Extended depth from focus reconstruction using NIH ImageJ plugins: Quality and resolution of elevation maps

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Stochastic Skellam model

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

LaTBP1: A Leishmania amazonensis DNA-binding protein that associates in vivo with telomeres and GT-rich DNA using a Myb-like domain

Different species of Leishmania can cause a variety of medically important diseases, whose control and treatment are still health problems. Telomere binding proteins (TBPs) have potential as targets for anti-parasitic chemotherapy because of their importance for genome stability and cell viability. Here, we describe LaTBP1 a protein that has a Myb-like DNA-binding domain, a feature shared by most double-stranded telomeric proteins. Binding assays using full-length and truncated LaTBP1 combined with spectroscopy analysis were used to map the boundaries of the Myb-like domain near to the protein only tryptophan residue. The Myb-like domain of LaTBP1 contains a conserved hydrophobic cavity implicated in DNA-binding activity. A hypothetical model helped to visualize that it shares structural homology with domains of other Myb-containing proteins. Competition assays and chromatin immunoprecipitation confirmed the specificity of LaTBP1 for telomeric and GT-rich DNAs, suggesting that LaTBP1 is a new TBP. (C) 2007 Elsevier B.V. All rights reserved.

The two-loop massless (lambda/4!)phi(4) model in nontranslational invariant domain

We study the (lambda/4!)phi(4) massless scalar field theory in a four-dimensional Euclidean space, where all but one of the coordinates are unbounded. We are considering Dirichlet boundary conditions in two hyperplanes, breaking the translation invariance of the system. We show how to implement the perturbative renormalization up to two-loop level of the theory. First, analyzing the full two and four-point functions at the one-loop level, we show that the bulk counterterms are sufficient to render the theory finite. Meanwhile, at the two-loop level, we must also introduce surface counterterms in the bare Lagrangian in order to make finite the full two and also four-point Schwinger functions. (c) 2006 American Institute of Physics.

Dental caries and the nutritional status of preschool children: a spatial analysis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Spatial and temporal profiles for anti-inflammatory gene expression in leukocytes during a resolving model of peritonitis

The recent appreciation of the role played by endogenous counterregulatory mechanisms in controlling the outcome of the host inflammatory response requires specific analysis of their spatial and temporal profiles. In this study, we have focused on the glucocorticoid-regulated anti-inflammatory mediator annexin 1. Induction of peritonitis in wild-type mice rapidly (4 h) produced the expected signs of inflammation, including marked activation of resident cells (e.g., mast cells), migration of blood-borne leukocytes, mirrored by blood neutrophilia. These changes subsided after 48-96 h. In annexin 1null mice, the peritonitis response was exaggerated (∼40% at 4 h), with increased granulocyte migration and cytokine production. In blood leukocytes, annexin 1 gene expression was activated at 4, but not 24, h postzymosan, whereas protein levels were increased ai both time points. Locally, endothelial and mast cell annexin 1 gene expression was not detectable in basal conditions, whereas it was switched on during the inflammatory response. The significance of annexin 1 system plasticity in the anti-inflammatory properties of dexamethasone was assessed. Clear induction of annexin 1 gene in response to dexamethasone treatment was evident in the circulating and migrated leukocytes, and in connective tissue mast cells; this was associated with the steroid failure to inhibit leukocyte trafficking, cytokine synthesis, and mast cell degranulation in the annexin 1null mouse. In conclusion, understanding how inflammation is brought under control will help clarify the complex interplay between pro- and anti-inflammatory pathways operating during the host response to injury and infection. Copyright © 2006 by The American Association of Immunologists, Inc.

Domain reduction using GRASP construction phase for transmission expansion planning problem

This paper proposes a new strategy to reduce the combinatorial search space of a mixed integer linear programming (MILP) problem. The construction phase of greedy randomized adaptive search procedure (GRASP-CP) is employed to reduce the domain of the integer variables of the transportation model of the transmission expansion planning (TM-TEP) problem. This problem is a MILP and very difficult to solve specially for large scale systems. The branch and bound (BB) algorithm is used to solve the problem in both full and the reduced search space. The proposed method might be useful to reduce the search space of those kinds of MILP problems that a fast heuristic algorithm is available for finding local optimal solutions. The obtained results using some real test systems show the efficiency of the proposed method. © 2012 Springer-Verlag.

Small-angle X-ray scattering and structural modeling of full-length: Cellobiohydrolase I from Trichoderma harzianum

Cellobiohydrolases hydrolyze cellulose releasing cellobiose units. They are very important for a number of biotechnological applications, such as, for example, production of cellulosic ethanol and cotton fiber processing. The Trichoderma cellobiohydrolase I (CBH1 or Cel7A) is an industrially important exocellulase. It exhibits a typical two domain architecture, with a small C-terminal cellulose-binding domain and a large N-terminal catalytic core domain, connected by an O-glycosylated linker peptide. The mechanism by which the linker mediates the concerted action of the two domains remains a conundrum. Here, we probe the protein shape and domain organization of the CBH1 of Trichoderma harzianum (ThCel7A) by small angle X-ray scattering (SAXS) and structural modeling. Our SAXS data shows that ThCel7A linker is partially-extended in solution. Structural modeling suggests that this linker conformation is stabilized by inter- and intra-molecular interactions involving the linker peptide and its O-glycosylations. © 2013 Springer Science+Business Media Dordrecht.

DNA for nano-bio scale computation of chemical formalisms using Higher Order Logic (HOL) and analysis using an interdisciplinary approach

Bio-molecular computing, 'computations performed by bio-molecules', is already challenging traditional approaches to computation both theoretically and technologically. Often placed within the wider context of ´bio-inspired' or 'natural' or even 'unconventional' computing, the study of natural and artificial molecular computations is adding to our understanding of biology, physical sciences and computer science well beyond the framework of existing design and implementation paradigms. In this introduction, We wish to outline the current scope of the field and assemble some basic arguments that, bio-molecular computation is of central importance to computer science, physical sciences and biology using HOL - Higher Order Logic. HOL is used as the computational tool in our R&D work. DNA was analyzed as a chemical computing engine, in our effort to develop novel formalisms to understand the molecular scale bio-chemical computing behavior using HOL. In our view, our focus is one of the pioneering efforts in this promising domain of nano-bio scale chemical information processing dynamics.

Modular Hyperthermostable Bacterial Endo-beta-1, 4-Mannanase: Molecular Shape, Flexibility and Temperature-Dependent Conformational Changes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

An Informatics Technical Note on Interaction of DNA - Graphene Chemical Sensor System as Reaction-Diffusion Wave-Based Computing System in Ionised Gaseous environments and their Applications Using Theoretical Studies and Scientific Computation Overview

The physics of plasmas encompasses basic problems from the universe and has assured us of promises in diverse applications to be implemented in a wider range of scientific and engineering domains, linked to most of the evolved and evolving fundamental problems. Substantial part of this domain could be described by R–D mechanisms involving two or more species (reaction–diffusion mechanisms). These could further account for the simultaneous non-linear effects of heating, diffusion and other related losses. We mention here that in laboratory scale experiments, a suitable combination of these processes is of vital importance and very much decisive to investigate and compute the net behaviour of plasmas under consideration. Plasmas are being used in the revolution of information processing, so we considered in this technical note a simple framework to discuss and pave the way for better formalisms and Informatics, dealing with diverse domains of science and technologies. The challenging and fascinating aspects of plasma physics is that it requires a great deal of insight in formulating the relevant design problems, which in turn require ingenuity and flexibility in choosing a particular set of mathematical (and/or experimental) tools to implement them.

A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Determination of quality parameters for mustard sauces in sealed packets using time-domain nuclear magnetic resonance spectroscopy and chemometrics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)