The modelling of fibre reorientation in soft tissue

In this paper, a hyperelastic and thermodynamically consistent model for soft tissue is developed that is able to describe the change of the initial orientation of the collagen fibres. Full numerical implementation is considered as well. The collagen architecture is assumed to reorient driven by a specific thermodynamical force. The anisotropy is described by a strain energy function, which is decomposed into a part related to the matrix and a part related to the fibres. The initial fibre orientation is defined by a structural tensor, while the current orientation is described by a time-dependent structural tensor, which results from the initial one by a rotational transformation. The rotation tensor is obtained via an integration process of a rate tensor, which depends on an adequately defined thermodynamical force. The integration is achieved via an exponential map algorithm, where it is shown that the rotation is necessarily a two-parametric one. Efficiency of the proposed formulation is demonstrated using some numerical examples.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

Rhesus monkey apolipoprotein(a). Sequence, evolution, and sites of synthesis

Human lipoprotein(a) is a low density lipoprotein-like lipoprotein whose concentration in plasma is correlated with atherosclerosis. The characteristic protein component of lipoprotein(a) is apolipoprotein(a) (apo(a)) which is disulfide-linked to apolipoprotein B-100. Sequencing of rhesus monkey apo(a) cDNA suggests that this protein, like human apo(a), is highly similar to plasminogen. Sequence data suggests that a plasminogen-like protease activity and kringle 1-, 2-, 3-, and 5-like domains are unnecessary for apo(a) function, but a highly repeated kringle four-like domain is important. Liver is the major site of apo(a) RNA synthesis; reduced amounts of message were also found in testes and brain. Co-expression with apoB-100 and plasminogen in rhesus tissues is not mandatory.     

A physical characterization of biological information and communication system model of ecosystems

What is information for living organisms? An answer to this question is given on a physical basis and a contrast between genetic information and sensory information is stressed with a relation to information theory. A simple model of an environment of living organisms is investigated on the basis of communication systems model proposed by the author and a cost of information transmission is taken into consideration through capacity cost theory. It is shown that channel capacity of information theory can be interpreted as an environment, and furthermore that a large diversity of genetic messages needs a large capacity of the environment. In addition, a definition of life in terms of information is proposed and a unified view on life processes is suggested.     

Forming sparse representations by local anti-Hebbian learning

How does the brain form a useful representation of its environment? It is shown here that a layer of simple Hebbian units connected by modifiable anti-Hebbian feed-back connections can learn to code a set of patterns in such a way that statistical dependency between the elements of the representation is reduced, while information is preserved. The resulting code is sparse, which is favourable if it is to be used as input to a subsequent supervised associative layer. The operation of the network is demonstrated on two simple problems.     

Toward an optimal design principle in relational biology

A vulnerability criterion is posed for a biological system within the context of representing the system as a relational set, i.e., a collection of components whose interdependency is described by means of a set of binary relations. The criterion provides a numerical value for each representation and therefore a means for comparing one representation against another. Choice of the criterion is such that the larger a numerical value a representation has then the less vulnerable to destruction is the system represented. Other things being equal, it is argued that the representation which endows the system with the least vulnerability is more likely to be a valid representation. A selection criterion is thereby achieved for narrowing down the choice ofa priori representations.     

Length control of extended protein structures in bacteria and bacteriophages

The length of the tail of bacteriophages is controlled by a protein which acts as a molecular ruler. The needle of the injectisome, which is assembled by the polymerization of subunits that are exported through the nascent injectisome, is functionally related to the tail of bacteriophages. Interestingly, its length is controlled by a protein, which is itself exported and acts as a molecular ruler that is coupled to a substrate specificity switch. The bacterial flagellum is evolutionarily related to the injectisome. The length of the hook is also controlled by a secreted protein. This protein acts as a substrate specificity switch and, possibly, also as a ruler.     

Evidence for a presynaptic blockage of transmission in a temperature-sensitive mutant of Drosophila

In the temperature sensitive mutant of Drosophila, shibirets1 (shi), synaptic transmission in the dorsal longitudinal flight muscles (DLM) is normal at 19 degrees C, but is diminished progressively as the temperature is raised, and is blocked at 29 degrees C. The purpose of this paper is to determine whether this defect is located presynaptically, postsynaptically, or both. It is demonstrated here that the postsynaptic sensitivity to L-glutamate, the putative transmitter for this synapse, is not decreased at 29 degrees C. Furthermore, studies conducted with genetic mosaics of this mutant show that transmission is blocked when a mutant motor neuron synapses on a wild-type muscle fiber, but is not blocked when a wild-type motor neuron synapses on a mutant muscle fiber. Thus, the shi phenotype (temperature dependent transmission block) correlates with a shi motor neuron, not with a shi muscle fiber. The data, therefore, suggest that the defect is not postsynaptic, but presynaptic.     

A self-organized chemical model and reaction cascade

Some reaction cascades in biological systems are analyzed by a self-organized chemical model, an autocatalytic reaction. This model is described by the coupling of a primary system which stabilizes the initial stage of the reaction rapidly and a partial system which controls the primary system slowly. By the internal force caused by a trigger above the threshold, the coupled system in near-equilibrium is broken and changed into a new state. From the rate equation for the coupled system, a dimensionless nonlinear state equation, n = -n3 - un - v, is derived, where n is the concentration of intermediate, and u, v are dynamic variables of the system. This equation is similar to a nonequilibrium tri-molecular reaction. By using this chemical network theory, fibrin polymerization. F + F----fm----fp + X, where F is a fibrinogen molecule, fm is a fibrin monomer, fp is fibrin polymer, and X is small peptides released from fibrinogen, is discussed as an excellent example of the enzyme reaction cascade.     

Formation of segregated regions of feature detecting cells in self-organizing nerve field

This paper investigates the formation of a segregated region for a specific set of input signals in a nerve field. The segregated region is formed by a feature detecting cell group which fires only for a specific set of input signals. This firing region is called the region of feature detecting cells for the corresponding input set. First, a basic self-organizing model is given. The model is composed of the first input layer, the second nerve cell layer with lateral inhibitory interactions (it is called a lateral-inhibition type nerve field) and an inhibitory nerve cell. An input signal is an-dimensional vector whose components assume continuous values. Next, the condition which gurantees the formation of a segregated region for a specific set of input signals is derived, and the properties of the model are discussed based on the derived condition. In addition, the behavior of the model is examined through computer-simulated experiments. The following observations are made: When a certain condition is satisfied, a segregated region is formed in the nerve field according to a specific set of input signals. By varying the parameters of learning, the region is formed depending on the similarity between input signals. The regions for similar input signals are formed near each other in the nerve field. The region is created depending on the occurence probability of the input signal and its norm.     

The Influence of Temperature on the Effect of Bacteriostatic Concentrations of Phenol Against Escherichia coli

S ummary . During early exponential growth of Escherichia coli in the absence of phenol there is a natural death rate at 20, 30, and 44° but at the optimum temperature around 37° there is little if any significant death. The influence of a rise in temperature from 20 to 44° is to decrease the generation time and at 44° the lower generation time compensates for a reduced generation index. The main effect of sub-bacteriostatic concentrations of phenol is to increase the generation time but at 30, 37 and 44° there is a significant reduction in the generation index at the higher concentrations resulting in a dynamic bacteriostasis. At 20° bacteriostasis is due mainly to a large generation time but there is a little growth and so bacteriostasis is essentially dynamic. There is also evidence to suggest that the effect of a particular concentration of phenol on the generation index is not merely influenced by the temperature but by the generation time under the particular set of conditions. If phenol is added to rapidly growing cultures of E. coli the effect of a rise in temperature is to reduce the concentration required for bacteriostasis but if it is added during the lag phase there is a maximum in the bacteriostatic concentration between 20 and 37°.     

Universal common ancestry,LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.     

Competition in chemostat-type equations with two habitats

Competition on a model with nutrient recycling is considered. The model is based on a chemostat-type equation which is used to study population dynamics of microorganisms. The model consists of four organisms competing for a limiting nutrient. Nutrient is supplied both from the in-flow of medium and a recycling with delay, the latter is generated from dead organisms by bacterial decomposition. This paper shows that the model undergoes a Hopf bifurcation through a critical value of time delay when the in-flow is small. Coexistence of four organisms competing for one limiting nutrient is indicated by numerical simulation results.     

The question of virginity testing in Turkey

Pre-marital sex for a woman is regarded as wrong in my country. As a result, it is socially forbidden for a woman to engage in this act. In order to present a woman as a virgin on her marriage day, she is subjected to pressure, and put under control both by her family and societal norms. However, a man is free and never made to suffer any of the above. A woman found to be a virgin on her first night of marriage is seen as a normal person while one suspected to have lost her virginity is made to undergo a series of medical examinations to bring clarity to her situation.     

A moral argument for frozen human embryo adoption

Some people (e.g., Drs. Paul and Susan Lim) and, with them, organizations (e.g., the National Embryo Donation Center) believe that, morally speaking, the death of a frozen human embryo is a very bad thing. With such people and organizations in mind, the question to be addressed here is as follows: if one believes that the death of a frozen embryo is a very bad thing, ought, morally speaking, one prevent the death of at least one frozen embryo via embryo adoption? By way of a three-premise argument, one of which is a moral principle first introduced by Peter Singer, my answer to this question is: at least some of those who believe this ought to. (Just who the “some” are is identified in the paper.) If this is correct, then, for said people, preventing the death of a frozen embryo via embryo adoption is not a morally neutral matter; it is, instead, a morally laden one. Specifically, their intentional refusal to prevent the death of a frozen embryo via embryo adoption is, at a minimum, morally criticizable and, arguably, morally forbidden. Either way, it is, to one extent or another, a moral failing.     

The elastic behavior of the urinary bladder for large deformations

The purpose of this paper is to investigate the theoretical basis for the pressure-distension behavior of the urinary bladder. A finite strain theory is developed for hollow spherical structures and it is shown that the Treloar model is a good prototype only for rubber balloons. The pressure-extension ratio relationship is inverted to lead a general form of strain energy function, and fitted by an empirical relation involving one exponential. The following form of strain energy function is derived: W(lambda, lambda, lambda -2) = C1 (P(1), a) + P(1)C2 (a, lambda)ea(lambda -1). Where C1(P(1), a) is a constant (N m-2), P(1) is the initial pressure, a is the rate of pressure increase and C2 (a, lambda) a third degree polynomial relation. P(1) and a are experimentally determined through volumetric pressure-distension data. It is verified that this type of energy function is also valid for uniaxial loading experiments by testing strips coming from the same bladder for which P(1) and a were computed. There is a good agreement between the experimental points and the theoretical stress-strain relation. Finally, the strain energy function is plotted as a function of the first strain invariant and appears to be of an exponential nature.     

Site-specific DNA splicing: a general procedure for the creation of a restriction site at a predetermined position in a DNA sequence

A method is described for creating any of a wide array of restriction sites at a predetermined position in a known DNA sequence. The method utilizes the exonuclease activity of BAL 31 and a specially designed bifunctional oligodeoxynucleotide linker. The desired restriction site is generated when the linker is ligated to those BAL 31-digested DNA fragments which end with the target sequence. The proper ligation product is then identified by a highly specific hybridization procedure. The method is versatile and specific and is especially useful in the isolation of functional elements of a gene.     

Design‐based inference on Bernstein type estimators for continuous populations

The estimation of the values of a variable at any point of a study area is performed using Bernstein polynomials when the sampling scheme is implemented by selecting a point in each polygon of a regular grid overimposed onto the area. The evaluation of the precision of the resulting estimates is investigated under a completely design‐based framework. Moreover, as the main contribution to the mean squared error of the Bernstein‐type estimator is due to the bias, also a pseudo‐jackknife estimator is proposed. The performance of both estimators is investigated theoretically and by means of a simulation study. An application to a soil survey performed in Berkshire Downs in Oxfordshire (UK) is considered.     

The cosmetic split-thickness skin graft donor site

Any split-thickness skin graft donor site is obvious to some degree because of pigment alterations and, at the worst, it can develop hypertrophic scarring. A predictably superior aesthetic result is possible if this site is converted to a full-thickness defect followed by primary closure, because a linear scar is the only residuum. Using a modified tumescent technique, the groin can also be readily used as a split-thickness donor site if a thin graft is preferred; it captures the attributes of an ideal donor site in which pain is diminished, healing rapid, and the scar inconspicuous, just as when it is used as a full-thickness skin graft donor site.