Comparison of Manual and Automated Nucleic Acid (RNA) Extraction Methods for the Detection of SARS-CoV-2 by qRT-PCR.

Objectives During the COVID-19 pandemic, several laboratories used different RNA extraction methods based on the resources available. Hence this study was done to compare the Ct values in qRT-PCR, time taken (sample processing-loading to PCR), manpower requirement, and cost of consumables between manual and automated methods. Materials and methods A cross-sectional study was done on 120 nasopharyngeal/oropharyngeal swabs received in VRDL for RT-PCR testing. Based on the results of automated RNA extraction (Genetix, HT 96 Purifier) and RT-PCR (Trivitron PCR Kit) detecting E gene (screening) and ORF gene (confirmatory), the division into Group- I (Ct 15-22), Group- II (Ct 23-29), Group-III (Ct 30-36) and Group-IV (Ct >36) was done. Manual RNA extraction was done using magnetic beads (Lab system, Trivitron). Statistical analysis Data were analyzed by SPSS 19.0 version software. Ct values obtained in the two methods were compared by paired t-test, GroupWise. Z test was used to compare the other parameters. Results The difference in Ct values for target genes was statistically significant (p<0.05) in Group-I to III; however, no variation in result interpretation. The difference in time, manpower, and cost were statistically significant (p<0.05). The manual method required twice more manpower; 40 minutes more time & automated method cost 3.5 times more for consumables. Conclusion The study showed that RNA yield was better with automated extraction in comparison to manual extraction. The samples extracted by the automated method detected the virus at a lower Ct range by PCR than the manual method. Automated method processed samples in less time and with less manpower. Considering the cost factor, manual extraction can be preferred in resource-limited settings as there was no difference in the results of the test. The manual method requires more hands-on time with potential chances of cross-contamination and technical errors.

Nanosynthesis by atmospheric arc discharges excited with pulsed-DC power: a review.

Plasma technology is actively used for nanoparticle synthesis and modification. All plasma techniques share the ambition of providing high quality, nanostructured materials with full control over their crystalline state and functional properties. Pulsed-DC physical/chemical vapour deposition, high power impulse magnetron sputtering, and pulsed cathodic arc are consolidated low-temperature plasma processes for the synthesis of high-quality nanocomposite films in vacuum environment. However, atmospheric arc discharge stands out thanks to the high throughput, wide variety, and excellent quality of obtained stand-alone nanomaterials, mainly core-shell nanoparticles, transition metal dichalcogenide monolayers, and carbon-based nanostructures, like graphene and carbon nanotubes. Unique capabilities of this arc technique are due to its flexibility and wide range of plasma parameters achievable by modulation of the frequency, duty cycle, and amplitude of pulse waveform. The many possibilities offered by pulsed arc discharges applied on synthesis of low-dimensional materials are reviewed here. Periodical variations in temperature and density of the pulsing arc plasma enable nanosynthesis with a more rational use of the supplied power. Parameters such as plasma composition, consumed power, process stability, material properties, and economical aspects, are discussed. Finally, a brief outlook towards future tendencies of nanomaterial preparation is proposed. Atmospheric pulsed arcs constitute promising, clean processes providing ecological and sustainable development in the production of nanomaterials both in industry and research laboratories.

SARS-CoV-2 seroprevalence in the city of Hyderabad, India in early 2021

BackgroundCOVID-19 emerged as a global pandemic in 2020, rapidly spreading to most parts of the world. The proportion of infected individuals in a population can be reliably estimated via sero-surveillance, making it a valuable tool for planning control measures. We conducted a serosurvey study to investigate SARS-CoV-2 seroprevalence in the urban population of Hyderabad at the end of the first wave of infections. MethodsThe cross-sectional survey conducted in January 2021 included males and females aged 10 years and above, selected by multi-stage random sampling. 9363 samples were collected from 30 wards distributed over 6 zones of Hyderabad and tested for antibodies against SARS-CoV-2 nucleocapsid antigen. ResultsOverall seropositivity was 54.2%, ranging from 50-60% in most wards. Highest exposure appeared to be among 30-39y and 50-59y olds, with women showing greater seropositivity. Seropositivity increased with family size, with only marginal differences among people with varying levels of education. Seroprevalence was significantly lower among smokers. Only 11% of the survey subjects reported any COVID-19 symptoms, while 17% had appeared for Covid testing. ConclusionOver half the citys population was infected within a year of onset of the pandemic. However, [~]46% people were still susceptible, contributing to subsequent waves of infection. Highlights National level serosurveys under-estimate localised prevalence in dense urban areas SARS-CoV-2 seroprevalence in Hyderabad city was 54.2% after the first wave A large proportion of the population remains at risk over a year into the pandemic

Transcranial approach for pituitary adenomas - An evaluation of surgical approaches over two decades and factors influencing peri-operative morbidity.

PURPOSE: Transcranial surgery(TCS) for pituitary adenoma(PA) is mostly reserved for lesions with widespread extensions. We sought to analyse the intraoperative challenges, morbidity and the factors associated with morbidity of transcranial approaches, in a large series from a tertiary neurosurgical institute. METHODS: We retrospectively evaluated 137 patients who underwent TCS for PA in our institute. The details of their clinical features, imaging, operative and peri-operative events and complications were collected and analysed. The factors associated with morbidity were evaluated. RESULTS: The mean age of the cohort was 40.86 ± 13.35 years. 21 (15.3%) patients developed significant post-operative hematoma, out of which 7 patients (5.1%) required re-exploration. Post-operative diabetes insipidus was noted in 45 patients (32.84%), while SIADH was noted in 10 patients (7.35%). Other complications were cranial nerve palsy in 14 patients (10.2%), visual deterioration in 7 patients (5.1%). Neither tumour characteristics nor the choice of approach was associated with occurrence of post op hematoma. SIADH was significantly associated with patients with tumours involving cavernous sinus (p = 0.019) and subfrontal extension (p = 0.031). Patients with post-operative hematoma had significantly higher incidence of post-op DI (57.1% vs 28.7%; p = 0.021), while similar correlation was not noticed with SIADH (4.7 vs 7.8%). CONCLUSION: TCS plays a distinct, albeit a small role in surgical management of pituitary adenoma. Tumour related or approach related factors are not significantly associated with the incidence of hematoma. Post-operative hematoma significantly influences the incidence of DI. A proper and judicious selection of approach and meticulous surgical technique should result in a reduction in associated morbidity and mortality.

An absolute sodium abundance for a cloud-free 'hot Saturn' exoplanet.

Broad absorption signatures from alkali metals, such as the sodium (Na I) and potassium (K I) resonance doublets, have long been predicted in the optical atmospheric spectra of cloud-free irradiated gas giant exoplanets1-3. However, observations have revealed only the narrow cores of these features rather than the full pressure-broadened profiles4-6. Cloud and haze opacity at the day-night planetary terminator are considered to be responsible for obscuring the absorption-line wings, which hinders constraints on absolute atmospheric abundances7-9. Here we report an optical transmission spectrum for the 'hot Saturn' exoplanet WASP-96b obtained with the Very Large Telescope, which exhibits the complete pressure-broadened profile of the sodium absorption feature. The spectrum is in excellent agreement with cloud-free, solar-abundance models assuming chemical equilibrium. We are able to measure a precise, absolute sodium abundance of logεNa = [Formula: see text], and use it as a proxy for the planet's atmospheric metallicity relative to the solar value (Zp/Zʘ = [Formula: see text]). This result is consistent with the mass-metallicity trend observed for Solar System planets and exoplanets10-12.

Helium in the eroding atmosphere of an exoplanet.

Helium is the second-most abundant element in the Universe after hydrogen and is one of the main constituents of gas-giant planets in our Solar System. Early theoretical models predicted helium to be among the most readily detectable species in the atmospheres of exoplanets, especially in extended and escaping atmospheres 1 . Searches for helium, however, have hitherto been unsuccessful 2 . Here we report observations of helium on an exoplanet, at a confidence level of 4.5 standard deviations. We measured the near-infrared transmission spectrum of the warm gas giant 3 WASP-107b and identified the narrow absorption feature of excited metastable helium at 10,833 angstroms. The amplitude of the feature, in transit depth, is 0.049 ± 0.011 per cent in a bandpass of 98 angstroms, which is more than five times greater than what could be caused by nominal stellar chromospheric activity. This large absorption signal suggests that WASP-107b has an extended atmosphere that is eroding at a total rate of 1010 to 3 × 1011 grams per second (0.1-4 per cent of its total mass per billion years), and may have a comet-like tail of gas shaped by radiation pressure.

Recent Advances and Structural Features of Enoyl-ACP Reductase Inhibitors of Mycobacterium tuberculosis.

Mycobacterium tuberculosis enoyl-ACP reductase (InhA) has been validated as a promising target for antitubercular agents. Isoniazid (INH), the most prescribed drug to treat tuberculosis (TB), inhibits a NADH-dependent InhA that provides precursors of mycolic acids, which are components of the mycobacterial cell wall. It is a pro-drug that needs activation to form the inhibitory INH-NAD adduct by KatG coding for catalase-peroxidase. The INH resistance of M. tuberculosis is caused by mutations in KatG, which may lead to multidrug-resistant TB (MDR-TB). Hence, there is a need for new drugs that can combat MDR-TB. The rationale for the development of new drugs to combat MDR-TB strains is the design of InhA inhibitors that can bypass bioactivation by KatG. In the present review, special attention was paid to discuss the chemical nature and recent developments of direct InhA inhibitors. The InhA inhibitors reported here have significant inhibitory effects against Mtb InhA. The diphenyl ether derivatives have shown slow onset, a tight-binding mechanism, and high affinity at the InhA active site. However, some of the diphenyl ethers have significant in vitro efficacy, which fails to transform into in vivo efficacy. Among the InhA inhibitors, 4-hydroxy-2-pyridones have emerged as a new chemical class with significant InhA inhibitory activity and better pharmacokinetic parameters when compared to diphenyl ethers.

A Case of Surgical Site Infection Caused by Mycobacterium fortuitum, following Herniorrhaphy.

Rapidly Growing Mycobacteria (RGM) are opportunistic pathogens found in the environment. Mycobacterium fortuitum, M. chelonae and M.abscessus are the important human pathogens of this group. They cause wound infections, disseminated cutaneous disease, pulmonary infection in patients with cystic fibrosis or bronchiectasis, bone and joint infections and keratitis. Infections due to these Non-Tuberculous Mycobacteria (NTM) are increasingly reported. Post laparoscopic wound infections, mesh site infections and other surgical site infections due to M. fortuitum and M. chelonae have been reported. Usually wound infections due to atypical mycobacteria have delayed onset and do not respond to conventional antibiotics. Identification of RGM can be done by a set of cumbersome biochemical tests, High Performance Liquid Chromatography (HPLC), molecular methods using DNA probes or by Polymerase Chain Reaction (PCR). We here report a case of post-herniorrhaphy wound infection due to M. fortuitum which was identified by molecular method (HAIN mycobacterial species system). This case report underscores the importance of examining Ziehl-Neelsen (ZN) stain of all exudates with sterile culture on day one for non fastidious bacteria. Timely identification can lead to prompt therapy of patients preventing further complications.

Structural insights of PA-824 derivatives: ligand-based 3D-QSAR study and design of novel PA824 derivatives as anti-tubercular agents.

With the purpose of designing novel chemical entities with improved inhibitory potencies against drug-resistant Mycobacterium tuberculosis, the 3D- quantitative structure-activity relationship (QSAR) studies were carried out on biphenyl analogs of the tuberculosis (TB) drug, PA-824. Anti-mycobacterial activity (MABA) was considered for the 3D-QSAR studies using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. The best CoMFA and CoMSIA models were found statistically significant with cross-validated coefficients (q(2)) of 0.784 and 0.768, respectively, and conventional coefficients (r(2)) of 0.823 and 0.981, respectively. The cross-validated and the external validation results revealed that both the CoMFA and CoMSIA models possesses high accommodating capacities and they would be reliable for predicting the pMIC values of new PA-824 derivatives. Based on the models and structural insights, a series of new PA-824 derivatives were designed and the anti-mycobacterial activities of the designed compounds were predicted based on the best 3D-QSAR model. The predicted data results suggest the designed compounds are more potent than existed ones.

Small field dosimetry and analysis of flattening filter free beams in true beam system.

AIM OF STUDY: The purpose of this study was to report the dosimetric characteristics of the small fields in flattening filter free (FFF) beams (output measurements, profile analysis, surface dose and consistency) generated by medical linear accelerator and its variation with respect to flattened beams (FB). MATERIALS AND METHODS: Surface doses were obtained for field sizes 1 × 1-40 × 40 cm(2). Field width and penumbra were analyzed for field sizes 1 × 1-40 × 40 cm(2). To take output factors for small fields, diode and micro chamber were used and data was taken at a source-to-surface distance (SSD) and extended SSD. Consistency checked for the dosimetric data for 1 year. RESULTS: Surface doses were higher in FFF compared with FB up to 20 × 20 cm(2) field size. Measured field sizes were slightly lesser in FFF and penumbra values were increased with respect to field size in both FB and FFF. For small fields, diode values have shown more promising results than micro chamber. Small field output measurements at nominal SSD and extended SSD were well in agreement with each other. FFF beams showed good data consistency in 1 year duration. CONCLUSION: Small field dosimetry, surface dose, profile analysis and consistency of FFF beams in FFF photon beams were derived and data shown good consistency during 1 year duration.

COMPOSITIONAL DIVERSITY IN THE ATMOSPHERES OF HOT NEPTUNES, WITH APPLICATION TO GJ 436b.

Neptune-sized extrasolar planets that orbit relatively close to their host stars - often called "hot Neptunes" - are common within the known population of exoplanets and planetary candidates. Similar to our own Uranus and Neptune, inefficient accretion of nebular gas is expected produce hot Neptunes whose masses are dominated by elements heavier than hydrogen and helium. At high atmospheric metallicities of 10-10,000× solar, hot Neptunes will exhibit an interesting continuum of atmospheric compositions, ranging from more Neptune-like, H2-dominated atmospheres to more Venus-like, CO2-dominated atmospheres. We explore the predicted equilibrium and disequilibrium chemistry of generic hot Neptunes and find that the atmospheric composition varies strongly as a function of temperature and bulk atmospheric properties such as metallicity and the C/O ratio. Relatively exotic H2O, CO, CO2, and even O2-dominated atmospheres are possible for hot Neptunes. We apply our models to the case of GJ 436b, where we find that a CO-rich, CH4-poor atmosphere can be a natural consequence of a very high atmospheric metallicity. From comparisons of our results with Spitzer eclipse data for GJ 436b, we conclude that although the spectral fit from the high-metallicity forward models is not quite as good as the best fit obtained from pure retrieval methods, the atmospheric composition predicted by these forward models is more physically and chemically plausible in terms of the relative abundance of major constituents. High-metallicity atmospheres (orders of magnitude in excess of solar) should therefore be considered as a possibility for GJ 436b and other hot Neptunes.

The demonstration of extension of high-grade glioma beyond magnetic resonance imaging defined edema by the use of (11) C-methionine positron emission tomography.

The use of magnetic resonance imaging (MRI) is the current standard for the delineation of target volumes for high-grade gliomas (HGG). While the peritumoral edema as per T2-weighted (T2W) imaging is utilized as basis to delineate the initial borders of the clinical target volume (CTV), those areas enhancing on T1-weighted (T1W) images with gadolinium contrast (T1-Gd) are considered for treatment with further boost. However, recent data has emerged concerning the use of positron emission tomography (PET) with 11 C-methionine, which seemingly provides additional information beyond MRI. We present the case of a gentleman with an inoperable HGG which was imaged with 11 C-methionine-PET ( 11 C-MET-PET)/CT as well as MRI as part of the radiotherapy treatment planning (RTP) process. The differences noted between the MRI and the PET defined volumes are presented. This being a patient who was not operated, the potentially confounding issue of surgery-induced PET-avidity is absent.

CHEMICAL CONSEQUENCES OF THE C/O RATIO ON HOT JUPITERS: EXAMPLES FROM WASP-12b, COROT-2b, XO-1b, AND HD 189733b.

Motivated by recent spectroscopic evidence for carbon-rich atmospheres on some transiting exo-planets, we investigate the influence of the C/O ratio on the chemistry, composition, and spectra of extrasolar giant planets both from a thermochemical-equilibrium perspective and from consideration of disequilibrium processes like photochemistry and transport-induced quenching. We find that although CO is predicted to be a major atmospheric constituent on hot Jupiters for all C/O ratios, other oxygen-bearing molecules like H2O and CO2 are much more abundant when C/O < 1, whereas CH4, HCN, and C2H2 gain significantly in abundance when C/O > 1. Other notable species like N2 and NH3 that do not contain carbon or oxygen are relatively unaffected by the C/O ratio. Disequilibrium processes tend to enhance the abundance of CH4, NH3, HCN, and C2H2 over a wide range of C/O ratios. We compare the results of our models with secondary-eclipse photometric data from the Spitzer Space Telescope and conclude that (1) disequilibrium models with C/O ~ 1 are consistent with spectra of WASP-12b, XO-1b, and CoRoT-2b, confirming the possible carbon-rich nature of these planets, (2) spectra from HD 189733b are consistent with C/O ≲ 1, but as the assumed metallicity is increased above solar, the required C/O ratio must increase toward 1 to prevent too much H2O absorption, (3) species like HCN can have a significant influence on spectral behavior in the 3.6 and 8.0 µm Spitzer channels, potentially providing even more opacity than CH4 when C/O > 1, and (4) the very high CO2 abundance inferred for HD 189733b from near-infrared observations cannot be explained through equilibrium or disequilibrium chemistry in a hydrogen-dominated atmosphere. We discuss possible formation mechanisms for carbon-rich hot Jupiters, including scenarios in which the accretion of CO-rich, H2O-poor gas dominates the atmospheric envelope, and scenarios in which the planets accrete carbon-rich solids while migrating through disk regions inward of the snow line. The C/O ratio and bulk atmospheric metallicity provide important clues regarding the formation and evolution of the giant planets.

Biodegradation of phenanthrene with biosurfactant production by a new strain of Brevibacillus sp.

In this work, a phenanthrene-degrading bacterial strain was isolated by enrichment method from hydrocarbon contaminated sludge samples and identified as Brevibacillus sp. PDM-3 based on morphological, biochemical, chemotaxonomic (FAMEs analysis) and molecular (16S rDNA sequencing) analysis. Growth parameters for efficient degradation of phenanthrene such as nutrient medium, pH, temperature, rpm and inoculum size were standardized and 93% of phenanthrene was degraded in 6 days as analysed by HPLC. The bacterial strain PDM-3 also has the ability to produce biosurfactant during phenanthrene degradation as detected by the surface tension measurements of the culture supernatant and the emulsification index (EI24). The biosurfactant was identified by its functional groups through FT-IR spectroscopy. Phenanthrene degradation and biosurfactant production are associated with each other and can be used in environmental biotechnology. Further, the strain has the ability to degrade other PAHs such as anthracene and fluorene by utilizing them as sole carbon and energy source.

Effect of maternal fluoride exposure on developing CNS of rats: protective role of Aloe vera, Curcuma longa and Ocimum sanctum.

Fluoride is toxic to neuronal development and its excessive intake during pregnancy cause adverse effects on neonatal development. The present study examined the presence of oxidative stress during maternal exposure of fluoride and the therapeutic strategy of Aloe vera, Curcuma longa and Ocimum sanctum extracts in functional prevention of fluoride led oxidative stress. The pregnant Wistar rats were exposed to 100 ppm fluoride in drinking water and pups born to them were supplemented with phytoextracts daily. On 21st postpartum day, the pups were sacrificed to analyse fluoride and oxidative stress markers. Fluoride exposure significantly increased its accumulation, lipid peroxidation and decreased the activities of catalase, superoxide dismutase, glutathione peroxidase, glutathione-S-transferase and glutathione levels in discrete regions of the central nervous system (CNS) of pups indicating oxidative stress and inhibited antioxidant defense. The results implied the vulnerability of developing CNS to fluoride toxicity. On phytoextract supplementation, the oxidant devastation was suppressed by regaining antioxidant homeostasis near normal level proving efficacy and therapeutic strategy. Among the phytoextracts supplemented the Ocimum sanctum is found to be more effective.