cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19161956.v2
title: Regulation of phenylpropanoid metabolism during moderate freezing and post-freezing recovery in <i>Dendrobium ofﬁcinale</i>

description: Freezing injury is a major environmental limiting factor affecting plant yield and geographical distribution. Little is known about the regulation of phenylpropanoid metabolism during freezing (FT) and post-freezing recovery (FR). <i>Dendrobium ofﬁcinale</i> is a valuable medicinal plant and hypersensitive to low temperature, especially freezing in winter. Here, we used metabolomics and transcriptomics analyses to reveal the regulation of of phenylpropanoid metabolism during FT and FR in <i>D. ofﬁcinale</i>. Most anthocyanin and flavonol signiﬁcantly increased during FR, including quercetin 3-O-glucoside (Q3G) and cyanidin 3-O-sophoroside (C3S) increased 104.6-fold and 66.8-fold in FR vs. CK. Transcriptomics analyses revealed the expression levels of <i>flavonoid 3′- hydroxylase</i> (<i>F3`H</i>) and <i>ﬂavonol synthase</i> (<i>FLS</i>), which were related to an increase in quercetin derivatives. Six phytohormone-related GO terms were enriched during FT and FR. Four genes were significantly affected by FT and FR, including <i>MYB97</i>, <i>MYB39</i>, <i>fructosyltransferase</i>, and <i>zinc finger</i> transcript factor. Four GA response-related genes, <i>2-oxoglutarate-dependent dioxygenases</i>, were specially induced during freezing stress. Moreover, jasmonic acid (JA) and salicylic acid (SA) were significantly increased during FT, and only SA decreased during FR. This study provided understanding of phenylpropanoid metabolism under freezing stress and will be useful for enhancing freezing tolerance <i>via</i> molecular breeding in <i>D. officinale</i>.
DOI: 10.6084/m9.figshare.19705596
title: Constitutive expression of <i>SlMX1</i> gene improves fruit yield and quality, health-promoting compounds, fungal resistance and delays ripening in transgenic tomato plants

description: Tomato is one of the major economically domesticated crops, and it is extensively used in different ways and purposes worldwide. Cell metabolism is the central core of all the biological processes to sustain life including cell growth, differentiation, maintenance, and response to environmental stress. To evaluate how genetic engineering can improve tomato fruit metabolome, the transcriptomic and metabolomic datasets of two transgenic tomatoes (<i>SlMX1</i> overexpression and RNAi lines) have been compared with wild-type. The combined results demonstrated that the constitutive expression of <i>SlMX1</i> not only increased trichome formation, carotenoids, and terpenoids as has been stated in several studies, but has also up- and down-regulated the expression of multiple genes related to cell growth (cell wall turnover), primary (carbohydrates, vitamins, and phytohormones), and secondary (phenylpropanoids, carotenoids, and terpenoids) metabolism, cell signaling, and stress responses. These changes in gene expression due to the constitutive expression of <i>SlMX1</i> promote the most important agroeconomic traits such as fruit yield and quality, biosynthesis of health-promoting phytochemicals (including phenolic acids, flavonoids, and anthocyanins), and finally, activate resistance to <i>Botrytis cinerea</i> and repress the expression of over-ripening-related genes, thus extending the fruit shelf-life. In conclusion, the traits improvement achieved by <i>SlMX1</i> overexpression can be harnessed in molecular breeding programs to engineer fruit size and yield, induce health-promoting secondary metabolites, promote fungal resistance, and finally extend the fruit shelf-life.
DOI: 10.6084/m9.figshare.20624797
title: Phosphoproteome analysis reveals chitosan-induced resistance to osmotic stress in rice (<i>Oryza sativa</i> L.) seedlings

description: This study sought to identify the mechanism underlying the response to chitosan at the posttranslational level. Khao Dawk Mali 105 seeds were soaked in 40 mg l<sup>−1</sup> of chitosan, and leaves of 2- and 4-week-old seedlings were sprayed with chitosan before starting osmotic stress conditions. Chitosan induced resistance to osmotic stress by enhancing shoot fresh and dry weights and maintained increased photosynthetic pigments. Leaf phosphoproteomes were examined using gel-free LC-MS/MS. Of the 60 phosphoproteins showed a significant difference in protein expressions under osmotically-stressed plants treated with chitosan. More than 40% of the phosphoproteins involved in signaling pathways, including OsCML12 calmodulin-related calcium sensor protein, ubiquitin carboxyl-terminal hydrolase 15, U-box domain-containing protein 45, HEAT repeat family protein, BRCA1 C terminus domain-containing protein, pectinesterase, protein kinase domain-containing protein, and receptor-like protein kinase. Chitosan enhanced rice seedling growth and drought resistance via multiple complex networks, including metabolism, transport, transcription, and signaling under osmotic stress.
DOI: 10.6084/m9.figshare.20624797.v1
title: Phosphoproteome analysis reveals chitosan-induced resistance to osmotic stress in rice (<i>Oryza sativa</i> L.) seedlings

description: This study sought to identify the mechanism underlying the response to chitosan at the posttranslational level. Khao Dawk Mali 105 seeds were soaked in 40 mg l<sup>−1</sup> of chitosan, and leaves of 2- and 4-week-old seedlings were sprayed with chitosan before starting osmotic stress conditions. Chitosan induced resistance to osmotic stress by enhancing shoot fresh and dry weights and maintained increased photosynthetic pigments. Leaf phosphoproteomes were examined using gel-free LC-MS/MS. Of the 60 phosphoproteins showed a significant difference in protein expressions under osmotically-stressed plants treated with chitosan. More than 40% of the phosphoproteins involved in signaling pathways, including OsCML12 calmodulin-related calcium sensor protein, ubiquitin carboxyl-terminal hydrolase 15, U-box domain-containing protein 45, HEAT repeat family protein, BRCA1 C terminus domain-containing protein, pectinesterase, protein kinase domain-containing protein, and receptor-like protein kinase. Chitosan enhanced rice seedling growth and drought resistance via multiple complex networks, including metabolism, transport, transcription, and signaling under osmotic stress.
DOI: 10.6084/m9.figshare.19161956
title: Regulation of phenylpropanoid metabolism during moderate freezing and post-freezing recovery in <i>Dendrobium ofﬁcinale</i>

description: Freezing injury is a major environmental limiting factor affecting plant yield and geographical distribution. Little is known about the regulation of phenylpropanoid metabolism during freezing (FT) and post-freezing recovery (FR). <i>Dendrobium ofﬁcinale</i> is a valuable medicinal plant and hypersensitive to low temperature, especially freezing in winter. Here, we used metabolomics and transcriptomics analyses to reveal the regulation of of phenylpropanoid metabolism during FT and FR in <i>D. ofﬁcinale</i>. Most anthocyanin and flavonol signiﬁcantly increased during FR, including quercetin 3-O-glucoside (Q3G) and cyanidin 3-O-sophoroside (C3S) increased 104.6-fold and 66.8-fold in FR vs. CK. Transcriptomics analyses revealed the expression levels of <i>flavonoid 3′- hydroxylase</i> (<i>F3`H</i>) and <i>ﬂavonol synthase</i> (<i>FLS</i>), which were related to an increase in quercetin derivatives. Six phytohormone-related GO terms were enriched during FT and FR. Four genes were significantly affected by FT and FR, including <i>MYB97</i>, <i>MYB39</i>, <i>fructosyltransferase</i>, and <i>zinc finger</i> transcript factor. Four GA response-related genes, <i>2-oxoglutarate-dependent dioxygenases</i>, were specially induced during freezing stress. Moreover, jasmonic acid (JA) and salicylic acid (SA) were significantly increased during FT, and only SA decreased during FR. This study provided understanding of phenylpropanoid metabolism under freezing stress and will be useful for enhancing freezing tolerance <i>via</i> molecular breeding in <i>D. officinale</i>.
DOI: 10.6084/m9.figshare.21591171
title: Physiological and transcriptomic analysis of antioxidant mechanisms in sweet sorghum seedling leaves in response to single and combined drought and salinity stress

description: The effects of drought, salinity, and combined stress on ROS and ROS metabolic physiology and transcriptomics in sweet sorghum seedling leaves were evaluated. The results showed that drought stress had little effect on photosynthesis, while the SOD activity, CAT activity, and the expression of their related genes were elevated in leaves, but no excessive accumulation of O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub>, or -OH was observed. Under salinity stress, photosynthesis was inhibited, the O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub> and -OH contents increased significantly, and the SOD, POD, CAT activities and the expression of their related genes in leaves were elevated. Under combined stress, photosynthesis was significantly inhibited, the highest accumulation of O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub> and -OH contents occurred, and the SOD and POD activities and the expression of related genes in leaves were significantly increased, but the CAT was significantly decreased. These results collectively indicate that oxidative damage to sweet sorghum seedling leaves was higher with combined stress than with either drought or salinity stress alone. Under combined stress the SOD and POD activities were increased, but the CAT activity in the AsA-GSH cycle was severely reduced, demonstrating that antioxidant mechanisms in seedlings did not play a normal protective role, leaving the plants severely damaged by oxidative stress. <b>Abbreviations:</b> AsA: Ascorbic acid; APX: Ascorbate peroxidase; CAT: Catalase; Chl a: Chlorophyll a; Chl b: Chlorophyll b; Ci: Intercellular CO2 concentration; DHAR: Dehydroascorbate reductase; DEGs: Differentially expressed genes; DW: Dry weight; ETR: Photosynthetic electron transport rate; FW: Fresh weight; Fv/Fm: Original light energy conversion efficiency; GPX: Glutathione peroxidase; GR: Glutathione reductase; Gs: Stomatal conductance; GSH: Oxidized glutathione; H2O2: Hydrogen peroxide; MDA: Malondialdehyde; MDHAR: Monodehydroascorbate reductase; O2-: Superoxide anion; PCA: Principal component analysis; PCD: Programed cell death; PEG-6000: Polyethylene glycol 6000; POD: Peroxidase; Pn: Photosynthetic rate; Pro: Proline; qRT–PCR: Quantitative real-time PCR; RNA-seq: RNA Sequencing; ROS: Reactive oxygen species; RWC: Relative water content; RMP: Relative membrane permeability; SOD: Superoxide dismutase; SW: Saturation weight; Tr: Transpiration rate; ΦPSII: Actual photochemical efficiency; -OH: Hydroxyl radical
DOI: 10.6084/m9.figshare.21591171.v1
title: Physiological and transcriptomic analysis of antioxidant mechanisms in sweet sorghum seedling leaves in response to single and combined drought and salinity stress

description: The effects of drought, salinity, and combined stress on ROS and ROS metabolic physiology and transcriptomics in sweet sorghum seedling leaves were evaluated. The results showed that drought stress had little effect on photosynthesis, while the SOD activity, CAT activity, and the expression of their related genes were elevated in leaves, but no excessive accumulation of O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub>, or -OH was observed. Under salinity stress, photosynthesis was inhibited, the O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub> and -OH contents increased significantly, and the SOD, POD, CAT activities and the expression of their related genes in leaves were elevated. Under combined stress, photosynthesis was significantly inhibited, the highest accumulation of O<sub>2</sub><sup>-</sup>, H<sub>2</sub>O<sub>2</sub> and -OH contents occurred, and the SOD and POD activities and the expression of related genes in leaves were significantly increased, but the CAT was significantly decreased. These results collectively indicate that oxidative damage to sweet sorghum seedling leaves was higher with combined stress than with either drought or salinity stress alone. Under combined stress the SOD and POD activities were increased, but the CAT activity in the AsA-GSH cycle was severely reduced, demonstrating that antioxidant mechanisms in seedlings did not play a normal protective role, leaving the plants severely damaged by oxidative stress. <b>Abbreviations:</b> AsA: Ascorbic acid; APX: Ascorbate peroxidase; CAT: Catalase; Chl a: Chlorophyll a; Chl b: Chlorophyll b; Ci: Intercellular CO2 concentration; DHAR: Dehydroascorbate reductase; DEGs: Differentially expressed genes; DW: Dry weight; ETR: Photosynthetic electron transport rate; FW: Fresh weight; Fv/Fm: Original light energy conversion efficiency; GPX: Glutathione peroxidase; GR: Glutathione reductase; Gs: Stomatal conductance; GSH: Oxidized glutathione; H2O2: Hydrogen peroxide; MDA: Malondialdehyde; MDHAR: Monodehydroascorbate reductase; O2-: Superoxide anion; PCA: Principal component analysis; PCD: Programed cell death; PEG-6000: Polyethylene glycol 6000; POD: Peroxidase; Pn: Photosynthetic rate; Pro: Proline; qRT–PCR: Quantitative real-time PCR; RNA-seq: RNA Sequencing; ROS: Reactive oxygen species; RWC: Relative water content; RMP: Relative membrane permeability; SOD: Superoxide dismutase; SW: Saturation weight; Tr: Transpiration rate; ΦPSII: Actual photochemical efficiency; -OH: Hydroxyl radical
DOI: 10.5281/zenodo.7463297
title: Data set for EMPIR project MeDDII Report A2.3.3

description: Data set for EMPIR project MeDDII Report A2.3.3 Characterization of devices for the in-line measurement of the dynamic viscosity and the density of Newtonian liquids
DOI: 10.5281/zenodo.7463298
title: Data set for EMPIR project MeDDII Report A2.3.3

description: Data set for EMPIR project MeDDII Report A2.3.3 Characterization of devices for the in-line measurement of the dynamic viscosity and the density of Newtonian liquids
DOI: 10.5281/zenodo.7463295
title: Data set for EMPIR project MeDDII Report A2.2.2

description: Data set for EMPIR project MeDDII Report A2.2.2 In-line calibration of in-line pressure sensors
DOI: 10.5281/zenodo.7463305
title: Data set for EMPIR project MeDDII Report A2.3.4 D4

description: Data set for EMPIR project MeDDII Report A2.3.4 D4 Report on the use of a calibrated microfluidic multi-parameter chip for the in-line measurement of pressure, viscosity and temperature
DOI: 10.5281/zenodo.7463306
title: Data set for EMPIR project MeDDII Report A2.3.4 D4

description: Data set for EMPIR project MeDDII Report A2.3.4 D4 Report on the use of a calibrated microfluidic multi-parameter chip for the in-line measurement of pressure, viscosity and temperature
DOI: 10.5281/zenodo.7463294
title: Data set for EMPIR project MeDDII Report A2.2.2

description: Data set for EMPIR project MeDDII Report A2.2.2 In-line calibration of in-line pressure sensors
DOI: 10.5281/zenodo.7463290
title: Data set for EMPIR project MeDDII Report A2.1.5 D3

description: Data set for EMPIR project MeDDII Report A2.1.5 D3 Validation report on the primary standards developed for the in-line measurement of the dynamic viscosity of Newtonian liquids with a target uncertainty of 2 % (k=2)
DOI: 10.5281/zenodo.7463291
title: Data set for EMPIR project MeDDII Report A2.1.5 D3

description: Data set for EMPIR project MeDDII Report A2.1.5 D3 Validation report on the primary standards developed for the in-line measurement of the dynamic viscosity of Newtonian liquids with a target uncertainty of 2 % (k=2)
DOI: 10.5281/zenodo.7463284
title: Data set for EMPIR project MeDDII Report A2.1.4

description: Data set for EMPIR project MeDDII Report A2.1.4 Validation of the pipe viscometers (primary standards) for the in-line measurement of the dynamic viscosity of Newtonian liquids
DOI: 10.5281/zenodo.7463285
title: Data set for EMPIR project MeDDII Report A2.1.4

description: Data set for EMPIR project MeDDII Report A2.1.4 Validation of the pipe viscometers (primary standards) for the in-line measurement of the dynamic viscosity of Newtonian liquids
DOI: 10.5281/zenodo.7463272
title: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID88

description: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID88 First comparison of inline measurements of dynamic viscosity
DOI: 10.5281/zenodo.7463273
title: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID88

description: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID88 First comparison of inline measurements of dynamic viscosity
DOI: 10.5281/zenodo.7462134
title: Data set for EMPIR project MeDDII Paper FMI 73 2020 101729

description: Data set for EMPIR project MeDDII Paper https://doi.org/10.1016/j.flowmeasinst.2020.101729
DOI: 10.5281/zenodo.7463265
title: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID90

description: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID90 Dynamic vs constant liquid flow calibrations down to 20 nL/min
DOI: 10.5281/zenodo.7463266
title: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID90

description: Data set for EMPIR project MeDDII Paper FLOMEKO 2022 ID90 Dynamic vs constant liquid flow calibrations down to 20 nL/min
DOI: 10.5281/zenodo.7462133
title: Data set for EMPIR project MeDDII Paper FMI 73 2020 101729

description: Data set for EMPIR project MeDDII Paper https://doi.org/10.1016/j.flowmeasinst.2020.101729
DOI: 10.6084/m9.figshare.21757133
title: Liu_Ecosphere.xlsx

description: Responses of nutrient resorption to interannual precipitation variability and nitrogen addition in a pine plantation
DOI: 10.34740/kaggle/dsv/4748920
title: Worldwide Internet users as % of populationti
DOI: 10.6084/m9.figshare.21657629.v2
title: DKK3 protective role in prostate cancer is partly due to the modulation of immune-related pathways

description: <br> <br> <br> <br> <br> While it is considered one of the most common cancers and the leading cause of death in men worldwide, prognostic stratification and treatment modalities are still limited for patients with prostate cancer (PCa). Recently, the introduction of genomic profiling, as well as, the use of new techniques like next-generation sequencing (NGS) in many cancers provides novel tools for the discovery of new molecular targets that might improve our understanding of the genomic aberrations in PCa and the discovery of novel prognostic and therapeutic targets. In this study, we investigated the possible mechanisms through which <em>Dickkopf-3</em> (DKK3) produces its possible protective role in prostate cancer using NGS in both the DKK3 overexpression PCa cell line (PC3) model, as well as, our patients’ cohort consisting of 9 prostate cancer and 5 benign prostatic hyperplasia. Interestingly, our results have shown that DKK3 transfection-modulated genes are involved in the regulation of cell motility, senescence-associated secretory phenotype (SASP), and cytokine signaling in the immune system, as well as, in the regulation of adaptive immune response. Further analysis of our NGS using our in vitro model revealed the presence of 36 differentially expressed genes between DKK3 transfected cells and PC3 empty vector. In addition, both <em>CP</em> and <em>ACE2 </em>genes were differentially expressed not only between the transfected and empty group but also between the transfected and mock cells. The top common differentially expressed genes (DEGs) between the DKK3 overexpression cell line and in our patients’ cohort showed the list of the following; <em>IL32, IRAK1, RIOK1, HIST1H2BB, SNORA31, AKR1B1,</em> <em>ACE2</em> and <em>CP</em>. The upregulated genes including <em>IL32</em>, <em>HIST1H2BB</em> and <em>SNORA31</em> showed tumor suppressor functions in various cancers including PCa. On the other hand, both <em>IRAK1</em> and <em>RIOK1</em> were downregulated and involved in tumor initiation, tumor progression, poor outcome and radiotherapy resistance. Together, our results highlighted the possible role of the DKK3 related genes in protecting against PCa initiation and progression.
DOI: 10.25403/upresearchdata.20480022
title: Tourists rewilding preferences for a National Park

description: Data were collected between December 2021 and March 2022, it covered 288 tourists that have previously visited Mokala National Park. Data included visitor profile such as socio-economic demographic factors, environmental management preferences, park quality and attraction preferences and a discrete choice experiment for natural characteristics of the national park. Data was obtained through a questionnaire done on qualtrics and distributed online. After successfully capturing and cleaning analysis of the data was done using R-statistical software, utilizing the Apollo packages. This resulted in a conditional logit model and a latent class model to be developed and willingness-to-pay to be determined.
DOI: 10.25403/upresearchdata.20480022.v1
title: Tourists rewilding preferences for a National Park

description: Data were collected between December 2021 and March 2022, it covered 288 tourists that have previously visited Mokala National Park. Data included visitor profile such as socio-economic demographic factors, environmental management preferences, park quality and attraction preferences and a discrete choice experiment for natural characteristics of the national park. Data was obtained through a questionnaire done on qualtrics and distributed online. After successfully capturing and cleaning analysis of the data was done using R-statistical software, utilizing the Apollo packages. This resulted in a conditional logit model and a latent class model to be developed and willingness-to-pay to be determined.
DOI: 10.6084/m9.figshare.21154609
title: Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River basin

description: 1. Alignment of all 569 COI sequences used in this study 2. Alignment of all 85 COI haplotypes generated in this study 3. Details of 85 COI haplotypes. Number of sequences, name of speicimens or reference sequences and accession numbers per haplotype were presented 4. COI haplotype frequency distribution in 14 geographic populations
DOI: 10.6084/m9.figshare.21154609.v1
title: Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River basin

description: 1. Alignment of all 569 COI sequences used in this study 2. Alignment of all 85 COI haplotypes generated in this study 3. Details of 85 COI haplotypes. Number of sequences, name of speicimens or reference sequences and accession numbers per haplotype were presented 4. COI haplotype frequency distribution in 14 geographic populations
DOI: 10.6073/pasta/65ea33e0d5a92b7c3aca0722d3143b47
title: Hemlock History Plots at Harvard Forest since 1995

description: Hemlock (Tsuga canadensis) forests in New England are changing rapidly with the invasion of the hemlock woolly adelgid (HWA, Adelges tsugae), an exotic insect pest that kills hemlock trees. The adelgid is just beginning to be observed at Harvard Forest, making this the right moment to begin intensive physiological, ecological and monitoring studies of our hemlock forests. We gathered detailed baseline information for several hemlock stands across Harvard Forest. We surveyed community vegetation structure and composition, and began to monitor soil nitrogen cycling. These measurements will allow us to link the long-term history of these hemlock stands to other current studies of hemlock response to adelgid infestation, and will provide the basis for intensive study of hemlock dynamics with the stands' anticipated decline.