Cycle-time and residence-time density approximations in a stochastic model for circulatory transport

The concentration of a drug in the circulatory system is studied under two different elimination strategies. The first strategy—geometric elimination—is the classical one which assumes a constant elimination rate per cycle. The second strategy—Poisson elimination—assumes that the elimination rate changes during the process of elimination. The problem studied here is to find a relationship between the residence-time distribution and the cycle-time distribution for a given rule of elimination. While the presented model gives this relationship in terms of Laplace-Stieltjes transform, the aim here is to determine the shapes of the corresponding probability density functions. From experimental data, we expect positively skewed, gamma-like distributions for the residence time of the drug in the body. Also, as some elimination parameter in the model approaches a limit, the exponential distribution often arises. Therefore, we use laguerre series expansions, which yield a parsimonious approximation of positively skewed probability densities that are close to a gamma distribution. The coefficients in the expansion are determined by the central moments, which can be obtained from experimental data or as a consequence of theoretical assumptions. The examples presented show that gamma-like densities arise for a diverse set of cycle-time distributions and under both elimination rules.     

Proliferation of anchorage-dependent contact-inhibited cells: I. Development of theoretical models based on cellular automata

We report the development of new class of discrete models that can accurately describe the contact-inhibited proliferation of anchorage-dependent cells. The models are based on cellular automata, and they quantitatively account for contact inhibition phenomena occurring during all stages of the proliferation process: (a) the initial stage of "exponential" growth of cells without contact inhibition; (b) the second stage where cell colonies form and grow with few colony mergings; and (c) the final stage where proliferation rates are dominated by colony merging events. Model prediction are presented and analyzed to study the complicated dynamics of large cell populations and determine how the initial spatial cell distribution, the seeding density, and the geometry of the growth surface affect the observed proliferation rates. Finally, we present a model variant that can simulate contact-inhibited proliferation of asynchronous cell populations with arbitrary cell cycle-time distribution. The latter model can also compute the percentage of cells that are in a specific phase of their division cycle at a given time.     

Animal body size distributions: patterns, mechanisms and implications

Documenting the shape of the frequency distribution of species body sizes for an animal taxon appears at first sight a straightforward task. However, a variety of patterns has been reported, and a consensus is only now being reached through an understanding of how potential biases may affect observed shapes of distributions. A new body of evidence suggests that, at large scales, size distributions are right-skewed, even on logarithmic axes. If body size distributions can be described with certainty, this will allow assessment of the mechanisms proposed to generate them, and will be an important step towards understanding the structure and dynamics of animal assemblages.     

Dynamics of transitional endoplasmic reticulum sites in vertebrate cells

A typical vertebrate cell contains several hundred sites of transitional ER (tER). Presumably, tER sites generate elements of the ER-Golgi intermediate compartment (ERGIC), and ERGIC elements then generate Golgi cisternae. Therefore, characterizing the mechanisms that influence tER distribution may shed light on the dynamic behavior of the Golgi. We explored the properties of tER sites using Sec13 as a marker protein. Fluorescence microscopy confirmed that tER sites are long-lived ER subdomains. tER sites proliferate during interphase but lose Sec13 during mitosis. Unlike ERGIC elements, tER sites move very little. Nevertheless, when microtubules are depolymerized with nocodazole, tER sites redistribute rapidly to form clusters next to Golgi structures. Hence, tER sites have the unusual property of being immobile, yet dynamic. These findings can be explained by a model in which new tER sites are created by retrograde membrane traffic from the Golgi. We propose that the tER-Golgi system is organized by mutual feedback between these two compartments.     

Decoy models for protein structure comparison score normalisation

A method is described to construct sets of decoy models that can be used to generate a background score distribution for protein structure comparison. The models are derived directly from the two proteins being compared and retain all the essential properties of the structures, including length, density, shape and secondary structure composition but have different folds. As each comparison involves a pair of proteins of the same length, no explicit normalisation is required to adjust for the length of the proteins being compared. This allows substructure (or domain) matches to score almost equally to the comparison of isolated domains. A normalised probability measure was derived that allows joint family/family comparison. The method was applied to some of the CASP6 models for targets with new folds.     

GIS在生物质能源研究中的应用

生物质资源分布广阔而分散,且与环境、气候、土壤、土地利用等关系密切.地理信息系统(geographic information systems,GIS)具有空间数据分析功能以及易于与其他应用模型和算法相结合等特性,使其在生物质能源研究中具有优势.本文系统总结了国内外学者在生物质能源GIS应用方面的研究,着重讨论了GIS在生物质能开发可行性、生物质资源量及分布评估、生物质开发利用布局、生物质燃烧气体排放评估以及生物质能源信息系统等方面的应用,进而提出了GIS在生物质能源方面应用的3个趋势,即丰富数据源、提升数据处理和决策支持能力以及方案在线生成.     

Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm

Protein libraries are essential to the field of protein engineering. Increasingly, probabilistic protein design is being used to synthesize combinatorial protein libraries, which allow the protein engineer to explore a vast space of amino acid sequences, while at the same time placing restrictions on the amino acid distributions. To this end, if site-specific amino acid probabilities are input as the target, then the codon nucleotide distributions that match this target distribution can be used to generate a partially randomized gene library. However, it turns out to be a highly nontrivial computational task to find the codon nucleotide distributions that exactly matches a given target distribution of amino acids. We first showed that for any given target distribution an exact solution may not exist at all. Formulated as a constrained optimization problem, we then developed a genetic algorithm-based approach to find codon nucleotide distributions that match as closely as possible to the target amino acid distribution. As compared with the previous gradient descent method on various objective functions, the new method consistently gave more optimized distributions as measured by the relative entropy between the calculated and the target distributions. To simulate the actual lab solutions, new objective functions were designed to allow for two separate sets of codons in seeking a better match to the target amino acid distribution.     

Lime treatment of shrimp head waste for the generation of highly digestible animal feed

In addition to approximately 20% ash, shrimp processing by-products contain 64% protein and chitin, both of which can be used to generate several valuable products. Chitin and chitosan production is currently based on several crustacean wastes, and at the present time the protein fraction is not being used. This paper describes the thermo-chemical treatment of shrimp processing wastes with lime to generate a protein-rich material with a well-balanced amino acid content that can be used as a monogastric animal feed supplement. The residual solid, rich in calcium carbonate and chitin, can still be used to generate chitin and chitosan through well-established processes.     

Maturation of the flight motor pattern without movement inManduca sexta

The development of the flight motor pattern was studied by recording acutely with fine wire electrodes inserted in the thoracic muscles of pharate moths of known age and by recording chronically for up to 8 days with implanted electrodes. Externally visible morphological characteristics by which the age of a pharateManduca sexta can be established were identified (Table 1). Bouts of activity lasting approximately 30 min to 2 h and alternating with inactive periods of similar duration were recorded as early as the ninth day after pupation and on all successive days until early on the day of eclosion, typically 19 days after pupation (Figs. 1,5). During the 3 days preceding the day of eclosion a rhythmic flight motor pattern was produced (Fig. 2). The rhythmic activity ceased 5^1/2–10^1/2 h before eclosion and only an occasional, large potential change was recorded from the thoracic muscles during this time (Fig. 3). During the 3 days of rhythmic activity the percent-age of time that the animal was active did not change (Fig. 4). The flight motor pattern matured, in that the cycle-time decreased and became less variable (Fig. 6). The approximate flight phase relationship between an elevator muscle and the dorsal longitudinal depressor muscle did not become less variable as the cycle-time improved. The flight motor pattern produced by pharate moths caused neither movement of the scutum nor an increase in thoracic temperature in marked contrast to the consequences of adult motor activity (Fig. 7). Intracellular recording from the dorsal longitudinal muscle of pharate moths 20–30 h before eclosion showed that, after repeated stimulation of the motor nerve at 2/s, only small junctional potentials were elicited (Fig. 8). A burst of 6 stimuli at 50/s elicited 2–5 active membrane responses and a contraction. These observations explain the absence of thoracic movement in immature animals producing the flight motor pattern and the presence of movement in immature animals stimulated to eclose. They also show that the neuromuscular junction matures rapidly during the day before eclosion.     

Bayesian inference in ecology

Bayesian inference is an important statistical tool that is increasingly being used by ecologists. In a Bayesian analysis, information available before a study is conducted is summarized in a quantitative model or hypothesis: the prior probability distribution. Bayes’ Theorem uses the prior probability distribution and the likelihood of the data to generate a posterior probability distribution. Posterior probability distributions are an epistemological alternative to P‐values and provide a direct measure of the degree of belief that can be placed on models, hypotheses, or parameter estimates. Moreover, Bayesian information‐theoretic methods provide robust measures of the probability of alternative models, and multiple models can be averaged into a single model that reflects uncertainty in model construction and selection. These methods are demonstrated through a simple worked example. Ecologists are using Bayesian inference in studies that range from predicting single‐species population dynamics to understanding ecosystem processes. Not all ecologists, however, appreciate the philosophical underpinnings of Bayesian inference. In particular, Bayesians and frequentists differ in their definition of probability and in their treatment of model parameters as random variables or estimates of true values. These assumptions must be addressed explicitly before deciding whether or not to use Bayesian methods to analyse ecological data.     

Smart Monte Carlo Algorithm for the Adsorption of Molecules at a Surface

Abstract

A modified grand canonical ensemble Monte Carlo (GCMC) technique has been developed to simulate adsorption isotherms for molecules on or near a surface. The speed and accuracy of the simulation is increased by using a non-uniform distribution function, related to the force field exerted by the surface and the current configuration, to generate coordinates for the creation of new particles in the simulation. With this method, isotherms are generated more efficiently than with current techniques in which the creation step relies on a uniform distribution to generate the coordinates of a new molecule. This is shown by comparing the calculation of an isotherm for a simple molecule adsorbed on a graphite substrate from a traditional GCMC simulation with that calculated using this new technique.     

Size and power required for motion with implication for the evolution of early hominids

The fossil record of early hominids (early human ancestors) suggests that their stature and weight had a tendency to increase, but their robusticity (the proportion of radius to length) to decrease. Using a simple musculo-skeletal model, this paper explores possible relationships between size, power required for motion (PRM) and cycle-time, deriving relationships which indicate that PRM per unit of mass and velocity is proportional to robusticity, but inversely proportional to stature. The results derived appear to be in general agreement with published data from physiological experiments. If the material properties of early hominids were similar to those of modern humans and the achievement of minimum PRM was the selective criterion, human stature might tend to increase slightly in human evolution (and, if selective pressures are not removed, might do so in the future but at lower rate). If mobility and stability under loading are the selective criteria, however, human size should not substantially increase in the future.     

Transport of chlorine in the proximal tubule. Its effects on water-electrolyte absorption

Several studies in rat kidney have established that an appreciable fraction of proximal absorption is passive in nature and occurs across the highly conductive paracellular pathway. Passive absorption is generally ascribed to the transepithelial Cl- distribution, luminal Cl- activity (alpha lCl) being higher than plasma Cl- activity (alpha pCl). The inequality alpha lCl greater than alpha pCl generates a transepithelial diffusion potential, lumen positive, which taken together with the chemical potential differences of Cl- and Na+ across the epithelium gives rise to transepithelial electrochemical potential differences for Cl- and Na+ favoring their absorption. The alpha lCl greater than alpha pCl distribution is traditionally ascribed to preferential bicarbonate absorption. We argue that HCO3- absorption alone cannot generate a non equilibrium transepithelial Cl- distribution. Other mechanisms are necessary. Our measurements in amphibian proximal tubule demonstrate that the intracellular Cl- activity, alpha cCl, is higher than the theoretical value predicted for equilibrium. This distribution is the result of two basolateral coupled transport processes (Cl-/HCO3- exchange and Cl-/Na+ cotransport). It contributes to the exit of Cl- from cell to lumen (by passive diffusion and K+/Cl- cotransport), yielding alpha lCl values higher than the theoretical value for equilibrium with regard to plasma. Thus, a small transcellular flux of Cl- (without solvent) proceeds from interstitium to lumen. It compensates the dissipative tendency of a much higher paracellular Cl- absorptive flux (in association with water) on the transepithelial Cl- gradient. The result is a steady-state luminal Cl- distribution above equilibrium, along the major part of the proximal tubule.     

Non-invasive measurements of skin pigmentation in situ

Objective in situ measurements of skin pigmentation are needed for accurate documentation of pigmentation disorders, in studies of constitutive and induced skin pigmentation, for testing of the efficacy of pro-pigmentation or de-pigmentation agents, etc. Non-invasive instrumental measurements of skin pigmentation have been used for many decades. All are based on the ability of melanin to attenuate light. However, hemoglobin in dermal capillaries also attenuates light and needs to be accounted for when pigmentation is assessed. The methods under consideration include: (a) single point measurements, in which light reflected from a defined skin area is collected and a pigment index is calculated representing the average pigmentation over the examined area, and (b) imaging methods that attempt to generate a concentration distribution map of melanin pigment for the skin area being imaged. In this article, we describe the potentials and the limitations of the different approaches to both single point and imaging methods.     

Non‐Invasive Measurements of Skin Pigmentation In Situ

Objective in situ measurements of skin pigmentation are needed for accurate documentation of pigmentation disorders, in studies of constitutive and induced skin pigmentation, for testing of the efficacy of pro‐pigmentation or de‐pigmentation agents, etc. Non‐invasive instrumental measurements of skin pigmentation have been used for many decades. All are based on the ability of melanin to attenuate light. However, hemoglobin in dermal capillaries also attenuates light and needs to be accounted for when pigmentation is assessed. The methods under consideration include: (a) single point measurements, in which light reflected from a defined skin area is collected and a pigment index is calculated representing the average pigmentation over the examined area, and (b) imaging methods that attempt to generate a concentration distribution map of melanin pigment for the skin area being imaged. In this article, we describe the potentials and the limitations of the different approaches to both single point and imaging methods.     

Replication origins in Xenopus egg extract Are 5-15 kilobases apart and are activated in clusters that fire at different times

When Xenopus eggs and egg extracts replicate DNA, replication origins are positioned randomly with respect to DNA sequence. However, a completely random distribution of origins would generate some unacceptably large interorigin distances. We have investigated the distribution of replication origins in Xenopus sperm nuclei replicating in Xenopus egg extract. Replicating DNA was labeled with [(3)H]thymidine or bromodeoxyuridine and the geometry of labeled sites on spread DNA was examined. Most origins were spaced 5-15 kb apart. This regular distribution provides an explanation for how complete chromosome replication can be ensured although origins are positioned randomly with respect to DNA sequence. Origins were grouped into small clusters (typically containing 5-10 replicons) that fired at approximately the same time, with different clusters being activated at different times in S phase. This suggests that a temporal program of origin firing similar to that seen in somatic cells also exists in the Xenopus embryo. When the quantity of origin recognition complexes (ORCs) on the chromatin was restricted, the average interorigin distance increased, and the number of origins in each cluster decreased. This suggests that the binding of ORCs to chromatin determines the regular spacing of origins in this system.     

Bio-electrosprays: the next generation of electrified jets

Biological electrosprays are rapidly becoming a robust means by which to engineer living organisms for applications ranging from tissue repair to developmental biology. We previously reported the ability to electrospray living organisms without compromising their viability, but found it challenging to achieve stability in the jetting of these organisms as a result of the chemical properties of the living cellular suspensions. Jet stability is required for the generation of a near-mono distribution of droplets, which is necessary for the development of electrospray technology as a "drop and place" biotechnique. Recently, we determined the conditions needed to achieve jet stability and were able to generate droplets with a near-mono distribution (<50 microm). In this communication, we elucidate the relationship between jet behaviour and droplet size under stable jetting conditions, with a view to further reducing the droplet size to deposit a single living cell within a droplet. We believe that this level of resolution will make electrospray jetting superior amongst the jet-based biotechnologies presently being developed for the engineering of biological architectures comprised of living cells.     

A new imaging technique to study 3-D plaque and shear stress distribution in human coronary artery bifurcations in vivo

OBJECTIVE: Bifurcations of coronary arteries are predilection sites for atherosclerosis and expansive remodeling, the latter being associated with plaque vulnerability. Both are related to blood flow-induced shear stress (SS). We present a new approach to generate 3-D reconstructions of coronary artery bifurcations in vivo and investigate the relationship between SS, wall thickness (WT) and remodeling. METHODS: The patient specific 3-D reconstruction of the main branch of the bifurcation was obtained by combining intravascular ultrasound and biplane angiography, and the 3-D lumen of the side branch was based on biplane angiography only. The two data sets were fused and computational methods were applied to determine the SS distribution, using patient derived flow and viscosity data. The intravascular ultrasound data allowed us to measure local WT and remodeling in the main branch. RESULTS: The lumen reconstruction procedure was successful and it was shown that the impact of the side branch on SS distribution in the main branch diminished within 3mm. Distal to the bifurcation, two continuous regions in the main branch were identified. In the proximal region, we observed lumen preservation, and expansive remodeling. Although a plaque was observed in the low SS region at the non-divider wall, no relationship between SS and WT was found. In the distal region, we observed lumen narrowing and a significant positive relationship between SS and WT. CONCLUSIONS: A new imaging technique was applied to generate a 3-D reconstruction of a human coronary artery bifurcation in vivo. The observed relationship between SS, WT and remodeling in this specific patient illustrates the spatial heterogeneity of the atherosclerosis in the vicinity of arterial bifurcations.     

Identification of human skin bacteria attractive to the Asian Tiger mosquito

Aedes albopictus is a vector of arboviruses and filarial nematodes. Originating from Asia, this mosquito has rapidly expanded its geographical distribution and colonized areas across both temperate and tropical regions. Due to the increase in insecticide resistance, the use of environmentally friendly vector control methods is encouraged worldwide. Using methods based on semiochemicals in baited traps are promising for management of mosquito populations. Interestingly, human skin microbiota was shown to generate volatile compounds that attract the mosquito species Anopheles gambiae and Aedes aegypti. Here, we investigated the composition of skin bacteria from different volunteers and the attractive potential of individual isolates to nulliparous Ae. albopictus females. We showed that three out of 16 tested isolates were more attractive and two were more repulsive. We identified dodecenol as being preferentially produced by attractive isolates and 2-methyl-1-butanol (and to a lesser extent 3-methyl-1-butanol) as being overproduced by these isolates compared with the other ones. Those bacterial volatile organic compounds represent promising candidates but further studies are needed to evaluate their potential application for baited traps improvement.