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  • 1990-1994  (129,562)
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  • 1984  (48,999)
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  • 1990-1994  (129,562)
  • 1980-1984  (48,999)
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  • 1
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 137-144 
    ISSN: 1476-5535
    Keywords: Composting ; Explosives ; Propellants ; Thermophilic ; Mesophilic ; Bioremediation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Composting was investigated as a bioremediation technology for clean-up of sediments contaminated with explosives and propellants. Two field demonstrations were conducted, the first using 2,4,6-trinitrotoluene (TNT), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine (HMX), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and N-methyl-N,2,4,6-tetranitroaniline (tetryl) contaminated sediment, and the second using nitrocellulose (NC) contaminated soil. Tests were conducted in thermophilic and mesophilic aerated static piles. Extractable TNT was reduced from 11840 mg/kg to 3 mg/kg, and NC from 13090 mg/kg to 16 mg/kg under thermophilic conditions. Under mesophilic conditions, TNT was reduced from 11 190 mg/kg to 50 mg/kg. The thermophilic and mesophilic half-lives were 11.9 and 21.9 days for TNT, 17.3 and 30.1 days for RDX, and 22.8 and 42.0 days for HMX, respectively. Known nitroaromatic transformation products increased in concentration over the first several weeks of the test period, but decreased to low concentrations thereafter.
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  • 2
    ISSN: 1476-5535
    Keywords: Fructo-oligosaccharide ; 1-Kestose ; Glycoprotein ; Fructosyl-transferring activity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Two extracellular β-fructofuranosidases (E-1 andE-2) fromAureobasidium sp. ATCC 20524, producing 1-kestose (1F-β-fructofuranosyl-sucrose) from sucrose, were purified to homogeneity. Molecular weights of the enzymes were estimated to be about 304000 (E-1) and 315000 (E-2) Da by gel filtration. The enzymes contained 33% (w/w) (E-1) and 27% (w/w) (E-2) carbohydrate. TheK m values for sucrose ofE-1 andE-2 andE-2 were 0.34 and 0.28 M, respectively. were 0.34 and 0.28 M, respectively. The enzymatic profiles of these enzymes were almost identical to intracellular enzymesP-1 andP-2 except for the differences in carbohydrate content andK m values ofE-2 andP-2.
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  • 3
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 149-161 
    ISSN: 1476-5535
    Keywords: Toxin ; Secondary plant metabolite ; Allelochemical ; Insecticide ; Mycotoxin ; Endocytobiont
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Many species of insects cultivate, inoculate, or contain symbiotic fungi. Insects feed on plant materials that contain plant-produced defensive toxins, or are exposed to insecticides or other pesticides when they become economically important pests. Therefore, it is likely that the symbiotic fungi are also exposed to these toxins and may actually contribute to detoxification of these compounds. Fungi associated with bark beetles, ambrosia beetles, termites, leaf-cutting ants, long-horned beetles, wood wasps, and drug store beetles can variously metabolize/detoxify tannins, lignins, terpenes, esters, chlorinated hydrocarbons, and other toxins. The fungi (Attamyces) cultivated by the ants and the yeast (Symbiotaphrina) contained in the cigarette beetle gut appear to have broad-spectrum detoxifying abilities. The present limiting factor for using many of these fungi for large scale detoxification of, for example, contaminated soils or agricultural commodities is their slow growth rate, but conventional strain selection techniques or biotechnological approaches should overcome this problem.
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  • 4
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 163-172 
    ISSN: 1476-5535
    Keywords: Biosensors ; Process control ; Enzyme thermistor ; Immunoassay ; Bio-field effect transistor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary A short review about the biosensor research activities for bioprocess monitoring in the F.R.G. after its reunification is given. The principles of biosensor applications are presented. In situ sensors and sensors based on the principles of flow injection analysis are studied. Some applications of a four-channel enzyme thermistor, bio-field effect transistors, and immunoanalysis systems for real process monitoring are presented.
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  • 5
    ISSN: 1476-5535
    Keywords: Vibrio vulnificus ; Oyster ; Monoclonal antibody ; Most probable number ; Enzyme immunoassay
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Oysters, suspended particulate matter (SPM), sediment and seawater samples were collected from West Galveston Bay, Texas over a 16-month period and analyzed for the presence ofVibrio vulnificus, a naturally-occurring human marine pathogen. Detection and enumeration ofV. vulnificus was performed using a species-specific monoclonal antibody (mAb FRBT37) in an enzyme immunoassay (EIA)-most probable number (MPN) procedure capable of detecting as few as 2000 target organisms.V. vulnificus was not detected in seawater, oyster or SPM samples during the cold weather months, but was detected at low levels in several sediment samples during this time period. Increased levels of the organism were first observed in early spring in the sediment, and then in SPM and oysters. The major increase inV. vulnificus occurred only after the seawater temperature had increased above 20°C and the winter-spring rainfall had lowered the salinity below 16‰. The highestV. vulnificus levels at each site were associated with suspended particulate matter. These results are consistent with the hypothesis that (1)V. vulnificus over-winters in a floc zone present at the sediment-water interface, (2) is resuspended into the water column in early spring following changes in climatic conditions, (3) colonizes the surfaces of zooplankton which are also blooming during early spring and (4) are ingested by oysters during their normal feeding process.
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  • 6
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 235-238 
    ISSN: 1476-5535
    Keywords: Biodegradation ; Pseudomonas putida ; Immobilization ; Sodium cyanide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Pseudomonas putida, isolated from contaminated industrial wastewaters and soil sites, was found to utilize sodium cyanide (NaCN) as a sole source of carbon and nitrogen. Cells, immobilized in calcium alginate beads (1–2 mm diameter) were aerated in air-uplift-type fluidized batch bioreactor containing 100–400 ppm of NaCN. Degradation of NaCN was monitored for 168 h by analyzing gaseous and dissolved ammonia (NH3), CO2, pH and optical density. The results indicated that the alginate-immobilized cells ofP. putida were able to degrade NaCN into NH3 and CO2 in a time-dependent manner.
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  • 7
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 229-234 
    ISSN: 1476-5535
    Keywords: Heat shock protein (HSP) ; Yeast ; Saccharomyces ; Viability ; Thermotolerance ; Ethanol tolerance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Heat shock and ethanol stress of brewing yeast strains resulted in the induction of a set of proteins referred to as heat shock proteins (HSPs). At least six strongly induced HSPs were identified in a lager brewing strain and four HSPs in an ale brewing strain. Four of these HSPs with molecular masses of approximately 70, 38, 26 and 23 kDa were also identified in two laboratory strains ofSaccharomyces cerevisiae. The appearance of HSPs correlated with increased survival of strains at elevated temperatures and high concentrations of ethanol. These results suggest that HSPs may play a role in the ethanol and thermotolerance of yeasts. The properties of these proteins and membrane fatty acids in relation to heat and ethanol shock are being investigated.
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  • 8
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 239-245 
    ISSN: 1476-5535
    Keywords: Novel polysaccharide ; Bacillus licheniformis ; Raffia venifera ; d-Glucose ; d-Mannose ; d-Xylose
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary A polysaccharide producing strain ofBacillus licheniformis was isolated from exudate of raffia palm,Raffia vinifera. The optimum conditions for growth and polysaccharide production have been investigated and established. No appreciable polysaccharide was formed on glucose. It grew best in Czapek-Dox media with sucrose as the carbon source. The polysaccharide has been characterized as a heteropolymer containingd-glucose,d-mannose andd-xylose.
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  • 9
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    Journal of industrial microbiology and biotechnology 9 (1992), S. 269-269 
    ISSN: 1476-5535
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
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  • 10
    ISSN: 1476-5535
    Keywords: β-Fructofuranosidase ; Deglycosylation ; Aureobasidium ; Enzymatic stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Most of the carbohydrate moiety of β-fructofuranosidaseP-1 fromAureobasidium sp. ATCC 20524 was removed by endo-β-N-acetylglucosaminidase F. A subunit of 94000 Da was observed in SDS-PAGE after deglycosylation. TheK m value for sucrose was not changed by deglycosylation but the stability at pH 4–5 and 50°C was decreased. The deglycosylated enzyme was more sensitive to proteases such as pronase E and subtilisin than the native enzyme. It is considered that the carbohydrate moiety of β-fructofuranosidaseP-1 contributes to the stability of the enzyme but is not essential in its catalytic function.
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  • 11
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    Bulletin of mathematical biology 46 (1984), S. 967-969 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract It is observed that a dynamical continuity equation for biomass distribution yields the asymptotic steady-state exponential dependencen=A exp( $$ - m/\bar m$$ ) exhibited by certain fishery data, wherem is the biomass of an individual,n is the number of individuals per unit biomass interval, andA, $$\bar m$$ are positive constants. This dynamical approach to biomass distribution is an alternative to the global maximization principle proposed recently by Lurié and Wagensberg.
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  • 12
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    Bulletin of mathematical biology 46 (1984), S. 971-972 
    ISSN: 1522-9602
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  • 13
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    Bulletin of mathematical biology 46 (1984), S. 973-974 
    ISSN: 1522-9602
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  • 14
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    Bulletin of mathematical biology 46 (1984), S. 11-17 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract Linear birth and death processes are used to derive simple expressions for sequential extinction times and gene fixation probabilities in asexual populations.
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  • 15
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    Bulletin of mathematical biology 46 (1984), S. 1-10 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract We are here concerned with the functionf which assigns to each pointP of an object the numberf(P) which is the shortest distance fromP to the border. This function appears in various guises in diverse biological studies. The functionf(P) is itself a measure of shape—or more precisely, an infinite set of measures, one for each point (and hence, in view of its geometric definition, usually in a form inconvenient for use). Thus in this paper we sought a reasonable representative of this infinite set of measures, namely themean of the numbersf(P) asP ranges over all points of the entity. Computability studies are developed for various classes of shapes. For example, (1) the mean for a lamina bounded by a polygon circumscribable about a circle of radiusr isr/3; (2) the mean for a domain bounded by a polyhedron circumscribable about a sphere of radiusr isr/4. The transition from pointwise to piecewisef(P), especially in the non-convex case, requires working with inequalities.
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  • 16
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    Bulletin of mathematical biology 46 (1984), S. 19-40 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract A mathematical model for traveling bands of motile and chemotactic bacteria in the presence of cell growth and death is examined. It is found that asymptotic traveling wave solutions exist in the absence of chemotaxis, due to the balance of growth, death and random motility. Thus random motility confers the ecological advantage of population propagation through migration into nutrient-rich regions. The presence of chemotaxis amplifies this advantage by moving more cells into higher nutrient concentration regions, resulting in larger and faster bands. Therefore there seem to be two types of traveling bands that can be attained by chemotactic bacteria in the presence of growth and death: (1) these growth/death/motility bands; and (2) pure chemotactic ‘Keller-Segel'-type bands. Comparison to experimental observations by Chapman in 1973 indicate that the latter seem to be formed. The relationship between these two types of solution is at present uncertain. The growth/death/motility bands may have relevance on longer time or distance scales characteristic of microbial ecological systems.
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  • 17
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    Bulletin of mathematical biology 46 (1984), S. 115-125 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Based on the principle of minimum power, a mathematical model of the pathological functional state of the oxygen transport system is presented. The model is used to determine the optimal functional parameters of the oxygen transport system in hyperthyroidism, anemia and hypertension. Theoretical results are compared with clinical data.
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  • 18
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    Bulletin of mathematical biology 46 (1984), S. 139-153 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract A modified SIRS model is developed as a framework for the study of epizootiological dynamics in an insect-pathogen system. Linearized stability analysis reveals that the system with one immune and one susceptible host class can exhibit stable, periodic or unstable behavior depending on model parameters. In general, high pathogenicity, short pathogen propagule lifespan and high host reproductive rate are stabilizing influences. Pathogen transmissibility and propagule production/host do not influence local stability. The effect of seasonal host reproduction is studied because most insect hosts are seasonal in temperate climates. The basic stability dependence on model parameters holds except as modified by the length of the reproduction interval. The results of this study are compared with the recent work of Anderson and May.
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    Bulletin of mathematical biology 46 (1984), S. 175-184 
    ISSN: 1522-9602
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    Notes: Abstract The random predator-prey type interactions of the population species in a random varying environment have been investigated. The Fokker-Planck equation for the transition probability, corresponding to the stochastic differential equations established from Lotka-Volterra equations by the introduction of randomness and variability, has been integrated in the form of a path integral. The transition probabilities for extinction or survival of one or several species have been approximately evaluated and investigated.
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    Bulletin of mathematical biology 46 (1984), S. 155-174 
    ISSN: 1522-9602
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    Notes: Abstract If two microbial populations compete for a single resource in a homogeneous environment with time invariant inputs they cannot coexist indefinitely if the resource competed for is not renewed by biological activity within the system. Mathematical studies have shown that in a predator-prey system, where the resource (prey) is self-renewing, the two competitors (predators) can coexist in a limit cycle. This suggests that if the resource competed for is renewed by biological activity within the system coexistence can occur in any microbial system provided that it exhibits the same features as, but without being, a predator-prey one. A food chain involving commensalism, competition and amensalism is presented here. Two subcases are considered. It is only when maintenance effects are taken into account that coexistence, in limit cycles, can occur for this system. Limit cycle solutions for the system are demonstrated with the help of computer simulations. Some necessary conditions for coexistence are presented, as are some speculations regarding the possible physical explanations of the results.
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    Bulletin of mathematical biology 46 (1984), S. 127-137 
    ISSN: 1522-9602
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    Notes: Abstract The branching structure of the mammalian arterial tree has been known to be close to that of an optimal conduit system of the minimum work model characterized as the branch system of constant wall shear rate. The physiological mechanism producing such construction was considered to be based on the local response of arterial caliber induced by the wall shear stress (shear rate × blood viscosity) and thereby maintaining this stress constant, which was previously observed at the canine common carotid artery shunted to the external jugular vein. The stress levels at various parts of the arterial system estimated from available data fell within ±50% of the mean (15 dyn/cm2), which was consistent with the value predicted from the model. Theoretical analyses on the cost function of the model indicated that the suspected variation of shear rate levels in the arterial tree due to the anomalous changes in blood viscosity which might bring about 3- to 4-fold differences between the minimum and maximum shear rates would cause less than 10% increase in the total energy cost. It was concluded that a local adaptive response to wall shear stress is the mechanism which effectively optimizes the design of the arterial tree.
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  • 22
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    Bulletin of mathematical biology 46 (1984), S. 185-185 
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    Bulletin of mathematical biology 46 (1984), S. 187-203 
    ISSN: 1522-9602
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    Notes: Abstract The structure of the genetic code is related to a Gray code, which is a plausible theoretical model for an amino acid code. The proposed model implies that the most important factor in shaping the code was the effects of mistakes in translation, not effects of mutations. Another possible implication is that the preservation of stiffness and flexibility at appropriate places in a protein chain is as important in protein structure as the appropriate placement of hydrophilic (external) and hydrophobic (internal) residues. Other results are a simple conceptualization of the relationships among the 20 amino acids and their relations to their codons. The detailed relationships are summarized in the following ‘similarity alphabet’: ala, thr, gly, pro, ser; asp, asn, glu, gln, lys; his, arg, trp, tyr, phe; leu, met, ile, val, cys; (ATGPS DNEQK HRWYF LMIVC in the one-letter code). This alphabet falls into four groups of amino acids: small, external, large, internal. The approximate relation of the groups to their codons is expressed as: the first base of a codon controls size—a purine means a small amino acid, a pyrimidine means large; the middle base controls cloisterednes—purine means external, pyrimidine means internal. These relationships express the minimum change principle upon which the code appears to be founded.
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    Bulletin of mathematical biology 54 (1992), S. 1-20 
    ISSN: 1522-9602
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    Notes: Abstract An organism persists only if it satisfies internal and external constraints. Within the organism networks of processes meet the constraints. In such networks a principle of matching often obtains: the pattern of coupling among processes matches the correlation among constraints. That is, a module—a cluster of coupled processes—meets a constraint. Dissociable modules meet dissociàble constraints. A hierarchy of modules meets a hierarchy of constraints. We have inquired whether such matching is predicted by an optimality criterion in a simple example. We find that in an ensemble of networks with unreliable processes, the networks that meet the constraints with highest reliability obey the principle of matching. The difference in reliability between modular and nonmodular networks that meet the same constraints is a function of the probability of success per process. Our results suggest that this difference is maximal at a probability of success that increases monotonically with the number of processes in the network.
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    Bulletin of mathematical biology 54 (1992), S. 59-75 
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    Notes: Abstract A method is described for estimating the distribution and hence testing the statistical significance of sequence similarity scores obtained during a data-bank search. Maximum-likelihood is used to fit a model to the scores, avoiding any costly simulation of random sequences. The method is applied in detail to the Smith-Waterman algorithm when gaps are allowed, and is shown to give results very similar to those obtained by simulation.
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    Bulletin of mathematical biology 46 (1984), S. 269-282 
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    Notes: Abstract A theoretical study of the Brusselator model with non-uniform distribution of component A and a concentration-dependent diffusion coefficient has been performed. Numerical simulation reveals that a variable diffusion coefficient alters the bifurcation pattern and the stability properties of the steady-state as well as periodic solutions. A simple approximate method, based on one-point collocation, has been proposed to analyze the bifurcation phenomena for the case of fixed boundary conditions and low system size.
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    Bulletin of mathematical biology 46 (1984), S. 283-294 
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    Notes: Abstract In this paper the effects of the occurrence of cut trees in the topological analysis of branching patterns have been studied. It is assumed that branches are removed at random from the trees. We prove that, for both the segmental and terminal growth models, the probability distributions of the cut trees are identical to those of complete trees.
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    Bulletin of mathematical biology 46 (1984), S. 247-268 
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    Notes: Abstract The goal of this work is an examination of capillary exchange models as mathematical operators. The concentration function relations for the Krogh cylinder of a single capillary, basic to many organ models, are studied via the theory of operators on the Lebesgue normed spacesL p[0,∞], (1〈-p〈-∞). A discussion is included of theL p -normsvis-à-vis the coefficient of variation currently used in finding capillary parameters and evaluating parameter searches. The capillary model determines two operators on the space of locally integrable functions: O K (relating extravascular concentration to intravascular) and K a, k (relating intravascular concentration to input), wherek is the ratio of permeabilitysurface area (PS) to extravascular volume, and α is the ratio of PS to flow. These operators are shown to induce contractive (‖O K ‖ p 〈-1, ‖K a, k ‖ p 〈-1), isotone, linear operators onL p . The uniform convergence relation $$K_{a,k} = \mathop {\lim _{(p)} }\limits_{N \to \infty } \left( {\sum\limits_{n = 0}^N {P_n (a)O_k^n } } \right)$$ (as operators onL p) is derived, whereP n (a) is the Poisson probabilitye −a a n /n!. For the important special cases ofp=∞, 1, 2 the norms are found (‖Ok‖=‖Ka,k‖p=1). Consideration is also given to the norms and operators when the functions involved are limited to a finite interval of time.
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    Bulletin of mathematical biology 46 (1984), S. 295-326 
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    Notes: Abstract One particular kind of structure offers possible explanations, for long-term memory, efficient consolidation of stored information from the environment, clustering of data strings and multimodal functioning. It is a possible model for pieces of neural structure and its use offers a uniform method for both studying and constructing an extensive class of mechanisms.
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    Bulletin of mathematical biology 46 (1984), S. 327-332 
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    Notes: Abstract Levenshtein dissimilarity measures are used to compare sequences in application areas including coding theory, computer science and macromolecular biology. In general, they measure sequence dissimilarity by the length of a shortest weighted sequence of insertions, deletions and substitutions required, to transform one sequence into another. Those Levenshtein dissimilarity measures based on insertions and deletions are analyzed by a model involving valuations on a partially ordered set. The model reveals structural relationships among poset, valuation and dissimilarity measure. As a consequence, certain Levenshtein dissimilarity measures are shown to be metrics characterized by betweenness properties and computable in terms of well-known measures of sequence similarity.
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    Bulletin of mathematical biology 46 (1984), S. 337-337 
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    Bulletin of mathematical biology 46 (1984), S. 333-336 
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    Notes: Abstract It is pointed out that the methane flux measured experimentally for certain ponds and swamps is quantitatively consistent with a commensal dependence of Methanobacteria on O2-chemotactic motile aerobic bacteria. The Methano species is thereby shielded from oxygen and provided with carbon dioxide for the anaerobic production of methane.
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    Bulletin of mathematical biology 46 (1984), S. 357-370 
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    Notes: Abstract A sufficient condition is given for stochastic boundedness persistence of a top predator in generalized Lotka-Volterra-type stochastic food web models in arbitrary bounded regions of state space. The main result indicates that persistence in the corresponding deterministic system is preserved in the stochastic system if the intensities of the random fluctuations are not too large.
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    Bulletin of mathematical biology 46 (1984), S. 371-377 
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    Notes: Abstract One of Bobisud's models for the evolution of cannibalism is reanalyzed by applying the method of finding evolutionarily stable strategies (or ESS's). It is demonstrated that ‘no cannibalism’ never will be an ESS if the initial rate of cannibalism is too large. It is further demonstrated that individual selection may even result in the evolution of cannibalism during food abundance. Some empirical case studies are briefly discussed in relation to this model.
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    Bulletin of mathematical biology 46 (1984), S. 379-387 
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    Notes: Abstract A computer algorithm is presented which equiprobably generates any member of the set of all directed trees withk labeled terminal nodes and unlabeled interior nodes. The algorithm requires roughlyk 2 /2 storage locations. The one-time initialization requiresO(k 2 ) time, while generating each tree requiresO(k) time.
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    Bulletin of mathematical biology 54 (1992), S. 401-412 
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    Notes: Abstract We develop a theory for host seeking decisions in mosquitoes that explicitly considers the tradeoffs mosquitoes face in allocation to somatic and gametic function. Specifically, we consider conditions under which mosquitoes should seek out nectar and blood hosts upon encountering host odours. Results from development of a dynamic model that considers free and crop energy states suggest that mosquitoes should seek out blood hosts under a wide variety of conditions but that decisions to seek nectar depends upon crop volume, concentration and free energy. This pattern arises because mosquitoes carrying large crop loads are constrained in their ability to obtain large blood meals due to space limitations in the abdomen. The predicted patterns of behaviour are supported by published observations of mosquito behaviour.
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    Bulletin of mathematical biology 54 (1992), S. 413-422 
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    Notes: Abstract In behavioral ecology, diet selection is often predicted by using a theory in which it is assumed that behaviors have evolved to maximize the rate of intake of energy. In this theory, it is assumed that fitness is a monotonic function of energy intake. An alternative is to deal directly with fitness, measured in terms of expected reproduction, and thus connect short term behavior with reproduction. Following the usual assumptions of the theory of diet choice, fitness satisfies a partial differential-difference equation. Conditions under which rate maximizing and state variable theories of diet selection yield identical predictions are identified. When predation, as well as starvation, is a source of mortality, the identification is not as complete.
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    Bulletin of mathematical biology 54 (1992), S. 445-464 
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    Notes: Abstract Environmental uncertainty can be both a cause and consequence of chance variation in many of the phenotypic factors associated with the control of clutch size in birds. When such uncertainty inflates or otherwise influences the variance associated with expected reproductive success for any genotype, it will also influence the resulting phenotypic optima. Random variation that affects the evolution of clutch size optima explicitly may occur both within (intra-) and across (inter-) generations. Examples of intra-generational uncertainty could include chance variation in: (1) the quality and quantity of offspring, (2) parental quality, and (3) temporal resources like food. Inter-generational uncertainty would include chance variation in demographic and population characters. With respect to clutch (or litter) size, almost all forms of uncertainty tend to favor an optimum (genetic) strategy with a clutch that is smaller than the clutch associated with the apparent or actual maximal fitness of an individual parent. The overall effect of all the components of uncertainty can be evaluated through the integration of all this phenotypic variation: however each step of the integration is a conditional expectation of each component. Therefore, a single factor analysis may indicate a false optimum, and an integrated analysis of all components is necessary to evaluate the importance of their individual and joint effects on the adaptive evolution of clutch size.
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    Bulletin of mathematical biology 54 (1992), S. 503-519 
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    Notes: Abstract A difference equation model for the dynamics of a semelparous size-structured species consisting of juvenile and adult individuals is derived and studied. The adult population consists of two size classes, a smaller class and a larger more fertile class. Negative feedback occurs through slowed juvenile growth due to increased total population levels during the developmental period and consequently a smaller adult size at maturation. Intra-specific competition coefficients are size dependent and measure the strength of intra-specific competition between juveniles and adults. It is shown that equilibrium states in which adults and juveniles occur together at all times are in general destabilized by significantly increased juvenilevs adults competition with the result that stable periodic cycles appear, in which the generations alternate in time and hence avoid competition. This result supports the tenet that intra-specific competition between juveniles and adults is destabilizing. Exceptions to this destabilization principle are found, however, in which populations exhibiting non-equilibrium, aperiodic dynamics can be equilibrated by increase competition between juveniles and adults. This occurs, for example, when adult fertility and competition coefficients are significantly size class dependent.
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    Bulletin of mathematical biology 54 (1992), S. 537-561 
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    Notes: Abstract An epithelial cell is modeled as a single compartment, bounded by apical and basolateral cell membranes, and containing two nonelectrolyte solute species, nominally NaCl and KCl. Membrane transport of these species may be metabolically driven, or it may follow the transmembrane concentration gradients, either singly (a channel) or jointly (a cotransporter). To represent the effect of stretch-activated channels or shrinkage-activated cotransporters, the membrane permeabilities and cotransport coefficients are permitted to be functions of cell volume. When this epithelium is considered as a dynamical system, conditions are indicated which guarantee the uniqueness and stability of equilibria. Experimentally, many epithelial cells can regulate their volume, and such volume regulatory capability is defined for this model. It is clearly distinct from dynamical stability of the equilibrium and requires more stringent conditions on the volume-dependent permeabilities and cotransporters. For a previously developed model of the toad urinary bladder (Strieteret al., 1990,J. gen. Physiol. 96, 319–344) the uniqueness and stability of its equilibria are indicated. The analysis also demonstrates that under some conditions a second stable equilibrium may appear, along with a saddle-node bifurcation. This is illustrated numerically in a modified model of the epithelium of the thick ascending limb of Henle.
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    Bulletin of mathematical biology 54 (1992), S. 687-694 
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    Bulletin of mathematical biology 54 (1992), S. 649-672 
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    Notes: Abstract Models of the dynamical interactions important in generating immune reactivity have generally assumed that the immune system is a single well-stirred compartment. Here we explicitly take into account the compartmentalized nature of the immune system and show that qualitative conclusions, such as the stability of the immune steady state, depend on architectural details. We examine a simple model idiotypic network involving only two types of B cells and antibody molecules. We show, for model parameters used by De Boeret al. (1990,Chem. Eng. Sci. 45, 2375–2382), that the immune steady state is unstable in a one compartmental model but stable in a two compartment model that contains both a lymphoid organ, such as the spleen, and the circulatory system.
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    Bulletin of mathematical biology 46 (1984), S. 515-527 
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    Notes: Abstract The comparison of several sequences is central to many problems of molecular biology. Finding consensus patterns that define genetic control regions or that determine structural or functional themes are examples of these problems. Previously proposed methods, such as dynamic programming, are not adequate for solving problems of realistic size. This paper gives a new and practical solution for finding unknown patterns that occur imperfectly above a preset frequency. Algorithms for finding the patterns are given as well as estimates of statistical significance.
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    Bulletin of mathematical biology 46 (1984), S. 501-514 
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    Notes: Abstract A new development is introduced here in the use of dynamic programming in finding pattern similarities in genetic sequences, as was first done by Needleman and Wunsch (1969). A condition of pattern similarity is defined and an algorithm is given which scans any set of similarities and screens out those which fail to meet the condition. When the set to be scanned contains every pair of segments, one from each of two given sequences of lengthsm andn (i.e. every possible location for a pattern similarity), then it completes the scan in a number of computational steps proportional tom·n, leaving those pairs of segments which satisfy the similarity condition. The algorithm is based on the concept of match density, as suggested by Goad and Kanehisa (1982).
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    Bulletin of mathematical biology 46 (1984), S. 529-543 
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    Notes: Abstract This paper concerns sequences of letters in which certain “distinguished” words are of interest. Such sequences arise as data in numerous fields including genetics and neuroscience. A probability distribution is given for the number of occurrences of a chosen word in a randomized sequence of letters. Such words are considered “favored” if they occur more than expected at random. Favored words have been discovered in nerve impulse trains and may reflect a neural coding scheme.
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    Bulletin of mathematical biology 46 (1984), S. 545-552 
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    Notes: Abstract As the volume of protein sequence data grows, rapid methods for searching the protein sequence database become of primary importance. Rigorous comparison of sequences is obtained with the well-known dynamic programming algorithms. However, these algorithms are not rapid enough to use for routinely searching the entire database. In this paper we discuss some methods that can be used for rapid searches.
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    Bulletin of mathematical biology 46 (1984), S. 553-566 
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    Notes: Abstract We give algorithms for computing the extent of similarity between two or three sequences of letters. The similarity measures we consider include a penalty for inserting gaps within the sequence in order to enhance similarity. The magnitude of the penalty for gaps is assumed to be independent of their size in order to accommodate certain biological applications. Our algorithm for three sequence comparisons, which is based on solving a system of recursive equations, improves upon the efficiency of existing methods. Although the system of recursive equations utilized by the algorithm is quite complicated as it stands, it has none the less been simplified by appeal to combinatorial considerations.
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    Bulletin of mathematical biology 46 (1984), S. 567-577 
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    Notes: Abstract Well-known dynamic programming algorithms exist for comparing two finite sequences inO(N 2) time and storage, whereN is the common sequence length. Extensions to the comparison ofM finite sequences requireO((2N) M) time and storage, making such algorithms difficult even forM=3. A simple generalization of the sequences makes it possible to obtain some results about the geometry of sequence alignments. These ideas suggest heuristic approaches to problems of comparing several sequences. IfM sequences are known to be related by a binary tree, they can be aligned inO(MN 2) time andO(N 2+NM) storage.
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    Bulletin of mathematical biology 54 (1992), S. 839-873 
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    Notes: Abstract Using the chromium release assay and the single cell assay in agarose, we study the cytotoxic reaction of the MHC-restricted T lymphocyte clones P89:15 and P1:3, which recognize distinct but specific tumour antigens on the surface of syngeneic P815 mastocytoma cells. We propose a mathematical model which describes these experiments, accounts for the strongly non-Michaelian behaviour of the reaction and permits us to estimate the kinetic parameters characterizing effector-target conjugation and lethal hit delivery. The results show that the binding and lytic activity of effector cells is modulated by the number of targets bound to them. The binding of a second target by an effector having already a target bound is facilitated; on the other hand, an effector having bound two targets delivers a lethal hit more slowly than one with a single target bound. We investigate the role of these kinetic properties in the competition between the process of tumour progression due to cancer cell replication and the process of tumour regression due to T lymphocyte cytotoxic activity. For both clones, we estimate the effector-target ratio beyond which rejection prevails. This ratio is nine times larger for P1:3 than for P89:15. Furthermore, our analysis suggests that there exists an optimal specificity minimizing this ratio. Deviations from this optimum, be it in the sense of an increase or decrease of specificity, tendsto stabilize the tumoural state: a situation which in the broader context of the immune response evolution and regulation can be viewed as animmune response dilemma.
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    Bulletin of mathematical biology 54 (1992), S. 929-938 
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    Notes: Abstract In this paper a stochastic model for a two-compartment system which incorporates Erlang residence time distributions (i.e. the residence times have the gamma distribution where the shape parameters assume integer values only) into each compartment is generalized to include random rate coefficients. Analytical forms of the model are derived for the case where the rate coefficients have gamma densities. A relationship is established between the new models and existing models that are in current practical usage.
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    Bulletin of mathematical biology 54 (1992), S. 939-955 
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    Notes: Abstract Oscillations and chaos can be modelled and observed in a realistic simulation model of interacting prey-predator populations based on Monte Carlo simulation methods. These nonlinear phenomena are linked with some biological and physical bifurcation parameters and mathematical tools from dynamical systems theory may be used in order to characterize this behaviour. Chaotic dynamics are therefore, in our simulation, more the rule than the exception, and are related to delays associated with spatial degrees of freedom.
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    Bulletin of mathematical biology 46 (1984), S. 661-672 
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    Notes: Abstract Protein sequences of the Dayhoff databank of 1984 have been analyzed to evaluate the occurrences of the 400 dipeptides and 8000 tripeptides. Expected values and standard deviations for the di- and tripeptides were determined by Monte Carlo and binomial approximation. A condensed format containing this information, labeled a uniqueness diagram, is presented and made available in the form of a microfiche.
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    Bulletin of mathematical biology 54 (1992), S. 1023-1038 
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    Notes: Abstract Cells displaying the classic multidrug resistant (MDR) phenotype possess a transmembrane protein (p170 or P-glycoprotein) which can actively extrude cytotoxic agents from the cytoplasm. A mathematical model of this drug efflux pump has been developed. Outward transport is modeled as a facilitated diffusion process. Since energy-dependent efflux of cytotoxic agents requires that ATP also bind to p170, the model includes a dynamic calculation for efflux rate which considers Michaelis-Menten kinetics for both the substrate agent and ATP. The final system consists of one partial differential equation (PDE) for the facilitated diffusion of substrate agents out of the cell a 2×2 ordinary differential equation (ODE) system for the dynamic calculation of the ATP-ADP pool, and a dynamic algebraic calculation of the efflux rate given substrate levels at the interior cell membrane interface and ATP levels in the cell. A stability analysis of the ATP-ADP pool distribution and a simplistic closed form solution of the linearized PDE are included. Numerical simulations are also provided.
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    Bulletin of mathematical biology 54 (1992), S. 1039-1056 
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    Notes: Abstract Reentry in the heart is the repeated excitation of the same tissue by a single excitation wave; it is responsible for several types of cardiac arrhythmia. The simplest model which permits the phenomenon of reentry is two laterally coupled excitable fibers; in this paper we examine such a model in order to establish a basis for the understanding of the fundamental physical processes underlying the process of reentry. Two versions of the FitzHugh-Nagumo equations are used to develop complementary numerical and analytical results for the coupled fiber model. On the basis of numerical studies, regions of qualitatively different behaviour are mapped in the parameter space of excitation threshold and coupling strength between the fibers, and the effect of the rate of recovery is explored. Some of these regions are also obtained analytically, in good agreement with the numerical results. Finally, the results are discussed in the light of recent work on the role of the anisotropy of cardiac tissue in the initiation of reentrant activity in the heart.
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    Bulletin of mathematical biology 54 (1992), S. 1069-1081 
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    Notes: Abstract A sigmoid curve with three fitting parameters is proposed as a descriptive model for the spatial velocity field in one-dimensional growth of plant organs. Analytic expressions are derived for the relative elemental growth (REG) rate, the position and value of the REG rate maximum, the length of the growth zone, the inverse of the growth trajectory and cell length in the “elongation only” zone. The expressions are fit to published data to characterize the effects of environmental variation on growth of monocotyledonous roots. The simple expressions for growth may prove useful in mechanistic models. The fitted curves summarize more than a decade of observations and thus provide a challenge to theorists.
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    Bulletin of mathematical biology 46 (1984), S. 827-844 
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    Notes: Abstract In two-state sliding filament models of muscle contraction a partial differential equation must be solved to find the cross-bridge distribution functionn(x, t). In this paper the analytical form of this function is obtained by integration along the characteristic line and special cases are presented in which the explicit expression forn(x, t) can be completely determined. These analytical solutions provide a direct mathematical connection between the microscopic contraction parameters contained in the kinetic theories and macroscopic muscle dynamics and are thus used to investigate what parameters influence the transient contractile tension in typical experimental conditions. The results of this investigation are consistent with relevant aspects of muscle physiology.
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    Bulletin of mathematical biology 46 (1984), S. 845-857 
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    Notes: Abstract Experiments on random binary, ternary, etc. (P=2, 3,…, 10) switching nets are reported. Behavioral cycle lengths are examined as functions of output variety,P, input connectance,K, and net size,N. Overall, output variety appears an influential, well-behaved net property. Strong, but well-behaved interactions appear among net variables. In high connectance nets, median cycle length grows approx. asP N/2. Other factors constant, one-connected nets show the shortest cycles, and connectance effects appear to converge asymptotically aroundN. Data for cycle length as a function of net size suggest a concavity not compatible with the Kauffman “square root law” (Kauffman, 1969). Evidence of a positive relationship between cycle length and run-in length is found in two-input nets; weaker evidence is obtained that in higher connectance nets this relationship becomes negative in sign. The “modular complexity” ofP〉2 nets is examined briefly.
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    Bulletin of mathematical biology 46 (1984), S. 869-877 
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    Notes: Abstract The influence of topographical situation on the spread of infection is studied. The investigation is based on a multigroup model. The population under consideration is thought to be divided into subpopulations living in regions that are separated from each other by natural barriers (mountains). Infection is carried from one region to another by migrating infectives. Migration is possible only along the river system so that the structure of the epidemiological network is that of a symmetric tree. The results allow comparison of the velocity of propagation of the epidemic for different geographical situations and allow quantification of the “channel-effect”, according to which mountainous regions are channels rather than barriers to the spread of an epidemic.
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    Bulletin of mathematical biology 56 (1994), S. 129-146 
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    Notes: Abstract More than 20 years after its proposal, Keller and Segel's model (1971,J. theor. Biol.,30, 235–248) remains by far the most popular model for chemical control of cell movement. However, before the Keller-Segel equations can be applied to a particular system, appropriate functional forms must be specified for the dependence on chemical concentration of the cell transport coefficients and the chemical degradation rate. In the vast majority of applications, these functional forms have been chosen using simple intuitive criteria. We focus on the particular case of eukaryotic cell movement, and derive an approximation to the detailed model of Sherrattet al. (1993,J. theor. Biol.,162, 23–40). The approximation consists of the Keller-Segel equations, with specific forms predicted for the cell transport coefficients and chemical degradation rate. Moreover, the parameter values in these functional forms can be directly measured experimentally. In the case of the much studied neutrophil-peptide system, we test our approximation using both the Boyden chamber and under-agarose assays. Finally, we show that for other cell-chemical interactions, a simple comparison of time scales provides a rapid check on the validity of our Keller-Segel approximation.
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    Bulletin of mathematical biology 56 (1994), S. 1-64 
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    Notes: Abstract The formal structure of evolutionary theory is based upon the dynamics of alleles, individuals and populations. As such, the theory must assume the prior existence of these entities. This existence problem was recognized nearly a century ago, when DeVries (1904,Species and Varieties: Their Origin by Mutation) stated. “Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” At the heart of the existence problem is determining how biological organizations arise in ontogeny and in phylogeny. We develop a minimal theory of biological organization based on two abstractions from chemistry. The theory is formulated using λ-calculus, which provides a natural framework capturing (i) the constructive feature of chemistry, that the collision of molecules generates specific new molecules, and (ii) chemistry's diversity of equivalence classes, that many different reactants can yield the same stable product. We employ a well-stirred and constrained stochastic flow reactor to explore the generic behavior of large numbers of applicatively interacting λ-expressions. This constructive dynamical system generates fixed systems of transformation characterized by syntactical and functional invariances. Organizations are recognized and defined by these syntactical and functional regularities. Objects retained within an organization realize and algebraic structure and possess a grammar which is invariant under the interaction between objects. An organization is self-maintaining, and is characterized by (i) boundaries established by the invariances, (ii) strong self-repair capabilities responsible for a robustness to perturbation, and (iii) a center, defined as the smallest kinetically persistent and self-maintaining generator set of the algebra. Imposition of different boundary conditions on the stochastic flow reactor generates different levels of organization, and a diversity of organizations within each level. Level 0 is defined by selfcopying objects or simple ensembles of copying objects. Level 1 denotes a new object class, whose objects are self-maintaining organizations made of Level 0 objects, and Level 2 is defined by self-maintaining metaorganizations composed of Level 1 organizations. These results invite analogy to the history of life, that is, to the progression from self-replication to self-maintaining procaryotic organizations to ultimately yield self-maintaining eucaryotic organizations. In our system self-maintaining organizations arise as a generic consequence of two features of chemistry, without appeal to natural selection. We hold these findings as calling for increased attention to the structural basis of biological order.
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    Bulletin of mathematical biology 56 (1994), S. 249-273 
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    Notes: Abstract A model is developed to describe neuronal elongation as a result of the polymerization of microtubules and elastic stretching of the neurites by force produced by the growth cone. The model for a single segment with a single growth cone revealed a constant elongation rate, while the concentration of tubulin in the soma rises, and the concentration of tubulin becomes constant in the growth cone. Extending the model to a neurite with a single branch point and two growth cones revealed the same results. When the assembly or the disassembly rate of microtubules is unequal in both growth cones, transient retraction of one of the terminal segments occurs, which results in complete retraction of the segment when the difference in (dis)assembly rate between the two growth cones is large enough. When the model is applied to large trees, a maximal sustainable number of terminal segments as a function of the production rate of tubulin appears. Mechanisms to stop outgrowth are discussed in relation to the establishment of synaptical contacts between cells.
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    Bulletin of mathematical biology 56 (1994), S. 225-247 
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    Notes: Abstract We have developed a new model describing the relationship between plasma and red cell tracers flowing through the lung. The model is the result of an analysis of the transport of radiolabeled plasma albumin between two flowing phases and shows that differences between red cell and plasma tracer curves are related to microvascular hematocrit. The model was tested in an isolated, blood-perfused dog lung preparation in which we injected51Cr-labeled red cells and125I-labeled plasma albumin into the pulmonary artery. From the tracer concentration-time curves at the venous outflow, we calculatedh r, the ratio of microvascular hematocrit to large-vessel hematocrit. In 18 baseline experiments,h r=0.92±0.01 (mn±sem) at a blood flow rate of 10.7±0.3 ml s−1. We determined the effects of (a) glass bead embolization, (b) alloxan, and (c) lobe ligation onh r. Embolization attenuated the separation between plasma and red cells (increasedh r), probably as a consequence of passive vasodilation. Alloxan enhanced separation of plasma and red cells (decreasedh r), possibly as a result of arteriolar vasoconstriction. Ligation of a fraction of the perfused tissue at constant flow did not cause significant change inh r in the remaining perfused tissue. The model assumes that large-vessel transit times are uniform and that all dispersion occurs in the microvasculature. A theoretical analysis apportioning dispersion between large and small vessels disclosed that the error associated with these assumptions is likely to be less than 15% of the measuredh r. We conclude from this study that the microvascular hematocrit model describes experimental plasma and red cell curves. The results imply thath r can be readily deduced from tagged red cells and plasma and can be accounted for in calculating permeability-surface area in diffusing tracer experiments.
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    Notes: Abstract We present a mathematical model of the cytotoxic T lymphocyte response to the growth of an immunogenic tumor. The model exhibits a number of phenomena that are seenin vivo, including immunostimulation of tumor growth, “sneaking through” of the tumor, and formation of a tumor “dormant state”. The model is used to describe the kinetics of growth and regression of the B-lymphoma BCL1 in the spleen of mice. By comparing the model with experimental data, numerical estimates of parameters describing processes that cannot be measuredin vivo are derived. Local and global bifurcations are calculated for realistic values of the parameters. For a large set of parameters we predict that the course of tumor growth and its clinical manifestation have a recurrent profile with a 3- to 4-month cycle, similar to patterns seen in certain leukemias.
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    Bulletin of mathematical biology 56 (1994), S. 275-294 
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    Notes: Abstract We present a new, practical algorithm to resolve the experimental data in restriction site analysis, which is a common technique for mapping DNA. Specifically, we assert that multiple digestions with a single restriction enzyme can provide sufficient information to identify the positions of the restriction sites with high probability. The motivation for the new approach comes from combinatorial results on the number of mutually homeometric sets in one dimension, where two sets ofn points are homeometric if the multiset ofn(n−1)/2 distances they determine are the same. Since experimental data contain errors, we propose algorithms for reconstructing sets from noisy interpoint distances, including the possibility of missing fragments. We analyse the performance of these algorithms under a reasonable probability distribution, establishing a relative error limit ofr=Θ(1/n 2) beyond which our technique becomes infeasible. Through simulations, we establish that our technique is robust enough to reconstruct data with relative errors of up to 7.0% in the measured fragment lengths for typical problems, which appears sufficient for certain biological applications.
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    Bulletin of mathematical biology 56 (1994), S. 323-336 
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    Notes: Abstract A simple chemical model of the idiotypic network of immune systems, namely the AB model, has been developed by De Boeret al. The complexity of the system, such as the steady states, periodic oscillations and chaotic motions, has been examined by the authors mentioned above. In the present paper, the periodic motions and chaotic behaviours exhibited by the system are intuitively described. To clarify in which parameter domains concerned the system exhibits periodic oscillations and in which parameter domains the system demonstrates chaotic behaviours the Lyapounov exponent is explored. To characterize the strangeness of the attractors, the fractal dimension problem is worked out.
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    Bulletin of mathematical biology 56 (1994), S. 359-363 
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    Bulletin of mathematical biology 56 (1994), S. 337-357 
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    Notes: Abstract We consider a stochastic mechanism of the loss of resistance of cancer cells to cytotoxic agents, in terms of unstable gene amplification. Two models being different versions of a time-continuous branching random walk are presented. Both models assume strong dependence in replication and segregation of the extrachromosomal elements. The mathematical part of the paper includes the expression for the expected number of cells with a given number of gene copies in terms of modified Bessel functions. This adds to the collection of rare explicit solutions to branching process models. Original asymptotic expansions are also demonstrated. Fitting the model to experimental data yields estimates of the probabilities of gene amplification and deamplification. The thesis of the paper is that purely stochastic mechanisms may explain the dynamics of reversible drug resistance of cancer cells. Various stochastic approaches and their limitations are discussed.
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    Bulletin of mathematical biology 56 (1994), S. 365-368 
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    Bulletin of mathematical biology 56 (1994), S. 369-389 
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    Notes: Abstract Dextran has been the most commonly employed test molecule for probing the selectivity of glomerular filtration to macromolecules of varying size. The usual theories for hindered transport of solid spheres through pores have limited utility in interpreting clearance data for dextran or other linear polymers because such polymers in solution more closely resemble random, solvent-filled coils than solid spheres. To provide a model for glomerular filtration of random-coil macromolecules, the equilibrium partitioning of random coils between cylindrical pores and bulk solution was simulated using Monte Carlo calculations, and those results were combined with a hydrodynamic theory for restricted motion of solvent-filled polymer coils in pores. The rates of transport predicted for either neutral random coils or for solid spheres of the same Stokes-Einstein radius were significantly lower than observed transport rates of dextran through the glomerular capillary wall or across synthetic porous membranes. This facilitation of dextran transport was modeled by postulating weak, attractive interactions between dextran monomers and the pore wall. The random-coil model with attractive interactions, modeled using a short-range, square-well potential, was found to adequately represent dextran sieving data in normal rats. Various limitations of this approach are discussed.
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    Bulletin of mathematical biology 56 (1994), S. 567-586 
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    Notes: Abstract Method-dependent mechanisms that may affect dynamic numerical solutions of a hyperbolic partial differential equation that models concentration profiles in renal tubules are described. Some numerical methods that have been applied to the equation are summarized, and ways by which the methods may misrepresent true solutions are analysed. Comparison of these methods demonstrates the need for thoughtful application of computational mathematics when simulating complicated time-dependent phenomena.
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    Bulletin of mathematical biology 56 (1994), S. 587-616 
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    Notes: Abstract The regulation of the interactions between the actin binding proteins and the actin filaments are known to affect the cytoskeletal structure of F-actin. We develop a model depicting the formation of actin cytoskeleton, bundles and orthogonal networks, via activation or inactivation of different types of actin binding proteins. It is found that as the actin filament density increases in the cell, a spontaneous tendency to organize into bundles or networks occurs depending on the active actin binding protein concentration. Also, a minute change in the relative binding affinity of the actin binding proteins in the cell may lead to a major change in the actin cytoskeleton. Both the linear stability analysis and the numerical results indicate that the structures formed are highly sensitive to changes in the parameters, in particular to changes in the parameter ϕ, denoting the relative binding affinity and concentration of the actin binding proteins.
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    Bulletin of mathematical biology 56 (1994), S. 633-664 
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    Notes: Abstract To investigate morphogenesis and in particular circularization mechanisms in young mycelia, we observe cultures of the zygomyceteMucor spinosus and develop discrete models of two-dimensional filamental branching growth. The models are based on the hypothesis that the fungus secretes a regulatory substance that diffuses into the surrounding medium and is detected by the growing hyphae. We also present a simple Markovian growth model without such a feedback, but yielding to analytical computations.
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    Bulletin of mathematical biology 56 (1994), S. 617-631 
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    Notes: Abstract In vivo volume growth of two murine tumor cell lines was compared by mathematical modeling to their volume growth as multicellular spheroids. Fourteen deterministic mathematical models were studied. For one cell line, spheroid growth could be described by a model simpler than needed for description of growthin vivo. A model that explicitly included the stimulatory role for cell-cell interactions in regulation of growth was always superior to a model that did not include such a role. The von Bertalanffy model and the logistic model could not fit the data; this result contradicted some previous literature and was found to depend on the applied least squares fitting method. By the use of a particularly designed mathematical method, qualitative differences were discriminated from quantitative differences in growth dynamics of the same cells cultivated in two different three-dimensional systems.
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    Bulletin of mathematical biology 56 (1994), S. 665-686 
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    Notes: Abstract This paper develops and applies a dynamic mathematical model for optimal scheduling of nitrogen fertilization and irrigation that minimizes nitrogen leaching subject to a target level of yield. The analysis assumes a single crop grown during a single growing season of a given length. It is shown that substitution of water for nitrogen along a given plant growth path decreases nitrogen leaching and, therefore, groundwater contamination. It is proved that a minimum leaching solution to the optimization problem is obtained with a single nitrogen application at the beginning of the season and irrigation scheduling that maintains a wet soil throughout the growing period. A numerical example utilizing experimental data for an irrigated summer corn in Israel confirms and quantifies the analytical findings.
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    Bulletin of mathematical biology 56 (1994), S. 875-898 
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    Notes: Abstract We analyse the stochastic properties of dynamical systems with finite populations of a few differentreplicator species. Our main interest is to evaluate the typicallifetime, i.e. the time for the extinction of the first species in the network, for different catalytic structures, as a function of the population size.
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    Bulletin of mathematical biology 56 (1994), S. 899-921 
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    Notes: Abstract The capacity of a model immune network in terms of the number of different antigens that can be vaccinated against without any memory lost is computed and tested by numerical simulations. We also investigate memory loss and failure to vaccinate due to overcrowding the network with too many antigens. The computations are done for two different strategies for proliferation, one implying all the antigen specific clones and the second one being more thrifty.
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    Bulletin of mathematical biology 56 (1994), S. 923-943 
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    Notes: Abstract The technique of model-building a protein of known sequence but unknown tertiary structure from the structures of homologous proteins is probably so far the most reliable means of mapping from primary to tertiary structure. A key step towards the realization of the aim is to develop ways of aligning three-dimensional structures of homologus proteins, thereby deriving the rules useful for protein modelling. We have developed a generalized differential-geometric representation of protein local conformation for use in a protein comparison program which aligns protein sequences on the basis of their sequence and conformational knowledge. Because the differetial-geometric distance measure between local conformations is independent of the coordinate frame and remains chirality information, the comparison program is easily implemented, relatively rational and reasonably fast. The utility of this program for aligning closely and distantly related homologous proteins is demonstrated by multiple alignment of globins, serine proteinases and aspartic proteinase domains. Particularly, the method has reached the rational alignment between the mammalian and microbial serine proteinases as compared with many published alignment programs.
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    Bulletin of mathematical biology 56 (1994), S. 945-957 
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    Notes: Abstract New formulas for deriving the sensitivities of stable stage structures and reproductive values to changes in vital rates are presented. They enable comparison of the sensities to changes of different elements in the projection matrix; in other words, comparison of partial derivatives of the eigenvectors. These kinds of sensitivities can be used in applied problems such as an analysis of the effect of harvesting on the population structure. However, in this paper, we examine the application of the sensitivities in a more general ecological context. We investigate why the stable stage structure of the mustard aphid,Lipaphis erysimi, changes very little in the temperature interval 10–30°C. The sensitivities of the stable stage structure at 15°C and 25°C were derived. The character of the sensitivites were the same in both temperatures although the stage structure was more sensitive to changes at 15°C than at 25°C. The sensitivity analysis also revealed that the temperature variation results in changes in fecundity and developmental rate that have a counteractive effect on the population structure.
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    Bulletin of mathematical biology 56 (1994), S. 981-998 
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    Notes: Abstract Plankton populations undergo dramatic surges. Rapid increases and decreases by a factor of 10 or more are observed, often separated by relatively stable interludes. We propose a description of plankton communities as excitable systems. In particular, we present a model for the evolution of phytoplankton and zooplankton populations which resembles models for the behaviour of excitable media. The parameter dependency of the various “excitable” phenomena, trigger mechanism, threshold, and slow recovery, is clear, and permits ready investigation of the influence of properties of the physical environment, including variations in nutrient fluxes, temperature or pollution levels.
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    Bulletin of mathematical biology 56 (1994), S. 959-980 
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    Notes: Abstract Analysis schemes for the classification of synergism and antagonism for mixed agents operate on the discrepancies between observed and calculated results. As such they cannot be confirmed by experiments and therefore have to be tested in terms of mathematical and logical self-consistency. The concept of independent action is close to the literal meaning of the term “non-interaction”. Since this concept does not depend on the mechanisms of actions nor on the type of effect scale used, it is suitable as one of the basic criterion for the definition of synergism and antagonism. A general mathematical framework of independent action is presented in this paper based on the concept of “relative effect” as used in the literature. The, different equations for independent action currently used in various areas are shown to be manifestations, of a general formula under different sets of boundary conditions, which are the natural limiting values of the effects of the corresponding system observed at low and at high doses of the agents. The framework can, be generalized to the combined action ofn-agents as well as to the interaction of an agent with itself. In addition, the differential form of the formula for independent action is derived. This framework of systematic definitions and derived equations enable a more in-depth study of the implications of the concept of independent action and its relation to other concepts of non-interaction.
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    Bulletin of mathematical biology 56 (1994), S. 999-1008 
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    Bulletin of mathematical biology 56 (1994), S. 1009-1040 
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    Notes: Abstract We model how auto-reactiveB cells are kept under control by an idiotypic network. Autoimmunity occurs when the control is broken by an infection or not achieved through an abnormal ontogenetic evolution. We describe the idiotypic network, viz., the central immune system, by idiotype-anti-idiotype pairs which are coupled to a set of highly connected clones, which interact with each clone of the network. Some clones of the central immune system recognize self-antigen. We find a huge variety of fixed points which can be classified as tolerant, autoimmune, and neutral states according to the concentration of the auto-reactive antibody. Most significant are auto-reactive clones which are a member of an idiotype-anti-idiotype pair. In a healthy individual, an autoimmune disease is induced by an antigen infection which triggers a transition from a tolerant to an autoimmune state. Autoimmunity is induced more readily by an antigen coupling to theanti-idiotype than by one interacting with the auto-reactive clone itself. We indicate a possible therapy which simply reverses the processes that have lead to the autoimmune disease. In the early development of the central immune system its highly connected, core part serves to draw the more specific clones of idiotype-anti-idiotype pairs into the network. In order to avoid autoimmunity in ontogenetic evolution the anti-idiotype of an auto-reactive clone must be formed in advance by a sufficiently long period of time. Thus, a well ordered succession of the appearance of the more specific clones is required.
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    Bulletin of mathematical biology 56 (1994), S. 1121-1141 
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    Notes: Abstract A method of dimensionless time-scaling based on extrinsic expectation of life at birth but intrinsic to a system generating a survival distribution is introduced. Such scaling allows the survival fraction function and its associated mortality function to serve as Green's functions for their generalized equivalents. i.e. a “population” function and a “death” function. The analytical mechanics of utilizing these concepts are formulated, applied to the classical Gompertz and Weibull survival models, and discussed with respect to biological relevance.
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    Bulletin of mathematical biology 56 (1994), S. 1095-1119 
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    Notes: Abstract It is now widely accepted that localized high concentrations of Ca2+ (Ca2+ domains) play a major role in controlling the time course of neurotransmitter release. In the present work we calculate the magnitude and the time course of Ca2+ domains that evolve in the vicinity of a Ca2+ channel and an adjacent release site. In the calculations we consider a accurately dimensioned Ca2+ channel. Moreover, the Ca2+ current is continuously adjusted with regard to the accumulated intracellular Ca2+ and, in addition, endogenous buffers are considered. The calculations, carried out by the software FIDAP, based on finite element method, show that the Ca2+ concentrations achieved near the release sites are significantly lower than claimed by other investigators. Furthermore, we present arguments indicating that the Ca2+ domains, regardless of their magnitude, do not play a role in controlling the time course of release of neurotransmitter.
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    Bulletin of mathematical biology 56 (1994), S. 1041-1093 
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    Notes: Abstract Mammalian white blood cells are known to bias the direction of their movement along concentration gradients of specific chemical stimuli, a phenomenon called chemotaxis. Chemotaxis of leukocyte cells is central to the acute inflammatory response in living organisms and other critical physiological functions. On a molecular level, these cells sense the stimuli termed chemotactic factor (CF) through specific cell surface receptors that bind CF molecules. This triggers a complex signal transduction process involving intracellular biochemical pathways and biophysical events, eventually leading to the observable chemotactic response. Several investigators have shown theoretically that statistical fluctuations in receptor binding lead to “noisy” intracellular signals, which may explain the observed imperfect chemotactic response to a CF gradient. The most recent dynamic model (Tranquillo and Lauffenburger,J. Math. Biol. 25, 229–262. 1987) couples a scheme for intracellular signal transduction and cell motility response with fluctuations in receptor binding. However, this model employs several assumptions regarding receptor dynamics that are now known to be oversimplifications. We extend the earlier model by accounting for several known and speculated chemotactic receptor dynamics, namely, transient G-protein signaling, cytoskeletal association, and receptor internalization and recycling, including statistical fluctuations in the numbers of receptors among the various states. Published studies are used to estimate associated constants and ensure the predicted receptor distribution is accurate. Model analysis indicates that directional persistence in uniform CF concentrations is enhanced by increasing rate constants for receptor cytoskeletal inactivation, ternary complex dissociation, and binary complex dissociation, and by decreasing rate constants for receptor internalization and recycling. For most rate constants, we have detected an optimal range that maximizes orientation bias in CF gradients. We have also examined different desensitization and receptor recycling mechanisms that yield experimentally documented orientation behavior. These yield novel insights into the relationship between receptor dynamics and leukocyte chemosensory movement behavior.
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    Bulletin of mathematical biology 56 (1994), S. 1143-1162 
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    Notes: Abstract Given two independent sequences of letters, we seek the probability distribution of the length of the longest matching word. This word can be in different positions in the two sequences and we consider both perfect and nearly perfect matching. We derive bounds and approximations for the probability and compare them with other bounds and approximations. The results can be applied to DNA sequences in molecular biology and generalized matching between two independent random sequences.
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    Bulletin of mathematical biology 56 (1994), S. 1163-1172 
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    Circuits, systems and signal processing 13 (1994), S. 273-293 
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    Notes: Abstract A basic control engineer's adage-the poles of a feedback compensator become zeros of the closed-loop system-admits difficulties of interpretation even in the most simple of cases; that of single-input, single-output. An earlier investigation has provided an analysis of this adage in a module-theoretic context for systems in state space form while avoiding restrictive assumptions on system minimality or squareness. The main result is expressed concisely in terms of an exact sequence of modules which include Ω-zero modules corresponding to the feedback system and the plant. Extended zero modules of Ω-type incorporate both finite invariant zero structure, and generic zero information which occurs when a system fails to be right-invertible. In the case of compensation in the feedback path, this main exact sequence reduces to a mathematically clear expression of the aforementioned adage: the Ω-zero module of the feedback system is precisely the direct sum of the Ω-zero module of the plant and the system pole module of the feedback compensator. This paper extends the previous work in order to avoid assumptions on causality in the plant. Implicit dynamical systems are employed, in lieu of systems in state space form. Once again, it is not assumed that the system is one-to-one or onto; and so the concepts of generic zeros and their modules are brought into the arena of implicit systems. The implicit system itself is assumed in this work to be regular; however, decoupling zeros are permitted. Moreover, input-decoupling zeros and system pole feedback relationships are considered.
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    Circuits, systems and signal processing 13 (1994), S. 387-388 
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    Circuits, systems and signal processing 13 (1994), S. 373-384 
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    Notes: Abstract When the problem is considered of obtaining a periodic description in state-space form of a linear process which can be modelled by linear difference equations with periodic coefficients, it is natural to ask whether it is possible to preliminarily derive a polynomial equivalent form of such equations, which in the periodic case plays a role similar to the Rosenbrock's polynomial matrix description of a linear time-invariant process. In this paper a polynomial time-invariant description of a linear periodic process is introduced. It is shown that such a polynomial description gives a simple characterization of the dimension of the space of the solutions corresponding to the null input function, i.e., of the order of the periodic model under consideration. In addition, it allows us to introduce a transfer matrix for the computation of the output responses corresponding to null initial conditions, and to deduce conditions for the periodic model to be causal. These results, as well as the possibility of defining strict system equivalence between two periodic models through their time-invariant polynomial descriptions, in a similar sense as in the time-invariant case, show the relevance of such a polynomial time-invariant description for the problem under consideration.
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    Circuits, systems and signal processing 13 (1994), S. 435-453 
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    Notes: Abstract An actual sampling process can be modeled as a random process, which consists of the regular (uniform) deterministic sampling process plus an error in the sampling times which constitutes a zero-mean noise (the jitter). In this paper we discuss the problem of estimating the jitter process. By assuming that the jitter process is an i.i.d. one, with standard deviation that is small compared to the regular sampling time, we show that the variance of the jitter process can be estimated from thenth order spectrum of the sampled data,n=2, 3, i.e., the jitter variance can be extracted from the 2nd-order spectrum or the 3rd-order spectrum (the bispectrum) of the sampled data, provided the continuous signal spectrum is known. However when the signal skewness exceeds a certain level, the potential performance of the bispectrum-based estimation is better than that of the spectrum-based estimation. Moreover, the former can also provide jitter variance estimates when the continuous signal spectrum is unknown while the latter cannot. This suggests that the bispectrum of the sampled data is potentially better for estimating any parameter of the sampling jitter process, once the signal skewness is sufficiently large.
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    The journal of Fourier analysis and applications 1 (1994), S. 67-85 
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    Topics: Mathematics
    Notes: Abstract Functions belonging to various Paley-Wiener spaces have representations in sampling series. When a function does not belong to such a space, the sampling series may converge, not to the object function but to an "alias" of it, and an aliasing error is said to occur. Aliasing error bounds are derived for one- and two-channel sampling series analogous to the Whittaker-Kotel’nikov-Shannon series, and for the multi-band sampling series, and a "derivative" extension of it, due to Dodson, Beaty, et al. The Poisson summation formula is a basic tool throughout. Aliasing in the one-channel case is shown to arise from a transformation with similarities to a projection. Where possible, the sharpness of the error bounds is discussed.
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    The journal of Fourier analysis and applications 1 (1994), S. 113-130 
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    Notes: Abstract This paper is devoted to a study of the Hausdorff-Young theorems from a historical perspective, beginning with the F. Riesz-Fischer theorem. Introduced by W. H. Young (1912), these theorems were considered and extended by F. Hausdorff (1923), F. Riesz (1923), E.C. Titchmarsh (1924), G. H. Hardy and J.E. Littlewood (1926), M. Riesz (1927), and O. Thorin (1939/48). Special emphasis is placed upon the development of the proofs of the two Hausdorff-Young inequalities and their impact upon Fourier analysis as a whole, in particular on the M. Riesz-Thorin convexity theoremand on the interpolation of operators. The golden thread connecting the various extensions and generalizations is the concept of logarithmic convexity, one that goes back to the work of J. Hadamard (1896), A. Liapounoff (1901), J.L.W.V. Jensen (1906), and O. Blumenthal (1907).
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    The journal of Fourier analysis and applications 1 (1994), S. 171-191 
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    Topics: Mathematics
    Notes: Abstract In this paper we give a further investigation of the method introduced by the author in [1, Frequency-domain bounds for nonnegative unsharply band-limited functions] for proving bounds for functions with nonnegative Fourier transforms. We also dealt with the question of how large the supremum KS of all numbers |f(u)| is with f the Fourier transform of a nonnegative integrable function F and f(0) = 1, |f(ku)| ≤ ε for k ∈ S. Here u 〉 0 and S ⊂ {2, 3, . . .}. This problem was related in [1] to finding the infimum MS of all numbers Mh = maxϑ [(1−h(ϑ))/(1− cos ϑ)] over all 2π-periodic even, smooth functions h whose Fourier cosine coefficients ak vanish for k ∉ S, and it was proved and announced for several cases that MS (1−KS ) = 1. In this paper we prove the results announced in [1]. To that end we generalize the method given in [1] to include Fourier transforms f of probability measures on R and a certain generalized function h, and we show that the numbers KS, MS are assumed as |f(u)|, Mh for certain allowed f,h. Moreover, we establish a fundamental relation between finding the numbers KS, MS and the numbers KT, MT where T = {2, 3, . . .}\S. In particular, we show that MT = 2KS (2KS − 1)−1,KT = 1/2 MS(MS − 1)−1 and that MT (1 − KT) = 1,KSKT = 1/2 , whenever MS (1 − KS) = 1.
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  • 95
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    The journal of Fourier analysis and applications 1 (1994), S. 281-295 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Finite energy band-limited functions are reconstructed iteratively from nonuniform sample values of the functions and its derivatives. It is shown that the maximum gap allowed between the sampling points increases linearly with the number of derivatives considered. Moreover, a more precise result is presented for the first derivative case and another reconstruction of the functions using the frame algorithm is deduced.
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  • 96
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    The journal of Fourier analysis and applications 1 (1994), S. 233-247 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract In the early 1960s research into radar signal synthesis produced important formulas describing the action of the two-dimensional Fourier transform on auto- and crossambiguity surfaces. When coupled with the Poisson Summation formula, these results become applicable to the theory of Weyl-Heisenberg systems, in the form of lattice sum formulas that relate the energy of the discrete crossambiguity function of two signals f and g over a lattice with the inner product of the discrete autoambiguity functions of f and g over a "complementary" lattice. These lattice sum formulas provide a framework for a new proof of a result of N.J. Munch characterizing tight frames and for establishing an important relationship between l1-summability (condition A) of the discrete ambiguity function of g over a lattice and properties of the Weyl-Heisenberg system of g over the complementary lattice. This condition leads to formulas for upper frame bounds that appear simpler than those previously published and provide guidance in choosing lattice parameters that yield the most snug frame at a stipulated density of basis functions.
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  • 97
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    The journal of Fourier analysis and applications 1 (1994), S. 403-436 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Let $a〉0, b〉0, ab〈1;$ and let $g\in L^2({\Bbb R}).$ In this paper we investigate the relation between the frame operator $S:f\in L^2({\Bbb R})\rightarrow \sum_{n,m}\,(f,g_{na,mb})\,g_{na,mb}$ and the matrix $H$ whose entries $H_{k,l\,;\,k',l'}$ are given by $(g_{k'/b,l'/a},g_{k/b,l/a})$ for $k,l,k',l'\in{\Bbb Z}.$ Here $f_{x,y}(t)={\rm exp}(2\pi iyt)\,f(t-x),$ $t\in{\Bbb R}$ , for any $f\in L^2({\Bbb R}).$ We show that $S$ is bounded as a mapping of $L^2({\Bbb R})$ into $L^2({\Bbb R})$ if and only if $H$ is bounded as a mapping of $l^2({\Bbb Z}^2)$ into $l^2({\Bbb Z}^2).$ Also we show that $AI\leq S\leq BI$ if and only if $AI\leq\frac{1}{ab}\,H\leq BI,$ where $I$ denotes the identity operator of $L^2({\Bbb R})$ and $l^2({\Bbb Z}^2),$ respectively, and $A\geq 0,$ $B〈\infty.$ Next, when $g$ generates a frame, we have that $(g_{k/b,l/a})_{k,l}$ has an upper frame bound, and the minimal dual function $^{\circ}\gamma$ can be computed as $ab\,\sum_{k,l}\,(H^{-1})_{k,l\,;\,o,o}\,g_{k/b,l/a}.$ The results of this paper extend, generalize, and rigourize results of Wexler and Raz and of Qian, D. Chen, K. Chen, and Li on the computation of dual functions for finite, discrete-time Gabor expansions to the infinite, continuous-time case. Furthermore, we present a framework in which one can show that certain smoothness and decay properties of a $g$ generating a frame are inherited by $^{\circ}\gamma.$ In particular, we show that $^{\circ}\gamma\in{\cal S}$ when $g\in{\cal S}$ generates a frame $({\cal S}$ Schwartz space). The proofs of the main results of this paper rely heavily on a technique introduced by Tolimieri and Orr for relating frame bound questions on complementary lattices by means of the Poisson summation formula.
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  • 98
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    The journal of Fourier analysis and applications 1 (1994), S. 103-112 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract For any ε 〉 0, we construct an orthonormal Schauder basis of C(K) consisting of trigonometric polynomials Tn n = 1, 2, . . . , such that deg(Tn) ≤ (1/2)(1 + ε)n. This is best possible with regard to the degree. The construction uses wavelet techniques.
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  • 99
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    The journal of Fourier analysis and applications 1 (1994), S. 131-170 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract We study the general question of the existence of self-similar lattice tilings of Euclidean space. A necessary and sufficient geometric condition on the growth of the boundary of approximate tiles is reduced to a problem in Fourier analysis that is shown to have an elegant simple solution in dimension one. In dimension two we further prove the existence of connected self-similar lattice tilings for parabolic and elliptic dilations. These results apply to produce Haar wavelet bases and certain canonical number systems.
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  • 100
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    The journal of Fourier analysis and applications 1 (1994), S. 201-232 
    ISSN: 1531-5851
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract In the spirit of work of Kerman and Sawyer, a condition is given that is necessary and sufficient for the Fourier transform norm inequality $\Big(\int_{{\Bbb R}_d} \vert\hat{f}\vert^q d\mu\Big)^{1/q} \leq C\Big(\int_{{\Bbb R}_d} \vert f\vert^p v\Big)^{1/p}$ provided v is a radial weight for which v−1/p is convexly decreasing and μ is a suitable measure. We also establish alternative conditions for such inequalities by proving corresponding trace type inequalities and maximal function inequalities that underlie the Fourier transform estimates. Our conditions are relatively simple to compute. Among applications we give extensions of a Sobolev restriction theorem.
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