cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851813.v1
title: Diversification of piRNAs expressed in PGCs and somatic cells during embryonic gonadal development

description: piRNAs are small non-coding RNAs known to play a main role in defence against transposable elements in germ cells. However, other potential functions, such as biogenesis and differences in somatic and germline expression of these regulatory elements, are not yet fully unravelled. Here, we analysed a variety of piRNA sequences detected in mouse male and female primordial germ cells (PGCs) and gonadal somatic cells at crucial stages during embryonic differentiation of germ cells (11.5–13.5 days post-coitum). NGS of sncRNA and bioinformatic characterization of piRNAs from PGCs and somatic cells, in addition to piRNAs associated with TEs, indicated functional diversification in both cell types. Differences in the proportion of the diverse types of piRNAs are detected between somatic and germline during development. However, the global diversified patterns of piRNA expression are mainly shared between germ and somatic cells, we identified piRNAs related with molecules involved in ribosome components and translation pathway, including piRNAs derived from rRNA (34%), tRNA (10%) and snoRNA (8%). piRNAs from both tRNA and snoRNA are mainly derived from 3ʹ and 5ʹ end regions. These connections between piRNAs and rRNAs, tRNAs or snoRNAs suggest important functions of specialized piRNAs in translation regulation during this window of gonadal development.
DOI: 10.6084/m9.figshare.12851819.v1
title: An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits

description: High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. We recently compared the performance (sensitivity, reliability, titration response and differential expression) of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. NEXTflex demonstrated the highest sensitivity, which may reflect its use of partially-randomized adapter sequences, but overall performance was lower than the QIAseq and TailorMix kits. NEBNext showed intermediate performance. We reaffirm that biases are kit specific, complicating the comparison of miRNA datasets generated using different kits.
DOI: 10.6084/m9.figshare.12851822.v1
title: Discovery of new group I-D introns leads to creation of subtypes and link to an adaptive response of the mitochondrial genome in fungi

description: Group I catalytic introns are widespread in bacterial, archaeal, viral, organellar, and some eukaryotic genomes, where they are reported to provide regulatory functions. The group I introns are currently divided into five types (A-E), which are themselves distributed into several subtypes, with the exception of group I type D intron (GI-D). GI-D introns belong to the rarest group with only 17 described to date, including only one with a putative role reported in fungi, where it would interfere with an adaptive response in the cytochrome b (COB) gene to quinone outside inhibitor (QoI) fungicide resistance. Using homology search methods taking into account both conserved sequences and RNA secondary structures, we analysed the mitochondrial genomes or COB genes of 169 fungal species, including some frequently under QoI selection pressure. These analyses have led to the identification of 216 novel GI-D introns, and the definition of three distinct subtypes, one of which being linked with a functional activity. We have further uncovered a homing site for this GI-D intron type, which helps refine the accepted model of quinone outside inhibitor resistance, whereby mobility of the intron across fungal mitochondrial genomes, would influence a fungus ability to develop resistance to QoIs.
DOI: 10.6084/m9.figshare.12851822
title: Discovery of new group I-D introns leads to creation of subtypes and link to an adaptive response of the mitochondrial genome in fungi

description: Group I catalytic introns are widespread in bacterial, archaeal, viral, organellar, and some eukaryotic genomes, where they are reported to provide regulatory functions. The group I introns are currently divided into five types (A-E), which are themselves distributed into several subtypes, with the exception of group I type D intron (GI-D). GI-D introns belong to the rarest group with only 17 described to date, including only one with a putative role reported in fungi, where it would interfere with an adaptive response in the cytochrome b (COB) gene to quinone outside inhibitor (QoI) fungicide resistance. Using homology search methods taking into account both conserved sequences and RNA secondary structures, we analysed the mitochondrial genomes or COB genes of 169 fungal species, including some frequently under QoI selection pressure. These analyses have led to the identification of 216 novel GI-D introns, and the definition of three distinct subtypes, one of which being linked with a functional activity. We have further uncovered a homing site for this GI-D intron type, which helps refine the accepted model of quinone outside inhibitor resistance, whereby mobility of the intron across fungal mitochondrial genomes, would influence a fungus ability to develop resistance to QoIs.
DOI: 10.6084/m9.figshare.12851840
title: A novel microRNA boosts hyper-β-oxidation of fatty acids in liver by impeding CEP350-mediated sequestration of PPARα and thus restricts chronic hepatitis C

description: Imbalance in lipid metabolism induces steatosis in liver during Chronic hepatitis C (CHC). Contribution of microRNAs in regulating lipid homoeostasis and liver disease progression is well established using small RNA-transcriptome data. Owing to the complexity in the development of liver diseases, the existence and functional importance of yet undiscovered regulatory miRNAs in disease pathogenesis was explored in this study using the unmapped sequences of the transcriptome data of HCV-HCC liver tissues following miRDeep2.pl pipeline. MicroRNA-c12 derived from the first intron of LGR5 of chromosome 12 was identified as one of the miRNA like sequences retrieved in this analysis that showed human specific origin. Northern blot hybridization has proved its existence in the hepatic cell line. Enrichment of premiR-c12 in dicer-deficient cells and miR-c12 in Ago2-RISC complex clearly suggested that it followed canonical miRNA biogenesis pathway and accomplished its regulatory function. Expression of this miRNA was quite low in CHC tissues than normal liver implying HCV-proteins might be regulating its biogenesis. Promoter scanning and ChIP analysis further revealed that under expression of p53 and hyper-methylation of STAT3 binding site upon HCV infection restricted its expression in CHC tissues. Centrosomal protein 350 (CEP350), which sequestered PPARα, was identified as one of the targets of miR-c12 using Miranda and validated by luciferase assay/western blot analysis. Furthermore, reduced triglyceride accumulation and enhanced PPARα mediated transcription of β-oxidation genes upon restoration of miR-c12 in liver cells suggested its role in lipid catabolism. Thus this study is reporting miR-c12 for the first time and showed its’ protective role during chronic HCV infection.
DOI: 10.25345/c52z0s
title: MassIVE MSV000086379 - Bottom-up proteomics with collision energies optimized for identification confidence
title: Collision energy dependent measurements on HeLa samples and performance assessment at optimized energies on QTof and Orbitrap instruments
DOI: 10.6084/m9.figshare.13150844
title: SOLID Study (Anthropometry and Blood Pressure)

description: Data was collected in SOLID (Study Of Lung function and Its Development) cohort from 2017-2019.
DOI: 10.6084/m9.figshare.13150844.v4
title: SOLID Study (Anthropometry and Blood Pressure)

description: Data was collected in SOLID (Study Of Lung function and Its Development) cohort from 2017-2019.
DOI: 10.6084/m9.figshare.13150844.v3
title: SOLID Study (Anthropometry and Blood Pressure)

description: Data was collected in SOLID (Study Of Lung function and Its Development) cohort from 2017-2019.
DOI: 10.6084/m9.figshare.13154312
title: R0312_20191130a_videos

description: Rat 0312, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13158080
title: Transition Readiness Assessment Solution 2

description: Presents the results of applying the Transition Readiness Assessment to "solution 2" as referenced in the associated publication.
DOI: 10.6084/m9.figshare.13158080.v1
title: Transition Readiness Assessment Solution 2

description: Presents the results of applying the Transition Readiness Assessment to "solution 2" as referenced in the associated publication.
DOI: 10.6084/m9.figshare.13158083
title: Transition Readiness Assessment Solution 1

description: The Transition Readiness Assessment for Solution 2
DOI: 10.6084/m9.figshare.13158083.v1
title: Transition Readiness Assessment Solution 1

description: The Transition Readiness Assessment for Solution 2
DOI: 10.5517/ccdc.csd.cc26hzvk
title: CCDC 2041159: Experimental Crystal Structure Determination

description: Related Article: S.A. Pogozhikh|2020|CSD Communication|||
DOI: 10.5281/zenodo.4134821
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.5281/zenodo.4134820
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.6084/m9.figshare.13158086
title: BGC files from selected Rhodococcus genomes

description: Biosynthetic gene cluster (BGC) files from selected Rhodoccocus genomes, as predicted by antiSMASH v4.1.0<br>
DOI: 10.6084/m9.figshare.13158086.v1
title: BGC files from selected Rhodococcus genomes

description: Biosynthetic gene cluster (BGC) files from selected Rhodoccocus genomes, as predicted by antiSMASH v4.1.0<br>
DOI: 10.6084/m9.figshare.13158059
title: Should be deleted

description: This is the code and datasets that support the findings of the IJGIS paper "Aligning geographic entities from historical maps for building knowledge graphs".
DOI: 10.6084/m9.figshare.13158059.v2
title: Should be deleted

description: This is the code and datasets that support the findings of the IJGIS paper "Aligning geographic entities from historical maps for building knowledge graphs".
DOI: 10.6084/m9.figshare.13158059.v1
title: Aligning geographic entities from historical maps for building knowledge graphs

description: This is the code and datasets that support the findings of the IJGIS paper "Aligning geographic entities from historical maps for building knowledge graphs".
DOI: 10.21227/7cqh-h078
title: Model 2.11

description: Model 2.11 Clustered-meter average monthly ratios Monthly (kWh) consumption clustering: 1. Twelve clustering models (one per month of signup): Spectral Clustering2. Clustering using (daily kWh) consumption extracted features. Cluster count set to 4 (empirically better than the 5 or 6 suggested by the elbow distortion method). Forecasting for a meter: Using the mean monthly consumption + in-cluster month-to-month ratios. Clustering Features (170) from weekend/weekday and full series:- Statistical: median, variance, quantiles, ...- Time-series: autocorrelations, trends, seasonalities, ... Month-to-month ratios:- Robust STL LOESS trend was used to calculate the month-to-month percentage ratios ---
DOI: 10.25919/5f99ee3285d35
title: Parkes observations for project P1050 semester 2020APRS_34

description: This is a request for observing time for the initial follow-up of pulsar discoveries from the re-processing of the low-latitude Galactic plane section of the HTRU survey (P630). We have now completed a first pass re-processing of the 60 % of the survey with GPU based coherent acceleration search and template bank search pipelines, and have discovered potential 54 previously unknown pulsars. Interesting science can usually only be derived from a new pulsar after confirmation and a follow-up timing campaign is carried out. One year of initial timing is the minimum timespan required to fully characterise any newly-discovered pulsars, essential for deriving pulsar parameters such as the characteristic age, magnetic field strength, spin-down rate, as well as to detect any unexpected behaviour of the pulsar which might result from emission instabilities. This follow-up and timing project is necessary for following up on any interesting pulsar systems discovered from the HTRU Galactic plane survey. Since all of the pulsars on the observing list here are being followed-up for the first time, they will produce completely new and exciting results. In addition, this timing project will enable a large-scale examination of the Galactic plane pulsar population, exploring the true boundaries of pulsar parameter space.
DOI: 10.5066/f71n7zms
title: Bathymetric Surveys of the Neosho River, Spring River, and Elk River, northeast Oklahoma and southwest Missouri, 201617

description: In February 2017, the Grand River Dam Authority filed to relicense the Pensacola Hydroelectric Project with the Federal Energy Regulatory Commission. The predominant feature of the Pensacola Hydroelectric Project is Pensacola Dam, which impounds Grand Lake O the Cherokees (locally called Grand Lake) in northeastern Oklahoma. Identification of information gaps and assessment of project effects on stakeholders are central aspects of the Federal Energy Regulatory Commission relicensing process. Some upstream stakeholders have expressed concerns about the dynamics of sedimentation and flood flows in the transition zone between major rivers and Grand Lake O the Cherokees. To relicense the Pensacola Hydroelectric Project with the Federal Energy Regulatory Commission, the hydraulic models for these rivers require high-resolution bathymetric data along the river channels. In support of the Federal Energy Regulatory Commission relicensing process, the U.S. Geological Survey, in cooperation with the Grand River Dam Authority, performed bathymetric surveys of (1) the Neosho River from the Oklahoma border to the U.S. Highway 60 bridge at Twin Bridges State Park, (2) the Spring River from the Oklahoma border to the U.S. Highway 60 bridge at Twin Bridges State Park, and (3) the Elk River from Noel, Missouri, to the Oklahoma State Highway 10 bridge near Grove, Oklahoma. The Neosho River and Spring River bathymetric surveys were performed from October 26 to December 14, 2016; the Elk River bathymetric survey was performed from February 27 to March 21, 2017. Only areas inundated during those periods were surveyed. The bathymetric surveys covered a total distance of about 76 river miles and a total area of about 5 square miles. Greater than 1.4 million bathymetric-survey data points were used in the computation and interpolation of bathymetric-survey digital elevation models and derived contours at 1-foot intervals. The minimum bathymetric-survey elevation of the Neosho River was 709.18 feet above North American Vertical Datum of 1988, which corresponds to a maximum depth of 34.22 feet. The minimum bathymetric-survey elevation of the Spring River was 714.18 feet above North American Vertical Datum of 1988, which corresponds to a maximum depth of 29.22 feet. The minimum bathymetric-survey elevation of the Elk River was 715.62 feet above North American Vertical Datum of 1988, which corresponds to a maximum depth of 27.78 feet.
DOI: 10.15131/shef.data.4834217.v1
title: Data relating to the publication "Expression and regulation of drug transporters in vertebrate neutrophils".

description: Data relating to the publication <b>Foulkes, M. J. et al. (2017) Expression and regulation of drug transporters in vertebrate neutrophils. Scientific Reports, 7, 4967. http://doi.org/10.1038/s41598-017-04785-4</b><br>Expression of SLC and ABC transporters in human and zebrafish neutrophils.<br>Protein sequences for both human and zebrafish transporters can be found in files named: Protein sequences_human and Protein sequences_zebrafish<br>Expression data can be found in files named:Expression data_human and Expression data_zebrafish<br>Methods involved in generating these data are documented in the paper.<br><br>Abbreviations:ABC - ATP-binding cassettedpf - days post fertilisationFPKM - fragments per kilobase of exon per million fragments mappedSLC - solute carrierUNTR - untreated<br>Zebrafish lines used:<i>mpx:GFP <sup>i114 </sup></i>neutrophil-specific GFP
DOI: 10.15131/shef.data.4834217
title: Data relating to the publication "Expression and regulation of drug transporters in vertebrate neutrophils".

description: Data relating to the publication <b>Foulkes, M. J. et al. (2017) Expression and regulation of drug transporters in vertebrate neutrophils. Scientific Reports, 7, 4967. http://doi.org/10.1038/s41598-017-04785-4</b><br>Expression of SLC and ABC transporters in human and zebrafish neutrophils.<br>Protein sequences for both human and zebrafish transporters can be found in files named: Protein sequences_human and Protein sequences_zebrafish<br>Expression data can be found in files named:Expression data_human and Expression data_zebrafish<br>Methods involved in generating these data are documented in the paper.<br><br>Abbreviations:ABC - ATP-binding cassettedpf - days post fertilisationFPKM - fragments per kilobase of exon per million fragments mappedSLC - solute carrierUNTR - untreated<br>Zebrafish lines used:<i>mpx:GFP <sup>i114 </sup></i>neutrophil-specific GFP
DOI: 10.6084/m9.figshare.13154312.v1
title: R0312_20191130a_videos

description: Rat 0312, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13154300
title: R0169_20170515a_videos

description: Rat 0169, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5066/p967bvql
title: Data used to describe hydrogeologic units and create contour maps and cross sections of the Boone and Roubidoux Aquifers, northeastern Oklahoma

description: The Ozark Plateau aquifer system stretches across approximately 70,000 square miles (mi2) of Arkansas, Missouri, Kansas and Oklahoma, and is composed of many hydrogeologic units, such as the Boone aquifer and the Roubidoux aquifer. However, this data release is focused on only 11,000 mi2 in northern Arkansas, southeastern Kansas, southwestern Missouri, and northeastern Oklahoma. The Boone aquifer covers approximately 10,700 mi2 of this area, and the Roubidoux aquifer covers the 11,000 mi2 area entirely. These aquifers are mostly made of Mississippian-aged and Ordovician-aged carbonate rock, and serve as the main sources of fresh groundwater in northeastern Oklahoma (Imes and Emmett, 1994). In 2017, the U.S. Geological Survey (USGS) and Oklahoma Water Resources Board (OWRB) began a hydrologic investigation to support a determination of maximum annual yields for the Boone and Roubidoux aquifers. This data release provides components of the hydrogeologic framework for that hydrologic investigation. To further characterize the hydrogeologic framework of the aquifers, contours and digital elevation models (DEMs) were created and modified on the following hydrogeologic units (listed from youngest to oldest): the Western Interior Plains confining unit, the Boone aquifer, the Ozark confining unit, and the Roubidoux aquifer. These contours and DEMs represent the altitudes of the bases of each hydrogeologic unit in feet. The hydrogeologic-unit names in this data release are consistent with those used in Oklahoma (Osborn, 2001; Czarnecki and others, 2009) and may differ from those used in regional reports describing the Ozark Plateaus aquifer system (Imes and Emmett, 1994; Westerman and others, 2016).
DOI: 10.5066/p9t3q6mb
title: RiverWare model outputs for flood calculations along the Arkansas River for a flood event in eastern and Northeastern Oklahoma during May-June 2019

description: As much as 22 inches of rain fell in Oklahoma in May 2019, resulting in historic flooding along the Arkansas River and its tributaries in eastern and northeastern Oklahoma. The flooding along the Arkansas River and its tributaries began in May continued into June 2019. Peaks of record were measured at nine U.S. Geological Survey (USGS) and U.S. Army Corps of Engineers (USACE) streamgages on various streams in eastern and northeastern Oklahoma. This data release documents the model output files for the Riverware model used to simulate regulated and unregulated conditions and the physical and operational input data, including spillway and outlet works, rating curves, established pool limits, and regulation criteria for modeling system operational constraints. The RiverWare model was developed and maintained by the USACE Tulsa District. RiverWare provides a stream basin modeling environment for operations and planning that allows a high degree of flexibility for users to model any stream basin, manage data input and output efficiently enough for near real-time operations, and provide a selection of solution algorithms. In addition to documenting the model output files, a copy of the model is provided for the convenience of the user.
DOI: 10.5066/p9b99tqz
title: Data Release of Basin Characteristics, Generalized Skew Map, and Peak-Streamflow Frequency Estimates in Oklahoma, 2017 (ver. 1.1, September 2020)

description: The U.S. Geological Survey (USGS) Oklahoma-Texas Water Science Center, in cooperation with the Oklahoma Department of Transportation, updated basin-characteristic data for Oklahoma streams with drainage areas of less than 2,510 square miles. Basin characteristics were updated or created for 248 streamgages. The previously published Oklahoma generalized skew map, a necessary element in the development of the peak-streamflow frequencies was updated. Compared to a previous dataset described in (Lewis, 2010), this dataset incorporates an additional 9 years of annual peak-streamflow data, including 2 years when major peak-streamflows were recorded (2015 and 2017). The additional years of data collection since the publication of Lewis (2010) also means that several additional streamgages now have an adequate number of years of record for frequency analysis. Some streamgages that provided data for Lewis (2010) have subsequently been determined to be influenced by regulation or were outside of the modified study area and were therefore omitted from this revised dataset. Basin characteristics were determined at each streamgage location by using a geographic information system (GIS) and Bulletin 17B methodology to create an updated Oklahoma generalized skew map. The basin-characteristic data and generalized skew map can be used to asses peak streamflows for unregulated streams in Oklahoma.
DOI: 10.25919/5f99f1deaf698
title: Database of chemical properties of Australian biomass and waste

description: This project sought to develop a database of fuel and energy characteristics for a range of Australian biomass and wastes to support their use in a range of thermochemical technologies. The database includes biomass sourced from agriculture (wheat straw, cotton trash, sugar cane trash, chicken manure, etc), forestry (mostly woody wastes from different forestry operations including some irrigated by effluent), industrial processing (timber residues, saw dust from timber mills, bagasse from sugar industry, rice hull from rice industry, paper sludge from paper industry, etc) and urban waste (municipal solid waste, green waste and biosolids and sewage from waste water treatment facilities). The database contains relatively simple-to-use information such as proximate analysis, ultimate analysis, calorific value as well as chemical composition of mineral matter to enable project proponents to draw conclusions as to likely plant capacity and annual output. It will be updated and expanded over time as more data are available.