Colour model analysis for microscopic image processing

This article presents a comparative study between different colour models (RGB, HSI and CIEL*a*b*) applied to a very large microscopic image analysis. Such analysis of different colour models is needed in order to carry out a successful detection and therefore a classification of different regions of interest (ROIs) within the image. This, in turn, allows both distinguishing possible ROIs and retrieving their proper colour for further ROI analysis. This analysis is not commonly done in many biomedical applications that deal with colour images. Other important aspects is the computational cost of the different processing algorithms according to the colour model. This work takes these aspects into consideration to choose the best colour model tailored to the microscopic stain and tissue type under consideration and to obtain a successful processing of the histological image.     

A procedure for differential staining of cartilage and bone in whole formalin-fixed vertebrates.

This paper describes a modification of the Simons and Van Horn (1971) procedure for rendering cartilage blue, bone red, and soft tissue translucent or transparent in whole vertebrate specimens. Alcian blue and alizarin red S are used to stain cartilage and bone respectively. In our procedure formalin is used as a fixative. This is a significant modification because formalin is the common fixative for museum specimens. This clearing and staining procedure is thus readily applicable to comparative studies in anatomy, embryology and systematic zoology.     

Crystallization kinetics of homopolymers: overall crystallization: a review

This paper is a brief review of the overall crystallization kinetics of synthetic homopolymers. The basic experimental results are presented and compared with theory that is currently available. It is found, surprisingly, that the more sophisticated theories do no better in explaining experimental results than does the free-growth approximation. This is contrary to what is observed for the crystallization of low molecular weight substances. The reason can be attributed to entanglements and other topological defects that are present in the pure melt and are relegated to the non-crystalline regions as crystallization progresses. This results in a more protracted crystallization than is predicted and is yet to be included in theory.     

Conservation analysis in biochemical networks: computational issues for software writers

Large scale genomic studies are generating significant amounts of data on the structure of cellular networks. This is in contrast to kinetic data, which is frequently absent, unreliable or fragmentary. There is, therefore, a desire by many in the community to investigate the potential rewards of analyzing the more readily available topological data. This brief review is concerned with a particular property of biological networks, namely structural conservations (e.g. moiety conserved cycles). There has been much discussion in the literature on these cycles but a review on the computational issues related to conserved cycles has been missing. This review is concerned with the detection and characterization of conservation relations in arbitrary networks and related issues, which impinge on simulation simulation software writers. This review will not address flux balance constraints or small-world type analyses in any significant detail.     

Frailty modelling of testicular cancer incidence using Scandinavian data

The incidence of testicular cancer is highest among young men, and then decreases sharply with age. This points towards a frailty effect, where some men have a much greater risk of testicular cancer than the majority of the male population. Those with the highest risk get cancer, drain the group of individuals at risk, and leave a healthy male population which has approximately zero risk of testicular cancer. This leads to the observed decrease in incidence. We discuss a frailty model, where the frailty is compound-Poisson-distributed. This allows for a non-susceptible group (of zero frailty). The model is successfully applied to incidence data from the Danish and Norwegian registries. It is indicated that there was a decrease in incidence for males born during World War II in both countries. Bootstrap analysis is used to find the degree of variation in the estimates. In the Armitage-Doll multistage model, the estimated number of transitions needed for a cell to become malignant is close to 3 for non-seminomas and 4 for seminomas in both the Danish and Norwegian data. This paper demonstrates that a model including a frailty effect fits the incidence data well and gives interesting results and interpretations, although this is no proof of the effect's truth.     

Application of isothermal titration calorimetry and column chromatography for identification of biomolecular targets

This protocol describes a method for identifying unknown target proteins from a mixture of biomolecules for a given drug or a lead compound. This method is based on a combination of chromatography and isothermal titration calorimetry (ITC) where ITC is used as a tracking tool. The first step involves the use of ITC to confirm the binding of ligand to a component in the biomolecular mixture. Subsequently, the biomolecular mixture is fractionated by chromatography, and the binding of the ligand with individual fractions (or subfractions) is verified by ITC. The iteration of chromatographic purification on the fractions combined with ITC results in identifying the target protein. This method is useful when the target protein or ligand is unknown and/or not amenable to labeling, chemical modification or immobilization. This protocol has been successfully used by our team and by others to identify both low-abundance and highly abundant target proteins present in biomolecular mixtures. With this protocol, it takes approximately 3-5 d to identify the target protein from a mixture.     

Pruning artificial neural networks using neural complexity measures

This paper describes a new method for pruning artificial neural networks, using a measure of the neural complexity of the neural network. This measure is used to determine the connections that should be pruned. The measure computes the information-theoretic complexity of a neural network, which is similar to, yet different from previous research on pruning. The method proposed here shows how overly large and complex networks can be reduced in size, whilst retaining learnt behaviour and fitness. The technique proposed here helps to discover a network topology that matches the complexity of the problem it is meant to solve. This novel pruning technique is tested in a robot control domain, simulating a racecar. It is shown, that the proposed pruning method is a significant improvement over the most commonly used pruning method Magnitude Based Pruning. Furthermore, some of the pruned networks prove to be faster learners than the benchmark network that they originate from. This means that this pruning method can also help to unleash hidden potential in a network, because the learning time decreases substantially for a pruned a network, due to the reduction of dimensionality of the network.     

Optimization of expression and the purification by organic extraction of the integral membrane protein EmrE

EmrE is a member of the small multidrug resistance family of proteins and functions as a efflux transporter of lipophilic cations. This integral membrane protein is composed of 110 amino acids and is very hydrophobic with small loops exposed to the aqueous environment. This protein has been purified in a variety of ways including extraction with chloroform:methanol mixtures. This study explored culture growth and induction conditions, the parameters of organic solvent extraction, running conditions of a lipophilic column for lipid removal, as well as solubilization conditions. Optimal expression and purification protocols are crucial to the characterization goals of this protein. The experiments presented here led to an improvement in the yield of pure EmrE obtained by organic solvent extraction methods at a level of 0.9+/-0.2mg/L of culture. This is on the order of a 60% improvement over previous reports.     

Experimental assessment of wall shear flow in models

The blood flow immediately adjacent to the wall of a blood vessel or an artificial surface is of great interest. This flow defines the shear stress at the wall and is known to have a great physiological importance. The use of models is a viable method to investigate this flow. However, even in models the shear stress at the wall is difficult to assess. A new optical method is based on transparent models and uses particles in the model fluid, which are only visible near the wall. This is achieved with a model fluid having a defined opacity. This fluid obscures particles in the center of the models, but permits the observation and recording of particles close to the wall. The method has been applied for Hagen-Poiseuille flow and for the likewise well researched flow in a tube with a sudden expansion.     

Time Space Translation: A Hox Mechanism for Vertebrate A-P Patterning

The vertebrate A-P axis is a time axis. The head is made first and more and more posterior levels are made at later and later stages. This is different to the situation in most other animals, for example, in Drosophila. Central to this timing is Hox temporal collinearity (see below). This occurs rarely in the animal kingdom but is characteristic of vertebrates and is used to generate the primary axial Hox pattern using time space translation and to integrate successive derived patterns (see below). This is thus a different situation than in Drosophila, where the primary pattern guiding Hox spatial collinearity is generated externally, by the gap and segmentation genes.     

Automation of Mode Locking in a Nonlinear Polarization Rotation Fiber Laser through Output Polarization Measurements

When a laser is mode-locked, it emits a train of ultra-short pulses at a repetition rate determined by the laser cavity length. This article outlines a new and inexpensive procedure to force mode locking in a pre-adjusted nonlinear polarization rotation fiber laser. This procedure is based on the detection of a sudden change in the output polarization state when mode locking occurs. This change is used to command the alignment of the intra-cavity polarization controller in order to find mode-locking conditions. More specifically, the value of the first Stokes parameter varies when the angle of the polarization controller is swept and, moreover, it undergoes an abrupt variation when the laser enters the mode-locked state. Monitoring this abrupt variation provides a practical easy-to-detect signal that can be used to command the alignment of the polarization controller and drive the laser towards mode locking. This monitoring is achieved by feeding a small portion of the signal to a polarization analyzer measuring the first Stokes parameter. A sudden change in the read out of this parameter from the analyzer will occur when the laser enters the mode-locked state. At this moment, the required angle of the polarization controller is kept fixed. The alignment is completed. This procedure provides an alternate way to existing automating procedures that use equipment such as an optical spectrum analyzer, an RF spectrum analyzer, a photodiode connected to an electronic pulse-counter or a nonlinear detecting scheme based on two-photon absorption or second harmonic generation. It is suitable for lasers mode locked by nonlinear polarization rotation. It is relatively easy to implement, it requires inexpensive means, especially at a wavelength of 1550 nm, and it lowers the production and operation costs incurred in comparison to the above-mentioned techniques.     

Microbial diversity: ex situ conservation of Indonesian microorganisms

This paper discusses the role of microbial resource collections in the ex situ conservation of microbial diversity and, in particular, the activities of a recently completed Darwin Initiative project to facilitate collection, identification and exploitation of Indonesian microbial diversity. This helped revitalize the collection of the Lembaga Ilmu Pengetahuea Indonesia (Indonesian Institute of Sciences), LIPI, Research and Development Centre for Biology, Bogor, Indonesia. It is suggested that a focus on microorganisms beneficial to man is essential to enable ex situ collections to be a useful tool in the conservation and sustainable utilization of microbial diversity. This task is enormous and far beyond the capabilities of one collection and its achievement will necessitate a network of collections.     

Effect of selenite on growth and protein synthesis in the phototrophic bacterium Rhodobacter sphaeroides

The effect of selenite on the growth rate and protein synthesis has been investigated in Rhodobacter sphaeroides. This photosynthetic bacterium efficiently reduces selenite with intracellular accumulation under both dark aerobic and anaerobic photosynthetic conditions. Addition of 1 mM selenite under these two growth conditions does not affect the final cell density, although a marked slowdown in growth rate is observed under aerobic growth. The proteome analysis of selenite response by two-dimensional gel electrophoresis shows an enhanced synthesis of some chaperones, an elongation factor, and enzymes associated to oxidative stress. The induction of these antioxidant proteins confirms that the major toxic effect of selenite is the formation of reactive oxygen species during its metabolism. In addition, we show that one mutant unable to precipitate selenite, selected from a transposon library, is affected in the smoK gene. This encodes a constituent of a putative ABC transporter implicated in the uptake of polyols. This mutant is less sensitive to selenite and does not express stress proteins identified in the wild type in response to selenite. This suggests that the entry of selenite into the cytoplasm is mediated by a polyol transporter in R. sphaeroides.     

A review of the involvement of proctolin as a cotransmitter and local neurohormone in the oviduct of the locust,Locusta migratoria

The pentapeptide proctolin, originally identified in the cockroach, has been shown to be widely distributed in many insects and to have a broad range of physiological functions. In the oviduct of the locust, Locusta migratoria, proctolin's role as a neurotransmitter/neuromodulator has been well documented; however, a neurohormonal role in the locust is less certain. This review will examine the various roles of proctolin in locust oviduct contraction and will present evidence that a substance chromatographically, immunologically and physiologically indistinguishable from proctolin is present in the hemolymph of the locust, L. migratoria. This material is concentrated in the plasma, rather than the hemocytes, and is present at concentrations ranging from 0.1 to 0.2nM. This review extends the role of proctolin in insects, and suggests that proctolin may play a neurohormonal role in the locust.     

A bound water molecule is crucial in initiating autocatalytic precursor activation in an N-terminal hydrolase

Cephalosporin acylase is a member of the N-terminal hydrolase family, which is activated from an inactive precursor by autoproteolytic processing to generate a new N-terminal nucleophile Ser or Thr. The gene structure of the precursor cephalosporin acylases generally consists of a signal peptide that is followed by an alpha-subunit, a spacer sequence, and a beta-subunit. The cephalosporin acylase precursor is post-translationally modified into an active heterodimeric enzyme with alpha- and beta-subunits, first by intramolecular cleavage and, second, by intermolecular cleavage. Intramolecular autocatalytic proteolysis is initiated by nucleophilic attack of the residue Ser-1beta onto the adjacent scissile carbonyl carbon. This study determined the precursor structure after disabling the intramolecular cleavage. This study also provides experimental evidence showing that a conserved water molecule plays an important role in assisting the polarization of the OG atom of Ser-1beta to generate a strong nucleophile and to direct the OG atom of the Ser-1beta to a target carbonyl carbon. Intramolecular proteolysis is disabled as a result of a mutation of the residues causing conformational distortion to the active site. This is because distortion affects the existence of the catalytically crucial water at the proper position. This study provides the first evidence showing that a bound water molecule plays a critical role in initiating intramolecular cleavage in the post-translational modification of the precursor enzyme.     

Non-equilibrium thermodynamic sensitivity of oxidative phosphorylation.

A new method was developed to analyse the dynamic properties of oxidative phosphorylation, in particular the sensitivity of the phosphate potential with respect to fluctuating cellular ATP utilization. This treatment is based on the eigenvalue sensitivity analysis of an experimentally supported non-equilibrium thermodynamic model of oxidative phosphorylation. Such an analysis allows direct access to the kinetic information, while circumventing the awkward conventional numerical integration of a set of nonlinear differential equations. This procedure revealed, for the parameters characteristic for liver of starved rats in vivo, that the sensitivity of oxidative phosphorylation to a fluctuating ATP utilization is minimal at a degree of coupling q = 0.95. This means that the phosphate potential is highly buffered with respect to fluctuating energy demands at the degree of coupling. This value of q agrees well with the degree of coupling qeef, at which net ATP production of oxidative phosphorylation--at optimal efficiency--occurs in the most economic way. This simultaneous maximization of kinetic stability and economic thermodynamic efficiency at the same degree of coupling appears to be a coincidence.     

Sectioning Refractory Animal Tissues

A method is described tor sectioning refractory material, particularly heavily yolked tissue. Fixation in a saturated picric acid-dioxan solution containing 10% formalin and 5% formic acid is recommended followed by dehydration in 2-ethoxyethanol. This greatly reduces pre-embedding hardening. Prior to clearing in three 4-hour changes of benzene, the tissue is placed for 12 hours in a bath of 2% celloidin in 2-ethoxyethanol. This impregnation prevents subsequent imbibition pressure from disrupting the anatomical relationships of the different parts. The material is embedded in wax and the block, trimmed to expose the tissue, is solvated for 12 hours in a 5% solution of Tergitol in pure ethane diol. This method has produced excellent sections and flaccid ribbons in a range of material which, prior to solvation, proved extremely refractory and, in some instances, impossible to cut.     

Variation and inheritance of sodium transport in rice

Sodium transport in rice is characterised by large variability between individual plants, and large environmental interaction. As a result of these two factors, plant sodium content is a continuous variable which is not distributed normally. This applies both to the quantity of sodium in the plant and to the concentration of sodium on a unit fresh or dry weight basis. This variability is in part because the transpirational by-pass flow, dependent upon root anatomy and development, contributes to sodium uptake. Variability in sodium content within designated cultivars is heritable and line selections diverge during recurrent selection, suggesting that selection is working on residual heterozygosity rather than on a family of homozygous lines. Varieties differ in average sodium uptake into the plant but the direct correlation of this with survival is weak. This is because other independent characters are important (and these have not been combined by natural selection nor by chance) and because overall performance is confounded by the spurious advantage of the tall (non-dwarf) plant type. This advantage is spurious because much of it is due to plant size rather than to any genetic information for salt tolerance. The benefit deriving from plant size will not be heritable in crosses with genotypes of the improved (dwarf), high-yielding plant type because the dwarfing genes are dominant. Sodium transport is heritable in crosses, and the results presented show that both low sodium transport and low sodium to potassium ratio can be selected independently of plant type. This allows the selection of dwarf plants (which are agronomically desirable) with low sodium transport (which will improve salt tolerance).     

Convection and diffusion in tissues and tissue cultures

The relative importance of transport by diffusion and convection in permeable tissues is investigated in three-dimensional structures. The transport of a solute takes place from a number of sources embedded in the tissue, to a number of sinks similarly embedded. An enhancement factor E is defined to be the ratio of the transport rate in the presence of a pressure difference between the sources and sinks, to the transport rate without a pressure difference. It is shown that E is a unique function of a parameter W, which characterizes the properties of the tissue and the pressure difference. This relation is independent of the number or the geometries of the sources and sinks.This relation is compared with experimental data obtained in a hollow fiber tissue culture device, with two sets of hollow fibers kept at different pressures. This relation is also used to estimate the importance of convection in vivo for a wide range of mammalian tissues and solute molecules.