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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.

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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

Non-NASA Center↗
NASA NTRS1993

Backward Assembly Planning With DFA Analysis

System of algorithms developed to automate planning of sequences of manufacturing or field operations in which components are put together into assemblies. Results of DFA analysis also used to modify designs to optimize them with respect to assembly considerations.

Lee, Sukhan↗
DOE OSTI2017

Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences

Abstract The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5ʹ upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

Chen, Zhen-Yong↗
DOE OSTI2024

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗
DOE OSTI2025

Feed status and skin injury modulate immunopathology, global gene expression, and survival in channel catfish during virulent Aeromonas hydrophila infection

Introduction VirulentAeromonas hydrophilais a major pathogen in channel catfish (Ictalurus punctatus), that causes motileAeromonassepticemia and significant economic losses. We investigated the effect of feeding status and skin integrity on the host immune response, disease survival, and gastrointestinal pathology following a vAh challenge. Methods Using a bath immersion model, channel catfish were divided into four treatment groups: fin clipped and fed (FCF), fin clipped but not fed (FCN), not fin clipped but fed (NCF), and not fin clipped nor fed (NCN) alongside non-challenged control groups The FCF and NCF groups were fed 2 h prior to the challenge, but the FCN and NCN groups were not. Survival analysis, histopathological assessment, and RNA sequencing were conducted across groups at different time intervals throughout the vAh challenge. Results Survival rates were lowest in the FCF and FCN groups (30% and 23% survival, respectively), suggesting that both feeding and skin damage contributed to disease severity. Histopathological analyses revealed more severe intestinal and gastric lesions in fed groups, characterized by epithelial necrosis, hemorrhage, and edema. Transcriptomic analysis among the groups identified significant differentially expressed genes associated with inflammation, apoptosis, and metabolic stress, with notable upregulation of interleukin 1-beta (il-1β), and complement C3 (c3). Gene ontology enrichment highlighted distinct immune activation patterns between fed and unfed groups, with enhanced pathogen recognition and pro-inflammatory responses in unfed fish. Discussion These findings suggest feeding prior to infection may exacerbate disease pathology, potentially by creating a physiological state conducive to facilitate pathogen proliferation and dampened early immune responses, whereas short-term fasting appears to promote early immune activation. This study provides novel insights into the complex interplay between feed status, physical injury, and immune response to vAh infection.

Immunology↗
DOE OSTI2023

Coupling SCALE with DAKOTA for Axial Burnup Profiles Assessment in Burnup Credit

This paper presents a computational study that demonstrates the application of the SCALE code system in conjunction with the Design Analysis Kit for Optimization and Terascale Applications (DAKOTA) for the analysis of key factors influencing the evaluation of burnup credit (BUC) in pressurized water reactors (PWRs). The primary objective of this analysis is to characterize the model by utilizing parameterization, uncertainty quantification, and optimization studies. Using this approach, we can comprehensively assess the system and conduct informed predictive studies. This study highlights the effectiveness of the SCALE code system integrated within the DAKOTA framework in terms of efficiency and capability. With the coupling of the burnup code ORIGAMI with the CSAS or TSUNAMI-3D sequence embedded in a DAKOTA analysis, we can characterize the factors that influence the k eff of PWR 17x17 spent nuclear fuel (SNF) in the GBC-32 computational benchmark cask for the assessment of BUC in criticality safety analysis. The coupling methodology used in this study is not exclusive to BUC analysis. However, the choice to apply this methodology to the BUC problem is particularly significant because of the diverse range of aspects it encompasses in nuclear criticality safety analyses. This problem presents a unique opportunity to explore and address multiple facets of such analyses related to BUC and illustrates the capability of the SCALE code system with DAKOTA. This analysis makes use of historical reference data for the axial burnup profile, where the entire space within the bounds is considered. Both SCALE and DAKOTA are currently integrated in the Nuclear Energy Advanced Modeling Simulation (NEAMS) Workbench code system, which has a user-friendly graphical interface that simplifies the setup of simulations and configuration of input parameters as well as the visualization of simulation results.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Porous Polymers as Universal Reversal Agents for Heparin Anticoagulants through an Inclusion–Sequestration Mechanism

Heparins are widely used anticoagulants for surgical procedures and extracorporeal therapies. However, all of them have bleeding risks. Protamine sulfate, the only clinically approved antidote for unfractionated heparin (UFH), has adverse effects. Moreover, protamine can only partially neutralize low-molecular-weight heparins (LMWHs) and is not effective for fondaparinux. In this report an inclusion–sequestration strategy for efficient neutralization of heparin anticoagulants by cationic porous supramolecular organic frameworks (SOFs) and porous organic polymers (POPs) is reported. Isothermal titration calorimetric and fluorescence experiments show strong binding affinities of these porous polymers toward heparins, whereas dynamic light scattering and zeta potential analysis confirm that the heparin sequences are adsorbed into the interior of the porous hosts. Activated partial thromboplastin time, anti-FXa, and thromboelastography assays indicate that their neutralization efficacies are higher than or as high as that of protamine for UFH and generally superior to protamine for LMWHs and fondaparinux, which is further confirmed by tail-transection model in mice and ex vivo aPTT or anti-FXa analysis in rats. Acute toxicity evaluations reveal that one of the SOFs displays outstanding biocompatibility. This work suggests that porous polymers can supply safe and rapid reversal of clinically used heparins, as protamine surrogates, providing an improved approach for their neutralization.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH 4 + :NO 2 - , where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH 4 + :NO 2 - ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH 4 + :NO 2 - ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89–202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169–200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0–89, compared to 85.49 ± 0.01% from day 89–169, and 83.04 ± 0.01% from day 169–200). When the ratio was slightly increased to 1:1.17–1:1.2 (day 202–253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH 4 + :NO 2 - ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Patient-Reported Outcomes From a Phase 3 Randomized Controlled Trial Exploring Optimal Sequencing of Short-Term Androgen Deprivation Therapy With Prostate Radiation Therapy in Localized Prostate Cancer

Two phase 3 randomized controlled trials (OTT-0101, RTOG-9413) and a meta-analysis have shown an impact of sequencing of androgen deprivation therapy (ADT) and radiation therapy on oncologic outcomes in prostate cancer (PCa). However, the impact of sequencing strategy on health-related quality of life (HR-QoL) is unclear. Here, we present the patient-reported HR-QoL outcomes from the OTT-0101 study.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

CasCollect: Detecting cas genes and CRISPR arrays in raw sequence data v1

This software examines raw Illumina sequence data files for cas genes and CRISPR arrays, either to be used as evidence of genome editing or for basic analysis of bacterial genomes. It translates sequencing reads into peptide sequences, and runs these against sensitive hidden Markov models for numerous Cas protein families. The set of hit read seeds is then expanded leftward and rightward by sequence matching to remaining reads, and after multiple cycles, this small fraction of the original reads is assembled to produce Cas operons. A separate mode using known CRISPR repeat sequences for a genus are used to identify CRISPR arrays that may be in genomic locations that are isolated from Cas genes.SAND2019-11770 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Williams, Kelly↗
DOE OSTI2022

Identification of new marker genes from plant single‐cell RNA‐seq data using interpretable machine learning methods

Summary An essential step in the analysis of single‐cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single‐cell predictive marker (SPmarker) to identify novel cell‐type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes. We have demonstrated that our method can: assign cell types based on cells that were labelled using published methods; project cell types identified by trajectory analysis from one data set to other data sets; and assign cell types based on internal GFP markers. Using SPmarker, we have identified hundreds of new marker genes that were not identified before. As compared to known marker genes, the new marker genes have more orthologous genes identifiable in the corresponding rice single‐cell clusters. The new root hair marker genes also include 172 genes with orthologs expressed in root hair cells in five non‐ Arabidopsis species, which expands the number of marker genes for this cell type by 35–154%. Our results represent a new approach to identifying cell‐type marker genes from scRNA‐seq data and pave the way for cross‐species mapping of scRNA‐seq data in plants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Description of Pegethrix niliensis sp. nov., a Novel Cyanobacterium from the Nile River Basin, Egypt: A Polyphasic Analysis and Comparative Study of Related Genera in the Oculatellales Order

In this paper, we examine the filamentous cyanobacterial strain NILCB16 and describe it as a new species within the genus Pegethrix. The original population was sampled from a mat growing in an irrigation canal in the Nile River, Egypt. Initially classified under Plectonema or Planktolyngbya, the strain is a potential producer of the toxins microcystin and β-N-Methylamino-L-Alanine (BMAA). Additionally, we reviewed the taxonomic relationships between the Oculatellales genera. To describe the new species, we conducted a polyphasic study, encompassing 16S rRNA gene phylogenetic analyses performed using both Maximum Likelihood and Bayesian methods, sequence identity (p-distance) analysis, 16S-23S ITS secondary structures, and morphological and habitat comparisons. The phylogenetic analysis revealed that strain NILCB16 clustered within the Pegethrix clade with strong phylogenetic support, but in a distinct position from other species in the genus. The strain shared a maximum 16S rRNA gene identity of 97.3% with P. qiandaoensis and 96.1% with the type species, P. bostrychoides. Morphologically, NILCB16 can be differentiated from other species in the genus by its lack of false branching. Our phylogenetic analyses also show that Pegethrix, Cartusia, Elainella, and Maricoleus are clustered with strong phylogenetic support. They exhibit high 16S rRNA gene identity and are morphologically indistinguishable, suggesting they could potentially be merged into a single genus in the future.

Hentschke, Guilherme Scotta (ORCID:000000034396024↗
NASA NTRS2002

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Non-NASA Center↗
DOE OSTI2019

Syntgen: a system to generate temporal networks with user-specified topology

Abstract In the last few years, the study of temporal networks has progressed markedly. The evolution of clusters of nodes (or communities) is one of the major focus of these studies. However, the time dimension increases complexity, introducing new constructs and requiring novel and enhanced algorithms. In spite of recent improvements, the relative scarcity of timestamped representations of empiric networks, with known ground truth, hinders algorithm validation. A few approaches have been proposed to generate synthetic temporal networks that conform to static topological specifications while in general adopting an ad hoc approach to temporal evolution. We believe there is still a need for a principled synthetic network generator that conforms to problem domain topological specifications from a static as well as temporal perspective. Here, we present such a system. The unique attributes of our system include accepting arbitrary node degree and cluster size distributions and temporal evolution under user control, while supporting tunable joint distribution and temporal correlation of node degrees. Theoretical contributions include the analysis of conditions for graphic sequences of inter- and intracluster node degrees and cluster sizes and the development of a heuristic to search for the cluster membership of nodes that minimizes the shared information distance between clusterings. Our work shows that this system is capable of generating networks under user controlled topology with up to thousands of nodes and hundreds of clusters with strong topology adherence. Much larger networks are possible with relaxed requirements. The generated networks support algorithm validation as well as problem domain analysis.

Pereira, Luis Ramada↗
DOE OSTI2026

Protocol for applying a network-enabled gene discovery pipeline to non-model plant species

Identifying upstream regulators of key genes is essential for understanding gene regulatory mechanisms and translating these insights into functional targets. Here, we present a protocol for applying the network-enabled gene discovery pipeline (NEEDLE) to non-model plant species. We describe steps for environment setup, data preparation, computational analysis, expected outputs, and parameter considerations. NEEDLE integrates RNA sequencing (RNA-seq) processing, weighted gene co-expression analysis (WGCNA), Gene Network Inference with Ensemble of trees (GENIE3), and promoter conservation analysis to prioritize candidate transcriptional regulators.

Plant Sciences↗
NASA NTRS2002

Smooth Pursuit Saccade Amplitude Modulation During Exposure to Microgravity

Russian investigators have reported changes in pursuit tracking of a vertically moving point stimulus during space flight. Early in microgravity, changes were manifested by decreased eye movement amplitude (undershooting) and the appearance of correction saccades. As the flight progressed, pursuit of the moving point stimulus deteriorated while associated saccadic movements were unchanged. Immediately postflight there was an improved execution of active head movements indicating that the deficiencies in pursuit function noted in microgravity may be of central origin. In contrast, tests of two cosmonauts showed that horizontal and vertical smooth pursuit were unchanged inflight. However, results of corresponding saccadic tasks showed a tendency toward the overshooting of a horizontal target early inflight with high accuracy developing later inflight, accompanied by an increased saccade velocity and a trend toward decreased saccade latency. Based on these equivocal results, we have further investigated the effects of space flight on the smooth pursuit mechanism during and after short duration flight, and postflight on returning MIR crewmembers. Sinusoidal target movement was presented horizontally at frequencies of 0.33 and 1.0 Hz. Subjects were asked to perform two trials for each stimulus combination: (1) moving eyes-only (EO) and (2) moving eyes and head (EH) with the target motion. Peak amplitude was 30 deg for 0.33 Hz trials and 15 deg for the 1.0 Hz trials. The relationship between saccade amplitude and peak velocity were plotted as a main sequence for each phase of flight, and linear regression analysis allowed us to determine the slope of each main sequence plot. The linear slopes were then combined for each flight phase for each individual subject. The main sequence for both EO and EH trials at both the 0.33 and 1.0 Hz frequencies during flight for the short duration flyers showed a reduction in saccade velocity and amplitude when compared to the preflight main sequence . This difference in the regression slopes between flight phase, head/eye condition (EO or EH), and pursuit target frequency was observed across all subjects (statistically significant at the p<0.02, df= 2). It is interesting to note that postflight for the short duration flyers there was an immediate recovery to the preflight main sequence across all trials. There were no significant differences observed between the preflight slopes for either head movement condition (EO vs. EH). When the immediate postflight (R+O) regression slopes were compared with the preflight slopes, there was a tendency (not significant) for both saccade amplitude and peak velocity to increase during the postflight testing. This tendency had vanished by R+ 1. Of particular interest was the redistribution of saccades during the latter stages of the flight and immediately postflight in the EO condition. At the 1.0 Hz frequency the saccades tended to be clustered near the lowest target velocity. It was also interesting to note that gaze performance (eye in skull + head in space) was consistently better during the EH condition; a finding also observed by our Russian colleagues. As the results of the long duration flight become available we expect that they will not only show that postflight effects will be similar to those observed during the short duration flights, but will also last for a greater period of time following flight. It is not clear what mechanism is responsible for the decreased peak saccadic velocity during flight unless the change is related to the control of retinal slip. For example, it is possible that saccades will tend to initially undershoot their targets by a small percentage and these saccades are then followed, if vision is available, by a small augmenting corrective saccade. It has been postulated that the functional significance of this undershooting tendency is to maintain the spatial representation of the target on the same side of the fovea (as opposedo racing across the fovea) and hence in the same cerebral hemisphere that initiated the primary saccade thus minimizing delays caused by an intra-hemispheric transfer of information . One could also speculate that with saccade velocities greater than normal, additional corrective saccades would be required to bring the target back on the fovea. A less plausible explanation of our findings could be fatigue. Yet it seems unlikely that our subjects would show lower velocities on all inflight test days while showing increased saccade velocities immediately following space flight where fatigue is usually the greatest. Finally, the redistribution effect noted late inflight is likely caused by adaptive changes. Overall, corrective saccades appeared to be used in maintaining gaze on target; reducing retinal slip and assisting space travelers in maintaining clear vision throughout the different phases of the space flight.

Reschke, M. F.↗
NASA NTRS2014

Rapid Polymer Sequencer

Solid-state nanopore-based analysis of nucleic acid polymers is revolutionary. No other technique can determine information content in single molecules of genetic material at the speed of 1 subunit per microsecond. Because individual molecules are counted, the output is intrinsically quantitative. The nanopore approach is more generalized than any other method and in principle may be used to analyze any polymer molecule, including proteins. The approach to the development of a solid-state nanopore device is novel in the use of nanofabrication, nanoelectronic components, and high-speed signal acquisition. A novel geometry of the solid-state nanopore (less than 5 nm in length and 5 nm in diameter) will enable 1 to 5 nucleotide resolution measurements. This means that maximum resolution will be improved at least 100-fold compared to biological ion-channel measurements. The solid-state nanopore sensor will be made to enable sequencing DNA at a much faster rate than presently possible without the need for extensive sample preparation procedures, such as enzymatic amplification and labeling reactions. It will analyze electronic properties of individual subunits of DNA or RNA, to obtain linear composition of each genetic polymer molecule.

technology opportunity↗