cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24257398.v1
title: The seaweed <i>Ascophyllum nodosum</i>-based biostimulant enhances salt stress tolerance in rice (<i>Oryza sativa</i> L.) by remodeling physiological, biochemical, and metabolic responses

description: This study explores the role of a biostimulant derived from the seaweed <i>Ascophyllum nodosum</i> (AN) in mitigating salt stress in rice plants. The weekly (S+W) and biweekly (S+B) biostimulant treatments exhibited enhanced shoot and root biomass, maintained ionic balance, and increased pigment content (total chlorophyll increased by 26.35% and 31%, carotenoids by 11.90% and 16.67% in S+W and S+B treatments, respectively) compared to untreated salt-stressed plants (CS). Improved gas exchange parameters and PSII efficiency were observed in S+W and S+B treatments. AN-biostimulant treatments mitigated salt-induced oxidative stress by positively regulating the antioxidant defense system. Notably, a strong negative correlation was observed between antioxidants and oxidative markers. Furthermore, AN-biostimulant treatments induced key metabolites (organic acids, sugars, amino acids, flavonoids), emphasizing the integrated role of multiple pathways in enhancing salt tolerance in rice. These findings highlight the potential of AN biostimulants as eco-friendly tools for crop enhancement in challenging environments.
DOI: 10.6084/m9.figshare.24297065
title: Basic leucine zipper (bZIP) family in Asparagus (<i>Asparagus officinalis</i>): genome-wide identification, evolutionary, structure, collinearity, and expression analyses under abiotic stress at the seeding stage

description: Asparagus (<i>Asparagus officinalis</i>) is a crop with medicinal, horticultural, and nutritional uses. The basic leucine zipper (bZIP) family is a transcription factor family distributed throughout eukaryotes, including plants, and whose members participate in various biological processes, including plant growth, development, flowering, and stress responses. However, a few genome-wide studies of the bZIP family members have been reported. Here, 46 Asparagus bZIP members, named AobZIP01–AobZIP46, were identified from the reference genome via PFAM search and could be divided into 14 subgroups which were shown to be similar via motif and gene structure analysis. The molecular evolution, motif, and gene structure comparative analysis between <i>A</i>. <i>officinalis</i> and <i>Arabidopsis</i> indicated the accuracy of AobZIP member identification. Additionally, the <i>cis</i>-acting elements of the <i>AobZIP</i> members revealed that they might be associated with plant hormones and responses to abiotic stress. The collinear analysis predicted that the function of <i>AobZIP</i> members might be comparable to that of other species. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that <i>AobZIP</i> genes were enriched in the abscisic acid (ABA) pathway. Furthermore, the tissue-specific expression at the seedling stage revealed that root tissue could be used as a target tissue because of its high expression level. The expression of <i>AobZIP</i> genes determined by quantitative real-time PCR under abiotic stress at the seeding stage revealed that some <i>AobZIP</i> members could be candidate genes for plant breeding. This study offers insights for future research in improving the abiotic stress resistance of asparagus utilizing the <i>AobZIP</i> genes.
DOI: 10.6084/m9.figshare.24297065.v1
title: Basic leucine zipper (bZIP) family in Asparagus (<i>Asparagus officinalis</i>): genome-wide identification, evolutionary, structure, collinearity, and expression analyses under abiotic stress at the seeding stage

description: Asparagus (<i>Asparagus officinalis</i>) is a crop with medicinal, horticultural, and nutritional uses. The basic leucine zipper (bZIP) family is a transcription factor family distributed throughout eukaryotes, including plants, and whose members participate in various biological processes, including plant growth, development, flowering, and stress responses. However, a few genome-wide studies of the bZIP family members have been reported. Here, 46 Asparagus bZIP members, named AobZIP01–AobZIP46, were identified from the reference genome via PFAM search and could be divided into 14 subgroups which were shown to be similar via motif and gene structure analysis. The molecular evolution, motif, and gene structure comparative analysis between <i>A</i>. <i>officinalis</i> and <i>Arabidopsis</i> indicated the accuracy of AobZIP member identification. Additionally, the <i>cis</i>-acting elements of the <i>AobZIP</i> members revealed that they might be associated with plant hormones and responses to abiotic stress. The collinear analysis predicted that the function of <i>AobZIP</i> members might be comparable to that of other species. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that <i>AobZIP</i> genes were enriched in the abscisic acid (ABA) pathway. Furthermore, the tissue-specific expression at the seedling stage revealed that root tissue could be used as a target tissue because of its high expression level. The expression of <i>AobZIP</i> genes determined by quantitative real-time PCR under abiotic stress at the seeding stage revealed that some <i>AobZIP</i> members could be candidate genes for plant breeding. This study offers insights for future research in improving the abiotic stress resistance of asparagus utilizing the <i>AobZIP</i> genes.
DOI: 10.6084/m9.figshare.24305292
title: Exploration of chemical interactions between <i>Viscum combreticola</i> Engl. and its hosts through a metabolic profiling approach and molecular networking

description: <i>Viscum combreticola</i> Engl., an evergreen semi-parasitic mistletoe plant, is utilized in herbal medicines<i>.</i> Herein, a UHPLC-q-TOF-MS profiling and molecular networking approach were used to investigate the chemical interactions between <i>V. combreticola</i> and two of its host plants, <i>Combretum erythrophyllum</i> and <i>Pseudolachnostylis maprouneifolia</i> Pax. Moreover, <i>in vitro</i> grown <i>V. combreticola</i> seedlings were used to explore the host independence of the phytochemistry of these plants. The phytochemistry of <i>V. combreticola</i> was found to be independent and distinct from that of the host plants. Moreover, both mature <i>V. combreticola</i> and in vitro seedlings displayed diverse polyphenolic compounds but exhibited distinct metabolic profiles. Notably, the esterification of phenolic acids (hydroxycinnamic and benzoic acids) to quinic acid was a unique chemistry that was observed in both mature and <i>in vitro</i> grown <i>V. combreticola</i>. Beyond providing metabolic fingerprints of the studied samples, the UHPLC-q-TOF-MS and molecular networking effectively visualized plant-plant chemical relationships at a metabolite level.
DOI: 10.6084/m9.figshare.24305292.v1
title: Exploration of chemical interactions between <i>Viscum combreticola</i> Engl. and its hosts through a metabolic profiling approach and molecular networking

description: <i>Viscum combreticola</i> Engl., an evergreen semi-parasitic mistletoe plant, is utilized in herbal medicines<i>.</i> Herein, a UHPLC-q-TOF-MS profiling and molecular networking approach were used to investigate the chemical interactions between <i>V. combreticola</i> and two of its host plants, <i>Combretum erythrophyllum</i> and <i>Pseudolachnostylis maprouneifolia</i> Pax. Moreover, <i>in vitro</i> grown <i>V. combreticola</i> seedlings were used to explore the host independence of the phytochemistry of these plants. The phytochemistry of <i>V. combreticola</i> was found to be independent and distinct from that of the host plants. Moreover, both mature <i>V. combreticola</i> and in vitro seedlings displayed diverse polyphenolic compounds but exhibited distinct metabolic profiles. Notably, the esterification of phenolic acids (hydroxycinnamic and benzoic acids) to quinic acid was a unique chemistry that was observed in both mature and <i>in vitro</i> grown <i>V. combreticola</i>. Beyond providing metabolic fingerprints of the studied samples, the UHPLC-q-TOF-MS and molecular networking effectively visualized plant-plant chemical relationships at a metabolite level.
DOI: 10.6084/m9.figshare.23734244
title: Genome-wide identification of papain-like cysteine proteases in <i>Citrus sinensis</i> and expression analysis in response to <i>Candidatus</i> Liberibacter asiaticus

description: Papain-like cysteine proteases (PLCPs) play important roles in plant-pathogen interactions. In citrus, PLCPs are targeted by effectors from <i>Candidatus</i> Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB). To study interactions between <i>Citrus sinensis</i> and CLas, we identified 33 candidate <i>CsPLCP</i> genes by HMMsearch with the Peptidase_C1 domain (PF00112), and further confirmed them using local BLAST with PLCP sequences from <i>Arabidopsis thaliana</i>. The 33 <i>CsPLCPs</i> were classified into 9 subfamilies. Analysis of the cis-acting elements in their promoters indicated that <i>CsPLCPs</i> are responsive to various phytohormones and stressors. Further qPCR analysis indicated that several <i>CsPLCPs</i> were up-regulated during CLas infection. Subcellular localization analysis indicated that five CsPLCPs were localized to the cytoplasm and nucleus, while CsXBCP2 was localized only to the cytoplasm. In summary, this study provides a sound basis for understanding the roles of <i>CsPLCPs</i> in the Citrus-CLas interaction.
DOI: 10.6084/m9.figshare.23734244.v1
title: Genome-wide identification of papain-like cysteine proteases in <i>Citrus sinensis</i> and expression analysis in response to <i>Candidatus</i> Liberibacter asiaticus

description: Papain-like cysteine proteases (PLCPs) play important roles in plant-pathogen interactions. In citrus, PLCPs are targeted by effectors from <i>Candidatus</i> Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB). To study interactions between <i>Citrus sinensis</i> and CLas, we identified 33 candidate <i>CsPLCP</i> genes by HMMsearch with the Peptidase_C1 domain (PF00112), and further confirmed them using local BLAST with PLCP sequences from <i>Arabidopsis thaliana</i>. The 33 <i>CsPLCPs</i> were classified into 9 subfamilies. Analysis of the cis-acting elements in their promoters indicated that <i>CsPLCPs</i> are responsive to various phytohormones and stressors. Further qPCR analysis indicated that several <i>CsPLCPs</i> were up-regulated during CLas infection. Subcellular localization analysis indicated that five CsPLCPs were localized to the cytoplasm and nucleus, while CsXBCP2 was localized only to the cytoplasm. In summary, this study provides a sound basis for understanding the roles of <i>CsPLCPs</i> in the Citrus-CLas interaction.
DOI: 10.5281/zenodo.10552500
title: A Stable High-Potential Na7V4(P2O7)4(PO4) Cathode for Sodium-Ion Batteries Developed from a Water-Based Slurry

description: These are the corresponding raw data related to the publication:

A Stable High-Potential Na7V4(P2O7)4(PO4) Cathode for Sodium-Ion Batteries Developed from a Water-Based Slurry

 

Ruihao Gong,+a Fabio Maroni,+a Mario Marinaro*a

 

aZentrum für Sonnenenergie- und Wasserstoff- Forschung, Baden-Württemberg (ZSW)

Helmholtzstraße 8 - 89081 Ulm, Germany

 

+: The authors contribute equally to this study.

*: Corresponding: mario.marinaro@zsw-bw.de
DOI: 10.5281/zenodo.10552501
title: A Stable High-Potential Na7V4(P2O7)4(PO4) Cathode for Sodium-Ion Batteries Developed from a Water-Based Slurry

description: These are the corresponding raw data related to the publication:

A Stable High-Potential Na7V4(P2O7)4(PO4) Cathode for Sodium-Ion Batteries Developed from a Water-Based Slurry

 

Ruihao Gong,+a Fabio Maroni,+a Mario Marinaro*a

 

aZentrum für Sonnenenergie- und Wasserstoff- Forschung, Baden-Württemberg (ZSW)

Helmholtzstraße 8 - 89081 Ulm, Germany

 

+: The authors contribute equally to this study.

*: Corresponding: mario.marinaro@zsw-bw.de
DOI: 10.6084/m9.figshare.25474912
title: <b>Plant anatomy: history and future directions</b><b>Supplementary Material – </b><b>Pollen morphology in the genus </b><b><i>Dyckia</i></b><b> (Bromeliaceae): endemic species from southern Brazil </b><b>comprising the proposed infrageneric grouping “</b><b><i>D. selloa</i></b><b> complex”</b>

description: <b>Table S1 – </b><b>Pollen grain measures comparison of the studied species. General characters with variation.</b><b>Table S2 – </b><b>Sporoderm strata comparison of the studied species. Exine measurements.</b>
DOI: 10.6084/m9.figshare.25474912.v1
title: <b>Plant anatomy: history and future directions</b><b>Supplementary Material – </b><b>Pollen morphology in the genus </b><b><i>Dyckia</i></b><b> (Bromeliaceae): endemic species from southern Brazil </b><b>comprising the proposed infrageneric grouping “</b><b><i>D. selloa</i></b><b> complex”</b>

description: <b>Table S1 – </b><b>Pollen grain measures comparison of the studied species. General characters with variation.</b><b>Table S2 – </b><b>Sporoderm strata comparison of the studied species. Exine measurements.</b>
DOI: 10.5281/zenodo.10637253
title: Ontogenetic variation in metabolic rate-temperature relationships during larval development

description: Predictive models of ectotherm responses to environmental change often rely on thermal performance data from the literature. For insects, the majority of these data focus on two traits, development rate and thermal tolerance limits. Data are also often limited to the adult stage. Consequently, predictions based on these data generally ignore other measures of thermal performance and do not account for the role of ontogenetic variation in thermal physiology across the complex insect life cycle. Theoretical syntheses for predicting metabolic rate also make similar assumptions despite the strong influence of body size as well as temperature on metabolic rate. The aim of this study was to understand the influence of ontogenetic variation on ectotherm physiology and its potential impact on predictive modeling. To do this we examined metabolic rate-temperature (MR-T) relationships across the larval stage in a laboratory strain of the Spongy moth (Lymantria dispar dispar). Routine metabolic rates (RMR) of larvae were assayed at nine temperatures across the first five instars of the larval stage. After accounting for differences in body mass, larval instars showed significant variation in MR-T. Both the temperature sensitivity and allometry of RMR increased and peaked during the third instar, then declined in the fourth and fifth instar. Generally, these results show that insect thermal physiology does not remain static during larval ontogeny and suggest that ontogenetic variation should be an important consideration when modeling thermal performance.
DOI: 10.5281/zenodo.10564937
title: Databases generated for Manuscript titled "Quantifying downward radiative fluxes from nighttime Martian water ice clouds: Applications to thermal modeling of surface temperatures"

description: Databases generated for manuscript "Quantifying downward radiative fluxes from nighttime Martian water ice clouds: Applications to thermal modeling of surface temperatures"

There are two zip files containing generated databases:

The zip file titled "database.zip" contains generated database for calculated fluxes using the methodology mentioned in the manuscript. The database spans calculated fluxes in one degree bins for latitudes spanning 30° to -10° N and longitudes spanning 0° to 360°. There are 14760 separate .csv files that are for each one by one degree bin. The title of each file contains its coordinates in the format XXXNXXXEtb.csv (e.g. 000N000Etb.csv for 0°N, 0°E). Each .csv file contains four separate columns and variable rows. The columns have headers corresponding to specific values. "ls" corresponds to solar longitude or date based on Mars' orbit around the Sun. "Flux" corresponds to calculated flux based on the methodology presented on the manuscript. "Delta-T" is the difference in temperature comparing modeled temperature compared to Thermal Emission Spectrometer (TES) measured temperature. "Tau" corresponds to calculated Dust visible opacities using the methodology presented in this work. The rows in each file vary based on the temporal observations from TES at each location. 

The zip file titled "fitdatabase.zip" contains generated database for fitted fluxes using the methodology mentioned in the manuscript. The database spans calculated fluxes in one degree bins for latitudes spanning 30° to -10° N and longitudes spanning 0° to 360°. There are 14760 separate .csv files that are for each one by one degree bin. The title of each file contains its coordinates in the format XXXNXXXEtbf.csv (e.g. 000N000Etbf.csv for 0°N, 0°E). Each .csv file contains six separate columns and three hundred and sixty rows. The columns have headers corresponding to specific values. "ls" corresponds to solar longitude or date based on Mars' orbit around the Sun. "Flux" corresponds to calculated flux based on the methodology presented on the manuscript. "Delta-T" is the difference in temperature comparing modeled temperature compared to measured temperature. The fitting algorithm interpolates points between values in the calculated flux database and applies a rolling mean fit with a window spanning ten degrees in solar longitude centered at each calculated flux point. "FLAG" indicates the amount of points of calculated flux points that exist within the ten degree window centered at each flux point to demonstrate to the user how much data had to be fitted. "From Ls" shows the leftmost edge of the rolling mean fit window. "To Ls" shows the rightmost edge of the rolling mean fit window. The rows in each file correspond to one degree of solar longitude the fitting algorithm was designed to cover each solar longitude bin.
DOI: 10.25390/caryinstitute.8120816.v3
title: Cary Environmental Monitoring Program Precipitation Chemistry Event-Based Data: 1984-2021

description: The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, water pollution and streamwater hydrology. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: Please click on the Data Cite button in Figshare.<br>Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org.
DOI: 10.57967/hf/1960
title: TACDEC
DOI: 10.13012/b2idb-1022017_v1
title: Data for "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States"

description: This is the dataset for the manuscript titled, "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States"
DOI: 10.5281/zenodo.10574109
title: Predicted genes from the Amblyomma americanum draft genome assembly

description: Data for pub "Predicted genes from the Amblyomma americanum draft genome assembly."



Amblyomma_americanum_filtered_assembly.fasta: Decontaminated A. americanum genome with bacterial contigs removed

Amblyomma_americanum_bacterial_contigs_info.tsv: Information about contigs classified as bacteria that were removed

Amblyomma_americanum_annotation_data.tar.gz: Directory of annotation data produced by EvidenceModeler as part of the nf-core/genomeannotator workflow. Includes files in FASTA format (predicted genes and proteins), set of proteins clustered at 99% identity in FASTA format, and annotations in both GFF3 and GTF formats. GTF file produced from the GFF3 file with AGAT.

Amblyomma_americanum_transcriptome_assembly_data.tar.gz: Directory of data generated for the transcriptome assembly that was used for gene prediction
DOI: 10.5281/zenodo.10574110
title: Predicted genes from the Amblyomma americanum draft genome assembly

description: Data for pub "Predicted genes from the Amblyomma americanum draft genome assembly."



Amblyomma_americanum_filtered_assembly.fasta: Decontaminated A. americanum genome with bacterial contigs removed

Amblyomma_americanum_bacterial_contigs_info.tsv: Information about contigs classified as bacteria that were removed

Amblyomma_americanum_annotation_data.tar.gz: Directory of annotation data produced by EvidenceModeler as part of the nf-core/genomeannotator workflow. Including set of proteins that were clustered at 99% identity

Amblyomma_americanum_transcriptome_assembly_data.tar.gz: Directory of data generated for the transcriptome assembly that was used for gene prediction
DOI: 10.5281/zenodo.10870487
title: Predicted genes from the Amblyomma americanum draft genome assembly

description: Data for pub "Predicted genes from the Amblyomma americanum draft genome assembly."



Amblyomma_americanum_filtered_assembly.fasta: Decontaminated A. americanum genome with bacterial contigs removed

Amblyomma_americanum_bacterial_contigs_info.tsv: Information about contigs classified as bacteria that were removed

Amblyomma_americanum_annotation_data.tar.gz: Directory of annotation data produced by EvidenceModeler as part of the nf-core/genomeannotator workflow. Includes files in FASTA format (predicted genes and proteins), set of proteins clustered at 99% identity in FASTA format, and annotations in both GFF3 and GTF formats. GTF file produced from the GFF3 file with AGAT.

Amblyomma_americanum_transcriptome_assembly_data.tar.gz: Directory of data generated for the transcriptome assembly that was used for gene prediction
DOI: 10.5281/zenodo.7007501
title: GSHHG: Global Self-consistent Hierarchical High-resolution Geography

description: Global Self-consistent, Hierarchical, High-resolution Geography Database (GSHHG) is a high-resolution geography data set, amalgamated from two databases: World Vector Shorelines (WVS) and CIA World Data Bank II (WDBII). The former is the basis for shorelines while the latter is the basis for lakes, although there are instances where differences in coastline representations necessitated adding WDBII islands to GSHHG. The WDBII source also provides political borders and rivers. GSHHG data have undergone extensive processing and should be free of internal inconsistencies such as erratic points and crossing segments. The shorelines are constructed entirely from hierarchically arranged closed polygons.GSHHG combines the older GSHHS shoreline database with WDBII rivers and borders, available in either ESRI shapefile format or in a native binary format. Geography data are in five resolutions: crude(c), low(l), intermediate(i), high(h), and full(f). Shorelines are organized into four levels: boundary between land and ocean (L1), boundary between lake and land (L2), boundary between island-in-lake and lake (L3), and boundary between pond-in-island and island (L4). Datasets are in WGS84 geographic (simple latitudes and longitudes; decimal degrees).

GSHHG is released under the GNU Lesser General Public license, and is developed and maintained by Dr. Paul Wessel, SOEST, University of Hawai'i, and Dr. Walter H. F. Smith, NOAA Laboratory for Satellite Altimetry. Please notify Dr. Paul Wessel and Dr. Walter H.F. Smith if any changes are made to the GSHHG data set for commercial use.

Processing and assembly of the GSHHG data:Wessel, P., and W. H. F. Smith (1996), A global, self-consistent, hierarchical, high-resolution shoreline database, J. Geophys. Res., 101(B4), 8741–8743, doi:10.1029/96JB00104.