A critical analysis of various post-harvest arsenic removal treatments of rice and their impact on public health due to nutrient loss.

Rice (Oryza sativa L.) is particularly susceptible to arsenic (As) accumulation. Currently, to decrease the level of As accumulated in rice, various post-harvest methods, i.e., polishing, parboiling, pH-dependent soaking, washing, and cooking at different rice-to-water ratios (r/w), are being focused, because it removes significant amount of As from rice grain. Depending upon the rice variety and type, i.e., rough (with husk), husked (without husk/brown), or polished rice, these methods can remove 39-54% As by parboiling, 38-55% by polishing, 37-63% by soaking, and 6-80% by washing and cooking. Infants are highly vulnerable to As exposure; thus, these methods can be helpful for the production of rice-based infant foods. Although concern arises during the use of these methods that apart from decreasing the level of As in rice grain, they also lead to a significant loss of nutrients, such as macro- and micro-elements present in rice. Among these discussed methods, parboiling curtails 5-59%, polishing curtails 6-96%, soaking curtails 33-83%, and washing and cooking in different r/w reduce 8-81% of essential nutrients resulting in 2-90% reduction in contribution to the RDI of these nutrients through rice-based diet. Thus, these post-harvest arsenic removal methods, although reduce arsenic induced health hazard, but may also lead to malnutrition and compromised health in the population based on rice diet. There is a need to explore another way to reduce As from rice without compromising the nutrient availability or to supplement these nutrients through grain enrichment or by introducing additional dietary sources by changing eating habits; however, this may impose an extra economic burden on people.

Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity.

Repair of uracils in DNA is initiated by uracil DNA glycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 (BdiUng) from Bradyrhizobium diazoefficiens. Although BdiUng contains the motif A (GQDPA), it has low sequence identity to known UDGs. BdiUng prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it. BdiUng is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits family 1 UDGs. Crystal structure of BdiUng shows similarity with the family 4 UDGs in its overall fold but with family 1 UDGs in key active site residues. However, instead of a classical motif B, BdiUng has a uniquely extended protrusion explaining the lack of Ugi inhibition. Structural and mutational analyses of BdiUng have revealed the basis for the accommodation of diverse substrates into its substrate binding pocket. Phylogenetically, BdiUng belongs to a new UDG family. Bradyrhizobium diazoefficiens presents a unique scenario where the presence of at least four families of UDGs may compensate for the absence of an efficient family 1 homologue.

Evolution of a multi-step phosphorelay signal transduction system in Ensifer: recruitment of the sigma factor RpoN and a novel enhancer-binding protein triggers acid-activated gene expression.

Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid-tolerant strain Ensifer medicae WSM419, the acid-activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi-step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer-binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid-induced. RACE mapping revealed that lpiA/acvB were co-transcribed as an operon from an RpoN promoter. In most Ensifer species, lpiA/acvB is located on the chromosome and the sequence upstream of lpiA lacks an RpoN-binding site. Nearly all Ensifer meliloti strains completely lack ebpA, tcrA, tcsA and fsrR regulatory loci. In contrast, E. medicae strains have lpiA/acvB and ebpA/tcrA/tcsA/fsrR co-located on the pSymA megaplasmid, with lpiA/acvB expression coupled to an RpoN promoter. Here we provide a model for the expression of lpiA/acvB in E. medicae. This unique acid-activated regulatory system provides insights into an evolutionary process which may assist the adaptation of E. medicae to acidic environmental niches.

Complete genome sequence of a Salimicrobium sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Salimicrobium sp. PL1-032A was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a single chromosome (2,705,688 bp) with a GC content of 47.2%. The isolation of Salimicrobium sp. PL1-032A contributes to the collection of culturable extremophiles and offers potential insight into the Pearse Lakes biome.

Complete genome sequence of a Marinococcus sp. PL1-022 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Marinococcus sp. PL1-022 was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a chromosome (3,140,198 bp; 48.2% GC) and two plasmids (58,083 bp and 19,399 bp; 41.4 and 50.7% GC-content, respectively). Isolation of Marinococcus sp. PL1-022 adds to the increasing repertoire of culturable extremophiles.

Complete genome sequence of Idiomarina sp. PL1-037 isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia.

Idiomarina sp. PL1-037 was isolated from Pearse Lakes, Rottnest Island, Western Australia. The sequenced completed genome for PL1-037 is composed of a single chromosome (2,804,934 bp) with a GC content of 47.1%. Isolation of Idiomarina sp. PL1-037 provides insights about culturable extremophiles from the Pearse lakes microbiome.

Evaluating the efficacy and feasibility of post harvest methods for arsenic removal from rice grain and reduction of arsenic induced cancer risk from rice-based diet.

Food-chain arsenic (As) contamination is a severe environmental and health problem worldwide, and its intake through rice affects billions of people. In this review, we have summarized the post harvest As removal methods from rice and their efficacy and feasibility. Rice grain subspecies (indica and japonica), size (short, medium and long), type (husked, parboiled or polished), soaking time, temperature and rice to water ratio (r/w) during washing and cooking are the major factors that affect the removal of total arsenic (tAs) from rice grain. The reduction in tAs was greater in japonica than indica rice and was directly proportional to As in husked rice. For the removal of As, a low water volume (1:2 r/w) was more effective during washing due to friction between rice grains, while high water (≥4 times water) during cooking was more effective. Up to 80 % As was removed by cooking in 1:10 (rice: water). Soaking rice in edible acids such as vinegar, acetic and ascorbic acid was not effective, except citric acid, which removes tAs up to 63 %. Human-health risk assessment showed that these post harvest and cooking methods reduce the non-carcinogenic and incremental lifetime cancer risk by up to 5-fold, as calculated on the basis of bioaccessible inorganic As. These post harvest methods also remove nutrient elements and vitamins. The recommended dietary intake (RDI) of Zn and Cu was particularly affected (up to 40 and 83 %). The levels of P, Mo, Mn and Co were still sufficient to meet the RDI through the rice-based diet, while rice is already poor in the RDI of Ca, K, Fe and Se, and their levels were further reduced by 0.22-44 %. In conclusion, these post harvest and cooking methods may significantly reduce As induced health risks; however, other dietary sources of nutrients need to be carefully evaluated and supplemented.

Cloud-Based Quad Deep Ensemble Framework for the Detection of COVID-19 Omicron and Delta Variants.

The mortality rates of patients contracting the Omicron and Delta variants of COVID-19 are very high, and COVID-19 is the worst variant of COVID. Hence, our objective is to detect COVID-19 Omicron and Delta variants from lung CT-scan images. We designed a unique ensemble model that combines the CNN architecture of a deep neural network-Capsule Network (CapsNet)-and pre-trained architectures, i.e., VGG-16, DenseNet-121, and Inception-v3, to produce a reliable and robust model for diagnosing Omicron and Delta variant data. Despite the solo model's remarkable accuracy, it can often be difficult to accept its results. The ensemble model, on the other hand, operates according to the scientific tenet of combining the majority votes of various models. The adoption of the transfer learning model in our work is to benefit from previously learned parameters and lower data-hunger architecture. Likewise, CapsNet performs consistently regardless of positional changes, size changes, and changes in the orientation of the input image. The proposed ensemble model produced an accuracy of 99.93%, an AUC of 0.999 and a precision of 99.9%. Finally, the framework is deployed in a local cloud web application so that the diagnosis of these particular variants can be accomplished remotely.

A comprehensive review on spatial and temporal variation of arsenic contamination in Ghaghara basin and its relation to probable incremental life time cancer risk in the local population.

Spatial and temporal variations have been found in the levels of arsenic (As) throughout the groundwater of the Ghaghara basin. Fifteen out of twenty-five districts in this basin are reported to be affected by As, where the levels of As in groundwater and soil exceed the permissible limits set by the WHO (10 µgl-1) and FAO (20 mgkg-1) respectively. These districts include a total of four municipalities in Nepal and eighty-six blocks in India, all of which have varying degrees of As contamination. Approximately 17 million people are at risk of As poisoning, with more than two orders of magnitude higher potential lifetime incremental cancer risk, constituting over 153 thousand potential additional cases of cancer due to As-contaminated drinking water. Out of the 90 As-contaminated blocks in the Ghaghara basin, 4 blocks have about 7-fold higher potential risk of developing cancer, 49 blocks have 8-37-fold higher risk, and 37 blocks have up to 375-fold higher risk compared to the upper limit of the USEPA acceptable range, which is 1 × 10-6-1 × 10-4. High accumulation of As has been reported in the nails, hair, and urine of local inhabitants, with higher levels observed in females than males. The toxicity of As is manifested in terms of a higher occurrence of various diseases. Reproductive endpoints, such as increased incidences of preterm birth, spontaneous abortion, stillbirth, low-birth weight, and neonatal death, have also been reported in the basin. The level of As in tube wells has been found to be negatively correlated with the depth (r = -0.906), and tube wells with high levels of As (>150 µgl-1) are generally located within close proximity (<10 km) to abandoned or present meander channels in the floodplain areas of the Ghaghara river. In addition to As contamination, the water quality index (WQI) in the Ghaghara basin is poor according to the BIS standards for drinking water. Groundwater in six out of fifteen districts is unsuitable for drinking purposes, with a WQI exceeding 100. The levels of As in agricultural soil in many villages of Ballia, Bahraich, and Lakhimpur Kheri districts have exceeded the FAO limit. Water from deep tube wells has been found to be relatively safe in terms of As content, and thus can be recommended for drinking purposes. However, the use of surface water needs to be encouraged for irrigation purposes in order to preserve soil health and reduce As contamination in the food chain, thereby minimizing the risk of cancer.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae Strain MUP20, Isolated from Frost-Damaged Wheat (Triticum aestivum cv. Scepter) in Western Australia.

Pseudomonas syringae MUP20 was isolated from Western Australian frost-damaged wheat. The MUP20 complete genome contained a 6,045,198-bp single circular chromosome with a GC content of 59.03%. IMG/M genome annotation identified 5,245 protein-coding genes, 1 of which encoded an ice nucleation protein containing 20 occurrences of a highly repetitive PF00818 domain.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae pv. pisi Isolate MUP32, Isolated from Frost-Damaged Pea (Pisum sativum subsp. arvense cv. Dundale) in New South Wales.

The genome of Pseudomonas syringae MUP32, which was isolated from frost-damaged pea in New South Wales, Australia, is tripartite and contains a circular chromosome (6,032,644 bp) and two plasmids (61,675 and 54,993 bp). IMG/M genome annotation identified 5,370 protein-coding genes, one of which encoded an ice-nucleation protein with 19 repetitive PF00818 domains.

Complete Genome Sequence of the Ice-Nucleation-Active Pseudomonas syringae Strain MUP17, Isolated from the Frost-Damaged Barley Cultivar Hordeum vulgare cv. La Trobe.

Pseudomonas syringae MUP17 was isolated from Western Australian frost-damaged barley. The MUP17 complete genome contained a 5,850,185-bp single circular chromosome with a GC content of 59.12%. IMG/M genome annotation identified 5,012 protein-coding genes, 1 of which encoded an ice-nucleation protein containing 19 occurrences of a highly repetitive PF00818 domain.

The critical appraisal of randomized controlled trials published in an Indian journal to assess the quality of reporting: A retrospective, cross-sectional study.

BACKGROUND: Although randomized controlled trials (RCTs) are the highest levels of evidence, they might not necessarily be of good quality. Hence, RCTs should always be appraised critically. Critical appraisal is the corroboration of evidence by methodically studying its validity, reliability, and applicability. OBJECTIVE: The primary objective of this study was to do a critical appraisal of the RCTs published in Indian Journal of Pharmacology (IJP) from 2011 to 2016. The secondary objective was to scrutinize how adequately the published RCTs adhere to the Consolidated Standards of Reporting Trials (CONSORT) declaration. MATERIALS AND METHODS: The present study included all RCTs published as full-text articles in IJP from January 2011 to December 2016. The identified RCTs were critically appraised using the critical appraisal checklist based on CONSORT 2010 guidelines and its extensions. RESULTS: According to this analysis, 75% (95% confidence interval [CI]: 0.56-0.87) of the articles had given details about the sample size calculation. Nearly 89.29% (95% CI: 0.72-0.96) of the articles described the method for generating random allocation sequence, but only 35.71% (95% CI: 0.20-0.54) of the articles described allocation concealment method. Almost 35.71% (95% CI: 0.20-0.54) of the trials reported results as per the principle of the intention to treat (ITT). Nearly 21.43% (95% CI: 0.10-0.39) of the studies reported CIs in the present study. CONCLUSION: Allocation concealment method, analysis of the data based on the ITT principle, and reporting CIs were found to be underreported in this study. There should be more emphasis on reporting of allocation concealment, ITT analysis, and CI.

A retrospective cross-sectional descriptive study to critically appraise the quality of reporting of health economic evaluations conducted in the Indian setting.

BACKGROUND: The reporting quality of economic research could benefit from enhanced quality assurance procedures. At present, there are small numbers of health economic researches being conducted with Indian context or setting. There is not much clarity about the reporting quality of health economic researches being conducted with Indian context or setting. OBJECTIVE: The primary objective is to of this study was to appraise the quality of reporting of health economic evaluations conducted in the Indian setting and published between January 2014 and December 2018. MATERIALS AND METHODS: This was a retrospective, cross-sectional, descriptive analysis. The MEDLINE in PubMed, Google Scholar, and Science Direct were systematically searched to search for economic evaluations. The consolidated health economic evaluation reporting standards statement checklist was utilized to assess the quality of reporting of the included studies. For grading the quality of the included health economic assessments, the Quality of Health Evaluation Studies (QHES) instrument was used. RESULTS: Thirty studies fulfilled the inclusion criteria and were included in the study. The mean QHES score was 80.26 (standard deviation = 8.06). Twenty-five (83.33%, 95% confidence interval [CI]: 0.66-0.92) of the article mentioned perspective of the study. Twenty-nine (96.66%, 95% CI: 0.83-0.99) of the article described the effects of uncertainty for all input parameters. Twenty (66.66%, 95% CI: 0.48-0.80) of the article reported all funding sources. CONCLUSIONS: Overall, the quality of reporting of the included health economic studies was good, which reemphasizes their usefulness in supporting the decision-making procedure about better medicine. The finding of this study will be a small step toward ensuring robust and high-quality health economics data in India.

Conceptualising a channel-based overlapping CNN tower architecture for COVID-19 identification from CT-scan images.

Convolutional Neural Network (CNN) has been employed in classifying the COVID cases from the lungs' CT-Scan with promising quantifying metrics. However, SARS COVID-19 has been mutated, and we have many versions of the virus B.1.1.7, B.1.135, and P.1, hence there is a need for a more robust architecture that will classify the COVID positive patients from COVID negative patients with less training. We have developed a neural network based on the number of channels present in the images. The CNN architecture is developed in accordance with the number of the channels present in the dataset and are extracting the features separately from the channels present in the CT-Scan dataset. In the tower architecture, the first tower is dedicated for only the first channel present in the image; the second CNN tower is dedicated to the first and second channel feature maps, and finally the third channel takes account of all the feature maps from all three channels. We have used two datasets viz. one from Tongji Hospital, Wuhan, China and another SARS-CoV-2 dataset to train and evaluate our CNN architecture. The proposed model brought about an average accuracy of 99.4%, F1 score 0.988, and AUC 0.99.

Root nodule bacteria isolated from South African Lotononis bainesii, L. listii and L. solitudinis are species of Methylobacterium that are unable to utilize methanol.

The South African legumes Lotononis bainesii, L. listii and L. solitudinis are specifically nodulated by highly effective, pink-pigmented bacteria that are most closely related to Methylobacterium nodulans on the basis of 16S rRNA gene homology. Methylobacterium spp. are characterized by their ability to utilize methanol and other C(1) compounds, but 11 Lotononis isolates neither grew on methanol as a sole carbon source nor were able to metabolize it. No product was obtained for PCR amplification of mxaF, the gene encoding the large subunit of methanol dehydrogenase. Searches for methylotrophy genes in the sequenced genome of Methylobacterium sp. 4-46, isolated from L. bainesii, indicate that the inability to utilize methanol may be due to the absence of the mxa operon. While methylotrophy appears to contribute to the effectiveness of the Crotalaria/M. nodulans symbiosis, our results indicate that the ability to utilize methanol is not a factor in the Lotononis/Methylobacterium symbiosis.

The model legume Medicago truncatula A17 is poorly matched for N2 fixation with the sequenced microsymbiont Sinorhizobium meliloti 1021.

Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, complementing the sequenced root nodule bacterial strain Sinorhizobium meliloti 1021 (Sm1021). In this study, the effectiveness of the Sm1021-M. truncatula symbiosis at fixing N(2) was evaluated. N(2) fixation effectiveness was examined with eight Medicago species and three accessions of M. truncatula with Sm1021 and two other Sinorhizobium strains. Plant shoot dry weights, plant nitrogen content and nodule distribution, morphology and number were analysed. Compared with nitrogen-fed controls, Sm1021 was ineffective or partially effective on all hosts tested (excluding M. sativa), as measured by reduced dry weights and shoot N content. Against an effective strain, Sm1021 on M. truncatula accessions produced more nodules, which were small, pale, more widely distributed on the root system and with fewer infected cells. The Sm1021-M. truncatula symbiosis is poorly matched for N(2) fixation and the strain could possess broader N(2) fixation deficiencies. A possible origin for this reduction in effectiveness is discussed. An alternative sequenced strain, effective at N(2) fixation on M. truncatula A17, is Sinorhizobium medicae WSM419.

LC and LC-MS/MS studies for the identification and characterization of degradation products of acebutolol.

The aim of the present investigation was to demonstrate an approach involving use of liquid chromatography (LC) and liquid chromatography-mass spectrometry (LC-MS) to separate, identify and characterize very small quantities of degradation products (DPs) of acebutolol without their isolation from the reaction mixtures. The drug was subjected to oxidative, hydrolytic, thermal and photolytic stress conditions as per International Conference on Harmonization (ICH) guideline Q1A(R2). Among all the stress conditions the drug was found to be labile in hydrolytic (acidic & basic) and photolytic stress conditions, while it was stable in water-induced hydrolysis, oxidative and thermal stress conditions. A total of four degradation products were formed. A C18 column was employed for the separation of all the DPs on a gradient mode by using high-performance liquid chromatography (HPLC). All the DPs were characterized with the help of their fragmentation pattern and the masses obtained upon LC-MS/MS and MSn analysis. All the hitherto unknown degradation products were identified as 1-(2-(2-hydroxy-3-(isopropylamino)propoxy)-5-(amino)phenyl)ethanone (DP-I), N-(4-(2-hydroxy-3-(isopropylamino)propoxy)-3-acetylphenyl)acrylamide (DP-II), 1-(2-(2-hydroxy-3-(isopropylamino)propoxy)-5-(hydroxymethylamino)phenyl)ethanone (DP-III) and 1-(6-(2-hydroxy-3-(isopropylamino)propoxy)-2,3-dihydro-2-propylbenzo[d]oxazol-5-yl)ethanone (DP-IV). Finally the in-silico carcinogenicity and hepatotoxicity predictions of the drug and all the DPs were performed by using toxicity prediction softwares viz., TOPKAT, LAZAR and Discovery Studio ADMET. The results of in-silico toxicity studies revealed that acebutolol (0.967) and DP-I (0.986) were found to be carcinogenic, while acebutolol (0.490) and DP-IV (0.437) were found to be hepatotoxic.

Prevalence and real-world assessment of central aortic blood pressure in adult patients with essential hypertension uncontrolled on single anti-hypertensive agents.

OBJECTIVE: To assess the prevalence of high central aortic pressure (CAP) in Indian patients with uncontrolled essential hypertension while on anti-hypertensive monotherapy. Also, to determine correlation between brachial blood pressure (BBP) and CAP, and ascertain if it is impacted by anti-hypertensive drug class and patients' age. METHODS: In this real-world, observational, prospective study, patients (30-70 years) with uncontrolled BBP (systolic BP [SBP] ≥140 mmHg or diastolic BP [DBP] ≥90 mmHg) were enrolled. Treatment was adjusted at Visit 1 (baseline), based on BBP and at treating physicians' discretion. Primary endpoint was proportion of patients with uncontrolled central aortic SBP (>125 mmHg) at baseline. Secondary endpoints were comparison of BBP and CAP across drugs classes and age groups at baseline and Visit 2 (End-of-study, ∼8 weeks post-baseline), and proportion of patients with uncontrolled central SBP at end-of-study. RESULTS: Of 2030 patients screened, 1949 patients reported at baseline and 1740 patients completed end-of-study visit. Central SBP was >125 mmHg for 84.3% patients at baseline, and 48% patients at end-of-study. Interestingly, at end-of-study, 6.6% patients still had uncontrolled brachial SBP and controlled central SBP, while 13.6% patients had uncontrolled central SBP and controlled brachial SBP. At both visits, brachial SBP and central SBP showed positive correlation across most drug classes and age groups. At baseline, ACE inhibitors showed better efficacy than other drug classes. At end-of-study, BP control was better with fixed-dose combinations, though free-drug combinations were more frequently prescribed. CONCLUSION: Measurement of CAP along with BBP can be vital in management of hypertension. CTRI REGISTRATION NUMBER: CTRI/2015/10/006302.

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence information and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.