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DOE OSTI2015

How well do CMIP5 climate simulations replicate historical trends and patterns of droughts?

Assessing the uncertainties and understanding the deficiencies of climate models are fundamental to developing adaptation strategies. The objective of this study is to understand how well Coupled Model Intercomparison-Phase 5 (CMIP5) climate model simulations replicate ground-based observations of continental drought areas and their trends. The CMIP5 multimodel ensemble encompasses the Climatic Research Unit (CRU) ground-based observations of area under drought at all time steps. However, most model members overestimate the areas under extreme drought, particularly in the Southern Hemisphere (SH). Furthermore, the results show that the time series of observations and CMIP5 simulations of areas under drought exhibit more variability in the SH than in the Northern Hemisphere (NH). The trend analysis of areas under drought reveals that the observational data exhibit a significant positive trend at the significance level of 0.05 over all land areas. The observed trend is reproduced by about three-fourths of the CMIP5 models when considering total land areas in drought. While models are generally consistent with observations at a global (or hemispheric) scale, most models do not agree with observed regional drying and wetting trends. Over many regions, at most 40% of the CMIP5 models are in agreement with the trends of CRU observations. The drying/wetting trends calculated using the 3 months Standardized Precipitation Index (SPI) values show better agreement with the corresponding CRU values than with the observed annual mean precipitation rates. As a result, pixel-scale evaluation of CMIP5 models indicates that no single model demonstrates an overall superior performance relative to the other models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

Propionate accumulation is a common indicator of process imbalances in anaerobic bioreactor systems. The accumulation of propionate can occur due to low retention rates, hydrogen accumulation, or mechanical changes affecting the proximity between propionate oxidizers and partner species, thereby preventing necessary electron transfer. Few studies, however, have observed the changes in microbial community structure during propionate accumulation. We used 454 pyrosequencing of 16S rDNA to evaluate the community membership during propionate accumulations in replicate bioreactors with rumen based cultures. Half of the culture volume from a parent reactor was transferred to a sterile “daughter” reactor, and both systems were run identically. Both reactors experienced a propionate accumulation after roughly 10 days, with the propionate accumulation being less pronounced in the parent reactor as compared to the daughter reactor. Non-metric multidimensional scaling (NMDS) was used to determine clustering patterns of the samples, and correlative methods were used to determine which OTUs were significantly associated with the movements of samples along the NMDS axes. The presence of Saccharofermentans characterized the position of early samples, whereas the presence of Ruminococcus and Succiniclasticum were more indicative of the positions of later samples. Hydrogen accumulation and low sequence counts indicated low methanogen activity. Although both reactor systems were closed to microbial inputs due to the sterilization of influent media, we recorded significant increases in reactor diversity over time. This suggests that changes in the abundances of dominant community members may affect the sequencing of rare taxa within samples.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Early growth response 2 (EGR2) is a novel regulator of the senescence programme

Abstract Senescence, a state of stable growth arrest, plays an important role in ageing and age‐related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up‐regulated during senescence, and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates the ARF and p16 promoters and directly binds to both the ARF and p16 promoters. Loss of EGR2 down‐regulates p16 levels and increases the pool of p16− p21− ‘reversed’ cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a direct transcriptional activator of the p16/pRB and ARF/p53/p21 pathways in senescence and a novel marker of senescence.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1997

Gravitational Wave Search with the Clock Mission

Doppler tracking of distant spacecraft is the only method currently available to search for gravitational waves in the low-frequency (approx. 0.0001-0.1 Hz) band. In this technique the Doppler system measures the relative dimensionless velocity 2(delta)v/c = (delta)f/f(sub o) between the earth and the spacecraft as a function of time, where (delta)f is the frequency perturbation and f(sub o) is the nominal frequency of the radio link. A gravitational wave of amplitude h incident on this system causes small frequency perturbations, of order h in (delta)f/f(sub o), replicated three times in the observed record (Estabrook and Wahlquist 1975). All experiments to date and those planned for the near future involve only 'two-way' Doppler-i.e., uplink signal coherently transponded by the spacecraft with Doppler measured using a frequency standard common to the transmit and receive chains of the ground station. If, as on the proposed Clock Mission, there is an additional frequency standard on the spacecraft and a suitable earth-spacecraft radio system, some noise sources can be isolated and removed from the data (Vessot and Levine 1978). Supposing that the Clock Mission spacecraft is transferred into a suitable interplanetary orbit, I discuss here how the on-board frequency standard could be employed with an all-Ka-band radio system using the very high stability Deep Space Network station DSS 25 being instrumented for Cassini. With this configuration, the Clock Mission could search for gravitational waves at a sensitivity limited by the frequency standards, rather than plasma or tropospheric scintillation effects, whenever the sun-earth-spacecraft angle is greater than 90 degrees.

Armstrong, J. W.↗

NASA NTRS2000

Measurements in a Transitional Boundary Layer Under Low-Pressure Turbine Airfoil Conditions

This report presents the results of an experimental study of transition from laminar to turbulent flow in boundary layers or in shear layers over separation zones on a convex-curved surface which simulates the suction surface of a low-pressure turbine airfoil. Flows with various free-stream turbulence intensity (FSTI) values (0.5%, 2.5% and 10%), and various Reynolds numbers (50,000, 100,000 200,000 and 300,000) are investigated. Reynold numbers in the present study are based on suction surface length and passage exit mean velocity. Flow separation followed by transition within the separated flow region is observed for the lower-Re cases at each of the FSTI levels. At the highest Reynolds numbers and at elevated FSn, transition of the attached boundary layer begins before separation, and the separation zone is small. Transition proceeds in the shear layer over the separation bubble. For both the transitional boundary layer and the transitional shear layer, mean velocity, turbulence intensity and intermittency (the fraction of the time the flow is turbulent) distributions are presented. The present data are compared to published distribution models for bypass transition, intermittency distribution through transition, transition start position, and transition length. A model developed for transition of separated flows is shown to adequately predict the location of the beginning of transition, for these cases, and a model developed for transitional boundary layer flows seems to adequately predict the path of intermittency through transition when the transition start and end are known. These results are useful for the design of low-pressure turbine stages which are known to operate under conditions replicated by these tests.

Simon, Terrence W.↗

NASA NTRSDate not supplied

Comprehensive 3D Multiphysics Model on Electrochemical Recovery of O 2 from Metabolic CO 2 at the International Space Station (ISS)

The International Space Station (ISS) is presently equipped with an elaborate, heavy, and high-power consuming system that recovers approximately 50% of O 2 from metabolic CO 2 as part of the atmospheric revitalization (AR) at the ISS habitat. Future long-duration missions will require a sustainable and efficient system capable of yielding a minimum of 75% O 2 recovery to reach the self-sufficiency required for long space missions beyond earth’s low orbit. A Macrofluidic Electrochemical Reactor (MFECR) technology development effort is currently underway at NASA Marshall Space Flight Center (MSFC) to not only increase significantly current O 2 recovery efficiency, improving self-sufficiency on AR at the ISS habitat and future long missions, but also reduce the complexity of the system. The authors have developed and deployed a comprehensive 3D multiphysics model that thoroughly replicates the actual configuration and fluid/material domains of the MFECR. The coupled physics in this multiphysics model include multicomponent-multiphase electrochemical-driven reactions, non-ideal mass transport mechanism, free and porous flow, heat transfer, CO 2 solubility on alkaline electrolyte, water condensation on porous medium, and DC electrical current generation along with Joule heating effect. This model is aimed to conduct quantitive benchmark on three different MFECR’s layouts, one without serpentine paths (plain) and two with serpentines leading to four and twelve paths respectively. Once experimental data is generated via a test matrix of 200 tests, the model will be validated to conduct MFECR’s process optimization and revalidate the quantitive benchmark on three different MFECR’s layouts.

Jesus A. Dominguez↗

NASA NTRSDate not supplied

Acoustic Characterization of the NASA Langley 14- by 22-Foot Subsonic Tunnel Using Single-Microphone Analysis Techniques

An experimental campaign was conducted to assess recent acoustic modifications to the NASA Langley Research Center 14- by 22-Foot Subsonic Tunnel. This effort was undertaken in preparation for future rotorcraft, Advanced Air Mobility, and airframe noise acoustic tests. The tunnel is a closed circuit and typically operates in an open-jet configuration for acoustic studies. A vertical linear array of microphones and a phased array were placed on traverses outside of the core flow. Pole-mounted acoustic sources with known waveforms were used to identify reflective surfaces under static conditions with no tunnel flow. A similar process was replicated with more compact sources in an aerodynamic fairing for flow speeds up to Mach 0.16. This enabled investigation of the test section core flow and bounding shear layer impacts on the acoustic measurements. Periodic averaging was employed and was shown to be capable of isolating periodic acoustic signals even for poor signal-to-noise ratio conditions. Benefits and limitations of single-microphone processing methods are identified. A companion paper utilizes a phased array in an effort to address the identified limitations to more traditional single-microphone data collection.

Acoustic Characterization↗

NASA NTRSDate not supplied

Acoustic Characterization of the NASA Langley 14- by 22-Foot Subsonic Tunnel Using Single-Microphone Analysis Techniques

Acoustic Characterization↗

NASA NTRS2019

Human Performance Contributions to Safety in Commercial Aviation

Every day in aviation, pilots, air traffic controllers, and other front-line personnel perform countless correct judgments and actions in a variety of operational environments. These judgments and actions are often the difference between an accident and a non-event. Ironically, data on these behaviors are rarely collected or analyzed. Data-driven decisions about safety management and design of safety-critical systems are limited by the available data, which influence how decision makers characterize problems and identify solutions. Large volumes of data are collected on the failures and errors that result in infrequent incidents and accidents, but in the absence of data on behaviors that result in routine successful outcomes, safety management and system design decisions are based on a small sample of nonrepresentative safety data. This assessment aimed to find and document “safety successes” made possible by human operators. With many Aeronautics Research Mission Directorate (ARMD) Programs and Projects focusing on increased automation and autonomy and decreased human involvement, failure to fully consider the human contributions to successful system performance in civil aviation represents a significant risk — a risk that has not been recognized to date. Without understanding how humans contribute to safety, any estimate of predicted safety of autonomous capabilities is incomplete and inherently suspect. Furthermore, understanding the ways in which humans contribute to safety can promote strategic interactions among safety technologies, functions, procedures and the people using them. Without this understanding, the full benefits of an integrated, optimized human/technology or autonomous system will not be realized. Historically, safety has been consistently defined in terms of the occurrence of accidents or recognized risks (i.e., in terms of things that go wrong). These adverse outcomes are explained by identifying their causes, and safety is restored by eliminating or mitigating these causes. An alternative to this approach is to focus on what goes right and identify how to replicate that process. Focusing on the rare cases of failures attributed to “human error” provides little information about why human performance routinely prevents adverse events. Hollnagel has proposed that things go right because people continuously adjust their work to match their operating conditions. These adjustments become increasingly important as systems continue to grow in complexity. Thus, the definition of safety should reflect not only “avoiding things that go wrong” but “ensuring that things go right.” The basis for safety management requires developing an understanding of everyday activities. However, few mechanisms to monitor everyday work exist in the aviation domain, which limits opportunities to learn how designs function in reality. This concept of safety thinking and safety management is reflected in the emerging field of resilience engineering. According to Hollnagel, a system is resilient if it can sustain required operations under expected and unexpected conditions by adjusting its functioning prior to, during, or following changes, disturbances, and opportunities. To explore “positive” behaviors that contribute to resilient performance in commercial aviation, the assessment team examined a range of existing sources of data about pilot and air traffic control (ATC) tower controller performance, including subjective interviews with domain experts and objective aircraft flight data records. These data were used to identify strategies that support resilient performance, methods for exploring and refining those strategies in existing data, and proposed methods for capturing and analyzing new data.

Null, Cynthia H.↗

DOE OSTI2014

Poster — Thur Eve — 69: Computational Study of DVH-guided Cancer Treatment Planning Optimization Methods

Purpose: To compare methods to incorporate the Dose Volume Histogram (DVH) curves into the treatment planning optimization. Method: The performance of three methods, namely, the conventional Mixed Integer Programming (MIP) model, a convex moment-based constrained optimization approach, and an unconstrained convex moment-based penalty approach, is compared using anonymized data of a prostate cancer patient. Three plans we generated using the corresponding optimization models. Four Organs at Risk (OARs) and one Tumor were involved in the treatment planning. The OARs and Tumor were discretized into total of 50,221 voxels. The number of beamlets was 943. We used commercially available optimization software Gurobi and Matlab to solve the models. Plan comparison was done by recording the model runtime followed by visual inspection of the resulting dose volume histograms. Conclusion: We demonstrate the effectiveness of the moment-based approaches to replicate the set of prescribed DVH curves. The unconstrained convex moment-based penalty approach is concluded to have the greatest potential to reduce the computational effort and holds a promise of substantial computational speed up.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Methods and apparatus for multi-resolution replication of files in a parallel computing system using semantic information

Techniques are provided for storing files in a parallel computing system using different resolutions. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a sub-file. The method comprises the steps of obtaining semantic information related to the file; generating a plurality of replicas of the file with different resolutions based on the semantic information; and storing the file and the plurality of replicas of the file in one or more storage nodes of the parallel computing system. The different resolutions comprise, for example, a variable number of bits and/or a different sub-set of data elements from the file. A plurality of the sub-files can be merged to reproduce the file.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Base excision repair and double strand break repair cooperate to modulate the formation of unrepaired double strand breaks in mouse brain

Abstract We lack the fundamental information needed to understand how DNA damage in the brain is generated and how it is controlled over a lifetime in the absence of replication check points. To address these questions, here, we integrate cell-type and region-specific features of DNA repair activity in the normal brain. The brain has the same repair proteins as other tissues, but normal, canonical repair activity is unequal and is characterized by high base excision repair (BER) and low double strand break repair (DSBR). The natural imbalance creates conditions where single strand breaks (SSBs) can convert to double strand breaks (DSBs) and reversibly switch between states in response to oxidation both in vivo and in vitro. Our data suggest that, in a normal background of repair, SSBs and DSBs are in an equilibrium which is pushed or pulled by metabolic state. Interconversion of SSB to DSBs provides a physiological check point, which would allow the formation of unrepaired DSBs for productive functions, but would also restrict them from exceeding tolerable limits.

Science & Technology - Other Topics↗

DOE OSTI2023

Development of Laboratory Testbeds Simulating Real-World Greenhouse Gas Emissions

Climate change leads to drastic variations in the environment that can threaten food security. To protect the security and prosperity of the environment, new agricultural practices that mitigate greenhouse gas emissions need to be developed. Agriculture plays a large role in the emissions of greenhouse gases, thus a need for new practices. At present, testing landscape management practices for carbon sequestration and reduction of greenhouse gas emissions are expensive because such tests often require intricate field experiments. Laboratory tests on landscape management practices often fail to simulate and accurately represent the natural systems researchers intend to study. There are methods that can be used to make these laboratory tests more closely replicate natural systems for the improvement of agricultural lands used in biofuel and food production. The goal of this project is to develop a laboratory testbed replicating field conditions that will mimic field greenhouse gas emissions. To achieve this goal, we used soil cores taken from agricultural and marginal lands, then attached fiberglass wicks to improve the drainage system in the soil core to simulate a more natural hydraulic system. The soil cores with the wicks were used to compared to greenhouse gas emissions observed in the field. Our preliminary results suggest that the soil carbon dioxide and nitrous oxide flux from the agricultural land site were comparable to the soil cores equipped with the drainage wicks. The data suggests that laboratory testbeds can be used to mimic field greenhouse gas emissions if parameters, such as soil water content were in a set range. The laboratory testbed produces similar greenhouse gas emissions to the agricultural site when the soil water content was between 15-25%.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Using Eye Tracking to Elucidate the Mechanisms Underlying Stimulation-Enhanced Visual Target Detection

Transcranial direct current stimulation (tDCS) is a noninvasive form of brain stimulation that involves passing a weak electrical current between electrodes on the scalp to modulate underlying neural tissue. TDCS has been shown to modulate cognition in a variety of domains, including memory, attention, and visual processing. Prior work from our laboratory has shown positive effects of tDCS on learning to detect target objects hidden in complex naturalistic visual scenes and learn rules for categorizing images, though the mechanism for these benefits remains unknown. One possibility is that tDCS optimizes visual search by modulating visual attention or via the reduction in search errors. One method of quantifying visual attention is to use eye tracking to record search patterns to determine if and how visual search is adjusted under verum stimulation conditions. Eye tracking data allows classification of errors into error types, including sampling errors (failing to look in the relevant region), recognition errors (looking at the critical portion of a scene, but failing to recognize it as such as evidenced by visual fixation), and decision-making errors (fixating on the relevant portion of a scene, but making the wrong determination). Our results indicate that the benefit tDCS confers on visual search for targets stems from the reduction in decision-making errors when targets are present (Cohen’s d = 0.86). Also reported is a replication of previous findings showing a tDCS-dependent improvement in learning this task, learning score (Cohen’s d = 0.88); d’ (Cohen’s d = 1.00). This provides support for moving tDCS into the application space by pairing it with analysts who are concerned with the type of search error that is corrected via stimulation.

attention↗

DOE OSTI2019

Investigating YAP’s role in Human Mammary Epithelial Cell (HMEC) Immortalization and Cancer Stem Cell (CSC) Phenotype Acquisition during Early Breast Cancer Progression

The malignant aspect of tumorigenesis in breast cancer is initiated when human mammary epithelial cells (HMEC) first immortalize (gain the ability to proliferate indefinitely) and subsequently undergo oncogenic activation. Our laboratory has developed a two-step HMEC immortalization process that we believe accurately models early breast cancer progression. Normal finite pre-stasis HMEC must overcome two distinct senescence barriers to achieve full immortality: stasis (stress-associated senescence) and replicative senescence, respectively. HMEC bypass stasis, and become post-stasis, when errors in the retinoblastoma pathway are present. Replicative senescence, a product of continuously shortening telomeres producing telomere dysfunction, is overcome by the reactivation of telomerase. Our lab has called HMEC that acquire the error allowing telomerase expression conditionally immortal (CI); CI cells may still have low telomerase expression. Full immortality is achieved when sufficient telomerase expression exists to maintain short stable telomeres following a process we have called conversion. The transcriptional coactivator YAP, upregulated in several human cancers, is closely correlated with a variety of oncogenic effects including proliferation and induction of cancer stem cell (CSC) properties. Our preliminary data have shown that YAP-transduced post-stasis HMEC expressed properties of CI cells. Growth curves indicated that some cell lines achieved full immortality; however, these cells had acquired an additional error – amplified expression of c-Myc, an oncogene known to induce telomerase in post-stasis or CI cells. The absence of uniform immortalization in the YAP-transduced cells suggests that YAP causes post-stasis HMEC to become conditionally immortal. This is further supported given that YAP-transduced post-stasis HMEC have decreased levels of the lncRNA MORT and rapidly go through conversion when p53 function is abrogated, well-documented attributes of CI HMEC. Previous studies have also reported that YAP controls the differentiation of breast progenitor cells; as a result, it is likely that YAP plays a role in inducing CSC phenotypes. In this study, we attempt to gain a greater understanding of YAP’s role in HMEC immortalization and induction of CSC properties in early breast cancer progression. We measured gene expression levels and attempted to identify proteins indicative of a CSC phenotype in YAP-transduced post-stasis HMEC. Our initial results did not reveal an association between YAP and HMEC conditional immortality or induction of CSC attributes in the cultures examined. However, using a YAP construct that promotes nuclear localization (where YAP is most active) has led to a potentially promising YAP-derived cell line that we presume to be immortal. We go on to demonstrate that YAP may be acting via non-transcriptional oncogenic roles in our HMEC specimens. Thus, we recommend future studies into YAP and the HMEC immortalization process given that they are promising targets for breast cancer prevention therapies.

Shah, Manav↗

DOE OSTI2020

Machine Learning for Automated Extraction of Building Geometry

As data science comes to buildings, the promise of using machine learning and novel sources of data has received much attention. Advances in machine learning and computer vision algorithms, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics – cost-effectively, and at scale. Acquisition of features such as footprint are time consuming and costly to acquire with today’s manual methods, but can be streamlined through intelligent software-based solutions applied to satellite images. When combined with aerial RGB and thermal images, full 3D geometries and thermal maps can be constructed to determine additional characteristics such as window to wall ratio, height, number of stories and envelope thermal characteristics. In this paper we present three contributions to accelerate these high potential opportunities: (1) a methodical analysis of how these features can be integrated into today’s simulation and data driven software tools to enhance efficiency measure identification and owner/operator decision making; (2) development and accuracy testing of open source deep neural network methods to extract building footprints from satellite imagery, including the curation and application of openly available GIS datasets for training and continued development by others; and (3) an open framework for drone-based image capture and creation of 3D building geometries. This work represents an important bridge between high-level studies that span diverse application areas and those that detail point solutions yet cannot be easily replicated or extended.

Touzani, Samir↗

DOE OSTI2017

Multi-platform ’Omics Analysis of Human Ebola Virus Disease Pathogenesis

The pathogenesis of human Ebola virus disease (EVD) is complex. EVD is characterized by high levels of virus replication and dissemination, dysregulated immune responses, extensive virus- and host-mediated tissue damage, and disordered coagulation. To clarify how host responses contribute to EVD pathophysiology, we performed multi-platform ’omics analysis of peripheral blood mononuclear cells and plasma from EVD patients. Our results indicate that EVD molecular signatures overlap with those of sepsis, imply that pancreatic enzymes contribute to tissue damage in fatal EVD, and suggest that Ebola virus infection may induce aberrant neutrophils whose activity could explain hallmarks of fatal EVD. Moreover, integrated biomarker prediction identified putative biomarkers from different data platforms that differentiated survivors and fatalities early after infection. We report this work reveals insight into EVD pathogenesis, suggests an effective approach for biomarker identification, and provides an important community resource for further analysis of human EVD severity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

TeMPI Shim

This is the manual for the TeMPI Shim library, whose goal is to facilitate scientific apps being loosely coupled through MPI. TeMPI Shim can be used to create and manage Message Passing Interface (MPI, see [MPI]) Communicators for Single Program, Multiple Data (SPMD, see [SPMD]) and Multiple Programs, Multiple Data (MPMD, see [MPMD]) workflows. MPI provides the MPI_APPNUM command number to each of the processes within its context. This number, starting at 0, is the application number being executed. In a case where 3 applications are being run in MPMD mode, there would be MPI_APPNUM values of 0, 1, and 2. TeMPI Shim creates intra- and inter-communicators between each pair of MPI_APPNUM values. In the aforementioned case, application 0 would have intra- and inter-communicators to speak to itself, application 1, and application 2. This is replicated for each of the applications. Additionally, TeMPI Shim creates intra- and inter-communicators for the first MPI rank of each application to directly communicate only with each other. Finally, TeMPI Shim creates its own copy of the default world communicator, i.e., MPI_COMM_WORLD. In the case where there is only a single application, it will have the communicators to only speak with itself. TeMPI Shim is useful in this case since it is considered good practice for MPI applications to copy the default world communicator and reference this copy (see [Duplicate World]_) anyways. Ultimately, it provides value independent of the number of applications present.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗