MK2a inhibitor CMPD1 abrogates chikungunya virus infection by modulating actin remodeling pathway.

Chikungunya virus (CHIKV) epidemics around the world have created public health concern with the unavailability of effective drugs and vaccines. This emphasizes the need for molecular understanding of host-virus interactions for developing effective targeted antivirals. Microarray analysis was carried out using CHIKV strain (Prototype and Indian) infected Vero cells and two host isozymes, MAPK activated protein kinase 2 (MK2) and MAPK activated protein kinase 3 (MK3) were selected for further analysis. The substrate spectrum of both enzymes is indistinguishable and covers proteins involved in cytokines production, endocytosis, reorganization of the cytoskeleton, cell migration, cell cycle control, chromatin remodeling and transcriptional regulation. Gene silencing and drug treatment were performed in vitro and in vivo to unravel the role of MK2/MK3 in CHIKV infection. Gene silencing of MK2 and MK3 abrogated around 58% CHIKV progeny release from the host cell and a MK2 activation inhibitor (CMPD1) treatment demonstrated 68% inhibition of viral infection suggesting a major role of MAPKAPKs during late CHIKV infection in vitro. Further, it was observed that the inhibition in viral infection is primarily due to the abrogation of lamellipodium formation through modulation of factors involved in the actin cytoskeleton remodeling pathway. Moreover, CHIKV-infected C57BL/6 mice demonstrated reduction in the viral copy number, lessened disease score and better survivability after CMPD1 treatment. In addition, reduction in expression of key pro-inflammatory mediators such as CXCL13, RAGE, FGF, MMP9 and increase in HGF (a CHIKV infection recovery marker) was observed indicating the effectiveness of the drug against CHIKV. Taken together it can be proposed that MK2 and MK3 are crucial host factors for CHIKV infection and can be considered as important target for developing effective anti-CHIKV strategies.

Effect of heat treatments on quinoa germ quality and its storage study.

Quinoa is a potential crop to address the situation as it offers a plethora of benefits as it is nutritionally rich and can adapt to extreme climatic and salt conditions. Quinoa germ consists of almost 25-30% of whole grain. Quinoa germ obtained using roller milling has remarkable nutritional properties with high protein, fat and mineral content. Presence higher fat content limits shelf-life of quinoa germ. The objective of the present investigation is to study the effect of different treatment on stabilization of quinoa germ and its storge study. Quinoa germ was subjected to microwave and infrared treatment for shelf-life extension. Colour properties of the germ has not changed drastically by both treatments. Sorption behavior of quinoa germ stored at different RH was studied and results showed typical sigmoid curve for all samples. Sorption studies revealed that treated quinoa germ were stable at 64% RH. The storage study was carried out at accelerated conditions using PET/PE packaging material. Based on the results of the study, it can be inferred that the quinoa germ can be kept up to three months at accelerated conditions. Study demonstrated that microwave treatments of quinoa germ showed highest shelf life of three months at accelerated conditions.

Telmisartan Restricts Chikungunya Virus Infection In Vitro and In Vivo through the AT1/PPAR-γ/MAPKs Pathways.

Chikungunya virus (CHIKV) has reemerged as a global public health threat. The inflammatory pathways of the renin-angiotensin system (RAS) and peroxisome proliferator-activated receptor-gamma (PPAR-γ) are usually involved in viral infections. Thus, telmisartan (TM), which is known to block the angiotensin 1 (AT1) receptor and activate PPAR-γ, was investigated for activity against CHIKV. The anti-CHIKV effect of TM was investigated in vitro (Vero cells, RAW 264.7 cells, and human peripheral blood mononuclear cells [hPBMCs]) and in vivo (C57BL/6 mice). TM was found to abrogate CHIKV infection efficiently (50% inhibitory concentration (IC50) of 15.34 to 20.89 µM in the Vero cells and RAW 264.7 cells, respectively). Viral RNA and proteins were reduced remarkably. Additionally, TM interfered in the early and late stages of the CHIKV life cycle with efficacy during pretreatment and posttreatment. Moreover, the agonist of the AT1 receptor and an antagonist of PPAR-γ increased CHIKV infection, suggesting that the antiviral potential of TM occurs through modulating host factors. In addition, reduced activation of all major mitogen-activated protein kinases (MAPKs), NF-κB (p65), and cytokines by TM occurred through the inflammatory axis and supported the fact that the anti-CHIKV efficacy of TM is partly mediated through the AT1/PPAR-γ/MAPKs pathways. Interestingly, at a human equivalent dose, TM abrogated CHIKV infection and inflammation significantly, leading to reduced clinical scores and complete survival of C57BL/6 mice. Additionally, TM reduced infection in hPBMC-derived monocyte-macrophage populations in vitro. Hence, TM was found to reduce CHIKV infection by targeting both viral and host factors. Considering its safety and in vivo efficacy, it can be a suitable candidate in the future for repurposing against CHIKV.

Secondary overtriage of isolated facial trauma.

DESIGN: Retrospective chart review. SETTING: Academic, tertiary care, level I trauma center in a rural state. BACKGROUND: Unnecessary transfer of certain facial trauma patients results in a burden of time, money, and other resources on both the patient and healthcare system; identification and development of outpatient treatment pathways for these patients is a significant opportunity for cost savings. OBJECTIVES: To investigate the treatment and disposition of un-complicated, stable, isolated facial trauma injuries transferred from outside hospitals and determine the significance of secondary overtriage. METHODS: Retrospective chart review utilizing our institutional trauma database, including patients transferred to our emergency department between January 2012 and December 2017. Patients were identified by ICD9 or ICD10 codes and only those with isolated facial trauma were included. RESULTS: We identified 538 isolated facial trauma patients who were transferred to our institution during the study period. The majority of those patients were transferred via ground ambulance for an average of 76 miles. Overall, 82% of patients (N = 440) were discharged directly from our institution's emergency department. Almost 30% of patients did not require any formal treatment for their injuries; the potential savings associated with elimination of these unnecessary transfers was estimated to be between $388,605 and $771,372. CONCLUSIONS: We identified a high rate of patients with stable, isolated facial trauma that could potentially be evaluated and treated without emergent transfer. The minimization of these unnecessary transfers represents a significant opportunity for cost and resource utilization savings. LEVEL OF EVIDENCE: 2b- Economic and Cost Analysis.

Molecular characterization of coxsackievirus A24 variants isolated from an outbreak of acute hemorrhagic conjunctivitis.

PURPOSE: Acute Hemorrhagic conjunctivitis (AHC) is associated with CVA24v. Recently there was a severe outbreak of conjunctivitis in months of July and August 2023 in India. This study emphasizes the identification of the distinct mutations in the CVA24v strains, which were isolated during the AHC outbreak and could have potentially played a role in the high transmission of AHC in India during the 2023 outbreak. METHODS: A total of 71 conjunctivitis patients aged 1-75 years comprising 47 males and 24 females who attended Ophthalmology department of a tertiary care hospital of easternIndia were studied.RNA was extracted from all conjunctival swab samples and converted into cDNA. Subsequently, the viral 5' UTR was amplified and the PCR positive samples were subjected to sequencing. The newly isolated viral 5' UTR sequences were aligned with other worldwide sequences using the Clustal W tool to conduct mutational analysis. A phylogenetic tree was built using the MEGA software for viral genotype identification. RESULTS: All of the current outbreak strains belonged to genotype IV of CVA24v. The present outbreak strains formed a distinct clade in the phylogenetic tree and were different from previously reported Indian strains. Two persistent mutations, specifically in domain IV (T213C) and domain V (C475T), were exclusively detected within the internal ribosome entry site (IRES) of the 5' UTR of the current strains causing the outbreak. These two alterations have previously been shown to impact the virulence of another enterovirus (CV B3), but they have not been described in CVA24v until now. CONCLUSION: Finding of the present study highlights the possibility and the significance of the aforementioned two mutations in enhancing the transmissibility of the newer CVA24v strains. Hence, these two distinct mutations should be investigated further for developing antiviral therapies to combat future AHC outbreaks associated with CVA24v.

Diagnostic Accuracy of Beta-2 Transferrin Gel Electrophoresis for Detecting Cerebrospinal Fluid Rhinorrhea.

OBJECTIVE: Unilateral thin clear rhinorrhea (UTCR) may represent a variety of pathologies including cerebrospinal fluid (CSF) rhinorrhea. Beta-2 transferrin (B2Tf) gel electrophoresis (GE) has become the preferred testing modality due to reportedly high sensitivity (87%-100%) and specificity (71%-100%). However, there have been relatively few studies assessing its diagnostic accuracy. The purpose of this single-institution study was to determine the accuracy of B2Tf GE in detecting CSF rhinorrhea. METHODS: A single-center retrospective review was conducted from 2016 and 2024 for all patients who presented with UTCR and underwent B2Tf GE. Institutional review board approval was obtained. The gold standard for diagnostic confirmation of true and false positives (TP, FP) as well as false negatives (FN) was endoscopic exploration. The gold standard for true negative (TN) was response to medical therapy. RESULTS: A total of 105 patients underwent 149 B2Tf GE tests. 40 (38.1%) patients were diagnosed with CSF rhinorrhea. Of the 149 B2-Tf GE tests, there were 51 TPs, 72 TNs, 20 FPs, and 6 FNs yielding 89.5% sensitivity, 78.3% specificity, 71.8% positive predictive value, and 92.3% negative predictive value, respectively. Of the false results the most common causes for error were purulent sinusitis (n = 6, 23.1%), possible mucous contamination from nose-blowing during collection (n = 3, 11.5%), patient collection error (n = 3, 11.5%), and blood contamination (n = 1, 3.8%). CONCLUSION: Although these single-institutional data demonstrate test accuracy within ranges previously reported in the literature, they also demonstrate diagnostic limitations. Future studies should explore reasons for erroneous B2Tf GE results and how these may change clinical decision-making. LEVEL OF EVIDENCE: IV Laryngoscope, 2024.

Salicylic Acid Conjugate of Telmisartan Inhibits Chikungunya Virus Infection and Inflammation.

There is no approved antiviral for the management of the Chikungunya virus (CHIKV). To develop an antiviral drug that can manage both CHIKV and arthritis induced by it, an ester conjugate of telmisartan (TM) and salicylic acid (SA) was synthesized (DDABT1). It showed higher potency (IC50 of 14.53 µM) and a good selectivity index [(SI = CC50/IC50) > 33]. On post-treatment of DDABT1, CHIKV infection was inhibited significantly by reducing CPE, viral titer, viral RNA, and viral proteins. Further, the time of addition experiment revealed >95% inhibition up to 4hpi indicating its interference predominantly in the early stages of infection. However, the late stages were also affected. This conjugate of SA and TM was found to increase the antiviral efficacy, and this might be partly attributed to modulating angiotensin II (Ang II) receptor type 1 (AT1). However, DDABT1 might have other modes of action that need further investigation. In addition, the in vivo experiments showed an LD50 of 5000 mg/kg in rats and was found to be more effective than TM, SA, or their combination against acute, subacute, and chronic inflammation/arthritis in vivo. In conclusion, DDABT1 showed remarkable anti-CHIKV properties and the ability to reduce inflammation and arthritis, making it a very good potential drug candidate that needs further experimental validation.

Maxillary Antrostomy Versus Complete Sinus Surgery for Odontogenic Sinusitis With Frontal Sinus Extension.

OBJECTIVES: Endoscopic sinus surgery (ESS) is often necessary when managing odontogenic sinusitis (ODS), but ESS extent for ODS with extramaxillary sinus involvement has been incompletely studied. This study compared outcomes after wide maxillary antrostomy (MA) alone versus complete ESS for ODS with frontal sinus involvement. METHODS: A multicenter prospective cohort study was conducted on patients with uncomplicated ODS (no extrasinus spread) who underwent ESS when computed tomography demonstrated maxillary, anterior ethmoid (AE), and frontal sinus opacification. Multiple preoperative and postoperative variables were recorded, including 22-item sinonasal outcome tests (SNOT-22) and endoscopic findings. Ultimate SNOT-22 and endoscopic resolution, and time to SNOT-22 and endoscopic resolution were compared between patients who underwent MA alone versus "complete" ESS (maxillary, ethmoid, frontal; not sphenoid). RESULTS: Of 70 patients, mean age was 59.2 years, and 55.7% were male. Thirty-five underwent MA alone, and 35 had complete ESS. At first postoperative visits (mean 9.3 days), AE sinus purulence was more likely resolved after complete ESS compared with MA (97.1% vs. 71.4%, p = 0.006). However, time to resolution of AE purulence was comparable by 6 weeks postoperatively (p = 0.158). There were no significant differences in times to foul smell resolution and achieving ≥9 point SNOT-22 reduction (p > 0.05). CONCLUSIONS: For ODS with frontal sinus involvement, MA alone and complete ESS both resulted in rapid and long-term symptomatic resolution. While ultimate resolution of sinus purulence was equivalent between surgery groups, complete ESS did lead to faster resolution of frontoethmoidal purulence in a significant number of cases. LEVEL OF EVIDENCE: 2 Laryngoscope, 2024.

A generalized Defries-Fulker regression framework for the analysis of twin data.

Twin studies compare the similarity between monozygotic twins to that between dizygotic twins in order to investigate the relative contributions of latent genetic and environmental factors influencing a phenotype. Statistical methods for twin data include likelihood estimation and Defries-Fulker regression. We propose a new generalization of the Defries-Fulker model that fully incorporates the effects of observed covariates on both members of a twin pair and is robust to violations of the Normality assumption. A simulation study demonstrates that the method is competitive with likelihood analysis. The Defries-Fulker strategy yields new insight into the parameter space of the twin model and provides a novel, prediction-based interpretation of twin study results that unifies continuous and binary traits. Due to the simplicity of its structure, extensions of the model have the potential to encompass generalized linear models, censored and truncated data; and gene by environment interactions.

Quinoa germ-enriched pasta: Technological, nutritional, textural, and morphological properties.

Germ is the most significant component of quinoa having good nutritional value. Quinoa germ (QG), with balanced amino acid profile and unsaturated fatty acid, is a unique ingredient for human nutrition. In present study, pasta supplemented with QG was characterized for physical, nutritional, morphological, and textural properties. Dough rheology showed increased farinograph water absorption and decreased dough stability with the addition of QG. Addition of QG up to 30% significantly improved the pasta protein content from 13.55% to 20.55%. The substitution of QG to pasta showed decrease in whiteness index and increase in optimum cooking time, swelling index, cooked weight, and cooking loss. It is reported that 20% QG supplement pasta was found to be acceptable; beyond, this level the pasta quality was inferior. Firmness value of pasta significantly increased up to 20% supplementation of QG from 157 to 178 g. The micrographs of pasta with the addition of QG observed increased protein matrix around the starch granules. The results inferred that the QG can serve as a potential functional ingredient for the development of nutritionally enhanced pasta for food industry. PRACTICAL APPLICATION: Quinoa germ (QG) is concentrated source of nutrient with unique nutrition and alternative source of protein. Pasta is the one the popular and fast-growing food in world and explored for enhancement of its nutritional composition to target a larger population with specific nutrient demand. Hence, pasta becomes important vehicle for the supplementation. Developed QG-enriched high-protein pasta will help industry to produce nutritious products at large scale.

Systematic review of errors on beta-2 transferrin gel electrophoresis testing of rhinorrhea and otorrhea.

BACKGROUND: Beta-2 transferrin (B2-Tf) gel electrophoresis (GE) is the preferred non-invasive diagnostic modality for confirming cerebrospinal fluid (CSF) in body fluids. While B2-Tf GE testing is highly sensitive and specific for CSF, false-positive (FP) and false-negative (FN) results can lead to diagnostic and therapeutic dilemmas. Several series have demonstrated potential causes of false B2-Tf GE results, but few studies have reported reasons for these errors. The purpose of this systematic review was to describe sources of B2-Tf GE errors. METHODS: A systematic review was performed by searching OVID, EMBASE, and Web of Science databases for B2-Tf GE studies. After applying exclusion criteria, original research studies directly addressing erroneous B2-Tf GE results underwent qualitative analysis. RESULTS: Of the 243 abstracts screened, 71 underwent full-text review and 18 studies reporting B2-Tf GE errors were included for analysis. There were 15 potential FPs, 12 actual FPs, 12 potential FNs, 19 actual FNs, and 14 indeterminate results. There were also 246 potentially indeterminate results from in vitro studies. Reasons for B2-Tf GE errors included serum transferrin alterations (n = 17; all potential), infection related (n = 13; 9 potential), orbital or salivary contamination (n = 2; 1 potential), and collection related (n = 255; 246 potential). There were 31 false or indeterminate results with unspecified reasons. There were no reported errors due to laboratory processing. CONCLUSIONS: Multiple potential or actual reasons for false or indeterminate results have been reported for B2-Tf GE testing of rhinorrhea and otorrhea. Future studies should explore reasons for B2-Tf testing errors and how these may affect clinical decision making.

Cadaveric analysis of autonomic nerve fiber density in posterior nasal, posterolateral nasal, and anterior ethmoid nerves.

KEY POINTS: Autonomic nerve densities were equivalent in posterior nasal (PNN), posterolateral nasal (PLNN), and anterior ethmoid nerves (AEN). Rhinitis studies should explore the utility of PLNN and/or AEN transection over PNN alone.

Development of an optimized preoperative computed tomography imaging checklist for endoscopic sinus surgery utilizing a systematic review of the literature and the modified Delphi method.

BACKGROUND: Critical review of computed tomography (CT) imaging is essential in preoperative planning for endoscopic sinus surgery. In this study, we used a systematic review and a modified Delphi method to develop a comprehensive checklist that facilitates preoperative review of sinus CT imaging. METHODS: We performed a systematic review of PubMed, Embase, CINAHL, Cochrane, and Web of Science databases to identify existing checklists developed to evaluate sinus CT imaging. An inclusive list of items from these checklists was compiled and a modified Delphi methodology was used to assign ranked priority. The Delphi process involved 14 rhinologists and had three phases: an initial survey with Likert priority (scale of 1-9) and two rounds of live discussions followed by survey to confirm consensus. RESULTS: Ninety-seven possible checklist items were identified from a systematic review and panelist input. On initial survey, 63 items reached a consensus score of 7+, and 13 items had near consensus scores between 6 and 7; two of these 13 borderline items were retained after subsequent panelist discussion. The resulting items were consolidated into an 11-item disease checklist and a 24-item anatomical checklist; the anatomical checklist was further divided into six subsections: nasal cavity, maxillary, ethmoid, sphenoid, frontal, skull base, and orbit. Additionally, panelists identified six core aspects of patient history to consider prior to surgery. CONCLUSIONS: After establishing content validity through a systematic literature review and a modified Delphi method, we developed a comprehensive checklist for preoperative sinus CT imaging review; implementation and evaluation of validity among trainees will suggest overall utility.

Aversive and reinforcing opioid effects: a pharmacogenomic twin study.

BACKGROUND: The clinical utility of opioids is limited by adverse drug effects including respiratory depression, sedation, nausea, and pruritus. In addition, abuse of prescription opioids is problematic. Gaining a better understanding of the genetic and environmental mechanisms contributing to an individual's susceptibility to adverse opioid effects is essential to identify patients at risk. METHODS: A classic twin study paradigm provided estimates for the genetic and familial (genetic and/or shared environment) contribution to acute adverse and affective opioid responses, all secondary outcomes of a larger dataset. One hundred twenty-one twin pairs were recruited in a single occasion, randomized, double-blind, and placebo-controlled study. The µ-opioid receptor agonist alfentanil and saline placebo were administered as target-controlled infusions under carefully monitored laboratory conditions. Measured outcomes included respiratory depression, sedation, nausea, pruritus, drug liking, and drug disliking. Demographic information was collected, and aspects of mood and sleep were evaluated. RESULTS: Significant heritability was detected for respiratory depression (30%), nausea (59%), and drug disliking (36%). Significant familial effects were detected for sedation (29%), pruritus (38%), dizziness (32%), and drug liking (26%). Significant covariates included age, sex, race, ethnicity, education, mood, and depression. Covariates affected sedation, pruritus, drug liking and disliking, and dizziness. CONCLUSIONS: This study demonstrates that large-scale efforts to collect quantitative and well-defined opioid response data are not only feasible but also produce data that are suitable for genetic analysis. Genetic, environmental, and demographic factors work together to control adverse and reinforcing opioid responses, but contribute differently to specific responses.

The Microbiology of Acute Exacerbations in Chronic Rhinosinusitis - A Systematic Review.

Background: Acute exacerbations (AE) in chronic rhinosinusitis (CRS) are a common and important clinical issue. However, relatively little is known regarding the underlying microbiology that drives exacerbations or how it relates to the microbiome of CRS. The purpose of this study is to examine the literature to characterize the microbiome associated with acute exacerbations in a chronic rhinosinusitis setting. Understanding this disease process may facilitate targeted antibiotic therapy, reduced antibiotic resistance, and offer more effective disease control and treatment efficacy. Objective: To characterize the microbiome associated with acute exacerbations of chronic rhinosinusitis (AECRS). Methods: We conducted a systematic review of the literature on Medline, Embase, and Web of Science databases from January 1990-June 2021 to identify studies related to AE in CRS. Exclusion criteria include non-English, non-human studies, and case reports. Studies without culture or PCR data were also excluded. Results: Fourteen studies were identified which provided detailed data regarding sinus microbiome in AECRS patients. In these patients, a total of 1252 individual isolates were identified. While common acute pathogens were identified in high frequencies in the sinonasal cultures (Staphylococcus pneumonia, Haemophilus influenza), the predominant bacteria were Staphylococcus aureus (including methicillin-sensitive Staphylococcus aureus) and Pseudomonas aeruginosa. Patient characteristics that may represent higher risk phenotypes were not consistently collected in the studies. Discussion of antimicrobial sensitivities and/or resistance were included in 7/14 studies. Conclusions: This systematic review identifies the predominant microbiology species that may contribute to AECRS. Further studies are needed to understand the pathogenic role of bacteria and viruses in AECRS and to identify associated comorbidities and patient phenotypes that may predispose to AE. The optimal treatment regimen for AECRS remains unclear.

Association Between Cardiometabolic Factors and Dizziness in African Americans: The Jackson Heart Study.

BACKGROUND: Balance dysfunction is a complex, disabling health condition that can present with multiple phenotypes and etiologies. Data regarding prevalence, characterization of dizziness, or associated factors is limited, especially in an African American population. PURPOSE: The aim of the study is to characterize balance dysfunction presentation and prevalence in an African American cohort, and balance dysfunction relationship to cardiometabolic factors. RESEARCH DESIGN: The study design is descriptive, cross sectional analysis. STUDY SAMPLE: The study sample consist of N = 1,314, participants in the Jackson Heart Study (JHS). DATA COLLECTION AND ANALYSIS: JHS participants were presented an initial Hearing health screening questionnaire (N = 1,314). Of these, 317 participants reported dizziness and completed a follow-up Dizziness History Questionnaire. Descriptive analysis was used to compare differences in the cohorts' social-demographic characteristics and cardiometabolic variables to the 997 participants who did not report dizziness on the initial screening questionnaire. Based on questionnaire responses, participants were grouped into dizziness profiles (orthostatic, migraine, and vestibular) to further examine differences in cardiometabolic markers as related to different profiles of dizziness. Logistical regression models were adjusted for age, sex, education, reported noise exposure, and hearing sensitivity. RESULTS: Participants that reported any dizziness were slightly older and predominantly women. Other significant complaints in the dizzy versus nondizzy cohort included hearing loss, tinnitus, and a history of noise exposure (p < 0.001). Participants that reported any dizziness had significantly higher prevalence of hypertension, blood pressure medication use, and higher body mass index (BMI). Individuals with symptoms alluding to an orthostatic or migraine etiology had significant differences in prevalence of hypertension, blood pressure medication use, and BMI (p < 0.001). Alternatively, cardiometabolic variables were not significantly related to the report of dizziness symptoms consistent with vestibular profiles. CONCLUSION: Dizziness among African Americans is comparable to the general population with regards to age and sex distribution, accordingly to previously published estimates. Participants with dizziness symptoms appear to have significant differences in BMI and blood pressure regulation, especially with associated orthostatic or migraine type profiles; this relationship does not appear to be conserved in participants who present with vestibular etiology symptoms.

Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India.

Purpose: The current global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to the investigation with clinical, biochemical, immunological, and genomic characterization from patients to understand the pathophysiology of viral infection. Methods: Samples were collected from six asymptomatic and six symptomatic SARS-CoV-2-confirmed hospitalized patients in Bhubaneswar, Odisha, India. Clinical details, biochemical parameters, and treatment regimen were collected from a hospital; viral load was determined by RT-PCR; and the levels of cytokines and circulating antibodies in plasma were assessed by Bio-Plex and isotyping, respectively. In addition, whole-genome sequencing of viral strains and mutational analysis were carried out. Results: Analysis of the biochemical parameters highlighted the increased levels of C-reactive protein (CRP), lactate dehydrogenase (LDH), serum SGPT, serum SGOT, and ferritin in symptomatic patients. Symptomatic patients were mostly with one or more comorbidities, especially type 2 diabetes (66.6%). The virological estimation revealed that there was no significant difference in viral load of oropharyngeal (OP) samples between the two groups. On the other hand, viral load was higher in plasma and serum samples of symptomatic patients, and they develop sufficient amounts of antibodies (IgG, IgM, and IgA). The levels of seven cytokines (IL-6, IL-1α, IP-10, IL-8, IL-10, IFN-α2, IL-15) were found to be highly elevated in symptomatic patients, while three cytokines (soluble CD40L, GRO, and MDC) were remarkably higher in asymptomatic patients. The whole-genome sequence analysis revealed that the current isolates were clustered with 19B, 20A, and 20B clades; however, 11 additional changes in Orf1ab, spike, Orf3a, Orf8, and nucleocapsid proteins were acquired. The D614G mutation in spike protein is linked with higher virus replication efficiency and severe SARS-CoV-2 infection as three patients had higher viral load, and among them, two patients with this mutation passed away. Conclusions: This is the first comprehensive study of SARS-CoV-2 patients from India. This will contribute to a better understanding of the pathophysiology of SARS-CoV-2 infection and thereby advance the implementation of effective disease control strategies.

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.

MOTIVATION: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more than one platform for the same set of samples, and it is natural to want to combine the different estimates in order to meet this demand. Estimates from different platforms show different degrees of attenuation of the true CN changes. Similar differences can be observed in CNs from the same platform run in different labs, or in the same lab, with different analytical methods. This is the reason why it is not straightforward to combine CN estimates from different sources (platforms, labs and analysis methods). RESULTS: We propose a single-sample multi source normalization that brings full-resolution CN estimates to the same scale across sources. The normalized CNs are such that for any underlying CN level, their mean level is the same regardless of the source, which make them better suited for being combined across sources, e.g. existing segmentation methods may be used to identify aberrant regions. We use microarray-based CN estimates from 'The Cancer Genome Atlas' (TCGA) project to illustrate and validate the method. We show that the normalized and combined data better separate two CN states at a given resolution. We conclude that it is possible to combine CNs from multiple sources such that the resolution becomes effectively larger, and when multiple platforms are combined, they also enhance the genome coverage by complementing each other in different regions. AVAILABILITY: A bounded-memory implementation is available in aroma.cn.

Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts.

Development of model systems that recapitulate the molecular heterogeneity observed among glioblastoma multiforme (GBM) tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from the Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7 gain/chromosome-10 loss, a poor-prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBM tumors, genomic amplification and overexpression of known GBM oncogenes, such as EGFR, MDM2, CDK6, and MYCN, and novel genes, including NUP107, SLC35E3, MMP1, MMP13, and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M phase, DNA replication, and chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis and cell-cycle module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M progression and/or checkpoint activation. Our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.

Otitis media: a genome-wide linkage scan with evidence of susceptibility loci within the 17q12 and 10q22.3 regions.

BACKGROUND: Otitis media (OM) is a common worldwide pediatric health care problem that is known to be influenced by genetics. The objective of our study was to use linkage analysis to map possible OM susceptibility genes. METHODS: Using a stringent diagnostic model in which only those who underwent tympanostomy tube insertion at least once for recurrent/persistent OM are considered affected, we have carried out a genome-wide linkage scan using the 10K Affymetrix SNP panel. We genotyped 403 Caucasian families containing 1,431 genotyped individuals and 377 genotyped affected sib pairs, and 26 African American families containing 75 genotyped individuals and 27 genotyped affected sib pairs. After careful quality control, non-parametric linkage analysis was carried out using 8,802 SNPs. RESULTS: In the Caucasian-only data set, our most significant linkage peak is on chromosome 17q12 at rs226088 with a p-value of 0.00007. Other peaks of potential interest are on 10q22.3 (0.00181 at rs1878001), 7q33 (0.00105 at rs958408), 6p25.1 (0.00261 at rs554653), and 4p15.2 (0.00301 at rs2133507). In the combined Caucasian and African American dataset, the 10q22.3 peak becomes more significant, with a minimal p-value of 0.00026 at rs719871. Family-based association testing reveals signals near previously implicated genes: 513 kb from SFTPA2 (10q22.3), 48 kb from IFNG (12q14), and 870 kb from TNF (6p21.3). CONCLUSION: Our scan does not provide evidence for linkage in the previously reported regions of 10q26.3 and 19q13.43. Our best-supported linkage regions may contain susceptibility genes that influence the risk for recurrent/persistent OM. Plausible candidates in 17q12 include AP2B1, CCL5, and a cluster of other CCL genes, and in 10q22.3, SFTPA2.