A cloud-based precision oncology framework for whole genome sequence analysis.

Cancer is one of the wide-ranging diseases which have a high mortality rate impacting globally. This scenario can be switched by early detection and correct precision treatment, a major concern for cancer patients. Clinicians can figure out the best-suited treatments for cancer patients by analyzing the patient's genome, which will treat the patient well and minimize the chances of side effects as well. Therefore, we have developed a fast, robust, and efficient solution as our precision oncology framework based on the whole genome sequencing of the individual's DNA. This platform can perform the entire genomic analysis, starting from the quality assessment of the input file to the variant annotation and functional prediction, followed by a certain level of interpretation. This analysis helps in the molecular profiling of the tumors for the identification of the targetable alterations. It takes in FASTQ or BAM file as an input and provides us with two output reports: a primary report, which consists of the patients' details, a summary of the analysis, and a secondary report, which is an elaborated report comprised of numerous results obtained from the analysis such as base changes, codon changes, amino acid changes, TMB analysis, MSI analysis, the variant frequency with its effects and impacts, affected biomarkers, etc. This framework can be effectively utilized for cancer treatment guidance, identification and validation of novel biomarkers, oncology research & development, genomic analysis, and gene manipulation.

Neuronal insulin signaling and resistance: a balancing act of kinases and phosphatases.

Insulin signaling cascade in peripheral insulin-sensitive tissues regulates whole-body glucose metabolism. Any deregulation in this pathway leads to insulin resistance, ultimately leading to metabolic diseases like type 1 diabetes, type 2 diabetes, and obesity. Insulin signaling in the brain has also been studied for many decades and associated with many primary functions like maintenance of synaptic plasticity, regulation of cognition, and circadian rhythm. Importantly, neuronal insulin signaling has also been associated with the regulation of neuronal glucose uptake. Any impairment in neuronal insulin signaling affecting neuronal glucose uptake has been associated with neurodegenerative disorders like Alzheimer's disease, the process now being termed as type 3 diabetes. Since the criticality lies in proper signaling cascade, determining important points of deregulation is important. In this review, we have discussed some critical points of such deregulation, dividing them into two classes of enzymes: kinases and phosphatases. We have highlighted their individual roles in neuronal insulin signaling, along with their possible implications in neuronal insulin resistance. Future strategies targeting these nodes in neuronal insulin signaling might be helpful in exploring potential therapeutic opportunities to overcome neuronal insulin resistance and related neurodegenerative diseases.

PP1γ regulates neuronal insulin signaling and aggravates insulin resistance leading to AD-like phenotypes.

BACKGROUND: PP1γ is one of the isoforms of catalytic subunit of a Ser/Thr phosphatase PP1. The role of PP1γ in cellular regulation is largely unknown. The present study investigated the role of PP1γ in regulating neuronal insulin signaling and insulin resistance in neuronal cells. PP1 was inhibited in mouse neuroblastoma cells (N2a) and human neuroblastoma cells (SH-SY5Y). The expression of PP1α and PP1γ was determined in insulin resistant N2a, SH-SY5Y cells and in high-fat-diet-fed-diabetic mice whole-brain-lysates. PP1α and PP1γ were silenced by siRNA in N2a and SH-SY5Y cells and effect was tested on AKT isoforms, AS160 and GSK3 isoforms using western immunoblot, GLUT4 translocation by confocal microscopy and glucose uptake by fluorescence-based assay. RESULTS: Results showed that, in one hand PP1γ, and not PP1α, regulates neuronal insulin signaling and insulin resistance by regulating phosphorylation of AKT2 via AKT2-AS160-GLUT4 axis. On the other hand, PP1γ regulates phosphorylation of GSK3ß via AKT2 while phosphorylation of GSK3α via MLK3. Imbalance in this regulation results into AD-like phenotype. CONCLUSION: PP1γ acts as a linker, regulating two pathophysiological conditions, neuronal insulin resistance and AD. Video Abstract.

Emerging roles of PHLPP phosphatases in the nervous system.

It has been more than a decade since the discovery of a novel class of phosphatase, the Pleckstrin Homology (PH) domain Leucine-rich repeat Protein Phosphatases (PHLPP). Over time, they have been recognized as crucial regulators of various cellular processes, such as memory formation, cellular survival and proliferation, maintenance of circadian rhythm, and others, with any deregulation in their expression or cellular localization causing havoc in any cellular system. With the ever-growing number of downstream substrates across multiple tissue systems, a web is emerging wherein the central point is PHLPP. A slight nick in the normal signaling cascade of the two isoforms of PHLPP, namely PHLPP1 and PHLPP2, has been recently found to invoke a variety of neurological disorders including Alzheimer's disease, epileptic seizures, Parkinson's disease, and others, in the neuronal system. Improper regulation of the two isoforms has also been associated with various disease pathologies such as diabetes, cardiovascular disorders, cancer, musculoskeletal disorders, etc. In this review, we have summarized all the current knowledge about PHLPP1 (PHLPP1α and PHLPP1ß) and PHLPP2 and their emerging roles in regulating various neuronal signaling pathways to pave the way for a better understanding of the complexities. This would in turn aid in providing context for the development of possible future therapeutic strategies.

PHLPP isoforms differentially regulate Akt isoforms and AS160 affecting neuronal insulin signaling and insulin resistance via Scribble.

BACKGROUND: The aim of the present study was to determine the role of individual PHLPP isoforms in insulin signaling and insulin resistance in neuronal cells. METHODS: PHLPP isoforms were either silenced or overexpressed individually, and the effects were observed on individual Akt isoforms, AS160 and on neuronal glucose uptake, under insulin sensitive and resistant conditions. To determine PHLPP regulation itself, we tested effect of scaffold protein, Scribble, on PHLPP isoforms and neuronal glucose uptake. RESULTS: We observed elevated expression of both PHLPP1 and PHLPP2 in insulin resistant neuronal cells (Neuro-2A, mouse neuroblastoma; SHSY-5Y, human neuroblastoma) as well as in the whole brain lysates of high-fat-diet mediated diabetic mice. In insulin sensitive condition, PHLPP isoforms differentially affected activation of all Akt isoforms, wherein PHLPP1 regulated serine phosphorylation of Akt2 and Akt3, while PHLPP2 regulated Akt1 and Akt3. This PHLPP mediated Akt isoform specific regulation activated AS160 affecting glucose uptake. Under insulin resistant condition, a similar trend of results were observed in Akt isoforms, AS160 and glucose uptake. Over-expressed PHLPP isoforms combined with elevated endogenous expression under insulin resistant condition drastically affected downstream signaling, reducing neuronal glucose uptake. No compensation was observed amongst PHLPP isoforms under all conditions tested, indicating independent roles and pointing towards possible scaffolding interactions behind isoform specificity. Silencing of Scribble, a scaffolding protein known to interact with PHLPP, affected cellular localization of both PHLPP1 and PHLPP2, and caused increase in glucose uptake. CONCLUSIONS: PHLPP isoforms play independent roles via Scribble in regulating Akt isoforms differentially, affecting AS160 and neuronal glucose uptake. Video abstract.

Reporting of Discrimination by Health Care Consumers Through Online Consumer Reviews.

IMPORTANCE: Little is known about how discrimination in health care relates to inequities in hospital-based care because of limitations in the ability to measure discrimination. Consumer reviews offer a novel source of data to capture experiences of discrimination in health care settings. OBJECTIVE: To examine how health care consumers perceive and report discrimination through public consumer reviews. DESIGN, SETTING, AND PARTICIPANTS: This qualitative study assessed Yelp online reviews from January 1, 2011, to December 31, 2020, of 100 randomly selected acute care hospitals in the US. Word filtering was used to identify reviews potentially related to discrimination by using keywords abstracted from the Everyday Discrimination Scale, a commonly used questionnaire to measure discrimination. A codebook was developed through a modified grounded theory and qualitative content analysis approach to categorize recurrent themes of discrimination, which was then applied to the hospital reviews. EXPOSURES: Reported experiences of discrimination within a health care setting. MAIN OUTCOMES AND MEASURES: Perceptions of how discrimination in health care is experienced and reported by consumers. RESULTS: A total of 10 535 reviews were collected. Reviews were filtered by words commonly associated with discriminatory experiences, which identified 2986 reviews potentially related to discrimination. Using the codebook, the team manually identified 182 reviews that described at least 1 instance of discrimination. Acts of discrimination were categorized by actors of discrimination (individual vs institution), setting (clinical vs nonclinical), and directionality (whether consumers expressed discriminatory beliefs toward health care staff). A total of 53 reviews (29.1%) were coded as examples of institutional racism; 89 reviews (48.9%) mentioned acts of discrimination that occurred in clinical spaces as consumers were waiting for or actively receiving care; 25 reviews (13.7%) mentioned acts of discrimination that occurred in nonclinical spaces, such as lobbies; and 66 reviews (36.3%) documented discrimination by the consumer directed at the health care workforce. Acts of discrimination are described through 6 recurrent themes, including acts of commission, omission, unprofessionalism, disrespect, stereotyping, and dehumanizing. CONCLUSIONS AND RELEVANCE: In this qualitative study, consumer reviews were found to highlight recurrent patterns of discrimination within health care settings. Applying quality improvement tools, such as the Plan-Do-Study-Act cycle, to this source of data and this study's findings may help inform assessments and initiatives directed at reducing discrimination within the health care setting.

Role of Akt isoforms in neuronal insulin signaling and resistance.

The aim of the present study was to determine the role of Akt isoforms in insulin signaling and resistance in neuronal cells. By silencing Akt isoforms individually and in pairs, in Neuro-2a and HT22 cells we observed that, in insulin-sensitive condition, Akt isoforms differentially reduced activation of AS160 and glucose uptake with Akt2 playing the major role. Under insulin-resistant condition, phosphorylation of all isoforms and glucose uptake were severely affected. Over-expression of individual isoforms in insulin-sensitive and resistant cells differentially reversed AS160 phosphorylation with concomitant reversal in glucose uptake indicating a compensatory role of Akt isoforms in controlling neuronal insulin signaling. Post-insulin stimulation Akt2 translocated to the membrane the most followed by Akt3 and Akt1, decreasing glucose uptake in the similar order in insulin-sensitive cells. None of the Akt isoforms translocated in insulin-resistant cells or high-fat-diet mediated diabetic mice brain cells. Based on our data, insulin-dependent differential translocation of Akt isoforms to the plasma membrane turns out to be the key factor in determining Akt isoform specificity. Thus, isoforms play parallel with predominant role by Akt2, and compensatory yet novel role by Akt1 and Akt3 to regulate neuronal insulin signaling, glucose uptake, and insulin-resistance.

Emergence of a smooth interface from growth of a dendritic network against a mechanosensitive contractile material.

Structures and machines require smoothening of raw materials. Self-organized smoothening guides cell and tissue morphogenesis and is relevant to advanced manufacturing. Across the syncytial Drosophila embryo surface, smooth interfaces form between expanding Arp2/3-based actin caps and surrounding actomyosin networks, demarcating the circumferences of nascent dome-like compartments used for pseudocleavage. We found that forming a smooth and circular boundary of the surrounding actomyosin domain requires Arp2/3 in vivo. To dissect the physical basis of this requirement, we reconstituted the interacting networks using node-based models. In simulations of actomyosin networks with local clearances in place of Arp2/3 domains, rough boundaries persisted when myosin contractility was low. With addition of expanding Arp2/3 network domains, myosin domain boundaries failed to smoothen, but accumulated myosin nodes and tension. After incorporating actomyosin mechanosensitivity, Arp2/3 network growth locally induced a surrounding contractile actomyosin ring that smoothened the interface between the cytoskeletal domains, an effect also evident in vivo. In this way, a smooth structure can emerge from the lateral interaction of irregular active materials.

AKT ISOFORMS-AS160-GLUT4: The defining axis of insulin resistance.

The Akt isoforms-AS160-GLUT4 axis is the primary axis that governs glucose homeostasis in the body. The first step on the path to insulin resistance is deregulated Akt isoforms. This could be Akt isoform expression, its phosphorylation, or improper isoform-specific redistribution to the plasma membrane in a specific tissue system. The second step is deregulated AS160 expression, its phosphorylation, improper dissociation from glucose transporter storage vesicles (GSVs), or its inability to bind to 14-3-3 proteins, thus not allowing it to execute its function. The final step is improper GLUT4 translocation and aberrant glucose uptake. These processes lead to insulin resistance in a tissue-specific way affecting the whole-body glucose homeostasis, eventually progressing to an overt diabetic phenotype. Thus, the relationship between these three key proteins and their proper regulation comes out as the defining axis of insulin signaling and -resistance. This review summarizes the role of this central axis in insulin resistance and disease in a new light.

Identification of Patterns of Cognitive Impairment for Early Detection of Dementia.

Early detection of dementia is crucial to devise effective interventions. Comprehensive cognitive tests, while being the most accurate means of diagnosis, are long and tedious, thus limiting their applicability to a large population, especially when periodic assessments are needed. The problem is compounded by the fact that people have differing patterns of cognitive impairment as they progress to different forms of dementia. This paper presents a novel scheme by which individual-specific patterns of impairment can be identified and used to devise personalized tests for periodic follow-up. Patterns of cognitive impairment are initially learned from a population cluster of combined normals and cognitively impaired subjects, using a set of standardized cognitive tests. Impairment patterns in the population are identified using a 2-step procedure involving an ensemble wrapper feature selection followed by cluster identification and analysis. These patterns have been shown to correspond to clinically accepted variants of Mild Cognitive Impairment (MCI), a prodrome of dementia. The learned clusters of patterns can subsequently be used to identify the most likely route of cognitive impairment, even for pre-symptomatic and apparently normal people. Baseline data of 24,000 subjects from the NACC database was used for the study.

Enhanced adjustable nasal transposition of split lateral rectus muscle for surgical management of oculomotor nerve palsy.

Lateral rectus transposition to the medial rectus muscle has recently generated interest in the management of oculomotor nerve palsy. We report 4 cases of complete oculomotor nerve palsy with a large-angle exotropia that were treated with a modified adjustable nasal transposition of the split lateral rectus muscle. Forced duction testing for the lateral rectus muscle showed good adduction in all 4 cases. Postoperative alignment within 10Δ in straight-ahead gaze was achieved in all 4 cases; adjustment was required in 2 cases.

Acquired Ocular Motor Palsy: Current Demographic and Etiological Profile.

PURPOSE: To describe the clinical, demographic, and etiological profile of patients of acquired ocular motor palsy presenting in a tertiary eye care center. DESIGN: A retrospective hospital record-based study was conducted in patients of paralytic strabismus presenting from April 2016 to December 2017. METHODS: Data included demographic and clinical details, diagnosis, underlying etiology, imaging, laboratory reports, and the outcome. RESULTS: Mean age of presentation of 345 patients included in the study was 38.2 ±â€Š19.5 years (range = 365 years). Pediatric patients (age: ≤16 years) constituted 9.5% of the entire cohort. Mean duration of complaints was 5.87 ±â€Š2 months. Of the 372 eyes of 345 cases, 42.7% were sixth nerve palsy, 34.7% were third nerve palsy, 17.7% were fourth nerve palsy, and 4.8% had multiple ocular motor nerve involvement. Third and sixth nerve palsies were mostly due to ischemic event (58.1% and 69.8% cases, respectively), whereas fourth nerve palsies were commonly caused by trauma (63.6%). Amongst traumatic cases, road traffic accident was the most common mode of trauma. Systemic risk factors were preexistent in 18.2% cases (n = 63); in the remaining (40.8%; n = 141), they were diagnosed after presentation. Complete or partial recovery was noted in 69.7% cases in third nerve palsy, 67.9% cases in sixth nerve palsy, and 45% cases in fourth nerve palsy. CONCLUSIONS: Acquired cranial nerve palsy has younger onset in Indian scenario. Ischemia is the most common etiology raising concerns about the health issues of young Indians. Sixth nerve is most commonly involved in all age groups. Low recovery rate in fourth nerve palsy can be attributed to traumatic etiology.

Knowledge of COVID-19 among Health Care Workers at a Tertiary Care Hospital of Nepal: A Descriptive Cross-sectional Study.

INTRODUCTION: Health care workers are at higher risk of infection with the coronavirus disease as they are directly involved in the treatment of infected patients and perform aerosol-generating procedures. Proper knowledge of this disease can influence the positive attitude, good practices and enhance their safety. We aim to study the knowledge of COVID-19 among health care workers of the tertiary care hospital of Nepal. METHODS: A descriptive cross-sectional study was conducted among health care workers of Shahid Gangalal National Heart Centre from May 20 to June 19, 2020. Ethical approval was taken from the Institutional Review Board (IRB No: 4-2020). Written informed consent was taken from all respondents. Correct answers were summated to reflect the mean knowledge, expressed as a percentage. Data analysis was done using Statistical Package for the Social Sciences version 21. RESULTS: The mean general knowledge score was 95.7%. The mean medical knowledge score was 70.5%. Only 42 (56.8%) of physicians and 103 (53.6%) of nurses had a higher level of medical knowledge regarding COVID-19. Likewise, very few lab technicians 7 (21.9%) and none of the pharmacists had a higher level of medical knowledge. CONCLUSIONS: The healthcare workers of this centre have adequate knowledge regarding COVID-19. However, periodic training for all workers, especially the nurses and allied workers, may help to update the knowledge and hence enhance their safety and that of their patients.

Persistent Basal Cell Hyperplasia Is Associated With Clinical and Endoscopic Findings in Patients With Histologically Inactive Eosinophilic Esophagitis.

BACKGROUND & AIMS: Although eosinophil count is the standard used to monitor disease activity in patients with eosinophilic esophagitis (EoE), there are often disparities between patient-reported symptoms and eosinophil counts. We examined the prevalence of epithelial alterations, namely basal cell hyperplasia (BCH) and spongiosis, among patients with inactive EoE (eosinophil counts below 15 following therapy) and aimed to determine whether maintenance of these changes in epithelial morphology are associated with persistent clinical findings. METHODS: Esophageal biopsies of 243 patients (mean age, 16.9 years) undergoing routine endoscopy at the University of Pennsylvania were evaluated for epithelial BCH and spongiosis. Univariable analysis was used to calculate the association between epithelial changes and symptoms as well as endoscopic findings and peak eosinophil count. We validated our findings using data from a cohort of patients at the University of North Carolina. RESULTS: The discovery and validation cohorts each included patients with inactive EoE, based on histologic factors, but ongoing BCH and spongiosis. Ongoing BCH, but not spongiosis, in patients with inactive EoE was associated with symptoms (odds ratio, 2.14; 95% CI, 1.03-4.42; P = .041) and endoscopic findings (odds ratio, 7.10; 95% CI, 3.12-16.18; P < .001). CONCLUSIONS: In patients with EoE, the presence of BCH might indicate ongoing disease activity, independent of eosinophil count. This might account for the persistent symptoms in patients who are considered to be in remission based on histologic factors.

Mining the biomass deconstructing capabilities of rice yellow stem borer symbionts.

BACKGROUND: Efficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable manner is a prerequisite for its global acceptance as a feedstock in bioethanol production. This is achieved in nature by suites of enzymes with the capability of efficiently depolymerizing all the components of lignocellulose. Here, we provide detailed insight into the repertoire of enzymes produced by microorganisms enriched from the gut of the crop pathogen rice yellow stem borer (Scirpophaga incertulas). RESULTS: A microbial community was enriched from the gut of the rice yellow stem borer for enhanced rice straw degradation by sub-culturing every 10 days, for 1 year, in minimal medium with rice straw as the main carbon source. The enriched culture demonstrated high cellulolytic and xylanolytic activity in the culture supernatant. Metatranscriptomic and metaexoproteomic analysis revealed a large array of enzymes potentially involved in rice straw deconstruction. The consortium was found to encode genes ascribed to all five classes of carbohydrate-active enzymes (GHs, GTs, CEs, PLs, and AAs), including carbohydrate-binding modules (CBMs), categorized in the carbohydrate-active enzymes (CAZy) database. The GHs were the most abundant class of CAZymes. Predicted enzymes from these CAZy classes have the potential to digest each cell-wall components of rice straw, i.e., cellulose, hemicellulose, pectin, callose, and lignin. Several identified CAZy proteins appeared novel, having an unknown or hypothetical catalytic counterpart with a known class of CBM. To validate the findings, one of the identified enzymes that belong to the GH10 family was functionally characterized. The enzyme expressed in E. coli efficiently hydrolyzed beechwood xylan, and pretreated and untreated rice straw. CONCLUSIONS: This is the first report describing the enrichment of lignocellulose degrading bacteria from the gut of the rice yellow stem borer to deconstruct rice straw, identifying a plethora of enzymes secreted by the microbial community when growing on rice straw as a carbon source. These enzymes could be important candidates for biorefineries to overcome the current bottlenecks in biomass processing.

Extended release granisetron: Review of pharmacologic considerations and clinical role in the perioperative setting.

In this review, we evaluate recent literature on use of ER granisetron in clinical practice as compared with current antiemetics and describe its potential uses for perioperative PONV prophylaxis and treatment. Recent literature was evaluated on ER granisetron use compared with currently used antiemetic agents ondansetron, droperidol, metoclopramide, promethazine, and dexamethasone with a focus on procedural anti-emesis. Though promising great effect, application of extended release granisetron to clinical use may be limited by it's increased relative cost.

Stem Cell Therapies for Treatment of Discogenic Low Back Pain: a Comprehensive Review.

PURPOSE OF REVIEW: Discogenic low back pain (DLBP) stems from pathology in one or more intervertebral discs identified as the root cause of the pain. It is the most common type of chronic low back pain (LBP), representing 26-42% of attributable cases. RECENT FINDINGS: The clinical presentation of DLBP includes increased pain when sitting, coughing, or sneezing, and experiencing relief when standing or ambulating. Dermatomal radiation of pain to the lower extremity and neurological symptoms including numbness, motor weakness, and urinary or fecal incontinence are signs of advanced disease with disc prolapse, nerve root compression, or spinal stenosis. Degenerative disc disease is caused by both a decrease in disc nutrient supply causing decreased oxygen, lowered pH, and lessened ability of the intervertebral disc (IVD) to respond to increased load or injury; moreover, changes in the extracellular matrix composition cause weakening of the tissue and skewing the extracellular matrix's (ECM) harmonious balance between catabolic and anabolic factors for cell turnover in favor of catabolism. Thus, the degeneration of the disc causes a shift from type II to type I collagen expression by NP cells and a decrease in aggrecan synthesis leads to dehydrated matrix cells ultimately with loss of swelling pressure needed for mechanical support. Cell-based therapies such as autologous nucleus pulposus cell re-implantation have in animal models and human trials shown improvements in LBP score, retention of hydration in IVD, and increased disc height. Percutaneously delivered multipotent mesenchymal stem cell (MSC) therapy has been proposed as a potential means to uniquely ameliorate discogenic LBP holistically through three mechanisms: mitigation of primary nociceptive disc pain, slow or reversal of the catabolic metabolism, and restoration of disc tissue. Embryonic stem cells (ESCs) can differentiate into cells of all three germ layers in vitro, but their use is hindered related to ethical concerns, potential for immune rejection after transplantation, disease, and teratoma formation. Another similar approach to treating back pain is transplantation of the nucleus pulposus, which, like stem cell therapy, seeks to address the underlying cause of intervertebral disc degeneration by aiming to reverse the destructive inflammatory process and regenerate the proteoglycans and collagen found in healthy disc tissue. Preliminary animal models and clinical studies have shown mesenchymal stem cell implantation as a potential therapy for IVD regeneration and ECM restoration via a shift towards favorable anabolic balance and reduction of pain.

Low Back Pain, a Comprehensive Review: Pathophysiology, Diagnosis, and Treatment.

PURPOSE OF REVIEW: Low back pain encompasses three distinct sources: axial lumbosacral, radicular, and referred pain. Annually, the prevalence of low back pain in the general US adult population is 10-30%, and the lifetime prevalence of US adults is as high as 65-80%. RECENT FINDINGS: Patient history, physical exam, and diagnostic testing are important components to accurate diagnosis and identification of patient pathophysiology. Etiologies of low back pain include myofascial pain, facet joint pain, sacroiliac joint pain, discogenic pain, spinal stenosis, and failed back surgery. In chronic back pain patients, a multidisciplinary, logical approach to treatment is most effective and can include multimodal medical, psychological, physical, and interventional approaches. Low back pain is a difficult condition to effectively treat and continues to affect millions of Americans every year. In the current investigation, we present a comprehensive review of low back pain and discuss associated pathophysiology, diagnosis, and treatment.