On an interacting particle system modeling an epidemic

We consider an interacting particle system onZ ^dto model an epidemic. Each site ofZ ^dcan be in either one of three states: empty, healthy or infected. Healthy and infected individuals give birth at different rates to healthy individuals on empty sites. Healthy individuals get infected by infected individuals. Infected and healthy individuals die at different rates. We prove that in dimension 1 and with nearest-neighbor interactions the epidemic may persist forever if and only if the rate at which infected individuals give birth to healthy individuals is high enough. This is in sharp contrast with models analysed by Andjel and Schinazi (1994) and Sato et al. (1994) where infected individuals do not give birth. We also show that some results in the latter reference can be obtained easily and rigorously using probabilistic coupling to the contact process.     

Optimal modeling of an arterial system

The aortic blood flow is described by a set of nonlinear hyperbolic partial differential equations that account for mass and momentum conservation, and nonlinear models for the mechanical properties of the artery. Identification is used for determining the wave speed, arterial taper, and cross section: these parameters reflect the elastic characteristics of the aorta wall and control the pulsatile response. The differential equations were numerically integrated by the Lax-Wendroff scheme of Abarbanel and Goldberg [J. Comput. Phys. 10:1–21 (1972)] that avoids nonlinear oscillations. The Gauss-Newton technique was used for the parameter identification. By reference to reported elocity and pressure input-output pairs, a parameter vector is found such that the distance in the L₂ norm between the predicted outputs and the measured functions is minimal. Calculations of the velocity and pressure waves show excellent compatibility of the model with reported experimental data: starting from arbitrary parameter estimates, which yield grossly distorted waveforms, the error is typically reduced to 7–8%. Introduction of viscoelastic behaviour for the arterial wall in the form of a Volterra integral for the cross section does not lead to significant improvement. Numerical examples are presented which prove the convergence, accuracy, and stability of the algorithm. Emphasis is placed on the computational feasibility of the proposed system identification.     

Self-organization of an oscillatory neural system

Hebbian dynamics is used to derive the differential equations for the synaptic strengths in the neural circuitry of the locomotive oscillator. Initially, neural connection are random. Under a specified arborization hypothesis relating to the density of neural connections, the differential equations are shown to model the self-organization and the stability of the oscillator.     

Hemostasis as an optimal system

Zymogen and procofactor concentrations in physiological biochemical systems (PBS) have not yet been explained. The problem in question is to determine optimal plasma clotting factor (factors II, VII, IX, and X and cofactors V and VIII) concentrations for coagulation system (CS) as a whole. Constrained optimization technique is used to solve this problem. The constraint is determined by the ability of the CS to perform its physiological function--thrombin generation (and hence clot formation)--under vessel injury conditions. The constraint statement is based on the CS dynamics equations. In solving the problem the Lagrange multiplier is used. A hypothesis is advanced that this problem can be solved based on principle of minimum protein consumption subject to an above constraint. The results obtained indicate that the optimal clotting factor concentrations are in good agreement with those measured by biochemical techniques. A comparison between the theoretical results and experimental data lends support for our hypothesis that zymogen and procofactor concentrations in the CS (and, probably, for other biochemical systems) are determined by the principle of minimum protein consumption.     

Molecular topography of an entire nervous system

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Development of an automated microbial sensor system

An automated whole cell biosensor system was developed by integration of immobilized microbial cells in a flow-through system with screen-printed flow-through electrodes as detectors. The detectors used were thick-film Pt-electrodes in a 3-electrode configuration constructed as sandwich flow-through cells with a volume of about 36 microliters polarized at -900 mV. The measuring principle was the determination of oxygen consumption due to the microbial metabolism. Fructose was used as model analyte. The microorganisms were immobilized on cellulose-acetate membranes and integrated into a newly created reaction chamber (membrane reactor). The microbial cells used were Rhodococcus erythropolis and Issatchenkia orientalis known to be suitable for the determination of biological oxygen demand.     

An analysis of an alternative scintimammography system

A novel system for scintimammography has been developed, which has high spatial resolution, good sensitivity, better energy resolution, and lower cost than conventional systems. In addition, the system incorporates the potential to provide additional information and functionality beyond imaging, including x,y and z lesion location, integration with a stereotatic biopsy system and images both breasts at the same time. Methods: The system uses sheet NaI (Tl) crystals, PM Tubes, and slant hole collimators allowing complete separation of the breast from the chest wall while remaining in contact with the breast at all depths. The physical characteristics are presented, with images and compared with other systems. Results: The limit of lesion detectability in terms lesion size, depth and contrast has been investigated and compared with a current conventional system. Using accepted patient dose data, the anticipated radiopharmaceutical activity related to the lesion size is used for imaging tests and provides a measure of expected of lesion detectability. Conclusion: Large area, sheet NaI (Tl) detector systems with slant hole collimators are capable of imaging features of below 5mm size at both surface and at clinical depths with the amount of activity expected in lesions of this size with patient administered doses in the clinically acceptable range.     

Contractile system of muscle as an auto-oscillator

It is widely known that the contractile system of muscle takes on either the state of contraction (force-generating) or the state of relaxation (non-force-generating), which is known as the "all-or-nothing" principle. However, it is important to note that under intermediate activation conditions there exists a third state, which demonstrates auto-oscillatory properties and is termed SPOC (SPontaneous Oscillatory Contraction) state. We present a phase diagram, in which the states of the contractile system of muscle are divided into three regions consisting of contraction, relaxation and SPOC states. In the present review, experimental data related to the characteristics of SPOC are summarized and the mechanism of SPOC is described. We propose that the bio-motile system itself is an auto-oscillator, even in a membrane-less supra-molecular structure composed of an assembly of molecular motors and cytoskeletons (actin filaments and microtubules). Finally, the physiological significance of SPOC is discussed.     

The beta-D-glucosidase system of an Actinoplanes sp

Actinoplanes sp. No. 1700, a sporangium-forming, filamentous, soil bacterium possesses a β-D-glucosidase (β-D-glucoside glucohydrolase, E.C. 3.2.1.21). The enzyme was induced to higher concentrations by addition of methyl or phenyl β-D-glucopyranoside, gentiobiose, or salicin to growing cultures. Addition of D-glucose, lactate, or acetate repressed enzyme induction back to the constitutive level, but never below it. The properties of this inducible system place it in the semi-constitutive category.Both the constitutive and the inducible enzyme were purified 60-fold; their properties were compared and found to be identical. Their pH optima lay between 5.8 and 6.0; the enzymes were stable for 2 h at 30° at pH 5.5 to 7.3. Rapid inactivation occurred at temperatures above 50°. The enzymes were inactivated by 100μM CU²⁺, Hg²⁺, Pb²⁺, and Ag⁺.Each of these β-D-glucosidases was inhibited by p-chloromercuribenzoate (100 μ/M); this effect was overcome by cysteine or 2-mercaptoethanol, indicating that the β-D-glucosidase is a sulfhydryl enzyme. Kinetic determinations with chromogenic p-nitrophenyl β-D-glucopyranoside established a K_m. of 2.5 x 10^-4 and an Arrhenius activation-energy of 8.5 kcal.mole^-1. The molecular weight of the induced enzyme was 165,000 as determined by elution from Sephadex G-200. Chromatographic studies showed the enzyme to be a hydrolase, not a transferase.     

Development of an automated plant culture system

An apparatus was constructed that could be used to grow plant tissues, organs, and whole plantlets under sterile conditions. This system accommodated independent or multiple concurrent growth of cultures. Growth of plants either equalled or exceeded that observed using the manual transfer procedure. The automated plant culture system (APCS) consists of silicone tubing, 2 impeller pumps, 2 glass medium reservoir bottles, a 3-way stainless steel valve, a plant culture chamber, and an interface module containing relay boards. Control of the APCS is through interfacing with a microcomputer (e.g. Apple IIe or Atari 400). The computer controlled medium introduction, evacuation, and replenishment in a sterile environment. The APCS was inexpensively constructed and provides a labor-saving, long-term method to culture plants in vitro.Mention of a trade name or proprietary product in the paper does not constitute a guarantee or warranty of the product by the US Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.     

Evaluation of an adjustable epidemiologic information system

Background

In order to facilitate public health response and to achieve early control of infectious disease epidemics, an adjustable epidemiologic information system (AEIS) was established in the Taiwan public health network in February 2006.

Methodology/Principal Findings

The performance of AEIS for the period 2006 through 2008 was evaluated based on a number of response times (RT) and the public health impact. After implementation of the system, the apparent overall shortened RT was mainly due to the shortening of personnel response time (PRT) and the time needed to draft a new questionnaire that incurred as personnel-system interface (PSI); PRT dropped from a fluctuating range of 9.8 ∼28.8 days in the first four months to <10 days in the following months and remained low till 2008 (0.88±1.52 days). The PSIs for newly emerged infectious diseases were 2.6 and 3.4 person-hours for H5N1 in 2007 and chikungunya in 2008, respectively, a much improvement from 1142.5 person-hours for SARS in 2003. The duration of each rubella epidemic cluster was evaluated as public health impact and showed a shortening trend (p = 0.019) that concurred with the shortening of PRT from 64.8±47.3 to 25.2±38.2 hours per cluster (p<0.0001).

Conclusions/Significance

The first evaluation of the novel instrument AEIS that had been used to assist Taiwan''s multi-level government for infectious diseases control demonstrated that it was well integrated into the existing public health infrastructure. It provided flexible tools and computer algorithms with friendly interface for timely data collection, integration, and analysis; as a result, it shortened RTs, filled in gaps of personnel lacking sufficient experiences, created a more efficient flow of response, and identified asymptomatic/mild cases early to minimize further spreading. With further development, AEIS is anticipated to be useful in the application of other acute public health events needing immediate orchestrated data collection and public health actions.     

Toward an integrated system of clade names

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An integrated system of clade names is described based on categories of clades defined with respect to lineages that have survived to the present time. In this system, the most widely known names are applied to crown clades, the names of total clades are formed by adding a standard prefix to the names of the corresponding crowns, and the names of apomorphy clades describe the specific apomorphies with which they originated. Relative to traditional approaches, this integrated approach to naming clades is both more precise concerning the associations of names with particular clades and more efficient with regard to the cognitive effort required to recognize the names of corresponding crown and total clades. It also seems preferable to five alternatives that could be used to make the same distinctions. The integrated system of clade names has several advantages, including the facilitation of communication among biologists who study distantly related clades, promoting a broader conceptualization of the origins of distinctive clades of extant organisms and emphasizing the continuous nature of evolution.     

Pathways database system: an integrated system for biological pathways

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.     

Cannibalism in an age-structured predator-prey system

Recently, Kohlmeier and Ebenhöh showed that cannibalism can stabilize population cycles in a Lotka-Volterra type predator-prey model. Population cycles in their model are due to the interaction between logistic population growth of the prey and a hyperbolic functional response. In this paper, we consider a predator-prey system where cyclic population fluctuations are due to the age structure in the predator species. It is shown that cannibalism is also a stabilizing mechanism when population oscillations are due to this age structure. We conclude that in predator-prey systems, cannibalism by predators can stabilize both externally generated (consumer-resource) as well as internally generated (agestructure) fluctuations.     

Calpains: an elaborate proteolytic system

Calpain is an intracellular Ca(2+)-dependent cysteine protease (EC 3.4.22.17; Clan CA, family C02). Recent expansion of sequence data across the species definitively shows that calpain has been present throughout evolution; calpains are found in almost all eukaryotes and some bacteria, but not in archaebacteria. Fifteen genes within the human genome encode a calpain-like protease domain. Interestingly, some human calpains, particularly those with non-classical domain structures, are very similar to calpain homologs identified in evolutionarily distant organisms. Three-dimensional structural analyses have helped to identify calpain's unique mechanism of activation; the calpain protease domain comprises two core domains that fuse to form a functional protease only when bound to Ca(2+)via well-conserved amino acids. This finding highlights the mechanistic characteristics shared by the numerous calpain homologs, despite the fact that they have divergent domain structures. In other words, calpains function through the same mechanism but are regulated independently. This article reviews the recent progress in calpain research, focusing on those studies that have helped to elucidate its mechanism of action. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.     

Metapopulation dynamics in an aphid-parasitoid system

Metapopulation theory makes a number of predictions concerning the effects of dispersal on the persistence of predator-prey or host-parasitoid systems. While the stabilising effects of dispersal have been shown in a number of laboratory studies, evidence from field studies remains scarce due to a lack of suitable model systems. I describe a host-parasitoid system that shows a classical metapopulation structure with frequent extinctions and colonisations consisting of the aphidiid Lysiphlebus hirticornisand the aphid Metopeurum fuscoviride. Both the parasitoid and the aphid are specialists on their respective hosts. I followed the dynamics of host and parasitoid on individually marked tansy (Tanacetum vulgare) plants, the host of M. fuscoviride. Dynamics of host and parasitoid populations were characterized by frequent extinctions and colonisations. Mean longevity of aphid colonies was only 3.1 weeks. Parasitism by L. hirticorniswas a main cause of extinction for the aphid as rates of parasitism often reached 100%, in particular towards the end of the field season. Patchiness in this system occurs at two spatial scales. Aphid colonies form on single tansy ramets = shoots but movements of aphid individuals among ramets within a particular tansy genet are frequent. Because aphids can persist on a genet for a large numer of generations, it is argued that local populations form on genets rather than ramets. The number of host and parasitoid extinctions described in this study exceeds the number of extinctions usually observed in field studies of host-parasitoid metapopulations. It is suggested that aphid-parasitoid systems such as the one studied in this paper may be good models to test the predictions of metapopulation theory.