply that induction of autophagic cancer cell death through activation of the EGFR pathway may be a potential therapeutic strategy for EGFR-disregulated gastric tumors.
DOI: 10.6084/m9.figshare.7109471.v1
title: Additional file 3: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Single copy genes in six phytoplasmas. (XLS 41 kb)
DOI: 10.25549/one-ouc17551637
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.6084/m9.figshare.7109483
title: Additional file 4: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Annotated CAZymes in jwb-nky. (XLS 1 kb)
DOI: 10.6084/m9.figshare.12872159
title: Additional file 6 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 6 : Table S6 KEGG enrichment analysis of the DEGs in C7–2 and C7–2t.
DOI: 10.6084/m9.figshare.7109447
title: Additional file 1: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Gene annotation of jwb-nky with different databases. (XLS 468 kb)
DOI: 10.25549/one-ouc17551638
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.6084/m9.figshare.7109447.v1
title: Additional file 1: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Gene annotation of jwb-nky with different databases. (XLS 468 kb)
DOI: 10.6084/m9.figshare.22313742
title: Inhibition of Integrin α<sub>v</sub>β<sub>3</sub>-FAK-MAPK signaling constrains the invasion of T-ALL cells

description: The role of adhesion receptor integrin αvβ3 in T-ALL was unclear. Firstly, we performed quantitative real-time PCR to assess medullary expression of integrin β3(ITGB3) in T-ALL patients and high ITGB3 expression was relevant with the central nervous system leukemia(CNSL) incidence. Decreasing of cell invasion was observed in Jurkat and Molt4 treated with integrin αvβ3 specific antibody and inhibitor as well as cells with ITGB3 interference. Further, phosphorylation of FAK, cRAF, MEK and ERK decreased in cells with integrin αvβ3 inhibition or interference. Invasion decreased in T-ALL cells treated with FAK and ERK inhibitors. In conclusion, inhibition of integrin αvβ3 signals significantly limits the cell invasion of T-ALL cells.
DOI: 10.6084/m9.figshare.12872147
title: Additional file 2 of Identification of drought tolerant mechanisms in a drought-tolerant maize mutant based on physiological, biochemical and transcriptomic analyses

description: Additional file 2 : Table S2 The DEGs detected in C7–2 and C7–2t.
DOI: 10.6084/m9.figshare.21789021
title: Divergence and relationships of <i>Cymbidium tortisepalum</i> and its kindred germplasms by EST-SSR markers

description: Molecular marker-based identification of Chinese orchids among species, genera, and hybrids before flowering has important breeding and genetic research value. In this study, the <i>Cymbidium tortisepalum</i> germplasm ‘Lianbansu’ was chosen for transcriptome sequencing, yielding 9,485 putative EST-SSRs discovered from 28,235 unigenes. Then, 192 primers were randomly selected from the designed primers, and 38 pairs of high-quality primers were screened out through experiments. These high-quality markers were used to examine the genetic diversity, population structure, and evolutionary history of 51 orchid germplasms. The number of alleles ranged from 3 to 12, with an average of 6. The observed and expected heterozygosity with an average of 0.4662 and 0.5973. The first two principal coordinates detected 39.66% of the total variation. It was found that the <i>ΔK</i>-value had one peak (When K = 2). Several germplasms of <i>C. tortisepalum</i>, <i>Cymbidium sinense</i>, <i>Cymbidium hybridum</i>, and some interspecific or intergeneric hybrids and unidentified germplasms could be effectively distinguished using these markers. In conclusion, a set of EST-SSR markers with outstanding transferability was created in this study that can be utilised for hybrid parent tracing and germplasm identification of orchids before flowering.
DOI: 10.6084/m9.figshare.7109315.v1
title: MOESM2 of Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

description: Additional file 2: Table S2. Amplicon primers designed for the WGS hotspot mutation (WHM) panel.
DOI: 10.6084/m9.figshare.7109483.v1
title: Additional file 4: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: Annotated CAZymes in jwb-nky. (XLS 1 kb)
DOI: 10.25549/one-ouc17551639
title: Mattachine Society, correspondence, Wallace O. Maxey (1953-1961)
DOI: 10.6084/m9.figshare.7109501.v1
title: Additional file 5: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: 87 putative effectors in JWB phytoplasma genome assigned to Virulence Factor Database. (XLS 32 kb)
DOI: 10.6084/m9.figshare.21789021.v1
title: Divergence and relationships of <i>Cymbidium tortisepalum</i> and its kindred germplasms by EST-SSR markers

description: Molecular marker-based identification of Chinese orchids among species, genera, and hybrids before flowering has important breeding and genetic research value. In this study, the <i>Cymbidium tortisepalum</i> germplasm ‘Lianbansu’ was chosen for transcriptome sequencing, yielding 9,485 putative EST-SSRs discovered from 28,235 unigenes. Then, 192 primers were randomly selected from the designed primers, and 38 pairs of high-quality primers were screened out through experiments. These high-quality markers were used to examine the genetic diversity, population structure, and evolutionary history of 51 orchid germplasms. The number of alleles ranged from 3 to 12, with an average of 6. The observed and expected heterozygosity with an average of 0.4662 and 0.5973. The first two principal coordinates detected 39.66% of the total variation. It was found that the <i>ΔK</i>-value had one peak (When K = 2). Several germplasms of <i>C. tortisepalum</i>, <i>Cymbidium sinense</i>, <i>Cymbidium hybridum</i>, and some interspecific or intergeneric hybrids and unidentified germplasms could be effectively distinguished using these markers. In conclusion, a set of EST-SSR markers with outstanding transferability was created in this study that can be utilised for hybrid parent tracing and germplasm identification of orchids before flowering.
DOI: 10.6084/m9.figshare.7109516
title: Additional file 6: of Comparative genome analysis of jujube witchesâ -broom Phytoplasma, an obligate pathogen that causes jujube witchesâ -broom disease

description: 92 genes in JWB phytoplasma genome assigned to Pathogen Host Interactions Database. (XLS 46 kb)
DOI: 10.6084/m9.figshare.7109384.v1
title: Additional file 1: of Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes

description: Table S1. Occurrence of theÂ Mo utilization trait in bacteria. Table S2. Occurrence of theÂ Mo utilization trait in archaea. Table S3. Occurrence of theÂ Mo utilization trait in eukaryotes. Table S4. Distribution of Mo transporters in Mo-utilizing bacteria. Table S5. Distribution of Mo transporters in Mo-utilizing archaea. Table S6. Distribution of Mo transporters in Mo-utilizing eukaryotes. Table S7. List of Mo transporters, Moco biosynthesis components and molybdoproteins. (XLSX 488 kb)
DOI: 10.25549/one-ouc17551640
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.5281/zenodo.10531986
title: iEPI - 1.2mm - 2shot
DOI: 10.5281/zenodo.10531987
title: iEPI - 1.2mm - 2shot
DOI: 10.6084/m9.figshare.20216669.v1
title: DYNC1LI2 regulates localization of the chaperone-mediated autophagy receptor LAMP2A and improves cellular homeostasis in cystinosis

description: The dynein motor protein complex is required for retrograde transport but the functions of the intermediate-light chains that form the cargo-binding complex are not elucidated and the importance of individual subunits in maintaining cellular homeostasis is unknown. Here, using mRNA arrays and protein analysis, we show that the dynein subunit, DYNC1LI2 (dynein, cytoplasmic 1 light intermediate chain 2) is downregulated in cystinosis, a lysosomal storage disorder caused by genetic defects in CTNS (cystinosin, lysosomal cystine transporter). Reconstitution of DYNC1LI2 expression in <i>ctns</i><sup>-/-</sup> cells reestablished endolysosomal dynamics. Defective vesicular trafficking in cystinotic cells was rescued by DYNC1LI2 expression which correlated with decreased endoplasmic reticulum stress manifested as decreased expression levels of the chaperone HSPA5/GRP78, and the transcription factors ATF4 and DDIT3/CHOP. Mitochondrial fragmentation, membrane potential and endolysosomal-mitochondrial association in cystinotic cells were rescued by DYNC1LI2. Survival of cystinotic cells to oxidative stress was increased by DYNC1LI2 reconstitution but not by its paralog DYNC1LI1, which also failed to decrease ER stress and mitochondrial fragmentation. DYNC1LI2 expression rescued the localization of the chaperone-mediated autophagy (CMA) receptor LAMP2A, CMA activity, cellular homeostasis and LRP2/megalin expression in cystinotic proximal tubule cells, the primary cell type affected in cystinosis. DYNC1LI2 failed to rescue phenotypes in cystinotic cells when LAMP2A was downregulated or when co-expressed with dominant negative (DN) RAB7 or DN-RAB11, which impaired LAMP2A trafficking. DYNC1LI2 emerges as a regulator of cellular homeostasis and potential target to repair underlying trafficking and CMA in cystinosis, a mechanism that is not restored by lysosomal cystine depletion therapies. <b>Abbreviations</b>: ACTB: actin, beta; ATF4: activating transcription factor 4; CMA: chaperone-mediated autophagy; DYNC1LI1: dynein cytoplasmic 1 light intermediate chain 1; DYNC1LI2: dynein cytoplasmic 1 light intermediate chain 2; ER: endoplasmic reticulum; LAMP1: lysosomal associated membrane protein 1; LAMP2A: lysosomal associated membrane protein 2A; LIC: light-intermediate chains; LRP2/Megalin: LDL receptor related protein 2; PTCs: proximal tubule cells; RAB: RAB, member RAS oncogene family; RAB11FIP3: RAB11 family interacting protein 3; RILP: Rab interacting lysosomal protein
DOI: 10.6084/m9.figshare.5012375
title: w09, a novel autophagy enhancer, induces autophagy-dependent cell apoptosis via activation of the EGFR-mediated RAS-RAF1-MAP2K-MAPK1/3 pathway

description: The EGFR (epidermal growth factor receptor) signaling pathway is frequently deregulated in many malignancies. Therefore, targeting the EGFR pathway is regarded as a promising strategy for anticancer drug discovery. Herein, we identified a 2-amino-nicotinonitrile compound (w09) as a novel autophagy enhancer, which potently induced macroautophagy/autophagy and consequent apoptosis in gastric cancer cells. Mechanistic studies revealed that EGFR-mediated activation of the RAS-RAF1-MAP2K-MAPK1/3 signaling pathway played a critical role in w09-induced autophagy and apoptosis of gastric cancer cells. Inhibition of the MAPK1/3 pathway with U0126 or blockade of autophagy by specific chemical inhibitors markedly attenuated the effect of w09-mediated growth inhibition and caspase-dependent apoptosis. Furthermore, these conclusions were supported by knockdown of <i>ATG5</i> or knockout of <i>ATG5</i> and/or <i>ATG7</i>. Notably, w09 increased the expression of SQSTM1 by transcription, and knockout of <i>SQSTM1</i> or deleting the LC3-interaction region domain of SQSTM1, significantly inhibited w09-induced PARP1 cleavage, suggesting the central role played by SQSTM1 in w09-induced apoptosis. In addition, in vivo administration of w09 effectively inhibited tumor growth of SGC-7901 xenografts. Hence, our findings not only suggested that activation of the EGFR-RAS-RAF1-MAP2K-MAPK1/3 signaling pathway may play a critical role in w09-induced autophagy and apoptosis, but also imply that induction of autophagic cancer cell death through activation of the EGFR pathway may be a potential therapeutic strategy for EGFR-disregulated gastric tumors.
DOI: 10.21227/h4dt-c995
title:  GHSL-based China’s Urban Boundaries

description: Accurately defining urban entity boundaries is crucial for analyzing urban expansion trends, understanding the impacts of urbanization on the environment, and planning and achieving sustainable urban development. In recent years, multiple global urban boundary products have emerged. However, cities’ definitions, formation processes, and morphology vary significantly across countries, making it particularly challenging to use a uniform method to delineate urban boundaries. This study proposes a top-down approach to urban boundary identification that considers China’s urban characteristics, ultimately constructing a high-precision GHSL-based China’s urban boundaries (GCUB) dataset for 2000, 2005, 2010, 2015, and 2020.The GCUB dataset outperforms existing urban boundary products in consistency and accuracy, with an impressive overall accuracy rate of 91.65%, effectively delineating urban boundaries across various regions and types within China.
DOI: 10.25549/one-ouc17551643
title: Mattachine Society, correspondence, Donald Stewart Lucas (1956-1965)
DOI: 10.25549/one-ouc17551645
title: Mattachine Society, correspondence, Gonzalo (Tony) Segura, Jr. (1956-1961)