cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10086108
title: PUDL Raw FERC Electric Quarterly Report EQR Form 920 2002-2013

description: Data from the FERC Electric Quarterly Report (also known as the EQR or Form 920) covering the years 2002-2013. This data was downloaded from the FERC website on 2022-01-24.

In theory, this data is available directly from FERC, but it is on a server that is limited to 3 concurrent connections. Given that it is ~15GB in size, it is functionally impossible to download. So, we thought we would archive it here to improve accessibility, and so we don't risk losing the only copy of it that we have!

More recent FERC EQR data (starting in Q3 of 2013) are actually downloadable through the FERC EQR Report Viewer.

Note that this is not one of our normal machine-readable PUDL raw input data archives, as it was hand-compiled, based on data downloaded from FERC on 2022-01-24.
DOI: 10.5281/zenodo.10086109
title: PUDL Raw FERC Electric Quarterly Report EQR Form 920 2002-2013

description: Data from the FERC Electric Quarterly Report (also known as the EQR or Form 920) covering the years 2002-2013. This data was downloaded from the FERC website on 2022-01-24.

In theory, this data is available directly from FERC, but it is on a server that is limited to 3 concurrent connections. Given that it is ~15GB in size, it is functionally impossible to download. So, we thought we would archive it here to improve accessibility, and so we don't risk losing the only copy of it that we have!

More recent FERC EQR data (starting in Q3 of 2013) are actually downloadable through the FERC EQR Report Viewer.

Note that this is not one of our normal machine-readable PUDL raw input data archives, as it was hand-compiled, based on data downloaded from FERC on 2022-01-24.
DOI: 10.6084/m9.figshare.9375800
title: The casein kinase MoYck1 regulates development, autophagy, and virulence in the rice blast fungus

description: Casein kinases are serine/threonine protein kinases that are evolutionarily conserved in yeast and humans and are involved in a range of important cellular processes. However, the biological functions of casein kinases in the fungus <i>Magnaporthe oryzae</i>, the causal agent of destructive rice blast disease, are not characterized. Here, two casein kinases, <i>MoYCK1</i> and <i>MoHRR25</i>, were identified and targeted for replacement, but only <i>MoYCK1</i> was further characterized due to the possible nonviability of the <i>MoHRR25</i> deletion mutant. Disruption of <i>MoYCK1</i> caused pleiotropic defects in growth, conidiation, conidial germination, and appressorium formation and penetration, therefore resulting in reduced virulence in rice seedlings and barley leaves. Notably, the <i>MoYCK1</i> deletion triggered quick lipidation of MoAtg8 and degradation of the autophagic marker protein GFP-MoAtg8 under nitrogen starvation conditions, in contrast to the wild type, indicating that autophagy activity was negatively regulated by MoYck1. Furthermore, we found that HOPS (homotypic fusion and vacuolar protein sorting) subunit MoVps41, a putative substrate of MoYck1, was co-located with MoAtg8 and positively required for the degradation of MoAtg8-PE and GFP-MoAtg8. In addition, <i>MoYCK1</i> is also involved in the response to ionic hyperosmotic and heavy metal cation stresses. Taken together, our results revealed crucial roles of the casein kinase MoYck1 in regulating development, autophagy and virulence in <i>M. oryzae</i>.
DOI: 10.6084/m9.figshare.9375800.v1
title: The casein kinase MoYck1 regulates development, autophagy, and virulence in the rice blast fungus

description: Casein kinases are serine/threonine protein kinases that are evolutionarily conserved in yeast and humans and are involved in a range of important cellular processes. However, the biological functions of casein kinases in the fungus <i>Magnaporthe oryzae</i>, the causal agent of destructive rice blast disease, are not characterized. Here, two casein kinases, <i>MoYCK1</i> and <i>MoHRR25</i>, were identified and targeted for replacement, but only <i>MoYCK1</i> was further characterized due to the possible nonviability of the <i>MoHRR25</i> deletion mutant. Disruption of <i>MoYCK1</i> caused pleiotropic defects in growth, conidiation, conidial germination, and appressorium formation and penetration, therefore resulting in reduced virulence in rice seedlings and barley leaves. Notably, the <i>MoYCK1</i> deletion triggered quick lipidation of MoAtg8 and degradation of the autophagic marker protein GFP-MoAtg8 under nitrogen starvation conditions, in contrast to the wild type, indicating that autophagy activity was negatively regulated by MoYck1. Furthermore, we found that HOPS (homotypic fusion and vacuolar protein sorting) subunit MoVps41, a putative substrate of MoYck1, was co-located with MoAtg8 and positively required for the degradation of MoAtg8-PE and GFP-MoAtg8. In addition, <i>MoYCK1</i> is also involved in the response to ionic hyperosmotic and heavy metal cation stresses. Taken together, our results revealed crucial roles of the casein kinase MoYck1 in regulating development, autophagy and virulence in <i>M. oryzae</i>.
DOI: 10.6084/m9.figshare.25308796
title: Hyperspectral pressure-volume curves to estimate leaf turgor loss

description: Turgor Loss Point (TLP) is an important proxy for plant drought tolerance, species habitat suitability, and drought-induced plant mortality risk. Thus, TLP serves as a critical tool for evaluating climate change impacts on plants, making it imperative to develop high-throughput and in-situ methods to measure TLP. We developed hyperspectral pressure-volume curves to estimate TLP using leaf spectral reflectance. First, we developed PLSR models to estimate leaf water potential (WP or psi) and relative water content (RWC) using spectral reflectance (400-2400 nm). We used estimated values to construct hyperspectral PV-curves and compared the accuracy of estimating TLP from reflectance to empirical PV-curves using the Pressure-Volume Analysis Spreadsheet tool (PVAST, the most widely used analytical method; Sack et al., 2010). Additionally, we compared TLPs extracted from PVAST to TLPs automatically extracted by segmented regression, a tool commonly used to automatically parameterize physiological.
DOI: 10.6084/m9.figshare.11971545
title: Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in <i>Camellia</i>

description: Direct single-molecule sequencing of full-length transcripts allows efficient identification of gene isoforms, which is apt to alternative splicing (AS), polyadenylation, and long non-coding RNA analyses. However, the identification of gene isoforms and long non-coding RNAs with novel regulatory functions remains challenging, especially for species without a reference genome. Here, we present a comprehensive analysis of a combined long-read and short-read transcriptome sequencing in <i>Camellia japonica</i>. Through a novel bioinformatic pipeline of reverse-tracing the split-sites, we have uncovered 257,692 AS sites from 61,838 transcripts; and 13,068 AS isoforms have been validated by aligning the short reads. We have identified the tissue-specific AS isoforms along with 6,373 AS events that were found in all tissues. Furthermore, we have analysed the polyadenylation (polyA) patterns of transcripts, and found that the preference for polyA signals was different between the AS and non-AS transcripts. Moreover, we have predicted the phased small interfering RNA (phasiRNA) loci through integrative analyses of transcriptome and small RNA sequencing. We have shown that a newly evolved phasiRNA locus from lipoxygenases generated 12 consecutive 21 bp secondary RNAs, which were responsive to cold and heat stress in <i>Camellia</i>. Our studies of the isoform transcriptome provide insights into gene splicing and functions that may facilitate the mechanistic understanding of plants.
DOI: 10.6084/m9.figshare.11971545.v1
title: Identification of Alternatively Spliced Gene Isoforms and Novel Noncoding RNAs by Single-Molecule Long-Read Sequencing in <i>Camellia</i>

description: Direct single-molecule sequencing of full-length transcripts allows efficient identification of gene isoforms, which is apt to alternative splicing (AS), polyadenylation and long non-coding RNA analyses. However, the identification of gene isoforms and long non-coding RNAs with novel regulatory functions remains challenging, especially for species without a reference genome. Here, we present a comprehensive analysis of a combined long-read and short-read transcriptome sequencing in <i>Camellia japonica</i>. Through a novel bioinformatic pipeline of reverse-tracing the split-sites, we have uncovered 257,692 AS sites from 61,838 transcripts; and 13,068 AS isoforms have been validated by aligning the short reads. We have identified the tissue-specific AS isoforms along with 6,373 AS events that were found in all tissues. Furthermore, we have analyzed the polyadenylation (polyA) patterns of transcripts, and found that the preference for polyA signals was different between the AS and non-AS transcripts. Moreover, we have predicted the phased small interfering RNA (phasiRNA) loci through integrative analyses of transcriptome and small RNA sequencing. We have shown that a newly evolved phasiRNA locus from lipoxygenases generated 12 consecutive 21 bp secondary RNAs, which were responsive to cold and heat stress in <i>Camellia</i>. Our studies of the isoform transcriptome provide insights into gene splicing and functions that may facilitate the mechanistic understanding of plants.
DOI: 10.6084/m9.figshare.11971545.v2
title: Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in <i>Camellia</i>

description: Direct single-molecule sequencing of full-length transcripts allows efficient identification of gene isoforms, which is apt to alternative splicing (AS), polyadenylation, and long non-coding RNA analyses. However, the identification of gene isoforms and long non-coding RNAs with novel regulatory functions remains challenging, especially for species without a reference genome. Here, we present a comprehensive analysis of a combined long-read and short-read transcriptome sequencing in <i>Camellia japonica</i>. Through a novel bioinformatic pipeline of reverse-tracing the split-sites, we have uncovered 257,692 AS sites from 61,838 transcripts; and 13,068 AS isoforms have been validated by aligning the short reads. We have identified the tissue-specific AS isoforms along with 6,373 AS events that were found in all tissues. Furthermore, we have analysed the polyadenylation (polyA) patterns of transcripts, and found that the preference for polyA signals was different between the AS and non-AS transcripts. Moreover, we have predicted the phased small interfering RNA (phasiRNA) loci through integrative analyses of transcriptome and small RNA sequencing. We have shown that a newly evolved phasiRNA locus from lipoxygenases generated 12 consecutive 21 bp secondary RNAs, which were responsive to cold and heat stress in <i>Camellia</i>. Our studies of the isoform transcriptome provide insights into gene splicing and functions that may facilitate the mechanistic understanding of plants.
DOI: 10.6084/m9.figshare.11473059
title: The lithospheric thickness control on the compositional variation of continental intraplate basalts: A demonstration using the Cenozoic basalts and clinopyroxene megacrysts from eastern China

description: This file contains supplementary tables 1-8 listing the data of Cenozoic basalts and cpx megacrysts in eastern continental China, the corrected primitive major element compositions and the calculated equilibrium pressures and temperatures of cpx megacrysts.
DOI: 10.5281/zenodo.10694886
title: iRON_Soil_Moisture_Uncalibrated_2023

description: These are minimally processed, near raw data. Potential sensor errors or equipment changes are not flagged. 

 

Rain values are from a tipping bucket rain gauge, and values may not accurately represent precipitation in winter months.These files have been corrected for data gaps and sensor label errors. V0 Files published prior to Feb 22, 2022 may contain errords.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.10719629
title: iRON_Soil_Moisture_Uncalibrated_2023

description: These are minimally processed, near raw data. Potential sensor errors or equipment changes are not flagged. 

 

Rain values are from a tipping bucket rain gauge, and values may not accurately represent precipitation in winter months.These files have been corrected for data gaps and sensor label errors. V0 Files published prior to Feb 22, 2022 may contain errords.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.1228346
title: Iron_Soil_Moisture_Uncalibrated_2013_2017

description: These data are the complete data set from installation through Dec 31, 2017 for AGCI's interactive Roaring Fork Observation Network (iRON). The network consists of 9 stations in the Southern Rockies (Colorado, USA). Descriptions of soil type and site locations can be found at: www.agci.org/iron/stations

<strong>Please note that these soil moisture data readings are uncalibrated</strong>. Measurements taken for rain are recorded via tipping bucket rain gauge and may not be accurate for winter precipitation events (e.g. snow). Blank spaces represent absent or false readings. -888.88, -138.25, or -162.469 represents a sensor error.

Sensors used for soil moisture readings are Decagon EC-5 Dielectric probe (5cm/2in depth); Decagon 10-HS (20cm/8in; 50cm/20in depths). All other equipment is Onset, and the logger device is the RX3000 model. Data collection is generally set to every 20 minutes (most stations) or every hour (Independence Pass station), but maintenance resets, etc. may occasionally have contributed to other collection intervals, e.g. every 5 minutes. Conversely, on occasions of logger failure, there may be full days of data absent.

<strong>A V1 set of the data, planned for release in summer of 2018 will provided cleaned and calibrated versions of the data.</strong>

Some instruments have been replaced over the life of a station. In 2015, all original U30 logger boxes were replaced with the RX3000 model.  For complete metadata or records of instrumentation, please contact project advisor E. Osenga at eliseo at agci.org.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request
DOI: 10.5281/zenodo.1250549
title: Iron_Soil_Moisture_Uncalibrated_2013_2017

description: These data are the complete data set from installation through Dec 31, 2017 for AGCI's interactive Roaring Fork Observation Network (iRON). The network consists of 9 stations in the Southern Rockies (Colorado, USA). Descriptions of soil type and site locations can be found at: www.agci.org/iron/stations

<strong>Please note that these soil moisture data readings are uncalibrated</strong>. Measurements taken for rain are recorded via tipping bucket rain gauge and may not be accurate for winter precipitation events (e.g. snow). Blank spaces represent absent or false readings. -888.88, -138.25, or -162.469 represents a sensor error.

Sensors used for soil moisture readings are Decagon EC-5 Dielectric probe (5cm/2in depth); Decagon 10-HS (20cm/8in; 50cm/20in depths). All other equipment is Onset, and the logger device is the RX3000 model. Data collection is generally set to every 20 minutes (most stations) or every hour (Independence Pass station), but maintenance resets, etc. may occasionally have contributed to other collection intervals, e.g. every 5 minutes. Conversely, on occasions of logger failure, there may be full days of data absent.

<strong>A V1 set of the data, planned for release in summer of 2018 will provided cleaned and calibrated versions of the data.</strong>

Some instruments have been replaced over the life of a station. In 2015, all original U30 logger boxes were replaced with the RX3000 model.  For complete metadata or records of instrumentation, please contact project advisor E. Osenga at eliseo at agci.org.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.1267837
title: Iron_Soil_Moisture_Uncalibrated_2013_2017

description: These data are the complete data set from installation through Dec 31, 2017 for AGCI's interactive Roaring Fork Observation Network (iRON). The network consists of 9 stations in the Southern Rockies (Colorado, USA). Descriptions of soil type and site locations can be found at: www.agci.org/iron/stations

<strong>Please note that these soil moisture data readings are uncalibrated</strong>. Measurements taken for rain are recorded via tipping bucket rain gauge and may not be accurate for winter precipitation events (e.g. snow). Blank spaces represent absent or false readings. -888.88, -138.25, or -162.469 represents a sensor error.

Sensors used for soil moisture readings are Decagon EC-5 Dielectric probe (5cm/2in depth); Decagon 10-HS (20cm/8in; 50cm/20in depths). All other equipment is Onset, and the logger device is the RX3000 model. Data collection is generally set to every 20 minutes (most stations) or every hour (Independence Pass station), but maintenance resets, etc. may occasionally have contributed to other collection intervals, e.g. every 5 minutes. Conversely, on occasions of logger failure, there may be full days of data absent.

<strong>A V1 set of the data, planned for release in summer of 2018 will provided cleaned and calibrated versions of the data.</strong>

Some instruments have been replaced over the life of a station. In 2015, all original U30 logger boxes were replaced with the RX3000 model.  For complete metadata or records of instrumentation, please contact project advisor E. Osenga at eliseo at agci.org.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.10724799
title: iRON_Soil_Moisture_Uncalibrated_2023

description: These are minimally processed, near raw data. Potential sensor errors or equipment changes are not flagged. 

 

Rain values are from a tipping bucket rain gauge, and values may not accurately represent precipitation in winter months.These files have been corrected for data gaps and sensor label errors. V0 Files published prior to Feb 22, 2022 may contain errords.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.10724811
title: iRON_Soil_Moisture_Uncalibrated_2023

description: These are minimally processed, near raw data. Potential sensor errors or equipment changes are not flagged. 

 

Rain values are from a tipping bucket rain gauge, and values may not accurately represent precipitation in winter months.These files have been corrected for data gaps and sensor label errors. V0 Files published prior to Feb 22, 2022 may contain errords.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.5281/zenodo.1228345
title: iRON_Soil_Moisture_Uncalibrated_2023

description: These are minimally processed, near raw data. Potential sensor errors or equipment changes are not flagged. 

 

Rain values are from a tipping bucket rain gauge, and values may not accurately represent precipitation in winter months.These files have been corrected for data gaps and sensor label errors. V0 Files published prior to Feb 22, 2022 may contain errords.
description: Snow data are available for Northstar Transition Zone and Independence Pass by request.

***An error has been caught in time codes. The time codes currently read GMT-5:00. The CORRECT time code is GMT-7:00 for all datasets.***
DOI: 10.6084/m9.figshare.19337498
title: Identification of a five-gene signature deriving from the vacuolar ATPase (V-ATPase) sub-classifies gliomas and decides prognoses and immune microenvironment alterations

description: Aberrant expression of coding genes of the V-ATPase subunits has been reported in glioma patients that can activate oncogenic pathways and result in worse prognosis. However, the predictive effect of a single gene is not specific or sensitive enough. In this study, by using a series of bioinformatics analyses, we identified five coding genes (ATP6V1C2, ATP6V1G2, TCIRG1, ATP6AP1 and ATP6AP2) of the V-ATPase that were related to glioma patient prognosis. Based on the expression of these genes, glioma patients were sub-classified into different prognosis clusters, of which C1 cluster performed better prognosis; however, C2 cluster showed more malignant phenotypes with oncogenic and immune-related pathway activation. The single-cell RNA-seq data revealed that ATP6AP1, ATP6AP2, ATP6V1G2 and TCIRG1 might be cell-type potential markers. Copy number variation and DNA promoter methylation potentially regulate these five gene expressions. A risk score model consisted of these five genes effectively predicted glioma prognosis and was fully validated by six independent datasets. The risk scores also showed a positive correlation with immune checkpoint expression. Importantly, glioma patients with high-risk scores presented resistance to traditional treatment. We also revealed that more inhibitory immune cells infiltration and higher rates of “non-response” to immune checkpoint blockade (ICB) treatment in the high-risk score group. In conclusion, our study identified a five-gene signature from the V-ATPase that could sub-classify gliomas into different phenotypes and their abnormal expression was regulated by distinct mechanisms and accompanied with immune microenvironment alterations potentially act as a biomarker for ICB treatment.