Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests.

Genomic epidemiology offers important insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 antigen tests to identify a wide range of respiratory viruses and generate full genome sequences, offering a streamlined mechanism for broad respiratory virus genomic surveillance.

A GUCY2D variant associated cone-rod dystrophy with electronegative ERG: A case report and review.

Purpose: Cone-rod dystrophies (CORD) are inherited retinal dystrophies characterized by primary cone degeneration with secondary rod involvement. We report two patients from the same family with a dominant variant in the guanylate cyclase 2D (GUCY2D) gene with different phenotypes in the electroretinogram (ERG). Observations: A 21-year-old lady (Patient 1) was referred due to experiencing blurry vision and color vision impairment. Visual field testing revealed a central scotoma. Spectral-domain optical coherence tomography (SD-OCT) and fundus autofluorescence (FAF) documented macula dysfunction. Reduced amplitude was observed in the photopic responses of ERG. Her 54-year-old father (Patient 2) had similar issues with blurry vision. A dilated fundus examination displayed bilateral macular atrophy. Loss of the ellipsoid zone line and collapse of the outer nuclear segment were noted on the SD-OCT. Photopic ERG responses were extinguished, and an electronegative ERG was observed in the dark-adapted 3.0 ERG. The gene report revealed a c.2512C > T (p.Arg838Cys) variant in GUCY2D for both patients. They were respectively diagnosed as cone dystrophy (COD) and cone-rod dystrophy (CORD). Conclusions: We report two different clinical phenotypes in GUCY2D-associated COD despite sharing the same variant. A dysfunction in the synaptic junction between the photoreceptor and the secondary neuron was proposed to explain the electronegative ERG. This explanation might extend to other gene-related cases of CORD with electronegative ERG.

Cross-Sectional Analysis of Outer Retinal Tubulation in Inherited Retinal Diseases: A Multicenter Study.

PURPOSE: This study aims to explore genetic variants that potentially lead to outer retinal tubulation (ORT), estimate the prevalence of ORT in these candidate genes, and investigate the clinical etiology of ORT in patients with inherited retinal diseases (IRDs), with respect to each gene. DESIGN: Retrospective cohort study. METHODS: A retrospective cross-sectional review was conducted on 565 patients with molecular diagnoses of IRD, confirming the presence of ORT as noted in each patient's respective spectral-domain optical coherence tomography (SD-OCT) imaging. Using SD-OCT imaging, the presence of ORT was analyzed in relation to specific genetic variants and phenotypic characteristics. Outcomes included the observed ORT frequencies across 2 gene-specific cohorts: non-retinal pigment epithelium (RPE)-specific genes, and RPE-specific genes; and to investigate the analogous characteristics caused by variants in these genes. RESULTS: Among the 565 patients included in this study, 104 exhibited ORT on SD-OCT. We observed ORT frequencies among the following genes from our patient cohort: 100% (23/23) for CHM, 100% (2/2) for PNPLA6, 100% (4/4) for RCBTB1, 100% for mtDNA [100% (4/4) for MT-TL1 and 100% (1/1) for mtDNA deletion], 100% (1/1) for OAT, 95.2% (20/21) for CYP4V2, 72.7% (8/11) for CHM female carriers, 66.7% (2/3) for C1QTNF5, 57.1% (8/14) for PROM1, 53.8% (7/13) for PRPH2, 42.9% (3/7) for CERKL, 28.6% (2/7) for CDHR1, 20% (1/5) for RPE65, 4% (18/445) for ABCA4. In contrast, ORT was not observed in any patients with photoreceptor-specific gene variants, such as RHO (n = 13), USH2A (n = 118), EYS (n = 70), PDE6B (n = 10), PDE6A (n = 4), and others. CONCLUSIONS: These results illustrate a compelling association between the presence of ORT and IRDs caused by variants in RPE-specific genes, as well as non-RPE-specific genes. In contrast, IRDs caused by photoreceptor-specific genes are typically not associated with ORT occurrence. Further analysis revealed that ORT tends to manifest in IRDs with milder intraretinal pigment migration (IPM), a finding that is typically associated with RPE-specific genes. These findings regarding ORT, genetic factors, atrophic patterns in the fundus, and IPM provide valuable insight into the complex etiology of IRDs. Future prospective studies are needed to further explore the association and underlying mechanisms of ORT in these contexts.

Protocol for the creation and characterization of SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing.

The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Alpha variant in 2020 demonstrated the need for reanalysis of diagnostic tests to ensure detection of emerging variants. Here, we present a protocol for creating and characterizing SARS-CoV-2 variant testing panels using remnant clinical samples for diagnostic assay testing. We describe steps for characterizing SARS-CoV-2 remnant clinical samples and preparing them into pools and their use in preparing varying quantities of virus. We then detail procedures for verifying variant detection using the resulting sample panel. For complete details on the use and execution of this protocol, please refer to Rao et al.1,2.

Physiological regulation of neuronal Wnt activity is essential for TDP-43 localization and function.

Nuclear exclusion of the RNA- and DNA-binding protein TDP-43 can induce neurodegeneration in different diseases. Diverse processes have been implicated to influence TDP-43 mislocalization, including disrupted nucleocytoplasmic transport (NCT); however, the physiological pathways that normally ensure TDP-43 nuclear localization are unclear. The six-transmembrane enzyme glycerophosphodiester phosphodiesterase 2 (GDE2 or GDPD5) cleaves the glycosylphosphatidylinositol (GPI) anchor that tethers some proteins to the membrane. Here we show that GDE2 maintains TDP-43 nuclear localization by regulating the dynamics of canonical Wnt signaling. Ablation of GDE2 causes aberrantly sustained Wnt activation in adult neurons, which is sufficient to cause NCT deficits, nuclear pore abnormalities, and TDP-43 nuclear exclusion. Disruption of GDE2 coincides with TDP-43 abnormalities in postmortem tissue from patients with amyotrophic lateral sclerosis (ALS). Further, GDE2 deficits are evident in human neural cell models of ALS, which display erroneous Wnt activation that, when inhibited, increases mRNA levels of genes regulated by TDP-43. Our study identifies GDE2 as a critical physiological regulator of Wnt signaling in adult neurons and highlights Wnt pathway activation as an unappreciated mechanism contributing to nucleocytoplasmic transport and TDP-43 abnormalities in disease.

Genetic underpinnings explored: OPA1 deletion and complex phenotypes on chromosome 3q29.

BACKGROUND: Copy number variations (CNVs) have emerged as significant contributors to the elusive genetic causality of inherited eye diseases. In this study, we describe a case with optic atrophy and a brain aneurysm, in which a de novo CNV 3q29 deletion was identified. CASE PRESENTATION: A 40-year-old female patient was referred to our department after undergoing aneurysm transcatheter arterial embolization for a brain aneurysm. She had no history of systemic diseases, except for unsatisfactory best-corrected visual acuity (BCVA) since elementary school. Electrophysiological tests confirmed the findings in retinal images, indicating optic nerve atrophy. Chromosomal microarray analysis revealed a de novo deletion spanning 960 kb on chromosome 3q29, encompassing OPA1 and six neighboring genes. Unlike previously reported deletions in this region associated with optic atrophy, neuropsychiatric disorders, and obesity, this patient displayed a unique combination of optic atrophy and a brain aneurysm. However, there is no causal relationship between the brain aneurysm and the CNV. CONCLUSION: In conclusion, the optic atrophy is conclusively attributed to the OPA1 deletion, and the aneurysm could be a coincidental association. The report emphasizes the likelihood of underestimating OPA1 deletions due to sequencing technology limitations. Recognizing these constraints, healthcare professionals must acknowledge these limitations and consistently search for OPA1 variants/deletions in Autosomal Dominant Optic Atrophy (ADOA) patients with negative sequencing results. This strategic approach ensures a more comprehensive exploration of copy-number variations, ultimately enhancing diagnostic precision in the field of genetic disorders.

The accuracy of artificial intelligence deformed nodal structures in cervical online cone-beam-based adaptive radiotherapy.

Background and Purpose: Online cone-beam-based adaptive radiotherapy (ART) adjusts for anatomical changes during external beam radiotherapy. However, limited cone-beam image quality complicates nodal contouring. Despite this challenge, artificial-intelligence guided deformation (AID) can auto-generate nodal contours. Our study investigated the optimal use of such contours in cervical online cone-beam-based ART. Materials and Methods: From 136 adaptive fractions across 21 cervical cancer patients with nodal disease, we extracted 649 clinically-delivered and AID clinical target volume (CTV) lymph node boost structures. We assessed geometric alignment between AID and clinical CTVs via dice similarity coefficient, and 95% Hausdorff distance, and geometric coverage of clinical CTVs by AID planning target volumes by false positive dice. Coverage of clinical CTVs by AID contour-based plans was evaluated using D100, D95, V100%, and V95%. Results: Between AID and clinical CTVs, the median dice similarity coefficient was 0.66 and the median 95 % Hausdorff distance was 4.0 mm. The median false positive dice of clinical CTV coverage by AID planning target volumes was 0. The median D100 was 1.00, the median D95 was 1.01, the median V100% was 1.00, and the median V95% was 1.00. Increased nodal volume, fraction number, and daily adaptation were associated with reduced clinical CTV coverage by AID-based plans. Conclusion: In one of the first reports on pelvic nodal ART, AID-based plans could adequately cover nodal targets. However, physician review is required due to performance variation. Greater attention is needed for larger, daily-adapted nodes further into treatment.

Multisite Mpox Infection and Viral Dynamics Among Persons With HIV in Metro Atlanta.

The 2022 mpox outbreak primarily involved sexual transmission among men who have sex with men and disproportionately affected persons with human immunodeficiency virus (HIV). We examined viral dynamics and clinical features in a cohort evaluated for mpox infection at a comprehensive HIV clinic in Atlanta, Georgia. Viral DNA was found in 8 oropharyngeal and 5 anorectal specimens among 10 mpox cases confirmed by lesion swab polymerase chain reaction. Within-participant anatomic site of lowest cycle threshold (Ct) value varied, and lower Ct values were found in oropharyngeal and anorectal swabs when corresponding symptoms were present. This provides insight into mpox infection across multiple anatomic sites among people with HIV.

Determinants of electrical propagation and propagation block in Arrhythmogenic Cardiomyopathy.

Gap junction and ion channel remodeling occur early in Arrhythmogenic Cardiomyopathy (ACM), but their pathogenic consequences have not been elucidated. Here, we identified the arrhythmogenic substrate, consisting of propagation slowing and conduction block, in ACM models expressing two different desmosomal gene variants. Neonatal rat ventricular myocytes were transduced to express variants in genes encoding desmosomal proteins plakoglobin or plakophilin-2. Studies were performed in engineered cells and anisotropic tissues to quantify changes in conduction velocity, formation of unidirectional propagation, cell-cell electrical coupling, and ion currents. Conduction velocity decreased by 71% and 63% in the two ACM models. SB216763, an inhibitor of glycogen synthase kinase-3 beta, restored conduction velocity to near normal levels. Compared to control, both ACM models showed greater propensity for unidirectional conduction block, which increased further at greater stimulation frequencies. Cell-cell electrical conductance measured in cell pairs was reduced by 86% and 87% in the two ACM models. Computer modeling showed close correspondence between simulated and experimentally determined changes in conduction velocity. The simulation identified that reduced cell-cell electrical coupling was the dominant factor leading to slow conduction, while the combination of reduced cell-cell electrical coupling, reduced sodium current and inward rectifier potassium current explained the development of unidirectional block. Expression of two different ACM variants markedly reduced cell-cell electrical coupling and conduction velocity, and greatly increased the likelihood of developing unidirectional block - both key features of arrhythmogenesis. This study provides the first quantitative analysis of cellular electrophysiological changes leading to the substrate of reentrant arrhythmias in early stage ACM.

Assessing Educational and Attitudinal Outcomes of a Student Learner Experience Focused on Homelessness.

BACKGROUND AND OBJECTIVES: Patient navigation programs help guide vulnerable populations, such as those experiencing homelessness, through the health care system. Medical students developed the student-run Patient Navigator Program (PNP) to serve persons experiencing homelessness (PEH) in the Dallas area. The objective of this study was to build on previously published data to determine how medical student attitudes, knowledge, and confidence working with PEH changed during involvement in the PNP, particularly after participating as a patient navigator. METHODS: Student fellows completed a survey prior to a training elective (time point 1), immediately after the training elective (time point 2), and after acting as a patient navigator (time point 3). The PNP survey, which intended to measure student attitudes and knowledge regarding PEH, included the Health Professionals' Attitudes Toward the Homeless Inventory (HPATHI) and the Student-Run Free Clinic Project (SRFCP) surveys. In our analysis, we compared responses among the different time points. RESULTS: Seventy-six of 88 students who completed the training elective chose to participate in the PNP fellowship. Skills, knowledge, and self-efficacy improved from time points 1 to 2, 1 to 3, and 2 to 3. Social advocacy also improved from time points 1 to 2 and 1 to 3. CONCLUSIONS: Improvements from time point 1 to 2 demonstrated the value of didactic learning, while further improvements from time point 2 to 3 demonstrated the added benefit of hands-on experiential learning. Our study illustrates the potential educational benefits that a PNP provides to medical students who may encounter or care for this population during their careers.

Evaluating bottoming-out of bariatric sized wheelchair cushions.

In the United States, wheelchair cushions are classified using HCPCS codes. Cushions classified as Skin Protection cushions are provided for wheelchair users who are at risk of tissue damage. Cushions designed for bariatric users fall into a category of cushions with width of 22 inches or greater. Current coding procedures require tests that are designed for 41-43-cm-wide cushion so cannot evaluate wider cushions. The objective of this study was to evaluate the performance of heavy-duty or bariatric wheelchair cushions using an anthropometrically appropriate buttock model and loading profile. A rigid buttock model, designed to reflect the anthropometry of persons using cushions over 55 cm in width was loaded onto six bariatric-sized wheelchair cushions. Two applied loads, 75 and 88 kg, represented the 50th and 80th percentile of persons who would be expected to use a 55-cm-wide cushion. None of the cushions indicated a bottomed-out state at the 88 kg load, suggesting that they could adequately support users weighing 135 kg. However, when evaluating cushions at their maximum rated loads, two of the six cushions were approaching or had bottomed-out. This study indicates that a more valid approach to classify Skin Protection bariatric cushions is needed.

Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA.

While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.

Regional Analgesia for Cesarean Delivery: A Narrative Review Toward Enhancing Outcomes in Parturients.

Introduction: With the current surge on peripheral nerve blocks in post-cesarean pain management and the historical lack of unequivocal evidence supporting its universal use, this review intended to re-examine the extended scope of literature on regional anesthesia and postoperative analgesia in low-transverse cesarean section. Methods: A literature search was conducted up to April 2023 using PubMed to identify articles relevant to our search words "cesarean section", "neuraxial morphine", "post-cesarean analgesia", as well as the name of each individual nerve block. The literature search was ultimately narrowed to systematic reviews and randomized controlled trials published between 2012 and 2023. We define, describe, and discuss the evidence surrounding each individual regional anesthetic technique in the presence and absence of intrathecal morphine, which is used as the gold standard when appropriate. Results: In the absence of neuraxial morphine, all regional anesthetic techniques have some level of analgesic benefit in the post-cesarean analgesia. Transversus Abdominis Plane blocks continue to have the most studies in their use. Newer fascia plane blocks including the anterior Quadratus Lumborum, and Erector Spinae Plane blocks provide significant analgesia. In addition, direct comparison among peripheral nerve blocks consistently favors the more proximal, centralized techniques. Conversely, in the presence of neuraxial morphine, no peripheral anesthetic technique has reliably and reproducibly demonstrated an added analgesic benefit regardless of the peripheral nerve block technique or location of local anesthetic injection in the post-cesarean population. Conclusion: Neuraxial morphine continues to be the gold standard for post-cesarean section analgesia, the benefit of additional single injection regional anesthetic is currently not evidence supported. In cases where neuraxial opioids have not or cannot be given, there is overwhelming evidence that regional anesthetic techniques improve post-cesarean section analgesia and decrease post-operative opioid consumption. Even though there is no consensus on the optimal peripheral nerve block, emerging evidence suggests more centralized abdominal fascia plane block trends towards better analgesia.

Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants.

Rapid antigen tests (RATs) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of 10 commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using both individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR cycle threshold (CT) value (a rough proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

Safety of Concurrent Radiation Therapy With Brentuximab Vedotin in the Treatment of Lymphoma.

Purpose: Purpose: Radiation therapy (RT) and the antibody-drug conjugate brentuximab vedotin (BV) are standard-of-care treatment options for patients with certain B and T-cell lymphomas; however, there are limited data exploring the safety of concurrent BV and RT (BVRT). Methods and Materials: We performed a single institutional retrospective review of 44 patients who received BVRT. Results: Twenty percent of patients (9/44) developed new grade 2 or higher (G2+) hematologic toxicity (HT) after BVRT, which was associated with radiation dose (median dose of 35 Gy in those with new G2+ HT compared with 15 Gy in those without; P < .001). Acute G2+ elevation in aspartate transaminase or alanine transaminase level was associated with administration of concurrent chemotherapy with BVRT (57% vs 21%; P = .047) but was not associated with any RT factors. Local control (LC) was achieved in 24 of 42 patients (57%) with available follow-up. Ten patients (23%) proceeded to stem cell transplant or cellular therapy after BVRT at a median of 48 days (interquartile range, 27-188 days). At last follow-up, 10 patients (23%) remained without evidence of disease. Conclusions: Our analysis demonstrates that the combination of BV and RT is well tolerated, though care should be taken during RT planning to reduce the risk of HT. This combination can be considered for patients in need of both local and systemic disease control.

Methods of Machine Learning-Based Chimeric Antigen Receptor Immunological Synapse Quality Quantification.

Chimeric Antigen Receptor (CAR)-mediated immunotherapy shows promising results for refractory blood cancers. Currently, six CAR-T drugs have been approved by U.S. Food and Drug Administration (FDA). Theoretically, CAR-T cells must form an effective immunological synapse (IS, an interface between effective cells and their target cells) with their susceptible tumor cells to eliminate tumor cells. Previous studies show that CAR IS quality can be used as a predictive functional biomarker for CAR-T immunotherapies. However, quantification of CAR-T IS quality is clinically challenging. Machine learning (ML)-based CAR-T IS quality quantification has been proposed previously.Here, we show an easy-to-use, step-by-step approach to predicting the efficacy of CAR-modified cells using ML-based CAR IS quality quantification. This approach will guide the users on how to use ML-based CAR IS quality quantification in detail, which include: how to image CAR IS on the glass-supported planar lipid bilayer, how to define the CAR IS focal plane, how to segment the CAR IS images, and how to quantify the IS quality using ML-based algorithms.This approach will significantly enhance the accuracy and proficiency of CAR IS prediction in research.

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 antigen self tests.

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants.

Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (C T ) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using C T value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests.

Widespread use of over-the-counter rapid diagnostic tests for SARS-CoV-2 has led to a decrease in availability of clinical samples for viral genomic surveillance. As an alternative sample source, we evaluated RNA isolated from BinaxNOW swabs stored at ambient temperature for SARS-CoV-2 rRT-PCR and full viral genome sequencing. 81 of 103 samples (78.6%) yielded detectable RNA, and 46 of 57 samples (80.7 %) yielded complete genome sequences. Our results illustrate that SARS-CoV-2 RNA extracted from used Binax test swabs provides an important opportunity for improving SARS-CoV-2 genomic surveillance, evaluating transmission clusters, and monitoring within-patient evolution.

Approaches to Reduce Use and Duration of Anti-MRSA Agents for Antimicrobial Stewardship Programs: A Review of Recent Literature.

Antimicrobial stewardship programs (ASPs) have the potential to effectively deescalate unnecessary methicillin-resistant Staphylococcus aureus (MRSA) coverage. This review summarizes literature published from 2014 through 2021 describing contemporary ASP methods and their resulting effectiveness at reducing anti-MRSA agent use (ie vancomycin, linezolid, daptomycin, ceftaroline, and clindamycin). This review of the literature examined the following strategies, which had reports of success in either decreasing the use or duration of anti-MRSA agents: prospective review and feedback, antibiotic timeouts, health system or department protocol changes, polymerase chain reaction (PCR) and rapid testing of patient samples. Most of the current literature continue to support most ASP interventions including antibiotic timeouts, pathways, and molecular testing including MRSA nasal PCRs and rapid diagnostic testing can be successful at reducing unnecessary anti-MRSA use.