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.     

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.     

Effect of binding on melting transitions in polymer–diluent systems

An expression is derived for the melting point of a polymer when in equilibrium with a solution in which binding of low molecular weight compounds to the polymer takes place. Allowance is made for the possibility that the crystalline polymer itself is a complex. The argument is a purely thermodynamic one and is based on a consideration of the change in free energy as a result of a change in binding. Allowance is made also for non-specific polymer–solvent interactions, in which the mixture of low molecular weight solvents is treated as a single solvent. Special attention is paid to “inverted” melting transitions, i.e., cases in which the melting point increases with increasing dilution of the polymer. It is shown that as a rule this is accompanied by a corresponding, inverted effect of the solvent composition on the melting point. It is further shown that-in the absence of binding, “normal” behavior at the critical point (i.e., phase separation is induced by lowering the temperature) is always accompanied by “normal” melting behavior (i.e., a decrease in melting point when the polymer is diluted). Also, “inverted” melting always implies that phase separation at the critical point is induced by heating, but the reverse is not necessarily true.     

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.     

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.     

On religious ritual as deference and communicative excess

I shall argue that most religious ritual is a performance that not only invokes but also performs communication. The ethnographic material from which I derive this argument is from China, in particular the temple rituals of local festivals. My argument is that a deep obeisance of welcome and departure that is both like and not like the normal ritual of greeting marks a religious from a non-religious ritual occasion and place. It is a ritual doubling that makes the honoured guest also a host. Religious ritual is a medium, and as a medium it is double in another sense. It is deference and deferral, a repeated transmission of obeisance to authority that has the authority of repetition. As well as doubling, religious ritual is excessively communicative. The medium is a performance not only of invitation and departure but also of communicative response, and it repeats this communication as a test of communicative response over and over again. Religious ritual performs both the opening and closing of communication, both the seeking and the responsive reciprocation of gift offerings with bounteousness. It is shadowed by the possibility of no response, of giving offence, of being abandoned. This possibility is acknowledged by being prevented, while the possibility that the performers are their own responders is disavowed.     

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.     

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.     

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 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.     

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.     

Human death--a view from the beginning of life

This paper presents a simple argument against definitions of the death of a human being in terms of death, or the cessation of functioning, of its brain: a human being is alive, and so is capable of dying, before it acquires a brain. Although a more accurate definition is sketched, it is stressed that it should not be taken for granted that it is ethically urgent to work out such a definition. What morally matters more than the death of a human being may be something for which its death is sufficient, but not necessary, namely the irreversible loss of its capacity for consciousness. It is when we lose this capacity that we lose our moral standing, as subjects who can be benefited and harmed, and who can have rights. But, as is also suggested, the loss of this capacity is ill suited to be what the death of a human being definitionally consists of.     

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.     

Finding and testing network communities by lumped Markov chains

Identifying communities (or clusters), namely groups of nodes with comparatively strong internal connectivity, is a fundamental task for deeply understanding the structure and function of a network. Yet, there is a lack of formal criteria for defining communities and for testing their significance. We propose a sharp definition that is based on a quality threshold. By means of a lumped Markov chain model of a random walker, a quality measure called "persistence probability" is associated to a cluster, which is then defined as an "α-community" if such a probability is not smaller than α. Consistently, a partition composed of α-communities is an "α-partition." These definitions turn out to be very effective for finding and testing communities. If a set of candidate partitions is available, setting the desired α-level allows one to immediately select the α-partition with the finest decomposition. Simultaneously, the persistence probabilities quantify the quality of each single community. Given its ability in individually assessing each single cluster, this approach can also disclose single well-defined communities even in networks that overall do not possess a definite clusterized structure.     

Does Computation Reveal Machine Cognition?

This paper seeks to understand machine cognition. The nature of machine cognition has been shrouded in incomprehensibility. We have often encountered familiar arguments in cognitive science that human cognition is still faintly understood. This paper will argue that machine cognition is far less understood than even human cognition despite the fact that a lot about computer architecture and computational operations is known. Even if there have been putative claims about the transparency of the notion of machine computations, these claims do not hold out in unraveling machine cognition, let alone machine consciousness (if there is any such thing). The nature and form of machine cognition remains further confused also because of attempts to explain human cognition in terms of computation and to model/simulate (aspects of) human cognitive processing in machines. Given that these problems in characterizing machine cognition persist, a view of machine cognition that aims to avoid these problems is outlined. The argument that is advanced is that something becomes a computation in machines only when a human interprets it, which is a kind of semiotic causation. From this it follows that a computing machine is not engaged in a computation unless a human interprets what it is doing; instead, it is engaged in machine cognition, which is defined as a member or subset of the set of all possible mappings of inputs to outputs. The human interpretation, which is a semiotic process, gives meaning to what a machine does, and then what it does becomes a computation.     

Marquis: A Defense of Abortion?

This is a reply to Don Marquis'Why Abortion is Immoral.' Marquis, who asserts that abortion is morally wrong, bases his argument on the following premise: Killing a being is morally wrong if that being is the sort of being who has a valuable future. I argue that this premise is false. I then assert that if I am correct about this premise being false, Marquis is faced with a dilemma. If he does not alter the premise in a way that makes it true, his argument is unsound. However, if he does make such an alteration, he must also alter a second premise in his argument, and this second change opens him to the charge of question begging. In addition, I conclude that such an alteration requires Marquis to adopt a position much like that taken by Judith J. Thompson in 'A Defense of Abortion,' a position he initially states is indefensible.     

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.     

Fluorescence polarization immunoassay: detection of antibody to Brucella abortus

Fluorescence polarization immunoassay (FPA) is a homogeneous immunoassay useful for rapid and accurate detection of antibody or antigen. The principle of the assay is that a fluorescent dye (attached to an antigen or an antibody fragment) can be excited by plane-polarized light at the appropriate wavelength. As a rule, a small molecule rotates faster when in solution than a larger molecule. The rotation rate may be assessed by measuring light intensity in the vertical and horizontal planes. Generally, the time it takes a molecule to rotate through a given angle is an indication of its size. When a small molecule that rotates rapidly is bound to a larger molecule, the rotation rate is decreased and this decrease is measured. Because it is a primary antigen-antibody interaction, the rate of reaction is very rapid and usually a result may be obtained in minutes. This technology was applied to the detection of antibody to Brucella abortus in serum and milk, providing for the first time a rapid primary binding assay that is cost effective for use in the field.     

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.