cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13714177.v1
title: HDS.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714180
title: CMS.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714165
title: DXS.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714168
title: MDS.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714168.v1
title: MDS.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714171.v1
title: HDR.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714171
title: HDR.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714174
title: DXR.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.6084/m9.figshare.13714174.v1
title: DXR.fas

description: <b>Background</b>Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.<b>Results</b>Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.<b>Conclusion</b>Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
DOI: 10.5519/qd.q6wmumau
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.15468/88cv5h
title: Additional contributions to the knowledge of Philippine predatory mites mainly of the subfamilies Cunaxinae and Cunaxoidinae (Acari: Prostigmata: Cunaxidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Corpuz-Raros, Leonila A., Naredo, Jeremy C. B., Garcia, Rufino C. (2019): Additional contributions to the knowledge of Philippine predatory mites mainly of the subfamilies Cunaxinae and Cunaxoidinae (Acari: Prostigmata: Cunaxidae). Acarologia 59 (1): 134-151, DOI: 10.24349/acarologia/20194318
DOI: 10.6073/pasta/97d8f5dada6505ae21e9bd443eda4e74
title: Synthesis of Sea level rise and carbon accumulation rates in United States tidal wetlands

description: Coastal wetlands accumulate soil carbon more efficiently than terrestrial systems, but sea level rise potentially threatens the persistence of this prominent carbon sink. Here, we combine a published dataset of 372 soil carbon accumulation rates from across the United States with new analysis of 131 sites in coastal Louisiana. The combined database featured 503 measurements of carbon accumulation, spanning broad gradients in mean annual temperature, tide range, and dominant vegetation.
DOI: 10.6084/m9.figshare.13715365
title: Dictionary Raw Dat

description: Raw data and dictionary for the paper: "A study of dramatic action and emotion using a systematic scan of stick figure configurations"
DOI: 10.6084/m9.figshare.13715365.v1
title: Dictionary Raw Dat

description: Raw data and dictionary for the paper: "A study of dramatic action and emotion using a systematic scan of stick figure configurations"
DOI: 10.5281/zenodo.4500851
title: Dataset related to article "Clinical performance of Xpert Bladder Cancer (BC) Monitor, a mRNA‐based urine test, in active surveillance (AS) patients with recurrent non‐muscle‐invasive bladder cancer (NMIBC): results from the Bladder Cancer Italian Active Surveillance (BIAS) project"

description: This record contains raw data related to article “ "Clinical performance of Xpert Bladder Cancer (BC) Monitor, a mRNA‐based urine test, in active surveillance (AS) patients with recurrent non‐muscle‐invasive bladder cancer (NMIBC): results from the Bladder Cancer Italian Active Surveillance (BIAS) project"" The paper investigates the clinical performance of a new mRNA-based urine test, aiming to avoid unnecessary follow-up cystoscopy in patients under active surveillance (AS) for recurrent NMIBC. This is a prospective cohort study enrolling patients with history of low-grade (LG) NMIBC, who developed a recurrence during the follow-up and underwent AS. Their urinary samples were analyzed by Xpert BC Monitor (Cepheid, Sunnyvale, CA, USA). The primary endpoint was to investigate if Xpert BC Monitor could avoid unnecessary cystoscopy during the follow-up period. Its sensitivity, specificity, PPVs and NPVs were calculated. A cutoff of 0.4 “linear discriminant analysis” (LDA) was optimized for the AS setting. The cohort consisted of 106 patients with a mean age of 72±9.52 and a median follow-up from AS start of 8.8 (range 0–56.5) months. No statistically significant difference was found for the mean age, smoker status, lesion size, and number of lesions with a cutoff of 0.4. Of 106 patients, 22 (20.8%) were deemed to require treatment because of cystoscopic changes in size and/or number of lesions during the follow-up period. Using a cutoff value of &lt; 0.4, 34 (33.7%) cystoscopies could be avoided due to low LDA value, missing 2/22 (9%) failures, none with high-grade (HG) NMIBC. Further research on larger population remains mandatory before its clinical use.Xpert BC Monitor seems to be a reliable assay, which might avoid unnecessary cystoscopies without missing HG NMIBC when its cutoff is optimized for the AS setting.
DOI: 10.5281/zenodo.4500850
title: Dataset related to article "Clinical performance of Xpert Bladder Cancer (BC) Monitor, a mRNA‐based urine test, in active surveillance (AS) patients with recurrent non‐muscle‐invasive bladder cancer (NMIBC): results from the Bladder Cancer Italian Active Surveillance (BIAS) project"

description: This record contains raw data related to article “ "Clinical performance of Xpert Bladder Cancer (BC) Monitor, a mRNA‐based urine test, in active surveillance (AS) patients with recurrent non‐muscle‐invasive bladder cancer (NMIBC): results from the Bladder Cancer Italian Active Surveillance (BIAS) project"" The paper investigates the clinical performance of a new mRNA-based urine test, aiming to avoid unnecessary follow-up cystoscopy in patients under active surveillance (AS) for recurrent NMIBC. This is a prospective cohort study enrolling patients with history of low-grade (LG) NMIBC, who developed a recurrence during the follow-up and underwent AS. Their urinary samples were analyzed by Xpert BC Monitor (Cepheid, Sunnyvale, CA, USA). The primary endpoint was to investigate if Xpert BC Monitor could avoid unnecessary cystoscopy during the follow-up period. Its sensitivity, specificity, PPVs and NPVs were calculated. A cutoff of 0.4 “linear discriminant analysis” (LDA) was optimized for the AS setting. The cohort consisted of 106 patients with a mean age of 72±9.52 and a median follow-up from AS start of 8.8 (range 0–56.5) months. No statistically significant difference was found for the mean age, smoker status, lesion size, and number of lesions with a cutoff of 0.4. Of 106 patients, 22 (20.8%) were deemed to require treatment because of cystoscopic changes in size and/or number of lesions during the follow-up period. Using a cutoff value of &lt; 0.4, 34 (33.7%) cystoscopies could be avoided due to low LDA value, missing 2/22 (9%) failures, none with high-grade (HG) NMIBC. Further research on larger population remains mandatory before its clinical use.Xpert BC Monitor seems to be a reliable assay, which might avoid unnecessary cystoscopies without missing HG NMIBC when its cutoff is optimized for the AS setting.
DOI: 10.6084/m9.figshare.13235537
title: Sartor_L.guttulus_x_L.geoffroyi.xlsx

description: Microsatellite data from 135 individuals of Leopardus guttulus, 140 individuals of L. geoffroyi and their hybrids. The samples were genotyped for 13 loci.
DOI: 10.7278/s50dssmbhhxn
title: Data for: A Pluto-Charon Concerto II. Formation of a Circumbinary Disk of Debris After the Giant Impact
DOI: 10.6073/pasta/d24a5ac199704f4be3dc32e34383af75
title: PIE LTER, Hach, OTT RLS measurements of water column depth at 15 minute intervals in the lower Plum Island Sound off the Ipswich Bay Yacht Club pier, Ipswich, MA, year 2020.

description: Measurements of water column depth at 15 minute intervals in Plum Island Sound at the Ipswich Bay Yacht Club, for year 2020. OTT radar level sensor (RLS) installed September 20, 2011 out of the water under the concrete pad on the Ipswich Bay Yacht Club pier, Ipswich, MA. RLS was mounted so that continuous year round measurements can be conducted without the concern of ice flows damaging the sensor.
DOI: 10.15468/cag4d8
title: Review of the Scorpaena papillosa species complex (Teleostei: Scorpaenidae) with description of a new species from southwestern Australia

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wibowo, Kunto, Motomura, Hiroyuki (2020): Review of the Scorpaena papillosa species complex (Teleostei: Scorpaenidae) with description of a new species from southwestern Australia. Zootaxa 4852 (5): 527-546, DOI: https://doi.org/10.11646/zootaxa.4852.5.2
DOI: 10.5517/ccdc.csd.cc25x8p2
title: CCDC 2023174: Experimental Crystal Structure Determination

description: Related Article: Xin Yang, Rui Wei, Yaping Shi, Liu Leo Liu, Yile Wu, Yufen Zhao, Douglas W. Stephan|2021|Chem.Commun.|57|1194|doi:10.1039/D0CC07736D