cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26186/147988
title: Exploring for the Future, Strontium, Oxygen and Carbon Isotopes from NDI Carrara 1, South Nicholson Region, Australia

description: Geoscience Australia’s Exploring for the Future program provides precompetitive information to inform decision-making by government, community and industry on the sustainable development of Australia's mineral, energy and groundwater resources.<br>In order to gain insights into the resource potential of the South Nicholson region, a key region of focus for EFTF, National Drilling Initiative (NDI) Carrara 1 stratigraphic drill hole was completed in late 2020, as a collaboration between Geoscience Australia, the Northern Territory Geological Survey (NTGS), and the MinEx CRC. NDI Carrara 1 is the first drill hole to intersect the, as yet, undifferentiated Proterozoic rocks of the newly defined Carrara Sub-Basin within the South Nicholson region. NDI Carrara 1 is located on the western flank of the Carrara Sub-basin, reaching a total depth of 1751 m, intersecting ca. 630 m of Cambrian Georgina Basin overlying ca. 1100 m of Proterozoic carbonates, black shales and minor siliciclastics.<br>Geoscience Australia is undertaking a range of investigations on the lithology, stratigraphy and geotechnical properties of NDI Carrara 1 based on wireline data, as well as undertaking a range of analyses of over 400 physical samples recovered through the entire core. These analyses include geochronology, isotopic studies, mineralogy, inorganic and organic geochemistry, petrophysics, geomechanics, thermal maturity, and petroleum systems investigations. Hylogger™ data is available at the NTGS Geoscience Exploration and Mining Information System (GEMIS) webpage.<br>This data release presents results for analyses on selected rock samples from NDI Carrara 1, conducted by the Mawson Analytical Spectrometry Services, University of Adelaide, under contract to Geoscience Australia. These results include:<br>1. Carbon (δ13C), oxygen (δ18O) and strontium (87Sr/86Sr) isotopes on carbonate bearing samples, and2. Trace element data on the leachates prepared for 87Sr/86Sr ratio analyses.<br>
DOI: 10.6084/m9.figshare.21755386
title: Toxicoproteomics reveals an effect of clozapine on autophagy in human liver spheroids

description: <b>Background:</b> Clozapine is an atypical antipsychotic drug used to treat treatment-resistant schizophrenia. Its side effects, including liver enzyme abnormalities, experienced by many patients preclude its more common use as a first-line therapy for schizophrenia. Toxicoproteomic approaches have been demonstrated to effectively guide the identification of toxicological mechanisms. <b>Methods:</b> To further our understanding of the molecular effects of clozapine, we performed a data-independent acquisition (DIA)-based quantitative proteomics investigation of clozapine-treated human liver spheroid cultures. <b>Results:</b> In total, we quantified 4479 proteins across the five treatment groups (vehicle; 15 µM, 30 µM, and 60 µM clozapine; and 10 ng/mL TNFα + IL-1β). Clozapine (60 µM) treatment yielded 36 differentially expressed proteins (FDR &lt; 0.05). Gene-set enrichment analysis indicated perturbation of several gene sets, including interferon gamma signaling (e.g. interferon gamma receptor 1) and prominent autophagy-related processes (e.g. upregulation of sequestosome-1 (SQSTM1), MAP1LC3B/LC3B2, GABARAPL2, and nuclear receptor coactivator 4). The effects of clozapine on autophagy were confirmed by targeted mass spectrometry and western blotting using conventional SQSTM1 and LC3B markers. <b>Conclusions:</b> Combined with prior literature, our work suggests a broad contribution of autophagy to both the therapeutic and side effects of clozapine. Overall, this study demonstrates how proteomics can contribute to the elucidation of physiological and toxicological mechanisms of drugs.
DOI: 10.6084/m9.figshare.21755386.v1
title: Toxicoproteomics reveals an effect of clozapine on autophagy in human liver spheroids

description: <b>Background:</b> Clozapine is an atypical antipsychotic drug used to treat treatment-resistant schizophrenia. Its side effects, including liver enzyme abnormalities, experienced by many patients preclude its more common use as a first-line therapy for schizophrenia. Toxicoproteomic approaches have been demonstrated to effectively guide the identification of toxicological mechanisms. <b>Methods:</b> To further our understanding of the molecular effects of clozapine, we performed a data-independent acquisition (DIA)-based quantitative proteomics investigation of clozapine-treated human liver spheroid cultures. <b>Results:</b> In total, we quantified 4479 proteins across the five treatment groups (vehicle; 15 µM, 30 µM, and 60 µM clozapine; and 10 ng/mL TNFα + IL-1β). Clozapine (60 µM) treatment yielded 36 differentially expressed proteins (FDR &lt; 0.05). Gene-set enrichment analysis indicated perturbation of several gene sets, including interferon gamma signaling (e.g. interferon gamma receptor 1) and prominent autophagy-related processes (e.g. upregulation of sequestosome-1 (SQSTM1), MAP1LC3B/LC3B2, GABARAPL2, and nuclear receptor coactivator 4). The effects of clozapine on autophagy were confirmed by targeted mass spectrometry and western blotting using conventional SQSTM1 and LC3B markers. <b>Conclusions:</b> Combined with prior literature, our work suggests a broad contribution of autophagy to both the therapeutic and side effects of clozapine. Overall, this study demonstrates how proteomics can contribute to the elucidation of physiological and toxicological mechanisms of drugs.
DOI: 10.6075/j0qr4vgp
title: Data from: Eddy-induced acceleration of Lagrangian floats

description: Simulated Argo float trajectories, with advection using velocities from the Estimating the Circulation and Climate of the Ocean, Phase II (ECCO2) project.
DOI: 10.6075/j0154fc9
title: Data from: Mesopelagic fishes dominate otolith record of past two millennia in the Santa Barbara Basin

description: The two data files (Excel) in this collection contain (a) individual fossil otolith data (geometric measurements, shape characteristics and elemental composition) and (b) time series over the past two millennia at 10-y intervals for otolith deposition rate and proxies for upper ocean temperature and primary productivity. The latter time series were provided to the authors by Dr. James Kennett. All data from sediment cores from the Santa Barbara Basin.
DOI: 10.6075/j0kw5ddx
title: Data from: Superconductivity Found in Meteorites

description: This data details the discovery and analysis of superconducting material in two meteorites. These are the first superconducting materials found in extraterrestrial samples and the superconducting phases are characterized as alloys of lead, tin and indium. The collection here is divided into components which consist of different analysis techniques. See the following paragraphs for a brief description of how these techniques were used together to analyze the meteorite samples. A diverse population of meteorites was selected and powder samples were dislodged or scraped from the meteorite, for measurement in MFMMS. Superconducting candidate samples were identified in two meteorites (Mundrabilla and GRA 95205) from peaks in the Magnetic Field Modulated Microwave Spectroscopy (MFMMS) response. The grains with the most superconducting material were isolated by subdividing these samples and measuring the subsamples in the MFMMS. These subsamples were subsequently measured with Vibrating Sample Magnetometry (VSM) to confirm that they were superconducting and images from an optical microscope were used to analyze the sample volume, which allowed an estimate of the average superconducting volume fraction in superconducting grains. The samples were measured with EDX in an SEM. This data showed that the likely superconducting phases were alloys of indium, lead and tin. To confirm this, EDX measurements were taken in a TEM, imaging the inside of a grain that exhibited superconductivity. In addition, the EDX data from the SEM was compared to the database of superconductors, SUPERCON, to determine all of the known superconducting compounds that could be made from the elements observed using EDX.
DOI: 10.6075/j08w3bqk
title: Data from: DNA damage induced during mitosis undergoes DNA repair synthesis

description: The files are best viewed in the open source, image processing package, FIJI, which is freely available on https://fiji.sc/.
description: Abstract: Understanding the mitotic DNA damage response (DDR) is critical to our comprehension of cancer, premature aging and developmental disorders which are marked by DNA repair deficiencies. In this study we use a micro-focused laser to induce DNA damage in selected mitotic chromosomes to study the subsequent repair response. Our findings demonstrate that (1) mitotic cells are capable of DNA repair as evidenced by DNA synthesis at damage sites, (2) Repair is attenuated when DNA-PKcs and ATM are simultaneously compromised, (3) Laser damage may permit the observation of previously undetected DDR proteins when damage is elicited by other methods in mitosis, and (4) Twenty five percent of mitotic DNA-damaged cells undergo a subsequent mitosis. Together these findings suggest that mitotic DDR is more complex than previously thought and may involve factors from multiple repair pathways that are better understood in interphase.
DOI: 10.6075/j0d21w00
title: The Atmospheric River-CONNected objECT (AR-CONNECT) algorithm applied to the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA V2) - 1983 to 2016

description: This collection contains the lifecycles of global atmospheric river (AR) objects. This data was produced by isolating regions of enhanced IVT transport events by applying the Atmospheric River-CONNected objECT (AR-CONNECT) algorithm. AR-CONNECT is a four-dimensional (4D) object-oriented algorithm, adapted from the CONNECT algorithm developed by a team of researchers from the University of California, Irvine [Sellars et al., 2013, 2015, 2017]. The algorithm uses a seeded region growing segmentation technique to segment AR lifecycles according to their high-intensity cores. AR-CONNECT determines the lifecycles of an AR by using a flood-filling algorithm to group discrete AR timeslices where they are contiguous over time and space. Each object has a unique ID and a set of selected characteristics.
DOI: 10.6075/j01v5c9v
title: Data from: The influence of a cross-reef channel on the wave-driven setup and circulation at Ipan, Guam

description: Currents, waves and water level observations from the field program of Clark et al. 2020 (https://doi.org/10.1029/2019JC015722). Abstract: The influence of a deep (30 m), narrow (30 m) cross-shore channel on the circulation and wave-induced setup over a shallow (~0.5 m) and wide (~400 m) shore-attached fringing reef is examined using field measurements collected at Ipan, Guam. Mean currents on the reef flat over a seven-week study period during mid and high tides when the reef is submerged are directed toward the channel with the alongshore component of the current increasing with proximity to the channel. The cross-shore component of the reef-flat current is directed onshore at the sensors in the far field of the channel with a weak offshore flow at the current meter located closest to the channel ~760 m to the north). Low-frequency fluctuations of the alongshore reef flat current and off-shore channel current are significantly correlated, and with the incident significant wave height. Mean and low frequency fluctuating currents are forced by the spatially variable wave-driven setup, modulated by tidal elevation, which creates a pressure gradient over the reef flat due to the channel where waves do not break. The dominant alongshore momentum balance on the reef flat is between the pressure gradient and bottom stress, with an inferred drag coefficient of C<sub>D</sub>~0.01. A simple analytical model is presented that is consistent with the observations and delineates the near- and far-field of the channel as a function of the aspect ratio of the reef. Observations from a longer deployment of channel currents are highly correlated with incident wave height in distinct tidal level bands.
DOI: 10.6084/m9.figshare.21082351
title: Models of topological barriers and molecular motors of bacterial DNA

description: Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins like the LacI repressor, which behave like topological barriers and block the diffusion of torsion along the DNA. Other proteins, like DNA gyrases and RNA polymerases, called molecular motors, use the energy released by the hydrolysis of ATP to apply forces and/or torques to the DNA and modify its superhelicity. Here, we report on simulation work aimed at enlightening the interplay between DNA supercoiling, topological barriers, and molecular motors. To this end, we developed a coarse-grained Hamiltonian model of topological barriers and a model of molecular motors and investigated their properties through Brownian dynamics simulations. We discuss their influence on the contact map of a model nucleoid and the steady state values of twist and writhe in the DNA. These coarse-grained models, which are able to predict the dynamics of plectonemes depending on the position of topological barriers and molecular motors, should prove helpful to back up experimental efforts, like the development of Chromosome Conformation Capture techniques, and decipher the organisational mechanisms of bacterial chromosomes.
DOI: 10.6084/m9.figshare.21082351.v1
title: Models of topological barriers and molecular motors of bacterial DNA

description: Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins like the LacI repressor, which behave like topological barriers and block the diffusion of torsion along the DNA. Other proteins, like DNA gyrases and RNA polymerases, called molecular motors, use the energy released by the hydrolysis of ATP to apply forces and/or torques to the DNA and modify its superhelicity. Here, we report on simulation work aimed at enlightening the interplay between DNA supercoiling, topological barriers, and molecular motors. To this end, we developed a coarse-grained Hamiltonian model of topological barriers and a model of molecular motors and investigated their properties through Brownian dynamics simulations. We discuss their influence on the contact map of a model nucleoid and the steady state values of twist and writhe in the DNA. These coarse-grained models, which are able to predict the dynamics of plectonemes depending on the position of topological barriers and molecular motors, should prove helpful to back up experimental efforts, like the development of Chromosome Conformation Capture techniques, and decipher the organisational mechanisms of bacterial chromosomes.
DOI: 10.6084/m9.figshare.21082351.v2
title: Models of topological barriers and molecular motors of bacterial DNA

description: Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins like the LacI repressor, which behave like topological barriers and block the diffusion of torsion along the DNA. Other proteins, like DNA gyrases and RNA polymerases, called molecular motors, use the energy released by the hydrolysis of ATP to apply forces and/or torques to the DNA and modify its superhelicity. Here, we report on simulation work aimed at enlightening the interplay between DNA supercoiling, topological barriers, and molecular motors. To this end, we developed a coarse-grained Hamiltonian model of topological barriers and a model of molecular motors and investigated their properties through Brownian dynamics simulations. We discuss their influence on the contact map of a model nucleoid and the steady state values of twist and writhe in the DNA. These coarse-grained models, which are able to predict the dynamics of plectonemes depending on the position of topological barriers and molecular motors, should prove helpful to back up experimental efforts, like the development of Chromosome Conformation Capture techniques, and decipher the organisational mechanisms of bacterial chromosomes.
DOI: 10.6075/j0rb734d
title: Data from: Cusp and mega cusp observations on a mixed sediment beach

description: Abstract: Frequent surveys using modern remote sensing technology enable observations of subaerial beach morphology and surface sediment type (sand versus gravel/cobble) with unprecedented spatial and temporal resolution. Here we show weekly terrestrial mobile LiDAR observations of cusps on a mixed sediment beach, consisting of sand and gravel/cobble, spanning ~2 km alongshore. Surface gravel/cobble coverage varied from almost complete to none (e.g. all sand), over times ranging from weekly to seasonal, and with location. Cusp morphologies also varied in space and time. Cusps with 11-20 m alongshore wavelengths (L) primarily developed in winter and were composite with gravel-cobble horns and sandy bays. Cusps with L between 21-40 m developed throughout the year and were either composite or entirely sandy. Previously not reported, composite mega cusps (L between 200-400 m) occurred in winter. Composite cusps, with L between 11-40 m, were clustered in gravel/cobble-rich mega cusp bays, and absent on the sandier mega cusp horns.
DOI: 10.6075/j0zs2v1m
title: Data from: Observations and Modeling of Ocean Circulation in the Seychelles Plateau Region

description: Observations and model data were processed using the Python open programming language. Codes used to process data and models from this collection are found in https://github.com/almacarolina/slomodata. Please refer to Castillo-Trujillo et al., 2020, and https://agu.confex.com/agu/os18/meetingapp.cgi/Paper/315049 for more information on the data and model setup.
description: This collection contains raw and processed data from a variety of instruments deployed from December 2016 to March 2019 over the Seychelles Plateau. This collection also contains a subset of an Ocean General Circulation POP model in the South Tropical Indian Ocean, encompassing the Seychelles Plateau. The data was deployed at three locations in the Seychelles Plateau; at the northern edge, and at the eastern and western side of the island of Mahé, the main island part of the Republic of Seychelles. The data include velocity and pressure measurements from two acoustic Doppler current profilers (ADCPs) at the eastern and northern moorings; temperature measurements from Seabird 56s, deployed across thermistor-chains at the western and eastern moorings and pressure, temperature, and salinity from two Seabird 37 at the eastern mooring. The ocean model is the Los Alamos National Laboratory Parallel Ocean Program (POP) Model 2 and it communicates with the sea-ice model and the atmospheric forcing via Flux Coupler version 7. It is forced with the Coordinated Ocean-ice Reference Experiment-II corrected interannually varying atmospheric forcing from 1948 to 2009 (CORE-II CIAF). It has 1.8-degree and 6-hour spatiotemporal resolution. The output used in this study consists of three-dimensional fields of temperature, potential density, and velocity as well as two-dimensional fields of Sea Surface Height, Mixed Layer Depth and wind stress over the South Tropical Indian Ocean (5N to 20S and 35E to 70E) from 1993 to 2009.
DOI: 10.13145/bacdive11746.20171208.2.1
title: Pasteurella oralis Christensen et al. 2012

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive11747.20171208.2.1
title: Bibersteinia trehalosi (Sneath and Stevens 1990) Blackall et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive9756.20171208.2.1
title: Myxococcus fulvus (Cohn 1875) Jahn 1911

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive9874.20171208.2.1
title: Myxococcus virescens Thaxter 1892 emend. Lang et al. 2008

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10282.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10283.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10284.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10285.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10286.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10287.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10288.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10289.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10290.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10291.20171208.2.1
title: Nannocystis exedens subsp. exedens Reichenbach

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10964.20171208.2.1
title: Rhodococcus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10965.20171208.2.1
title: Rhodococcus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive10966.20171208.2.1
title: Rhodococcus sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.