Topology-controlled volume rendering

Topology provides a foundation for the development of mathematically sound tools for processing and exploration of scalar fields. Existing topology-based methods can be used to identify interesting features in volumetric data sets, to find seed sets for accelerated isosurface extraction, or to treat individual connected components as distinct entities for isosurfacing or interval volume rendering. We describe a framework for direct volume rendering based on segmenting a volume into regions of equivalent contour topology and applying separate transfer functions to each region. Each region corresponds to a branch of a hierarchical contour tree decomposition, and a separate transfer function can be defined for it. The novel contributions of our work are: 1) a volume rendering framework and interface where a unique transfer function can be assigned to each subvolume corresponding to a branch of the contour tree, 2) a runtime method for adjusting data values to reflect contour tree simplifications, 3) an efficient way of mapping a spatial location into the contour tree to determine the applicable transfer function, and 4) an algorithm for hardware-accelerated direct volume rendering that visualizes the contour tree-based segmentation at interactive frame rates using graphics processing units (GPUs) that support loops and conditional branches in fragment programs     

Phase-error-free quadrature sampling technique in the ultrasonic B-scan imaging system and its application to the synthetic focusing system

The quadrature sampling technique as a means of detecting the envelope of RF waveform in the baseband is well known. If this technique is applied to a focused ultrasound imaging system using an array transducer, whether it is a synthetic or nonsynthetic focusing system, unwanted phase terms appear in the expressions of the inphase and quadrature components of the baseband signal when an appropriate delay time is introduced to each channel signal for the purpose of focusing. The expressions of the inphase and quadrature components from the point of focusing are derived and analyzed in detail, and a scheme to eliminate the unwanted phase terms is proposed. The resulting phase-error-free quadrature sampling technique is applied to the synthetic focusing system; a system block diagram together with the simulation and experimental results are presented.     

Denitrification of nitrate-contaminated groundwater using a simple immobilized activated sludge bioreactor

A simple anaerobic-activated sludge system, in which microorganisms are immobilized by a novel functional carrier, was used for removing nitrate in groundwater. The operating conditions, including hydraulic retention time (HRT), C/N ratio, temperature and NO(3)(-)-N loading concentration were investigated. The NO(3)(-)-N concentration, residual chemical oxygen demand (COD) and nitrite accumulation were used as indicators to assess the water quality of the effluent. The anaerobic biomass loading capacity in the carrier was 12.8 g/L and the denitrifying Pseudomonas sp. and Rhodocyclaceae bacterium were dominant among the immobilized microorganisms in the anaerobic-activated sludge. Under operating conditions of HRT= 1.5 h, C/N= 2-3 and T= 16.8-20 °C, the removal efficiency of NO(3)(-)-N exceeded 93%, corresponding to a relatively high denitrification rate of 0.73 kg NO(3)(-)-N m(-3) d(-1), when the NO(3)(-)-N loading concentration was 50 mg/L. The NO(3)(-)-N concentration of the effluent always met regulatory criteria for drinking water (<10 mg/L) in the main developed and developing countries. The effluent COD was also below 10 mg/L. Although some nitrite accumulated (0-1.77 mg/L) during the operating period, it can be decreased through adjusting the operating pH and HRT. The immobilized activated sludge system may be useful for the removal of nitrate from groundwater.     

Degenerative process and cell death in salivary glands of Rhipicephalus sanguineus (Latreille, 1806) (Acari: Ixodidae) semi-engorged female exposed to the acaricide permethrin

Ticks are ectoparasites of great medical and veterinary importance around the world and synthetic chemicals such as permethrin have been used for their control. This study provides a cytochemistry analysis of both degenerative and cell death processes in salivary glands of the brown dog tick Rhipicephalus sanguineus semi-engorged females exposed to 206, 1,031, and 2,062 ppm of permethrin. The results presented herein demonstrate that permethrin is a potent chemical acaricide that would act on the glandular tissue's morphophysiology in this tick species by eliciting severe changes in the acinus shape, intense vacuolation of the acinar cells' cytoplasm, marked glandular tissue disorganization, culminating in an advanced degenerative stage with consequent formation of many apoptotic bodies (cell death). In addition, permethrin induced major changes in the acinar cells' nucleus, such as a change both in its shape and size, chromatin marginalization, nuclear fragmentation, and appearance of picnotic nuclei, especially when the highest concentrations of the product were used. Thus, permethrin induced early degeneration of this tissue characterized by significant changes in the structure of acinar cells and production of enzymes related to the cell death process, in addition to interfering directly in the genetic material of these cells.     

Morphological characterization of the nymphs Rhipicephalus sanguineus ticks (Latreille, 1806) (Acari: Ixodidae). Description of the testes, integument, Malpighian tubules, and midgut on the detachment day

This study presents the morpho-histological and histochemical characterization of the testes, integument, Malpighian tubules, and midgut of engorged Rhipicephalus sanguineus nymphs on the detachment day, showing the morphological and physiological characteristics to this phase in the life cycle of these individuals. The testis is constituted by germinative cells (only spermatogonia) with large, round-shaped and strongly stained nuclei which are organized into cysts by a thin layer of somatic cells. The integument consists of a cuticle subdivided into epicuticle (lipoprotein) and procuticle (glycoproteic), and a layer of epithelial cells which present glycolipoprotein elements. The procuticle presents two distinct regions: the exocuticle (next to the epicuticle) and the endocuticle (next to the epithelial layer). The Malpighian tubules present a simple epithelium with small flat and/or cubic cells, which form its wall and delimitates a lumen full of lipoprotein material. The midgut consists of an epithelial wall formed by two types of digestive cells, spent cells and empty digest cells, and by generative cells supported by a basal lamina and a thin layer of muscular tissue. This study described the main organs of engorged nymphs of R. sanguineus, to generate information that can help researchers to better understand the biology of these ectoparasites; which is fundamental for the development of compounds that are less aggressive to the environment. In addition, if the immature stages of the ticks are controlled, the number of adult ticks able to cause damages to the animals--and to the man as well--is also under control.     

Single-molecular AFM probing of specific DNA sequencing using RecA-promoted homologous pairing and strand exchange

The specific sequence in a linearlized double-stranded DNA target has been identified at a single-molecular level by atomic force microscopy (AFM). This was accomplished using RecA-coated, single-stranded DNA probes which were paired with a specific complementary DNA sequence in a linear double-stranded DNA target by strand-exchange reaction at a homologous sequence site with target DNA. The sites of interaction between the nucleoprotein filaments and the double-stranded DNA targets were directly visualized by AFM in solution containing 4 mM magnesium acetate. Measurements of the position of RecA-coated probes paired to individual target DNA showed that DNA probes specifically paired at their corresponding homologous target sequences. Strand exchange promoted by RecA and the visualization by AFM provided a rapid and efficient way to identify homologous sequence on a single-molecule target DNA.     

The substrate specificity of a recombinant cysteine protease from Leishmania mexicana: application of a combinatorial peptide library approach

The substrate specificity of CPB2.8DeltaCTE, a recombinant cysteine protease from Leishmania mexicana, was mapped by screening a fluorescence-quenched combinatorial peptide library. Results from library screening indicated a preference for Arg or Lys in the S(3) subsite and for hydrophobic residues, both aliphatic and aromatic, in S(2). The S(1) subsite exhibited a specificity for the basic residues Arg and Lys. Generally, the specificity of the primed subsites was less strict compared with the non-primed side which showed preference for Arg, Lys and Ala in S'(1), Arg, Pro and Gly in S'(2) and Lys, Arg and Ser in S'(4). By contrast, a strict preference for the basic residues Arg and Lys was found for S'(3). Overall, there was a trend for basic residues in alternating subsites and smaller residues in the primed sites compared with the non-primed sites. In addition, there were strict requirements for the amino acids in subsites S(3)--S(1). Fluorescence-quenched peptides from the library with the highest on-resin cleavage were resynthesised and their kinetics of hydrolysis by CPB2.8DeltaCTE assessed in solution phase assays. Several good substrates containing the quintessential dipeptide particular to cathepsin-L-like enzymes, -F-R/K-, in P(2) and P(1) were identified (e.g. Y(NO(2))-EKFR down arrow RGK-K(Abz)G, Abz=2-aminobenzoyl; k(cat)K(m)(-1)=4298 mM(-1)s(-1)). However, novel substrates containing the dipeptide -L/I-Q- in P(2) and P(1) were also well hydrolysed (e.g. Y(NO(2))-YLQ down arrow GIQK-K(Abz)G; k(cat)K(m)(-1)=2583 mM(-1)s(-1)). The effect of utilising different fluorescent donor--quencher pairs on the value of k(cat)K(m)(-1) was examined. Generally, the use of the Abz/Q-EDDnp donor--quencher pair (EDDnp=N-(2,4-dinitrophenyl)ethylenediamine) instead of K(Abz)/Y(NO(2)) resulted in higher k(cat)K(m)(-1) values for analogous substrates.     

Improvement of intact human lipocortin-I production in Saccharomyces cerevisiae by inhibiting proteolysis

Human lipocortin-I (hLC1), when was expressed as a secretory product in Saccharomyces cerevisiae, was cleaved to a significant extent by endoproteolytic processing, resulting in the accumulation of des1-26-hLC1 in the culture supernatant. This proteolytic cleavage was inhibited significantly by the addition of high concentrations of l-arginine and l-lysine, with a resultant marked improvement in the yield of intact hLC1. When the hLC1 was expressed in S. cerevisiae mutants deficient in one or two of the following endoproteases, Kex2p, Mkc7p and Yps1p (Yap3p), the mutants exhibited no reduction in the extent of hLC1 proteolysis, indicating that these endoproteases are not involved in the proteolytic cleavage of hLC1.