cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7227332.v1
title: USP1 (ubiquitin specific peptidase 1) targets ULK1 and regulates its cellular compartmentalization and autophagy

description: ULK1 (unc-51 like autophagy activating kinase 1) is a core component at multiple steps of canonical macroautophagy/autophagy. The activity of ULK1 is tightly regulated by several post-translational modifications, including ubiquitination, yet the deubiquitinase (DUB) responsible for its reversible deubiquitination has not been described. Here, we identified USP1 (ubiquitin specific peptidase 1) as a key player in the modulation of ULK1 K63-linked deubiquitination. Moreover, both USP1 depletion and its chemical inhibition by pimozide are coupled to a reduction of ULK1 in Triton X-100 soluble cellular lysates, and its compartmentalization to a fraction that can be solubilized in 5 M urea. In USP1-depleted cells this fraction is also enriched in SQSTM1 (sequestosome 1), the aggresome marker HDAC6 (histone deacetylase 6), and the prototype of USP1 targets FANCD2 (FA complementation group D2). Consistently, in USP1-depleted and pimozide-treated cells, ULK1 forms protein aggregates enriched in SQSTM1, as detected by both immummunofluorescence and co-immunoprecipitation studies. Notably, depletion of USP1 inhibits canonical autophagic flux and promotes an alternative route leading to lysosomal-mediated degradation of SQSTM1. Our findings reveal a novel function of the USP1-ULK1 axis as a modulator of the switch between canonical and unconventional autophagy. Further, we provide the first evidence supporting the existence of a subset of breast tumors co-expressing ULK1 and MAP1LC3B (microtubule associated protein 1 light chain 3 beta) proteins. Because the USP1 inhibitor pimozide affects breast cancer cell growth, targeting USP1 in those tumors relying on autophagy for growth might prove to be a convenient therapeutic strategy. <b>Abbreviations</b>: ATG13: autophagy related 13; BECN1: beclin 1; BZ: bortezomib; CAPN1: calpain 1; DUB: deubiquitinase; FANCI: FA complementation group I; FANCD2: FA complementation group D2; FZR1: fizzy and cell division cycle 20 related 1; HDAC6: histone deacetylase 6; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; PMZ: pimozide; SH3GLB1: SH3 domain containing GRB2 like, endophilin B1; SQSTM1: sequestosome 1; TRAF6: TNF receptor associated factor 6; ULK1: unc-51 like autophagy activating kinase 1; USP1: ubiquitin specific peptidase 1; WDR48: WD repeat domain 48
DOI: 10.6084/m9.figshare.7227284
title: Fluvial-aeolian sedimentary facies, Sossusvlei, Namib Desert

description: Aeolian sedimentary processes and corresponding facies shape the Earth’s surface and control the evolution of dune fields. The Namib Sand Sea with its Sossusvlei playa-lake is a perfect example to investigate the spatial distribution of fluvially influenced aeolian deposits. Remote sensing in combination with ground observations allowed for mapping of the facies distribution pattern of associated fluvial and aeolian sediments. Laboratory spectral signature measurements were used to further improve the separation between six groups of facies: modern aeolian sand, deflation surface, mud pool/mud drapes, heavy mineral lag, reworked fluvial–aeolian sediments, and fossil dune remnant. The best results were achieved through a supervised classification algorithm trained by field observations, a combination of Principal Component Analysis, band ratios, texture and geomorphologic indices. Consequently, a map outlining the facies distribution pattern of the Sossusvlei area at a scale of 1:10,000 was created. We propose this as a possible workflow to efficiently map and monitor desert environments and to investigate the interplay of aeolian and fluvial sediments.
DOI: 10.7284/128777
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SP1711 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7227284.v1
title: Fluvial-aeolian sedimentary facies, Sossusvlei, Namib Desert

description: Aeolian sedimentary processes and corresponding facies shape the Earth’s surface and control the evolution of dune fields. The Namib Sand Sea with its Sossusvlei playa-lake is a perfect example to investigate the spatial distribution of fluvially influenced aeolian deposits. Remote sensing in combination with ground observations allowed for mapping of the facies distribution pattern of associated fluvial and aeolian sediments. Laboratory spectral signature measurements were used to further improve the separation between six groups of facies: modern aeolian sand, deflation surface, mud pool/mud drapes, heavy mineral lag, reworked fluvial–aeolian sediments, and fossil dune remnant. The best results were achieved through a supervised classification algorithm trained by field observations, a combination of Principal Component Analysis, band ratios, texture and geomorphologic indices. Consequently, a map outlining the facies distribution pattern of the Sossusvlei area at a scale of 1:10,000 was created. We propose this as a possible workflow to efficiently map and monitor desert environments and to investigate the interplay of aeolian and fluvial sediments.
DOI: 10.7284/128773
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1711 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7227260
title: A catalog of stars observed simultaneously by Kepler and TESS

description: A small region of the sky was observed simultaneously by both TESS and Kepler as part of TESS Sector 2 (Aug 22 - Sep 20, 2018) and Kepler's K2 Campaign 19 (Sep 7 - Sep 26, 2018). The overlap region was 0.5 sq. deg.<br>We identified 171 K2 targets that fell inside TESS Sector 2 field of view, all of which are observed at 30-minute cadence by both missions. This is the catalog of these 171 targets.
DOI: 10.6084/m9.figshare.7226945
title: Progressing from direct instruction to structured and open inquiry-based teaching in a bachelor of soil sciences program: Experience at the National University in Oman

description: Revising standard structured academic programs by incorporating research throughout the curriculum is a modern trend at universities worldwide. There are numerous publications on inquiry-based learning (IBL) in individual courses, but few provide evidence both of success at the program level and of synergy in the teaching–research nexus. Our strategy in inquiry-based teaching (IBT) relies on three intertwined premises: (a) advancing the soil BSc program from direct instruction through structured learning toward IBL, (b) including outreach activities executed by undergraduates, and (c) facilitating students’ initiatives to compete for and fulfill grants from national research agencies. Our evaluation is based on students’ self-reported evaluations in program courses, data obtained from the questionnaires administered at two workshops organized by students, and the progress of elite students who won a research grant. Students reported improved confidence and perception of an increase in teamwork skills.
DOI: 10.6084/m9.figshare.7227260.v1
title: A catalog of stars observed simultaneously by Kepler and TESS

description: A small region of the sky was observed simultaneously by both TESS and Kepler as part of TESS Sector 2 (Aug 22 - Sep 20, 2018) and Kepler's K2 Campaign 19 (Sep 7 - Sep 26, 2018). The overlap region was 0.5 sq. deg.<br>We identified 171 K2 targets that fell inside TESS Sector 2 field of view, all of which are observed at 30-minute cadence by both missions. This is the catalog of these 171 targets.
DOI: 10.7284/128774
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1711 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7226945.v1
title: Progressing from direct instruction to structured and open inquiry-based teaching in a bachelor of soil sciences program: Experience at the National University in Oman

description: Revising standard structured academic programs by incorporating research throughout the curriculum is a modern trend at universities worldwide. There are numerous publications on inquiry-based learning (IBL) in individual courses, but few provide evidence both of success at the program level and of synergy in the teaching–research nexus. Our strategy in inquiry-based teaching (IBT) relies on three intertwined premises: (a) advancing the soil BSc program from direct instruction through structured learning toward IBL, (b) including outreach activities executed by undergraduates, and (c) facilitating students’ initiatives to compete for and fulfill grants from national research agencies. Our evaluation is based on students’ self-reported evaluations in program courses, data obtained from the questionnaires administered at two workshops organized by students, and the progress of elite students who won a research grant. Students reported improved confidence and perception of an increase in teamwork skills.
DOI: 10.7284/128775
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1711 using a Furuno GP-90D instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7224347
title: Smooth Pursuit Data

description: This dataset includes eye tracking data from seven human subjects in a smooth pursuit task. Each mat file includes all the data from one subject for different conditions.
DOI: 10.7284/128776
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1711 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7224347.v1
title: Smooth Pursuit Data

description: This dataset includes eye tracking data from seven human subjects in a smooth pursuit task. Each mat file includes all the data from one subject for different conditions.
DOI: 10.7284/128772
title: Gyrocompass data collected during research cruise SP1711 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128771
title: Meteorological Station data collected during research cruise SP1711 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7224293
title: Sv genotyping talk ASHG: Giab workshop

description: My slides from my ASHG Giab workshop talk summarizing our work about SV genotyping based on short reads.
DOI: 10.6084/m9.figshare.7224317
title: questPlusInitializationFile

description: The instructions how to use this data set are available in a text file titled 'The relative contribution of color and material in object selection.txt' which can be found at https://github.com/BrainardLab/ColorMaterial .The instructions how to use this data set are available in a text file titled 'The relative contribution of color and material in object selection.txt' which can be found at https://github.com/BrainardLab/ColorMaterial .
DOI: 10.6084/m9.figshare.7224317.v1
title: questPlusInitializationFile

description: The instructions how to use this data set are available in a text file titled 'The relative contribution of color and material in object selection.txt' which can be found at https://github.com/BrainardLab/ColorMaterial .The instructions how to use this data set are available in a text file titled 'The relative contribution of color and material in object selection.txt' which can be found at https://github.com/BrainardLab/ColorMaterial .
DOI: 10.6084/m9.figshare.7224293.v1
title: Sv genotyping talk ASHG: Giab workshop

description: My slides from my ASHG Giab workshop talk summarizing our work about SV genotyping based on short reads.
DOI: 10.7284/128770
title: Winch data collected during research cruise SP1711 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128778
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1712 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128786
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SP1712 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128782
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1712 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128783
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1712 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128784
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1712 using a Furuno GP-90D instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7224104
title: Deliberation-Without-Attention in Solving Insight & Analytic Problems

description: Three experimental conditions were used in the study: conscious, unconscious with differing distractor task, and unconscious with like-kind distractor task. Additionally, problem type manipulation was achieved through the presentation of two problem types (insight and analytic).
DOI: 10.6084/m9.figshare.7224104.v1
title: Deliberation-Without-Attention in Solving Insight & Analytic Problems

description: Three experimental conditions were used in the study: conscious, unconscious with differing distractor task, and unconscious with like-kind distractor task. Additionally, problem type manipulation was achieved through the presentation of two problem types (insight and analytic).
DOI: 10.7284/128785
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1712 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128781
title: Gyrocompass data collected during research cruise SP1712 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128780
title: Meteorological Station data collected during research cruise SP1712 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128779
title: Winch data collected during research cruise SP1712 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128787
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1713 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128791
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1713 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128792
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1713 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7223876
title: Supplementary Material for: Age-Related Macular Degeneration in Chronic Kidney Disease: A Meta-Analysis of Observational Studies

description: <b><i>Background:</i></b> Age-related macular degeneration (AMD) is an important cause of blindness in aged people. Chronic kidney disease (CKD) was reported to be associated with a higher risk of AMD. However, supporting evidence was inconsistent between studies. This work intends to examine whether a positive association exists between CKD and AMD by systematic review and meta-analysis. <b><i>Methods:</i></b> A systematic search of electronic databases (Medline, PubMed, Cochrane and EMBASE) and reference lists on June 2017. The key inclusion criteria were controlled trials that investigated the relationship between AMD and CKD. The outcome measures included risk ratios and/or occurrence rates of AMD in CKD vs. non-CKD population. Data were pooled according to the type of AMD by random effect model. <b><i>Results:</i></b> Twelve observational studies (3 cohorts, 2 case controls, and 7 cross-sectionals) with a total 335,601 participants were included. Eleven studies reported risk ratios and 9 reported occurrence rates. Pooled prevalence for early, advanced, and any AMD were all higher in the CKD population than in the non-CKD population. The pooled multivariate adjusted OR of CKD vs. non-CKD was 1.49 (95% CI 1.11–2.02) for early, 1.55 (95% CI 1.05–2.27) for exudative, 1.58 (95% CI 1.12–2.23) for advanced, and 1.35 (95% CI 1.05–1.73) for any AMD. However, high statistical heterogeneity and methodological diversity existed. Moreover, results were inconsistent between different study designs. <b><i>Conclusions:</i></b> The overall results support a positive association between CKD and AMD, although some limitations exist. Given the risk that AMD is increased in CKD, regular eye screenings for the CKD population is recommended for an early detection and intervention.
DOI: 10.7284/128793
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1713 using a Furuno GP-90D instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128794
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1713 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128790
title: Gyrocompass data collected during research cruise SP1713 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7223750
title: Supplementary Material for: The Number of Items on Each Stroop Test Card Is Unrelated to Its Sensitivity

description: <b><i>Objects:</i></b> Different variations of the Stroop Color-Word Test (SCWT) exist and the tests differ in the number of items on each test card. The optimal number of items per card of the SCWT<b><i></i></b> is unclear. <b><i>Methods:</i></b> A comprehensive neuropsychological battery including the SCWT was administered to 237 cognitively normal controls (NC), 221 patients with mild cognitive impairment (MCI), and 160 patients with Alzheimer’s disease (AD). We compared the accuracy for different items of card C (SCWT-C10<sub>accuracy</sub>, SCWT-C24<sub>accuracy</sub>, and SCWT-C50<sub>accuracy</sub>) in distinguishing patients with MCI and AD from NC. <b><i>Results:</i></b> The correct responses for different items of card C were ranked in the order: NC &gt; MCI &gt; AD group and mild AD &gt; moderate AD, except for SCWT-C24<sub>accuracy</sub>. The validity of SCWT-C24<sub>accuracy</sub> was similar to that of SCWT-C50<sub>accuracy</sub> for discriminating MCI and AD from NC, as well as different levels of AD. <b><i>Conclusion:</i></b> We concluded that the number of items on the accuracy of the response was unrelated to its sensitivity to deficits and we preferred the 24-item version in daily clinical use.
DOI: 10.7284/128789
title: Meteorological Station data collected during research cruise SP1713 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128788
title: Winch data collected during research cruise SP1713 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128795
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1714 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128804
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SP1714 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128800
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1714 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128801
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1714 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7223618
title: Table 3.2. Palynofacies Analysis & Optical Kerogen Analysis

description: Palynofacies Analysis & Optical Kerogen Analysis
DOI: 10.6084/m9.figshare.7223621
title: STL_REDLINING_Analysis.csv

description: A tract-level data set of segregation, redlining, and demographic data combined with health outcomes measures from the Centers for Disease Control. This data set is specific to the City of St. Louis.
DOI: 10.6084/m9.figshare.7223618.v1
title: Table 3.2. Palynofacies Analysis & Optical Kerogen Analysis

description: Palynofacies Analysis & Optical Kerogen Analysis
DOI: 10.7284/128802
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1714 using a Furuno GP-90D instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7223612
title: Groundwater geochemistry data in Jianghan Plain, China

description: Long-term (1992-2014) groundwater geochemistry data (in mg/L except pH; n.d. represents value below the detection limit) in Jianghan Plain by the Geological Environmental Center of Hubei Province, China used in our manuscript "Understanding Spatial and Temporal Patterns and Controlling Factors of Groundwater Geochemistry in a Regional Aquifer by Using Cluster Analysis". <br><br>
DOI: 10.6084/m9.figshare.7223615
title: Table 3.1. Palynofacies Analysis & Optical Kerogen Analysis

description: Palynofacies Analysis & Optical Kerogen Analysis
DOI: 10.7284/128803
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1714 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition