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All sourcesNASA NTRSDOE OSTI
DOE OSTI1996

Nuclear Safety [Vol. 37, No. 2, April-June 1996]

Nuclear Safety is a journal that covers significant issues in the field of nuclear safety. Its primary scope is safety in the design, construction, operation, and decommissioning of nuclear power reactors worldwide and the research and analysis activities that promote this goal, but it also encompasses the safety aspects of the entire nuclear fuel cycle, including fuel fabrication, spent-fuel processing and handling, and nuclear waste disposal, the handling of fissionable materials and radioisotopes, and the environmental effects of all these activities. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 97 The Nuclear Community and the Public: Cognitive and Cultural Influences on Thinking About Nuclear Risk, M. A. Meyer; 109 Twenty-Third Water Reactor Safety Information Meeting, D. A. Copinger; ACCIDENT ANALYSIS: 126 Analysis of a PWR LBLOCA Without SCRAM, Trevor N. Tyler, Rafael Macian-Juan and John H. Mahaffy; DESIGN FEATURES: 139 Vulnerability of Multiple-Barrier Systems, N. C. Lind; ENVIRONMENTAL EFFECTS: 149 A Study of Wet Catalytic Oxidation of Radioactive Spent Ion Exchange Resin by Hydrogen Peroxide, Xingchao Jian, Tianbao Wu, and Guichun Yun; 157 A Comparison Study and Resolution of Differences Between Emergency Response and Safety Analysis Codes Used at the Savannah River Site, A. A. Simpkins; OPERATING EXPERIENCES: 164 Reactor Shutdown Experience, Compiled by J. W. Cletcher; RECENT DEVELOPMENTS: 167 Reports, Standards, and Safety Guides, D. S. Queener; 172 Proposed Rule Changes as of Dec. 31,1995; ANNOUNCEMENTS: 178 American Nuclear Society 1997 Annual Meeting; 178 American Nuclear Society Nuclear Criticality and Safety Division Topical Meeting; 176 The Authors.

05 NUCLEAR FUELS↗
DOE OSTI2024

Vascular endothelial growth factor receptor-1 (FLT1) interactions with amyloid-beta in Alzheimer’s disease: A putative biomarker of amyloid-induced vascular damage

We have identified FLT1 as a protein that changes during Alzheimer's disease (AD) whereby higher brain protein levels are associated with more amyloid, more tau, and faster longitudinal cognitive decline. Given FLT1's role in angiogenesis and immune activation, we hypothesized that FLT1 is upregulated in response to amyloid pathology, driving a vascular-immune cascade resulting in neurodegeneration and cognitive decline. We sought to determine (1) if in vivo FLT1 levels (CSF and plasma) associate with biomarkers of AD neuropathology or differ between diagnostic staging in an aged cohort enriched for early disease, and (2) whether FLT1 expression interacts with amyloid on downstream outcomes, such as phosphorylated tau levels and cognitive performance. Additionally, we sought to replicate FLT1 interactions in the brain. The results showed that higher levels of FLT1 in CSF and post-mortem brain tissue related to increased tau, particularly among amyloid positive individuals. These analyses help clarify the potential utility of FLT1 as a biomarker among individuals with evidence of brain amyloidosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Protein–protein interactions between tenascin-R and RPTPζ/phosphacan are critical to maintain the architecture of perineuronal nets

Neural plasticity, the ability to alter the structure and function of neural circuits, varies throughout the age of an individual. The end of the hyperplastic period in the central nervous system coincides with the appearance of honeycomb-like structures called perineuronal nets (PNNs) that surround a subset of neurons. PNNs are a condensed form of neural extracellular matrix that include the glycosaminoglycan hyaluronan and extracellular matrix proteins such as aggrecan and tenascin-R (TNR). PNNs are key regulators of developmental neural plasticity and cognitive functions, yet our current understanding of the molecular interactions that help assemble them remains limited. Disruption of Ptprz1, the gene encoding the receptor protein tyrosine phosphatase RPTPζ, altered the appearance of nets from a reticulated structure to puncta on the surface of cortical neuron bodies in adult mice. The structural alterations mirror those found in Tnr -/- mice, and TNR is absent from the net structures that form in dissociated cultures of Ptprz1 -/- cortical neurons. These findings raised the possibility that TNR and RPTPζ cooperate to promote the assembly of PNNs. Here, we show that TNR associates with the RPTPζ ectodomain and provide a structural basis for these interactions. Furthermore, we show that RPTPζ forms an identical complex with tenascin-C, a homolog of TNR that also regulates neural plasticity. Finally, we demonstrate that mutating residues at the RPTPζ–TNR interface impairs the formation of PNNs in dissociated neuronal cultures. Overall, this work sets the stage for analyzing the roles of protein–protein interactions that underpin the formation of nets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Machine-learning-aided cognitive reconfiguration for flexible-bandwidth HPC and data center networks [Invited]

This paper proposes a machine-learning (ML)-aided cognitive approach for effective bandwidth reconfiguration in optically interconnected datacenter/high-performance computing (HPC) systems. The proposed approach relies on a Hyper-X-like architecture augmented with flexible-bandwidth photonic interconnections at large scales using a hierarchical intra/inter-POD photonic switching layout. We first formulate the problem of the connectivity graph and routing scheme optimization as a mixed-integer linear programming model. A two-phase heuristic algorithm and a joint optimization approach are devised to solve the problem with low time complexity. Then, we propose an ML-based end-to-end performance estimator design to assist the network control plane with intelligent decision making for bandwidth reconfiguration. Numerical simulations using traffic distribution profiles extracted from HPC applications traces as well as random traffic matrices verify the accuracy performance of the ML design estimator ( < <#comment/> 9 % <#comment/> error) and demonstrate up to 5 × <#comment/> throughput gain from the proposed approach compared with the baseline Hyper-X network using fixed all-to-all intra/inter-portable data center interconnects.

Chen, Xiaoliang (ORCID:0000000278056237)↗
DOE OSTI2020

An Unobstructive Sensing Method for Indoor Air Quality Optimization and Metabolic Assessment within Vehicles

This work investigates the use of an intelligent and unobstructive sensing technique for maintaining vehicle cabin’s indoor air quality while simultaneously assessing the driver metabolic rate. CO 2 accumulation patterns are of great interest because CO 2 can have negative cognitive effects at higher concentrations and also since CO 2 accumulation rate can potentially be used to determine a person’s metabolic rate. The management of the vehicle’s ventilation system was controlled by periodically alternating the air recirculation mode within the cabin, which was actuated based on the CO 2 levels inside the vehicle’s cabin. The CO 2 accumulation periods were used to assess the driver’s metabolic rate, using a model that considered the vehicle’s air exchange rate. In the process of the method optimization, it was found that the vehicle’s air exchange rate (λ [h –1 ]) depends on the vehicle speeds, following the relationship: λ = 0.060 × (speed) – 0.88 when driving faster than 17 MPH. An accuracy level of 95% was found between the new method to assess the driver’s metabolic rate (1620 ± 140 kcal/day) and the reference method of indirect calorimetry (1550 ± 150 kcal/day) for a total of N = 16 metabolic assessments at various vehicle speeds. The new sensing method represents a novel approach for unobstructive assessment of driver metabolic rate while maintaining indoor air quality within the vehicle cabin.

passive sensing↗
DOE OSTI2020

Glucuronidation of Methylated Quercetin Derivatives: Chemical and Biochemical Approaches

Botanical supplements derived from grapes are functional in animal model systems for the amelioration of neurological conditions, including cognitive impairment. Rats fed with grape extracts accumulate 3'-O-methyl-quercetin-3-O-β-Dglucuronide (3) in their brains, suggesting 3 as a potential therapeutic agent. To develop methods for the synthesis of 3 and the related 4'-O-methyl-quercetin-7-O-β-D-glucuronide (4), 3-O-methyl-quercetin-3'-O-β-D-glucuronide (5), and 4'-O-methylquercetin-3'-O-β-D-glucuronide (6), which are not found in the brain, we have evaluated both enzymatic semisynthesis and full chemical synthetic approaches. Biocatalysis by mammalian UDP-glucuronosyltransferases generated multiple glucuronidated products from 4'-O-methylquercetin, and is not cost-effective. Chemical synthetic methods, on the other hand, provided good results; 3, 5, and 6 were obtained in six steps at 12, 18, and 30% overall yield, respectively, while 4 was synthesized in five steps at 34% overall yield. Furthermore, a mechanistic study on the unexpected regioselectivity observed in the quercetin glucuronide synthetic steps is also presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A hidden demethylation pathway removes mercury from rice plants and mitigates mercury flux to food chains

Dietary exposure to methylmercury (MeHg) causes irreversible damage to human cognition and is mitigated by photolysis and microbial demethylation of MeHg. Rice (Oryza sativa L.) has been identified as a major dietary source of MeHg. However, it remains unknown what drives the process within plants for MeHg to make its way from soils to rice and the subsequent human dietary exposure to Hg. Here we report a hidden pathway of MeHg demethylation independent of light and microorganisms in rice plants. This natural pathway is driven by reactive oxygen species generated in vivo, rapidly transforming MeHg to inorganic Hg and then eliminating Hg from plants as gaseous Hg°. MeHg concentrations in rice grains would increase by 2.4- to 4.7-fold without this pathway, which equates to intelligence quotient losses of 0.01–0.51 points per newborn in major rice-consuming countries, corresponding to annual economic losses of US$30.7–84.2 billion globally. Importantly, this discovered pathway effectively removes Hg from human food webs, playing an important role in exposure mitigation and global Hg cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The phylogenetic roots of addiction: compulsive drug seeking, natural and drug-sensitive reward, and the acquisition of learned habits

Our rational faculties permit us humans to maximize the utility of our actions. We perform a fundamental type of cost-benefit analysis in which we frame a problem, assign values to the different paths, and then choose from among a set of available options, the course that promises the most favorable outcome. So why then does addiction appear to be so impervious to the associated costs, so unaffected by undesired consequences, and ultimately so resistant to cognitive oversight? The answer may likely be found in the fact that the drivers for compulsive drug seeking and drug taking are located in affective brain circuits, circuits that are structured and patterned by learning with repeated activation. These deep processes exhibit significant resistance to control by our cognitive faculties. The general consensus is that addiction arises from mechanisms that overvalue the magnitude of reward, discount the associated risks, and thereby bias individuals towards compulsive pursuit of addictive drugs. Behavioral disruption and dependence appear to arise at the intersection of a number of connected but separate phenomena: expectations for the occurrence of specific events, behaviors that seek encounters with them, the ability to notice and learn nonrandom, co-occurring conditions, the prediction and valuation of consequences, the forming of enduring memories, and the drivers of focused behavior through compulsion, habits, and acquired routines. It is important to recognize that each one of these individual faculties are present and well developed across the entire phylogenetic tree of bilateral metazoans. The goal of this special volume is dedicated to exploring the degree to which inherent elements can account for addiction and addiction-associated phenomena. In much of the literature on addiction, the underlying processes are often viewed as distinctly mammalian, arising, in part, from the strong cognitive capacities of this taxon. Some phenomena may even be regarded to exist only in primates, or even solely in humans. This supposition arises from the fact that studies are conducted almost exclusively in mammals and primates, while evolutionary antecedents of the behavior are rarely considered. A more comprehensive perspective that examines drug reward and reinforcement in a wider range of organisms demonstrates that many of the component traits are actually well developed across the greater metazoan lineage, and they may well predate the emergence of a mammalian clade by a wide margin. The collection of papers assembled here supports the notion that the capacity to associate cues and quences has not arisen in mammals de novo. Rather, the neural mechanisms for detecting contingencies and for predicting future outcomes are very deeply rooted across broad phylogenetic divisions. Our understanding of an ability to associate paired events has been enriched by work in invertebrate preparations in both classical and operant conditioning scenarios [Cook and Carew, 1986, 1989a, 1989b]. The ability to learn allows us to connect cues and behavioral actions to their associated consequences. Pavlovian conditioning enriches surrounding cues with predictive value. Outcomes with positive valence generate appetitive responses and approach to the associated cues, while those perceived as aversive bring cue avoidance and withdrawal. Humans are not the only life forms capable of such short- and long-term modulations of behavior

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Eucalyptus Wood Smoke Extract Elicits a Dose-Dependent Effect in Brain Endothelial Cells

The frequency, duration, and size of wildfires have been increasing, and the inhalation of wildfire smoke particles poses a significant risk to human health. Epidemiological studies have shown that wildfire smoke exposure is positively associated with cognitive and neurological dysfunctions. However, there is a significant gap in knowledge on how wildfire smoke exposure can affect the blood–brain barrier and cause molecular and cellular changes in the brain. Our study aims to determine the acute effect of smoldering eucalyptus wood smoke extract (WSE) on brain endothelial cells for potential neurotoxicity in vitro. Primary human brain microvascular endothelial cells (HBMEC) and immortalized human brain endothelial cell line (hCMEC/D3) were treated with different doses of WSE for 24 h. WSE treatment resulted in a dose-dependent increase in IL-8 in both HBMEC and hCMEC/D3. RNA-seq analyses showed a dose-dependent upregulation of genes involved in aryl hydrocarbon receptor (AhR) and nuclear factor erythroid 2-related factor 2 (NRF2) pathways and a decrease in tight junction markers in both HBMEC and hCMEC/D3. When comparing untreated controls, RNA-seq analyses showed that HBMEC have a higher expression of tight junction markers compared to hCMEC/D3. In summary, our study found that 24 h WSE treatment increases IL-8 production dose-dependently and decreases tight junction markers in both HBMEC and hCMEC/D3 that may be mediated through the AhR and NRF2 pathways, and HBMEC could be a better in vitro model for studying the effect of wood smoke extract or particles on brain endothelial cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The False Dilemma: Rethinking AF Science and Technology Officer Talent Management

In 2019, Secretary of the Air Force (SECAF) Heather Wilson launched the 2030 Science and Technology (S&T) Strategy by stating, “The advantage will go to those who create the best technologies and who integrate and field them in creative operational ways that provide military advantages.” In 2021, 15% of Air Force general officers responsible for creating and integrating this technological edge had a science, technology, engineering, and math (STEM) graduate degree, and less than 1% of generals had a STEM doctorate. As one point of comparison, at least 32% and 13% of founding CEOs of Fortune 500 technology companies had a master’s and doctoral STEM degree, respectively. The gulf is larger when you consider that these CEOs used their technical degrees throughout their careers whereas most general officers do not. In large organizations, if the leader does not possess technical knowledge, it is difficult to drive innovation systems and connect ideas to reality. The evidence for this disconnect is abundant in acquisition challenges for high-tech systems, significant pushback to the “revolution in military affairs”, and failure of the “Third Offset” to take hold and deliver capabilities to offset Chinese and Russian capabilities. Indeed, when the former Air Force and Space Force Chief Software Officer, Nicolas M. Chaillan, offered his resignation, one of the main reasons for leaving was “the failure of OSD and the Joint Staff to deliver on their own alleged top ‘priority’, JADC2 – they couldn’t ‘walk the walk.’” Senior leaders have recognized this disconnect, and several inquiries and studies regarding STEM competency have been conducted. Many have posed a false dilemma: a large, STEM-cognizant or small, STEM-expert force. However, current and future STEM human capital needs are managed at the unit and functional area level. This leads to “silos” and the tactical “needs of the present” dominating the strategic “needs of the future”, highlighted by only two functional areas systematically tracking future STEM needs. Therefore, the decision on force structure appears to have been historically made by default through these and other perceived structural realities, and a vast majority of recommendations have focused on the small STEM community – an exercise in diminishing returns. In essence, the solution often boils down to finding unicorns – officers that have chartered the unforgiving pathway through the traditional “gates” to general officer while obtaining sufficient STEM proficiency along the way. Fortunately for the Air Force, these officers exist, albeit at a rate below what the evidence would suggest is necessary. However, this approach fundamentally limits the ability to develop a deep pool of officers with the ability to create and integrate technologies and ensures the Dunning-Kruger effect is prevalent. The Dunning-Kruger effect is a cognitive bias where those with limited knowledge in an area lack the expertise necessary to recognize their lack of expertise and consequently are prone to overestimate their knowledge and performance. In short, we need less leaders overestimating their STEM knowledge and more with hard-earned STEM competency required to “walk the walk” to create and integrate technologies for military advantage. This will not be accomplished by restricting the emphasis to the traditional scientists and engineering (S&E) career fields – the pool, only 10% of line officers, and general officer progression is just too small. Fortunately, the recent SECAF’s Management Initiatives and Chief of Staff’s (CSAF) Action Orders, both containing emphasis on organic expertise to “accrue advantage in military-technological competition,” present an opportunity to truly develop a framework for the force of the future.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Investigating the clinico-anatomical dissociation in the behavioral variant of Alzheimer disease

We previously found temporoparietal-predominant atrophy patterns in the behavioral variant of Alzheimer’s disease (bvAD), with relative sparing of frontal regions. Here, we aimed to understand the clinico-anatomical dissociation in bvAD based on alternative neuroimaging markers. We retrospectively included 150 participants, including 29 bvAD, 28 “typical” amnestic-predominant AD (tAD), 28 behavioral variant of frontotemporal dementia (bvFTD), and 65 cognitively normal participants. Patients with bvAD were compared with other diagnostic groups on glucose metabolism and metabolic connectivity measured by [ 18 F]FDG-PET, and on subcortical gray matter and white matter hyperintensity (WMH) volumes measured by MRI. A receiver-operating-characteristic-analysis was performed to determine the neuroimaging measures with highest diagnostic accuracy. bvAD and tAD showed predominant temporoparietal hypometabolism compared to controls, and did not differ in direct contrasts. However, overlaying statistical maps from contrasts between patients and controls revealed broader frontoinsular hypometabolism in bvAD than tAD, partially overlapping with bvFTD. bvAD showed greater anterior default mode network (DMN) involvement than tAD, mimicking bvFTD, and reduced connectivity of the posterior cingulate cortex with prefrontal regions. Analyses of WMH and subcortical volume showed closer resemblance of bvAD to tAD than to bvFTD, and larger amygdalar volumes in bvAD than tAD respectively. The top-3 discriminators for bvAD vs. bvFTD were FDG posterior-DMN-ratios (bvAD bvFTD, area under the curve [AUC] range 0.85–0.91, all p < 0.001). The top-3 for bvAD vs. tAD were amygdalar volume (bvAD>tAD), MRI anterior-DMN-ratios (bvAD<tAD), FDG anterior-DMN-ratios (bvAD<tAD, AUC range 0.71–0.84, all p < 0.05). Subtle frontoinsular hypometabolism and anterior DMN involvement may underlie the prominent behavioral phenotype in bvAD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

In-vivo neuronal dysfunction by Aβ and tau overlaps with brain-wide inflammatory mechanisms in Alzheimer’s disease

The molecular mechanisms underlying neuronal dysfunction in Alzheimer’s disease (AD) remain uncharacterized. Here, we identify genes, molecular pathways and cellular components associated with whole-brain dysregulation caused by amyloid-beta (Aβ) and tau deposits in the living human brain. We obtained in-vivo resting-state functional MRI (rs-fMRI), Aβ- and tau-PET for 47 cognitively unimpaired and 16 AD participants from the Translational Biomarkers in Aging and Dementia cohort. Adverse neuronal activity impacts by Aβ and tau were quantified with personalized dynamical models by fitting pathology-mediated computational signals to the participant’s real rs-fMRIs. Then, we detected robust brain-wide associations between the spatial profiles of Aβ-tau impacts and gene expression in the neurotypical transcriptome (Allen Human Brain Atlas). Within the obtained distinctive signature of in-vivo neuronal dysfunction, several genes have prominent roles in microglial activation and in interactions with Aβ and tau. Moreover, cellular vulnerability estimations revealed strong association of microglial expression patterns with Aβ and tau’s synergistic impact on neuronal activity (q < 0.001). These results further support the central role of the immune system and neuroinflammatory pathways in AD pathogenesis. Neuronal dysregulation by AD pathologies also associated with neurotypical synaptic and developmental processes. In addition, we identified drug candidates from the vast LINCS library to halt or reduce the observed Aβ-tau effects on neuronal activity. Top-ranked pharmacological interventions target inflammatory, cancer and cardiovascular pathways, including specific medications undergoing clinical evaluation in AD. Our findings, based on the examination of molecular-pathological-functional interactions in humans, may accelerate the process of bringing effective therapies into clinical practice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Contributions of major tau kinase activation and phospho-tau accumulation to cortical and hippocampal tangle formation and cognition in older adults

Aberrant activation of tau kinases (tauK) has been proposed as a major step in tau hyperphosphorylation and misfolding, and subsequent formation of neurofibrillary tangles (NFT) in Alzheimer's disease (AD). However, evidence of tauK hyperactivation in actual AD brains is scarce and inconsistent, and their role in age-related cognitive decline remains undocumented. We evaluated activated/inhibited species of CDK5/p35/p25, GSK3a/ß, and ERK1/2 as well as ten tau/phospho-tau (ptau) peptides (mapping Ser 202 , Thr 217 , Ser 262 , Ser 305 , and Ser 404 phospho-residues) by Western blot or selected reaction monitoring proteomics, respectively, in postmortem dorsolateral prefrontal cortex (DLPFC) and hippocampal samples of 150 participants from the Rush Memory and Aging Project (MAP). Regression models and mediation analyses assessed the contributions of these variables to tau phosphorylation, NFT deposition and antemortem cognitive status of MAP participants. Surprisingly, greater p25 and p35 (indices for CDK5 activation) and lower pSer 21/9 -GSK3a/ß (inhibited species) immunodensities were associated with lower ptau peptide amounts. Individuals with higher p25 cortical densities displayed better cognitive outcomes, particularly working memory. Statistical mediation analyses indicated that the beneficial effect of CDK5/p25 on cognition was mediated by lower densities of phospho-Thr 217 -tau and NFT deposition in DLPFC, and also identified Thr 217 and Ser 262 as the ptau sites with greatest influence in both NFT accumulation and cognitive impairment. The present data suggest that tau hyperphosphorylation, tangle deposition, and the subsequent cognitive impairment do not rely on aberrant activation of major tauKs. Additionally, novel evidence was provided for the beneficial contribution of cortical CDK5/p25 to the maintenance of working memory.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Feasibility and preliminary efficacy for morning bright light therapy to improve sleep and plasma biomarkers in US Veterans with TBI. A prospective, open-label, single-arm trial

Mild traumatic brain injury (TBI) is associated with persistent sleep-wake dysfunction, including insomnia and circadian rhythm disruption, which can exacerbate functional outcomes including mood, pain, and quality of life. Present therapies to treat sleep-wake disturbances in those with TBI (e.g., cognitive behavioral therapy for insomnia) are limited by marginal efficacy, poor patient acceptability, and/or high patient/provider burden. Thus, this study aimed to assess the feasibility and preliminary efficacy of morning bright light therapy, to improve sleep in Veterans with TBI (NCT03578003). Thirty-three Veterans with history of TBI were prospectively enrolled in a single-arm, open-label intervention using a lightbox (~10,000 lux at the eye) for 60-minutes every morning for 4-weeks. Pre- and post-intervention outcomes included questionnaires related to sleep, mood, TBI, post-traumatic stress disorder (PTSD), and pain; wrist actigraphy as a proxy for objective sleep; and blood-based biomarkers related to TBI/sleep. The protocol was rated favorably by ~75% of participants, with adherence to the lightbox and actigraphy being ~87% and 97%, respectively. Post-intervention improvements were observed in self-reported symptoms related to insomnia, mood, and pain; actigraphy-derived measures of sleep; and blood-based biomarkers related to peripheral inflammatory balance. The severity of comorbid PTSD was a significant positive predictor of response to treatment. Morning bright light therapy is a feasible and acceptable intervention that shows preliminary efficacy to treat disrupted sleep in Veterans with TBI. A full-scale randomized, placebo-controlled study with longitudinal follow-up is warranted to assess the efficacy of morning bright light therapy to improve sleep, biomarkers, and other TBI related symptoms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures

Fentanyl is one of the most common opioid analgesics administered to patients undergoing surgery or for chronic pain management. While the side effects of chronic fentanyl abuse are recognized (e.g., addiction, tolerance, impairment of cognitive functions, and inhibit nociception, arousal, and respiration), it remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome. Here, we examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 μM) and high (10 μM) dose. Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, were seeded in wells on either a 6-well multi-electrode array (MEA, for electrophysiology) or a 96-well tissue culture plate (for serial endpoint bulk RNA sequencing analysis). Once networks matured (at 28 days in vitro ), co-cultures were treated with 0.01 or 10 μM of fentanyl for 4 days and monitored daily. Only high dose exposure to fentanyl resulted in a decline in features of spiking and bursting activity as early as 30 min post-exposure and sustained for 4 days in cultures. Transcriptomic analysis of the complex cultures after 4 days of fentanyl exposure revealed that both the low and high dose induced gene expression changes involved in synaptic transmission, inflammation, and organization of the extracellular matrix. Collectively, the findings of this in vitro study suggest that while neuroadaptive changes to neural network activity at a systems level was detected only at the high dose of fentanyl, transcriptomic changes were also detected at the low dose conditions, suggesting that fentanyl rapidly elicits changes in plasticity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cognitive analysis of metabolomics data for systems biology

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

In-depth quantitative proteomic characterization of organotypic hippocampal slice culture reveals sex-specific differences in biochemical pathways

Sex differences in the brain of mammals range from neuroarchitecture through cognition to cellular metabolism. The hippocampus, a structure mostly associated with learning and memory, presents high vulnerability to neurodegeneration and aging. Therefore, we explored basal sex-related differences in the proteome of organotypic hippocampal slice culture, a major in vitro model for studying the cellular and molecular mechanisms related to neurodegenerative disorders. Results suggest a greater prevalence of astrocytic metabolism in females and significant neuronal metabolism in males. The preference for glucose use in glycolysis, pentose phosphate pathway and glycogen metabolism in females and high abundance of mitochondrial respiration subunits in males support this idea. An overall upregulation of lipid metabolism was observed in females. Upregulation of proteins responsible for neuronal glutamate and GABA synthesis, along with synaptic associated proteins, were observed in males. In general, the significant spectrum of pathways known to predominate in neurons or astrocytes, together with the well-known neuronal and glial markers observed, revealed sex-specific metabolic differences in the hippocampus. TEM qualitative analysis might indicate a greater presence of mitochondria at CA1 synapses in females. These findings are crucial to a better understanding of how sex chromosomes can influence the physiology of cultured hippocampal slices and allow us to gain insights into distinct responses of males and females on neurological diseases that present a sex-biased incidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗