Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

Mitigating abiotic stresses using natural and modified stilbites synergizing with changes in oxidative stress markers in aquaculture.

In-depth mineralogical understanding and characterization are necessary to explore potential applications of clinoptilolites. In this study, the clinoptilolite collected from quarries and identified as stilbite microscopically and spectroscopically was subjected to physical and chemical treatments for the synthesis of modified stilbites, which were further evaluated for determining their removal efficiencies on ammonical contaminant in a predetermined concentration range from various source of aquaculture water namely fish pond, aquaponics and ornamental under laboratory condition. High-resolution transmission electron microscope results revealed that stilbite was rod-shaped in all forms but physically modified stilbite contains some nano-zeolite particles, synthesized probably due to heat treatment. The natural zeolite (stilbite) and microwave sodium acetate treated stilbite were found to be most effective in ammonia removal, hence both these products were further evaluated for the removal of cadmium and lead under laboratory conditions and for the ammonia removal in fish pond water under wet lab conditions. The results showed that these zeolites at 10-100 mg/L and 100-200 mg/L had a better removal efficiency of ammonical and metallic contaminants, respectively. Fish samples were taken at particular intervals to determine oxidative stress parameters, i.e., superoxide dismutase and catalase enzyme activities were found to be increased in control fish samples without treatment due to abiotic stress caused by higher ammonia concentration. The levels of oxidative stress markers are decreased in the treatments with zeolite-stilbite which brings to light its potential efficiency in alleviating stress in fish. This study revealed the potential of natural and abundantly available native zeolite-stilbite and its chemically modified form in relieving ammonical stress from the aquaculture system. This work has potential applications for the environmental management of aquaculture, ornamental fisheries, and aquaponics.

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021.

In this article, we - the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) - summarise the results of our activities for the period March 2020 - March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.

Retrospective genomic analysis of Vibrio cholerae O1 El Tor strains from different places in India reveals the presence of ctxB-7 allele found in Haitian isolates.

A total of 45 strains of Vibrio cholerae O1 isolated from 10 different places in India where they were associated with cases of cholera between the years 2007 and 2008 were examined by molecular methods. With the help of phenotypic and genotypic tests the strains were confirmed to be O1 El Tor biotype strains with classical ctxB gene. Polymerase chain reaction (PCR) analysis by double - mismatch amplification mutation assay PCR showed 16 of these strains carried the ctxB-7 allele reported in Haitian strains. Sequencing of the ctxB gene in all the 45 strains revealed that in 16 strains the histidine at the 20th amino acid position had been replaced by asparagine and this single nucleotide polymorphism did not affect cholera toxin production as revealed by beads enzyme-linked immunosorbent assay. This study shows that the new ctxB gene sequence was circulating in different places in India. Seven representatives of these 45 strains analysed by pulsed - field gel electrophoresis showed four distinct Not I digested profiles showing that multiple clones were causing cholera in 2007 and 2008.

Oscillation quenching in third order phase locked loop coupled by mean field diffusive coupling.

We explored analytically the oscillation quenching phenomena (amplitude death and parameter dependent inhomogeneous steady state) in a coupled third order phase locked loop (PLL) both in periodic and chaotic mode. The phase locked loops were coupled through mean field diffusive coupling. The lower and upper limits of the quenched state were identified in the parameter space of the coupled PLL using the Routh-Hurwitz technique. We further observed that the ability of convergence to the quenched state of coupled PLLs depends on the design parameters. For identical systems, both the systems converge to the homogeneous steady state, whereas for non-identical parameter values they converge to an inhomogeneous steady state. It was also observed that for identical systems, the quenched state is wider than the non-identical case. When the system parameters are so chosen that each isolated loop is chaotic in nature, we observe narrowing down of the quenched state. All these phenomena were also demonstrated through numerical simulations.

Challenges in HbA1c Analysis and Reporting in Patients with Variant Hemoglobins.

Hemoglobin A1c (HbA(1)c) is a well-established indicator of mean glycemia. The presence of genetic variants of hemoglobin can profoundly affect the accuracy of HbA(1)c measurements. Variants of hemoglobin especially Hemoglobin E (HbE) is prevalent in South East Asia including Bangladesh. The objective of our study is to compare the HbA(1)c values measured on high performance liquid chromatography (HPLC) and Turbidimetric Inhibition Immunoassay (TINIA) in diabetic patients with variant hemoglobins including HbE. A total of 7595 diabetic patients receiving treatment at BIRDEM General Hospital were analyzed for HbA(1)c results within a period of two months from December 2013 to January 2014. Seventy two cases out of 7595 (0.95%) had either undetectable or below normal HbA(1)c levels (males-33 and females-39; ratio = 0.82:1) by HPLC method. In 34(0.45%) cases, HbA(1)c value was undetectable by HPLC method but was in the reportable range by TINIA method. In the other 38 (0.55%) cases, HbA(1)c levels were below the reportable range (<4%) by HPLC method but were in the normal or higher range by TINIA method. TINIA method did not agree with HPLC method on Bland Altman plot in the 38 cases with below normal HbA(1)c levels, [Mean bias -5.2(-9.3 to 1.0), 95% CI] but agreed very well [mean bias -0.21 (-0.84 to 0.42), y=1.1037+0.776X; r(2)=0.30, p<0.01] in controls. In control group mean MCV was 83.80±7.48 and in study group was 73.65±10.44. Alkaline electrophoresis confirmed the variant hemoglobin to be HbE. The fasting blood sugar levels of all the 72 cases correlated strongly with TINIA method (r(2) =0.75, p<0.0001) but not with HPLC (r = 0.24, p=0.13). In our regions where populations have a high prevalence of Hb variant, proper knowledge of hemoglobin variants which affect the measurements HbA(1)c level is essential. MCV of 80fl or below may serve as a rough guide to select samples that require analysis by TINIA method. Moreover, HPLC may be a convenient and inexpensive tool for screening of hemoglobinopathies especially among diabetic population in Bangladesh. It may therefore be helpful in improving management of complications related to both anaemia and iron overload.

Therapeutic plasma exchange in paediatric SLE: a case series from India.

Therapeutic plasma exchange (TPE) has been reported to be a useful adjunct in severe systemic lupus erythematosus (SLE) but paediatric literature continues to be scanty. We hereby present three cases of refractory paediatric SLE (pSLE) with thrombotic thrombocytopenic purpura (TTP), diffuse alveolar haemorrhage (DAH) and crescentic glomerulonephritis which were treated with TPE as an adjunctive therapy. TPE was carried out in haemodialysis units using the membrane filtration technique. Demonstrable benefit of TPE was seen in all three cases. In refractory pSLE, TPE may be a useful tool and should be considered. The report additionally highlights the feasibility of undertaking TPE in haemodialysis units, which is important as haemodialysis units are more readily available than dedicated apheresis units in developing countries.

Genotypic variability in physiological, biomass and yield response to drought stress in pigeonpea.

Three pigeonpea (Cajanus cajan L. Millsp.) genotypes- GT-1, AKP-1 and PRG-158 with varying crop duration, growth habit and flowering pattern were evaluated for variability in their response for drought stress. Drought stress was imposed at initiation of flowering and the observations on biomass and seed yield parameters were recorded at harvest. The magnitude of response of individual component to drought stress was found to be genotype specific. Drought stress significantly decreased photosynthetic rate (PN), transpiration rate (Tr) and relative water content (RWC) in all the genotypes, however the magnitude of reduction differed with genotype. With drought stress, the reduction of PN was highest in GT-1 while reduction in Tr was highest in PRG-158. The genotype AKP-1, accumulated significantly higher concentrations of osmotic solutes especially proline under water deficit stress, this facilitated it to maintain higher relative water content (RWC) and lower malondialdehyde (MDA) content as compared to other genotypes. Drought stress also impacted biomass production and their partitioning to vegetative and reproductive components at harvest. There was significant variability between the genotypes for seed yield under drought stress while it was non-significant under well-watered condition. Drought stress enhanced flower drop and decreased flower to pod conversion resulting in reduced pod number and seed number in PRG-158 and GT-1. The genotype AKP-1 recorded superior performance for seed yield under stress environment due to its ability in maintaining pod and seed number as well as improved test weight (100 seed weight). Under drought stress, significant positive association of seed yield with proline, seed number, pod number and test weight clearly indicating their role in drought tolerance.

Spatiotemporal dynamics of a digital phase-locked loop based coupled map lattice system.

We explore the spatiotemporal dynamics of a coupled map lattice (CML) system, which is realized with a one dimensional array of locally coupled digital phase-locked loops (DPLLs). DPLL is a nonlinear feedback-controlled system widely used as an important building block of electronic communication systems. We derive the phase-error equation of the spatially extended system of coupled DPLLs, which resembles a form of the equation of a CML system. We carry out stability analysis for the synchronized homogeneous solutions using the circulant matrix formalism. It is shown through extensive numerical simulations that with the variation of nonlinearity parameter and coupling strength the system shows transitions among several generic features of spatiotemporal dynamics, viz., synchronized fixed point solution, frozen random pattern, pattern selection, spatiotemporal intermittency, and fully developed spatiotemporal chaos. We quantify the spatiotemporal dynamics using quantitative measures like average quadratic deviation and spatial correlation function. We emphasize that instead of using an idealized model of CML, which is usually employed to observe the spatiotemporal behaviors, we consider a real world physical system and establish the existence of spatiotemporal chaos and other patterns in this system. We also discuss the importance of the present study in engineering application like removal of clock-skew in parallel processors.

Poly[(µ3-3,5-di-nitro-benzoato-κ(3) O (1):O (1'):O (3))(µ2-hydroxido-κ(2) O:O)copper(II)].

The title complex, [Cu{µ3-O2CC6H3(NO2)2-3,5}(µ-OH)] n , features zigzag chains in which successive pairs of Cu(II) atoms are connected by OH bridges and bidentate carboxyl-ate ligands, leading to six-membered Cu(O)(OCO)Cu rings. The zigzag chains are connected into a three-dimensional architecture by Cu-O(nitro) bonds. The coordination geometry of the Cu(II) atom is square-pyramidal, with the axial position occupied by the nitro O atom, which forms the longer Cu-O bond. Bifurcated hy-droxy-nitro O-H⋯O hydrogen bonds contribute to the stability of the crystal structure.

Dose to Organ at Risk and its Characteristic Variation with the Clinically Used Different Prescription Levels for Early-stage Left-sided Breast Cancer.

AIMS: To evaluate the organ at risk (OAR) dose and its characteristic variation with different clinically usable prescription doses (RxD) for breast and chest wall radiotherapy in patients with early-stage left-sided breast cancer. MATERIALS AND METHODS: In total, 145 patients with early-stage breast cancers (T1N0M0-T2N0M0) on the left side were treated with radiotherapy after a modified radical mastectomy or breast conservation surgery, with a mean age of 45.1 ± 21.6 years. The patient received 4050 cGy of field-in-field (three-dimensional conformal radiotherapy) treatment limited to the breast or chest wall, excluding the supraclavicular node, axillary node and internal mammary chain, over 15 fractions. Additional plans of 5000 cGy/25 fractions, 4500 cGy/20 fractions and 2600 cGy/5 fractions were created with no or minor changes to the original plan. Mathematical modelling was used to study the distinctive change in the dose-volume characteristics for various OARs as a function of the RxD. OAR dosages, both absolute and normalised, were expressed in terms of the RxD. The mathematical (functional) relationship between OAR doses and different prescription levels was deduced by the least squares fit method. RESULT: The left lung mean dose, V5Gy (%), V10Gy (%) and V20Gy (%) and the heart mean dose, V10Gy (%) and V20Gy (%) were evaluated. The dose-volume parameters showed a parabolic variation (x2) with the RxD. Prescription normalised OAR doses showed a linear relationship with the RxD; relative dose increased with diminishing RxD. Normalised lung and heart mean doses exhibited saturation (linear relationship) with RxD variation. Paired sample t-test results between RxD versus all evaluated parameters were found to be statistically significant (P = 0.004). The Pearson correlation coefficient between different prescription levels for left lung mean dose (range 0.942-1.0), heart mean dose (range 1.0-1.0), left lung V5Gy (%) (range 0.987-1.0), left lung V10Gy (%) (range 0.991-0.999), heart V10Gy (%) (range 0.998-1.0). CONCLUSION: The functional form of absolute OAR dose-volume parameters versus RxD is parabolic and the RxD normalised OAR dose-volume parameter versus RxD is a straight line with a negative slope as RxD increases. This indicates an increase in the relative OAR dose-volume parameters if the RxD is reduced. This study is the first of its kind to compare the OAR doses as a function of clinically used degenerate prescription levels. These data will help to comprehend the OAR doses while adopting a new dose fractionation regimen and reviewing the radiotherapy treatment plans.

Elevated CO2 ameliorates the high temperature stress effects on physio-biochemical, growth, yield traits of maize hybrids.

The rising temperatures and levels of carbon dioxide in the atmosphere are anticipated to have a significant impact on the productivity of agricultural crops. Although, the individual effects of elevated CO2 and temperature have been extensively studied in C3 and C4 crops, there remains a scarcity of research investigating their interactive effects specifically on maize hybrids. The impact of elevated temperature and its interaction with elevated CO2 on phenology, physiology, biomass, and grain yield of maize hybrids was assessed in a field experiment using Free Air Temperature Elevation (FATE) facility. The results showed that elevated temperature (eT) increased the anthesis silking interval (ASI), while the presence of elevated CO2 along with elevated temperature (eT + eCO2) mitigated this effect. The differential expression were observed between hybrids depending on their genetic potential. Furthermore, the net photosynthetic rate (Anet), stomatal conductance (gs), and transpiration rate (Tr) of hybrids decreased under elevated temperature but eT + eCO2 condition helped in reverting its impact to some extent. In term of leaf composition, the highest level of total soluble sugars (TSS) and starch was observed under eT + eCO2 conditions, possibly due to improved Anet in the presence of elevated eCO2. The negative impact of eT was also evident through increased proline and MDA content, but eT + eCO2 ameliorated the adverse effect of eT. The biomass and grain yield also responded similarly, among the hybrids 900M GOLD recorded superior performance for grain yield at eT condition exceeding 35 °C. On the other hand, DHM117 experienced a significant reduction in grain yield under eT, but performed better under eT + eCO2 due to its improved physiological response to eCO2. The study indicated that elevated levels of carbon dioxide can actually mitigate the detrimental effects of elevated temperature on maize crop. This positive impact on maize crop can be attributed to an enhanced physiological performance in the presence of eCO2 which enables the plants to maintain satisfactory yield levels despite the challenging environmental conditions.

Spontaneous remission in a case of idiopathic retroperitoneal fibrosis.

A 54-year-old lady being investigated at the medical clinic for back pain and weight loss, was diagnosed with idiopathic retroperitoneal fibrosis on the basis of CT imaging, biopsy findings and absence of known secondary causes. After lengthy discussions with the patient during several clinic visits she declined the use of corticosteroid treatment due to concerns for the potential side effects. Serial monitoring of inflammatory markers and interval imaging suggested a spontaneous remission in the inflammatory process. We describe the case and discuss the management of retroperitoneal fibrosis.

Vibrio cholerae typing phage N4: genome sequence and its relatedness to T7 viral supergroup.

OBJECTIVES: In countries where cholera is endemic, Vibrio cholerae O1 bacteriophages have been detected in sewage water. These have been used to serve not only as strain markers, but also for the typing of V. cholerae strains. Vibriophage N4 (ATCC 51352-B1) occupies a unique position in the new phage-typing scheme and can infect a larger number of V. cholerae O1 biotype El Tor strains. Here we characterized the complete genome sequence of this typing vibriophage. METHODS: The complete DNA sequence of the N4 genome was determined by using a shotgun sequencing approach. RESULTS: Complete genome sequence explored that phage N4 is comprised of one circular, double-stranded chromosome of 38,497 bp with an overall GC content of 42.8%. A total of 47 open reading frames were identified and functions could be assigned to 30 of them. Further, a close relationship with another vibriophage, VP4, and the enterobacteriophage T7 could be established. DNA-DNA hybridization among V. cholerae O1 and O139 phages revealed homology among O1 vibriophages at their genomic level. CONCLUSIONS: This study indicates two evolutionary distinctive branches of the possible phylogenetic origin of O1 and O139 vibriophages and provides an unveiled collection of information on viral gene products of typing vibriophages.

Mathematical modelling of thin layer hot air drying of carrot pomace.

Thin layer carrot pomace drying characteristics were evaluated in a laboratory scale hot air forced convective dryer. The drying experiments were carried out at 60, 65, 70 & 75 °C and at an air velocity of 0.7 m/s. Mathematical models were tested to fit drying data of carrot pomace. The whole drying process of carrot pomace took place in a falling rate period except a very short accelerating period at the beginning. The average values of effective diffusivity ranged from 2.74 × 10(-9) to 4.64 × 10(-9) m(2)/s for drying carrot pomace. The activation energy value was 23.05 kJ/mol for the whole falling rate period.

Thigh Pain and Peri-Implant Fractures with the Use of Short Cephalo-medullary Nails: A Retrospective Study of 122 Patients.

Introduction: To assess the incidence and causes of persistent thigh pain and peri-implant fractures after union in patients of intertrochanteric fractures treated with short cephalo-medullary nails. Materials and methods: A retrospective observational study conducted at a Level 1 Trauma centre. A total of 122 patients of intertrochanteric fractures who were operated using short cephalo-medullary nails (170mm and 200mm lengths) between January 2018 to June 2019 were included in the study. Main outcomes measured were the incidence of thigh pain and peri-implant fractures. Results: Out of the 122 patients with a mean follow-up of 14.1 month, 12 patients had persistent thigh pain. Six patients had the helical blade protruding from the lateral cortex, two of them had distal tip of nail abutting on the anterior cortex and four cases had prominent proximal segment of nail which may explain the cause of their pain. Five of these patients had a combination of these findings. Two patients had pain for which no other obvious cause was found. There were no cases of peri-implant fractures in our study. Conclusion: Thigh pain associated with the use of short cephalon-medullary nails is often unrelated to nail length and can be prevented by using proper surgical technique. There seems to be no association between the use of short nails and peri-implant fractures.

Growth Characteristics of Female Radiation/Clinical Oncologists in South Asia: Assessment of Gender Neutrality and Leadership Position.

AIM: To evaluate the temporal growth pattern of female radiation/clinical oncologists (FRCOs) and, if applicable, predict the gender neutrality in different countries of South Asia. MATERIALS AND METHODS: South Asia is composed of Afghanistan, Bhutan, Maldives, Bangladesh, India, Nepal, Pakistan and Sri Lanka. The growth pattern of FRCOs in the latter five countries having radiation oncology facilities was evaluated from respective national registration data. Based on the average annual differential growth rate, together with the already existing female and male radiation/clinical oncologists (MRCOs), the cumulative numbers of FRCOs and MRCOs were forecasted for the next 10 years. The data regarding FRCOs in a leadership position were also calculated from different sources. RESULTS: The total number of radiation/clinical oncologists in the region was 4074, of which 91.8% were in India, because of its vast population. The overall number of FRCOs and MRCOs stood at 1370 and 2704, with a 1:2 female:male ratio. The average incremental annual growth of FRCOs in India was the highest (12.7 persons/year) and Nepal was the lowest (0.4 persons/year), with no data from Pakistan. If the current growth rate is sustained, Indian gender neutrality will be achieved by 2027-2030. In other countries, gender neutrality is unlikely to be achieved in the near future. With regards to leadership positions, 56-77 radiation oncology departments in India, one each in Bangladesh and Sri Lanka are headed by FRCOs, whereas Nepal and Pakistan have none. CONCLUSIONS: With the current growth rate of FRCOs and MRCOs, India will achieve gender parity within a decade; however, the rest of the countries will not achieve this in the near future. Analysis of radiation/clinical oncologists' registration data with their respective national bodies revealed an encouraging growth in the number of FRCOs as against their male counterparts in the last 5 years, compared with previous decades, especially in Bangladesh, Sri Lanka and India. Sri Lanka show high gender neutrality and adopted a multi-tasking and holistic approach of clinical oncology practices as also seen in Scandinavian countries. Such practice may be helpful to improve gender equality in radiation/clinical oncology practice for the other countries in the South Asian region.

High-resolution dissection of photosystem II electron transport reveals differential response to water deficit and heat stress in isolation and combination in pearl millet [Pennisetum glaucum (L.) R. Br.].

Heat and Water Deficit Stress (WDS) tend to impede and restrict the efficiency of photosynthesis, chlorophyll fluorescence, and maximum photochemical quantum yield in plants based on their characteristic ability to interfere with the electron transport system in photosystem II. Dissection of the electron transport pathway in Photosystem II (PSII) under water deficit and Heat Stress (HS) can be insightful in gaining knowledge on the various attributes of the photosynthetic performance of a plant. We attempt a high-resolution dissection of electron transport in PSII with studies on chlorophyll a fast fluorescence kinetics and non-photochemical quenching (NPQ) as a response to and recovery from these stresses in pearl millet [Pennisetum glaucum (L.) R. Br.] in isolation and combination. In this study, we bring out the mechanisms by which both heat and water stress, in isolation and in combination, affect the photosynthetic electron transport in Photosystem II. Our results indicate that oxygen evolution complex (OEC) damage is the primary effect of heat stress and is not seen with the same intensity in the water-stressed plants. Low exciton absorption flux in heat stress and combined stress was seen due to OEC damage, and this caused an electron transport traffic jam in the donor side of PS II. Both the specific energy flux model and the phenomenological flux model developed from the derived values in our study show that water deficit stress in combination with heat stress has a much stronger effect than the stresses in isolation on the overall electron transport pathway of the PS II in pearl millet plants.

Generalized Born-Oppenheimer treatment of Jahn-Teller systems in Hilbert spaces of arbitrary dimension: theory and application to a three-state model potential.

Generalized Born-Oppenheimer equations including the geometrical phase effect are derived for three- and four-fold electronic manifolds in Jahn-Teller systems near the degeneracy seam. The method is readily extendable to N-fold systems of arbitrary dimension. An application is reported for a model threefold system, and the results are compared with Born-Oppenheimer (geometrical phase ignored), extended Born-Oppenheimer, and coupled three-state calculations. The theory shows unprecedented simplicity while depicting all features of more elaborated ones.