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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

The relation of motion sickness to the spatial-temporal properties of velocity storage

Tilting the head in roll to or from the upright while rotating at a constant velocity (roll while rotating, RWR) alters the position of the semicircular canals relative to the axis of rotation. This produces vertical and horizontal nystagmus, disorientation, vertigo, and nausea. With recurrent exposure, subjects habituate and can make more head movements before experiencing overpowering motion sickness. We questioned whether promethazine lessened the vertigo or delayed the habituation, whether habituation of the vertigo was related to the central vestibular time constant, i.e., to the time constant of velocity storage, and whether the severity of the motion sickness was related to deviation of the axis of eye velocity from gravity. Sixteen subjects received promethazine and placebo in a double-blind, crossover study in two consecutive 4-day test series 1 month apart, termed series I and II. Horizontal and vertical eye movements were recorded with video-oculography while subjects performed roll head movements of approx. 45 degrees over 2 s to and from the upright position while being rotated at 138 degrees /s around a vertical axis. Motion sickness was scaled from 1 (no sickness) to an endpoint of 20, at which time the subject was too sick to continue or was about to vomit. Habituation was determined by the number of head movements that subjects made before reaching the maximum motion sickness score of 20. Head movements increased steadily in each session with repeated testing, and there was no difference between the number of head movements made by the promethazine and placebo groups. Horizontal and vertical angular vestibulo-ocular reflex (aVOR) time constants declined in each test, with the declines being closely correlated to the increase in the number of head movements. The strength of vertiginous sensation was associated with the amount of deviation of the axis of eye velocity from gravity; the larger the deviation of the eye velocity axis from gravity, the more severe the motion sickness. Thus, promethazine neither reduced the nausea associated with RWR, nor retarded or hastened habituation. The inverse relationship between the aVOR time constants and number of head movements to motion sickness, and the association of the severity of motion sickness with the extent, strength, and time of deviation of eye velocity from gravity supports the postulate that the spatiotemporal properties of velocity storage, which are processed between the nodulus and uvula of the vestibulocerebellum and the vestibular nuclei, are likely to represent the source of the conflict responsible for producing motion sickness.

NASA Discipline Neuroscience↗
NASA NTRS2002

Effect of morphine on sympathetic nerve activity in humans

There are conflicting reports for the role of endogenous opioids on sympathetic and cardiovascular responses to exercise in humans. A number of studies have utilized naloxone (an opioid-receptor antagonist) to investigate the effect of opioids during exercise. In the present study, we examined the effect of morphine (an opioid-receptor agonist) on sympathetic and cardiovascular responses at rest and during isometric handgrip (IHG). Eleven subjects performed 2 min of IHG (30% maximum) followed by 2 min of postexercise muscle ischemia (PEMI) before and after systemic infusion of morphine (0.075 mg/kg loading dose + 1 mg/h maintenance) or placebo (saline) in double-blinded experiments on separate days. Morphine increased resting muscle sympathetic nerve activity (MSNA; 17 +/- 2 to 22 +/- 2 bursts/min; P < 0.01) and increased mean arterial pressure (MAP; 87 +/- 2 to 91 +/- 2 mmHg; P < 0.02), but it decreased heart rate (HR; 61 +/- 4 to 59 +/- 3; P < 0.01). However, IHG elicited similar increases for MSNA, MAP, and HR between the control and morphine trial (drug x exercise interaction = not significant). Moreover, responses to PEMI were not different. Placebo had no effect on resting, IHG, and PEMI responses. We conclude that morphine modulates cardiovascular and sympathetic responses at rest but not during isometric exercise.

Non-NASA Center↗
NASA NTRS2002

Selective norepinephrine reuptake inhibition as a human model of orthostatic intolerance

BACKGROUND: Observations in patients with functional mutations of the norepinephrine transporter (NET) gene suggest that impaired norepinephrine uptake may contribute to idiopathic orthostatic intolerance. METHODS AND RESULTS: We studied the effect of the selective NET blocker reboxetine and placebo in a randomized, double-blind, crossover fashion on cardiovascular responses to cold pressor testing, handgrip testing, and a graded head-up tilt test (HUT) in 18 healthy subjects. In a subset, we determined isoproterenol and phenylephrine sensitivities. Subjects ingested 8 mg reboxetine or placebo 12 hours and 1 hour before testing. In the supine position, heart rate was 65+/-2 bpm with placebo and 71+/-3 bpm with reboxetine. At 75 degrees HUT, heart rate was 84+/-3 and 119+/-4 bpm with placebo and with reboxetine (P<0.0001). Mean arterial pressure was 85+/-2 with placebo and 91+/-2 mm Hg with reboxetine while supine (P<0.01) and 88+/-2 mm Hg and 90+/-3 mm Hg at 75 degrees HUT. Blood pressure responses to cold pressor and handgrip testing were attenuated with reboxetine. Reboxetine increased the sensitivity to the chronotropic effect of isoproterenol and the pressor effect of phenylephrine. Vasovagal reactions occurred in 9 subjects on placebo and in 1 subject on reboxetine. CONCLUSIONS: Selective NET blockade creates a phenotype that resembles idiopathic orthostatic intolerance. This observation supports the hypothesis that disordered norepinephrine uptake mechanisms can contribute to human cardiovascular disease. Our study also suggests that NET inhibition might be useful in preventing vasovagal reactions.

Non-NASA Center↗
NASA NTRS2000

Pyruvate ingestion for 7 days does not improve aerobic performance in well-trained individuals

The purposes of the present studies were to test the hypotheses that lower dosages of oral pyruvate ingestion would increase blood pyruvate concentration and that the ingestion of a commonly recommended dosage of pyruvate (7 g) for 7 days would enhance performance during intense aerobic exercise in well-trained individuals. Nine recreationally active subjects (8 women, 1 man) consumed 7, 15, and 25 g of pyruvate and were monitored for a 4-h period to determine whether blood metabolites were altered. Pyruvate consumption failed to significantly elevate blood pyruvate, and it had no effect on indexes of carbohydrate (blood glucose, lactate) or lipid metabolism (blood glycerol, plasma free fatty acids). As a follow-up, we administered 7 g/day of either placebo or pyruvate, for a 1-wk period to seven, well-trained male cyclists (maximal oxygen consumption, 62.3 +/- 3.0 ml. kg(-1). min(-1)) in a randomized, double-blind, crossover trial. Subjects cycled at 74-80% of their maximal oxygen consumption until exhaustion. There was no difference in performance times between the two trials (placebo, 91 +/- 9 min; pyruvate, 88 +/- 8 min). Measured blood parameters (insulin, peptide C, glucose, lactate, glycerol, free fatty acids) were also unaffected. Our results indicate that oral pyruvate supplementation does not increase blood pyruvate content and does not enhance performance during intense exercise in well-trained cyclists.

Randomized Controlled Trial↗
NASA NTRS1999

Acute effect of ephedrine on 24-h energy balance

Ephedrine is used to help achieve weight control. Data on its true efficacy and mechanisms in altering energy balance in human subjects are limited. We aimed to determine the acute effect of ephedrine on 24-h energy expenditure, mechanical work and urinary catecholamines in a double-blind, randomized, placebo-controlled, two-period crossover study. Ten healthy volunteers were given ephedrine (50 mg) or placebo thrice daily during each of two 24-h periods (ephedrine and placebo) in a whole-room indirect calorimeter, which accurately measures minute-by-minute energy expenditure and mechanical work. Measurements were taken of 24-h energy expenditure, mechanical work, urinary catecholamines and binding of (+/-)ephedrine in vitro to human beta1-, beta2- and beta3-adrenoreceptors. Twenty-four-hour energy expenditure was 3.6% greater (8965+/-1301 versus 8648+/-1347 kJ, P<0.05) with ephedrine than with placebo, but mechanical work was not different between the ephedrine and placebo periods. Noradrenaline excretion was lower with ephedrine (0.032+/-0.011 microg/mg creatinine) compared with placebo (0.044+/-0.012 microg/mg creatinine) (P<0.05). (+/-)Ephedrine is a relatively weak partial agonist of human beta1- and beta2-adrenoreceptors, and had no detectable activity at human beta3-adrenoreceptors. Ephedrine (50 mg thrice daily) modestly increases energy expenditure in normal human subjects. A lack of binding of ephedrine to beta3-adrenoreceptors and the observed decrease in urinary noradrenaline during ephedrine treatment suggest that the thermogenic effect of ephedrine results from direct beta1-/beta2-adrenoreceptor agonism. An indirect beta3-adrenergic effect through the release of noradrenaline seems unlikely as urinary noradrenaline decreased significantly with ephedrine.

Non-NASA Center↗
NASA NTRS1998

Three-dimensional echocardiographic planimetry of maximal regurgitant orifice area in myxomatous mitral regurgitation: intraoperative comparison with proximal flow convergence

OBJECTIVES: We sought to validate direct planimetry of mitral regurgitant orifice area from three-dimensional echocardiographic reconstructions. BACKGROUND: Regurgitant orifice area (ROA) is an important measure of the severity of mitral regurgitation (MR) that up to now has been calculated from hemodynamic data rather than measured directly. We hypothesized that improved spatial resolution of the mitral valve (MV) with three-dimensional (3D) echo might allow accurate planimetry of ROA. METHODS: We reconstructed the MV using 3D echo with 3 degrees rotational acquisitions (TomTec) using a transesophageal (TEE) multiplane probe in 15 patients undergoing MV repair (age 59 +/- 11 years). One observer reconstructed the prolapsing mitral leaflet in a left atrial plane parallel to the ROA and planimetered the two-dimensional (2D) projection of the maximal ROA. A second observer, blinded to the results of the first, calculated maximal ROA using the proximal convergence method defined as maximal flow rate (2pi(r2)va, where r is the radius of a color alias contour with velocity va) divided by regurgitant peak velocity (obtained by continuous wave [CW] Doppler) and corrected as necessary for proximal flow constraint. RESULTS: Maximal ROA was 0.79 +/- 0.39 (mean +/- SD) cm2 by 3D and 0.86 +/- 0.42 cm2 by proximal convergence (p = NS). Maximal ROA by 3D echo (y) was highly correlated with the corresponding flow measurement (x) (y = 0.87x + 0.03, r = 0.95, p < 0.001) with close agreement seen (AROA (y - x) = 0.07 +/- 0.12 cm2). CONCLUSIONS: 3D echo imaging of the MV allows direct visualization and planimetry of the ROA in patients with severe MR with good agreement to flow-based proximal convergence measurements.

NASA Discipline Cardiopulmonary↗
NASA NTRS1996

Pre-exercise glycerol hydration improves cycling endurance time

The effects of glycerol ingestion (GEH) on hydration and subsequent cycle ergometer submaximal load exercise were examined in well conditioned subjects. We hypothesized that GEH would reduce physiologic strain and increase endurance. The purpose of Study I (n = 11) was to determine if pre-exercise GEH (1.2 gm/kg glycerol in 26 ml/kg solution) compared to pre-exercise placebo hydration (PH) (26 ml/kg of aspartame flavored water) lowered heart rate (HR), lowered rectal temperature (Tc), and prolonged endurance time (ET) during submaximal load cycle ergometry. The purpose of Study II (n = 7) was to determine if the same pre-exercise regimen followed by carbohydrate oral replacement solution (ORS) during exercise also lowered HR, Tc, and prolonged ET. Both studies were double-blind, randomized, crossover trials, performed at an ambient temperature of 23.5-24.5 degrees C, and humidity of 25-27%. Mean HR was lower by 2.8 +/- 0.4 beats/min (p = 0.05) after GEH in Study I and by 4.4 +/- 1.1 beats/min (p = 0.01) in Study II. Endurance time was prolonged after GEH in Study I (93.8 +/- 14 min vs. 77.4 +/- 9 min, p = 0.049) and in Study II (123.4 +/- 17 min vs. 99.0 +/- 11 min, p = 0.03). Rectal temperature did not differ between hydration regimens in both Study I and Study II. Thus, pre-exercise glycerol-enhanced hyperhydration lowers HR and prolongs ET even when combined with ORS during exercise. The regimens tested in this study could potentially be adapted for endurance activities.

Non-NASA Center↗
NASA NTRS1995

A two-year program of aerobics and weight training enhances bone mineral density of young women

Previous research suggests that physical activity may have a beneficial effect on bone mineral density (BMD) in women. This relationship was explored in a 2-year, randomized, intervention trial investigating the efficacy of exercise and calcium supplementation on increasing peak bone mass in young women. One hundred and twenty-seven subjects (ages of 20-35 years) were randomly assigned either to an exercise program that contained both aerobics and weight training components or to a stretching program. Calcium supplementation (up to 1500 mg/day including dietary intake) or placebo was given in a double-blinded design to all subjects. Spinal trabecular BMD was determined using quantitative computed tomography (QCT). Spinal integral, femoral neck, and trochanteric BMD were measured by dual X-ray absorptiometry (DXA) and calcaneal BMD by single photon absorptiometry (SPA). Fitness variables included maximal aerobic capacity (VO2max), and isokinetic muscle performance of the trunk and thigh. Measurements were made at baseline, 1 year, and 2 years. Sixty-three subjects (32 exercise, 31 stretching) completed the study, and all the measured bone parameters indicated a positive influence of the exercise intervention. There were significant positive differences in BMD between the exercise and stretching groups for spinal trabecular (2.5%), femoral neck (2.4%), femoral trochanteric (2.3%), and calcaneal (6.4%) measurements. The exercise group demonstrated a significant gain in BMD for spinal integral (1.3 +/- 2.8%, p < 0.02), femoral trochanteric (2.6 +/- 6.1%, p < 0.05), and calcaneal (5.6 +/- 5.1, p < 0.01) measurements. In contrast to exercise, the calcium intervention had no positive effect on any of the bone parameters. In regard to fitness parameters, the exercise group completed the study with significant gains in VO2max and isokinetic (peak torque) values for the knee flexion and extension and trunk extension. This study indicates that over a 2-year period, a combined regimen of aerobics and weight training has beneficial effects on BMD and fitness parameters in young women. However, the addition of daily calcium supplementation does not add significant benefit to the intervention.

Randomized Controlled Trial↗
NASA NTRS1994

Effect of inducing nocturnal serum melatonin concentrations in daytime on sleep, mood, body temperature, and performance

We examined effects of very low doses of melatonin (0.1-10 mg, orally) or placebo, administered at 1145 h, on sleep latency and duration, mood, performance, oral temperature, and changes in serum melatonin levels in 20 healthy male volunteers. A repeated-measure double-blind Latin square design was used. Subjects completed a battery of tests designed to assess mood and performance between 0930 and 1730 h. The sedative-like effects of melatonin were assessed by a simple sleep test: at 1330 h subjects were asked to hold a positive pressure switch in each hand and to relax with eyes closed while reclining in a quiet darkened room. Latency and duration of switch release, indicators of sleep, were measured. Areas under the time-melatonin concentration curve varied in proportion to the different melatonin doses ingested, and the 0.1- and 0.3-mg doses generated peak serum melatonin levels that were within the normal range of nocturnal melatonin levels in untreated people. All melatonin doses tested significantly increased sleep duration, as well as self-reported sleepiness and fatigue, relative to placebo. Moreover, all of the doses significantly decreased sleep-onset latency, oral temperature, and the number of correct responses on the Wilkinson auditory vigilance task. These data indicate that orally administered melatonin can be a highly potent hypnotic agent; they also suggest that the physiological increase in serum melatonin levels, which occurs around 2100 h daily, may constitute a signal initiating normal sleep onset.

Non-NASA Center↗
NASA NTRS1994

(abstract) Transmission Electron Microscopy of Al(sub x)Ga(sub 1-x)N/SiC Multilayer Structures

The potential of wide-band-gap III-V nitrides as solar-blind ultraviolet sensors and light emitters has prompted an increasing amount of work recently, including the fabrication of the first UV sensors from as-deposited single crystal GaN. We have used high resolution transmission electron microscopy (TEM) to study the microstructure of two novel developments of wide-band-gap III-V nitrides: the growth of ultra-short period GaN/AlN super lattices (digital alloys); and the incorporation of SiC layers into Al(sub x)Ga(sub 1-x)N structures. By varying the relative periods in a GaN/AlN superlattice, it should be possible to tailor the band gap of the composite to lie between the elemental values of 365 nm for GaN and 200 nm for AlN. The group IV semiconductor, SiC, has a close lattice match (< 3%) to Al(sub x)Ga(sub 1-x)N for growth on the basal plane. Demonstration of epitaxial growth for Al(sub x)Ga(sub 1-x)N/SiC multilayers could enable an extension of direct band-gap material towards the visible.

microscopy GaN AlN semiconductor SiC↗
NASA NTRSDate not supplied

Intelligent Change Detection System: Autonomous Intelligent Machine Agent Model Development

NASA’s significant role in facilitating the harmonious integration of unmanned aircraft systems (UAS), with other aerial vehicles operating in the National Airspace System (NAS), has revealed a need for more advanced technological tools than are being utilized currently. This technology would lend itself to significantly assisting Direct-Action Aviation Personnel (DAAP) with the ingress and egress of UAS operations within the NAS. Providing research findings that would reduce technical barriers, associated with UAS-NAS integration, has been a persistent effort by both NASA and the FAA. One such research effort, pursued by NASA’s Transformative Tools and Technologies – Revolutionary Aviation Mobility (T3-RAM) project, is the development of an autonomous intelligent machine (AIM) agent that would aid DAAP functioning as implemented in remote ground control stations (RGCS). This evolution of the “human-machine” symbiosis, within the aviation environment, is necessary for many reasons. For example, there are projections of large increases to the 864,000 registered UAS and 45,000 aviation operations taking place in the NAS each day. With a data output range from 1 to 20 terabytes per flight or each aerial vehicle, which is projected to have proportional rate increase to that of registered UASs. It is evident, that due to the projected increase of UASs and their generated data, the human-agent’s data managing capabilities will be quickly overwhelmed by the enormous amounts of data emanating in the NAS. The research efforts presented in this paper puts forward results from the development, assessment, and verification of a previously conceptualized AIM-Agent that combats actionable-data (information) errors resulting from the visual perception phenomenon known as “change blindness” (CB). CB has been identified as one of the main culprits of information erroring encountered within the ground control station operator (GCSO) community.

Change Blindness↗
DOE OSTI2023

Evaluation of Plasma Phosphorylated Tau217 for Differentiation Between Alzheimer Disease and Frontotemporal Lobar Degeneration Subtypes Among Patients With Corticobasal Syndrome

Plasma phosphorylated tau217 (p-tau217), a biomarker of Alzheimer disease (AD), is of special interest in corticobasal syndrome (CBS) because autopsy studies have revealed AD is the driving neuropathology in up to 40% of cases. This differentiates CBS from other 4-repeat tauopathy (4RT)–associated syndromes, such as progressive supranuclear palsy Richardson syndrome (PSP-RS) and nonfluent primary progressive aphasia (nfvPPA), where underlying frontotemporal lobar degeneration (FTLD) is typically the primary neuropathology. To validate plasma p-tau217 against positron emission tomography (PET) in 4RT-associated syndromes, especially CBS. This multicohort study with 6, 12, and 24-month follow-up recruited adult participants between January 2011 and September 2020 from 8 tertiary care centers in the 4RT Neuroimaging Initiative (4RTNI). All participants with CBS (n = 113), PSP-RS (n = 121), and nfvPPA (n = 39) were included; other diagnoses were excluded due to rarity (n = 29). Individuals with PET-confirmed AD (n = 54) and PET-negative cognitively normal control individuals (n = 59) were evaluated at University of California San Francisco. Operators were blinded to the cohort. Plasma p-tau217, measured by Meso Scale Discovery electrochemiluminescence, was validated against amyloid-β (Aβ) and flortaucipir (FTP) PET. Imaging analyses used voxel-based morphometry and bayesian linear mixed-effects modeling. Clinical biomarker associations were evaluated using longitudinal mixed-effect modeling. Of 386 participants, 199 (52%) were female, and the mean (SD) age was 68 (8) years. Plasma p-tau217 was elevated in patients with CBS with positive Aβ PET results (mean [SD], 0.57 [0.43] pg/mL) or FTP PET (mean [SD], 0.75 [0.30] pg/mL) to concentrations comparable to control individuals with AD (mean [SD], 0.72 [0.37]), whereas PSP-RS and nfvPPA showed no increase relative to control. Within CBS, p-tau217 had excellent diagnostic performance with area under the receiver operating characteristic curve (AUC) for Aβ PET of 0.87 (95% CI, 0.76-0.98; P < .001) and FTP PET of 0.93 (95% CI, 0.83-1.00; P < .001). At baseline, individuals with CBS-AD (n = 12), defined by a PET-validated plasma p-tau217 cutoff 0.25 pg/mL or greater, had increased temporoparietal atrophy at baseline compared to individuals with CBS-FTLD (n = 39), whereas longitudinally, individuals with CBS-FTLD had faster brainstem atrophy rates. Individuals with CBS-FTLD also progressed more rapidly on a modified version of the PSP Rating Scale than those with CBS-AD (mean [SD], 3.5 [0.5] vs 0.8 [0.8] points/year; P = .005). In this cohort study, plasma p-tau217 had excellent diagnostic performance for identifying Aβ or FTP PET positivity within CBS with likely underlying AD pathology. Plasma P-tau217 may be a useful and inexpensive biomarker to select patients for CBS clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Time‐Lapse Image Classification Using a Diffractive Neural Network

Diffractive deep neural networks (D 2 NNs), comprised of spatially engineered passive surfaces, collectively process optical input information at the speed of light propagation through a thin diffractive volume, without any external computing power. Diffractive networks were demonstrated to achieve all‐optical object classification and perform universal linear transformations. Herein, a “time‐lapse” image classification scheme using a diffractive network is demonstrated for the first time, significantly advancing its classification accuracy and generalization performance on complex input objects by using the lateral movements of the input objects and/or the diffractive network, relative to each other. In a different context, such relative movements of the objects and/or the camera are routinely being used for image super‐resolution applications; inspired by their success, a time‐lapse diffractive network is designed to benefit from the complementary information content created by controlled or random lateral shifts. The design space and performance limits of time‐lapse diffractive networks are numerically explored, revealing a blind testing accuracy of 62.03% on the optical classification of objects from the CIFAR‐10 dataset. This constitutes the highest inference accuracy achieved so far using a single diffractive network on the CIFAR‐10 dataset. Time‐lapse diffractive networks will be broadly useful for the spatiotemporal analysis of input signals using all‐optical processors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Gender gap in perspectives of the impacts of degradation and restoration on ecosystem services in Ethiopia

Abstract The importance of land restoration has garnered increasing attention on the global stage through large‐scale initiatives such as the Bonn Challenge. However, policies and strategies are often gender‐blind and designed in compliance with entrenched social hierarchies, exacerbating pre‐existing social inequalities that affect restoration initiatives. The challenge of developing gender‐responsive policies and initiatives is accentuated by a persistent lack of sex‐disaggregated data concerning men's and women's differing perceptions and experiences. This study aims to help fill this gap by capturing the differences in men and women's perceptions of ecosystem services before and after restoration interventions in Ethiopia. Towards that end, in October 2021, we collected data from fifty‐nine (59) paired husband‐wife households and six gender‐segregated focus group discussions in two regions of Ethiopia: Amhara and Southern Nations, and Nationalities and Peoples (SNNP). Kendall's concordance analysis established a strong degree of disagreement between men's and women's ratings of restoration outcomes for most indicators. Men attributed degradation to landscape conditions and natural forces, while women considered the lack of appropriate restoration strategies as a precursor for accelerated degradation. The study also reveals that men tended to benefit more than women from enhanced ecosystem services post‐restoration, with increased labour and land management burdens often falling on the shoulders of women. Based on these findings, we argue that including men's and women's perspectives from the earliest planning phases of restoration initiatives is essential to ensure greater equity in benefit‐sharing, mitigate trade‐offs for women, and build more nuanced, just and successful approaches to restoration.

Mponela, Powell↗
DOE OSTI2025

Detection of non‐native species formed during fibrillization of the myocilin olfactomedin domain

Abstract Glaucoma is a group of neurodegenerative diseases that together are the leading cause of irreversible blindness worldwide. Myocilin‐associated glaucoma is an inherited form of this disease, caused by intracellular aggregation of misfolded mutant myocilin. In vitro, the myocilin C‐terminal olfactomedin domain (OLF), the relevant domain for glaucoma pathogenesis, can be driven to form amyloid‐like fibrils under mild conditions. Here we characterize a species present during in vitro fibrillization. Purified OLF was subjected to fibrillization at concentrations required for downstream electron microscopy imaging and NMR spectroscopy. Additional biophysical techniques, including analytical ultracentrifugation and X‐ray crystallography, were employed to further characterize the multicomponent mixture. Negative stain transmission electron microscopy (TEM) shows a non‐native species reminiscent of known prefibrillar oligomers from other amyloid systems, NMR indicates a minor population of partially misfolded species is present in solution, and cryo‐EM imaging shows two‐dimensional protein arrays. The predominant soluble species remaining in solution after the fibril reaction is natively folded, as evidenced by X‐ray crystallography. In summary, after incubating OLF under fibrillization‐promoting conditions, there is a heterogeneous mixture consisting of soluble folded protein, mature amyloid‐like fibrils, and partially misfolded intermediate species that at present belie additional molecular detail. The characterization of OLF fibrillar species illustrates the challenges associated with developing a comprehensive understanding of the fibrillization process for large, non‐model amyloidogenic proteins.

Scelsi, Hailee F. [School of Chemistry and Biochem↗
DOE OSTI2022

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Protein model quality assessment using rotation–equivariant transformations on point clouds

Machine learning research concerning protein structure has seen a surge in popularity over the last years with promising advances for basic science and drug discovery. Working with macromolecular structure in a machine learning context requires an adequate numerical representation, and researchers have extensively studied representations such as graphs, discretized 3D grids, and distance maps. As part of CASP14, we explored a new and conceptually simple representation in a blind experiment: atoms as points in 3D, each with associated features. These features—initially just the basic element type of each atom—are updated through a series of neural network layers featuring rotation-equivariant convolutions. Starting from all atoms, we further aggregate information at the level of alpha carbons before making a prediction at the level of the entire protein structure. We find that this approach yields competitive results in protein model quality assessment despite its simplicity and despite the fact that it incorporates minimal prior information and is trained on relatively little data. As a result, its performance and generality are particularly noteworthy in an era where highly complex, customized machine learning methods such as AlphaFold 2 have come to dominate protein structure prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

Abstract Estimating the accuracy of quaternary structural models of protein complexes and assemblies (EMA) is important for predicting quaternary structures and applying them to studying protein function and interaction. The pairwise similarity between structural models is proven useful for estimating the quality of protein tertiary structural models, but it has been rarely applied to predicting the quality of quaternary structural models. Moreover, the pairwise similarity approach often fails when many structural models are of low quality and similar to each other. To address the gap, we developed a hybrid method (MULTICOM_qa) combining a pairwise similarity score (PSS) and an interface contact probability score (ICPS) based on the deep learning inter‐chain contact prediction for estimating protein complex model accuracy. It blindly participated in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 and performed very well in estimating the global structure accuracy of assembly models. The average per‐target correlation coefficient between the model quality scores predicted by MULTICOM_qa and the true quality scores of the models of CASP15 assembly targets is 0.66. The average per‐target ranking loss in using the predicted quality scores to rank the models is 0.14. It was able to select good models for most targets. Moreover, several key factors (i.e., target difficulty, model sampling difficulty, skewness of model quality, and similarity between good/bad models) for EMA are identified and analyzed. The results demonstrate that combining the multi‐model method (PSS) with the complementary single‐model method (ICPS) is a promising approach to EMA.

59 BASIC BIOLOGICAL SCIENCES↗