Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics.

Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3' and 5' flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user's query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.

The role of transportation in developing the tourism sector at high altitude destination, Kinnaur.

As a supporting factor, transportation is an important element of destination image that provides a base for the successful tourism industry. It is like the blood vessels of an area and is considered a determinant in developing a tourist destination. The article aims to characterize the status or problem of transportation accessibility in Kinnaur. GARMIN hand GPS (Global Positioning System) has been used to identify the damaged roads from their start to endpoints. In addition, a simple random sample technique has been used to register the opinion of 280 tourists about the transport facilities. Study results suggest that the bad condition of National Highway-22 is one of the barriers to tourism development in Kinnaur. There were no significant differences found between the selected destinations. Overall, the district headquarters, Kalpa, has been perceived significantly higher agreements by tourists. The government should ensure that the Border Road Organization, the organization entrusted with the responsibility of construction and maintenance of roads in international border areas, has sufficient resources to invest in transport development and its maintenance.

Manganese substitution induced magnetic transformation and magnetoelectricity in SrFe12O19.

In this study, manganese substituted strontium hexaferrite (SrFe12-xMnxO19; x = 0, 3, 5, and 7) prepared by the sol-gel auto-combustion method are studied. We observed that the substituted Mn preferentially goes to the 2a and 12k sites of Fe. Raman modes related to the 12k site suggest the stiffening of the lattice. The transformation of the grain's shape from hexagonal (x = 0 and 3) to rhombohedral (x = 7) was observed, as shown in the micrographs obtained from FESEM. The thermomagnetic curves show the shift of TC to lower temperatures with the increase in the Mn content. From x = 5 onwards, the growth of another magnetic phase (FiM2) of lower coercivity apart from the parent phase (FiM1) of higher coercivity is seen. The FiM2 phase was found to increase with the Mn content in the sample (16.4(3)% for x = 5 but 66.2(5)% for x = 7). Although the magnetization for both FiM1 and FiM2 decreases with the increase in temperature, both magnetic phases behave in contrast to each other for x = 5 and x = 7. The study suggests a transformation of the compound from high magnetic anisotropy (x = 0) to low magnetic anisotropy (x = 7). The x = 5 composition sample displays the highest value of the first-order ME coefficient (0.83(2) mV × cm-1 × Oe-1). The observed value for x = 5 composition is ∼2.5 times higher than that of the parent x = 0 composition sample (0.33(2) mV × cm-1 × Oe-1). The studies thus suggest that the x = 5 composition is one of the viable candidates for magnetoelectric applications.

Lunar lenses - Acquired lens colobomas.

Acquired lens colobomas secondary to ocular surgeries are scarcely described in the literature. We describe two cases of acquired lens coloboma in two infants with glaucoma who underwent ocular surgery. The coloboma in the first case was likely because of direct trauma to the lens zonules during an optical iridectomy with a vitrectomy cutter, resulting in localized loss of zonules and consequently localized lens coloboma. The coloboma in the second case was noticed during examination under anesthesia after scleral buckling and cryopexy for retinal detachment. The cause for coloboma development in this case could be disruption of the lens zonules because of stretching of the globe after scleral buckle surgery or because of injury to zonules during scleral buckling and the cryopexy procedure.

In-vitro antiviral activity of Carica papaya formulations against dengue virus type 2 and chikungunya viruses.

Dengue and chikungunya are diseases of global health significance and currently, no antivirals are available to treat these arboviral diseases. Carica papaya leaves extract is traditionally used to treat thrombocytopenia in patients infected with the dengue virus. The current study was undertaken to study the antiviral activity of commercially available Carica papaya leaves extract (CPLE) based products and CPLE prepared in four formulations against dengue virus type 2 (DENV-2) and chikungunya virus (CHIKV). Maximum nontoxic concentrations of the commercially available CPLE based products and CPLE based formulations (Carica papaya leaves in powder form, Carica papaya leaves in lyophilized form, Carica papaya leaves based silver nanoparticles and supercritical fluid extract of Carica papaya leaves) were used for screening the antiviral activity. The antiviral activity against DENV-2 and CHIKV were assessed post infection using focus forming unit assay. Effective formulations were tested under different conditions i.e. pretreatment, cotreatment and posttreatment. The virus output after treatment was assessed by real-time RT-PCR, immunofluorescence assay and focus forming unit assay. The results revealed Carica papaya leaves based silver nanoparticles and supercritical fluid extract of Carica papaya leaves formulations showed significant inhibition in case of DENV while papaya leaves in powder form showed significant reduction in case of CHIKV. This study demonstrates the antiviral activity of CPLE formulations against DENV-2 and CHIKV infection in in-vitro system and needs further validation in in-vivo models.

Findings of second multicentric follow-up serosurvey among Health Care Workers in government hospitals.

Background: The change in serological status of community may be used as input for guiding the public health policy. Hence, the present study was conducted to determine change in seroprevalence of COVID-19 among healthcare workers (HCWs). Methods: From the baseline multicentric study sample, a subsample was followed up, and a seroepidemiological study was conducted among them between 6 and 22 weeks after the second dose of the vaccination. Multistage population proportion to size sampling was performed for the selection of subsample of HCWs. The serosurvey was conducted using the enzyme-linked immunosorbent assay-based IgG antibody test (COVID KAVACH). Results: Follow-up serological testing was done in subsample of 1122 participants of original 3253 participants. The mean age of the participants was 34.6 (8.13) years. A total of 300 (26.7%) participants were females. The seroprevalence was 78.52, (95%CI:76-80.1). Among those who were seronegative at initial test, 708 (77.04%) were seroconverted. Those who were not seroconverted (241 (21.5%)) have longer duration from the second dose of the vaccination (93 (31.4) vs. 56 (38.4); p value < 0.001). The COVID-19 infection was significantly associated with seropositive status and being a medical staff was associated with remaining seronegative on follow-up. The higher age (≥50 years) was found to be significantly associated with seroreversion. Conclusion: Four in five HCWs had detectable antibodies. Seroepidemiological studies carry vital information to control the public health response in the course of the pandemic. The study can also further help as a platform to study the seroconversion and effect of vaccination among HCWs for newer variants of SARS-CoV-2.

Epidemiological analysis of SARS-COV-2 B.1.617.2 (delta variant) transmission in an educational institute.

Background: Despite having an effective COVID-19 vaccine, the COVID-19 pandemic is far from over and the delta variant continues to cause havoc across several continents. The present study was conducted to analyze and describe the occurrence of COVID-19 cases among completely vaccinated individuals. Methods: In an educational institute in Western Maharashtra, we analyzed a cluster of RTPCR positive COVID-19 cases among fully vaccinated students which occurred in 12 days. The cases were linked to a series of curricular and co-curricular events in the institute. A detailed epidemiological investigation and genome sequencing of cases were conducted. IgG antibodies against S1 protein of novel SARS-CoV-2 were estimated for cases and age, sex, and vaccination status matched controls. Results: All 37 identified cases were mild COVID. 188 high risk (HR) contacts of the cases were identified. The overall secondary attack was 9.5%. Out of 31 cases and 50 controls, 09 (29%) cases and 08 (16%) controls were found to have IgG antibodies against S1 protein of novel SARS-CoV-2 titer of more than 60 U/ml. Whole-genome sequencing of 15 samples of the cluster showed the presence of the Delta variant of SARS-CoV-2. No correlation was observed between Ct value and IgG S1 antibody titers. Conclusion: The study provides significant evidence that only vaccination alone does not completely protect against SARS-CoV-2 B.1.617.2 (Delta) variant infection. An all-encompassing multicomponent strategy involving implementation of NPIs, robust contact tracing, early identification and isolation of cases, and high vaccination coverage is the way forward for the prevention of COVID-19.

Post-trabeculectomy early bleb localization mimicking a 'ring of steel'.

A 54-year-old-man underwent trabeculectomy with mitomycin-C (0.02%). At 4-week follow-up, there was an elevated, well-circumscribed bleb with raised intra-ocular pressure (IOP) of 32-mmHg, with a classic "ring of steel" appearance, typically seen in a tenon's cyst. A sub-tenon needle revision re-established aqueous flow. Two weeks later, the IOP was 8-mmHg without any anti-glaucoma medications. A diffuse well formed bleb was noted. Careful ocular examination helps to identify early post-operative localized bleb that may appear like a "ring of steel" but can be managed by needling, unlike a tenon's cyst, which would require more extensive intervention.

Analysis and Evaluation of a Deep Learning Reconstruction Approach with Denoising for Orthopedic MRI.

PURPOSE: To evaluate two settings (noise reduction of 50% or 75%) of a deep learning (DL) reconstruction model relative to each other and to conventional MR image reconstructions on clinical orthopedic MRI datasets. MATERIALS AND METHODS: This retrospective study included 54 patients who underwent two-dimensional fast spin-echo MRI for hip (n = 22; mean age, 44 years ± 13 [standard deviation]; nine men) or shoulder (n = 32; mean age, 56 years ± 17; 17 men) conditions between March 2019 and June 2020. MR images were reconstructed with conventional methods and the vendor-provided and commercially available DL model applied with 50% and 75% noise reduction settings (DL 50 and DL 75, respectively). Quantitative analytics, including relative anatomic edge sharpness, relative signal-to-noise ratio (rSNR), and relative contrast-to-noise ratio (rCNR) were computed for each dataset. In addition, the image sets were randomized, blinded, and presented to three board-certified musculoskeletal radiologists for ranking based on overall image quality and diagnostic confidence. Statistical analysis was performed with a nonparametric hypothesis comparing derived quantitative metrics from each reconstruction approach. In addition, inter- and intrarater agreement analysis was performed on the radiologists' rankings. RESULTS: Both denoising settings of the DL reconstruction showed improved edge sharpness, rSNR, and rCNR relative to the conventional reconstructions. The reader rankings demonstrated strong agreement, with both DL reconstructions outperforming the conventional approach (Gwet agreement coefficient = 0.98). However, there was lower agreement between the readers on which DL reconstruction denoising setting produced higher-quality images (Gwet agreement coefficient = 0.31 for DL 50 and 0.35 for DL 75). CONCLUSION: The vendor-provided DL MRI reconstruction showed higher edge sharpness, rSNR, and rCNR in comparison with conventional methods; however, optimal levels of denoising may need to be further assessed.Keywords: MRI Reconstruction Method, Deep Learning, Image Analysis, Signal-to-Noise Ratio, MR-Imaging, Neural Networks, Hip, Shoulder, Physics, Observer Performance, Technology Assessment Supplemental material is available for this article. © RSNA, 2021.

Manifestation of dissimilar types of magnetism in iron- and chromium-substituted Mn2SnS4.

Mn2SnS4 belongs to the MII2AIVQ4 (M = transition metal; A = Si, Ge and Sn; Q = S, Se and Te) class of compounds that crystallizes in the orthorhombic space group Cmmm and shows complex magnetic properties. Here we report the synthesis and magnetic properties of Fe- and Cr-substituted Mn2SnS4 quaternary chalcogenides. All these compounds have been synthesized using a high-temperature solid-state route. Room temperature neutron diffraction studies on the specific compositions of chromium- and iron-substituted compounds were performed to obtain the site occupancy of different elements in the unit cell. The neutron diffraction analysis by employing the Rietveld refinement shows that for the Fe-substituted compound, most of the Fe goes to the Mn site with a small amount at the Sn site, while in the Cr-substituted sample, all the Cr occupy the Mn site. However, the Sn site almost remains intact in the case of the Fe-substituted compound, while it is significantly disordered for the Cr-substituted sample as a fraction of Mn occupies the Sn site and an equivalent amount of Sn occupies the Mn site. XPS study shows that both Cr and Fe exist in the +3 oxidation state, while Mn exists in the +2 state and Sn exists in a mixture of +2 and +4 oxidation states. Magnetic property study of these substituted compounds shows different types of magnetism, which is attributed to the variation of d-electrons of the substituent atom. The chromium-doped compounds show ferrimagnetic character along with two transitions: one transition at ∼37 K and another at ∼152 K. However, in Fe-substituted Mn2SnS4 samples, the low-temperature transition disappears and an increase in the high-temperature antiferromagnetic ordering temperature i.e. from 152 K (Mn2SnS4) to 174 K (Mn1.82Fe0.18SnS4) is observed. The increase in the antiferromagnetic ordering temperature in Mn2-xFexSnS4 may be attributed to the increase in the covalence of Mn/Fe-S-Mn/Fe bonds (shorter) with iron substitution.

Effectiveness of ChAdOx1 nCOV-19 Vaccine: Experience of a tertiary care institute.

BACKGROUND: The first dose of the ChAdOx1 nCoV- 19 Corona Virus Vaccine (Covishield) was administered to the eligible beneficiaries of tertiary care institute of Western Maharashtra on 16 Jan 21 and in the past three months almost 97% of the staff has been vaccinated. The present study analyses the incidence of COVID cases in the unvaccinated and vaccinated population of the institute. METHODS: All Covid 19 infections (RT-PCR positive) from 01 February 21 to 25 April 21 were included in the study and analyzed as per their vaccination status. To assess the COVID 19 transmission in contacts, Secondary Attack Rates (SAR) of the pre-vaccination period (Jun-Oct 20) was compared with the present SAR. RESULTS: A total of 113 cases occurred in the study period (01 Feb to 25 Apr 21). Lower number of infections were observed among the fully vaccinated as compared to partially vaccinated and non-vaccinated. The overall vaccine effectiveness was found to be 88.6% (81.55-92.37) and 44.1% (4.55-67.3) in completely and partially vaccinated individuals respectively. Hazard Ratios for getting infected dropped significantly after 28 days of the second dose. The SAR in high risk contacts (HRCs) was found to be 4.25%, which was lower than SAR (20.6%) of pre-vaccination period. CONCLUSION: This is one of the earliest studies in India to report the impact of COVID-19 vaccination. The results indicate that the vaccine provides effective protection against COVID-19 infection. However, given the complex dynamics of vaccination, the role of NPIs and implementation of COVID appropriate behavior cannot be undermined.

An analysis of mortality and survival of COVID 19 patients admitted to a tertiary care hospital in Maharashtra, India.

BACKGROUND: After nine months of responding to the coronavirus disease-19 (COVID-19) pandemic, the scientific fraternity is yet to unravel the mystery of those who are at most risk from mortality. Despite resistance to wear masks, the global public health response has beaten the grimmer projections of millions of deaths. The present study seeks to analyze the survival of COVID-19 patients at a tertiary care hospital and identify the risk factors of mortality. METHODS: Medical records of 1233 RT PCR confirmed COVID-19 patients admitted in a tertiary care hospital between 01 April and 30 September 2020 were retrospectively analyzed for calculating overall survival and to investigate the independent predictors of survival of COVID-19 patients. RESULTS: There were 72 (5.8%) deaths; which occurred in 24.9% of the elderly (age > 60yrs) people (P < 0.001), 76.0% in people with multiple comorbidities (having more than one comorbidity) (P < 0.001), 75.6% in people with diabetes (P < 0.001), and 75.5% in people with hypertension (P < 0.001). A significantly higher risk of mortality was observed in elderly patients, patients with comorbidities, and patients requiring oxygen while admitted in the hospital. CONCLUSION: Survival reflects the cure rates and is used by health professionals and policymakers to plan and implement disease control measures. The insights provided by the study would help facilitate the identification of patients at risk and timely provision of specialized care for the prevention of adverse outcomes in the hospital setting.

Estimating the proportion and IgG antibody response to SARS-CoV-2 in individuals joining a central educational institute from different parts of India by Enzyme-linked immunosorbent assay (ELISA) based serology.

BACKGROUND: Antibody response to SARS-CoV may be estimated to give trends and patterns emerging in a population during an evolving epidemic. The novel coronavirus has opened a new chapter in the history of pandemics and understanding the disease epidemiology. METHODS: The study was a cross-sectional descriptive study. Institutional Ethical clearance and informed consent were taken for participation in the study. The study population included all personnel reporting to the institute for training courses, permanent posting or joining back from leave during the study period of 2 months (16 June to 16 August 2020). The sample size was calculated assuming the prevalence of COVID-19 to be 1% with the absolute precision of 0.5% and 5% level of significance, and finite correction for population size of 500, and the calculated sample size was 377. Inclusion criteria were all personnel reporting to the institute from different states and districts. Exclusion criteria-Any personnel reported for a short visit of lesser than 14 days. Demographic details and details of any likely exposure to a confirmed COVID-19 case were noted. A blood sample was collected, and serological tests were done using ErbaLisa COVID-19 IgG kit by Calbiotech, as per the manufacturer's instructions. RESULTS: Overall seropositivity of IgG COVID-19 antibodies was 7.5% (31/413) (95% CI: 5.3-10.4%). Study population (n = 413) comprised of an adult population in the age range of 21 years-53 years, and the mean age was 31.4 years (SD = 6.2 years). CONCLUSION: As the personnel joining the institute have come from various parts of the country the study provides an estimation of antibodies against COVID-19.

Seroconversion among COVID-19 patients admitted in a dedicated COVID hospital: A longitudinal prospective study of 1000 patients.

BACKGROUND: The immune response after SARS-CoV-2 is complex and may be affected by severity of the disease, race, etc. The present study was conducted to assess the serial antibody response among the COVID-19 patients admitted in the hospital. METHODS: The study was conducted between July and October 2020 in a dedicated COVID-19 hospital. All consented patients underwent serial testing of antibodies using a rapid chromatographic immunoassay-based qualitative IgG/IgM kit every third day until their discharge or death. The data about age, sex, severity of disease, length of stay, onset of symptoms, date of molecular testing were also collected. Appropriate statistical tests were used. RESULTS: The mean age of 1000 COVID-19 patients was 47.5 ± 17.9 years. Out of the total, 687 (68.7%) were males. With respect to severity, 682 (68.2%) were asymptomatic/mild, 200 (20%) were moderate and 118 (11.8%) were severe cases. The seroconversion percentage increased from 12.8% to 97.9% and 16.3% to 80.9% for IgG and IgM respectively in 21 days. The median time for seroconversion was 10 days (IQR:6-12 days) for IgG and eight days (IQR: 6-11 days) for IgM. At the time of discharge (median nine days), detectable IgG and IgM antibodies were present in 502 (52.46%) and 414 (43.26%) participants respectively. Seroconversion was associated with days after the symptoms, increasing severity of the disease and the presence of co-morbidity. CONCLUSION: Seroconversion increased during the period of observation. The severe/moderate cases of COVID-19 tend to have an early seroconversion as compared to the asymptomatic/mild cases. Only half of the patients were seroconverted at discharge.

Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.

SAD phasing can be challenging when the signal-to-noise ratio is low. In such cases, having an accurate estimate of the substructure content can determine whether or not the substructure of anomalous scatterer positions can successfully be determined. Here, a likelihood-based target function is proposed to accurately estimate the strength of the anomalous scattering contribution directly from the measured intensities, determining a complex correlation parameter relating the Bijvoet mates as a function of resolution. This gives a novel measure of the intrinsic anomalous signal. The SAD likelihood target function also accounts for correlated errors in the measurement of intensities from Bijvoet mates, which can arise from the effects of radiation damage. When the anomalous signal is assumed to come primarily from a substructure comprising one anomalous scatterer with a known value of f'' and when the protein composition of the crystal is estimated correctly, the refined complex correlation parameters can be interpreted in terms of the atomic content of the primary anomalous scatterer before the substructure is known. The maximum-likelihood estimation of substructure content was tested on a curated database of 357 SAD cases with useful anomalous signal. The prior estimates of substructure content are highly correlated to the content determined by phasing calculations, with a correlation coefficient (on a log-log basis) of 0.72.

Understanding factors associated with continuation of intrauterine device use in Gujarat and Rajasthan, India: a cross-sectional household study.

The Government of India has promoted the expansion of access to and uptake of intrauterine devices (IUDs), during both the interval (IIUD) and postpartum (PPIUD) periods, as part of its Family Planning 2020 initiative. This study, conducted by EngenderHealth as part of the Expanding Access to IUD Services in India project, examines IIUD and PPIUD continuation rates over time and investigates factors associated with IUD continuation. We recruited respondents (N = 5024) through a repeated cross-sectional household study between February and December 2019. We identified respondents using IUD client data from public health facility registers in 20 districts of Gujarat and Rajasthan. We compared continuation rates for IIUD and PPIUD adopters and used regression analyses to measure the association between continuation and demographic, quality of care, and counselling variables. IIUD continuation rates decreased from 85.6% to 78.3% and PPIUD rates decreased from 78.5% to 70.7% between month 3 and month 12. Clients experiencing side effects or other problems were 15 times more likely to discontinue IUD use than clients who did not. Clients who received IUD counselling prior to insertion were more likely to continue than those who did not. IUD continuation increased significantly in cases where both partners jointly selected the method compared to situations where women decided alone. Several sociodemographic factors were associated with continuation. Our study demonstrates the value and benefits of programmes offering IUD services emphasising quality counselling and client-centred care to increase access, uptake, and continuation.