PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.

The dynamic evolution of the severe acute respiratory syndrome coronavirus 2 virus is primarily driven by mutations in its genetic sequence, culminating in the emergence of variants with increased capability to evade host immune responses. Accurate prediction of such mutations is fundamental in mitigating pandemic spread and developing effective control measures. This study introduces a robust and interpretable deep-learning approach called PRIEST. This innovative model leverages time-series viral sequences to foresee potential viral mutations. Our comprehensive experimental evaluations underscore PRIEST's proficiency in accurately predicting immune-evading mutations. Our work represents a substantial step in utilizing deep-learning methodologies for anticipatory viral mutation analysis and pandemic response.

Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts.

The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently invaded by novel TEs through horizontal transfer. These invading TEs are not targeted by host small RNAs, and their unregulated activity can cause DNA damage in germline cells and ultimately lead to sterility. Here we use hybrid dysgenesis-a sterility syndrome of Drosophila caused by transposition of invading P-element DNA transposons-to uncover host genetic variants that modulate dysgenic sterility. Using a panel of highly recombinant inbred lines of Drosophila melanogaster, we identified two linked quantitative trait loci (QTL) that determine the severity of dysgenic sterility in young and old females, respectively. We show that ovaries of fertile genotypes exhibit increased expression of splicing factors that suppress the production of transposase encoding transcripts, which likely reduces the transposition rate and associated DNA damage. We also show that fertile alleles are associated with decreased sensitivity to double-stranded breaks and enhanced DNA repair, explaining their ability to withstand high germline transposition rates. Together, our work reveals a diversity of mechanisms whereby host genotype modulates the cost of an invading TE, and points to genetic variants that were likely beneficial during the P-element invasion.

Quantifying the subjective: length-to-height ratio characterizes achalasia esophageal tortuosity.

BACKGROUND: Esophageal morphology in achalasia is thought to affect outcomes, with "end-stage" sigmoidal morphology faring poorly; however, evaluation of morphology's role in outcomes has been limited by lack of objective characterization. Hence, the goals of this study were twofold: characterize the variability of timed barium esophagram (TBE) interpretation and evaluate an objective classification of TBE tortuosity: length-to-height ratio (LHR). We hypothesized that the esophagus must elongate to become sigmoidal such that sigmoidal morphology would demonstrate a larger LHR. METHODS: Ninety pre-operative TBEs were selected from an institutional database. Esophageal morphology was categorized as straight, intermediate, or sigmoidal. Esophageal length was measured by a mid-lumen line from the aortic knob to the esophagogastric junction on TBE; height was measured vertically from the aortic knob to the level of the esophagogastric junction. The length divided by the height generated the LHR. Descriptive statistics and frequency of expert agreement were calculated. Median LHR was compared between consensus morphologies. A receiver operating characteristic (ROC) determined the optimal LHR for sigmoidal vs non-sigmoidal characterization. RESULTS: From a total of 90 pre-operative TBEs, expert consensus morphology was reached in 56 (62.2%) cases. Pairs of experts agreed on morphology in 62-74% of TBEs, with all three experts agreeing on 46.7-48.9% of cases. Median LHR between expert consensus morphologies was 1.03, 1.09, and 1.24 for straight, intermediate, and sigmoidal morphologies, respectively (p < 0.001). ROC demonstrated that an LHR cutoff of 1.13 was 100% sensitive and 95% specific (AUC 0.99) for ruling out sigmoidal morphology. CONCLUSION: These findings confirm our anecdotal experience that subjective morphology interpretation is variable, even between experts at a high-volume center. LHR provides an objective method for classification, allowing us to overcome the limitations of inter-observer variability, thus paving the way for future study of the role of morphology in achalasia outcomes.

Antenatal depression among women with gestational diabetes mellitus: a pilot study.

BACKGROUND: Gestational diabetes mellitus (GDM) is quite prevalent in low- and middle-income countries, and has been proposed to increase the risk of depression. There is only a prior study assessing antenatal depression among the subjects with GDM in the Bangladesh, which leads this study to be investigated. OBJECTIVE: To determine the prevalence of depressive symptoms and potential associations among pregnant women diagnosed with GDM. METHODS: A cross-sectional study was carried out among 105 pregnant women diagnosed with GDM over the period of January to December 2017 in 4- hospitals located in two different cities (Dhaka and Barisal). A semi-structured questionnaire was developed consisting of items related to socio-demographics, reproductive health history, diabetes, anthropometrics, and depression. RESULTS: Mild to severe antenatal depression was present in 36.2% of the subjects (i.e., 14.3%, 19% and 2.9% for mild, moderate and severe depression, respectively). None of the socio-demographic factors were associated with depression, but the history of reproductive health-related issues (i.e., abortion, neonatal death) and uncontrolled glycemic status were associated with the increased risk of depressive disorders. CONCLUSIONS: GDM is associated with a high prevalence of depressive symptoms, which is enhanced by poor diabetes control. Thus, in women presenting with GDM, screening for depression should be pursued and treated as needed.

Genotypic and phenotypic profiles of antibiotic-resistant bacteria isolated from hospitalised patients in Bangladesh.

OBJECTIVES: Characterisation of resistance phenotype and genotype is crucial to understanding the burden and transmission of antimicrobial resistance (AMR). This study aims to determine the spectrum of AMR and associated genes encoding aminoglycoside, macrolide and ß-lactam classes of antimicrobials in bacteria isolated from hospitalised patients in Bangladesh. METHODS: 430 bacterial isolates from patients with respiratory, intestinal, wound infections and typhoid fever, presenting to clinical care from 2015 to 2019, were examined. They included Escherichia coli (n = 85); Staphylococcus aureus (n = 84); Salmonella typhi (n = 82); Klebsiella pneumoniae (n = 42); Streptococcus pneumoniae (n = 36); coagulase-negative staphylococci (n = 28); Enterococcus faecalis (n = 27); Pseudomonas aeruginosa (n = 26); and Acinetobacter baumannii (n = 20). Reconfirmation of these clinical isolates and antimicrobial susceptibility tests was performed. PCR amplification using resistance gene-specific primers was done, and the amplified products were confirmed by Sanger sequencing. RESULTS: 53% of isolates were multidrug-resistant (MDR), including 97% of Escherichia coli. There was a year-wise gradual increase in MDR isolates from 2015 to 2018, and there was an almost twofold increase in the number of MDR strains isolated in 2019 (P = 0.00058). Among the 5 extended-spectrum ß-lactamases investigated, CTX-M-1 was the most prevalent (63%) followed by NDM-1 (22%); Escherichia coli was the major reservoir of these genes. The ermB (55%) and aac(6')-Ib (35%) genes were the most frequently detected macrolide and aminoglycoside resistance genes, respectively. CONCLUSION: MDR pathogens are highly prevalent in hospital settings of Bangladesh.

Effects of proton pump inhibitor use on the esophageal microbial community.

BACKGROUND: Changes in the esophageal microbiome correlate with esophageal disease, but the effects of proton pump inhibitor (PPI) drugs are incompletely characterized. Our objective was to identify the effects of PPI use on the microbial community of the esophagus. METHODS: Mucosal biopsies of the distal esophagus were analyzed using a customized esophageal microbiome qPCR panel array (EMB). Patient demographics, use of PPIs, duration of use and dose were recorded. RESULTS: Fifty-eight patients were included. Mean age was 60.5 years. Ninety percent (52/58) of patients were on PPIs. Mean dose was 42.7 mg. Mean duration of use was 2.5 years. The use of PPIs led to a significant difference in absolute levels of only one organism, Actinomyces, in the entire array (p < 0.01). Among patients who used proton pump inhibitors, there was no significant association between dose and absolute levels of any organism. Similarly, there was no association between duration of use and absolute levels of any organism. CONCLUSIONS: PPI use does not seem to cause significant changes in the distal esophageal microbial community. Future studies with larger sample sizes and esophageal pH testing should be performed to determine the level of acidity and its relationship to the microbial community.

p53 is required for female germline stem cell maintenance in P-element hybrid dysgenesis.

Hybrid dysgenesis is a sterility syndrome resulting from the mobilization of certain transposable elements in the Drosophila germline. Particularly extreme is the hybrid dysgenesis syndrome caused by P-element DNA transposons, in which dysgenic female ovaries often contain few or no germline cells. Those offspring that are produced from dysgenic germlines exhibit high rates of de novo mutation and recombination, implicating transposition-associated DNA damage as the cause of germline loss. However, how this loss occurs, in terms of the particular cellular response that is triggered (cell cycle arrest, senescence, or cell death) remains poorly understood. We demonstrate that two components of the DNA damage response, Checkpoint kinase 2 and its downstream target p53, determine the frequency of ovarian atrophy that is associated with P-element hybrid dysgenesis. We further show that p53 is strongly induced in the germline stem cells (GSCs) of dysgenic females, and is required for their maintenance. Our observations support the critical role for p53 in conferring tolerance of transposable element activity in stem cells.

CELF1 contributes to aberrant alternative splicing patterns in the type 1 diabetic heart.

Dysregulated alternative splicing (AS) that contributes to diabetes pathogenesis has been identified, but little is known about the RNA binding proteins (RBPs) involved. We have previously found that the RBP CELF1 is upregulated in the diabetic heart; however, it is unclear if CELF1 contributes to diabetes-induced AS changes. Utilizing genome wide approaches, we identified extensive changes in AS patterns in Type 1 diabetic (T1D) mouse hearts. We discovered that many aberrantly spliced genes in T1D hearts have CELF1 binding sites. CELF1-regulated AS affects key genes within signaling pathways relevant to diabetes pathogenesis. Disruption of CELF1 binding sites impairs AS regulation by CELF1. In sum, our results indicate that CELF1 target RNAs are aberrantly spliced in the T1D heart leading to abnormal gene expression. These discoveries pave the way for targeting RBPs and their RNA networks as novel therapies for cardiac complications of diabetes.

Surgical Diaphragm: Anatomy and Physiology.

The diaphragm is a musculoaponeurotic structure separating the thoracic and abdominal cavities. It plays important roles in both respiration and maintaining gastrointestinal function. A careful consideration of anatomy should be taken during surgical procedures to minimize injury to this crucial organ.

Survey results of COVID-19 pandemic on female surgical trainees: New normal work environment.

BACKGROUND: The COVID-19 pandemic has had a profound impact on surgical training globally. We aimed to explore and identify the specific challenges faced by women surgeons during the pandemic and provide recommendations for improvement. METHODS: A survey was conducted among trainee members of the Association of Women Surgeons, assessing various aspects of clinical training, mental well-being, and personal and professional life. RESULTS: The respondents were distributed across the United States, with the majority (28%) from the Midwest and Northeast. Training settings were predominantly academic university hospital programs (85%). The majority (92%) were resident trainees and 32% were in research. General surgery, constituting 86% of the respondents, was the most common specialty. There was a decline in surgical cases, research, mental health, and quality of didactics. Limited learning opportunities and challenges in job search were reported. Although virtual conferences were deemed affordable, the lack of networking was noted to be significant. CONCLUSION: The study highlights the need for ongoing support and adaptation in surgical training programs. These programs include the optimization of virtual platforms, prioritizing mental well-being, and ensuring equal opportunities. Strategies to mitigate the impact of future disruptions and promote gender equality are essential. Further research and workflow changes are warranted for effective capacity building.

The Value of Fundoplication in the Treatment of Type I Achalasia.

BACKGROUND: Type I achalasia comprises 20% of achalasia and has nearly absent esophageal motor activity. Concerns that fundoplication decreases the effectiveness of Heller myotomy in these patients has increased adoption of peroral endoscopic myotomy (POEM). Hence, we compared outcomes after Heller myotomy with Dor fundoplication vs POEM. METHODS: From 2005 to 2020, 150 patients with type I achalasia underwent primary surgical myotomy (117 Heller myotomy, 33 POEM). Patient demographics, prior treatments, timed barium esophagrams, Eckardt scores, and reinterventions were assessed between the 2 groups. Median follow-up was 5 years for Heller myotomy and 2.5 years for POEM. RESULTS: The Heller myotomy group was younger, had fewer comorbidities, and lower body mass index vs POEM. Risk-adjusted models demonstrated clinical success (Eckardt ≤3) in 83% of Heller myotomies and 87% of POEMs at 3 years; longitudinal complete timed barium esophagram emptying and reintervention were also similar. An abnormal pH test result was documented in 10% (6 of 60) after Heller myotomy and in 45% (10 of 22) after POEM (P < .001). CONCLUSIONS: Despite nearly absent esophageal contractility, Heller myotomy with Dor fundoplication and POEM result in similar long-term symptom relief, esophageal emptying, and occurrence of reintervention in patients with type I achalasia. There is decreased esophageal acid exposure with the addition of a fundoplication, without compromised esophageal drainage, allaying fears of a detrimental effect of a fundoplication. Hence, choice of procedure may be personalized based on patient characteristics and esophageal morphology and not solely on manometric subtype.

Paraconduit hernia following esophagectomy: Is it safe to watch and wait?

OBJECTIVES: We hypothesized that emergency complications related to asymptomatic paraconduit hernias may occur less often than generally believed. Therefore, we assessed the occurrence and timing of paraconduit hernia diagnosis after esophagectomy, as well as outcomes of these asymptomatic patients managed with a watch-and-wait approach. METHODS: From 2006 to 2021, 1214 patients underwent esophagectomy with reconstruction at the Cleveland Clinic. Among these patients, computed tomography scans were reviewed to identify paraconduit hernias. Medical records were reviewed for timing of hernia diagnosis, hernia characteristics, and patient symptoms, complications, and management. During this period, patients with asymptomatic paraconduit hernias were typically managed nonoperatively. RESULTS: Paraconduit hernias were identified in 37 patients. Of these, 31 (84%) had a pre-esophagectomy hiatal hernia. Twenty-one hernias (57%) contained colon, 7 hernias (19%) contained pancreas, and 9 hernias (24%) contained multiple organs. Estimated prevalence of paraconduit hernia was 3.3% at 3 years and 7.7% at 10 years. Seven patients (19%) had symptoms, 4 of whom were repaired electively, with 2 currently awaiting repairs. No patient with a paraconduit hernia experienced an acute complication that required emergency intervention. CONCLUSIONS: The risk of paraconduit hernia increases with time, suggesting that long-term symptom surveillance is reasonable. Emergency complications as a result of asymptomatic paraconduit hernias are rare. A small number of patients will experience hernia-related symptoms, sometimes years after hernia diagnosis. Our findings suggest that observation of asymptomatic paraconduit hernias (watch and wait) may be considered, with repair considered electively in patients with persistent symptoms.

Thoracoabdominal Esophagectomy: Then and Now.

BACKGROUND: Open approaches for esophagectomy are often still useful; of these, left thoracoabdominal esophagectomy (TAE) is poorly understood and often criticized. Hence, we examined TAE's worldwide utilization, survival, and present-day use and outcomes at our institution compared with contemporary national averages. METHODS: The Worldwide Esophageal Cancer Collaboration database includes 8854 patients who underwent esophagectomy for cancer between 2005 and 2014, a period when TAE was our center's most common approach. Two propensity score-matched models were constructed: worldwide TAE vs worldwide non-TAE (751 matched pairs); and our high-volume center TAE vs worldwide non-TAE (273 matched pairs). All-cause mortality was compared between matched groups. Institutional TAE data from 2017 to 2021 were assessed for present-day use and outcomes. RESULTS: Worldwide, propensity score-matched patients undergoing TAE had a median of 20 lymph nodes resected vs 17 after non-TAE (P < .0001). Five-year survival was 34% for worldwide TAE vs 42% for worldwide non-TAE groups (P = .04). Three-year matched survival was 52% for high-volume TAE compared with 54% for worldwide non-TAE groups (P = .1). From 2017 to 2021 at our institution, 90 (26%) of 346 esophagectomies were performed by TAE. Pneumonia developed in 5 patients (5.6%), with 88 patients (98%) alive at 30 days, comparable to contemporary averages of The Society of Thoracic Surgeons. CONCLUSIONS: When it is performed as the primary approach in high volumes, TAE can have comparable outcomes to non-TAE with low morbidity. At present, we find that TAE is most useful in patients with truncal obesity, prior abdominal operations, and locally advanced cardia tumors with potential for variable extent of resection.

Development and validation of a universal esophageal patient-reported outcome measure: The Cleveland Clinic Esophageal Questionnaire (CEQ).

OBJECTIVE: Currently, there is no validated patient-reported outcome measure (PROM) applicable to all esophageal diseases. Our objective was to create a psychometrically robust, validated universal esophageal PROM that can also objectively assess patients' quality of life (QoL). METHODS: The pilot PROM constructed based on expert opinions, literature review, and previous unpublished institutional research had 27 items covering 8 domains. It was completed by 30 patients in the outpatient clinic followed by a structured debriefing interview, which allowed for refining the PROM. The final PROM: Cleveland Clinic Esophageal Questionnaire (CEQ) included 34 items across 6 domains (Dysphagia, Eating, Pain, Reflux & Regurgitation, Dyspepsia, Dumping), each accompanied by a corresponding QoL component. Further psychometric assessment of the PROM was conducted by evaluating (1) acceptability, (2) construct validity, (3) reliability, and (4) responsiveness. RESULTS: Five hundred forty-six unique patients (median 63.7 years [54.3-71.7], 53% male [287], 86% White) completed CEQ at >90% completion within 5 minutes. Construct validity was demonstrated by differentiating scores across esophageal cancer (n = 146), achalasia (n = 170), hiatal hernia (n = 160), and other diagnoses (n = 70). Internal reliability (Cronbach alpha 0.83-0.89), and test-retest reliability (intraclass correlation coefficients 0.63-0.85) were strong. Responsiveness was demonstrated through CEQ domains improving for 53 patients who underwent surgery for achalasia or hiatal hernia (Cohen d 0.86-2.59). CONCLUSIONS: We have constructed a psychometrically robust, universal esophageal PROM that allows concise, consistent, objective quantification of symptoms and their effect on the patient. The CEQ is valuable in prognostication and tracking of longitudinal outcomes in both benign and malignant esophageal diseases.

Clinical T2 N0 M0 Esophageal Cancer: Identifying Predictive Factors of Upstaging.

BACKGROUND: Inaccuracy of clinical staging renders management of clinical T2 N0 M0 (cT2 N0 M0) esophageal cancer difficult. When an underlying advanced-stage disease is understaged to cT2 N0 M0, patients miss the opportunity to gain the potential benefits of neoadjuvant therapy. This study aimed to identify preoperative factors that predict underlying advanced-stage esophageal cancer. METHODS: From 2000 to 2020, 1579 patients with esophageal cancer underwent esophagectomy. Sixty patients who underwent upfront surgery for cT2 N0 M0 esophageal cancer were included in this study. The median age was 62.5 years, and 78% (n = 47) of these patients were male. Radiologic, clinical, and endoscopic factors were evaluated as preoperative markers. The Fisher exact and the Wilcoxon rank sum tests were used for categoric and continuous variables, respectively. Random forest classification was used to identify preoperative factors for predicting upstaging and downstaging. RESULTS: Of the 60 patients, 8 (13%) were found to have pathologic T2 N0 M0 esophageal cancer. Sixteen (27%) patients had cancer that was pathologically downstaged, and 36 (60%) had upstaged disease. Seven (19%) patients had upstaged cancer on the basis of the pathologic T stage, 14 (39%) had upstaging on the basis of the pathologic N stage, and 15 (42%) had upstaging on the basis of both T and N stages. Dysphagia (P = .003) and tumor maximum standardized uptake value (P = .048) were predictors of upstaging, with a combined predictive value of up to 75%. CONCLUSIONS: The presence of dysphagia and of high maximum standardized uptake value (≥5) of the tumor is predictive of more advanced underlying disease for patients with cT2 N0 M0 esophageal cancer, and these patients should be considered for neoadjuvant therapy.

Achalasia: Surgery Versus Per-Oral Endoscopic Myotomy.

Approaches to achalasia include non-operative and operative techniques with Heller Myotomy and Per-Oral Endoscopic Myotomy (POEM) at the forefront of palliative strategies. Given the diverse subtypes and the time-dependent failure pattern for achalasia, there is no standard approach. We elect for a POEM for type III achalasia, poor functional status, hostile abdomen, and salvage after the previous myotomy. A Heller myotomy is elected over a POEM for type II achalasia, presence of diverticulum, and hiatal hernia. As long-term outcomes become available, an optimal customized strategy will become clearer.

Preoperative predictors of spread through air spaces in lung cancer.

OBJECTIVE: Spread through air spaces (STAS) is a new histologic feature of invasion of non-small cell lung cancer that lacks sensitivity and specificity on frozen sections and is associated with higher recurrence and worse survival with sublobar resections. Our objective is to identify preoperative characteristics that are predictive of STAS to guide operative decisions. METHODS: From January 2018 through December 2021, 439 cT1-3N0 M0 patients with non-small cell lung cancer and a median age of 68 years, 255 (58%) women, who underwent primary surgery at our institution were included. Patients who received neoadjuvant therapy and whose STAS status was not documented were excluded. Age, sex, smoking status, tumor size, ground-glass opacities, maximum standardized uptake values, and molecular markers on preoperative biopsy were evaluated as preoperative markers. Comparisons between groups were conducted using standardized mean differences and random forest classification was used for prediction modeling. RESULTS: Of the 439 patients, 177 had at least 1 STAS-positive tumor, and 262 had no STAS-positive tumors. Overall, 179 STAS tumors and 293 non-STAS tumors were evaluated. Younger age (50 years or younger), solid tumor, size ≥2 cm, and maximum standardized uptake value ≥2.5 were independently predictive of STAS with prediction probabilities of 50%, 40%, 38%, and 40%, respectively. STAS tumors were more likely to harbor KRAS mutations and be PD-L1 negative. CONCLUSIONS: Young age (50 years or younger), larger (≥2 cm) solid tumors, high maximum standardized uptake values, and presence of KRAS mutation, are risk factors for STAS and can be considered for lobectomy. Smoking status and gender are still controversial risk factors for STAS.