cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5363560.v1
title: Supplementary Material for: Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98

description: A 41-year-old Asian woman with bilateral renal angiomyolipomas (AML) was incidentally identified to have a balanced translocation, 46,XX,t(11;12)(p15.4;q15). She had no other features or family history to suggest a diagnosis of tuberous sclerosis. Her healthy daughter had the same translocation and no renal AML at the age of 3 years. Whole-genome sequencing was performed on genomic maternal DNA isolated from blood. A targeted de novo assembly was then conducted with ABySS for chromosomes 11 and 12. Sanger sequencing was used to validate the translocation breakpoints. As a result, genomic characterization of chromosomes 11 and 12 revealed that the 11p breakpoint disrupted the <i>NUP98 </i>gene in intron 1, causing a separation of the promoter and transcription start site from the rest of the gene. The translocation breakpoint on chromosome 12q was located in a gene desert. <i>NUP98</i> has not yet been associated with renal AML pathogenesis, but somatic <i>NUP98</i> alterations are recurrently implicated in hematological malignancies, most often following a gene fusion event. We also found evidence for complex structural events involving chromosome 12, which appear to disrupt the <i>TDG</i> gene. We identified a <i>TDGP1</i> partially processed pseudogene at 12p12.1, which adds complexity to the de novo assembly. In conclusion, this is the first report of a germline constitutional structural chromosome rearrangement disrupting <i>NUP98</i> that occurred in a generally healthy woman with bilateral renal AML.
DOI: 10.6084/m9.figshare.5363545
title: Data for paper submitted to BMC Bioinformatics

description: The data stem fromI. Cantone, L. Marucci, F. Iorio, M.A. Ricci, V. Belcastro, M. Bansal, S. Santini, M. di Bernardo, D. di Bernardo and M.P. Cosma (2009): A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches, Cell, 137, 172-181.Grzegorczyk, M. and Husmeier, D. (2012): A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology, Statistical Applications in Genetics and Molecular Biology (SAGMB), 11(4), Article 7.<br>Please see those publications for details. <br>
DOI: 10.6084/m9.figshare.5363551
title: Supplementary Material for: Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

description: Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (<i>Acipenser ruthenus</i>) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.<br>
DOI: 10.6084/m9.figshare.5363551.v1
title: Supplementary Material for: Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus)

description: Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (<i>Acipenser ruthenus</i>) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.<br>
DOI: 10.6084/m9.figshare.5363545.v1
title: Data for paper submitted to BMC Bioinformatics

description: The data stem fromI. Cantone, L. Marucci, F. Iorio, M.A. Ricci, V. Belcastro, M. Bansal, S. Santini, M. di Bernardo, D. di Bernardo and M.P. Cosma (2009): A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches, Cell, 137, 172-181.Grzegorczyk, M. and Husmeier, D. (2012): A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology, Statistical Applications in Genetics and Molecular Biology (SAGMB), 11(4), Article 7.<br>Please see those publications for details. <br>
DOI: 10.6084/m9.figshare.5363494
title: Upper body Inertial motion data of human grasp dataset

description: File containing intertial motion data of upper body acquired using Xsens MVN suit during grasping experiments
DOI: 10.6084/m9.figshare.5363545.v2
title: Data for paper submitted to BMC Bioinformatics

description: The data stem fromI. Cantone, L. Marucci, F. Iorio, M.A. Ricci, V. Belcastro, M. Bansal, S. Santini, M. di Bernardo, D. di Bernardo and M.P. Cosma (2009): A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches, Cell, 137, 172-181.Grzegorczyk, M. and Husmeier, D. (2012): A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology, Statistical Applications in Genetics and Molecular Biology (SAGMB), 11(4), Article 7.<br>Please see those publications for details. <br>
DOI: 10.6084/m9.figshare.5363494.v1
title: Upper body Inertial motion data of human grasp dataset

description: File containing intertial motion data of upper body acquired using Xsens MVN suit during grasping experiments
DOI: 10.6084/m9.figshare.5363428
title: Dataset of telemonitored blood pressure readings to investigate if they are affected by end digit preference

description: Systolic and diastolic blood pressure readings from patients using one of two telemonitoring systems: "patient-texted" or "automatic-transmission". See corresponding publication "Are self-reported telemonitored blood pressure readings affected by end digit preference: a prospective cohort study".
DOI: 10.6084/m9.figshare.5363386
title: Explaining the evolving role of national parliaments under the European Semester

description: This contribution examines and explains the role of national parliaments in the European Semester process. It builds on original survey-based evidence and traces whether national parliaments discuss and vote on Stability/Convergence and on National Reform Programmes; how their involvement changed over time; and what might condition national varieties of parliamentary scrutiny over European Union (EU) affairs. We find significant cross-country variation in whether the debate is taking place at the parliamentary level; whether it is European Affairs or finance committees that are involved; and whether there is involvement <i>ex ante</i> (before submission) and/or <i>ex post</i> (after country-specific recommendations). From 2012 to 2015, finance committees played an increasingly prominent role. Traditional measures of the strength of parliament do not explain what we observe. We do find that non-euro area member states were most likely to monitor EU recommendations under the European Semester and that this effect increased over time.
DOI: 10.6084/m9.figshare.5363386.v1
title: Explaining the evolving role of national parliaments under the European Semester

description: This contribution examines and explains the role of national parliaments in the European Semester process. It builds on original survey-based evidence and traces whether national parliaments discuss and vote on Stability/Convergence and on National Reform Programmes; how their involvement changed over time; and what might condition national varieties of parliamentary scrutiny over European Union (EU) affairs. We find significant cross-country variation in whether the debate is taking place at the parliamentary level; whether it is European Affairs or finance committees that are involved; and whether there is involvement <i>ex ante</i> (before submission) and/or <i>ex post</i> (after country-specific recommendations). From 2012 to 2015, finance committees played an increasingly prominent role. Traditional measures of the strength of parliament do not explain what we observe. We do find that non-euro area member states were most likely to monitor EU recommendations under the European Semester and that this effect increased over time.
DOI: 10.6084/m9.figshare.5363377
title: Environmental correlates of breeding abundance and population change of Eurasian Curlew <i>Numenius arquata</i> in Britain

description: <b>Capsule:</b> Across Britain, breeding Eurasian Curlew <i>Numenius arquata</i> are less numerous and have shown greater population declines in areas with more arable farming, woodland cover and higher generalist predator abundance. <b>Aims:</b> We present the first national-scale analysis of the potential drivers of Curlew population change in Britain, which is needed to guide conservation action for this globally near-threatened, declining species. <b>Methods:</b> Breeding Bird Survey data and environmental predictors were used to model variation in Curlew abundance in 1995–99 and 2007–11, and population change between these periods. <b>Results:</b> Arable farming and woodland cover were negatively associated with Curlew abundance and population declines. Curlew abundance was positively associated with extent of protected area coverage and gamebird numbers. Abundance and population change were positively associated with cooler temperatures and higher summer rainfall, but negatively associated with numbers of generalist predators. <b>Conclusions:</b> We found support for the negative effects of intensive agriculture, forestry, increases in generalist predator populations and climate warming on Curlew abundance and population change. Effective site protection and measures to reduce generalist predator abundance may be important conservation measures, together with improving breeding habitat quality in the wider countryside.
DOI: 10.6084/m9.figshare.12901610
title: dummy.bw

description: UCSC test
DOI: 10.6084/m9.figshare.12901610.v1
title: dummy.bw

description: UCSC test
DOI: 10.17608/k6.auckland.5362726
title: GCM simulation data - 2017

description: General-Circulation-Model simulations of fast atmospheric adjustment following CO2 increase. Data used in Dinh and Fueglistaler, 2017, Journal of Advances in Modeling Earth System.
DOI: 10.17608/k6.auckland.5362726.v2
title: GCM simulation data - 2017

description: General-Circulation-Model simulations of fast atmospheric adjustment following CO2 increase. Data used in Dinh and Fueglistaler, 2017, Journal of Advances in Modeling Earth System.
DOI: 10.17608/k6.auckland.5362726.v1
title: GCM simulation data - 2017

description: General-Circulation-Model Simulations of fast atmospheric adjustment following CO2 increase
DOI: 10.6084/m9.figshare.5362627
title: Benchmark datasets for bilateral lower limb neuromechanical signals from wearable sensors during unassisted locomotion in able-bodied individuals

description: This dataset, the <b>EN</b>cyclopedia of <b>A</b>ble-bodied <b>B</b>ilateral <b>L</b>ower <b>L</b>imb <b>L</b>ocomotor <b>S</b>ignals <b>(ENABL3S)</b>,<b> </b>represents a benchmark for lower limb neuromechanical signals recorded using wearable sensors from 10 able-bodied individuals during unassisted locomotion. In addition to sitting and standing, subjects freely transitioned between level ground walking, ramp ascent/descent, and stair ascent/descent at their self-selected speed. Subjects were bilaterally instrumented with surface electromyography (EMG) from seven lower limb muscles, goniometers at the knee and ankle, and inertial measurement units (IMU) at the shank, thigh. An additional IMU was worn around the waist. Features commonly used in lower limb intent recognition for prosthesis control have been extracted from windows near heel contact and toe off gait events.<br>If you use this dataset, please cite as:Hu, B., Rouse, E. and Hargrove, L. (2018). Benchmark Datasets for Bilateral Lower-Limb Neuromechanical Signals from Wearable Sensors during Unassisted Locomotion in Able-Bodied Individuals. Frontiers in Robotics and AI 5:14.
DOI: 10.6084/m9.figshare.5362603
title: Table S2: U–Pb data. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S2: Isotope dilution thermal ionization mass spectrometry U–Pb.
DOI: 10.6084/m9.figshare.5362603.v1
title: Table S2: U–Pb data. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S2: Isotope dilution thermal ionization mass spectrometry U–Pb.
DOI: 10.6084/m9.figshare.5362597
title: Table S1: Trace elements. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S1: Laser ablation inductively coupled plasma mass spectrometry trace element data table.
DOI: 10.6084/m9.figshare.5362600
title: Table S3: Results of the Bayesian age modelling. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S3: Results of the Bayesian age modelling.
DOI: 10.6084/m9.figshare.5362597.v1
title: Table S1: Trace elements. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S1: Laser ablation inductively coupled plasma mass spectrometry trace element data table.
DOI: 10.6084/m9.figshare.5362600.v1
title: Table S3: Results of the Bayesian age modelling. High-resolution stratigraphy and zircon U–Pb geochronology of the Middle Triassic Buchenstein Formation (Dolomites, northern Italy): precession-forcing of hemipelagic carbonate sedimentation and calibration of the Anisian–Ladinian boundary interval

description: Table S3: Results of the Bayesian age modelling.
DOI: 10.6084/m9.figshare.5362588
title: Raw data_Ohno-2017-elife

description: Raw data_Ohno et al., 2017, eLife, 6:e28877<br>
DOI: 10.6084/m9.figshare.5362627.v1
title: Benchmark datasets for bilateral lower limb neuromechanical signals from wearable sensors during unassisted locomotion in able-bodied individuals

description: This dataset, the <b>EN</b>cyclopedia of <b>A</b>ble-bodied <b>B</b>ilateral <b>L</b>ower <b>L</b>imb <b>L</b>ocomotor <b>S</b>ignals <b>(ENABL3S)</b>,<b> </b>represents a benchmark for lower limb neuromechanical signals recorded using wearable sensors from 10 able-bodied individuals during unassisted locomotion. In addition to sitting and standing, subjects freely transitioned between level ground walking, ramp ascent/descent, and stair ascent/descent at their self-selected speed. Subjects were bilaterally instrumented with surface electromyography (EMG) from seven lower limb muscles, goniometers at the knee and ankle, and inertial measurement units (IMU) at the shank, thigh. An additional IMU was worn around the waist. Features commonly used in lower limb intent recognition for prosthesis control have been extracted from windows near heel contact and toe off gait events.
DOI: 10.6084/m9.figshare.5362216
title: Operationalizing Conflict & Coordination Between Automated Software Agents (datasets)

description: Datasets related to the Operationalizing Conflict & Coordination Between Automated Software Agents paper.<br>For the paper, see:https://commons.wikimedia.org/wiki/File:Operationalizing-conflict-bots-wikipedia-cscw-preprint.pdf<br><br>For the code, see: https://github.com/halfak/are-the-bots-really-fighting<br>
DOI: 10.6084/m9.figshare.5362354
title: RobustLinks

description: Robust Links. http://robustlinks.mementoweb.org
DOI: 10.6084/m9.figshare.5361601
title: Signposting

description: Some Signposting images. http://signposting.org
DOI: 10.6084/m9.figshare.5362588.v2
title: Raw data_Ohno-2017-elife

description: Raw data_Ohno et al., 2017, eLife, 6:e28877<br>
DOI: 10.6084/m9.figshare.5361601.v1
title: Signposting

description: Some Signposting images. http://signposting.org
DOI: 10.6084/m9.figshare.5362216.v1
title: CSCW data and code

description: Datasets related to the Operationalizing Conflict & Coordination Between Automated Software Agents paper.
DOI: 10.6084/m9.figshare.5362546.v1
title: USGS Surface Water Data for Coastal States

description: A collection of data pulled from the USGS Surface Water database, sorted by parameter of interest (e.g. chlorophyll, discharge, DOM...). The fileset contains all data for coastal states within the categories ocean, coastal, estuary, and tidal stream.
DOI: 10.6084/m9.figshare.5362588.v1
title: Ohno-2017-elife

description: Raw data in Ohno et al., 2017, eLife, 6:e28877<br>
DOI: 10.6084/m9.figshare.5361016
title: Uploaded ICIDR files.zip

description: ICIDR project, TIanjin, China 2011-2015.<br>
DOI: 10.6084/m9.figshare.5362354.v2
title: RobustLinks

description: Robust Links. http://robustlinks.mementoweb.org
DOI: 10.6084/m9.figshare.5361016.v1
title: Uploaded ICIDR files.zip

description: ICIDR project, TIanjin, China 2011-2015.<br>
DOI: 10.6084/m9.figshare.5361013
title: Simulation data for RNA benchmark

description: A collection of files generated by a PBSIM tool during the creation of simulated datasets for RNAseq benchmark.<br>These files are used to evaluate the results of mapping tools on simulated datasets.
DOI: 10.6084/m9.figshare.5361013.v1
title: Simulation data for RNA benchmark

description: A collection of files generated by a PBSIM tool during the creation of simulated datasets for RNAseq benchmark.<br>These files are used to evaluate the results of mapping tools on simulated datasets.
DOI: 10.6084/m9.figshare.5362216.v2
title: Operationalizing Conflict & Coordination Between Automated Software Agents (datasets)

description: Datasets related to the Operationalizing Conflict & Coordination Between Automated Software Agents paper.
DOI: 10.6084/m9.figshare.5362546.v2
title: USGS Surface Water Data for Coastal States

description: A collection of data pulled from the USGS Surface Water database, sorted by parameter of interest (e.g. chlorophyll, discharge, DOM...). The fileset contains all data for coastal states within the categories ocean, coastal, estuary, and tidal stream.
DOI: 10.6084/m9.figshare.5360950
title: RNA_benchmark_references.zip

description: Reference genomes, gene annotations and gene expression information used for RNAseq benchmark.
DOI: 10.6084/m9.figshare.5360998
title: RNA benchmark datasets

description: Real and simulated datasets for RNAseq benchmark.
DOI: 10.6084/m9.figshare.5362216.v3
title: Operationalizing Conflict & Coordination Between Automated Software Agents (datasets)

description: Datasets related to the Operationalizing Conflict & Coordination Between Automated Software Agents paper.<br>For the paper, see:https://commons.wikimedia.org/wiki/File:Operationalizing-conflict-bots-wikipedia-cscw-preprint.pdf<br><br>For the code, see: https://github.com/halfak/are-the-bots-really-fighting<br>
DOI: 10.6084/m9.figshare.5360950.v1
title: RNA_benchmark_references.zip

description: Reference genomes, gene annotations and gene expression information used for RNAseq benchmark.
DOI: 10.6084/m9.figshare.5360416
title: Generation of genome-modified <i>Drosophila</i> cell lines using SwAP

description: The ease of generating genetically modified animals and cell lines has been markedly increased by the recent development of the versatile CRISPR/Cas9 tool. However, while the isolation of isogenic cell populations is usually straightforward for mammalian cell lines, the generation of clonal <i>Drosophila</i> cell lines has remained a longstanding challenge, hampered by the difficulty of getting <i>Drosophila</i> cells to grow at low densities. Here, we describe a highly efficient workflow to generate clonal Cas9-engineered <i>Drosophila</i> cell lines using a combination of cell pools, limiting dilution in conditioned medium and PCR with allele-specific primers, enabling the efficient selection of a clonal cell line with a suitable mutation profile. We validate the protocol by documenting the isolation, selection and verification of eight independently Cas9-edited <i>armadillo</i> mutant <i>Drosophila</i> cell lines. Our method provides a powerful and simple workflow that improves the utility of <i>Drosophila</i> cells for genetic studies with CRISPR/Cas9.
DOI: 10.6084/m9.figshare.5358562
title: Complete data for 96 countries

description: Contains data on UV radiation, complex cognitive ability, genetic distance from South Africa and other variables.<br><br>