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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Assessing the use of portable air cleaners for reducing exposure to airborne diseases in a conference room with thermal stratification

The COVID-19 pandemic has highlighted the need for strategies that mitigate the risk of aerosol disease transmission in indoor environments with different ventilation strategies. It is necessary for building operators to be able to estimate and compare the relative impacts of different mitigation strategies to determine suitable strategies for a particular situation. Using a validated CFD model, this study simulates the dispersion of exhaled contaminants in a thermally stratified conference room with overhead heating. The impacts of portable air-cleaners (PACs) on the room airflow and contaminant distribution were evaluated for different PAC locations and flow rates, as well as for different room setups (socially distanced or fully occupied). To obtain a holistic view of a strategy's impacts under different release scenarios, we simultaneously model the steady-state distribution of aerosolized virus contaminants from eight distinct sources in 18 cases for a total of 144 release scenarios. The simulations show that the location of the source, the PAC settings, and the room set-up can impact the average exposure and PAC effectiveness. For this studied case, the PACs reduced the room average exposure by 31%-66% relative to the baseline case. Some occupant locations were shown to have a higher-than-average exposure, particularly those seated near the airflow outlet, and occupants closest to sources tended to see the highest exposure from said source. We found that these PACs were effective at reducing the stratification caused by overhead heating, and also identified at least one sub-optimal location for placing a PAC in this space.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Resource distribution under spatiotemporal uncertainty of disease spread: Stochastic versus robust approaches

We consider the problem of optimizing locations of distribution centers (DCs) and plans for distributing resources such as test kits and vaccines, under spatiotemporal uncertainties of disease spread and demand for the resources. We aim to balance the operational cost (including costs of deploying facilities, shipping, and storage) and quality of service (reflected by demand coverage), while ensuring equity and fairness of resource distribution across multiple populations. We compare a sample-based stochastic programming (SP) approach with a distributionally robust optimization (DRO) approach using a moment-based ambiguity set. Numerical studies are conducted on instances of distributing COVID-19 vaccines in the United States and test kits, to compare SP and DRO models with a deterministic formulation using estimated demand and with the current resource distribution plans implemented in the US. We demonstrate the results over distinct phases of the pandemic to estimate the cost and speed of resource distribution depending on scale and coverage, and show the “demand-driven” properties of the SP and DRO solutions. Furthermore, our results further indicate that if the worst-case unmet demand is prioritized, then the DRO approach is preferred despite of its higher overall cost. Nevertheless, the SP approach can provide an intermediate plan under budgetary restrictions without significant compromises in demand coverage.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Individualized Adaptive Radiation Therapy Allows for Safe Treatment of Hepatocellular Carcinoma in Patients With Child-Turcotte-Pugh B Liver Disease

Previous reports of stereotactic body radiation therapy (SBRT) for hepatocellular carcinoma (HCC) suggest unacceptably high rates of toxicity in patients with Child-Turcotte-Pugh (CTP) B liver disease. We hypothesized that an individualized adaptive treatment approach based on midtreatment liver function would maintain good local control while limiting toxicity in this population.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Pneumonia After Bacterial or Viral Infection Preceded or Followed by Radiation Exposure: A Reanalysis of Older Radiobiologic Data and Implications for Low-Dose Radiation Therapy for Coronavirus Disease 2019 Pneumonia

Currently, there are about 15 ongoing clinical studies on low dose radiation therapy for Coronavirus Disease 2019 pneumonia. One of the underlying assumptions is that irradiation of 0.5 to 1.5 Gy is effective at ameliorating viral pneumonia. We aimed to reanalyze all available experimental radiobiologic data to assess evidence for such amelioration.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

ALKBH5-Modified HMGB1-STING Activation Contributes to Radiation Induced Liver Disease via Innate Immune Response

Radiation therapy, which is vital for the treatment of primary liver cancer, comes with unavoidable liver injury, which limits its implementation. N6-methyladenosine (m6A) methylation is involved in many molecular functions. However, its role in radiation-induced liver diseases (RILD) remains unknown. Herein, we investigate the role of m6A methylation in RILD.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

The rapid increase in computing power, especially with the integration of graphics processing units, has dramatically increased the capabilities of molecular dynamics simulations. To date, these capabilities extend from running very long simulations (tens to hundreds of microseconds) to thousands of short simulations. However, the expansive data generated in these simulations must be made interpretable not only by the investigator who performs them but also by others as well. Here, we demonstrate how integrating learning techniques, such as artificial intelligence, machine learning, and neural networks, into analysis pipelines can reveal the kinetics of Alzheimer's disease (AD) protein aggregation. Finally, we review select AD targets, describe current simulation methods, and introduce learning concepts and their application in AD, highlighting limitations and potential solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Spatial Glycomics and Kidney Disease

Glycans are critical for the kidney's physiological and pathological cellular functions, and our ability to reveal their spatial distributions within tissues has helped us reveal how these carbohydrate moieties are involved in many of these processes. This review discusses the role of different types of glycans in kidney biology and disease, common approaches used for glycan imaging, and how glycan imaging has helped us better understand kidney pathology. Here, we mainly focus on emerging methods using mass spectrometry imaging (MSI) because this technology is untargeted and provides complete information on glycan composition compared to the other methods, such as lectin and metabolite labeling, which are targeted and often inform only on the specific part of a glycan structure. We especially focus on protein N-glycosylation, as this is one of the most common post-translational modifications, and these moieties play a vital role in renal structure and function. The recent advancements in MSI of N-glycans we reviewed have provided new insights into the pathophysiology of the kidney and paved the way for clinical application.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Galectin-1 secreted by bone marrow-derived mesenchymal stem cells mediates anti-inflammatory responses in acute airway disease

The hallmarks of allergic airway disease (AAD) include infiltration of inflammatory cells into the bronchoalveolar space. Bone marrow derived mesenchymal stem cells (BMSCs) show anti-inflammatory properties in AAD. In addition, galectin-1 (Gal-1) is a lectin significantly upregulated upon inflammation and is also known to mediate potential anti-inflammatory responses. We hypothesized that BMSCs regulated inflammatory responses by secretion of Gal-1 during AAD pathogenesis. BMSCs were isolated from murine femurs and tibiae and adoptively transferred into an ovalbumin-induced AAD mouse model. Knockdown of Gal-1 in BMSCs was performed using shRNA. Flow cytometry, ELISAs, and immunohistology were performed to analyze inflammatory responses in mice, and a Transwell system was used to establish an in vitro co-culture system of lung epithelial cells (MLE-12) and BMSCs. Administration of BMSCs significantly upregulated Gal-1 expression upon inflammation and decreased infiltration of inflammatory cells and secretion of proinflammatory cytokines in vivo. In addition, we showed that this function was mediated by reduced activation of the MAPK p38 signaling pathway. Similar observations were found using an in vitro lipopolysaccharide-induced model when MLE-12 cells were co-cultured with BMSCs. Gal-1 secretion by BMSCs alleviated inflammatory responses observed in AAD and hence provides a promising therapeutic alternative to AAD patients insensitive to conventional drug treatments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

MIG/CXCL9 exacerbates the progression of metabolic-associated fatty liver disease by disrupting Treg/Th17 balance

CD4{sup +}CD25{sup +} regulatory T (Treg) cells and Th17 cells play important roles in the progression of metabolic-associated fatty liver disease (MAFLD). However, the contribution of monokine induced by interferon-gamma (MIG)/CXCL9 to the Treg/Th17 imbalance in MAFLD is only partially understood. In the present study, we detected increased levels of MIG/CXCL9 and a Treg/Th17 imbalance in the setting of metabolic-associated steatohepatitis (MASH). Recombinant adeno-associated virus-mediated gene transfer and silencing of MIG/CXCL9 expression in mice alleviated MASH and increased the Treg/Th17 ratio. Furthermore, the percentage of Th17 cells, but not Treg cells, differentiated from splenic CD4{sup +} T cells was significantly increased by administration of MIG/CXCL9. MIG/CXCL9 also promoted Th17 cell proliferation, and its effects were dose dependent. Levels of phosphorylated c-Jun N-terminal kinase (JNK) decreased dramatically when MIG/CXCL9 was inhibited in a murine MASH model. In cultured Treg cells, phosphorylated JNK levels decreased dose-dependently in response to MIG/CXCL9 inhibition, but increased in cultured Th17 cells. This effect was blocked in the presence of a JNK inhibitor. These findings underline the fundamental importance of MIG/CXCL9 in maintaining the Treg/Th17 balance in MAFLD and provide the foundations for a novel approach to preventing and treating MAFLD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Evaluation of Extreme Soil Moisture Conditions During the 2020 Sahel Floods and Implications for Disease Outbreaks

The June-October 2020 growing season was characterized by sustained and extreme flooding across the African Sahel. One consequence of flooding events such as this is outbreaks of vector borne diseases (VBDs) which are often associated with climate anomalies. In this study, data from the soil moisture active passive (SMAP) mission is used with other soil moisture and precipitation data to show that the 2020 Sahelian growing season was the most extreme over the past four decades, ranking first in seasonally accumulated precipitation, which on average exceeded the climatology by around 300 mm. VBD outbreaks of Rift Valley fever and Chikungunya followed in Mauritania/Senegal and Chad, respectively. In some cases, soil moisture is a better indicator of VBD outbreak risk than precipitation, which has so far been more commonly used in studies of VBD outbreaks. It is expected that this finding will inform future monitoring and prediction efforts for VBD risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Abstract XPD is a key nucleotide excision repair (NER) protein whose function is vital for genome integrity. During NER, XPD serves as a 5′−3′ single-strand DNA translocase that enables lesion scanning and verification in genomic DNA. Yet, its translocation mechanism is incompletely understood. Here we use molecular simulations and chain-of-replicas path optimization methods to model the ATP-driven translocation mechanisms of XPD and its bacterial homolog DinG, revealing all on-path metastable intermediates and corresponding kinetic rates. We identify the XPD(DinG) global domain motions that modulate the strength of DNA association at the opposing ends of the DNA-binding groove. During the ATP hydrolysis cycle, alternating weak and strong interactions at two defined groove constrictions enable DNA reptation and forward displacement of the ATPase. Moreover, we show that DNA- or ATP-binding residues directly involved in translocation are hotspots for genetic disease mutations. Thus, our findings shed light on the etiology of XPD-associated genetic syndromes.

Paul, Tanmoy↗
DOE OSTI2023

Impaired neuron differentiation in GBA-associated Parkinson’s disease is linked to cell cycle defects in organoids

The mechanisms underlying Parkinson’s disease (PD) etiology are only partially understood despite intensive research conducted in the field. Recent evidence suggests that early neurodevelopmental defects might play a role in cellular susceptibility to neurodegeneration. To study the early developmental contribution of GBA mutations in PD we used patient-derived iPSCs carrying a heterozygous N370S mutation in the GBA gene. Patient-specific midbrain organoids displayed GBA-PD relevant phenotypes such as reduction of GCase activity, autophagy impairment, and mitochondrial dysfunction. Genome-scale metabolic (GEM) modeling predicted changes in lipid metabolism which were validated with lipidomics analysis, showing significant differences in the lipidome of GBA-PD. In addition, patient-specific midbrain organoids exhibited a decrease in the number and complexity of dopaminergic neurons. This was accompanied by an increase in the neural progenitor population showing signs of oxidative stress-induced damage and premature cellular senescence. These results provide insights into how GBA mutations may lead to neurodevelopmental defects thereby predisposing to PD pathology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genomic analyses implicate noncoding de novo variants in congenital heart disease

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10 -4 ). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10 -5 ). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10 -3 ). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10 -5 ). Overall, our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Electrocardiographic changes predate Parkinson’s disease onset

Autonomic nervous system involvement precedes the motor features of Parkinson’s disease (PD). Our goal was to develop a proof-of-concept model for identifying subjects at high risk of developing PD by analysis of cardiac electrical activity. We used standard 10-s electrocardiogram (ECG) recordings of 60 subjects from the Honolulu Asia Aging Study including 10 with prevalent PD, 25 with prodromal PD, and 25 controls who never developed PD. Various methods were implemented to extract features from ECGs including simple heart rate variability (HRV) metrics, commonly used signal processing methods, and a Probabilistic Symbolic Pattern Recognition (PSPR) method. Extracted features were analyzed via stepwise logistic regression to distinguish between prodromal cases and controls. Stepwise logistic regression selected four features from PSPR as predictors of PD. The final regression model built on the entire dataset provided an area under receiver operating characteristics curve (AUC) with 95% confidence interval of 0.90 [0.80, 0.99]. The five-fold cross-validation process produced an average AUC of 0.835 [0.831, 0.839]. We conclude that cardiac electrical activity provides important information about the likelihood of future PD not captured by classical HRV metrics. Machine learning applied to ECGs may help identify subjects at high risk of having prodromal PD.

59 BASIC BIOLOGICAL SCIENCES↗