Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor

SARS-CoV-2 is a unique event, having emerged suddenly as a highly infectious viral pathogen for human populations. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus detected in bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor-binding domain or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and in situ molecular dynamics simulations to examine the Spike-RBD's functional evolution, finding that the common ancestral virus with RaTG13, dating to no later than 2013, possessed high binding affinity to the human ACE2 receptor. This suggests that SARS-CoV-2 likely possessed a latent capacity to bind to human cellular targets (though this may not have been sufficient for successful infection) and emphasizes the importance of expanding efforts to catalog and monitor viruses circulating in both human and non-human populations.

Role of α- and β-adrenergic signaling in phenotypic targeting: significance in benign and malignant urologic disease

The urinary tract is highly innervated by autonomic nerves which are essential in urinary tract development, the production of growth factors, and the control of homeostasis. These neural signals may become dysregulated in several genitourinary (GU) disease states, both benign and malignant. Accordingly, the autonomic nervous system is a therapeutic target for several genitourinary pathologies including cancer, voiding dysfunction, and obstructing nephrolithiasis. Adrenergic receptors (adrenoceptors) are G-Protein coupled-receptors that are distributed throughout the body. The major function of α1-adrenoceptors is signaling smooth muscle contractions through GPCR and intracellular calcium influx. Pharmacologic intervention of α-and β-adrenoceptors is routinely and successfully implemented in the treatment of benign urologic illnesses, through the use of α-adrenoceptor antagonists. Furthermore, cell-based evidence recently established the antitumor effect of α1-adrenoceptor antagonists in prostate, bladder and renal tumors by reducing neovascularity and impairing growth within the tumor microenvironment via regulation of the phenotypic epithelial-mesenchymal transition (EMT). There has been a significant focus on repurposing the routinely used, Food and Drug Administration-approved α1-adrenoceptor antagonists to inhibit GU tumor growth and angiogenesis in patients with advanced prostate, bladder, and renal cancer. In this review we discuss the current evidence on (a) the signaling events of the autonomic nervous system mediated by its cognate α- and β-adrenoceptors in regulating the phenotypic landscape (EMT) of genitourinary organs; and (b) the therapeutic significance of targeting this signaling pathway in benign and malignant urologic disease. Video abstract.

Integrin-mediated interactions with a laminin-presenting substrate modulate biosynthesis and phenotypic expression for cells of the human nucleus pulposus

With aging and pathology, cells of the nucleus pulposus (NP) de-differentiate towards a fibroblast-like phenotype, a change that contributes to degeneration of the intervertebral disc (IVD). Laminin isoforms are a component of the NP extracellular matrix during development but largely disappear in the adult NP tissue. Exposing human adult NP cells to hydrogels made from PEGylated-laminin-111 (PEGLM) has been shown to regulate NP cell behaviors and promote cells to assume a biosynthetically active state with gene/protein expression and morphology consistent with those observed in juvenile NP cells. However, the mechanism regulating this effect has remained unknown. In the present study, the integrin subunits that promote adult degenerative NP cell interactions with laminin-111 are identified by performing integrin blocking studies along with assays of intracellular signaling and cell phenotype. The findings indicate that integrin α3 is a primary regulator of cell attachment to laminin and is associated with phosphorylation of signaling molecules downstream of integrin engagement (ERK 1/2 and GSK3β). Sustained effects of blocking integrin α3 were also demonstrated including decreased expression of phenotypic markers, reduced biosynthesis, and altered cytoskeletal organization. Furthermore, blocking both integrin α3 and additional integrin subunits elicited changes in cell clustering, but did not alter the phenotype of single cells. These findings reveal that integrin- mediated interactions through integrin α3 are critical in the process by which NP cells sense and alter phenotype in response to culture upon laminin and further suggest that targeting integrin α3 has potential for reversing or slowing degenerative changes to the NP cell.

Discovery and validation of a cross-platform 21-gene prognostic signature in neuroblastoma

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Background: Neuroblastoma (NB) is the most common extracranial solid tumor in children. Despite the development of risk stratification tools to improve prognostication, prediction of patient survival outcomes in NB remains poor. In this study we used an unbiased machine-learning algorithm to develop and validate a transcriptomic signature capable of predicting 5-year overall (OS) and event-free survival (EFS) in these patients. Methods: The TARGET-Neuroblastoma dataset (n = 243) was used as the training set. Two independent NB cohorts, E-MTAB-179 (n = 478) and GSE85047 (n = 266) were used as validation sets. Elastic net regression was employed to identify transcripts associated with EFS. Association of the developed signature with EFS and OS was evaluated using univariate Cox proportional hazards (CoxPH), Kaplan-Meier, and 5-year receiver-operator characteristic curves in validation cohorts. Further, the independent prognostic value of the signature was assessed using multivariate CoxPH models with relevant clinicopathologic variables including age, INSS stage, and N-Myc amplification status in both validation sets. Finally, a nomogram was developed to integrate the signature with prognostic clinicopathologic variables to evaluate their combined efficacy for prediction of 5-year EFS and OS. Results: We identified a 21-gene signature that demonstrates significant association with EFS and OS in both E-MTAB-178 and GSE49710 validation cohorts. Moreover, the signature is independent of clinicopathological variables and can be effectively incorporated into a risk model, improving the prognostic performance. Several genes within the signature have been previously implicated in NB, including ECEL1, HOXC9 and ARAF1. Conclusions: To the best of our knowledge, we are the first to use an unbiased machine learning approach to generate a transcriptomic gene signature for neuroblastoma prognosis externally validated in multiple cohorts across platforms. This 21-gene transcriptomic signature significantly associated with EFS and OS in this disease. Combining this signature with current prognostic clinicopathologic variables will improve risk stratification of affected patients and may inform effective clinical decision-making.[Table: see text]

Novel deep transfer learning model for COVID-19 patient detection using X-ray chest images

Around the world, more than 250 countries are affected by the COVID-19 pandemic, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This outbreak can be controlled only by the diagnosis of the COVID-19 infection in early stages. It is found that the radiographic images are ideal for the fastest diagnosis of COVID-19 infection. This paper proposes an ensemble model which detects the COVID-19 infection in the early stage with the use of chest X-ray images. The transfer learning enables to reuse the pretrained models. The ensemble learning integrates various transfer learning models, i.e., EfficientNet, GoogLeNet, and XceptionNet, to design the proposed model. These models can categorize patients as COVID-19 (+), pneumonia (+), tuberculosis (+), or healthy. The proposed model enhances the classifier's generalization ability for both binary and multiclass COVID-19 datasets. Two popular datasets are used to evaluate the performance of the proposed ensemble model. The comparative analysis validates that the proposed model outperforms the state-of-art models in terms of various performance metrics.

Transcriptional and translational abundance of visfatin (NAMPT) in buffalo ovary during estrous cycle and its in vitro effect on steroidogenesis

Visfatin is a highly conserved adipokine protein having multiple biological effects, including regulation of reproduction. Evidence in recent years has shown a pivotal role of visfatin in ovarian functions. The present study was conducted to evaluate the mRNA and protein abundance of visfatin in ovarian follicles and corpora lutea (CL) during different stages of their development in the ovary of water buffalo (Bubalus bubalis) and to investigate the role of visfatin on estradiol (E₂) and progesterone (P₄) secretion. Ovarian follicles were categorized in to small (F1), medium (F2), large (F3), and preovulatory (F4) follicles, whereas the CL were categorized into early (CL1), mid (CL2), late (CL3), and regressing (CL4) CL stage. In follicles, the mRNA and protein abundance of visfatin increased with an increase in follicle size in granulosa cells (GCs) and theca interna (TI) cells. In CL, the transcript of visfatin was significantly (P < 0.05) higher in the late luteal phase (CL3) than that in other phases. The translational abundance of visfatin was significantly higher in the mid and late luteal phase. Visfatin was localized in the cytoplasm of GC and TI of ovarian follicles and small and large luteal cells of CL. GCs were cultured in vitro and treated at 0, 1, and 10 ng/mL visfatin either alone or in the presence of FSH (30 ng/mL) or IGF-I (10 ng/mL) for 48 h. The luteal cells were treated with visfatin at 0, 1, and 10 ng/mL dose for 48h. There was significant (P < 0.05) increase in estradiol (E₂) secretion from GCs at 10 ng/mL dose of visfatin and visfatin (10 ng/mL) +IGF-I (10 ng/mL). Visfatin also increased (P < 0.05) progesterone (P₄) secretion from cultured luteal cells at both 1 and 10 ng/mL dose. In GCs, visfatin in the presence of IGF-I increased the transcriptional abundance of cytochrome P45019A1 (CYP19A1), the gene for key enzyme aromatase. In luteal cells, the visfatin increased mRNA abundance of factors involved in progesterone synthesis viz. steroidogenic acute regulatory protein (StAR), cytochrome P45011A1 (CYP11A1), 3beta-hydroxysteroid dehydrogenase (HSD3B1). The present study provided evidence that visfatin is expressed in ovarian follicles and CL of buffalo ovary and visfatin has a stimulatory effect on estradiol and progesterone secretion in ovarian cells of water buffalo.

Accurate Simulation of the Four Modes of Post-Die Extrudate Shape Distortion

A combined flow, thermal and structural analysis is employed to simulate post-die extrudate distortion in different profile dies. All four factors which can cause extrudate distortion, namely, nonuniform exit velocity distribution, extrudate shrinkage, extrudate draw down, and deformed shape of the calibrator or sizer profile, are simulated. To analyze the effect of exit velocity variation on extrudate distortion, the parameterized geometry of a simple profile die is optimized using an extrusion die optimization software. The simulation results presented for a bi-layer profile die successfully demonstrate how gradually changing profile shape in successive calibrators/sizers can be used to simplify the die design for extrusion of complex profiles. The predicted extrudate shape and layer structure for the bi-layer die are found to accurately match with those in the extruded product.

A139 IMPROVED QUALITY OF LIFE AFTER ENDOSCOPIC THERAPY FOR BARRETT’S ESOPHAGUS AND EARLY ESOPHAGEAL CANCER IN SOUTHERN ALBERTA

Background

In patients with Barrett’s esophagus (BE), endoscopic therapy reduces the risk of progression to invasive esophageal adenocarcinoma (EAC). Data on the impact of endoscopic therapy on patient quality of life (QoL) is limited.

Aims

We aimed to assess: (1) change in QoL during the course of endoscopic therapy for BE, (2) factors which predict this change, (3) whether achieving complete remission of dysplasia (CRD) or intestinal metaplasia (CRIM) affect the degree of change.

Methods

We conducted a retrospective observational study using a prospectively maintained database of BE patients treated in Calgary, Alberta from 2013–2020 containing data on demographics, BE disease characteristics and therapeutics, QoL, and follow-up. QoL was determined prior to initiation of therapy and after each treatment session using a validated questionnaire. Descriptive statistics were calculated and change in QoL was compared using a Wilcoxon signed ranks test. Backwards multiple linear regression analysis was performed to determine predictors of change in QoL.

Results

Of 130 BE patients, 112 (86.1%) were male and 104 (80%) had dysplastic histology or intramucosal carcinoma on index endoscopy. Mean (SD) age was 65.6 (12.0) years. At time of analysis, 76 patients (58.5%) had completed endoscopic therapy, of whom 69 (90.8%) achieved CRIM; 54 patients (41.5%) were still undergoing treatment. There was significant improvement in all QoL measures during the treatment course except for “depression” (Table 1). Patients with CRIM or CRD had reductions in “sleep difficulty” and “negative impact on life” to a significantly greater degree vs patients not achieving CRIM (Δ sleep -0.45 vs 0.0, P=0.002; Δ negative impact -0.4 vs -0.05, P=0.014) or CRD (Δ sleep -0.40 vs +0.60, P=0.002; Δ negative impact -0.40 vs +0.20, P=0.04). Multiple linear regression revealed older age (B=-0.03, P=0.008) and fewer number of EMR sessions (B=0.254, P=0.008) were correlated with greater improvement in QoL.

Conclusions

Endoscopic therapy improves QoL in BE patients, especially in those achieving CRIM/CRD. Older age and fewer EMRs are correlated with greater improvement in QoL. These results further reinforce the role of endoscopic therapy as the first line treatment of BE and early EAC.

Funding Agencies

None

A systematic review of reports of quality improvement for bronchopulmonary dysplasia

Bronchopulmonary dysplasia (BPD) is the most common morbidity of preterm infants, and its incidence has not responded to research and intervention efforts to the same degree as other major morbidities associated with prematurity. The complexity of neonatal respiratory care as well as persistent inter-institutional variability in BPD rates suggest that BPD may be amenable to quality improvement (QI) efforts. We present a systematic review of QI for BPD in preterm infants. We identified 22 reports from single centers and seven from collaborative efforts published over the past two decades. In almost all of the reports, respiratory QI interventions successfully reduced BPD or other key respiratory measures, particularly for infants with birth weight over 1000 g. Several themes and lessons from existing reports may help inform future efforts in both research and QI to impact the burden of BPD.

Correlation between pre-operative endoscopic findings with reflux symptom score for gastro-oesophageal reflux disease in bariatric patients

Introduction:

There is a strong association between gastro-oesophageal reflux disease and morbid obesity.

Methods:

Two hundred and eleven morbidly obese patients operated between September 2007 and June 2017 were retrospectively reviewed. All patients underwent pre-operative upper gastrointestinal endoscopy and assessment by reflux symptomatic score questionnaire.

Results:

Of the total 211 patients, 156 (73.94%) were females; mean body mass index of the cohort was 46.23 ± 3.1 kg/m². There was no evidence of Barrett's oesophagus or malignancy on pre-operative endoscopy. 63.04% of the patients (n = 133) in the study cohort had normal endoscopy. Pre-operative evaluation by reflux symptom score (RSS) questionnaire revealed no evidence of gastro-oesophageal reflux disease in 61.13% of patients (n = 129). The total number of patients with symptoms was 82 (38.86%). They were further divided into two categories based on severity of symptoms, namely, mild + moderate 60 (73.17%) and severe + very severe 22 (26.83%). From the cohort of symptomatic patients, the sub-cohort of 60 mild + moderate symptomatic patients had equal number of patients with normal 30 (50%) and abnormal endoscopy 30 (50%). In the sub-cohort of patients with severe + very severe symptoms (n = 22; 26.83%), endoscopy was abnormal in 6 (27.7%) patients. Whereas, out of 129 (61.13%) asymptomatic patients, one-third (n = 42) had abnormal endoscopy. The weighted kappa score was used between pre-operative endoscopic findings and RSS was statistically not significant (k - 0.0986).

Conclusion:

Pre-operative endoscopy is a must in all bariatric patients as significant percentage of asymptomatic patients can have abnormal endoscopy and vice versa.