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.

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.

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.

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).

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.

High-resolution melting curve analysis of heat shock protein 65 for identification of mycobacterial isolates.

Infections caused by non-tuberculous mycobacteria (NTM) often escape detection on traditional diagnostics. We evaluated the ability of heat shock protein 65 (hsp65) polymerase chain reaction and high-resolution melting curve (HRMC) analysis to identify and differentiate Mycobacterium tuberculosis complex (MTC) from NTM in 150 clinical mycobacterial isolates from extra-pulmonary sites. A hundred MTC and 50 NTM isolates were identified. We were able to simultaneously differentiate between seven mycobacterial species using HRMC analysis; a concordance of 100% between hsp65 HRMC analysis, polymerase chain reaction + restriction analysis and hsp65 sequencing was observed.

Role of inflammatory and hemostatic biomarkers in Alzheimer's and vascular dementia - A pilot study from a tertiary center in Northern India.

INTRODUCTION: A reliable plasma biomarker in differentiating between Alzheimer's disease (AD) and Vascular dementia (VaD) is the need of the hour, in most memory clinics. Even though there is no disease modifying treatment, it is important to know the type of dementia for both symptomatic treatment and prognostication. METHODS: Neuropsychological assessment, MRI brain, FDG-PET brain and CSF biomarkers of AD (Aß42 and total tau) were used for establishing the diagnosis of Mild Cognitive Impairment (MCI), AD or VaD. RESULTS: 68 diagnosed patients of AD/MCI/VaD were included. FDG PET brain, plasma fibrinogen, d dimer, IL6 and CRP were done in all 68 patients while 48 patients underwent CSF biomarker analysis. Sixteen patients had MCI, of which 11 were MCI-AD and 5 were MCI-VaSC. There were 41 patients with AD (Mild AD-9, Mod AD-23, Severe AD-9) and 11 patients with VaD. Alzheimer group (MCI-AD and AD) and Vascular group (MCI VaSC & VaD) consisted of 52 and 16 patients respectively. Alzheimer and Vascular groups did not exhibit significant difference in IL6 and CRP levels. Plasma fibrinogen levels were significantly higher in VaD and vascular group as compared to Alzheimer group. But MCI-VaSC was not significantly different from MCI-AD. Plasma d dimer levels were significantly higher in all vascular subgroups compared to Alzheimer subgroups except between MCI-VaSC and MCI-AD. CONCLUSION: Hemostatic biomarkers were higher in Vascular group compared to Alzheimer group whereas there was no difference in inflammatory biomarkers. But the sensitivity and specificity of fibrinogen and d-dimer were not high enough for routine clinical use. Further studies in a larger sample are required to confirm these results.

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.

Clinical and radiological predictors of outcome in tubercular meningitis: A prospective study of 209 patients.

OBJECTIVES: The predictors of poor outcome in tuberculous meningitis (TBM) remain to be delineated. We determined role of various clinical, radiological and cerebrospinal fluid (CSF) parameters in prediction of outcome in TBM. PATIENTS AND METHODS: Current study was a prospective observational study including 209 patients of TBM. All patients underwent detailed evaluation including Gadolinium enhanced Magnetic resonance imaging (GdMRI) of brain as well as tests to detect evidence of tuberculosis elsewhere in body. They also underwent GdMRI at three and nine month follow up. All patients received treatment as per standard guidelines. RESULTS: Mean age was 30.4±13.8years. 139 (66.5%) patients had definite TBM while 70 (34.5%) had highly probable TBM. 53 (25.4%) patients died. On univariate analysis, longer duration of illness, altered sensorium, stage III TBM, hydrocephalus and exudates correlated with poor outcome. On multivariate analysis presence of hydrocephalus (p=0.003; OR=3.2; 95% CI=1.5-6.7) and stage III TBM (p<0.0001; OR=8.7; 95% CI=3.7-20.2) correlated with higher risk of mortality. In addition, there was significant positive association between presence of hydrocephalus (p=0.05; OR=2.2; 95% CI=0.97-5.1), stage III TBM (p<0.0001; OR=28; 95% CI=4.9-158) and presence of altered sensorium (p=0.05; OR=22; 95% CI=0.99-4.8) with either death or survival with severe disability. CONCLUSIONS: It is possible to prognosticate TBM using a combination of clinical and radiological. The duration of illness (65.9±92days) before diagnosis of TBM continues to be unacceptably long and this stresses on need to educate primary care physicians about TBM. Future studies where intensity and duration of treatment is guided by these cues may help in sorting out some of the most difficult questions in TBM, namely duration of antitubercular therapy as well as dose and duration of steroid therapy etc.

Cytokines do play a role in pathogenesis of tuberculous meningitis: A prospective study from a tertiary care center in India.

BACKGROUND: Though animal studies have suggested a role for proinflammatory cytokines in pathogenesis their exact role in pathogenesis of human meningeal tuberculosis continues to be controversial with different studies yielding contradictory results. AIM AND OBJECTIVES: To study the levels of proinflammatory cytokines in serum and cerebrospinal fluid (CSF) of patients with tubercular meningitis (TBM) and to determine whether these correlate with disease severity. PATIENTS AND METHODS: Present study included 146 patients with TBM (90- Definite TBM; 56- Probable TBM), diagnosed according to criteria laid by Ahuja et al. which were modified to include CSF nucleic acid based tests. Serum (n=146) and CSF (n=140) levels of various proinflammatory cytokines (IL-1ß, IL-2, IL-6, TNF-α and IFNγ) were compared between TBM patients and healthy volunteers (n=99). These levels were correlated with various clinical, radiological and CSF parameters of TBM patients. RESULTS: Proinflammatory cytokines include cytokines which promote systemic inflammation. In current study, the serum and CSF levels of various cytokines (IL-2, IL-4, IL-6, IL-1ß, IFN-γ and TNF-α) were significantly elevated in TBM patients compared to controls. A significant correlation was found between a) Higher stage of TBM and various cytokines (except for serum IL-6 and CSF IFN-γ); b) High CSF TNF-α, IL-4 and IL-1ß with severity of hydrocephalus; c) High CSF IL1ß and IFN-γ with presence of exudates on MRI; d) Serum and CSF levels of all cytokines with poor outcome as determined by death or as defined by S and E ADL (Schwab and England activities of daily living) score or by GOS (Glasgow outcome scale) (except for interferon gamma); and e) Serum and CSF IL-4 and IL1ß with presence of infarcts on MRI brain. CONCLUSION: Proinflammatory cytokines play an important role in the pathogenesis of TBM and contribute significantly towards severity of disease.

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.

Multitargeted loop-mediated isothermal amplification for rapid diagnosis of tuberculous meningitis.

SETTING: Rapid and accurate diagnosis of tuberculous meningitis (TBM) is imperative for the optimal management of patients. Loop-mediated isothermal amplification (LAMP) is a promising nucleic-acid amplification assay, especially for resource-poor, endemic countries. OBJECTIVE: Evaluating LAMP assay using insertion sequence (IS) 6110 and MPB64 targets for the Mycobacterium tuberculosis complex (MTC) for the rapid diagnosis of TBM. Results were compared with culture and the composite reference standard. DESIGN: The LAMP assay was performed using six MTC-specific primers each for IS6110 and MPB64 on the cerebrospinal fluid of 150 TBM patients (50 confirmed, 100 suspected) and 100 non-TBM control subjects. RESULTS: Multitargeted LAMP had a sensitivity and specificity of 96% and 100% for confirmed (50 culture-positive) TBM cases. The sensitivity of IS6110 polymerase chain reaction (PCR), IS6110 LAMP and MPB64 LAMP for probable cases was respectively 70 (70%), 78 (78%) and 82 (82%). In a total of 150 TBM patients, the overall sensitivity of microscopy, IS6110 PCR, IS6110 LAMP, MPB64 LAMP and the multitargeted LAMP was respectively 4%, 74.6%, 82.7%, 86.7% and 88%. The specificity for all was 100%. Six cases were missed by IS6110 LAMP and two cases by MPB64 LAMP. CONCLUSION: The LAMP assay using two targets is a promising and accurate technique for the rapid diagnosis of TBM.

Anesthetic Management of a Patient with DRESS Syndrome for Renal Transplantation.

Drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome is a rare but potentially life-threatening hypersensitivity reaction characterized by widespread erythematous skin eruptions with fever, lymphadenopathy and visceral involvement-hepatitis, nephritis, pericarditis, and pneumonitis. There are numerous reports describing the management of such patients in intensive care units but hardly any describing the intraoperative anesthetic management of such patients. Herein, we report on a patient with DRESS syndrome who was scheduled for renal transplantation. The main goal in this case was to prevent a hypersensitive drug reaction intraoperatively and develop a safe alternative anesthesia plan for the patient. After pre-operative skin and intradermal tests, we chose the drugs that could be safely used for anesthesia. Usually general anesthesia is preferred for renal transplantation but in this patient we opted for combined spinal epidural anesthesia. Precautions that are to taken in such a case and the anesthetic management are discussed in detail herewith.