Generative artificial intelligence performs rudimentary structural biology modeling.

Natural language-based generative artificial intelligence (AI) has become increasingly prevalent in scientific research. Intriguingly, capabilities of generative pre-trained transformer (GPT) language models beyond the scope of natural language tasks have recently been identified. Here we explored how GPT-4 might be able to perform rudimentary structural biology modeling. We prompted GPT-4 to model 3D structures for the 20 standard amino acids and an α-helical polypeptide chain, with the latter incorporating Wolfram mathematical computation. We also used GPT-4 to perform structural interaction analysis between nirmatrelvir and its target, the SARS-CoV-2 main protease. Geometric parameters of the generated structures typically approximated close to experimental references. However, modeling was sporadically error-prone and molecular complexity was not well tolerated. Interaction analysis further revealed the ability of GPT-4 to identify specific amino acid residues involved in ligand binding along with corresponding bond distances. Despite current limitations, we show the capacity of natural language generative AI to perform basic structural biology modeling and interaction analysis with atomic-scale accuracy.

Medical Education in Armenia: An Overview.

This article serves to describe the medical education system of Armenia, a country located in the cross-section of Europe and Asia. Similar to other countries in the region, its medical education system is structured into undergraduate (6 years), postgraduate (1-4 years), and continuing education components. Its largest medical university, Yerevan State Medical University (YSMU), is the predominant institute for medical education and has enrollment of not only Armenian citizens, but also international students from India, Iran, Russia, and other countries. According to publication metrics, research activity at YSMU is increasing. Finally, the unique relationship between the country and its global diaspora has facilitated collaborative efforts in not only medical education, but also the delivery of care and capacity building. Significant challenges remain for each stage of medical education, such as the lack of standardized licensing or board examinations and oversight of the number of resident physicians per specialty.

Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion.

Given the COVID-19 pandemic, there is interest in understanding ligand-receptor features and targeted antibody-binding attributes against emerging SARS-CoV-2 variants. Here, we developed a large-scale structure-based pipeline for analysis of protein-protein interactions regulating SARS-CoV-2 immune evasion. First, we generated computed structural models of the Spike protein of 3 SARS-CoV-2 variants (B.1.1.529, BA.2.12.1, and BA.5) bound either to a native receptor (ACE2) or to a large panel of targeted ligands (n = 282), which included neutralizing or therapeutic monoclonal antibodies. Moreover, by using the Barnes classification, we noted an overall loss of interfacial interactions (with gain of new interactions in certain cases) at the receptor-binding domain (RBD) mediated by substituted residues for neutralizing complexes in classes 1 and 2, whereas less destabilization was observed for classes 3 and 4. Finally, an experimental validation of predicted weakened therapeutic antibody binding was performed in a cell-based assay. Compared with the original Omicron variant (B.1.1.529), derivative variants featured progressive destabilization of antibody-RBD interfaces mediated by a larger set of substituted residues, thereby providing a molecular basis for immune evasion. This approach and findings provide a framework for rapidly and efficiently generating structural models for SARS-CoV-2 variants bound to ligands of mechanistic and therapeutic value.

A modeling-based approach to optimize COVID-19 vaccine dosing schedules for improved protection.

While the development of different vaccines slowed the dissemination of SARS-CoV-2, the occurrence of breakthrough infections has continued to fuel the COVID-19 pandemic. To secure at least partial protection in the majority of the population through 1 dose of a COVID-19 vaccine, delayed administration of boosters has been implemented in many countries. However, waning immunity and emergence of new variants of SARS-CoV-2 suggest that such measures may induce breakthrough infections due to intermittent lapses in protection. Optimizing vaccine dosing schedules to ensure prolonged continuity in protection could thus help control the pandemic. We developed a mechanistic model of immune response to vaccines as an in silico tool for dosing schedule optimization. The model was calibrated with clinical data sets of acquired immunity to COVID-19 mRNA vaccines in healthy and immunocompromised participants and showed robust validation by accurately predicting neutralizing antibody kinetics in response to multiple doses of COVID-19 mRNA vaccines. Importantly, by estimating population vulnerability to breakthrough infections, we predicted tailored vaccination dosing schedules to minimize breakthrough infections, especially for immunocompromised individuals. We identified that the optimal vaccination schedules vary from CDC-recommended dosing, suggesting that the model is a valuable tool to optimize vaccine efficacy outcomes during future outbreaks.

A modeling-based approach to optimize COVID-19 vaccine dosing schedules for improved protection.

While the development of different vaccines has slowed the dissemination of SARS-CoV-2, the occurrence of breakthrough infections continues to fuel the pandemic. As a strategy to secure at least partial protection, with a single dose of a given COVID-19 vaccine to maximum possible fraction of the population, delayed administration of subsequent doses (or boosters) has been implemented in many countries. However, waning immunity and emergence of new variants of SARS-CoV-2 suggest that such measures may jeopardize the attainment of herd immunity due to intermittent lapses in protection. Optimizing vaccine dosing schedules could thus make the difference between periodic occurrence of breakthrough infections or effective control of the pandemic. To this end, we have developed a mechanistic mathematical model of adaptive immune response to vaccines and demonstrated its applicability to COVID-19 mRNA vaccines as a proof-of-concept for future outbreaks. The model was thoroughly calibrated against multiple clinical datasets involving immune response to SARS-CoV-2 infection and mRNA vaccines in healthy and immunocompromised subjects (cancer patients undergoing therapy); the model showed robust clinical validation by accurately predicting neutralizing antibody kinetics, a correlate of vaccine-induced protection, in response to multiple doses of mRNA vaccines. Importantly, we estimated population vulnerability to breakthrough infections and predicted tailored vaccination dosing schedules to maximize protection and thus minimize breakthrough infections, based on the immune status of a sub-population. We have identified a critical waiting window for cancer patients (or, immunocompromised subjects) to allow recovery of the immune system (particularly CD4+ T-cells) for effective differentiation of B-cells to produce neutralizing antibodies and thus achieve optimal vaccine efficacy against variants of concern, especially between the first and second doses. Also, we have obtained optimized dosing schedules for subsequent doses in healthy and immunocompromised subjects, which vary from the CDC-recommended schedules, to minimize breakthrough infections. The developed modeling tool is based on generalized adaptive immune response to antigens and can thus be leveraged to guide vaccine dosing schedules during future outbreaks.

Gross Total Resection of a Ruptured Micro-arteriovenous Malformation within the Cerebellar Peduncle: A Case Report and Qualitative Review of the Literature.

Deep-seated micro-arteriovenous malformations (micro-AVMs) may pose a challenge for complete yet safe resection. We propose the strategic placement of two to three microaneurysm clips throughout the hemorrhage cavity to successfully localize the micro-AVM nidus via digital subtraction angiography (DSA). We successfully demonstrate this novel method in a 15-year-old adolescent boy with cerebellar intraparenchymal hemorrhage who underwent hematoma evacuation and expansile duraplasty. He was found to have a 1-cm nidus of a micro-AVM with early venous drainage located in the right middle cerebellar peduncle. Five days later, we proceeded to resect the micro-AVM; however, a clear nidus or bleeding source was unable to be localized intraoperatively despite the use of stereotactic neuronavigation. In turn, we placed two mini-aneurysm clips superiorly and inferiorly within the hematoma cavity, which led to successful localization via DSA and complete resection. No surgical complications occurred. The patient completely recovered from right-sided weakness and dysarthria 6 to 12 months postoperatively. Our technique allows for the rapid localization and complete resection of micro-AVM nidi when stereotactic neuronavigation is inadequate.

Self-efficacy and knowledge in pediatrics among family medicine physicians in Armenia: A survey study.

Background: Armenia has trained physicians to practice family medicine (FM) for over 20 years. The pediatric population comprises a significant proportion of patients seen by FM practices, yet to date, there have been no studies assessing the knowledge and self-efficacy of FM physicians regarding pediatric care. As the first step is needs assessment to improve the quality of care, this study aims to assess the self-efficacy and knowledge of FM physicians regarding the care of pediatric patients. Materials and Methods: We distributed a survey to attendees at an FM conference in Lori Province, Armenia. The survey instrument assessed demographics and experience, self-efficacy in providing pediatric care, and pediatric knowledge via questions adapted from the American Board of Family Medicine (ABFM). Results: Eighty-seven percent of participants were female. Roughly half (45%) had trained through an FM residency program, while the remainder had retrained to become FM physicians following a residency in another field. Almost all (97%) practiced outside of the capital city, Yerevan. About half believed that their didactic (51%) and clinical education (48%) prepared them either "extremely" or "very" well. Overall, there was no clear relationship between participants' reported self-efficacy in a given area of pediatrics and their score in that area on the knowledge portion of the survey. Conclusions: Our findings reveal opportunities for improvement in knowledge related to pediatric care in FM physicians in Armenia, as well as a lack of relationship between reported self-efficacy and knowledge. Thus, future programs should not rely solely on self-reported gaps to identify or prioritize areas of focus. Further study is recommended in other specialties in Armenia and internationally to improve future programs.

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662-C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662-C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662-C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

Corpus Callosotomy in the Modern Era: Origins, Efficacy, Technical Variations, Complications, and Indications.

Corpus callosotomy is among the oldest surgeries performed for drug-resistant epilepsy. Since it was first performed in 1940, numerous studies have assessed its outcomes in various patient populations in addition to describing different extents of sectioning and emerging technologies (i.e., endoscopic, laser interstitial thermal therapy, and radiosurgery). To capture the current state and offer a reappraisal, we comprehensively review the origins of corpus callosotomy, efficacy for various seizure types, technical variations, complications, and indications and compare the procedure with vagus nerve stimulation therapy, which has similar indications. We consider corpus callosotomy to be a safe and efficacious procedure, which should be considered by clinicians when appropriate. Furthermore, it can play an important role in treating patients with drug-resistant epilepsy when appropriate in low-to-middle-income countries where resources are limited.

Underutilization of advanced presurgical studies and high rates of vagus nerve stimulation for drug-resistant epilepsy: a single-center experience and recommendations.

INTRODUCTION: Epilepsy surgery continues to be profoundly underutilized despite its safety and effectiveness. We sought to investigate factors that may contribute to this phenomenon, with a particular focus on the antecedent underutilization of appropriate preoperative studies. METHODS: We reviewed patient data from a pediatric epilepsy clinic over an 18-month period. Patients with drug-resistant epilepsy (DRE) were categorized according to brain magnetic resonance imaging (MRI) findings (lesional, MRI-negative, or multifocal abnormalities) and type of epilepsy diagnosis based on semiology and electroencephalography (EEG) (focal or generalized). We then analyzed the rates of diagnostic test utilization, surgical referral, and subsequent epilepsy surgery as well as vagus nerve stimulation (VNS). RESULTS: Of the 249 patients with a diagnosis of epilepsy, 138 (55.4%) were found to have DRE. Excluding the 10 patients with DRE who did not undergo MRI, 76 patients (59.4%) were found to be MRI-negative (non-lesional epilepsy), 37 patients (28.9%) were found to have multifocal abnormalities, and 15 patients (11.7%) were found to have a single epileptogenic lesion on MRI (lesional epilepsy). Positron emission tomography (PET) and single-photon emission computed tomography (SPECT) were each completed in nine patients (7.0%) and magnetoencephalography (MEG) in four patients (3.1%). Despite the low utilization rate of adjunctive studies, over half (56.3%) ultimately underwent VNS alone, and 8.6% ultimately underwent definitive intracranial resection or disconnection surgery. CONCLUSIONS: The underutilization of appropriate non-invasive, presurgical testing in patients with focal DRE may in part explain the continued underutilization of definitive, resective/disconnective surgery. For patients without access to a high-volume, multidisciplinary surgical epilepsy center, adjunctive presurgical studies [e.g., PET, SPECT, MEG, electrical source imaging (ESI), EEG-functional magnetic resonance imaging (fMRI)], even when available, are rarely ordered, and this may contribute to excessive rates of VNS in lieu of definitive intracranial surgery.

Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces.

There is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape ( e.g ., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies ( e.g ., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.

Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools.

Targeted bacteriophage (phage) particles are potentially attractive yet inexpensive platforms for immunization. Herein, we describe targeted phage capsid display of an immunogenically relevant epitope of the SARS-CoV-2 Spike protein that is empirically conserved, likely due to the high mutational cost among all variants identified to date. This observation may herald an approach to developing vaccine candidates for broad-spectrum, towards universal, protection against multiple emergent variants of coronavirus that cause COVID-19.

Completion Posterior Quadrant Disconnection After Failed Temporal Lobectomy: 2-Dimensional Operative Video.

Epilepsy is a chronic seizure disorder that affects about 1% of the global population.1 When seizure freedom cannot be obtained solely through antiseizure medicines (ASMs), the condition is termed medically refractory epilepsy (MRE).2,3 Though posterior quadrant disconnection (PQD) is underutilized in our experience, it is a highly effective surgical procedure for MRE restricted to the temporal, parietal, and/or occipital lobes.4-12 In this operative video, we demonstrate a right-sided completion PQD following failed temporal lobectomy in an 8-yr-old female with focal MRE. We review technical nuances, including (1) extension/revision of prior scalp incision, (2) placement of subdural strip for the identification of phase reversal and central sulcus, (3) disconnection of parietal and occipital lobes, (4) extension of the corticectomy to the pia overlying the falcotentorial junction and into the prior temporal lobectomy defect, and (5) posterior disconnection of the corpus callosum. Postoperatively, the patient experienced subtle left-arm weakness and central fever, both of which resolved. An external ventricular drain (EVD) was placed in the ventricle/operative cavity and left for 3 to 4 d until the draining cerebrospinal fluid (CSF) cleared. As of 3-mo follow-up, she has been seizure-free without complications. In summary, PQD is a safe and effective treatment option for MRE that can be utilized not only as an initial operation but also after failed surgery. Appropriate patient consent was obtained to perform this procedure and present this clinical case and surgical video for academic purposes. Image at 4:00 licensed under CC BY-2.5, 2006, modified from http://upload.wikimedia.org/wikipedia/commons/7/70/Lateral_head_skull.jpg (flipped and rotated). Image at 4:42, Public Domain: Gray H. Anatomy of the Human Body. 1918. Bartleby.com, https://commons.wikimedia.org/wiki/File:Lobes_of_the_brain_NL.svg; flipped, modified. Image at 6:42, Public Domain: House EL, Pansky B. A Functional Approach to Neuroanatomy. 1960. McGraw-Hill Book Company; https://upload.wikimedia.wikipedia.commons/5/52/Lawrence_1960_2.3.png; modified.

Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.

Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the development and initial evaluation of two targeted phage-based vaccination approaches against SARS-CoV-2: dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. For peptide-targeted phage, we performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein. One of these epitopes displayed on the major capsid protein pVIII of phage induced a specific and sustained humoral response when injected in mice. These phage were further engineered to simultaneously display the peptide CAKSMGDIVC on the minor capsid protein pIII to enable their transport from the lung epithelium into the systemic circulation. Aerosolization of these "dual-display" phage into the lungs of mice generated a systemic and specific antibody response. In the second approach, targeted AAVP particles were engineered to deliver the entire S protein gene under the control of a constitutive CMV promoter. This induced tissue-specific transgene expression, stimulating a systemic S protein-specific antibody response in mice. With these proof-of-concept preclinical experiments, we show that both targeted phage- and AAVP-based particles serve as robust yet versatile platforms that can promptly yield COVID-19 vaccine prototypes for translational development.