RepEx: Repeat extractor for biological sequences

Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence (s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy. (C) 2013 Elsevier Inc. All rights reserved.

Conflict-tolerant specifications for hybrid systems

We propose a framework for developing and reasoning about hybrid systems that are comprised of a plant with multiple controllers, each of which controls the plant intermittently. The framework is based on the notion of a ``conflict tolerant'' specification for a controller, and provides a modular way of developing and reasoning about such systems. We propose a novel mechanism of defining conflict-tolerant specifications for general hybrid systems, using ``acceptor'' and ``advisor'' components. We also give a decision procedure for verifying whether a controller satisfies its conflict-tolerant specification, in the special case when the components are modeled using initialized rectangular hybrid automata.

On Using Nanoporous Alumina Films as Tribological Coating

Anodization of aluminum alloys is a common surface treatment procedure employed for the protection against corrosion. A thin amorphous layer of alumina is formed on the surface of alloy, which seals the alloy surface from the surrounding. This alumina layer being harder than the base aluminum alloy can be useful as a tribological coating. But since this alumina layer is randomly formed with disordered voids and pores, predicting the mechanical properties is difficult. Specific anodizing conditions can be used to form highly ordered anodic nanoporous alumina films 1] on the aluminum alloy surface. These nanoporous alumina layer can be effectively used as a tribological coating, because of the highly ordered controllable geometry and the empty pores which can be used as reservoirs for lubricant.

Nonequilibrium noise in electrophoresis: The microion wind

A colloid supported against gravitational settling by means of an imposed electric field behaves, on average, as if it is at equilibrium in a confining potential T. M. Squires, J. Fluid Mech. 443, 403 (2001)]. We show, however, that the effective Langevin equation for the colloid contains a nonequilibrium noise source, proportional to the field, arising from the thermal motion of dissolved ions. The position fluctuations of the colloid show strong, experimentally testable signatures of nonequilibrium behavior, including a highly anisotropic, frequency-dependent ``effective temperature'' obtained from the fluctuation-dissipation ratio.

Synthesis, characterization and spectroscopic investigation of Cr3+ doped wollastonite nanophosphor

This work explores the preparation of nanocrystalline Cr3+ (1-5 mol%) doped CaSiO3 phosphors by solution combustion process and study of its photoluminescence (PL) behavior. The nanopowders are well characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Fourier transform infra-red (FTIR) spectroscopy. PXRD results confirm monoclinic phase upon calcination at 950 degrees C for 3 h. SEM micrographs indicates that the powder is highly porous and agglomerated. The TEM images show the powder to consist of spherical shaped particles of size similar to 30-60 nm. Upon 323 nm excitation, the emission profile of CaSiO3:Cr3+ exhibits a narrow red emission peak at 641 nm due to E-2 -> (4)A(2) transition and broad band at 722 nm due to T-4(2g) -> (4)A(2g). It is observed that PL intensity increases with increase in Cr3+ concentration and highest PL intensity is observed for 3 mol% doped sample. The PL intensity decreases with further increase in Cr3+ doping. This decrease in PL intensity beyond 3 mol% is ascribed to concentration quenching. Racah parameters are calculated to describe the effects of electron-electron repulsion within the crystal lattice. The parameters show 21% reduction in the Racah parameter of free ion and the complex, indicating the moderate nephelauxetic effect in the lattice. (C) 2014 Elsevier B.V. All rights reserved.

Non-polio enterovirus association with persistent diarrhea in children as revealed by a follow-up study of an Indian cohort during the first two years of life

Background: We recently reported significant association of non-polio enteroviruses (NPEVs) with acute diarrhea in children. Persistent diarrhea (PD) remains a major cause of morbidity and mortality in infants below two years of age in developing countries. Understanding age-dependent frequency and duration of NPEV infections is important to determine their association with persistent diarrhea and disease burden. Objectives: A cohort of 140 infants was followed for 6 months to 2 years of age to determine the frequency, duration, and association with PD of NPEV infections in comparison with rotavirus and other agents. Study design: Stool samples were collected every 14 days, and diarrheal episodes and their duration were recorded. Enteroviruses were characterized by RT-PCR and VP1 gene sequence analysis, rotavirus by electropherotyping, and other agents by PCR. Results: Of 4545 samples, negative for oral polio vaccine strains, 3907 (85.96%) and 638 (14.04%) were NPEV-negative and NPEV-positive, respectively, representing 403 (8.87%) infection episodes. About 68% of NPEV infections occurred during the first year with every child having at least one episode lasting between four days and four months. Approximately 38% and 22% of total diarrheal episodes were positive for NPEV and RV, respectively. While about 18% of NPEV infection episodes were associated with diarrhea, 6% being persistent, 13% of total diarrheal episodes were persistent involving infections by monotype NPEV strains or sequential infections by multiple strains and other agents. Conclusions: This is the first report revealing NPEVs as the single most frequently and persistently detected viral pathogen in every PD episode. (C) 2014 Elsevier B.V. All rights reserved.

Influence of Surface Texture and Roughness of Softer and Harder Counter Materials on Friction During Sliding

Surface texture influences friction during sliding contact conditions. In the present investigation, the effect of surface texture and roughness of softer and harder counter materials on friction during sliding was analyzed using an inclined scratch testing system. In the experiments, two test configurations, namely (a) steel balls against aluminum alloy flats of different surface textures and (b) aluminum alloy pins against steel flats of different surface textures, are utilized. The surface textures were classified into unidirectionally ground, 8-ground, and randomly polished. For a given texture, the roughness of the flat surfaces was varied using grinding or polishing methods. Optical profilometer and scanning electron microscope were used to characterize the contact surfaces before and after the experiments. Experimental results showed that the surface textures of both harder and softer materials are important in controlling the frictional behavior. The softer material surface textures showed larger variations in friction between ground and polished surfaces. However, the harder material surface textures demonstrated a better control over friction among the ground surfaces. Although the effect of roughness on friction was less significant when compared to textures, the harder material roughness showed better correlations when compared to the softer material roughness.

Direct measurements of growing amorphous order and non-monotonic dynamic correlations in a colloidal glass-former

The transformation of flowing liquids into rigid glasses is thought to involve increasingly cooperative relaxation dynamics as the temperature approaches that of the glass transition. However, the precise nature of this motion is unclear, and a complete understanding of vitrification thus remains elusive. Of the numerous theoretical perspectives(1-4) devised to explain the process, random first-order theory (RFOT; refs 2,5) is a well-developed thermodynamic approach, which predicts a change in the shape of relaxing regions as the temperature is lowered. However, the existence of an underlying `ideal' glass transition predicted by RFOT remains debatable, largely because the key microscopic predictions concerning the growth of amorphous order and the nature of dynamic correlations lack experimental verification. Here, using holographic optical tweezers, we freeze a wall of particles in a two-dimensional colloidal glass-forming liquid and provide direct evidence for growing amorphous order in the form of a static point-to-set length. We uncover the non-monotonic dependence of dynamic correlations on area fraction and show that this non-monotonicity follows directly from the change in morphology and internal structure of cooperatively rearranging regions(6,7). Our findings support RFOT and thereby constitute a crucial step in distinguishing between competing theories of glass formation.

Inhibition of protein synthesis leading to unfolded protein response is the major event in abrin-mediated apoptosis

Abrin obtained from the plant Abrus precatorius inhibits protein synthesis and also triggers apoptosis in cells. Previous studies from our laboratory suggested a link between these two events. Using an active site mutant of abrin A-chain which exhibits 225-fold lower protein synthesis inhibitory activity than the wild-type abrin A-chain, we demonstrate in this study that inhibition of protein synthesis induced by abrin is the major factor triggering unfolded protein response leading to apoptosis. Since abrin A-chain requires the B-chain for internalization into cells, the wild-type and mutant recombinant abrin A-chains were conjugated to native ricin B-chain to generate hybrid toxins, and the toxic effects of the two conjugates were compared. The rate of inhibition of protein synthesis mediated by the mutant ricin B-rABRA (R167L) conjugate was slower than that of the wild-type ricin B-rABRA conjugate as expected. The mutant conjugate activated p38MAPK and caspase-3 similar to its wild-type counterpart although at later time points. Overall, these results confirm that inhibition of protein synthesis is the major event contributing to abrin-mediated apoptosis.

Stability analysis of thick piezoelectric metal based FGM plate using first order and higher order shear deformation theory

This paper presents the stability analysis of functionally graded plate integrated with piezoelectric actuator and sensor at the top and bottom face, subjected to electrical and mechanical loading. The finite element formulation is based on first order and higher order shear deformation theory, degenerated shell element, von-Karman hypothesis and piezoelectric effect. The equation for static analysis is derived by using the minimum energy principle and solutions for critical buckling load is obtained by solving eigenvalue problem. The material properties of the functionally graded plate are assumed to be graded along the thickness direction according to simple power law function. Two types of boundary conditions are used, such as SSSS (simply supported) and CSCS (simply supported along two opposite side perpendicular to the direction of compression and clamped along the other two sides). Sensor voltage is calculated using present analysis for various power law indices and FG (functionally graded) material gradations. The stability analysis of piezoelectric FG plate is carried out to present the effects of power law index, material variations, applied mechanical pressure and piezo effect on buckling and stability characteristics of FG plate.

Investigation on Depth of Heat Affected Zone of Discharge Spot by High Repetitive Rate YAG Laser-Induced Discharge Texturing

It is known that the press formability and the elongation of laser textured sheet are improved, and the service life of textured roll is longer than that of the un-textured roll due to hardening of the treated surface. One of the goals to develop high repetitive rate YAG laser-induced discharge texturing (LIDT) is to get deeper hardening zone. By observing and measuring cross-section of LIDT spots in different discharge conditions, it is found that the single-crater, which is formed by the discharge conditions of anode, which is covered by an oil film and with rectangular current waveform, has the most depth of heat affected zone (HAZ) comparing with other crater shapes when discharge energy is the same. The depth of HAZ is mainly depends on pulse duration when the discharge spot is single-crater. The results are analyzed.

The challenge of cancer control in Africa.

While the world is focused on controlling the spread of diseases such as HIV and malaria in the developing world, another approaching epidemic has been largely overlooked. The World Heath Organization predicts that there will be 16 million new cancer cases per year in 2020 and 70% of these will be in the developing world. Many of these cancers are preventable, or treatable when detected early enough. Establishing effective, affordable and workable cancer control plans in African countries is one step in the right direction toward limiting this epidemic.

Estudio retrospectivo de mortalidad (1994-1998) y manejo sanitario en períodos de desarrollo y engorde (marzo-septiembre, 1999) de conejos comerciales en la Granja Experimental de FACA-UNA

El presente estudio se realizó en la granja cunícula de la Facultad de Ciencia Animal de la Universidad Nacional Agraria, ubicada en el Km. 12 1/2 de la carretera Norte, Managua, Nicaragua. El cual abarca una fase retrospectiva y una prospectiva, realizándose con ayuda de los registros productivos y reproductivos de cada animal. El objetivo del estudio fue establecer retrospectivamente las tasas de mortalidad del período de enero de 1994 a diciembre de 1998, e implementar un plan sanitario en forma prospectiva con el fin de disminuir la mortalidad encontrada en los años anteriores. Las fases del estudio realizado se enfocaron en el análisis de la mortalidad de los animales, teniendo como variables las diferentes categorías, raza, destino, mes y año. En la fase retrospectiva, la mortalidad de las hembras por raza dio como resultado, un porcentaje de muertos mayor en la raza Neozelandés Blanca con 27 hembras muertas representando el 48.2 % de la mortalidad entre 8 diferentes razas, presentándose las muertes en su mayoría en los meses de época seca, así como también 403 gazapos muertos lo que representa un porcentaje de 58 %. En la fase prospectiva, el total de conejos estudiados fue de 112, de los cuales se obtuvo un total de 4 hembras muertas para un porcentaje de 14.28% en lo que respecta a su categoría. El porcentaje de mortalidad de los gazapos al nacimiento fue de 25.8% dándose el número mayor de muertos en la época seca. En la categoría de engorde fue un total de 11 conejos muertos lo que representa el 13.9% de mortalidad en esa categoría. Los resultados demuestran que la implementación de un plan sanitario es indispensable para una alta producción de conejos, ya que sin este el índice de mortalidad e incidencia de enfermedades se aumentan, igualmente el factor económico haciendo gastos innecesarios en medicamentos para curar las enfermedades.