cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.j4kq7p
title: Occurrence Download

description: A dataset containing 560 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is one of (China, Viet Nam, Chinese Taipei, Hong Kong)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Taxus chinensis (Pilg.) Rehd."
 ]
}

 The dataset includes 560 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035622-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3637763_d1.v1
title: Additional file 2: of Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetleâ  plant interface

description: Large supporting tables. (XLSX 344 kb)
DOI: 10.6084/m9.figshare.c.3637748_d1.v1
title: MOESM3 of Development and validation of new glomerular filtration rate predicting models for Chinese patients with type 2 diabetes

description: Additional file 3. A simple EXCEL software to calculate eGFR by ANN3.
DOI: 10.6084/m9.figshare.c.3637727_d11.v1
title: Additional file 11: of High-frequency, precise modification of the tomato genome

description: Annotated sequence of the vector pTC223. (GB 33 kb)
DOI: 10.15468/dl.g73j79
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phocaena crassidens Owen, 1846",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035623-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3637601_d1.v1
title: Additional file 1: of A new mechanism of trastuzumab resistance in gastric cancer: MACC1 promotes the Warburg effect via activation of the PI3K/AKT signaling pathway

description: Figures S1 to S6. Figure S1: The expression of proteins in GC cells and the sequences of ectopic MACC1 and shRNA. Figure S2: The combination of trastuzumab and glycolysis inhibitors synergisticly inhibit glycolysis in HER2 positive GC cells. Figure S3: The combination of trastuzumab and glycolysis inhibitors synergisticly inhibit glycolysis in HER2 positive GC cells. Figure S4: MACC1 enhanced the Warburg effect in vivo. Figure S5: Combination of trastuzumab and oxamate effectively inhibited the Warburg effect in vivo. Figure S6: The apoptosis of indicated cells after treated with Ttzm. (ZIP 38363Â kb)
DOI: 10.6084/m9.figshare.c.3637550_d1.v1
title: Additional file 1: Table S1. of VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams

description: Sample data for the user to upload. Hypergeometric testing was conducted on samples of rat and mouse liver tissue to identify similar transcriptomic profiles [14]. (XLS 189Â kb)
DOI: 10.6084/m9.figshare.c.3637529_d1.v1
title: Additional file 1: of The Klotho gene G-395A polymorphism and metabolic syndrome in very elderly people

description: the SNP data of the study population. (XLS 36Â kb)
DOI: 10.6084/m9.figshare.25425920
title: A library of electrophysiological responses in plants - a model of transversal education and open science

description: Electrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here, we report on an investigation in open science, whereby scientists worked with high school students, faculty, and undergraduates from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of &gt;15 plant species in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response, with a delay of ~ 3-6 s after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ~ 2–9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.
DOI: 10.6084/m9.figshare.25425920.v2
title: A library of electrophysiological responses in plants - a model of transversal education and open science

description: Electrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here, we report on an investigation in open science, whereby scientists worked with high school students, faculty, and undergraduates from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of &gt;15 plant species in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response, with a delay of ~ 3-6 s after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ~ 2–9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.
DOI: 10.6084/m9.figshare.26093454
title: Comparative analysis of geotypic variations in the proteome of <i>Nostoc commune</i>

description: Cyanobacterium <i>Nostoc commune</i> is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of <i>N. commune</i> with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of <i>N. commune</i> from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN <i>N. commune</i>. The last two proteins suggest a more stressful condition in AN <i>N. commune</i>. In summary, our findings highlight biochemical processes that safeguard the AN geotype of <i>N. commune</i> from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of <i>N. commune</i>, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
DOI: 10.6084/m9.figshare.26093454.v1
title: Comparative analysis of geotypic variations in the proteome of <i>Nostoc commune</i>

description: Cyanobacterium <i>Nostoc commune</i> is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of <i>N. commune</i> with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of <i>N. commune</i> from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN <i>N. commune</i>. The last two proteins suggest a more stressful condition in AN <i>N. commune</i>. In summary, our findings highlight biochemical processes that safeguard the AN geotype of <i>N. commune</i> from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of <i>N. commune</i>, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
DOI: 10.6084/m9.figshare.25425920.v1
title: A library of electrophysiological responses in plants - a model of transversal education and open science

description: Electrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here, we report on an investigation in open science, whereby scientists worked with high school students, faculty, and undergraduates from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of &gt;15 plant species in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response, with a delay of ~ 3-6 s after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ~ 2–9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.
DOI: 10.6084/m9.figshare.25790343
title: A pharmacological approach to investigating effector translocation in rice-<i>Magnaporthe</i> oryzae interactions

description: Fungal pathogens deliver effector proteins into living plant cells to suppress plant immunity and control plant processes that are needed for infection. During plant infection, the devastating rice blast fungus, <i>Magnaporthe oryzae</i>, forms the specialized biotrophic interfacial complex (BIC), which is essential for effector translocation. Cytoplasmic effectors are first focally secreted into BICs, and subsequently packaged into dynamic membranous effector compartments (MECs), then translocated via clathrin-mediated endocytosis (CME) into the host cytoplasm. This study demonstrates that clathrin-heavy chain inhibitors endosidin-9 (ES9) and endosidin-9–17 (ES9–17) blocked the internalization of the fluorescently labeled effectors Bas1 and Pwl2 in rice cells, leading to swollen BICs lacking MECs. In contrast, ES9–17 treatment had no impact on the localization pattern of the apoplastic effector Bas4. This study provides further evidence that cytoplasmic effector translocation occurs by CME in BICs, suggesting a potential role for <i>M. oryzae</i> effectors in co-opting plant endocytosis.
DOI: 10.6084/m9.figshare.25790343.v1
title: A pharmacological approach to investigating effector translocation in rice-<i>Magnaporthe</i> oryzae interactions

description: Fungal pathogens deliver effector proteins into living plant cells to suppress plant immunity and control plant processes that are needed for infection. During plant infection, the devastating rice blast fungus, <i>Magnaporthe oryzae</i>, forms the specialized biotrophic interfacial complex (BIC), which is essential for effector translocation. Cytoplasmic effectors are first focally secreted into BICs, and subsequently packaged into dynamic membranous effector compartments (MECs), then translocated via clathrin-mediated endocytosis (CME) into the host cytoplasm. This study demonstrates that clathrin-heavy chain inhibitors endosidin-9 (ES9) and endosidin-9–17 (ES9–17) blocked the internalization of the fluorescently labeled effectors Bas1 and Pwl2 in rice cells, leading to swollen BICs lacking MECs. In contrast, ES9–17 treatment had no impact on the localization pattern of the apoplastic effector Bas4. This study provides further evidence that cytoplasmic effector translocation occurs by CME in BICs, suggesting a potential role for <i>M. oryzae</i> effectors in co-opting plant endocytosis.
DOI: 10.6084/m9.figshare.25955918
title: The 14-3-3 protein nt GF14e interacts with CIPK2 and increases low potassium stress in tobacco

description: Potassium (K<sup>+</sup>) plays a role in enzyme activation, membrane transport, and osmotic regulation processes. An increase in potassium content can significantly improve the elasticity and combustibility of tobacco and reduce the content of harmful substances. Here, we report that the expression analysis of <i>Nt GF14e</i>, a <i>14-3-3</i> gene, increased markedly after low-potassium treatment (LK). Then, chlorophyll content, POD activity and potassium content, were significantly increased in overexpression of <i>Nt GF14e</i> transgenic tobacco lines compared with those in the wild type plants. The net K<sup>+</sup> efflux rates were severely lower in the transgenic plants than in the wild type under LK stress. Furthermore, transcriptome analysis identified 5708 upregulated genes and 2787 downregulated genes between <i>Nt GF14e</i> overexpressing transgenic tobacco plants. The expression levels of some potassium-related genes were increased, such as CBL-interacting protein kinase 2 (<i>CIPK2</i>), <i>Nt CIPK23</i>, <i>Nt CIPK25</i>, H<sup>+</sup>-ATPase isoform 2 <i>a</i> (<i>AHA2a</i>), <i>Nt AHA4a</i>, Stelar K<sup>+</sup> outward rectifier 1(<i>SKOR1</i>), and high affinity K<sup>+</sup> transporter 5 (<i>HAK5</i>). The result of yeast two-hybrid and luciferase complementation imaging experiments suggested Nt GF14e could interact with CIPK2. Overall, these findings indicate that NtGF14e plays a vital roles in improving tobacco LK tolerance and enhancing potassium nutrition signaling pathways in tobacco plants.
DOI: 10.6084/m9.figshare.25955918.v1
title: The 14-3-3 protein nt GF14e interacts with CIPK2 and increases low potassium stress in tobacco

description: Potassium (K<sup>+</sup>) plays a role in enzyme activation, membrane transport, and osmotic regulation processes. An increase in potassium content can significantly improve the elasticity and combustibility of tobacco and reduce the content of harmful substances. Here, we report that the expression analysis of <i>Nt GF14e</i>, a <i>14-3-3</i> gene, increased markedly after low-potassium treatment (LK). Then, chlorophyll content, POD activity and potassium content, were significantly increased in overexpression of <i>Nt GF14e</i> transgenic tobacco lines compared with those in the wild type plants. The net K<sup>+</sup> efflux rates were severely lower in the transgenic plants than in the wild type under LK stress. Furthermore, transcriptome analysis identified 5708 upregulated genes and 2787 downregulated genes between <i>Nt GF14e</i> overexpressing transgenic tobacco plants. The expression levels of some potassium-related genes were increased, such as CBL-interacting protein kinase 2 (<i>CIPK2</i>), <i>Nt CIPK23</i>, <i>Nt CIPK25</i>, H<sup>+</sup>-ATPase isoform 2 <i>a</i> (<i>AHA2a</i>), <i>Nt AHA4a</i>, Stelar K<sup>+</sup> outward rectifier 1(<i>SKOR1</i>), and high affinity K<sup>+</sup> transporter 5 (<i>HAK5</i>). The result of yeast two-hybrid and luciferase complementation imaging experiments suggested Nt GF14e could interact with CIPK2. Overall, these findings indicate that NtGF14e plays a vital roles in improving tobacco LK tolerance and enhancing potassium nutrition signaling pathways in tobacco plants.
DOI: 10.6084/m9.figshare.25513847
title: Harsh environmental conditions promote cooperative behavior in an epiphytic fern

description: Harsh, unpredictable environments are known to favor cooperative groups in animals. Whether plants exhibit similar relationships is unknown. Staghorn ferns (<i>Platycerium bifurcatum</i>, Polypodiaceae) are epiphytes that form cooperative groups which build communal water and nutrient ‘nests’ at the tops of trees, a habitat characterized by water and nutrient stress. We conducted field observations to test whether staghorn ferns continue to live in large, reproductively active groups after they become dislodged from the canopy and fall to the forest floor, where they are less limited by water and nutrient deprivation. To rule out the potentially confounding effects of light limitation on the forest floor, we also conducted a multi-year glasshouse experiment where we transplanted individual plants into soil and onto vertically oriented boards under standardized light conditions. Results from field observations showed that dislodged colonies formed smaller groups that reproduced less than epiphytic colonies. Results from the glasshouse experiment showed that even when growing in full sun, terrestrial individuals tended to remain solitary, while epiphytic individuals tended to recruit new individuals into colonies. Results also showed that plants growing in potting soil and exposed to full sunlight sporulated more heavily than plants growing epiphytically. However, localities that are characterized by both elevated soil and light resources are generally not available to staghorn ferns in the wild, perhaps with the exception of large, epiphytic colonies with well-developed nests at the top of tree canopies. Overall results indicate that the harsh environmental conditions at the tops of trees trigger the formation of colonies in staghorn ferns, similarly to group living animals.
DOI: 10.6084/m9.figshare.25513847.v1
title: Harsh environmental conditions promote cooperative behavior in an epiphytic fern

description: Harsh, unpredictable environments are known to favor cooperative groups in animals. Whether plants exhibit similar relationships is unknown. Staghorn ferns (<i>Platycerium bifurcatum</i>, Polypodiaceae) are epiphytes that form cooperative groups which build communal water and nutrient ‘nests’ at the tops of trees, a habitat characterized by water and nutrient stress. We conducted field observations to test whether staghorn ferns continue to live in large, reproductively active groups after they become dislodged from the canopy and fall to the forest floor, where they are less limited by water and nutrient deprivation. To rule out the potentially confounding effects of light limitation on the forest floor, we also conducted a multi-year glasshouse experiment where we transplanted individual plants into soil and onto vertically oriented boards under standardized light conditions. Results from field observations showed that dislodged colonies formed smaller groups that reproduced less than epiphytic colonies. Results from the glasshouse experiment showed that even when growing in full sun, terrestrial individuals tended to remain solitary, while epiphytic individuals tended to recruit new individuals into colonies. Results also showed that plants growing in potting soil and exposed to full sunlight sporulated more heavily than plants growing epiphytically. However, localities that are characterized by both elevated soil and light resources are generally not available to staghorn ferns in the wild, perhaps with the exception of large, epiphytic colonies with well-developed nests at the top of tree canopies. Overall results indicate that the harsh environmental conditions at the tops of trees trigger the formation of colonies in staghorn ferns, similarly to group living animals.
DOI: 10.6084/m9.figshare.26539235.v1
title: Requirement of two simultaneous environmental signals for activation of Arabidopsis <i>ELIP2</i> promoter in response to high light, cold, and UV-B stresses

description: Arabidopsis EARLY LIGH-INDUCIBLE PROTEIN 2 (ELIP2) is a chlorophyll- and carotenoid-binding protein and is involved in photoprotection under stress conditions. Because its expression is induced through high light, cold, or UV-B stressors, its mechanism of induction has been studied. It is known that a functional unit found in the promoter, which is composed of Element B and Element A, is required and sufficient for full activation by these stressors. In this study, the role of each element in the unit was analyzed by introducing weak mutations in each element as synthetic promoters in addition to intensive repeat constructs of each single element. The results suggest that a stressor like cold stress generates two parallel signals in plant cells, and they merge at the promoter region for the activation of <i>ELIP2</i> expression, which constitutes an “AND” gate and has a potential to realize strong response with high specificity by an environmental trigger.
DOI: 10.6084/m9.figshare.26067997
title: Views and perspectives on the indoleamines serotonin and melatonin in plants: past, present and future

description: In the decades since their discovery in plants in the mid-to-late 1900s, melatonin (<i>N</i>-acetyl-5-methoxytryptamine) and serotonin (5-methoxytryptamine) have been established as their own class of phytohormone and have become popular targets for examination and study as stress ameliorating compounds. The indoleamines play roles across the plant life cycle from reproduction to morphogenesis and plant environmental perception. There is growing interest in harnessing the power of these plant neurotransmitters in applied and agricultural settings, particularly as we face increasingly volatile climates for food production; however, there is still a lot to learn about the mechanisms of indoleamine action in plants. A recent explosion of interest in these compounds has led to exponential growth in the field of melatonin research in particular. This concept paper aims to summarize the current status of indoleamine research and highlight some emerging trends.
DOI: 10.6084/m9.figshare.26067997.v1
title: Views and perspectives on the indoleamines serotonin and melatonin in plants: past, present and future

description: In the decades since their discovery in plants in the mid-to-late 1900s, melatonin (<i>N</i>-acetyl-5-methoxytryptamine) and serotonin (5-methoxytryptamine) have been established as their own class of phytohormone and have become popular targets for examination and study as stress ameliorating compounds. The indoleamines play roles across the plant life cycle from reproduction to morphogenesis and plant environmental perception. There is growing interest in harnessing the power of these plant neurotransmitters in applied and agricultural settings, particularly as we face increasingly volatile climates for food production; however, there is still a lot to learn about the mechanisms of indoleamine action in plants. A recent explosion of interest in these compounds has led to exponential growth in the field of melatonin research in particular. This concept paper aims to summarize the current status of indoleamine research and highlight some emerging trends.