The impact of implementation of rapid blood culture identification panels on antimicrobial optimization: a retrospective cohort study.

Objective: Determine the impact of limited implementation of a rapid blood culture identification (BCID) panel. Design: Retrospective cohort study. Methods: From February to April 2022, positive blood cultures identified via e-Plex BCID (Roche, Carlsbad, CA) were compared to those identified using standard microbial identification techniques. The primary outcomes assessed were time to optimal therapy, time to de-escalation of anti-MRSA (methicillin-resistant Staphylococcus aureus) agents, and time to de-escalation of anti-pseudomonal agents. Additional analysis investigated the impact of the availability of antimicrobial stewardship program support. This study was conducted at Grady Health System, a large metropolitan safety-net hospital in the southeastern United States. Results: A total of 253 blood cultures were included in this study (153 BCID and 100 standard). Blood culture identification use was associated with a reduction in median time to optimal antimicrobial therapy (43.4 vs 72.1 h, P < .001) and median time to de-escalation of anti-MRSA agents (27.7 vs 46.7 h, P = .006), and a trend towards reduction of median time to de-escalation of anti-pseudomonal agents (38.8 vs 54.8 h, P = .07). These reductions persisted when controlling for patient age, sex, intensive care unit status, Charlson Comorbidity Index, and antimicrobial stewardship program availability. Conclusions: Despite restricted use and lack of 24/7 antimicrobial stewardship program availability, BCID panel utilization was associated with earlier initiation of optimal therapy and pathogen identification with subsequent de-escalation of broad-spectrum antimicrobials, as compared to standard antimicrobial techniques. This suggests the potential for benefit from adopting novel diagnostic technologies outside of idealized fully-resourced settings.

Conceptualizing Educational Comparability in Distributed Health Professions Education: A Scoping Review.

PURPOSE: This study aimed to create greater clarity about the current understanding and formulate a model of how educational comparability has been used in the literature to inform practice. METHOD: The authors conducted a literature search of 9 online databases, seeking articles published on comparability in distributed settings in health professions education before August 2021, with an updated search conducted in May 2023. Using a structured scoping review approach, 2 reviewers independently screened articles for eligibility with inclusion criteria and extracted key data. All authors participated in the descriptive analysis of the extracted data. RESULTS: Twenty-four articles published between 1987 and 2021 met the inclusion criteria. Most articles were focused on medical education programs (n = 21) and located in North America (n = 18). The main rationale for discussing comparability was accreditation. These articles did not offer definitions or discussions about what comparability means. The program logic model was used as an organizing framework to synthesize the literature on practices that schools undertake to facilitate and demonstrate comparability in the design (inputs), implementation (activities), and evaluation (outcomes) of distributed education. Inputs include common learning objectives, identical assessment tools and policies, governance models that enable clear communication, and reporting structure that is supported by technological infrastructure. Activities include faculty planning meetings and faculty development training. Outcomes include student experiences and academic performances. CONCLUSIONS: This study demonstrated that a more complex understanding of the dynamics of educational processes and practices is required to better guide the practice of educational comparability within distributed education programs. In addition to highlighting the need to develop an accepted definition of educational comparability, further elucidation of the underlying dynamics among input, activities, and outcomes would help to better determine what drivers should be prioritized when considering educational change with attention to context within distributed education.

Saponin TQL1055 adjuvant-containing vaccine confers protection upon Mycobacterium tuberculosis challenge in mice.

Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis (Mtb), affects the lungs of infected individuals (pulmonary TB) but can also affect other sites (extrapulmonary TB). The only licensed vaccine Mycobacterium bovis bacillus Calmette-Guerin (BCG) protects infants and young children but exhibits variable efficacy in protecting against adult pulmonary TB. Poor compliance and prolonged treatment regimens associated with the use of chemotherapy has contributed to the development of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb. Thus, there is an urgent need for the design of more effective vaccines against TB. The development of safe and novel adjuvants for human use is critical. In this study, we demonstrate that saponin-based TQL1055 adjuvant when formulated with a TLR4 agonist (PHAD) and Mtb specific immunodominant antigens (ESAT-6 and Ag85B) and delivered intramuscularly in mice, the SA-TB vaccine induced potent lung immune responses. Additionally, the SA-TB vaccine conferred significant protection against Mtb infection, comparable with levels induced by BCG. These findings support the development of a SA-TB vaccine comprising TQL1055, as a novel, safe and effective TB vaccine for potential use in humans.

Correlating the Diffusion of Water to Performance in Model Reverse Osmosis Polyamides with Controlled Crosslink Densities.

We systematically reduce the cross-link density of a PA network based on m-phenylene diamine by substituting a fraction of the trifunctional trimesoyl chloride cross-linking agent with a difunctional isophthaloyl analog that promotes chain extension, in order to elucidate robust design cues for improving the polyamide (PA) separation layer in reverse osmosis (RO) membranes for desalination. Thin films of these model PA networks are fully integrated into a composite membrane and evaluated in terms of their water flux and salt rejection. By incorporating 15 mol % of the difunctional chain extender, we reduce the cross-link density of the network by a factor of two, which leads to an 80 % increase in the free or unreacted amine content. The resulting swelling of the PA network in liquid water increases by a factor of two accompanied by a 30 % increase in the salt passage through the membrane. Surprisingly, this leads to a 30 % decrease in the overall permeance of water through the membrane. This conundrum is resolved by quantifying the microscopic diffusion coefficient of water inside the PA network with quasi-elastic neutron scattering. In the highest and lowest cross-link density networks, water shows strong signatures of confined diffusion. At short length scales, the water exhibits a translational diffusion that is consistent with the jump-diffusion mechanism. This translational diffusion coefficient is approximately five times slower in the lowest cross-linked density network, consistent with the reduced water permeance. This is interpreted as water molecules interacting more strongly with the increased free amine content. Over longer length scales the water diffusion is confined, exhibiting mobility that is independent of length scale. The length scales of confinement from the quasi-elastic neutron scattering experiments at which this transition from confined to translational diffusion occurs is on the order of (5 to 6) Å, consistent with complementary X-ray scattering, small angle neutron scattering, and positron annihilation lifetime spectroscopy measurements. The confinement appears to come from heterogeneities in the average inter-atomic distances, suggesting that diffusion occurs by water bouncing between chains and occasionally sticking to the polar functional groups. The results obtained here are compared with similar studies of water diffusion through both rigid porous silicates and ion exchange membranes, revealing robust design cues for engineering high-performance RO membranes.

CyRSoXS: a GPU-accelerated virtual instrument for polarized resonant soft X-ray scattering.

Polarized resonant soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines the principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and chemical heterogeneity in soft materials such as polymers and biomaterials. Quantitative extraction of orientation information from P-RSoXS pattern data is challenging, however, because the scattering processes originate from sample properties that must be represented as energy-dependent three-dimensional tensors with heterogeneities at nanometre to sub-nanometre length scales. This challenge is overcome here by developing an open-source virtual instrument that uses graphical processing units (GPUs) to simulate P-RSoXS patterns from real-space material representations with nanoscale resolution. This computational framework - called CyRSoXS (https://github.com/usnistgov/cyrsoxs) - is designed to maximize GPU performance, including algorithms that minimize both communication and memory footprints. The accuracy and robustness of the approach are demonstrated by validating against an extensive set of test cases, which include both analytical solutions and numerical comparisons, demonstrating an acceleration of over three orders of magnitude relative to the current state-of-the-art P-RSoXS simulation software. Such fast simulations open up a variety of applications that were previously computationally unfeasible, including pattern fitting, co-simulation with the physical instrument for operando analytics, data exploration and decision support, data creation and integration into machine learning workflows, and utilization in multi-modal data assimilation approaches. Finally, the complexity of the computational framework is abstracted away from the end user by exposing CyRSoXS to Python using Pybind. This eliminates input/output requirements for large-scale parameter exploration and inverse design, and democratizes usage by enabling seamless integration with a Python ecosystem (https://github.com/usnistgov/nrss) that can include parametric morphology generation, simulation result reduction, comparison with experiment and data fitting approaches.

Emerging Trends in Machine Learning: A Polymer Perspective.

In the last five years, there has been tremendous growth in machine learning and artificial intelligence as applied to polymer science. Here, we highlight the unique challenges presented by polymers and how the field is addressing them. We focus on emerging trends with an emphasis on topics that have received less attention in the review literature. Finally, we provide an outlook for the field, outline important growth areas in machine learning and artificial intelligence for polymer science and discuss important advances from the greater material science community.

Divalent cations in human liver pyruvate kinase exemplify the combined effects of complex-equilibrium and allosteric regulation.

There is growing recognition that the functional outcome of binding of an allosteric regulator to a protein/enzyme is influenced by the presence of other ligands. Here, this complexity is exemplified in the allosteric regulation of human liver pyruvate kinase (hLPYK) that is influenced by the presence of a range of divalent cation types and concentrations. For this system, fructose-1,6-bisphosphate (activator) and alanine (inhibitor) both influence the protein's affinity for the substrate, phosphoenolpyruvate (PEP). Mg2+, Mn2+, Ni2+, and Co2+ were the primary divalent cations evaluated, although Zn2+, Cd2+, V2+, Pb2+, Fe2+, and Cu2+also supported activity. Allosteric coupling between Fru-1,6-BP and PEP and between Ala and PEP varied depending on divalent cation type and concentration. Due to complicating interactions among small molecules, we did not attempt the fitting of response trends and instead we discuss a range of potential mechanisms that may explain those observed trends. Specifically, observed "substrate inhibition" may result from substrate A in one active site acting as an allosteric regulator for the affinity for substrate B in a second active site of a multimer. We also discuss apparent changes in allosteric coupling that can result from a sub-saturating concentration of a third allosteric ligand.

Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.

OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep. METHODS: Adolescents aged 15-17 years in Philadelphia completed 7 days of continuous smartphone GPS tracking, which was used to identify daily levels of exposure to geocoded neighborhood factors (eg, crime, green space). Four daily EMA surveys assessed home sleep environment (eg, noise, light), stress, health behaviors, and neighborhood perceptions. Feasibility and acceptability of GPS tracking and EMA were assessed, and distributions of daily environmental exposures were examined. RESULTS: Among 25 teens (mean age 16, 56% male), there was a high level of GPS location data captured (median daily follow-up: 24 hours). Seventy-eight percent of EMA surveys were completed overall. Most participants (96%) reported no privacy concerns related to GPS tracking and minimal burden from EMA surveys. Exposures differed between participants' home neighborhoods and locations visited outside the home neighborhood (eg, higher crime away from home). Sleep environment disruptions were present on 29% of nights (most common: uncomfortable temperature) and were reported by 52% of adolescents. CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.

Qualities of the dying experience of persons who access medical assistance in dying: A scoping review.

Defining a "good death" is complex and grounded in diverse cultural, social, and personal factors. Although there is a significant body of literature exploring the broad concepts of death and dying, there is a dearth in literature that has explored what constitutes a good death for persons undergoing assisted dying such as Medical Assistance in Dying (MAiD). In this scoping review of 19 articles, we explore dying experiences and what a good death entails for people accessing MAiD. Understanding personal values and ideas about positive dying experiences can guide patients, care partners, and clinicians in their preparation toward, and facilitation of, a good death experience particularly among persons who access MAiD.

Odd one out? Functional tuning of Zymomonas mobilis pyruvate kinase is narrower than its allosteric, human counterpart.

Various protein properties are often illuminated using sequence comparisons of protein homologs. For example, in analyses of the pyruvate kinase multiple sequence alignment, the set of positions that changed during speciation ("phylogenetic" positions) were enriched for "rheostat" positions in human liver pyruvate kinase (hLPYK). (Rheostat positions are those which, when substituted with various amino acids, yield a range of functional outcomes). However, the correlation was moderate, which could result from multiple biophysical constraints acting on the same position during evolution and/or various sources of noise. To further examine this correlation, we here tested Zymomonas mobilis PYK (ZmPYK), which has <65% sequence identity to any other PYK sequence. Twenty-six ZmPYK positions were selected based on their phylogenetic scores, substituted with multiple amino acids, and assessed for changes in Kapp-PEP . Although we expected to identify multiple, strong rheostat positions, only one moderate rheostat position was detected. Instead, nearly half of the 271 ZmPYK variants were inactive and most others showed near wild-type function. Indeed, for the active ZmPYK variants, the total range of Kapp,PEP values ("tunability") was 40-fold less than that observed for hLPYK variants. The combined functional studies and sequence comparisons suggest that ZmPYK has evolved functional and/or structural attributes that differ from the rest of the family. We hypothesize that including such "orphan" sequences in MSA analyses obscures the correlations used to predict rheostat positions. Finally, results raise the intriguing biophysical question as to how the same protein fold can support rheostat positions in one homolog but not another.

Role of nanoparticle size and surface chemistry on ion transport and nanostructure of perfluorosulfonic acid ionomer nanocomposites.

Herein, we present a systematic investigation of the impact of silica nanoparticle (SiNP) size and surface chemistry on the nanoparticle dispersion state and the resulting morphology and vanadium ion permeability of the composite ionomer membranes. Specifically, Nafion containing a mass fraction of 5% silica particles, ranging in nominal diameters from 10 nm to >1 µm and with both sulfonic acid- and amine-functionalized surfaces, was fabricated. Most notably, an 80% reduction in vanadium ion permeability was observed for ionomer membranes containing amine-functionalized SiNPs at a nominal diameter of 200 nm. Further, these membranes exhibited an almost 400% increase in proton selectivity when compared to pristine Nafion. Trends in vanadium ion permeability within a particular nominal diameter were seen to be a function of the surface chemistry, where, for example, vanadyl ion permeability was observed to increase with increasing particle size for membranes containing unfunctionalized SiNPs, while it was seen to remain relatively constant for membranes containing amine-functionalized SiNPs. In general, the silica particles tended to exhibit a higher extent of aggregation as the size of the particles was increased. From small-angle neutron scattering experiments, an increase in the spacing of the hydrophobic domains was observed for all composite membranes, though particle size and surface chemistry were seen to have varying impacts on the spacing of the ionic domains of the ionomer.

Examining the Macrosystem Level of Influence on Community Health Worker Effectiveness in the State of Nebraska: A Qualitative Approach.

Community health workers (CHWs) serve as the linkage between community and providers and are stakeholders for bridging services to the public. However, integration of CHWs into health care organizations is often lacking. This study explored macrosystem level barriers faced by CHWs and their ability to do their jobs effectively. Using qualitative interviews from CHWs (n = 28) in Nebraska, we used an abductive approach to derive the following themes: (1) CHWs and client macrosystem barriers, (2) CHW workforce supports, and (3) macrosystem solutions for CHW workforce sustainability. Study results also found various macrosystem barriers affecting CHW workforces including immigration policies, insurance policies, funding sources, supervisor support, and obstacles for health seeking of clients. Moreover, through the lens of CHWs, results revealed the need to provide and advocate for solutions that prioritize the needs of CHWs as they continue to fill a crucial gap in community healthcare systems.

Effect of Carbohydrate Mouth Rinse on Resistance Exercise Performance.

ABSTRACT: Green, MS, Kimmel, CS, Martin, TD, Mouser, JG, and Brune, MP. Effect of carbohydrate mouth rinse on resistance exercise performance. J Strength Cond Res 36(7): 1916-1921, 2022-A carbohydrate mouth rinse (CMR) has been shown to enhance short duration endurance performance and raises the possibility that a similar strategy could improve performance during resistance exercise. Eighteen male and female (N = 36) resistance trained subjects (mean values ± SD; age: 21.5 ± 1.6 years, height: 1.72 ± 0.09 m, body mass: 72.8 ± 13.4 kg, and body fat: 16.7 ± 5.8%) performed 3 experimental visits during which bench press resistance exercise (4 × 10 repetitions at 65% of 1 repetition maximum [1RM] with 120 seconds recovery) and repetitions to failure at 60% 1RM were performed. Subjects rinsed 25 ml of water (WAT), noncaloric placebo (PLA), or 6.4% maltodextrin (CHO) solution for 10 seconds during exercise in a crossover, counter-balanced manner. Rating of perceived exertion (RPE), pleasure-displeasure (FS), number of repetitions to fatigue (REPS), and postexercise blood glucose (GLU) and lactate (LA) were measured. Compared to WAT (17.7 ± 0.8), PLA (19.0 ± 0.7; p = 0.025), and CHO (18.7 ± 0.8; p = 0.039) treatments resulted in higher REPS, with no difference between PLA and CHO treatments (p = 0.310). Rating of perceived exertion progressively increased each set (p < 0.0001), but was not affected by treatment (p = 0.897). Pleasure-displeasure declined during recovery from sets 3 and 4 (p < 0.05) but was also not affected by treatment (p = 0.692). Postexercise GLU (p = 0.103) and LA (p = 0.620) were not different between treatments. Although a placebo effect was present for REPS, this study failed to detect an effect of CMR on REPS, RPE, FS, GLU, or LA on upper-body resistance exercise.

Substitutions at a rheostat position in human aldolase A cause a shift in the conformational population.

Some protein positions play special roles in determining the magnitude of protein function: at such "rheostat" positions, varied amino acid substitutions give rise to a continuum of functional outcomes, from wild type (or enhanced), to intermediate, to loss of function. This observed range raises interesting questions about the biophysical bases by which changes at single positions have such varied outcomes. Here, we assessed variants at position 98 in human aldolase A ("I98X"). Despite being ~17 Å from the active site and far from subunit interfaces, substitutions at position 98 have rheostatic contributions to the apparent cooperativity (nH ) associated with fructose-1,6-bisphosphate substrate binding and moderately affected binding affinity. Next, we crystallized representative I98X variants to assess structural consequences. Residues smaller than the native isoleucine (cysteine and serine) were readily accommodated, and the larger phenylalanine caused only a slight separation of the two parallel helixes. However, the diffraction quality was reduced for I98F, and further reduced for I98Y. Intriguingly, the resolutions of the I98X structures correlated with their nH values. We propose that substitution effects on both nH and crystal lattice disruption arise from changes in the population of aldolase A conformations in solution. In combination with results computed for rheostat positions in other proteins, the results from this study suggest that rheostat positions accommodate a wide range of side chains and that structural consequences manifest as shifted ensemble populations and/or dynamics changes.

Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation.

When amino acids vary during evolution, the outcome can be functionally neutral or biologically-important. We previously found that substituting a subset of nonconserved positions, "rheostat" positions, can have surprising effects on protein function. Since changes at rheostat positions can facilitate functional evolution or cause disease, more examples are needed to understand their unique biophysical characteristics. Here, we explored whether "phylogenetic" patterns of change in multiple sequence alignments (such as positions with subfamily specific conservation) predict the locations of functional rheostat positions. To that end, we experimentally tested eight phylogenetic positions in human liver pyruvate kinase (hLPYK), using 10-15 substitutions per position and biochemical assays that yielded five functional parameters. Five positions were strongly rheostatic and three were non-neutral. To test the corollary that positions with low phylogenetic scores were not rheostat positions, we combined these phylogenetic positions with previously-identified hLPYK rheostat, "toggle" (most substitution abolished function), and "neutral" (all substitutions were like wild-type) positions. Despite representing 428 variants, this set of 33 positions was poorly statistically powered. Thus, we turned to the in vivo phenotypic dataset for E. coli lactose repressor protein (LacI), which comprised 12-13 substitutions at 329 positions and could be used to identify rheostat, toggle, and neutral positions. Combined hLPYK and LacI results show that positions with strong phylogenetic patterns of change are more likely to exhibit rheostat substitution outcomes than neutral or toggle outcomes. Furthermore, phylogenetic patterns were more successful at identifying rheostat positions than were co-evolutionary or eigenvector centrality measures of evolutionary change.

Nurtured in Nature: a Pilot Randomized Controlled Trial to Increase Time in Greenspace among Urban-Dwelling Postpartum Women.

Spending time in nature is associated with numerous mental health benefits, including reduced depression and improved well-being. However, few studies examine the most effective ways to nudge people to spend more time outside. Furthermore, the impact of spending time in nature has not been previously studied as a postpartum depression (PPD) prevention strategy. To fill these gaps, we developed and pilot tested Nurtured in Nature, a 4-week intervention leveraging a behavioral economics framework, and included a Nature Coach, digital nudges, and personalized goal feedback. We conducted a randomized controlled trial among postpartum women (n = 36) in Philadelphia, PA between 9/9/2019 and 3/27/2020. Nature visit frequency and duration was determined using GPS data. PPD was measured using the Edinburgh Postnatal Depression Scale (EPDS). Participants were from low-income, majority Black neighborhoods. Compared to control, the intervention arm had a strong trend toward longer duration and higher frequency of nature visits (IRR 2.6, 95%CI 0.96-2.75, p = 0.059). When analyzing women who completed the intervention (13 of 17 subjects), the intervention was associated with three times higher nature visits compared to control (IRR 3.1, 95%CI 1.16-3.14, p = 0.025). No significant differences were found in the EPDS scores, although we may have been limited by the study's sample size. Nurture in Nature increased the amount of time postpartum women spent in nature, and may be a useful population health tool to leverage the health benefits of nature in majority Black, low-resourced communities.

Radiology Workload Changes During the COVID-19 Pandemic: Implications for Staff Redeployment.

RATIONALE AND OBJECTIVES: Quantify changes in total and by-subspecialty radiology workload due to deferring nonurgent services during the initial COVID-19 pandemic, and describe operational strategies implemented due to shifts in priority. MATERIALS AND METHODS: This retrospective, Institutional Review Board-exempt, study was performed between February 3, 2020 and April 19, 2020 at a large academic medical center. During March 9-15 (intervention period), nonurgent outpatient service deferments began. Five-week periods pre- (baseline) and postintervention (COVID) were defined. Primary outcomes were radiology volume (reports per day) overall and in 11 subspecialty divisions. Linear regression assessed relationship between baseline vs. COVID volumes stratified by division. Secondary outcomes included changes in relative value units (RVUs), inpatient and outpatient volumes. RESULTS: There were 62,791 baseline reports vs. 23,369 during COVID; a 60% overall precipitous volume decrease (p < 0.001). Mean volume decrease pre- and during-COVID was significant (p < 0.001) amongst all individual divisions. Mean volume decrease differed amongst divisions: Interventional Radiology experienced least disruption (29% volume decrease), 7 divisions experienced 40%-60% decreases, and Musculoskeletal, Breast, and Cardiovascular imaging experienced >75% volume decrease. Total RVUs decreased 60% (71,186 baseline; 28,476 COVID). Both outpatient and inpatient report volumes decreased; 72% (41,115 baseline; 11,326 COVID) and 43% (12,626 baseline vs. 6,845 COVID), respectively. In labor pool tracking data, 21.8% (162/744) total radiology employees were reassigned to other hospital duties during the intervention period. CONCLUSION: Precipitous radiology workload reductions impacted subspecialty divisions with marked variation. Data-driven operational decisions during COVID-19 assisted workflow and staffing assignment changes. Ongoing adjustments will be needed as healthcare systems transition operations to a "new normal."

Addressing the challenges of modeling the scattering from bottlebrush polymers in solution.

Small-angle scattering measurements of complex macromolecules in solution are used to establish relationships between chemical structure and conformational properties. Interpretation of the scattering data requires an inverse approach where a model is chosen and the simulated scattering intensity from that model is iterated to match the experimental scattering intensity. This raises challenges in the case where the model is an imperfect approximation of the underlying structure, or where there are significant correlations between model parameters. We examine three bottlebrush polymers (consisting of polynorbornene backbone and polystyrene side chains) in a good solvent using a model commonly applied to this class of polymers: the flexible cylinder model. Applying a series of constrained Monte-Carlo Markov Chain analyses demonstrates the severity of the correlations between key parameters and the presence of multiple close minima in the goodness of fit space. We demonstrate that a shape-agnostic model can fit the scattering with significantly reduced parameter correlations and less potential for complex, multimodal parameter spaces. We provide recommendations to improve the analysis of complex macromolecules in solution, highlighting the value of Bayesian methods. This approach provides richer information for understanding parameter sensitivity compared to methods which produce a single, best fit.

Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression.

Expression of the Human Endogenous Retrovirus Type K (HERV-K), the youngest and most active HERV, has been associated with various cancers and neurodegenerative diseases. As in all retroviruses, a fraction of HERV-K transcripts is exported from the nucleus in unspliced or incompletely spliced forms to serve as templates for translation of viral proteins. In a fraction of HERV-K loci (Type 2 proviruses), nuclear export of the unspliced HERV-K mRNA appears to be mediated by a cis-acting signal on the mRNA, the RcRE, and the protein Rec-these are analogous to the RRE-Rev system in HIV-1. Interestingly, the HIV-1 Rev protein is able to mediate the nuclear export of the HERV-K RcRE, contributing to elevated HERV-K expression in HIV-infected patients. We aimed to understand the structural basis for HIV Rev-HERV-K RcRE recognition. We examined the conformation of the RcRE RNA in solution using small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM). We found that the 433-nt long RcRE can assume folded or extended conformations as observed by AFM. SAXS analysis of a truncated RcRE variant revealed an "A"-shaped topological structure similar to the one previously reported for the HIV-1 RRE. The effect of the overall topology was examined using several deletion variants. SAXS and biochemical analyses demonstrated that the "A" shape is necessary for efficient Rev-RcRE complex formation in vitro and nuclear export activity in cell culture. The findings provide insight into the mechanism of HERV-K expression and a structural explanation for HIV-1 Rev-mediated expression of HERV-K in HIV-infected patients. IMPORTANCE: Expression of the human endogenous retrovirus type K (HERV-K) has been associated with various cancers and autoimmune diseases. Nuclear export of both HIV-1 and HERV-K mRNAs is dependent on the interaction between a small viral protein (Rev in HIV-1 and Rec in HERV-K) and a region on the mRNA (RRE in HIV-1 and RcRE in HERV-K). HIV-1 Rev is able to mediate the nuclear export of RcRE-containing HERV-K mRNAs, which contributes to elevated production of HERV-K proteins in HIV-infected patients. We report the solution conformation of the RcRE RNA-the first three-dimensional topological structure for a HERV molecule-and find that the RcRE resembles the HIV-1 nuclear export signal, RRE. The finding reveals the structural basis for the increased HERV-K expression observed in HIV-infected patients. Elevated HERV expression, mediated by HIV infection or other stressors, can have various HERV-related biological consequences. The findings provide structural insight for regulation of HERV-K expression.