Multi-Dataset Comparison of Vision Transformers and Convolutional Neural Networks for Detecting Glaucomatous Optic Neuropathy from Fundus Photographs.

Glaucomatous optic neuropathy (GON) can be diagnosed and monitored using fundus photography, a widely available and low-cost approach already adopted for automated screening of ophthalmic diseases such as diabetic retinopathy. Despite this, the lack of validated early screening approaches remains a major obstacle in the prevention of glaucoma-related blindness. Deep learning models have gained significant interest as potential solutions, as these models offer objective and high-throughput methods for processing image-based medical data. While convolutional neural networks (CNN) have been widely utilized for these purposes, more recent advances in the application of Transformer architectures have led to new models, including Vision Transformer (ViT,) that have shown promise in many domains of image analysis. However, previous comparisons of these two architectures have not sufficiently compared models side-by-side with more than a single dataset, making it unclear which model is more generalizable or performs better in different clinical contexts. Our purpose is to investigate comparable ViT and CNN models tasked with GON detection from fundus photos and highlight their respective strengths and weaknesses. We train CNN and ViT models on six unrelated, publicly available databases and compare their performance using well-established statistics including AUC, sensitivity, and specificity. Our results indicate that ViT models often show superior performance when compared with a similarly trained CNN model, particularly when non-glaucomatous images are over-represented in a given dataset. We discuss the clinical implications of these findings and suggest that ViT can further the development of accurate and scalable GON detection for this leading cause of irreversible blindness worldwide.

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens - assessing 18,905 protein-coding and 10,678 lncRNA loci - and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.

Synthetic Vulnerabilities in the KRAS Pathway.

Mutations in Kristen Rat Sarcoma viral oncogene (KRAS) are among the most frequent gain-of-function genetic alterations in human cancer. Most KRAS-driven cancers depend on its sustained expression and signaling. Despite spectacular recent success in the development of inhibitors targeting specific KRAS alleles, the discovery and utilization of effective directed therapies for KRAS-mutant cancers remains a major unmet need. One potential approach is the identification of KRAS-specific synthetic lethal vulnerabilities. For example, while KRAS-driven oncogenesis requires the activation of a number of signaling pathways, it also triggers stress response pathways in cancer cells that could potentially be targeted for therapeutic benefit. This review will discuss how the latest advances in functional genomics and the development of more refined models have demonstrated the existence of molecular pathways that can be exploited to uncover synthetic lethal interactions with a promising future as potential clinical treatments in KRAS-mutant cancers.

On-table hepatopancreatobiliary surgical consults for difficult cholecystectomies: A 7-year audit.

BACKGROUND: Cholecystectomy is considered a general surgical operation. However, general surgeons are not trained to manage severe complications such as bile duct injury (BDI) and should refer to hepatopancreatobiliary (HPB) surgeons when difficulty arises. This study aimed to investigate the outcomes of patients who had on-table HPB consults during cholecystectomy. METHODS: This is an audit of 50 patients who required on-table HPB consult during cholecystectomy from 2011 to 2017. Consultations were classified as "proactive" and "reactive", where consults were made before or after surgical incision, respectively. Patient demographics and perioperative details were collected. RESULTS: The median age of the patients was 62.5 years [interquartile range (IQR) 50.8-71.3 years]. Eight (16%) patients had underlying HPB co-morbidity. Gallbladder wall was thickened in all patients (median 5 mm, IQR 4-7 mm), and common bile duct was of normal caliber in all patients (median 5 mm, IQR 4-6 mm). Median length of operation and length of stay were 165 min (IQR 124-209 min) and five days (IQR 3-7 days), respectively. Subtotal cholecystectomy was performed in 18 (36%) patients. Forty-eight patients were initially managed by laparoscopic approach, 15 (31%) required open conversion; majority (9/15, 60%) were initiated before on-table consult. Majority of referrals (98%) were reactive. Common reasons for referral included unclear anatomy or anatomical variations (30%), presence of dense adhesions and/or contracted gallbladder (18%) and impacted stones in Hartmann's pouch (16%). Three (6%) patients were referred for BDI (2 Strasberg D and 1 Strasberg E1), and two (4%) were referred for torrential bleeding from arterial injury (1 cystic artery and 1 right hepatic artery). Any morbidity and 30-day readmission were 22% and 6%, respectively. There was no 90-day mortality. CONCLUSIONS: Calling for help in BDI is obligatory, but in other instances is a personal choice. Calling for help prior to open conversion is lacking and this awareness should be raised. Whether surgical outcomes could be improved by early HPB consult needs to be determined by larger multicenter reports.

A descriptive analysis of an on-demand telehealth approach for remote COVID-19 patient screening.

INTRODUCTION: COVID-19 requires methods for screening patients that adhere to physical distancing and other Centers for Disease Control and Prevention guidelines. There is little data on the use of on-demand telehealth to meet this need. METHODS: The functional performance of on-demand telehealth as a COVID-19 remote patient screening approach was conducted by analysing 9270 patient requests. RESULTS: Most on-demand telehealth requests (5712 of 9270 total requests; 61.6%) had a visit reason that was likely COVID-19 related. Of these, 79.1% (4518 of 5712) resulted in a completed encounter and 20.9% (1194 of 5712) resulted in left without being seen. Of the 4518 completed encounters, 19.1% were referred to an urgent care centre, emergency department or COVID-19 testing centre. The average completed encounter wait time was 26.5 min and the mean visit length was 8.8 min. For patients that completed an encounter 42.8% (1935 of 4518) stated they would have sought in-person care and 9.1% stated they would have done nothing if on-demand telehealth was unavailable. DISCUSSION: On-demand telehealth can serve as a low-barrier approach to screen patients for COVID-19. This approach can prevent patients from visiting healthcare facilities, which reduces physical contact and reduces healthcare worker use of personal protective equipment.

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma.

The core cohesin subunit STAG2 is recurrently mutated in Ewing sarcoma but its biological role is less clear. Here, we demonstrate that cohesin complexes containing STAG2 occupy enhancer and polycomb repressive complex (PRC2)-marked regulatory regions. Genetic suppression of STAG2 leads to a compensatory increase in cohesin-STAG1 complexes, but not in enhancer-rich regions, and results in reprogramming of cis-chromatin interactions. Strikingly, in STAG2 knockout cells the oncogenic genetic program driven by the fusion transcription factor EWS/FLI1 was highly perturbed, in part due to altered enhancer-promoter contacts. Moreover, loss of STAG2 also disrupted PRC2-mediated regulation of gene expression. Combined, these transcriptional changes converged to modulate EWS/FLI1, migratory, and neurodevelopmental programs. Finally, consistent with clinical observations, functional studies revealed that loss of STAG2 enhances the metastatic potential of Ewing sarcoma xenografts. Our findings demonstrate that STAG2 mutations can alter chromatin architecture and transcriptional programs to promote an aggressive cancer phenotype.

Pharmacogenetics in Practice: Estimating the Clinical Actionability of Pharmacogenetic Testing in Perioperative and Ambulatory Settings.

Most literature describing pharmacogenetic implementations are within academic medical centers and use single-gene tests. Our objective was to describe the results and lessons learned from a multisite pharmacogenetic pilot that utilized panel-based testing in academic and nonacademic settings. This was a retrospective analysis of 667 patients from a pilot in 4 perioperative and 5 outpatient cardiology clinics. Recommendations related to 12 genes and 65 drugs were classified as actionable or not actionable. They were ascertained from Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines and US Food and Drug Administration (FDA) labeling. Patients displayed a high prevalence of actionable results (88%, 99%) and use of medications (28%, 46%) with FDA or CPIC recommendations, respectively. Sixteen percent of patients had an actionable result for a current medication per CPIC compared with 5% per FDA labeling. A systematic approach by a health system may be beneficial given the quantity and diversity of patients affected.

The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo.

While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development in vivo, particularly with genetic strategies that establish cis versus trans mechanisms. Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2. Here, we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination. Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene. Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo. Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.

High-throughput Chemical Screening Identifies Focal Adhesion Kinase and Aurora Kinase B Inhibition as a Synergistic Treatment Combination in Ewing Sarcoma.

PURPOSE: Ewing sarcoma is an aggressive solid tumor malignancy of childhood. Although current treatment regimens cure approximately 70% of patients with localized disease, they are ineffective for most patients with metastases or relapse. New treatment combinations are necessary for these patients. EXPERIMENTAL DESIGN: Ewing sarcoma cells are dependent on focal adhesion kinase (FAK) for growth. To identify candidate treatment combinations for Ewing sarcoma, we performed a small-molecule library screen to identify compounds synergistic with FAK inhibitors in impairing Ewing cell growth. The activity of a top-scoring class of compounds was then validated across multiple Ewing cell lines in vitro and in multiple xenograft models of Ewing sarcoma. RESULTS: Numerous Aurora kinase inhibitors scored as synergistic with FAK inhibition in this screen. We found that Aurora kinase B inhibitors were synergistic across a larger range of concentrations than Aurora kinase A inhibitors when combined with FAK inhibitors in multiple Ewing cell lines. The combination of AZD-1152, an Aurora kinase B-selective inhibitor, and PF-562271 or VS-4718, FAK-selective inhibitors, induced apoptosis in Ewing sarcoma cells at concentrations that had minimal effects on survival when cells were treated with either drug alone. We also found that the combination significantly impaired tumor progression in multiple xenograft models of Ewing sarcoma. CONCLUSIONS: FAK and Aurora kinase B inhibitors synergistically impair Ewing sarcoma cell viability and significantly inhibit tumor progression. This study provides preclinical support for the consideration of a clinical trial testing the safety and efficacy of this combination for patients with Ewing sarcoma.

Unmasking host and microbial strategies in the Agrobacterium-plant defense tango.

Coevolutionary forces drive adaptation of both plant-associated microbes and their hosts. Eloquently captured in the Red Queen Hypothesis, the complexity of each plant-pathogen relationship reflects escalating adversarial strategies, but also external biotic and abiotic pressures on both partners. Innate immune responses are triggered by highly conserved pathogen-associated molecular patterns, or PAMPs, that are harbingers of microbial presence. Upon cell surface receptor-mediated recognition of these pathogen-derived molecules, host plants mount a variety of physiological responses to limit pathogen survival and/or invasion. Successful pathogens often rely on secretion systems to translocate host-modulating effectors that subvert plant defenses, thereby increasing virulence. Host plants, in turn, have evolved to recognize these effectors, activating what has typically been characterized as a pathogen-specific form of immunity. Recent data support the notion that PAMP-triggered and effector-triggered defenses are complementary facets of a convergent, albeit differentially regulated, set of immune responses. This review highlights the key players in the plant's recognition and signal transduction pathways, with a focus on the aspects that may limit Agrobacterium tumefaciens infection and the ways it might overcome those defenses. Recent advances in the field include a growing appreciation for the contributions of cytoskeletal dynamics and membrane trafficking to the regulation of these exquisitely tuned defenses. Pathogen counter-defenses frequently manipulate the interwoven hormonal pathways that mediate host responses. Emerging systems-level analyses include host physiological factors such as circadian cycling. The existing literature indicates that varying or even conflicting results from different labs may well be attributable to environmental factors including time of day of infection, temperature, and/or developmental stage of the host plant.

Early virologic responses and hematologic safety of direct-acting antiviral therapies in veterans with chronic hepatitis C.

BACKGROUND & AIMS: There are limited data on the early effectiveness of direct-acting antiviral (DAA) therapies for patients with hepatitis C virus (HCV) infection in routine medical practice. We aimed to evaluate real-world experience with DAA-based regimens. METHODS: By using the Veterans Affairs' Clinical Case Registry, we conducted a prospective observational intent-to-treat analysis of veterans infected with HCV genotype 1 who began treatment with pegylated interferon, ribavirin, and boceprevir (BOC, n = 661) or telaprevir (TVR, n = 198) before January 2012. We determined rates of virologic response at treatment weeks 4, 8, 12, and 24; futility; early discontinuation; and adverse hematologic events. RESULTS: About one third of patients discontinued treatment by week 24 (30% BOC, 34% TVR). A higher percentage of treatment-naive, noncirrhotic patients receiving BOC had undetectable levels of virus at week 24 than patients receiving TVR (74% vs 60%; P = .03). There were no significant differences in rates of early response within subgroups of cirrhotic patients, prior relapsers, prior partial responders, or prior null responders. By week 24, treatment was determined to be futile for 14% of patients receiving BOC and 17% of those receiving TVR. No differences were observed in overall rates of anemia (50% BOC, 49% TVR) or thrombocytopenia (16% BOC, 18% TVR); higher rates of neutropenia were observed in BOC-treated patients (34% BOC, 21% TVR; P = .008). CONCLUSIONS: HCV-infected veterans treated in routine medical practice with DAA-based regimens (BOC or TVR) had rates of early response comparable with those reported in clinical trials. However, they had higher rates of futility and early discontinuation than clinical trial participants. Further studies are needed to determine rates of sustained viral response.

Assessment and utilization of rapid virologic response in US veterans with chronic hepatitis C: evaluating provider adherence to practice guidelines.

BACKGROUND AND GOALS: There are limited data on the extent to which medical providers adhere to practice guidelines for the antiviral treatment of patients with chronic hepatitis C virus (HCV) infection. As representative of overall provider adherence to practice guidelines, provider adherence to specific recommendations regarding rapid virologic response (RVR) was assessed. STUDY: From the Department of Veterans Affairs' Clinical Case Registry, all patients with HCV genotype 1 who initiated peginterferon and ribavirin between January 1, 2007 and December 31, 2008 were identified. The rate of testing for RVR was determined. Patient, provider, and facility characteristics were assessed to determine the factors that predicted improved provider adherence. For patients who achieved RVR, the overall treatment duration was calculated as a secondary measure of provider adherence. RESULTS: About one half of the cohort (54%) had HCV RNA testing for RVR. Among several significant predictors, testing for RVR was more likely in gastroenterology/hepatology specialty clinics, by midlevel providers such as nurse practitioners and physician assistants, and in facilities with a higher volume of HCV patients. Most patients who achieved RVR completed a treatment course within the recommended range. However, 27% of the cohort received more or less than the recommended duration of treatment, thereby unnecessarily increasing their risk for adverse events or decreasing their potential for cure. CONCLUSIONS: More aggressive education is needed to improve provider adherence to HCV antiviral treatment guidelines and optimize the outcomes of HCV patients, especially with the recent approval of complicated direct-acting antiviral regimens.

Lysostaphin-functionalized cellulose fibers with antistaphylococcal activity for wound healing applications.

With the emergence of "super bacteria" that are resistant to antibiotics, e.g., methicillin-resistant Staphylococcus aureus, novel antimicrobial therapies are needed to prevent associated hospitalizations and deaths. Bacteriophages and bacteria use cell lytic enzymes to kill host or competing bacteria, respectively, in natural environments. Taking inspiration from nature, we have employed a cell lytic enzyme, lysostaphin (Lst), with specific bactericidal activity against S. aureus, to generate anti-infective bandages. Lst was immobilized onto biocompatible fibers generated by electrospinning homogeneous solutions of cellulose, cellulose-chitosan, and cellulose-poly(methylmethacrylate) (PMMA) from 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), room temperature ionic liquid. Electron microscopic analysis shows that these fibers have submicron-scale diameter. The fibers were chemically treated to generate aldehyde groups for the covalent immobilization of Lst. The resulting Lst-functionalized cellulose fibers were processed to obtain bandage preparations that showed activity against S. aureus in an in vitro skin model with low toxicity toward keratinocytes, suggesting good biocompatibility for these materials as antimicrobial matrices in wound healing applications.

Sarcoidosis in patients with celiac disease.

PURPOSE: Several case reports and European studies have suggested an association between sarcoidosis and celiac disease; however, they have been inconsistent. We therefore analyzed a large cohort of celiac-disease patients to assess this association. METHODS: An anonymized database of patients with celiac disease was reviewed to determine the number of patients with sarcoidosis. Age- and gender-adjusted standardized morbidity ratios with corresponding 95% confidence intervals (CI) were calculated by comparing results to US-population-derived prevalence data. RESULTS: Ten patients were found to have a comorbid diagnosis of sarcoidosis, representing an age- and gender-adjusted standardized morbidity ratio of 36.8 (95% CI 26.7-50.9). CONCLUSIONS: In this cohort of patients with celiac disease, there was a significantly increased risk of sarcoidosis when compared with the American white population. This further strengthens prior associations that have been made suggesting a shared mechanism behind the etiologies of celiac disease and sarcoidosis.