GWAS to spot candidate genes associated with grain quality traits in diverse rice accessions of North East India.

INTRODUCTION: North East (NE) India is the second centre for the origin of rice and is enriched with a diverse collection of traditional rice accessions. These genotypes possess unique traits of breeding interest and are rich in grain nutritional and cooking qualities. Therefore, quantitative trait loci (QTLs)/genes associated with the various quality traits may be identified through genome-wide association studies (GWAS) and used in crop improvement programmes. METHODS AND RESULTS: A pool of 526 unique rice accessions from Assam, North East (NE) India were characterized by using 9 grain-quality traits and grouped into 16 clusters. Among these, the highest number of 156 (29.65%) genotypes belongs to diverse phenotypic classes; Sali, Lahi, and Chokuwa were grouped into cluster 6. The first three principal components showed 54.76% of morphological variability with Eigenvalue >1. Genome-wide association studies (GWAS) was performed in 103 rice accessions using 42,446 SNP markers. A total of 11 significant marker-trait associations were detected for 5 grain-quality traits, explaining 0.22-8.86% of phenotypic variation (PV). In-silico mining of QTLs detected 'candidate genes' associated with the quality traits. CONCLUSIONS: The phenotypic diversity among the 526 rice accessions of NE India was studied using grain quality traits and grouped into 16 significantly different clusters. The QTLs, or candidate genes identified for various grain quality traits, may be used in breeding programmes for the development of improved rice varieties.

Genome-wide association studies for agronomical traits in winter rice accessions of Assam.

The 297 winter rice accessions of Assam, North East India were genotyped by sequencing (GBS). The 50,985 high-quality SNPs were filtered and assigned to 12 rice chromosomes. The population structure analysis revealed three major subgroups SG1, SG2, and SG3 consisting of 30, 8, and 143 accessions respectively. The remaining 116 accessions were grouped as admixture population. Phenotypic data were recorded on13 agronomical traits for genome-wide association studies (GWAS). The 60 significant marker-trait associations (MTAs) were identified for 11 agronomical traits, which explained 0 to 15% of phenotypic variance (PV). A QTL 'hot spot' was detected near the centromeric region on chromosome 6. The identified QTLs may be validated and utilized in 'genomics assisted breeding' for improvement of existing rice cultivars of Assam and North East India.

Interface modification of Cr/Ti multilayers with C barrier layer for enhanced reflectivity in the water window regime.

The influence of a carbon barrier layer to improve the reflectivity of Cr/Ti multilayers, intended to be used in the water window wavelength regime, is investigated. Specular grazing-incidence X-ray reflectivity results of Cr/Ti multilayers with 10 bilayers show that interface widths are reduced to ∼0.24 nm upon introduction of a ∼0.3 nm C barrier layer at each Cr-on-Ti interface. As the number of bilayers increases to 75, a multilayer with C barrier layers maintains almost the same interface widths with no cumulative increase in interface imperfections. Using such interface-engineered Cr/C/Ti multilayers, a remarkably high soft X-ray reflectivity of ∼31.6% is achieved at a wavelength of 2.77 nm and at a grazing angle of incidence of 16.2°, which is the highest reflectivity reported so far in the literature in this wavelength regime. Further investigation of the multilayers by diffused grazing-incidence X-ray reflectivity and grazing-incidence extended X-ray absorption fine-structure measurements using synchrotron radiation suggests that the improvement in interface microstructure can be attributed to significant suppression of inter-diffusion at Cr/Ti interfaces by the introduction of C barrier layers and also due to the smoothing effect of the C layer promoting two-dimensional growth of the multilayer.

Carbon removal from a mirror-like gold surface by UV light, RF plasma, and IR laser exposure: a comparative study.

A decrease in photon intensity due to carbon contamination on optical elements is a serious issue in synchrotron radiation (SR) beamlines. Photon intensity can be regained by refurbishment of optical elements using suitable techniques. In the literature, three suitable techniques [radio frequency (RF) plasma, ultraviolet (UV) radiation (λ=172nm), and infrared (IR) laser (λ=1064nm) exposure] are reported to remove carbon contaminations from optical elements. These techniques are used independently to remove carbon, and, to the best of our knowledge, no systematic study is available on their relative efficiencies and effects on a mirror surface. We have applied these techniques independently for removal of carbon contamination from a gold surface, and detailed surface characterizations are carried out using soft x-ray reflectivity, x-ray photoelectron spectroscopy, Raman spectroscopy, and atomic force microscopy techniques. Characterization results suggest that all three techniques are capable of removing carbon contamination with certain limitations. Here, detailed relative effects on a gold surface after cleaning experiments with three techniques are discussed.

Refurbishment of an Au-coated toroidal mirror by capacitively coupled RF plasma discharge.

Deposition of synchrotron-radiation-induced carbon contamination on beamline optics causes their performance to deteriorate, especially near the carbon K edge. The photon flux losses due to carbon contamination have spurred researchers to search for a suitable decontamination technique to restore the optical surface and retain its performance. Several in situ and ex situ refurbishing strategies for beamline optics are still under development to solve this serious issue. In this work, the carbon contamination is removed from a large (340 mm × 60 mm) Au-coated toroidal mirror surface using a capacitively coupled low-pressure RF plasma. Before and after RF plasma cleaning, the mirror was characterized by Raman spectroscopy, soft X-ray reflectivity (SXR) and atomic force microscopy (AFM) techniques. The Raman spectra of the contaminated mirror clearly show the G (1575-1590 cm-1) and D (1362-1380 cm-1) bands of graphitic carbon. The SXR curve of the contaminated mirror shows a clear dip near the critical momentum transfer of carbon, indicating the presence of carbon contamination on the mirror surface. This dip disappears after removal of the contamination layer by RF plasma exposure. A decrease in the intensities of the CO bands is also observed by optical emission spectrometry during plasma exposure. The AFM and SXR results suggest that the root-mean-square (r.m.s.) roughness of the mirror surface does not increase after plasma exposure.

Characterization and in silico proteomic analysis of C2 and C3 proteins of squash leaf curl China virus associated with pumpkin leaf curl disease in Assam, India.

The pumpkin leaf curl disease is an emerging disease of pumpkin in Assam, India. Symptomatic pumpkin leaf samples from different locations were immunologically tested using Begomovirus specific antibody. PCR with the ELISA-positive samples, using Geminivirus universal primers amplified 1.4 kb virus-specific fragments. Sequence of these amplicons showed around 95% identity with squash leaf curl China virus-[Pumpkin: Varanasi] (SLCCV-Pumpkin: Varanasi EU573715). To investigate the possible functions of the viral proteins present in the fragment, the full-length C2 and C3 genes were conceptually translated and were subjected to in silico proteomic analyses. The phylogenetic analysis of both the proteins divulged the relationship of our isolate with related viruses and isolates. Multiple sequence alignment (MSA) of the proteins revealed the presence of the known viral conserved motifs, viz., zinc-finger (ZNF) motif [36CXCX(7)CX(6)H53], the arginine-rich nuclear localization signal (NLS) motif (28RRRR31) as well as the minimal activation domain in C2 protein. In the C3 protein, the 91LKYLD95 and the replication enhancer motif (30YFK32) were found to be conserved. Finally, 3-D models of the two proteins were predicted via ab initio approach and subsequently, the models were validated. To our knowledge, this study is a pioneering attempt to construct the ab initio 3-D models of two begomoviral proteins taking a SLCCV isolate as a model. Keywords: begomovirus; ELISA; ZNF motif; NLS motif; ab initio modelling.

Structural variation in a synchrotron-induced contamination layer (a-C:H) deposited on a toroidal Au mirror surface.

A carbon layer deposited on an optical component is the result of complex interactions between the optical surface, adsorbed hydrocarbons, photons and secondary electrons (photoelectrons generated on the surface of optical elements). In the present study a synchrotron-induced contamination layer on a 340 mm × 60 mm Au-coated toroidal mirror has been characterized. The contamination layer showed a strong variation in structural properties from the centre of the mirror to the edge region (along the long dimension of the mirror) due to the Gaussian distribution of the incident photon beam intensity/power on the mirror surface. Raman scattering measurements were carried out at 12 equidistant (25 mm) locations along the length of the mirror. The surface contamination layer that formed on the Au surface was observed to be hydrogenated amorphous carbon film in nature. The effects of the synchrotron beam intensity/power distribution on the structural properties of the contamination layer are discussed. The I(D)/I(G) ratio, cluster size and disordering were found to increase whereas the sp2:sp3 ratio, G peak position and H content decreased with photon dose. The structural parameters of the contamination layer in the central region were estimated (thickness ≃ 400 Å, roughness ≃ 60 Å, density ≃ 72% of bulk graphitic carbon density) by soft X-ray reflectivity measurements. The amorphous nature of the layer in the central region was observed by grazing-incidence X-ray diffraction.

Performance of Co/Ti multilayers in a water window soft x-ray regime.

The DC magnetron sputter grown Co/Ti multilayers, with ultra-low bi-layer thicknesses and with Co layers deposited under mixed ambience of argon and dry air, have been investigated for use in the water window soft x-ray regime of 23-44 Å. Initially, deposition parameters have been optimized for obtaining smooth and continuous low thickness Co and Ti single-layer films, and, then, multilayers with five bi-layers of various bi-layer thicknesses were deposited. The samples have been primarily characterized by the grazing incidence x-ray reflectivity (GIXR) measurements with a hard x-ray laboratory source. Subsequently, a set of multilayers with an increasing number of bi-layers has been deposited with a constant bi-layer thickness of 42 Å. GIXR results show that hard x-ray reflectivity at the first Bragg peak is maximum for the 20 bi-layer sample, beyond which the reflectivity decreases. Finally, the samples with the most promising hard x-ray GIXR have been used for soft x-ray reflectivity measurement with synchrotron radiation, and ∼2.5% peak reflectivity has been obtained in the multilayer sample at a 30.7 Å wavelength for a 21.5° grazing angle of incidence. The fitting results for both hard and soft x-ray reflectivities have been thoroughly investigated to find out the cause of the saturation of reflectivity with the increase in the number of bi-layers.

Laparoscopic Transplantation Following Transvaginal Insertion of the Kidney: Description of Technique and Outcome.

Laparoscopic kidney transplantation (LKT) is well accepted modality of treatment for ESRD patients at our center. Usually, the kidney is inserted through small Pfannenstiel incision. With the permission of the Internal Review Board, we carried out LKT in eight female recipients following insertion of the kidney through the vagina. The kidney was procured by the retroperitoneoscopic approach. Antibiotic prophylaxis was given. All cases were carried out successfully with immediate graft function and 100% graft and patient survival at 1 year of follow-up. Estimated glomerular filtration rate at 1 month and 1 year was similar to eight randomly selected female recipients who underwent open kidney transplantation (OKT). No analgesia was required in seven out of eight patients after the 3rd postoperative day. In summary, vaginal insertion of kidney and LKT is safe and feasible in a selected group of patients. It is associated with better analgesia and has similar allograft function as compare to OKT.

Catatonia in systemic lupus erythematosus: a case report and review of literature.

Although, neuropsychiatric morbidity is quite high in patients with systemic lupus erythematosus (SLE), catatonia has been rarely reported. We report a case of a 22-year-old female who presented with catatonic symptoms at the time of relapse of SLE and have discussed the presentation in the context of existing literature with regard to phenomenology of catatonia, psychiatric co-morbidity and treatment of catatonia in patients with SLE.

Study on effective cleaning of gold layer from fused silica mirrors using nanosecond-pulsed Nd:YAG laser.

A study on effective laser cleaning of gold layer deposited on fused silica substrates used in beamlines of synchrotron radiation (SR) sources using nanosecond-pulsed Nd:YAG laser has been carried out. The influence of pulse duration, beam incidence angle, spot overlapping, laser fluence, and number of passes on cleaning efficiency has been investigated. An approximately 48 nm thick gold layer from a mirror surface area of ~48 cm2 has been cleaned in 3 min. Laser clean quality and efficiency has been analyzed using microscope, scanning electron microscope (SEM), and angle-dependent reflectivity measurement techniques using SR beamline. Optimization of cleaning parameters resulted in a cleaning efficiency of ~98%. This study provides an alternate and low-cost solution for reuse of gold-coated, damaged mirrors.

A novel mutation (S227T) in domain II of the envelope gene of Japanese encephalitis virus circulating in North India.

Japanese encephalitis (JE) is an important arboviral infection of public health concern. There is a significant variation in mortality (10-30%) in JE viral infection. Epidemics of JE have become regular features in the northern states of India. The recent resurgence of the A226V mutation leading to a widespread Chikungunya epidemic motivated the investigators to search for any such mutational occurrence with Japanese encephalitis virus (JEV) isolated from this region. This study looked for mutation of clinical strains at amino-acid positions 176, 177, 227, 244, 264 and 279. A novel mutation S227T was detected corresponding to the loop region of domain II, E gene of JEV in comparison to Indian and other isolates from different parts of the world. Genotype III was found to be circulating in this geographical area. Further studies are required to ascertain its role in JE pathogenesis and vector competency.

Unilateral common peroneal nerve palsy following renal transplantation: a case report of tacrolimus neurotoxicity.

Neurologic complications are not uncommon in renal transplant recipients. Acute femoral neuropathy, lumbosacral plexopathy, and sciatic neuropathy have been reported after kidney transplantation probably due to perioperative nerve compression and ischemia. To the best of our knowledge, common peroneal nerve (CPN) palsy has not been described in the early postoperative period following renal transplantation. Also, mononeuropathy due to tacrolimus (TAC) therapy has not been described so far. We report a case of isolated CPN palsy presenting as unilateral foot drop following renal transplantation and that improved only after replacing TAC with cyclosporine.

Campylobacter jejuni infection in Guillain-Barré syndrome: a prospective case control study in a tertiary care hospital.

BACKGROUND: Guillain-Barré syndrome (GBS), is a common post-infectious polyradiculoneuropathy worldwide. The commonest implicated causative organism the world over is Campylobacter jejuni (C. jejuni). This study was carried out to determine the relationship between C. jejuni infection and GBS in an Indian setting. MATERIALS AND METHODS: This prospective study was carried out on a cohort of 50 patients with GBS who were treated in a tertiary care hospital in India. Based on electrophysiological findings the patients were divided into various subtypes. Serology for C. jejuni (Immunoglogulin G, IgG and Immunoglogulin, IgM) using an enzyme-linked immunosorbent assay method (ELISA) was done both in patients and 40 age, sex and geographically matched controls. RESULTS: Evidence of recent C. jejuni infection was present in 30% of GBS patients compared to 8% of controls (15/50 vs. 3/40 P<0.005). Eight (47%) C. jejuni-positive patients reported symptoms of gastroenteritis 4-30 days (mean 13 days) prior to onset of GBS. Of the 15 patients with evidence of C. jejuni infection, 10 (67%) patients had axonal type of GBS. Axonal variety of GBS presented in a younger age group compared to acute inflammatory demyelinating polyradiculoneuropathy (AIDP) patients (mean age: axonal vs. AIDP: 30.11 + 13.73 vs. 40.2 + 18.77). C. jejuni-positive patients presented mainly in spring and winter and had a similar age and sex incidence as compared to the rest of the GBS patients. CONCLUSIONS: Preceding C. jejuni infection is common among GBS patients and is often associated with the axonal variety of GBS. Axonal variety of GBS generally presents in a younger age group as compared to AIDP.

Comparative analysis of Truenat™ MTB Plus and Xpert® Ultra in diagnosing tuberculous meningitis.

BACKGROUND: Diagnostic delay and drug resistance not only worsen the outcomes of tuberculous meningitis (TBM), but are also important impediments to TB elimination efforts. Given the need for a near point-of-care test suitable for primary healthcare centres and simultaneous detection of resistance, Truenat™ MTB Plus assay was evaluated on a large cohort of TBM patients.METHODS: Truenat assay was performed on 148 cerebrospinal fluid specimens (76 definite TBM, 32 probable TBM and 40 non-TBM controls) and its performance was compared with Xpert® Ultra.RESULTS: The overall sensitivity of Truenat and Ultra was respectively 78.7% and 67.6% in diagnosing TBM, and respectively 85.5% and 96% in diagnosing definite TBM. Twenty-three additional cases were detected using Truenat and 11 using Ultra. Truenat missed seven cases of rifampicin (RIF) resistance and indicated false RIF resistance in four cases.CONCLUSION: Performance of Truenat was comparable to that of Ultra in diagnosing TBM and inferior to Xpert Ultra in determining RIF resistance.

Head to head comparison between neurology residents and a mobile medical application for diagnostic accuracy in cognitive neurology.

BACKGROUND: A novel Mobile Medical Application (App) App was created on iOS platform (Neurology Dx®) to deduce Differential Diagnoses (DDx) from a set of user selected Symptoms, Signs, Imaging data and Lab findings. The DDx generated by the App was compared for diagnostic accuracy with differentials reasoned by participating neurology residents when presented with same clinical vignettes. METHODS: Hundred neurology residents in seven leading Neurology centers across India participated in this study. A panel of experts created 60 clinical vignettes of varying levels of difficulty related to Cognitive neurology. Each neurology resident was instructed to formulate DDx from a set of 15 cognitive neurology vignettes. Experts in Cognitive Neurology made the gold standard DDx answers to all 60 clinical vignettes. The differentials generated by the App and neurology residents were then compared with the Gold standard. RESULTS: Sixty clinical vignettes were tested on 100 neurology residents (15 vignettes each) and also on the App (60 vignettes). The frequency of gold standard high likely answers accurately documented by the residents was 25% compared with 65% by the App (95% CI 33.1-46.3), P < 0.0001. Residents correctly identified the first high likely gold standard answer as their first high likely answer in 35% (95% CI 30.7-36.6) compared with 62% (95% CI 14.1-38.5), P < 0.0001. CONCLUSION: An App with adequate knowledge-base and appropriate algorithm can augment and complement human diagnostic reasoning in drawing a comprehensive list of DDx in the field of Cognitive Neurology (CTRI/2017/06/008838).

Human immunodeficiency virus associated intracranial aneurysms: report of three adult patients with an overview of the literature.

BACKGROUND AND PURPOSE: Aneurysms have been described in HIV infected patients. These involve predominantly extracranial blood vessels with specific histological and clinical features. Intracranial aneurysms are rare and have been identified mainly in children. METHODS: Case reports and literature review. RESULTS: Three black South African HIV positive adult patients with intracranial aneurysms were identified. The clinical, laboratory and radiological features are described. CONCLUSIONS: Intracranial aneurysms occur in both adults and children infected with HIV. More information is required on this association. The frequency in terms of numbers of cases indicates that it is an uncommon association or manifestation of HIV. The characteristics of the aneurysms suggest that they are distinctive and not a chance or coincidental co-occurrence of congenital or arteriosclerotic aneurysms.

Combined epidural and general anesthesia for paediatric renal transplantation-a single center experience.

BACKGROUND: Appropriate anesthesia for pediatric renal transplantation requires stable intraoperative hemodynamics, optimal perfusion of the newly transplanted kidney and good analgesia during recovery. The aim of this study was to assess the preliminary application, success and safety of combined epidural and general anesthesia in pediatric renal transplantation in a small cohort. METHODS: We retrospectively reviewed the anesthesia records of 46 consecutive pediatric patients who received renal transplantation under combined epidural and general anesthesia from January 2003-2007. RESULTS: The mean patient age and weight were 13.2 +/- 2.4 years and 25.7 +/- 5.46 kg, respectively. The infused crystalloids, 20% albumin and red blood cell concentrates were 120 +/- 2 mL/kg to achieve a CVP of 13 to 15 mm Hg. Brisk diuresis was observed in all patients. Epidural tramadol (2 mg/kg) provided good postoperative analgesia in 89% patients. 15% patients developed radiological evidence of pulmonary edema, only one required mechanical ventilation for hypoxemia. Minor adverse effects were nausea and vomiting (17.5%) and convulsions (8.5%). No perioperative mortality or major morbidity was recorded. CONCLUSION: Epidural anesthesia is a useful adjunct to general anesthesia due to stable intraoperative haemodynamics and good postoperative analgesia.

The "Christmas Tree" Sign on MR Cholangiogram in Left-Sided Cholangiohepatitis.

We report the "Christmas tree" sign on the magnetic resonance cholangiogram in two patients with left-sided cholangiohepatitis.