Biomarker discovery and authentication of cold-slaughtered chicken through classical analytical procedures and mass spectrometry based proteomic approaches.

1. This study evaluated the suitability of routine analytical procedures and used mass spectrometry-based proteomic approaches to distinguish meat from dead chicken/ cold-slaughtered birds (CS), electrically stunned and slaughtered birds, as per standard protocols (ES), and birds slaughtered according to halal guidelines (HS).2. Meat from CS birds had lower (P < 0.05) pH, water-holding capacity and higher (P < 0.05) lipid oxidation, haem iron content, residual blood and total viable counts relative to ES and HS meat indicating poor quality.3. The results demonstrated the presence of unique protein bands on SDS-PAGE only in CS meat that can be used for routine screening.4. Protein analysis using MALDI-TOF mass spectrometry identified haemoglobin subunit alpha-A and alpha-D; Adenylate kinase isoenzyme 1 as reliable and stable marker proteins for authentication of dead chicken meat under raw and cooked conditions and halal slaughtered chicken, respectively.5. The methods used may be employed by the food safety and regulatory agencies for regular screening of meat quality and to authenticate CS or HS chicken.

Drug Repurposing: An Effective Tool in Modern Drug Discovery.

Drug repurposing is using an existing drug for a new treatment that was not indicated before. It has received immense attention during the COVID-19 pandemic emergency. Drug repurposing has become the need of time to fasten the drug discovery process and find quicker solutions to the over-exerted healthcare scenario and drug needs. Drug repurposing involves identifying the drug, evaluating its efficiency using preclinical models, and proceeding to phase II clinical trials. Identification of the drug candidate can be made through computational and experimental approaches. This approach usually utilizes public databases for drugs. Data from primary and translational research, clinical trials, anecdotal reports regarding off-label uses, and other published human data information available are included. Using artificial intelligence algorithms and other bioinformatics tools, investigators systematically try to identify the interaction between drugs and protein targets. It can be combined with genetic data, clinical analysis, structure (molecular docking), pathways, signatures, targets, phenotypes, binding assays, and artificial intelligence to get an optimum outcome in repurposing. This article describes the strategies involved in drug repurposing and enlists a series of repurposed drugs and their indications.

Design, synthesis, and computational studies of phenylacetamides as antidepressant agents.

In the present work, a hit molecule obtained from zinc 'clean drug-like database' by systematically performed computational studies was modified chemically to obtain different derivatives (VS1-VS25). Structures of synthesized derivatives were confirmed by IR, 1H-NMR, 13C-NMR, 13C-DEPT, MS, and elemental analysis. All the synthesized compounds were biologically evaluated for their antidepressant activity by using tail suspension test and forced swimming test in albino mice. All these derivatives showed moderate to good antidepressant activity. The most potent compound (VS25) among the synthesized compounds showed better antidepressant potential than the standard drugs moclobemide, imipramine, and fluoxetine. To understand the time-dependent interactions of this most active compound with MAO-A molecular dynamics was carried out and reported here. Additionally, acute oral toxicity was performed for the most active compound as per OECD guidelines.

Pharmacophore mapping, molecular docking, chemical synthesis of some novel pyrrolyl benzamide derivatives and evaluation of their inhibitory activity against enoyl-ACP reductase (InhA) and Mycobacterium tuberculosis.

In an effort to produce new lead antimycobacterial compounds, herein we have reported the synthesis of a sequence of new pyrrolyl benzamide derivatives. The new chemical entities were screened to target enoyl-ACP reductase enzyme, which is one of the key enzymes of M. tuberculosis that are involved in type II fatty acid biosynthetic pathway. Compound 3q exhibited H-bonding interactions with Tyr158, Thr196 and co-factor NAD+ that binds the active site of InhA. All the pyrrolyl benzamide compounds were evaluated as inhibitors of M. tuberculosis H37Rv as well as inhibitors of InhA. Among them, few representative compounds were tested for mammalian cell toxicity on the human lung cancer cell-line (A549) and MV cell line that presented no cytotoxicity. Five of these compounds exhibited a good activity against InhA.

The CFTR gene mild variants poly-T, TG repeats and M470V detection in Indian men with congenital bilateral absence of vas deferens.

The aim of the study was to detect the frequency of the CFTR gene variants poly-T, TG repeats and c.1408A>G p.Met470Val (M470V) in Indian men with congenital bilateral absence of the vas deferens (CBAVD). Men diagnosed with CBAVD (n = 76), their female partners (n = 76) and healthy men from general population (n = 50) were recruited. Genomic DNA was isolated and the polymorphic regions of IVS9- c.1210-12T [5] and M470V were amplified using specific primers followed by Sanger's DNA sequencing. A statistically significant increase in the frequency of heterozygous IVS9- c.1210-12T [5] (39.4%) was observed in CBAVD men as compared to controls (14%). The allelic distribution of c.1210-12T [5], c.1210-12T [7] and c.1210-12T [9] in CBAVD men was 21%, 64.4% and 13% and that in healthy controls was 7%, 73% and 20% respectively. Longest TG repeat c.1210-34TG [13] was found in association with c.1210-12T [5] with an allelic frequency of 5.9% in CBAVD men. We found a significant association of c.1210-34TG [12]/c.1210-34TG [13] - c.1210-12[5] -V470 allele in CBAVD men. Twelve female partners harboured a heterozygous c.1210-12T [5] allele. The study emphasises the need to screen both partners for the polymorphisms M470V, poly-T, TG tract repeats in addition to population-specific known CFTR gene mutations.

Non-destructive evaluation of teeth restored with different composite resins using synchrotron based micro-imaging.

BACKGROUND: Application of high resolution synchrotron micro-imaging in microdefects studies of restored dental samples. OBJECTIVE: The purpose of this study was to identify and compare the defects in restorations done by two different resin systems on teeth samples using synchrotron based micro-imaging techniques namely Phase Contrast Imaging (PCI) and micro-computed tomography (MCT). With this aim acquired image quality was also compared with routinely used RVG (Radiovisiograph). METHODS: Crowns of human teeth samples were fractured mechanically involving only enamel and dentin, without exposure of pulp chamber and were divided into two groups depending on the restorative composite materials used. Group A samples were restored using a submicron Hybrid composite material and Group B samples were restored using a Nano-Hybrid restorative composite material. Synchrotron based PCI and MCT was performed with the aim of visualization of tooth structure, composite resin and their interface. RESULTS: The quantitative and qualitative comparison of phase contrast and absorption contrast images along with MCT on the restored teeth samples shows comparatively large number of voids in Group A samples. CONCLUSIONS: Quality assessment of dental restorations using synchrotron based micro-imaging suggests Nano-Hybrid resin restorations (Group B) are better than Group A.

Species identification of cattle and buffalo fat through PCR assay.

A method was standardized to isolate quality DNA from cattle and buffalo fat for species identification using QIAamp DNA stool mini kit. The quality of the DNA was sufficient enough to amplify universal primers viz., mt 12S rRNA and mt 16S rRNA, and species specific D loop primers for cattle and buffalo. The sensitivity of the PCR assay in the species specific D loop primer amplification was with a detection level of 0. 47 ng cattle DNA and 0.23 ng buffalo DNA in simplex and, 0. 47 ng cattle DNA and 0.12 ng buffalo DNA in duplex PCR. It is a potentially reliable method for DNA detection to authenticate animal fat.

Intramuscular delivery of heterodimeric IL-15 DNA in macaques produces systemic levels of bioactive cytokine inducing proliferation of NK and T cells.

Interleukin-15 (IL-15) is a common γ-chain cytokine that has a significant role in the activation and proliferation of T and NK cells and holds great potential in fighting infection and cancer. We have previously shown that bioactive IL-15 in vivo comprises a complex of the IL-15 chain with the soluble or cell-associated IL-15 receptor alpha (IL-15Rα) chain, which together form the IL-15 heterodimer. We have generated DNA vectors expressing the heterodimeric IL-15 by optimizing mRNA expression and protein trafficking. Repeated administration of these DNA plasmids by intramuscular injection followed by in vivo electroporation in rhesus macaques resulted in sustained high levels of IL-15 in plasma, with no significant toxicity. Administration of DNAs expressing heterodimeric IL-15 also resulted in an increased frequency of NK and T cells undergoing proliferation in peripheral blood. Heterodimeric IL-15 led to preferential expansion of CD8(+)NK cells, all memory CD8(+) T-cell subsets and effector memory CD4(+) T cells. Expression of heterodimeric IL-15 by DNA delivery to the muscle is an efficient procedure to obtain high systemic levels of bioactive cytokine, without the toxicity linked to the high transient cytokine peak associated with protein injection.

NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.

BACKGROUND: Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool 'HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. METHODS: We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a 'quick mode' to identify presence of HPV types and an 'integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. RESULTS: On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. CONCLUSIONS: HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.

Effect of three different pastes on remineralization of initial enamel lesion: an in vitro study.

OBJECTIVE: Dental caries in enamel is unique as enamel is both acellular and avascular. Fluoride is one of the most effective remineralizing agents in caries prevention. The purpose of the study was to assess whether nano-hydroxyapatite and CPP-ACP can be used as an alternative to fluoride for remineralization of early carious lesions. STUDY DESIGN: Initial artificial carious lesions were prepared in enamel with demineralization solution. The treatment materials used as remineralizing agents were Nano-hydroxyapatite (10%), CPP - ACP (10%), NaF (1000 ppm) and Deionized water (negative control). Surface microhardness (SMH) measurements were performed before/after demineralization and after 3, 6, 9 and 12 days of pH cycling and the percentage surface microhardness recovery (%SMHR) was calculated. The specimens were then examined by scanning electron microscope. RESULTS: Percentage surface microhardness recovery of nano-hydroxyapatite and fluoride was significantly greater than CPP - ACP and negative control. There was no significant difference of %SMHR between n-HA and fluoride at different time periods in the pH cycling. SEM analysis revealed n-HA particles were deposited on the demineralized enamel surface which formed a new surface layer. When observed under SEM CPP - ACP failed to show any significant surface remineralization while surface globular crystal depositions with multiple discrete porosities were evident with fluoride. CONCLUSION: It was concluded that nano-hydroxyapatite and fluoride had the potential to remineralize initial enamel lesions. CPP - ACP can be used as an effective adjunct to fluoride therapy but cannot be used as an alternative to fluoride.

Use of exhaled nitric oxide in children with bronchial asthma.

BACKGROUND: Inflammation is an important aspect of the pathophysiology of bronchial asthma and measurement of inflammatory markers of airways can aid in management. Nitric oxide measurement in exhaled breath is a non-invasive method of determining airway inflammation which can be used in assessing severity and response to treatment in children with bronchial asthma. METHODS: Thirty children in the age group 6-14 years with previously or newly diagnosed bronchial asthma reporting for the first time to a tertiary care hospital constituted the study group. Assessment was done by history, clinical examination, spirometry and measurement of fractional excretion of nitric oxide (FeNO) before commencement of treatment as per standard guidelines and on follow up at 2 to 4 weeks intervals for a minimum of three times. RESULTS: There was significant correlation between FeNO values, spirometry parameters and clinical profile in the first visit before the initiation of therapy. Children with higher FeNO in the first visit responded better to Inhaled Corticosteroids (ICS) with good clinical and spirometry responses and fall in FeNO on second visit. However, in subsequent visits no significant correlation was observed between clinical control, FeNO levels and spirometry. CONCLUSION: High FeNO values at first presentation could give us a clue as to whether or not a child would respond to ICS but FeNO monitoring may not be helpful in long term follow up as various other factors can affect its value.

Impact of maternal hepatitis B virus coinfection on mother-to-child transmission of HIV.

OBJECTIVES: Despite high hepatitis B virus (HBV) endemicity in various resource-limited settings (RLSs), the impact of maternal HIV/HBV coinfection on infant health outcomes has not been defined. We aimed to assess the prevalence of HBV coinfection among HIV-infected pregnant women and its impact on HIV transmission and infant mortality. METHODS: In this study, the seroprevalence of HBV coinfection was determined among HIV-infected pregnant women enrolled in the Six-Week Extended-Dose Nevirapine (SWEN) India trial. The impact of maternal HIV/HBV coinfection on mother-to-child transmission (MTCT) of HIV and infant mortality was assessed using univariate and multivariate logistic regression analysis. RESULTS: Among 689 HIV-infected pregnant Indian women, 32 (4.6%) had HBV coinfection [95% confidence interval (CI) 3.4%, 5.3%]. HBV DNA was detectable in 18 (64%) of 28 HIV/HBV-coinfected women; the median HBV viral load was 155 copies/mL [interquartile range (IQR) < 51-6741 copies/mL]. Maternal HIV/HBV coinfection did not increase HIV transmission risk [adjusted odds ratio (aOR) 1.06; 95% CI 0.30, 3.66; P = 0.93]. Increased odds of all-cause infant mortality was noted (aOR 3.12; 95% CI 0.67, 14.57; P = 0.15), but was not statistically significant. CONCLUSIONS: The prevalence of active maternal HBV coinfection in HIV-infected pregnant women in India was 4.6%. HIV/HBV coinfection was not independently associated with HIV transmission.

Bacterial penetration along different root canal fillings in the presence or absence of smear layer in primary teeth.

AIMS: To study the effect of the smear layer on the penetration of bacteria along different root canal fillings and to compare the sealing ability of new endodontic material Apexit plus as compared to Zinc Oxide Eugenol (ZOE) in primary teeth. STUDY DESIGN: A total of 60 human root segments were instrumented for endodontic treatment. Half of the sample size was irrigated with normal saline and in other half 3% NaOCl, 3% H2O2 and 17% EDTA was used alternatively as irrigant during instrumentation. The roots were rinsed thoroughly with distilled water and sterilized by autoclaving for 20 min at 121 +/- 2 degrees C. Roots with and without smear layer were obturated with Apexit plus, Zinc oxide eugenol. Following storage in humid conditions at 37 degrees C for 2 days, the specimens were mounted into a bacterial leakage test model for 180 days. RESULTS: At 180 days, there is statistically significant difference with a P value of < 0.05 among all groups except ZOE-smear and -nonsmear. In the presence of smear layer Apexit plus demonstrated more leakage. No leakage was observed in ZOE groups. ZOE demonstrated better sealing ability than Apexit plus. CONCLUSIONS: Removal of smear layer helps in better resistance to bacterial penetration along Apexit plus root canal fillings but no effect is seen along ZOE root canal fillings.

Preparation and storage stability of retort processed Chettinad chicken.

Chettinad chicken was prepared using boneless meat derived from spent hen and boiler breeder packed in retort pouches (250 g) and processed in retort at the product temperature of 121.1 °C and the corresponding F0 value of 5.2. The product was stored at ambient temperature (35 ± 2 °C) up to 180 days. The sensory scores for texture of the Chettinad chicken prepared from spent hen and broiler breeder meat decreased significantly however the scores were rated very acceptable even on 180th day. The thiobarbituric acid (TBA), tyrosine values and acid value increased gradually during storage but E. coli, Salmonella spp, Clostridium spp, Staphylococci spp, Streptococci spp, yeast and mould could not be detected during the entire storage period. The cost of production of Chettinad chicken (250 g) prepared from spent hen meat and broiler breeder meat was Rs.37 and Rs.50, respectively. It was concluded that the retort processed Chettinad chicken prepared from spent hen and broiler breeder meat can be safely stored up to 180 days at ambient temperature.

Validation of a Deep Learning Model for Detecting Chest Pathologies from Digital Chest Radiographs.

Purpose: Manual interpretation of chest radiographs is a challenging task and is prone to errors. An automated system capable of categorizing chest radiographs based on the pathologies identified could aid in the timely and efficient diagnosis of chest pathologies. Method: For this retrospective study, 4476 chest radiographs were collected between January and April 2021 from two tertiary care hospitals. Three expert radiologists established the ground truth, and all radiographs were analyzed using a deep-learning AI model to detect suspicious ROIs in the lungs, pleura, and cardiac regions. Three test readers (different from the radiologists who established the ground truth) independently reviewed all radiographs in two sessions (unaided and AI-aided mode) with a washout period of one month. Results: The model demonstrated an aggregate AUROC of 91.2% and a sensitivity of 88.4% in detecting suspicious ROIs in the lungs, pleura, and cardiac regions. These results outperform unaided human readers, who achieved an aggregate AUROC of 84.2% and sensitivity of 74.5% for the same task. When using AI, the aided readers obtained an aggregate AUROC of 87.9% and a sensitivity of 85.1%. The average time taken by the test readers to read a chest radiograph decreased by 21% (p < 0.01) when using AI. Conclusion: The model outperformed all three human readers and demonstrated high AUROC and sensitivity across two independent datasets. When compared to unaided interpretations, AI-aided interpretations were associated with significant improvements in reader performance and chest radiograph interpretation time.

Correlation of clinical and histopathological classification of leprosy in post elimination era.

Clinical and histopathological correlative study was carried out in 171 cases of leprosy using the criteria laid down by Ridley and Jopling. There was male preponderance in the study with majority of patients (35.7%) in the age goup of 21-30 years. The overall concordance between the clinical and histopathological diagnosis was 57.3%. Maximum concordance was seen in the polar ends of the spectrum with 76.9% in LL and 75.0% in TT. The concordance rate was lower in the borderline groups with 57.3% in BT, 40.0% in BL and least concordance of 16.7% in BB. However the concordance for IL was higher than the borderline groups with 66.7%. Cases in borderline group are in continuously changing immunological spectrum. Histological classification because of its definitive features gives a better indication than clinical classification for any recent shift of a case in the spectrum. Therefore skin biopsy should be done in all cases for correct classification of leprosy.

Concomitant pulmonary disease is common among patients with extrapulmonary TB.

BACKGROUND: Microbiologic screening of extrapulmonary TB (EPTB) patients could inform recommendations for aerosol precautions and close contact prophylaxis. However, this is currently not routinely recommended in India. Therefore, we estimated the proportion of Indian patients with EPTB with microbiologic evidence of pulmonary TB (PTB).METHODS: We characterized baseline clinical, radiological and sputum microbiologic data of 885 adult and pediatric TB patients in Chennai and Pune, India, between March 2014 and November 2018.RESULTS: Of 277 patients with EPTB, enhanced screening led to the identification of 124 (45%) with concomitant PTB, including 53 (19%) who reported a cough >2 weeks; 158 (63%) had an abnormal CXR and 51 (19%) had a positive sputum for TB. Of 70 participants with a normal CXR and without any cough, 14 (20%) had a positive sputum for TB. Overall, the incremental yield of enhanced screening of patients with EPTB to identify concomitant PTB disease was 14% (95% CI 12-16).CONCLUSIONS: A high proportion of patients classified as EPTB in India have concomitant PTB. Our results support the need for improved symptom and CXR screening, and recommends routine sputum TB microbiology screening of all Indian patients with EPTB.

A study on pulmonary manifestations in patients with malaria from northwestern India (Bikaner).

BACKGROUND & OBJECTIVES: Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) are responsible for most of the global burden of malaria. With changing spectrum of clinical presentation in malaria, pulmonary system involvement has always been under diagnosed. The present study was planned to estimate the pulmonary system involvement in patients with malaria from north- western India (Bikaner). STUDY DESIGN & DESCRIPTION OF THE PATIENTS: Our study was conducted during 2007 to 2009 in 200 cases of severe malaria [Pf , Pv, and mixed (Pf + Pv)] with pulmonary involvement. It included adult patients of both sexes (145 males and 55 females) belonging to all age groups. The diagnosis of Pf and Pv was confirmed by demonstrating asexual form of parasites in peripheral blood smear and OptiMal test. MAIN OUTCOME MEASURES: Pulmonary involvement was observed in 30% (60/200) patients among which cough in 24% , dyspnea in 12%, acute respiratory distress syndrome (ARDS) in 7% , bronchitis in 3% and pneumonia in 1.5% were the major clinical manifestations of malaria. Metabolic acidosis and low oxygen saturation was observed in 7% patients. Chest X- ray abnormality in 11.5% patients, 7% had bilateral infiltrates, 1.5% had inflammatory patch and 3% had findings suggestive of bronchitis. Spirometry findings showed 17% patients had early small airway obstruction. All the patients with ARDS had poor disease outcome. RESULTS & CONCLUSION: Our results suggest that pulmonary system involvement was observed in patients infected with Pf and Pv. If these clinical presentations are ignored, it may lead to delay in diagnosis and can alter the outcome and prognosis of the disease. Therefore, early diagnosis of malaria induced ARDS can significantly affect the outcome.

Efficacy of modified cell block cytology compared to fine needle aspiration cytology for diagnostic oral cytopathology.

Cell blocks and fine needle aspirations can be used for cytopathological diagnosis. Conventional fine needle aspiration smears provide limited material for diagnosis. The cell block technique provides more tissue, which improves diagnostic accuracy. We compared a modified cell block cytology to fine needle aspiration for providing optimal preservation of histochemical and immunocytochemical properties. We used 30 fine needle aspirates from oral lesions in two groups: group 1, fine needle aspiration cytology; group 2, cell block cytology. Smears of fine needle aspirates were stained with Papanicolaou. For the modified cell block technique, aspirated material was centrifuged to create a cell pellet, which then was fixed with Nathan alcohol formalin substitute. After routine histopathological processing, cell pellets were embedded in paraffin, then sectioned and stained with hematoxylin and eosin. Sections were compared to Papanicolaou stained smears of fine needle samples. Cellular morphology and staining quality of modified cell block samples were superior to fine needle aspiration cytology; both methods exhibited distinct nuclear morphology. Modified cell blocks provide excellent cytopathologic features compared to fine needle aspiration cytology.

Measuring TB drug levels in the hair in adults and children to monitor drug exposure and outcomes.

INTRODUCTION: Testing for anti-TB drugs in small hair samples may serve as a non-invasive tool to measure cumulative drug exposure and/or adherence, as these determine treatment success. We aimed to assess how well hair assays of TB drugs predict TB treatment outcomes.METHODS: A small thatch of hair, ~30 strands, was cut from the occipital region in adults and children from a prospective TB cohort in India. Isoniazid (INH), acetyl-INH and pyrazinamide (PZA) were extracted from the hair samples and quantified using liquid-chromatography-tandem mass spectrometry. The relationship between drug concentrations in hair and time to unfavourable outcomes was assessed using Cox-proportional hazards regression models.RESULTS: A two-fold increase in hair acetyl-INH concentrations in the 264 participants in our cohort with hair assays for TB drugs indicated a lower hazard of unfavourable TB treatment outcomes (aHR 0.67, 95%CI 0.44-1.02) and TB treatment failure (aHR 0.65, 95%CI 0.42-1.01). Higher summed concentrations (a summed measure of INH and acetyl-INH) indicated a lower hazard of treatment failure (aHR 0.69, 95%CI 0.45-1.05)CONCLUSION: Hair levels of INH and its metabolite may predict TB treatment outcomes, indicating the potential utility of this measure to assess and optimise TB treatment outcomes.