Layerwise decomposition of water dynamics in reverse micelles: A simulation study of two-dimensional infrared spectrum

We present computer simulation study of two-dimensional infrared spectroscopy (2D-IR) of water confined in reverse micelles (RMs) of various sizes. The present study is motivated by the need to understand the altered dynamics of confined water by performing layerwise decomposition of water, with an aim to quantify the relative contributions of different layers water molecules to the calculated 2D-IR spectrum. The 0-1 transition spectra clearly show substantial elongation, due to in-homogeneous broadening and incomplete spectral diffusion, along the diagonal in the surface water layer of different sized RMs. Fitting of the frequency fluctuation correlation functions reveal that the motion of the surface water molecules is sub-diffusive and indicate the constrained nature of their dynamics. This is further supported by two peak nature of the angular analogue of van Hove correlation function. With increasing system size, the water molecules become more diffusive in nature and spectral diffusion almost completes in the central layer of the larger size RMs. Comparisons between experiments and simulations establish the correspondence between the spectral decomposition available in experiments with the spatial decomposition available in simulations. Simulations also allow a quantitative exploration of the relative role of water, sodium ions, and sulfonate head groups in vibrational dephasing. Interestingly, the negative cross correlation between force on oxygen and hydrogen of O-H bond in bulk water significantly decreases in the surface layer of each RM. This negative cross correlation gradually increases in the central water pool with increasing RMs size and this is found to be partly responsible for the faster relaxation rate of water in the central pool. (C) 2013 AIP Publishing LLC.

Mechanism design for cost optimal PAC learning in the presence of strategic noisy annotators

We consider the problem of Probably Ap-proximate Correct (PAC) learning of a bi-nary classifier from noisy labeled exam-ples acquired from multiple annotators(each characterized by a respective clas-sification noise rate). First, we consider the complete information scenario, where the learner knows the noise rates of all the annotators. For this scenario, we derive sample complexity bound for the Mini-mum Disagreement Algorithm (MDA) on the number of labeled examples to be ob-tained from each annotator. Next, we consider the incomplete information sce-nario, where each annotator is strategic and holds the respective noise rate as a private information. For this scenario, we design a cost optimal procurement auc-tion mechanism along the lines of Myer-son’s optimal auction design framework in a non-trivial manner. This mechanism satisfies incentive compatibility property,thereby facilitating the learner to elicit true noise rates of all the annotators.

Modeling and analysis of MOS capacitor controlled by independent double gates

This paper, for the first time, explores the charcatersictics of MOS capacitor controlled by independent double gates by numerical simulation and analytical modeling for its possible use in RF circuit design as a varactor. By numerical simulation it is shown how the quasi-static and non-quasi-static characteristics of the first gate capacitance could be tuned by the second gate biases. Effect of body doping and energy quantization are also discussed in this regard. A semi-empirical quasi-static model is also developed by using the existing incomplete Poisson solution of independent double gate transistors. Proposed model, which is valid from accumulation to inversion, is shown to have excellent agreement with numerical simulation for practical bias conditions.

Inhibition of cancer cell proliferation and apoptosis-inducing activity of fungal taxol and its precursor baccatin III purified from endophytic Fusarium solani

Background: Taxol (generic name paclitaxel), a plant-derived antineoplastic agent, used widely against breast, ovarian and lung cancer, was originally isolated from the bark of the Pacific yew, Taxus brevifolia. The limited supply of the drug has prompted efforts to find alternative sources, such as chemical synthesis, tissue and cell cultures of the Taxus species both of which are expensive and yield low levels. Fermentation processes with microorganisms would be the methods of choice to lower the costs and increase yields. Previously we have reported that F. solani isolated from T. celebica produced taxol and its precursor baccatin III in liquid grown cultures J Biosci 33: 259-67, 2008. This study was performed to evaluate the inhibition of proliferation and induction of apoptosis of cancer cell lines by the fungal taxol and fungal baccatin III of F. solani isolated from T. celebica. Methods: Cell lines such as HeLa, HepG2, Jurkat, Ovcar3 and T47D were cultured individually and treated with fungal taxol, baccatin III with or without caspase inhibitors according to experimental requirements. Their efficacy on apoptotic induction was examined. Results: Both fungal taxol and baccatin III inhibited cell proliferation of a number of cancer cell lines with IC50 ranging from 0.005 to 0.2 mu M for fungal taxol and 2 to 5 mu M for fungal baccatin III. They also induced apoptosis in JR4-Jurkat cells with a possible involvement of anti-apoptotic Bcl2 and loss in mitochondrial membrane potential, and was unaffected by inhibitors of caspase-9,-2 or -3 but was prevented in presence of caspase-10 inhibitor. DNA fragmentation was also observed in cells treated with fungal taxol and baccatin III. Conclusions: The cytotoxic activity exhibited by fungal taxol and baccatin III involves the same mechanism, dependent on caspase-10 and membrane potential loss of mitochondria, with taxol having far greater cytotoxic potential.

Effects of elastase and collagenase on the nonlinearity and anisotropy of porcine aorta

We use enzymatic manipulation methods to investigate the individual and combined roles of elastin and collagen on arterial mechanics. Porcine aortic tissues were treated for differing amounts of time using enzymes elastase and collagenase to cause degradation in substrate proteins elastin and collagen and obtain variable tissue architecture. We use equibiaxial mechanical tests to quantify the material properties of control and enzyme treated tissues and histological methods to visualize the underlying tissue microstructure in arterial tissues. Our results show that collagenase treated tissues were more compliant in the longitudinal direction as compared to control tissues. Collagenase treatment also caused a decrease in the tissue nonlinearity as compared to the control samples in the study. A one hour collagenase treatment was sufficient to cause fragmentation and degradation of the adventitial collagen. In contrast, elastase treatment leads to significantly stiffer tissue response associated with fragmented and incomplete elastin networks in the tissue. Thus, elastin in arterial walls distributes tensile stresses whereas collagen serves to reinforce the vessel wall in the circumferential direction and also contributes to tissue anisotropy. A microstructurally motivated strain energy function based on circumferentially oriented medial fibers and helically oriented collagen fibers in the adventitia is useful in describing these experimental results.

Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

ELLIPSE FITTING USING FINITE RATE OF INNOVATION PRINCIPLES

We address the problem of parameter estimation of an ellipse from a limited number of samples. We develop a new approach for solving the ellipse fitting problem by showing that the x and y coordinate functions of an ellipse are finite-rate-of-innovation (FRI) signals. Uniform samples of x and y coordinate functions of the ellipse are modeled as a sum of weighted complex exponentials, for which we propose an efficient annihilating filter technique to estimate the ellipse parameters from the samples. The FRI framework allows for estimating the ellipse parameters reliably from partial or incomplete measurements even in the presence of noise. The efficiency and robustness of the proposed method is compared with state-of-art direct method. The experimental results show that the estimated parameters have lesser bias compared with the direct method and the estimation error is reduced by 5-10 dB relative to the direct method.

Lineage delimitation and description of nine new species of bush frogs (Anura: Raorchestes, Rhacophoridae) from the Western Ghats Escarpment

Bush frogs of the genus Raorchestes are distributed mainly in the Western Ghats Escarpment of Peninsular India. The inventory of species in this genus is incomplete and there is ambiguity in the systematic status of species recognized by morphological criteria. To address the dual problem of taxon sampling and systematic uncertainty in bush frogs, we used a large-scale spatial sampling design, explicitly incorporating the geographic and ecological heterogeneity of the Western Ghats. We then used a hierarchical multi-criteria approach by combining mitochondrial phylogeny, genetic distance, geographic range, morphology and advertisement call to delimit bush frog lineages. Our analyses revealed the existence of a large number of new lineages with varying levels of genetic divergence. Here, we provide diagnoses and descriptions for nine lineages that exhibit divergence across multiple axes. The discovery of new lineages that exhibit high divergence across wide ranges of elevation and across the major massifs highlights the large gaps in historical sampling. These discoveries underscore the significance of addressing inadequate knowledge of species distribution, namely the ``Wallacean shortfall'', in addressing the problem of taxon sampling and unknown diversity in tropical hotspots. A biogeographically informed sampling and analytical approach was critical in detecting and delineating lineages in a consistent manner across the genus. Through increased taxon sampling, we were also able to discern a number of well-supported sub-clades that were either unresolved or absent in earlier phylogenetic reconstructions and identify a number of shallow divergent lineages which require further examination for assessment of their taxonomic status.

Estimation of `drainable' storage - A geomorphological approach

Storage of water within a river basin is often estimated by analyzing recession flow curves as it cannot be `instantly' estimated with the aid of available technologies. In this study we explicitly deal with the issue of estimation of `drainable' storage, which is equal to the area under the `complete' recession flow curve (i.e. a discharge vs. time curve where discharge continuously decreases till it approaches zero). But a major challenge in this regard is that recession curves are rarely `complete' due to short inter-storm time intervals. Therefore, it is essential to analyze and model recession flows meaningfully. We adopt the wellknown Brutsaert and Nieber analytical method that expresses time derivative of discharge (dQ/dt) as a power law function of Q : -dQ/dt = kQ(alpha). However, the problem with dQ/dt-Q analysis is that it is not suitable for late recession flows. Traditional studies often compute alpha considering early recession flows and assume that its value is constant for the whole recession event. But this approach gives unrealistic results when alpha >= 2, a common case. We address this issue here by using the recently proposed geomorphological recession flow model (GRFM) that exploits the dynamics of active drainage networks. According to the model, alpha is close to 2 for early recession flows and 0 for late recession flows. We then derive a simple expression for drainable storage in terms the power law coefficient k, obtained by considering early recession flows only, and basin area. Using 121 complete recession curves from 27 USGS basins we show that predicted drainable storage matches well with observed drainable storage, indicating that the model can also reliably estimate drainable storage for `incomplete' recession events to address many challenges related to water resources. (C) 2014 Elsevier Ltd. All rights reserved.

Expression of Bioactive Callithrix jacchus Follicle-Stimulating Hormone in Pichia pastoris

Callithrix jacchus (common marmoset) is a New World primate monkey, used as an animal model in biomedical research. Marmoset-specific follicle-stimulating hormone (FSH) preparation is required to improve superovulation protocols and to develop homologous FSH monitoring assays in these monkeys. In this study, we document the large-scale expression of recombinant marmoset FSH in methylotropic yeast, Pichia pastoris. The recombinant preparation was found to be immunologically active in Western blotting and radioimmunoassay. The preparation displayed receptor binding ability in radioreceptor assay. Based on the receptor binding ability, the yield of fermentation was estimated to be 7.2 mg/L. FSH-induced cAMP assay and estradiol assay revealed that the recombinant hormone is able to induce signal transduction. Both immunological and in vitro biological activity of marmoset FSH was found to be comparable to purified human pituitary FSH, which served as reference hormone for these assays. Thus, the study suggests that a Pichia expression system can be used for large-scale expression of bioactive recombinant marmoset FSH.

Cytotoxicity of Ultrasmall Gold Nanoparticles on Planktonic and Biofilm Encapsulated Gram-Positive Staphylococci

The emergence of multidrug resistant bacteria, especially biofilm-associated Staphylococci, urgently requires novel antimicrobial agents. The antibacterial activity of ultrasmall gold nanoparticles (AuNPs) is tested against two gram positive: S. aureus and S. epidermidis and two gram negative: Escherichia coli and Pseudomonas aeruginosa strains. Ultrasmall AuNPs with core diameters of 0.8 and 1.4 nm and a triphenylphosphine-monosulfonate shell (Au0.8MS and Au1.4MS) both have minimum inhibitory concentration (MIC) and minimum bactericidal concentration of 25 x 10(-6)m Au]. Disc agar diffusion test demonstrates greater bactericidal activity of the Au0.8MS nanoparticles over Au1.4MS. In contrast, thiol-stabilized AuNPs with a diameter of 1.9 nm (AuroVist) cause no significant toxicity in any of the bacterial strains. Ultrasmall AuNPs cause a near 5 log bacterial growth reduction in the first 5 h of exposure, and incomplete recovery after 21 h. Bacteria show marked membrane blebbing and lysis in biofilm-associated bacteria treated with ultrasmall AuNP. Importantly, a twofold MIC dosage of Au0.8MS and Au1.4MS each cause around 80%-90% reduction in the viability of Staphylococci enveloped in biofilms. Altogether, this study demonstrates potential therapeutic activity of ultrasmall AuNPs as an effective treatment option against staphylococcal infections.

Regional hydrological impacts of climate change: implications for water management in India

Climate change is most likely to introduce an additional stress to already stressed water systems in developing countries. Climate change is inherently linked with the hydrological cycle and is expected to cause significant alterations in regional water resources systems necessitating measures for adaptation and mitigation. Increasing temperatures, for example, are likely to change precipitation patterns resulting in alterations of regional water availability, evapotranspirative water demand of crops and vegetation, extremes of floods and droughts, and water quality. A comprehensive assessment of regional hydrological impacts of climate change is thus necessary. Global climate model simulations provide future projections of the climate system taking into consideration changes in external forcings, such as atmospheric carbon-dioxide and aerosols, especially those resulting from anthropogenic emissions. However, such simulations are typically run at a coarse scale, and are not equipped to reproduce regional hydrological processes. This paper summarizes recent research on the assessment of climate change impacts on regional hydrology, addressing the scale and physical processes mismatch issues. Particular attention is given to changes in water availability, irrigation demands and water quality. This paper also includes description of the methodologies developed to address uncertainties in the projections resulting from incomplete knowledge about future evolution of the human-induced emissions and from using multiple climate models. Approaches for investigating possible causes of historically observed changes in regional hydrological variables are also discussed. Illustrations of all the above-mentioned methods are provided for Indian regions with a view to specifically aiding water management in India.

Modeling harvest rates and numbers from age and sex ratios: A demonstration for elephant populations

Illegal harvest rates of wildlife populations are often unknown or difficult to estimate from field data due to under-reporting or incomplete detection of carcasses. This is especially true for elephants that are killed for ivory or in conflicts with people. We describe a method to infer harvest rates from coarse field data of three population parameters, namely, adult female to male ratio, male old-adult to young-adult ratio, and proportion of adult males in the population using Jensen's (2000) 2-sex, density-dependent Leslie matrix model. The specific combination of male and female harvest rates and numbers can be determined from the history of harvest and estimate of population size. We applied this technique to two populations of elephants for which data on age structure and records of mortality were available-a forest-dwelling population of the Asian elephant (at Nagarahole, India) and an African savannah elephant population (at Samburu, Kenya) that had experienced male-biased harvest regimes over 2-3 decades. For the Nagarahole population, the recorded numbers of male and female elephants killed illegally during 1981-2000 were 64% and 88% of the values predicted by the model, respectively, implying some non-detection or incomplete reporting while for the Samburu population the recorded and modeled numbers of harvest during 1990-1999 closely matched. This technique, applicable to any animal population following logistic growth model, can be especially useful for inferring illegal harvest numbers of forest elephants in Africa and Asia. (C) 2013 Elsevier Ltd. All rights reserved.

Folivory as a Constraint on Social Behaviour of Langurs in South India

Folivory, being a dietary constraint, can affect the social time of colobines. In the present study, we compared food items and activity budgets of two closely related species of colobines inhabiting South India, i.e. the Hanuman langur (Semnopithecus hypoleucos) and Nilgiri langur (Semnopithecus johnii), to determine whether folivory had an impact on social time in these species. Our study established that Nilgiri langurs were more folivorous than Hanuman langurs. Nilgiri langurs spent much less time on social activities, but more time on resting, although the social organization of S. hypoleucos was similar to that of the Nilgiri langur. The enforced resting time for fermentation of leafy food items may have reduced the time available for social interactions, which in turn affected the social time in Nilgiri langurs. By comparing the data from previous studies on other Hanuman langur species, we found that S. hypoleucos spent a similar amount of time on social activities as Semnopithecus entellus. Hence, the social behaviour of S. entellus and S. hypoleucos is phylogenetically highly conservative. (C) 2015 S. Karger AG, Basel

Boron clusters in luminescent materials

In recent times, luminescent materials with tunable emission properties have found applications in almost all aspects of modern material sciences. Any discussion on the recent developments in luminescent materials would be incomplete if one does not account for the versatile photophysical features of boron containing compounds. Apart from triarylboranes and tetra-coordinate borate dyes, luminescent materials consisting of boron clusters have also found immense interest in recent times. Recent studies have unveiled the opportunities hidden within boranes, carboranes and metalloboranes, etc. as active constituents of luminescent materials. From simple illustrations of luminescence, to advanced applications in LASERs, OLEDs and bioimaging, etc., the unique features of such compounds and their promising versatility have already been established. In this review, recent revelations about the excellent photophysical properties of such materials are discussed.