Supplementary data for the biological age linked to oxidative stress modifies breast cancer aggressiveness
Not Available
Sáez-Freire, María del Mar↗
SEARCH · Search NASA
Results for “linked data”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
A compendium of multi-omic sequence information from the Saanich Inlet water column
Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
Hawley, Alyse K. (ORCID:0000000235164043)↗
Parallel transport studies of high-Z impurities in the core of Alcator C-Mod plasmas
Measurements of poloidal variation, ñ{sub z}/ , in high-Z impurity density have been made using photodiode arrays sensitive to vacuum ultraviolet and soft x-ray emission in Alcator C-Mod plasmas. In/out asymmetries in the range of −0.2 <0.3 are observed for r/a<0.8, and accumulation on both the high-field side, n{sub z,cos}<0, and low-field side, n{sub z,cos}>0, of a flux surface is found to be well described by a combination of centrifugal, poloidal electric field, and ion-impurity friction effects. Up/down asymmetries, −0.05 <0.10, are observed over 0.5 0 corresponding to accumulation opposite the ion ∇B drift direction. Measurements of the up/down asymmetry of molybdenum are found to disagree with predictions from recent neoclassical theory in the trace limit, n{sub z}Z{sup 2}/n{sub i}≪1. Non-trace levels of impurities are expected to modify the main-ion poloidal flow and thus change friction-driven impurity density asymmetries and impurity poloidal rotation, v{sub θ,z}. Artificially modifying main-ion flow in parallel transport simulations is shown to impact both ñ{sub z}/ and v{sub θ,z}, but simultaneous agreement between measured and predicted up/down and in/out asymmetry as well as impurity poloidal rotation is not possible for these C-Mod data. This link between poloidal flow and poloidal impurity density variation outlines a more stringent test for parallel neoclassical transport theory than has previously been performed. Measurement and computational techniques specific to the study of poloidal impurity asymmetry physics are discussed as well.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Spectral state dependence of the 0.4–2 MeV polarized emission in Cygnus X-1 seen with INTEGRAL/IBIS, and links with the AMI radio data
Polarization of the ≳400 keV hard tail of the microquasar Cygnus X-1 has been independently reported by INTEGRAL/Imager on Board the INTEGRAL Satellite (IBIS), and INTEGRAL/SPectrometer on INTEGRAL and interpreted as emission from a compact jet. These conclusions were, however, based on the accumulation of all INTEGRAL data regardless of the spectral state. We utilize additional INTEGRAL exposure accumulated until 2012 December, and include the AMI/Ryle (15 GHz) radio data in our study. We separate the observations into hard, soft, and intermediate/transitional states and detect radio emission from a compact jet in hard and intermediate states (IS), but not in the soft. The 10–400 keV INTEGRAL (JEM-X and IBIS) state resolved spectra are well modeled with thermal Comptonization and reflection components. We detect a hard tail in the 0.4–2 MeV range for the hard state only. We extract the state dependent polarigrams of Cyg X-1, which are all compatible with no or an undetectable level of polarization except in the 400–2000 keV range in the hard state where the polarization fraction is 75% ± 32% and the polarization angle 40.°0 ± 14.°3. An upper limit on the 0.4–2 MeV soft state polarization fraction is 70%. Due to the short exposure, we obtain no meaningful constraint for the IS. The likely detection of a >400 keV polarized tail in the hard state, together with the simultaneous presence of a radio jet, reinforce the notion of a compact jet origin of the >400 keV emission.
79 ASTRONOMY AND ASTROPHYSICS↗
The implementation of Global Feature EXtractor (gFEX) - the ATLAS Calorimeter Level 1 Trigger system for LHC Run-3 upgrade
As part of the ATLAS Phase-I Upgrade, the global Feature EXtractor (gFEX) is one of several hardware modules designed to help maintain the ATLAS Level-1 trigger acceptance rate with the increasing Large Hadron Collider (LHC) luminosity and the increasing Pile-Up conditions. The gFEX is used to identify patterns of energy associated with the hadronic decays of high momentum Higgs, W & Z bosons, top quarks, and exotic particles in real time at the 40 MHz LHC bunch crossing rate. The board is required to receive coarse-granularity (Δη×Δphiv = 0.2×0.2 gTower) information from the entire ATLAS calorimeters on 276 optical fibers. A prototype v1 with one Xilinx ZYNQ FPGA, and one Vertex-7 FPGA for technology validation has been designed and tested in 2015. With the lessons learned from the prototype v1, a prototype v2 with three Vertex UltraScale FPGAs and one ZYNQ FPGA has been implemented to verify full functionalities of gFEX in 2016. Based on the prototype v2 design, a prototype v3, the final gFEX prototype, is implemented, which is an ATCA module consisting of three Vertex UltraScale+ FPGAs, one ZYNQ UltraScale+ SoC, and 35 MiniPODs. This board receives up to 300 fiber optical links from calorimeters and transmits trigger data on 96 links to the to the ATLAS Level-1 Topological trigger (L1Topo [1]) at the speed up to 12.8 Gb/s. There are also 24 electrical links on board for communication between two FPGAs with the speed up to 25.6 Gb/s. The performance of three prototype boards have been tested and evaluated. For the prototype v3 board, the high-speed optical links are stable at 12.8 Gb/s with Bit Error Ratio (BER) < 1 × 10 -15 . The low-latency parallel GPIO (General Purpose I/O) buses between FPGAs are stable at 1.12 Gb/s. The peripheral components of ZYNQ UltraScale+ SoC, such as 16 GB DDR4 DIMM, UART, SPI flashes, and Ethernet, have also been verified. Here, the test results of the prototype v3 board validate the gFEX technologies, architecture and full functionalities. Now the final production board is being produced.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Planting a Lyman alpha forest on ABACUSSUMMIT
The full-shape correlations of the Lyman alpha (Ly$α$) forest contain a wealth of cosmological information through the Alcock Paczynski effect. However, these measurements are challenging to model without robustly testing and verifying the theoretical framework used for analyzing them. Here, we leverage the accuracy and volume of the $N$-body simulation suite ABACUSSUMMIT to generate high-resolution Ly$α$ skewers and quasi-stellar object (QSO) catalogs. One of the main goals of our mocks is to aid in the full-shape Ly$α$ analysis planned by the Dark Energy Spectroscopic Instrument (DESI) team. We provide optical depth skewers for six of the fiducial cosmology base-resolution simulations ($L$ box = 2 $h$ -1 Gpc, $N$ = 6912 3 ) at $z$ = 2.5. We adopt a simple recipe based on the Fluctuating Gunn-Peterson Approximation (FGPA) for constructing these skewers from the matter density in an $N$-body simulation and calibrate it against the 1D and 3D Ly$α$ power spectra extracted from the hydrodynamical simulation IllustrisTNG (TNG; $L$ box = 205 $h$ -1 Mpc, $N$ = 2500 3 ). As an important application, we study the non-linear broadening of the baryon acoustic oscillation (BAO) peak and show the cross-correlation between DESI-like QSOs and our Ly$α$ forest skewers. We find differences on small scales between the Kaiser approximation prediction and our mock measurements of the Ly$α$×QSO cross-correlation, which would be important to account for in upcoming analyses. The ABACUSSUMMIT Ly$α$ forest mocks open up the possibility for improved modelling of cross correlations between Ly$α$ and cosmic microwave background (CMB) lensing and Ly$α$ and QSOs, and for forecasts of the 3-point Ly$α$ correlation function. Furthermore, our catalogues and skewers are publicly available on Globus via the National Energy Research Scientific Computing Center (NERSC) (full link under Data Availability).
79 ASTRONOMY AND ASTROPHYSICS↗
Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data
The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. In conclusion, this will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.
59 BASIC BIOLOGICAL SCIENCES↗
A Compact Low-Power Driver Array for VCSELs in 65-nm CMOS Technology
This article presents a compact low-power 4 x 10 Gb/s quad-driver module for Vertical-Cavity Surface-Emitting Laser (VCSEL) arrays in a 65 nm CMOS technology. The side-by-side drivers can be directly wire bonded to the VCSEL diode array, supporting up to 4 channels. To increase the bandwidth of the driver, an internal feed-forward path is added for pole-zero cancellation, without increasing the power consumption. An edge-configurable pre-emphasis technique is proposed to achieve high bandwidth and minimize the asymmetry of the fall and rise times of the driver output current. Measurement results demonstrate a RMS jitter of 0.68 ps for 10 Gb/s operation. Tests demonstrate negligible crosstalk between channels. Under irradiation, the modulation amplitude degrades less than 5% up to 300 Mrad ionizing dose. Finally, the area of the quaddriver array is 500 μm by 1000 μm and the total power consumption for the entire driver array chip is 130 mW for the typical current setting.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Machine learning enables interpretable discovery of innovative polymers for gas separation membranes
Polymer membranes perform innumerable separations with far-reaching environmental implications. Despite decades of research, design of new membrane materials remains a largely Edisonian process. To address this shortcoming, we demonstrate a generalizable, accurate machine learning (ML) implementation for the discovery of innovative polymers with ideal performance. Specifically, multitask ML models are trained on experimental data to link polymer chemistry to gas permeabilities of He, H 2 , O 2 , N 2 , CO 2 , and CH 4 . We interpret the ML models and extract valuable insights into the contributions of different chemical moieties to permeability and selectivity. We then screen over 9 million hypothetical polymers and identify thousands that lie well above current performance upper bounds, including hundreds of never-before-seen ultrapermeable polymer membranes with O 2 and CO 2 permeability greater than 10 4 and 10 5 Barrers, respectively. High-fidelity molecular dynamics simulations confirm the ML-predicted gas permeabilities of the promising candidates, which suggests that many can be translated to reality.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dual Targeting Factors Are Required for LXG Toxin Export by the Bacterial Type VIIb Secretion System
Bacterial type VIIb secretion systems (T7SSb) are multisubunit integral membrane protein complexes found in Firmicutes that play a role in both bacterial competition and virulence by secreting toxic effector proteins. The majority of characterized T7SSb effectors adopt a polymorphic domain architecture consisting of a conserved N-terminal Leu-X-Gly (LXG) domain and a variable C-terminal toxin domain. Recent work has started to reveal the diversity of toxic activities exhibited by LXG effectors; however, little is known about how these proteins are recruited to the T7SSb apparatus. In this work, we sought to characterize genes encoding domains of unknown function (DUFs) 3130 and 3958, which frequently cooccur with LXG effector-encoding genes. Using coimmunoprecipitation-mass spectrometry analyses, in vitro copurification experiments, and T7SSb secretion assays, we found that representative members of these protein families form heteromeric complexes with their cognate LXG domain and in doing so, function as targeting factors that promote effector export. Additionally, an X-ray crystal structure of a representative DUF3958 protein, combined with predictive modeling of DUF3130 using AlphaFold2, revealed structural similarity between these protein families and the ubiquitous WXG100 family of T7SS effectors. Interestingly, we identified a conserved FxxxD motif within DUF3130 that is reminiscent of the YxxxD/E “export arm” found in mycobacterial T7SSa substrates and mutation of this motif abrogates LXG effector secretion. Overall, our data experimentally link previously uncharacterized bacterial DUFs to type VIIb secretion and reveal a molecular signature required for LXG effector export.
24 antibacterial toxins↗
Provenance infrastructure for multimodal x-ray experiments and reproducible analysis
Exploring relationships between material structures and desired properties for material discovery and synthesis requires mining machine-readable databases and linking experimental data with sufficiently rich annotations. There are vast gaps both in these data sources and in the connections between them. We present a provenance-based data management and analysis framework that enables capturing, persisting, and reanalyzing experimental data from the BNL National Synchrotron Light Source II (NSLS-II). Our system leverages NSLS-II Bluesky for experimental data acquisition, captures analysis parameters, and enriches the search space with results from the scientific literature. We describe in detail the challenges and benefits of data-driven approaches when comparing computational and experimental data, such as the multiple possible scenarios of interest in often ill-posed inverse problems and missing data. Our infrastructure utilizes the NSLS-II event model and includes discovery mechanisms across multiple beamlines. A text and data mining module using natural language processing classification techniques extracts relevant information from the literature that is added to data sources. We describe a provenance acquisition and analysis rerun workflow based on a directed acyclic graph that keeps track of process and data provenance and allows to replay analysis.
97 MATHEMATICS AND COMPUTING↗
Characteristics of Veterans With Depression Who Use the Veterans Choice Program of the Veterans Health Administration
Objective: The Veterans Choice Program (VCP) of the Veterans Health Administration (VHA) allowed eligible veterans to use their benefits with participating providers outside the VHA. The authors aimed to identify characteristics of veterans with depression who used or did not use mental health care through the VCP. Methods: In this cross-sectional study, the authors analyzed secondary data from the national VHA Corporate Data Warehouse. VHA administrative data were linked with VCP claims to examine characteristics of VCP-eligible veterans with depression. Further, the study sample included 595,943 unique veterans who were enrolled in the VHA before 2013, were eligible for the VCP in 2016, were alive in 2018, and had an assessed Patient Health Questionnaire–9 (PHQ-9) score or depressive disorder diagnosis documented in the VHA between 2016 and 2018. Results: Veterans who used the VCP had lower medical comorbidity scores and lived in less socioeconomically disadvantaged counties, compared with veterans who received only VHA care. VCP veterans were also more likely to have a PHQ-9 score assessment and to have higher mean depression scores. Mean counts of annual mental health visits per 1,000 veterans were markedly higher for direct VHA care than for care provided via the VCP. As a percentage of the total counts of visits per 1,000 veterans across the VCP and VHA, residential programs and outpatient procedures were the services that were most frequently delivered through the VCP. Conclusions: Between 2016 and 2018, the VCP was used primarily to augment mental health care provided by the VHA, rather than to fill a gap in care.
60 APPLIED LIFE SCIENCES↗
CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline
In silico prediction of a protein’s tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three ‘assisted’ protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data.
59 BASIC BIOLOGICAL SCIENCES↗
Preliminary performance of HT datalink
Preliminary performance of HT HS datalink at room temperature over 5000ft of wireline. The data shows ablility of the datalink to adapt by decreasing speed.
15 GEOTHERMAL ENERGY↗
January 2014 Dixie Valley Binary Cycle Production Data
Dixie Valley production data for January 2014, for a DOE Report. Used to demonstrate the techno-economic feasibility of utilizing the available unused heat to generate additional electric power from a binary power plant. *Note - This data is incomplete. See link below "Monthly Production Data September 2014" for more complete data set.
15 GEOTHERMAL ENERGY↗
Low Temperature Geothermal Resource Assessment for Desalination in United States
This data is a compilation of well observations from the Southern Methodist University (SMU) and Association of American State Geologists (AASG), location of identified low temperature geothermal systems from United States Geological Survey (USGS), and low temperature geothermal wells and springs from Oregon Institute of Technology Geo-Heat Center (OIT-GHC). The data is linked to NREL`s Geothermal Prospector online tool and shape files can be downloaded from the provided links. This study is also published at GRC Annual meeting on October 25th, 2016.
15 GEOTHERMAL ENERGY↗
Custom NEON AOP reflectance mosaics and maps of shade masks, canopy water content
This mosaic of visible to shortwave infrared (VSWIR) data was derived from the assignable asset NEON AOP radiance data that was collected by LBNL’s Watershed Function SFA during the summer of 2018 (DOI: 10.15485/1617204). This atmospheric correction was completed to take into account site-specific terrain variability in the 334 km2 survey area centered around Crested Butte, CO. The atmospheric correction was completed using ACORN atmospheric correction software executed on 200 x 200 pixel kernels rather than line by line in order to capture local flight altitude conditions. Manual cloud delineation removed any small shaded areas that occurred within the data collection areas. Mosaics were developed based on preference for days that were in close timing proximity to the coincident ground campaign and with mosaicing criteria that minimized the angle between the sun and the sensor to retrieve the most consistent reflectance (min_phase_refl_tiled). Finally, we generated shade masks based on the geometry between the sun angle at time of flight, the ground surface, and the sensor. Here we provide the orthomosaiced estimated reflectance data (min_phase_refl_tiled.tif), canopy water content (wtrl), estimated atmospheric water vapor (wtrv), the observational data (obs) for this particular mosaic, the estimated visibility (vis), shade masks derived from the digital surface elevation model (shade) and the digital terrain model (shade_tch) added to the canopy height model (DOI: 10.15485/1617203), and a wavelength metadata file. Each image file is provided as a GeoTiff with internal tiling and LZW compression. These data can also be found on Google Earth Engine for extraction, download, and analysis of smaller extents (Google Earth Engine data is linked in external link table).
2018 NEON and 2025 CHESS Campaigns↗