cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7140374.v1
title: Supplementary Material for: Brain Diffusion Imaging and Tractography to Distinguish Clinical Severity of Human <b><i>PLP1</i></b>-Related Disorders

description: <b><i>Aims:</i></b> We performed quantitative diffusion tensor imaging and brain tractography to distinguish clinical severity in a series of 35 patients with hypomyelinating <i>PLP1</i>-related disorders classified using the Motor Developmental Score according to the best motor function acquired before the age of 5 years and the gross motor function measure (GMFM) at the time of magnetic resonance imaging acquisition. <b><i>Methods:</i></b> We calculated fractional anisotropy and diffusivity values in 26 regions of interest and the numbers of fibers and volumes of hemisphere tractograms. Fiber bundles on tractograms were characterized according to 3 criteria: size, direction of main-stream fibers, and connectivity of bundles (extratelencephalic projections, commissural fibers, and intrahemispheric connections). <b><i>Results:</i></b> Age-adjusted multivariate analysis in 3 severity groups revealed increased isotropic diffusion in the superior cerebellar peduncle and grey matter in the most severe group, and larger tractogram volumes and increased numbers of fibers in the least severely affected group. Tractogram patterns showed preserved extratelencephalic projections and a main anterior-posterior aspect of intrahemispheric fibers in most patients, whereas interhemispheric connectivity was variable. The most severely affected and intermediate patients had less intrahemispheric connectivity, with a frequent predominant anterior-posterior direction of main-stream fibers. <b><i>Interpretation:</i></b> Diffusion tensor imaging and tractographic parameters can operate as biomarkers to distinguish clinical severity in <i>PLP1</i>-related disorders and could improve our understanding of hypomyelinating leukodystrophies.
DOI: 10.6084/m9.figshare.7140347
title: Evaluation of imputation accuracy using the combination of two high density panels in Nelore beef cattle

description: Files used to produce the results in the paper "Evaluation of imputation accuracy using the combination of two high density panels in Nelore beef cattle". There are genotype files in Plink format after quality control (three files - *.bed,*.bim and *.fam) for each panel used in the analysis.
DOI: 10.6084/m9.figshare.7140350
title: Subiculum scRNA-seq

description: Single-cell data and code accompanying Cembrowski et al., 2018
DOI: 10.7284/122768
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15234 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122769
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15234 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140290
title: SEM Image of Samples 1 - 2 - 3.jpg

description: 1. High-res SEM image of Sample 1 triaxially deformed at Peff = 5MPa.<br>2. High-res SEM image of Sample 1 triaxially deformed at Peff = 15MPa.<br><br>3. 1. High-res SEM image of Sample 1 triaxially deformed at Peff = 30MPa.
DOI: 10.6084/m9.figshare.7140215
title: Supplementary Material for: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

description: <b><i>Background:</i></b> Propofol induces acute neurotoxicity (e.g., neuroapoptosis) followed by impairment of long-term memory and learning in animals. However, underlying mechanisms remain largely unknown. Long non-coding RNAs (lncRNAs) are found to participate in various pathological processes. We hypothesized that lncRNA profile and the associated signaling pathways were altered, and these changes might be related to the neurotoxicity observed in the neonatal mouse hippocampus following propofol exposure. <b><i>Methods:</i></b> In this laboratory experiment, 7-day-old mice were exposed to a subanesthetic dose of propofol for 3 hours, with 4 animals per group. Hippocampal tissues were harvested 3 hours after propofol administration. Neuroapoptosis was analyzed based on caspase 3 activity using a colorimetric assay. A microarray was performed to investigate the profiles of 35,923 lncRNAs and 24,881 messenger RNAs (mRNAs). Representative differentially expressed lncRNAs and mRNAs were validated using reverse transcription quantitative polymerase chain reaction. All mRNAs dysregulated by propofol and the 50 top-ranked, significantly dysregulated lncRNAs were subject to bioinformatics analysis for exploring the potential mechanisms and signaling network of propofol-induced neurotoxicity. <b><i>Results:</i></b> Propofol induced neuroapoptosis in the hippocampus, with differential expression of 159 lncRNAs and 100 mRNAs (fold change ± 2.0, P&lt; 0.05). Bioinformatics analysis demonstrated that these lncRNAs and their associated mRNAs might participate in neurodegenerative pathways (e.g., calcium handling, apoptosis, autophagy, and synaptogenesis). <b><i>Conclusion:</i></b> This novel report emphasizes that propofol alters profiles of lncRNAs, mRNAs, and their cooperative signaling network, which provides novel insights into molecular mechanisms of anesthetic-induced developmental neurodegeneration and preventive targets against the neurotoxicity.
DOI: 10.7284/122770
title: Gyrocompass data collected during research cruise WS15234 using a SGB Meridian instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140209
title: Urban link travel speed dataset from a megacity road network

description: Link travel speeds in road networks are fundamental data in many research areas of traffic, transportation, and logistics. To support the research in these areas, we develop a dataset, containing the travel speeds on each road link and in different time periods together with the real road network map. The dataset is collected from a representative megacity in Western China, Chengdu. The road network of this city involves different urban road network structures. The dataset shows the realistic variations and randomness of urban link travel speeds. This enables the research of real data-driven decision-making problems in traffic, transportation and logistics areas.<i></i>
DOI: 10.6084/m9.figshare.7140215.v1
title: Supplementary Material for: Propofol Alters Long Non-Coding RNA Profiles in the Neonatal Mouse Hippocampus: Implication of Novel Mechanisms in Anesthetic-Induced Developmental Neurotoxicity

description: <b><i>Background:</i></b> Propofol induces acute neurotoxicity (e.g., neuroapoptosis) followed by impairment of long-term memory and learning in animals. However, underlying mechanisms remain largely unknown. Long non-coding RNAs (lncRNAs) are found to participate in various pathological processes. We hypothesized that lncRNA profile and the associated signaling pathways were altered, and these changes might be related to the neurotoxicity observed in the neonatal mouse hippocampus following propofol exposure. <b><i>Methods:</i></b> In this laboratory experiment, 7-day-old mice were exposed to a subanesthetic dose of propofol for 3 hours, with 4 animals per group. Hippocampal tissues were harvested 3 hours after propofol administration. Neuroapoptosis was analyzed based on caspase 3 activity using a colorimetric assay. A microarray was performed to investigate the profiles of 35,923 lncRNAs and 24,881 messenger RNAs (mRNAs). Representative differentially expressed lncRNAs and mRNAs were validated using reverse transcription quantitative polymerase chain reaction. All mRNAs dysregulated by propofol and the 50 top-ranked, significantly dysregulated lncRNAs were subject to bioinformatics analysis for exploring the potential mechanisms and signaling network of propofol-induced neurotoxicity. <b><i>Results:</i></b> Propofol induced neuroapoptosis in the hippocampus, with differential expression of 159 lncRNAs and 100 mRNAs (fold change ± 2.0, P&lt; 0.05). Bioinformatics analysis demonstrated that these lncRNAs and their associated mRNAs might participate in neurodegenerative pathways (e.g., calcium handling, apoptosis, autophagy, and synaptogenesis). <b><i>Conclusion:</i></b> This novel report emphasizes that propofol alters profiles of lncRNAs, mRNAs, and their cooperative signaling network, which provides novel insights into molecular mechanisms of anesthetic-induced developmental neurodegeneration and preventive targets against the neurotoxicity.
DOI: 10.7284/122777
title: INS (Inertial Navigation System) data collected during research cruise WS15234 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122797
title: Multiplexed data collected during research cruise WS15251 using a Miami VIDS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140197
title: Supplementary Material for: Nicotinamide Phosphoribosyltransferase Inhibitor APO866 Prevents IL-1β-Induced Human Nucleus Pulposus Cell Degeneration via Autophagy

description: <b><i>Background/Aims</i></b><b><i>:</i></b> Intervertebral discs consist of an extracellular matrix (ECM) with a central gelatinous nucleus pulposus (NP) enclosed in an outer layer known as the annulus fibrosus. ECM metabolic disorders result in loss of boundary between the annulus fibrosus and NP, which can lead to intervertebral disc degeneration (IDD). Proinflammatory cytokines, such as interleukin (IL)-1β, mediate the progression of IDD. Nicotinamide phosphoribosyltransferase (Nampt) catalyzes the first step in the biosynthesis of nicotinamide adenine dinucleotide (NAD) and is known to be induced by IL-1β. APO866 is an inhibitor of NAD biosynthesis and is involved in autophagy. LC3 (microtubule-associated protein 1 light chain 3) is a key regulator of autophagy and is used as an indicator of increased autophagy. Herein, we investigate the role of APO866 in regulating autophagy in NP cells and IL-1β mediated NP cell degeneration and apoptosis. <b><i>Methods:</i></b> NP cells were extracted from IDD tissues and cultured in DMEM/F12 medium. Nampt was induced by different concentrations of IL-1β (0, 0.5, 1, 5, 10 ng/mL) for 24 h or NP cells were treated with 10 ng/mL IL-1β for 0, 6, 12, 48 h. QRT-PCR and western blots were used to detect Nampt and ECM-related protein expression in NP tissue of patients with IDD and in NP cells. Confocal analysis was used to detect membrane-bound LC3, Aggrecan, and Collagen II. <b><i>Results:</i></b> Nampt is expressed in NP tissue at higher levels in severe grades of IDD (Grade IV and V) compared with low grades (Grade II and III). In NP cells, 10 ng/mL IL-1β induced Nampt expression for 48 h, increased expression of the degradative-associated proteins, ADAMTS4/5 and MMP-3/13, and decreased expression of ECM-related proteins, Aggrecan and Collagen II. However, the Nampt inhibitor APO866 blocked IL-1β induction, and the knockdown of Nampt expression increased the expression of ECM proteins that were inhibited by IL-1β. Moreover, evidence provided by the autophagic markers LC3 and Beclin-1 indicated that APO866 induced NP cell autophagy. Furthermore, although APO866 inhibited the downregulated expression of ECM-related proteins by IL-1β, this function was blocked by autophagy inhibitor, 3-methyladenine. <b><i>Conclusion:</i></b> APO866 protects NP cells and induces autophagy by inhibiting IL-1β-induced NP cell degeneration and apoptosis, which may have therapeutic potential in IDD.
DOI: 10.6084/m9.figshare.7140209.v2
title: Urban link travel speed dataset from a megacity road network

description: Link travel speeds in road networks are fundamental data in many research areas of traffic, transportation, and logistics. To support the research in these areas, we develop a dataset, containing the travel speeds on each road link and in different time periods together with the real road network map. The dataset is collected from a representative megacity in Western China, Chengdu. The road network of this city involves different urban road network structures. The dataset shows the realistic variations and randomness of urban link travel speeds. This enables the research of real data-driven decision-making problems in traffic, transportation and logistics areas.<i></i>
DOI: 10.7284/122799
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise WS15251 using a Hawaii UHDAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140209.v3
title: Urban link travel speed dataset from a megacity road network

description: Link travel speeds in road networks are fundamental data in many research areas of traffic, transportation, and logistics. To support the research in these areas, we develop a dataset, containing the travel speeds on each road link and in different time periods together with the real road network map. The dataset is collected from a representative megacity in Western China, Chengdu. The road network of this city involves different urban road network structures. The dataset shows the realistic variations and randomness of urban link travel speeds. This enables the research of real data-driven decision-making problems in traffic, transportation and logistics areas.<i></i>
DOI: 10.7284/122796
title: Anemometer data collected during research cruise WS15251 using a RM Young 05106 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140149
title: Supplementary Material for: NCOA3 Loss Disrupts Molecular Signature of Chondrocytes and Promotes Posttraumatic Osteoarthritis Progression

description: <b><i>Background/Aims:</i></b> Osteoarthritis (OA) is the most common joint disease. Recently, a novel variant near the nuclear receptor coactivator 3 (<i>NCOA3</i>) has been identified in association with greater risk of developing OA. However, how NCOA3 is regulated in chondrocytes and involved in OA pathogenesis remain elusive. <b><i>Methods:</i></b> The expression and DNA methylation of <i>NCOA3</i> in knee OA cartilage and <i>in vitro</i> dedifferentiated chondrocytes with or without rs6094710 SNP were analyzed by qRT-PCR, immunoblotting, methylation-specific PCR and bisulfite sequencing. NCOA3 was depleted by siRNA or shRNA or inhibited by a chemical inhibitor to assess its role in chondrocyte dedifferentiation or OA pathogenesis in posttraumatic OA animal model established by cruciate ligament transection surgery. <b><i>Results:</i></b> We found that compared with normal counterparts, samples with rs6094710 SNP failed to upregulate NCOA3. Further evidence associated this phenotype with DNMT1-mediated hypermethylation in gene promoter region. Moreover, we showed that NCOA3 maintained the molecular signature of chondrocytes dedifferentiating <i>in vitro</i> or exposed to IL-1β, nevertheless, NCOA3 appeared dispensable for preventing OA initiation, since NCOA3 loss did not trigger OA in young mice. Instead, NCOA3 loss promoted posttraumatic OA progression, and in parallel, enhanced NF-κB activation. Finally, the promoted posttraumatic OA progression was significantly retarded when administrated with NF-κB pathway inhibitor, suggesting that NCOA3 lose promotes posttraumatic OA at least partially by enhancing NF-κB activation. <b><i>Conclusion:</i></b> Thus, our findings indicate a critical role of NCOA3 in chondrocytes, and imply that manipulating NCOA3 might present a potential therapeutic approach to interfere OA progression.
DOI: 10.7284/122794
title: Fluorometer data collected during research cruise WS15251 using a Turner Cyclops-7 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122784
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15251 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140140
title: BNS simulations - ascii table

description: Simulated BNS mergers with gravitational wave detection<br>
DOI: 10.6084/m9.figshare.7140140.v1
title: BNS simulations - ascii table

description: Simulated BNS mergers with gravitational wave detection<br>
DOI: 10.7284/122785
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15251 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122786
title: Gyrocompass data collected during research cruise WS15251 using a SGB Meridian instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122795
title: Hygrometer data collected during research cruise WS15251 using a RM Young 41372VC instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122793
title: INS (Inertial Navigation System) data collected during research cruise WS15251 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122787
title: Radiometer data collected during research cruise WS15251 using a Eppley PSP instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122788
title: Radiometer data collected during research cruise WS15251 using a Eppley TUV instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122792
title: Radiometer data collected during research cruise WS15251 using a Eppley PIR instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122791
title: Rain Gauge data collected during research cruise WS15251 using a OSI ORG-815 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122798
title: Singlebeam Echosounder data collected during research cruise WS15251 using a Knudsen 3260 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122789
title: Water Temperature data collected during research cruise WS15251 using a Sea-Bird SBE-38 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122790
title: TSG (Thermosalinograph) data collected during research cruise WS15251 using a Sea-Bird SBE-45 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122814
title: Multiplexed data collected during research cruise WS15264 using a Miami VIDS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122816
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise WS15264 using a Hawaii UHDAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122813
title: Anemometer data collected during research cruise WS15264 using a RM Young 05106 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122809
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise WS15264 using a Sea-Bird SBE-911+ instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140053
title: Data.sav

description: The major aim of our study was to investigate the influence of anxiety and fear on pain with the NPU paradigm. Additionally, we were interested in the influence of anxiety sensitivity (AS) on pain perception, in interaction with anxiety and fear. Forty healthy subjects were selected for inclusion in the HAS or LAS group based on cut-off-scores of the Anxiety Sensitivity Index- 3 (ASI-III). Subjects rated the painfulness of electric stimuli in three conditions of the NPU paradigm: N (no shocks), P (predictable shocks, fear), and U (unpredictable shocks, anxiety). Startle reflex and anxiety ratings were determined as manipulation check.
DOI: 10.7284/122811
title: Fluorometer data collected during research cruise WS15264 using a Turner Cyclops-7 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140053.v1
title: Data.sav

description: The major aim of our study was to investigate the influence of anxiety and fear on pain with the NPU paradigm. Additionally, we were interested in the influence of anxiety sensitivity (AS) on pain perception, in interaction with anxiety and fear. Forty healthy subjects were selected for inclusion in the HAS or LAS group based on cut-off-scores of the Anxiety Sensitivity Index- 3 (ASI-III). Subjects rated the painfulness of electric stimuli in three conditions of the NPU paradigm: N (no shocks), P (predictable shocks, fear), and U (unpredictable shocks, anxiety). Startle reflex and anxiety ratings were determined as manipulation check.
DOI: 10.7284/122800
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15264 using a Raytheon 300 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7140035
title: mutations_pos.bed

description: List of the mutated sites of the hg19 reference genome used in de Filippo et al. "Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences".