A comprehensive review on electrochemical and optical aptasensors for organophosphorus pesticides.

There has been a rise in pesticide use as a result of the growing industrialization of agriculture. Organophosphorus pesticides have been widely applied as agricultural and domestic pest control agents for nearly five decades, and they remain as health and environmental hazards in water supplies, vegetables, fruits, and processed foods causing serious foodborne illness. Thus, the rapid and reliable detection of these harmful organophosphorus toxins with excellent sensitivity and selectivity is of utmost importance. Aptasensors are biosensors based on aptamers, which exhibit exceptional recognition capability for a variety of targets. Aptasensors offer numerous advantages over conventional approaches, including increased sensitivity, selectivity, design flexibility, and cost-effectiveness. As a result, interest in developing aptasensors continues to expand. This paper discusses the historical and modern advancements of aptasensors through the use of nanotechnology to enhance the signal, resulting in high sensitivity and detection accuracy. More importantly, this review summarizes the principles and strategies underlying different organophosphorus aptasensors, including electrochemical, electrochemiluminescent, fluorescent, and colorimetric ones.

Xpert Ultra in diagnosing extrapulmonary TB: accuracy and trace calls.

INTRODUCTION: Xpert Ultra (Ultra) was developed to improve the detection of TB; however, data on Ultra´s diagnostic accuracy in extrapulmonary TB (EPTB) are limited.METHODS: In this prospective diagnostic accuracy study, 242 EPTB samples were subjected to Ultra and Xpert MTB/Rif (Xpert) testing, and these were compared with both culture and a composite gold standard.RESULTS: Compared to culture, Ultra sensitivity and specificity using bone, cerebrospinal fluid (CSF), lymph node and tissue samples, and overall were respectively 100% and 77.3%, 75% and 100%, 87.5% and 87.5%, 100% and 87%, and 89.7% and 87.4%; in comparison to the composite gold standard, Ultra´s sensitivity and specificity were respectively 66.7% and 100%, 17.6% and 100%, 46.9% and 95.7%, 38.5% and 94.1%, and 46.2% and 96.9%. Using latent class analysis, sensitivity and specificity were respectively 94.5% and 96.3% for Ultra, 65.5% and 99.8% for Xpert, and 58.6% and 99.2% for culture. There were 22/242 (9%) trace calls on Ultra.CONCLUSION: We found improved sensitivity for Ultra compared to Xpert, although Ultra specificity was lower, with a large number of trace results (9%).

The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae).

The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.

Enteric fever in India: current scenario and future directions.

Enteric fever is a major cause of morbidity and mortality in tropical areas worldwide. The Indian subcontinent bears the brunt of the disease, both in terms of absolute case numbers and drug-resistant strains. Recent phylogenetic studies suggest that the multidrug-resistant clade H58 originated in India and subsequently expanded through Asia and Africa. In Africa, it caused unrecognised outbreaks in areas previously considered free of the disease. In this study, we discuss the current status of enteric fever in India, the factors preventing its control and its future directions in this rapidly developing nation.

Learning the sequence determinants of alternative splicing from millions of random sequences.

Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Toward better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of over two million (M) synthetic mini-genes, which include degenerate subsequences totaling over 100 M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing, as well as to gain new mechanistic insights. Our results show that the vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5' splicing also enhance (suppress) exon inclusion in alternative 3' or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.

Adsorption-desorption and leaching behavior of kresoxim-methyl in different soils of India: kinetics and thermodynamic studies.

The sorption and leaching behavior of kresoxim-methyl was explored in four different soils, viz., clay, sandy loam, loamy sand, and sandy loam (saline), representing vegetables and fruits growing regions of India. Adsorption of kresoxim-methyl in all the soils reached equilibrium within 48 h. The rate constants for adsorption and desorption at two different temperatures were obtained from the Lindstrom model, which simultaneously evaluated adsorption and desorption kinetics. The data for rate constants, activation energies, enthalpy of activation, entropy of activation, and free energy indicated physical adsorption of kresoxim-methyl on soil. The relative adsorptivity of the test soils could be attributed to different organic matter and clay contents of the soils. A good fit to the linear and Freundlich isotherms was observed for both adsorption as well as desorption. The groundwater ubiquity score (GUS) for different soils varied between 0 and 2.26. The GUS and leaching study indicated moderately low leaching potential of kresoxim-methyl. The adsorption on four soil types largely depended on the soil physicochemical properties such as organic carbon content, cation-exchange capacity, and texture of the soil.

In-situ preparation of N-TiO2/graphene nanocomposite and its enhanced photocatalytic hydrogen production by H2S splitting under solar light.

Highly monodispersed nitrogen doped TiO2 nanoparticles were successfully deposited on graphene (N-TiO2/Gr) by a facile in-situ wet chemical method for the first time. N-TiO2/Gr has been further used for photocatalytic hydrogen production using a naturally occurring abundant source of energy i.e. solar light. The N-TiO2/Gr nanocomposite composition was optimized by varying the concentrations of dopant nitrogen and graphene (using various concentrations of graphene) for utmost hydrogen production. The structural, optical and morphological aspects of nanocomposites were studied using XRD, UV-DRS, Raman, XPS, FESEM, and TEM. The structural study of the nanocomposite shows existence of anatase N-TiO2. Further, the details of the components present in the composition were confirmed with Raman and XPS. The morphological study shows that very tiny, 7-10 nm sized, N-TiO2 nanoparticles are deposited on the graphene sheet. The optical study reveals a drastic change in absorption edge and consequent total absorption due to nitrogen doping and presence of graphene. Considering the extended absorption edge to the visible region, these nanocomposites were further used as a photocatalyst to transform hazardous H2S waste into eco-friendly hydrogen using solar light. The N-TiO2/Gr nanocomposite with 2% graphene exhibits enhanced photocatalytic stable hydrogen production i.e. ∼5941 µmol h(-1) under solar light irradiation using just 0.2 gm nanocomposite, which is much higher as compared to P25, undoped TiO2 and TiO2/Gr nanocomposite. The enhancement in the photocatalytic activity is attributed to 'N' doping as well as high specific surface area and charge carrier ability of graphene. The recycling of the photocatalyst shows a good stability of the nanocomposites. This work may provide new insights to design other semiconductor deposited graphene novel nanocomposites as a visible light active photocatalyst.

Kresoxim methyl dissipation kinetics and its residue effect on soil extra-cellular and intra-cellular enzymatic activity in four different soils of India.

The rate of degradation of kresoxim methyl and its effect on soil extra-cellular (acid phosphatase, alkaline phosphatase and ß-glucosidase) and intra-cellular (dehydrogenase) enzymes were explored in four different soils of India. In all the tested soils, the degradation rate was faster at the beginning, which slowed down with time indicating a non-linear pattern of degradation. Rate of degradation in black soil was fastest followed by saline, brown and red soils, respectively and followed 1st or 1st + 1st order kinetics with half-life ranging between 1-6 days for natural soil and 1-19 days for sterile soils. The rate of degradation in natural against sterilized soils suggests that microbial degradation might be the major pathway of residue dissipation. Although small changes in enzyme activities were observed, kresoxim methyl did not have any significant deleterious effect on the enzymatic activity of the various test soils in long run. Simple correlation studies between degradation percentage and individual enzyme activities did not establish any significant relationships. The pattern and change of enzyme activity was primarily due to the effect of the incubation period rather than the effect of kresoxim methyl itself.

Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation.

In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of eExon mutations is not well known. Here, using massively parallel reporter assays, we dissect the enhancer activity of three liver eExons (SORL1 exon 17, TRAF3IP2 exon 2, PPARG exon 6) at single nucleotide resolution in the mouse liver. We find that both synonymous and non-synonymous mutations have similar effects on enhancer activity and many of the deleterious mutation clusters overlap known liver-associated transcription factor binding sites. Carrying a similar massively parallel reporter assay in HeLa cells with these three eExons found differences in their mutation profiles compared to the liver, suggesting that enhancers could have distinct operating profiles in different tissues. Our results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types.

Quantum confinement controlled solar hydrogen production from hydrogen sulfide using a highly stable CdS(0.5)Se(0.5)/CdSe quantum dot-glass nanosystem.

We have demonstrated unique CdS0.5Se0.5 and CdSe quantum dot-glass nanosystems with quantum confinement effect. The stable, monodispersed CdS0.5Se0.5 and CdSe quantum dots (QDs) of size 2 to 12 nm have been grown in a germanate glass matrix by a simple melt quench technique at moderate temperature. XRD and Raman studies show formation of hexagonal CdS0.5Se0.5 and CdSe in the glass matrix. The quantum confinement of CdS0.5Se0.5 and CdSe was studied using TEM and UV-Vis spectroscopy. The band gap of the glass nanosystem was tuned from 3.6 to 1.8 eV by controlling the CdS0.5Se0.5 quantum dot size in the glass matrix. It can be further tuned to 1.68 eV using growth of CdSe quantum dots in the glass matrix. Considering the tuneable band gap of the CdS0.5Se0.5 and CdSe quantum dot-glass nanosystem for the visible light absorption, a study of size tuneable photocatalytic activity for hydrogen generation from hydrogen sulfide splitting was performed under visible light irradiation for the first time. The utmost hydrogen evolution, i.e. 8164.53 and 7257.36 µmol h(-1) g(-1) was obtained for the CdS0.5Se0.5 and CdSe quantum dot-glass nanosystems, respectively. The apparent quantum yield (AQY) was observed to be 26% and 21% for the CdS0.5Se0.5 and CdSe quantum dot-glass nanosystems, respectively. It is noteworthy that the present glass nanosystem as a photocatalyst was found to be very stable as compared to naked powder photocatalysts.

Does first line antiretroviral therapy increase the prevalence of cardiovascular risk factors in Indian patients?: A cross sectional study.

CONTEXT: Antiretroviral therapy (ART) is associated with a myriad of metabolic complications which are potential cardiovascular risk factors. Early detection of these risk factors could help in alleviating morbidity and mortality in human immunodeficiency virus (HIV) infected patients on ART. AIMS: To study the prevalence of cardiovascular risk factors in patients on a combination of nucleoside reverse transcriptase inhibitors (NRTIs) and non-NRTIs (NNRTIs) - the standard combination first line ART regimen used in tertiary referral center. SETTINGS AND DESIGN: The prevalence of cardiovascular risk factors in HIV infected subjects with stage 1t disease on standard first line ART for at least 1 year, HIV infected subjects with stage 1 disease and not on ART and HIV negative subjects was assessed. The study was a cross-sectional study design. MATERIALS AND METHODS: Basic demographic data was collected and patients were examined for anthropometric data and blood was collected for analysis of blood glucose, serum lipids, and fasting insulin levels. STATISTICAL ANALYSIS: Chi-square test was used to calculate significance. Statistical Package for Social Sciences (SPSS) software version 16.0 was used for data analysis. RESULTS: The prevalence of hypercholesterolemia and hypertriglyceridemia was higher in the patients on ART when compared to patients not on ART (P<0.001). There was no difference in the prevalence of abnormal glycemic status, obesity, abdominal obesity, insulin resistance, and hyperinsulinemia between patients on ART and those not on ART. CONCLUSIONS: First line ART is associated with increased prevalence of dyslipidemia. Early detection and treatment of dyslipidemia should help in reducing the cardiovascular morbidity in patients on ART.

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project. To address this problem, we need scalable, cost-effective methods to obtain assemblies with chromosome-scale contiguity. Here we show that genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres. To exploit this finding, we developed an algorithm that uses Hi-C data for ultra-long-range scaffolding of de novo genome assemblies. We demonstrate the approach by combining shotgun fragment and short jump mate-pair sequences with Hi-C data to generate chromosome-scale de novo assemblies of the human, mouse and Drosophila genomes, achieving--for the human genome--98% accuracy in assigning scaffolds to chromosome groups and 99% accuracy in ordering and orienting scaffolds within chromosome groups. Hi-C data can also be used to validate chromosomal translocations in cancer genomes.

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Despite continual progress in the cataloging of vertebrate regulatory elements, little is known about their organization and regulatory architecture. Here we describe a massively parallel experiment to systematically test the impact of copy number, spacing, combination and order of transcription factor binding sites on gene expression. A complex library of ∼5,000 synthetic regulatory elements containing patterns from 12 liver-specific transcription factor binding sites was assayed in mice and in HepG2 cells. We find that certain transcription factors act as direct drivers of gene expression in homotypic clusters of binding sites, independent of spacing between sites, whereas others function only synergistically. Heterotypic enhancers are stronger than their homotypic analogs and favor specific transcription factor binding site combinations, mimicking putative native enhancers. Exhaustive testing of binding site permutations suggests that there is flexibility in binding site order. Our findings provide quantitative support for a flexible model of regulatory element activity and suggest a framework for the design of synthetic tissue-specific enhancers.

Disseminated histoplasmosis: a comparative study of the clinical features and outcome among immunocompromised and immunocompetent patients.

BACKGROUND: Disseminated histoplasmosis is a chronic granulomatous disease caused by the dimorphic fungus, Histoplasma capsulatum. Clinical presentation can vary from the acute pulmonary to the chronic disseminated form. In India, disseminated histoplasmosis often presents with pyrexia of unknown origin with a presentation similar to 'disseminated tuberculosis' involving the adrenal glands and bone marrow. Due to rarity of the disease, data are lacking regarding its clinical presentation and outcome among immunocompromised and immunocompetent patients. METHODS: During January 2000 to December 2010, we identified 37 patients of disseminated histoplasmosis and attempted to characterize the differences between immuno- compromised and immunocompetent patients. Demographic characteristics, clinical presentation, risk factors, laboratory findings, diagnostic yield, treatment received and prognosis were noted and compared between the two groups. RESULTS: Eleven of 37 patients with disseminated histo- plasmosis were immunocompromised and 26 were immuno- competent. Comparison of their clinical features showed a higher frequency of skin lesions in the immunocompromised compared to the immunocompetent group (54.5% v. 11.5%). Pancytopenia and anaemia were more common among the immunocompromised (81.8%) compared to the immunocompetent (46.2%) group. In the immuno- compromised patients, the diagnosis was made most often by bone marrow aspirate and culture (72.7%) compared to the immunocompromised group where the diagnosis was most often obtained by adrenal gland biopsy and fungal cultures (57.7%). The cure rate was significantly higher in the immunocompetent group (73% v. 45%). CONCLUSION: The clinical presentation and outcome of patients with disseminated histoplasmosis differs among immunocompromised and immunocompetent patients.

Spatio-temporal mapping cortical neuroplasticity in carpal tunnel syndrome.

Neuroimaging data demonstrate that carpal tunnel syndrome, a peripheral neuropathy, is accompanied by maladaptive central neuroplasticity. To further investigate this phenomenon, we collected magnetoencephalography data from 12 patients with carpal tunnel syndrome and 12 healthy control subjects undergoing somatosensory stimulation of the median nerve-innervated Digits 2 and 3, as well as Digit 5, which is innervated by the ulnar nerve. Nerve conduction velocity and psychophysical data were acquired to determine whether standard clinical measures correlated with brain response. In subjects with carpal tunnel syndrome, but not healthy controls, sensory nerve conduction velocity for Digits 2 and 3 was slower than Digit 5. However, somatosensory M20 latencies for Digits 2 and 3 were significantly longer than those of Digit 5. The extent of the M20 delay for median nerve-innervated Digit 2 was positively correlated with decreasing nerve conduction velocity and increasing pain severity. Thus, slower peripheral nerve conduction in carpal tunnel syndrome corresponds to greater delays in the first somatosensory cortical response. Furthermore, spectral analysis demonstrated weaker post-stimulus beta event-related desynchronization and earlier and shorter event-related synchronization in subjects with carpal tunnel syndrome. The extent of the decreased event-related desynchronization for median nerve-innervated digits was positively correlated with paraesthesia severity. We propose that ongoing paraesthesias in median nerve-innervated digits render their corresponding sensorimotor cortical areas 'busy', thus reducing their capacity to process external stimulation. Finally, subjects with carpal tunnel syndrome demonstrated a smaller cortical source separation for Digits 2 and 3 compared with healthy controls. This supports our hypothesis that ongoing paraesthesias promote blurring of median nerve-innervated digit representations through Hebbian plasticity mechanisms. In summary, this study reveals significant correlation between the clinical severity of carpal tunnel syndrome and the latency of the early M20, as well as the strength of long latency beta oscillations. These temporal magnetoencephalography measures are novel markers of neuroplasticity in carpal tunnel syndrome and could be used to study central changes that may occur following clinical intervention.

Atypical mucocutaneous involvement with Leishmania donovani.

Mucocutaneous leishmaniasis has rarely been reported from India. The usual causative organisms of this infection are Leishmania braziliensis and L. tropica. Another species, L. donovani, which usually causes visceral leishmaniasis, has recently been reported to cause mucocutaneous disease in a few patients from Sri Lanka. We report two patients who had undiagnosed chronic skin lesions for several years. Skin biopsies revealed Leishmania and the species was characterized as L. donovani in both patients. There was considerable improvement in the skin lesions following treatment with liposomal amphotericin B.

Understanding Immersivity: Image Generation and Transformation Processes in 3D Immersive Environments.

Most research on three-dimensional (3D) visual-spatial processing has been conducted using traditional non-immersive 2D displays. Here we investigated how individuals generate and transform mental images within 3D immersive (3DI) virtual environments, in which the viewers perceive themselves as being surrounded by a 3D world. In Experiment 1, we compared participants' performance on the Shepard and Metzler (1971) mental rotation (MR) task across the following three types of visual presentation environments; traditional 2D non-immersive (2DNI), 3D non-immersive (3DNI - anaglyphic glasses), and 3DI (head mounted display with position and head orientation tracking). In Experiment 2, we examined how the use of different backgrounds affected MR processes within the 3DI environment. In Experiment 3, we compared electroencephalogram data recorded while participants were mentally rotating visual-spatial images presented in 3DI vs. 2DNI environments. Overall, the findings of the three experiments suggest that visual-spatial processing is different in immersive and non-immersive environments, and that immersive environments may require different image encoding and transformation strategies than the two other non-immersive environments. Specifically, in a non-immersive environment, participants may utilize a scene-based frame of reference and allocentric encoding whereas immersive environments may encourage the use of a viewer-centered frame of reference and egocentric encoding. These findings also suggest that MR performed in laboratory conditions using a traditional 2D computer screen may not reflect spatial processing as it would occur in the real world.

Massively parallel functional dissection of mammalian enhancers in vivo.

The functional consequences of genetic variation in mammalian regulatory elements are poorly understood. We report the in vivo dissection of three mammalian enhancers at single-nucleotide resolution through a massively parallel reporter assay. For each enhancer, we synthesized a library of >100,000 mutant haplotypes with 2-3% divergence from the wild-type sequence. Each haplotype was linked to a unique sequence tag embedded within a transcriptional cassette. We introduced each enhancer library into mouse liver and measured the relative activities of individual haplotypes en masse by sequencing the transcribed tags. Linear regression analysis yielded highly reproducible estimates of the effect of every possible single-nucleotide change on enhancer activity. The functional consequence of most mutations was modest, with ∼22% affecting activity by >1.2-fold and ∼3% by >2-fold. Several, but not all, positions with higher effects showed evidence for purifying selection, or co-localized with known liver-associated transcription factor binding sites, demonstrating the value of empirical high-resolution functional analysis.

Differences in cortical response to acupressure and electroacupuncture stimuli.

BACKGROUND: FMRI studies focus on sub-cortical effects of acupuncture stimuli. The purpose of this study was to assess changes in primary somatosensory (S1) activity over the course of different types of acupuncture stimulation. We used whole head magnetoencephalography (MEG) to map S1 brain response during 15 minutes of electroacupuncture (EA) and acupressure (AP). We further assessed how brain response changed during the course of stimulation. RESULTS: Evoked brain response to EA differed from AP in its temporal dynamics by showing clear contralateral M20/M30 peaks while the latter demonstrated temporal dispersion. Both EA and AP demonstrated significantly decreased response amplitudes following five minutes of stimulation. However, the latency of these decreases were earlier in EA (~30 ms post-stimulus) than AP (> 100 ms). Time-frequency responses demonstrated early onset, event related synchronization (ERS), within the gamma band at ~70-130 ms and the theta band at ~50-200 ms post-stimulus. A prolonged event related desynchronization (ERD) of alpha and beta power occurred at ~100-300 ms post-stimulus. There was decreased beta ERD at ~100-300 ms over the course of EA, but not AP. CONCLUSION: Both EA and AP demonstrated conditioning of SI response. In conjunction with their subcortical effects on endogenous pain regulation, these therapies show potential for affecting S1 processing and possibly altering maladaptive neuroplasticity. Thus, further investigation in neuropathic populations is needed.