Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria

A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease. In this context, we surveyed and compared variation databases along with in silico prediction programs to assess the effects of deleterious functional variants on protein functions. In other respects, we attempted these methods to work as first-pass filter to identify the deleterious substitutions worth pursuing for further experimental research. In this analysis, we used the existing computational methods to explore the mutation-structure-function relationship in HGD gene causing alkaptonuria

Produção de acessos de mangarito em função do tamanho de mudas e níveis de adubação fosfada.

Com o objetivo de incrementar a produtividade foram avaliados dois acessos (CNPH 276 E CNPH 177), dois tamanhos de muda (tamanho pequeno - TP e muito pequeno - TPM) e doses de adubação fosfatada.Suplemento. Trabalho apresentado no 52. Congresso Brasileiro de Olericultura, Salvador, 2012

Chromatic Dynamics of an Electron Beam in a Plasma Based Accelerator

We present a theoretical investigation of the chromatic dynamics of the witness beam within a plasma based accelerator. We derive the single particle motion of an electron in an ion column within a nonlinear, blowout wake including adiabatic dampening and adiabatic variations in plasma density. Using this, we calculate the evolution of the beam moments and emittance for an electron beam. Our model can handle near arbitrary longitudinal phase space distributions. We include the effects of energy change in the beam, imperfect wake loading, initial transverse offsets of the beam, and mismatch between the beam and plasma. We use our model to derive analytic saturation lengths for the projected, longitudinal slice, and energy slice emittance under different beam loading conditions. Further, we show that the centroid oscillations and spot sizes vary between the slices and the variation depends strongly on the beam loading. Next, we show how a beam evolves in a full plasma source with density ramps and show that the integral of the plasma density along the ramp determines the impact on the beam. Finally, we derive several simple scaling laws that show how to design a plasma based injector to produce a target beam energy and energy spread.Comment: 17 pages, 10 figure

Mixed-mode oscillations and interspike interval statistics in the stochastic FitzHugh-Nagumo model

We study the stochastic FitzHugh-Nagumo equations, modelling the dynamics of neuronal action potentials, in parameter regimes characterised by mixed-mode oscillations. The interspike time interval is related to the random number of small-amplitude oscillations separating consecutive spikes. We prove that this number has an asymptotically geometric distribution, whose parameter is related to the principal eigenvalue of a substochastic Markov chain. We provide rigorous bounds on this eigenvalue in the small-noise regime, and derive an approximation of its dependence on the system's parameters for a large range of noise intensities. This yields a precise description of the probability distribution of observed mixed-mode patterns and interspike intervals.Comment: 36 page

Seleção de clones de mandioquinha-salsa em áreas naturalmente infestadas pelo nematoide-das-galhas por meio de escala de notas.

Realizou-se este trabalho com o objetivo de avaliar clones de mandioquinha-salsa quanto à reação a Meloidogyne spp. por meio da elaboração de uma escala de notas.bitstream/item/85035/1/bpd-93.pd

The 1995-1996 Decline of R Coronae Borealis - High Resolution Optical Spectroscopy

A set of high-resolution optical spectra of RCrB acquired before, during, and after its 1995-1996 decline is discussed. All of the components reported from earlier declines are seen. This novel dataset provides new information on these components including several aspects not previously seen in declines of RCrB and other RCBs. In the latter category is the discovery that the decline's onset is marked by distortions of absorption lines of high-excitation lines, and quickly followed by emission in these and in low excitation lines. This 'photospheric trigger' implies that dust causing the decline is formed close to the star. These emission lines fade quickly. After 1995 November 2, low excitation narrow (FWHM ~12 km s-1) emission lines remain. These appear to be a permanent feature, slightly blue-shifted from the systemic velocity, and unaffected by the decline except for a late and slight decrease of flux at minimum light. The location of the warm, dense gas providing these lines is uncertain. Absorption lines unaffected by overlying sharp emission are greatly broadened, weakened, and red-shifted at the faintest magnitudes when scattered light from the star is a greater contributor than direct light transmitted through the fresh soot cloud. A few broad lines are seen at and near minimum light with approxiamately constant flux: prominent among these are the He I triplet series, Na I D, and [N II] lines. These lines are blue-shifted by about 30 km s(-1) relative to the systemic velocity with no change in velocity over the several months for whicht he lines were seen. It is suggested that these lines, especially the He I lines, arise from an accretion disk around an unseen compact companion, which may be a low-mass white dwarf. If so, R CrB is similar to the unusual post-AGB star 89 Her.Comment: 31 pages, 26 figure

An extensive computational approach to analyze and characterize the functional mutations in the galactose-1-phosphate uridyl transferase (GALT) protein responsible for classical galactosemia

Type I galactosemia is a very rare autosomal recessive genetic metabolic disorder that occurs because of the mutations present in the galactose-1-phosphate uridyl transferase (GALT) gene, resulting in a deficiency of the GALT enzyme. The action of the GALT enzyme is to convert galactose-1-phosphate and uridine diphosphate glucose into glucose-1-phosphate (G1P) and uridine diphosphate-galactose, a crucial second step of the Leloir pathway. A missense mutation in the GALT enzyme leads to variable galactosemia's clinical presentations, ranging from mild to severe. Our study aimed to employ a comprehensive computational pipeline to analyze the most prevalent missense mutations (p.S135L, p.K285 N, p.Q188R, and p.N314D) responsible for galactosemia; these genes could serve as potential targets for chaperone therapy. We analyzed the four mutations through different computational analyses, including amino acid conservation, in silico pathogenicity and stability predictions, and macromolecular simulations (MMS) at 50 ns The stability and pathogenicity predictors showed that the p.Q188R and p.S135L mutants are the most pathogenic and destabilizing. In agreement with these results, MMS analysis demonstrated that the p.Q188R and p.S135L mutants possess higher deviation patterns, reduced compactness, and intramolecular H-bonds of the protein. This could be due to the physicochemical modifications that occurred in the mutants p.S135L and p.Q188R compared to the native. Evolutionary conservation analysis revealed that the most prevalent mutations positions were conserved among different species except N314. The proposed research study is intended to provide a basis for the therapeutic development of drugs and future treatment of classical galactosemia and possibly other genetic diseases using chaperone therapy

Maximum Azimuthal Anisotropy of Neutrons from Nb-Nb Collisions at 400 AMeV and the Nuclear Equation of State

We measured the first azimuthal distributions of triple--differential cross sections of neutrons emitted in heavy-ion collisions, and compared their maximum azimuthal anisotropy ratios with Boltzmann--Uehling--Uhlenbeck (BUU) calculations with a momentum-dependent interaction. The BUU calculations agree with the triple- and double-differential cross sections for positive rapidity neutrons emitted at polar angles from 7 to 27 degrees; however, the maximum azimuthal anisotropy ratio for these free neutrons is insensitive to the size of the nuclear incompressibility modulus K characterizing the nuclear matter equation of state.Comment: Typeset using ReVTeX, with 3 ps figs., uuencoded and appende

Neutrons from multiplicity-selected La-La and Nb-Nb collisions at 400A MeV and La-La collisions at 250A MeV

Triple-differential cross sections for neutrons from high-multiplicity La-La collisions at 250 and 400 MeV per nucleon and Nb-Nb collisions at 400 MeV per nucleon were measured at several polar angles as a function of the azimuthal angle with respect to the reaction plane of the collision. The reaction plane was determined by a transverse-velocity method with the capability of identifying charged-particles with Z=1, Z=2, and Z > 2. The flow of neutrons was extracted from the slope at mid-rapidity of the curve of the average in-plane momentum vs the center-of-mass rapidity. The squeeze-out of the participant neutrons was observed in a direction normal to the reaction plane in the normalized momentum coordinates in the center-of-mass system. Experimental results of the neutron squeeze-out were compared with BUU calculations. The polar-angle dependence of the maximum azimuthal anisotropy ratio $r(\theta)$ was found to be insensitive to the mass of the colliding nuclei and the beam energy. Comparison of the observed polar-angle dependence of the maximum azimuthal anisotropy ratio $r(\theta)$ with BUU calculations for free neutrons revealed that $r(\theta)$ is insensitive also to the incompressibility modulus in the nuclear equation of state.Comment: ReVTeX, 16 pages, 17 figures. To be published in Physical Review

Inundation mapping – a study based on December 2004 Tsunami Hazard along Chennai coast, Southeast India

Tsunami impact study has been undertaken along Chennai coast starting from Pulicat to Kovalam. The study area Chennai coast is mainly devoted to prepare large scale action plan maps on tsunami inundation incorporating land use details derived from satellite data along with cadastral data using a GIS tool. Under tsunami inundation mapping along Chennai coast an integrated approach was adopted to prepare thematic maps on land use/land cover and coastal geomorphology using multispectral remote sensing data. The RTK dGPS instruments are used to collect elevation contour data at 0.5 m intervals for the Chennai coast. The GIS tool has been used to incorporate the elevation data, tsunami inundation markings obtained immediately after tsunami and thematic maps derived from remote sensing data. The outcome of this study provides an important clue on variations in tsunami inundation along Chennai coast, which is mainly controlled by local geomorphologic set-up, coastal zone elevation including coastal erosion protection measures and near shore bathymetry. This study highlights the information regarding most vulnerable areas of tsunami and also provides indication to demarcate suitable sites for rehabilitation