Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR.

The highly conserved 5' untranslated region (5'UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5'UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed. According to this model the conformation of the 5'UTR determines the fate of the genome. In this work, the dynamics of this proposed conformational switch and the factors that regulate it were probed using multiple single-molecule and in-gel ensemble FRET assays. Our results show that the HIV-1 5'UTR intrinsically samples conformations that are stabilized by both viral and host factor binding. Annealing of tRNALys3, the primer for initiation of reverse transcription, can promote the kissing dimer but not the extended dimer. In contrast, HIV-1 nucleocapsid (NC) promotes formation of the extended dimer in both the absence and presence of tRNALys3 Our data are consistent with an ordered series of events that involves primer annealing, genome dimerization, and virion assembly.

Relating the metatranscriptome and metagenome of the human gut.

Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. Within-subject microbial species, gene, and transcript abundances were highly concordant across sampling methods, with only a small fraction of transcripts (<5%) displaying between-method variation. Next, we investigated relationships between the oral and gut microbial communities, identifying a subset of abundant oral microbes that routinely survive transit to the gut, but with minimal transcriptional activity there. Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substantial fraction (41%) of microbial transcripts were not differentially regulated relative to their genomic abundances. Of the remainder, consistently underexpressed pathways included sporulation and amino acid biosynthesis, whereas up-regulated pathways included ribosome biogenesis and methanogenesis. Across subjects, metatranscriptional profiles were significantly more individualized than DNA-level functional profiles, but less variable than microbial composition, indicative of subject-specific whole-community regulation. The results thus detail relationships between community genomic potential and gene expression in the gut, and establish the feasibility of metatranscriptomic investigations in subject-collected and shipped samples.

Surfing the COVID-19 Tsunami with Teleophthalmology: the Advent of New Models of Eye Care.

Purpose of Review: In this article, we reviewed the impact resulting from the COVID-19 pandemic on the traditional model of care in ophthalmology. Recent Findings: Though virtual eye care has been present for more than 20 years, the COVID-19 pandemic has established a precedent to seriously consider its role in the evolving paradigm of vision and eye care. New hybrid models of care have enhanced or replaced traditional synchronous and asynchronous visits. The increased use of smart phoneography and mobile applications enhanced the remote examination of patients. Use of e-learning became a mainstream tool to continue accessing education and training. Summary: Teleophthalmology has demonstrated its value for screening, examining, diagnosing, monitoring treatment, and increasing access to education. However, much of the progress made following the COVID-19 pandemic is at risk of being lost as society pushes to reestablish normalcy. Further studies during the new norm are required to prove a more permanent role for virtual eye care.

Association Between Preresidency Peer-reviewed Publications and Future Academic Productivity or Career Choice Among Ophthalmology Residency Applicants.

Importance: Ophthalmology-residency selection committees require robust metrics to review applicants. Participation in research activities is a core component of the application process for its perceived association with future academic productivity. Objective: To evaluate the correlation between the number of preresidency peer-reviewed publications (PPPs) and subsequent peer-reviewed publications or career choices of ophthalmology residency graduates. Design, Setting, and Participants: In this cross-sectional study, names of ophthalmology residency graduates were obtained. PubMed-indexed publication records were generated and publications were categorized as preresidency, intraresidency, and postresidency. First author and journal publications with an impact factor (IF) score of 3 or more were recorded. Current academic and community-based career statuses were designated. Names were obtained from cohort and alumni lists on residency program websites or by emailing program directors. Participants included US Accreditation Council for Graduate Medical Education-accredited ophthalmology residency graduates from 2013 to 2016. Main Outcomes and Measures: The primary outcome measure was association of PPPs with later publications, first authorship, and journal publications with an IF score of 3 or more. The secondary outcome measure was difference in characteristics associated with academic vs community-based ophthalmologist. Results: A total of 964 ophthalmologists (52% of graduates) were studied and most (85.5%) had PubMed-indexed publications. First authorship (ρ = 0.71; 95% CI, 0.67-0.74; P < .001) had a strong positive correlation with intraresidency publications, while journal publications with an IF score of 3 or more (ρ = 0.56; 95% CI, 0.51-0.60; P < .001) and PPPs (ρ = 0.38; 95% CI, 0.32-0.43; P < .001) had moderate and weak positive correlations, respectively. For postresidency publications, journal publications with an IF score of 3 or more (ρ = 0.86; 95% CI, 0.84-0.87; P < .001) had the strongest positive correlation followed by first authorship (ρ = 0.77; 95% CI, 0.74-0.79; P < .001) and PPPs (ρ = 0.26; 95% CI, 0.20-0.31; P < .001). Preresidency (t = 3.3; P = .001), intraresidency (t = 4.1; P < .001), postresidency (t = 7.5; P < .001), first author (t = 6.6; P < .001), and journal publications with an IF score of 3 or more (t = 5.9; P < .001) were greater for academic ophthalmologists compared with community-based ophthalmologists. Conclusions and Relevance: Preresidency publication history is at least weakly correlated with future publications or work in an academic setting among ophthalmologists. Multiple factors associated with academic productivity were evaluated; however, adjustment for multiple analyses was not done and further testing is required to prove whether these factors are predictive.

Chiari I malformation management in patients with heritable connective tissue disorders.

Background: Chiari malformation type I (CMI) is relatively common neurosurgical condition typically treated with posterior fossa decompression. However, the management of CMI in patients with heritable connective tissue disorders (CTDs), such as Ehlers-Danlos Syndrome, Marfan Syndrome, or Osteogenesis Imperfecta, involves a unique set of perioperative challenges. Objective: This study aims to define the demographic information, comorbidities, and perioperative course of patients with concomitant CMI and CTD. Methods: Patients with CMI admitted for surgical decompression from 2008 to 2015 were captured using the National Inpatient Sample (NIS). Information was collected based on ICD-9 codes. Descriptive and regression analyses were performed in SPSS (version 26). Results: 38,169 CMI patients, 353 of whom had CTD (0.92%), were identified. CMI patients with CTD were more likely to be female (p < 0.001) and present during teenage (p = 0.033) or young adult years (p < 0.001). They had more chronic issues (p < 0.001): systemic comorbidities include postural orthostatic tachycardia syndrome, cardiac dysrhythmias, and gastroparesis (all p < 0.001). CNS comorbidities include migraine, tethered spinal cord, and epilepsy (all p < 0.001). They have increased joint instability (both p < 0.001), as well as craniocervical instability (CCI). More posterior cervical fusion surgeries and application of cervical halo devices were seen during the same inpatient stay (both p < 0.001). Conclusions: Patients with concurrent CTD and CMI were more likely to present with complex Chiari and associated CCI. They were also younger, more often female, and had more systemic, CNS, and joint abnormalities. As such, preoperative recognition of an underlying CTD is imperative to achieve optimal outcomes in this patient population.

The Effect of Market Competition on the Price of Topical Eye Drops.

PURPOSE: To describe the relationship between the number of Federal Drug Administration (FDA)-approved manufacturers and the price change of generic and branded topical eye drops. METHODS: Retrospective analysis of topical eye drop medications with formulations listed in the FDA Orange Book and the National Average Drug Acquisition Cost database from 2013 to 2017. RESULTS: The most frequently prescribed generic topical drugs were glaucoma medications (34%), antimicrobials (32%), anti-inflammatories (24%), mydriatics (5%), and anesthetics (5%). The most frequently prescribed branded topical drugs were anti-inflammatories (45%), glaucoma medications (32%), antimicrobials (21%) and dry eye medications (3%). From 2013 to 2017, generic eye drops had a median price decrease of 20% (IQR 32%) while branded eye drops had a median price increase of 44% (IQR 28%) (P < .001). A significant inverse association was identified between the price change of generic eye drops and the total number of all manufacturers (r = -.41, P = .010), generic drug manufacturers (r = -.32, P = .0496), and alternative branded drug manufacturers (r = -.57, P = .002). There was no significant association between the price change of branded eye drops and number of manufacturers. Glaucoma (r = -.58, P = .039) and anti-inflammatory (r = -.69, P = .047) eye drops also had significant inverse associations with the number of generic manufacturers. CONCLUSION: From 2013 to 2017, the price of generic eye drops decreased whereas the price of branded eye drops increased. Market competition was significantly inversely associated with price changes of generic eye drops but not branded eye drops.

Evaluating the Efficacy of Two Regional Pain Management Modalities in Autologous Breast Reconstruction.

At our institution, multimodal opiate-sparing pain management is the cornerstone of our enhanced recovery program for autologous breast reconstruction. The purpose of this study was to compare postoperative outcomes and pain control metrics following implementation of an enhanced recovery program with two different regional analgesia approaches. METHODS: This retrospective cohort study identified 145 women who underwent autologous breast reconstruction from 2015 to 2017. Three groups were included: historical control patients (n = 46) and enhanced recovery patients that received multimodal pain management including a postoperative transversalis abdominis plane block with either a continuous local anesthetic catheter (n = 60) or a single-shot of liposomal bupivacaine (n = 39). The primary outcome was pain scores in the first three postoperative days. Secondary outcomes were opioid consumption in oral morphine equivalents and length of stay. RESULTS: Postoperative pain scores were similar across all three groups until postoperative day 3. Length of stay was significantly shorter in both of the enhanced recovery cohorts (3.0 [3.0, 4.0]) compared with control patients (4.0 [4.0, 5.0], P < 0.001). Likewise, average total oral morphine equivalents consumption was significantly reduced in enhanced recovery patients (continuous catheter 215.9 (95% CI, 165.4-266.3); liposomal bupivacaine 211.0 (95% CI, 154.8-267.2); control 518.4 (95% CI 454.2-582.7), P < 0.001). Neither length of stay (P = 0.953), nor oral morphine equivalents consumption (P = 0.883) differed by type of regional analgesia. CONCLUSION: Compared with control patients, both approaches to regional transversalis abdominis plane block analgesia as part of an opiate-sparing enhanced recovery pain management strategy were successful, but neither superior to the other.

Survey of provider perceptions of enhanced recovery after surgery and perioperative surgical home protocols at a tertiary care hospital.

ABSTRACT: Enhanced recovery after surgery (ERAS) and perioperative surgical home (PSH) initiatives are widely utilized to improve quality of patient care. Despite their established benefits, implementation still has significant barriers. We developed a survey for perioperative clinicians to gather information on perception and knowledge of ERAS/PSH programs to guide future expansion of these programs at our institution. The survey included questions about familiarity with ERAS/PSH and perceived value, perceived barriers to protocol implementation, preferred learning methods and prioritization of various ERAS/PSH protocol elements into care delivery and provider education. Faculty surgeons and anesthesiologists, in addition to advanced practice nurses and postgraduate physician trainees in the Departments of Surgery and Anesthesiology were asked to complete the survey. Overall survey participation was 25% (223/888). About half of survey respondents had provided care to a patient on an ERAS/PSH protocol, and a majority felt at least somewhat knowledgeable about ERAS/PSH protocols. Perception of the value of ERAS/PSH was positive. Participants were enthusiastic about on-going learning, with multimodal pain management being the topic of most interest and learning by direct participation in care of protocol patients being the favored educational approach. A significant majority of participants felt that upcoming health providers should receive formal ERAS/PSH education as part of their training. Based on our survey results, we plan to explore teaching methods that successfully engage learners of all levels of clinical expertise and also overcome the major barriers to gaining knowledge about ERAS/PSH identified by study participants, most notably lack of time for busy clinicians.

Effect of Cognitive Prehabilitation on the Incidence of Postoperative Delirium Among Older Adults Undergoing Major Noncardiac Surgery: The Neurobics Randomized Clinical Trial.

Importance: Postoperative delirium in older adults is a common and costly complication after surgery. Cognitive reserve affects the risk of postoperative delirium, and thus preoperative augmentation of reserve as a preventive technique is of vital interest. Objective: To determine whether cognitive prehabilitation reduces the incidence of postoperative delirium among older adults. Design, Setting, and Participants: This was a prospective, single-blinded randomized clinical trial conducted from March 2015 to August 2019 at the Ohio State University Wexner Medical Center in Columbus. Patients 60 years and older undergoing major, noncardiac, nonneurological surgery under general anesthesia, with an expected hospital stay of at least 72 hours, were eligible for trial inclusion. Patients were excluded for preoperative cognitive dysfunction and active depression. Interventions: Participation in electronic, tablet-based preoperative cognitive exercise targeting memory, speed, attention, flexibility, and problem-solving functions. Main Outcomes and Measures: The primary outcome was incidence of delirium between postoperative day 0 to day 7 or discharge, as measured by a brief Confusion Assessment Method, Memorial Delirium Assessment Scale, or a structured medical record review. Secondary outcomes compared delirium characteristics between patients in the intervention and control groups. Results: Of the 699 patients approached for trial participation, 322 completed consent and 268 were randomized. Subsequently, 17 patients were excluded, leaving 251 patients in the primary outcome analysis. A total of 125 patients in the intervention group and 126 control patients were included in the final analysis (median [interquartile range] age, 67 [63-71] years; 163 women [64.9%]). Ninety-seven percent of the patients in the intervention group completed some brain exercise (median, 4.6 [interquartile range, 1.31-7.4] hours). The delirium rate among control participants was 23.0% (29 of 126). With intention-to-treat analysis, the delirium rate in the intervention group was 14.4% (18 of 125; P = .08). Post hoc analysis removed 4 patients who did not attempt any cognitive exercise from the intervention group, yielding a delirium rate of 13.2% (16 of 121; P = .04). Secondary analyses among patients with delirium showed no differences in postoperative delirium onset day or duration or total delirium-positive days across study groups. Conclusions and Relevance: The intervention lowered delirium risk in patients who were at least minimally compliant. The ideal activities, timing, and effective dosage for cognitive exercise-based interventions to decrease postoperative delirium risk and burden need further study. Trial Registration: ClinicalTrials.gov Identifier: NCT02230605.

Incidence of Refeeding Syndrome in Children With Failure to Thrive.

OBJECTIVES: To determine the incidence of refeeding syndrome in otherwise healthy children <3 years of age admitted for failure to thrive (FTT). METHODS: A multicenter retrospective cohort study was performed on patients aged ≤36 months admitted with a primary diagnosis of FTT from January 1, 2011, to December 31, 2016. The primary outcome measure was the percentage of patients with laboratory evidence of refeeding syndrome. Exclusion criteria included admission to an ICU, parenteral nutrition, history of prematurity, gastrostomy tube feeds, and any complex chronic conditions. RESULTS: Of the 179 patients meeting inclusion criteria, none had laboratory evidence of refeeding syndrome. Of these, 145 (81%) had laboratory work done at the time of admission, and 69 (39%) had laboratory work repeated after admission. A small percentage (6%) of included patients experienced an adverse event due to repeat laboratory draw. CONCLUSIONS: In otherwise healthy hospitalized patients <3 years of age with a primary diagnosis of FTT, routine laboratory monitoring for electrolyte derangements did not reveal any cases of refeeding syndrome. More robust studies are needed to determine the safety and feasibility of applying low-risk guidelines to this patient population to reduce practice variability and eliminate unnecessary laboratory evaluation and monitoring.

Functional Equivalence of Retroviral MA Domains in Facilitating Psi RNA Binding Specificity by Gag.

Retroviruses specifically package full-length, dimeric genomic RNA (gRNA) even in the presence of a vast excess of cellular RNA. The "psi" (Ψ) element within the 5'-untranslated region (5'UTR) of gRNA is critical for packaging through interaction with the nucleocapsid (NC) domain of Gag. However, in vitro Gag binding affinity for Ψ versus non-Ψ RNAs is not significantly different. Previous salt-titration binding assays revealed that human immunodeficiency virus type 1 (HIV-1) Gag bound to Ψ RNA with high specificity and relatively few charge interactions, whereas binding to non-Ψ RNA was less specific and involved more electrostatic interactions. The NC domain was critical for specific Ψ binding, but surprisingly, a Gag mutant lacking the matrix (MA) domain was less effective at discriminating Ψ from non-Ψ RNA. We now find that Rous sarcoma virus (RSV) Gag also effectively discriminates RSV Ψ from non-Ψ RNA in a MA-dependent manner. Interestingly, Gag chimeras, wherein the HIV-1 and RSV MA domains were swapped, maintained high binding specificity to cognate Ψ RNAs. Using Ψ RNA mutant constructs, determinants responsible for promoting high Gag binding specificity were identified in both systems. Taken together, these studies reveal the functional equivalence of HIV-1 and RSV MA domains in facilitating Ψ RNA selectivity by Gag, as well as Ψ elements that promote this selectivity.

Laser Ablation of Newly Diagnosed Malignant Gliomas: a Meta-Analysis.

BACKGROUND: Magnetic resonance-guided laser-interstitial thermotherapy (MR-LITT) is a minimally invasive technique that shows promise in neuro-oncology because of its superiority in delivering precise minimally invasive thermal energy with minimal collateral damage. OBJECTIVE: In this analysis, we investigate initial data on the use of MR-LITT in the treatment of newly diagnosed high-grade gliomas. METHODS: With the use of the PubMed, OVID, and Google-scholar database systems, a comprehensive search of the English literature was performed. Eighty-five articles were identified plus 1 that is pending publication. Four articles were accounted for in this review, including 25 patients with newly diagnosed high-grade gliomas who underwent MR-LITT treatment. We evaluated safety, progression-free survival, and overall survival. RESULTS: Twenty-five patients with a mean age of 53.8 years underwent LITT treatments. On average, 82.9% of the pretreatment lesion volume was ablated. The average tumor volume treated was 16.5 cm. The mean follow-up time was 7.6 months. Median overall survival was found to be 14.2 months (range 0.1-23 months). The median progression-free survival was 5.1 months (range 2.4-23 months); however, these data are limited by the relatively short follow-up of the patients reviewed and small sample size of only 25 patients. There was 1 (3.4%) major perioperative complication, which was a central nervous system infection. CONCLUSION: MR-LITT is a promising technology for the treatment of small, yet difficult-to-treat newly diagnosed high-grade gliomas. This study demonstrates that MR-LITT is safe, and future randomized studies are needed to evaluate its role as a treatment adjunct for newly diagnosed high-grade gliomas. ABBREVIATIONS: BBB, blood-brain barrierHGG, high-grade gliomaLITT, laser-interstitial thermal therapyWHO, World Health Organization.

An application of evolutionary game theory to social dilemmas: the traveler's dilemma and the minimum effort coordination game.

The Traveler's Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler's Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.

A case of central serous chorioretinopathy associated with use of deer antler spray supplement.

This case report describes central serous chorioretinopathy (CSC) in a healthy man associated with the use of deer antler spray, an athletic supplement purported to contain insulin-like growth factor-1 (IGF-1). The CSC resolved after cessation of the supplement. Currently, there are no reports in the literature linking IGF-1 and CSC. We conclude that agents containing IGF-1, such as deer antler supplements, may be correlated with the development of CSC.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

BACKGROUND: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status. RESULTS: Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. CONCLUSIONS: This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.