Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming (Open Access publication)

An approach for optimising genetic contributions of candidates to control inbreeding in the offspring generation using semidefinite programming (SDP) was proposed. Formulations were done for maximising genetic gain while restricting inbreeding to a preset value and for minimising inbreeding without regard of gain. Adaptations to account for candidates with fixed contributions were also shown. Using small but traceable numerical examples, the SDP method was compared with an alternative based upon Lagrangian multipliers (RSRO). The SDP method always found the optimum solution that maximises genetic gain at any level of restriction imposed on inbreeding, unlike RSRO which failed to do so in several situations. For these situations, the expected gains from the solution obtained with RSRO were between 1.5–9% lower than those expected from the optimum solution found with SDP with assigned contributions varying widely. In conclusion SDP is a reliable and flexible method for solving contribution problems.     

Frequency response model of skeletal muscle and its association with contractile properties of skeletal muscle

The aims of the present study were to develop a mathematical model of the skeletal muscle based on the frequency transfer function, referred to as frequency response model, and to presume the relationship between the model elements and skeletal muscle contractile properties. Twitch force in elbow flexion was elicited by applying a single electrical stimulation to the motor point of biceps brachii muscles, and then analyzed visually by the Bode gain and phase diagram of the force signal. The frequency response model was represented by a frequency transfer function consisting of five basic control elements (proportional element, dead time element, and three first-order lag elements). The model element constants were estimated by best-fitting to the Bode gain and phase diagram of the twitch force signal. The proportional constant and the dead time in the frequency response model correlated significantly with the peak torque and the latency in the actual twitch force, respectively. In addition, the time constants of the three first-order lag elements in the model correlated strongly with the contraction time and the half relaxation time in the actual twitch force. The results suggested a possibility that the individual elements in the frequency response model would reflect the biochemical and biomechanical properties in the excitation–contraction coupling process of skeletal muscle.     

Avirulence proteins from haustoria-forming pathogens

A major insight that has emerged in the study of haustoria-forming plant pathogens over the last few years is that these eukaryotic biotrophs deliver suites of secreted proteins into host cells during infection. This insight has largely derived from successful efforts to identify avirulence (Avr) genes and their products from these pathogens. These Avr genes, identified from a rust and a powdery mildew fungus and three oomycete species, encode small proteins that are recognized by resistance proteins in the host plant cytoplasm, suggesting that they are transported inside plant cells during infection. These Avr proteins probably represent examples of fungal and oomycete effector proteins with important roles in subverting host cell biology during infection. In this respect, they represent a new opportunity to understand the basis of disease caused by these biotrophic pathogens. Elucidating how these pathogen proteins gain entry into plant cells and their biological function will be key questions for future research.     

Applications of ultrasound streaming and radiation force in biosensors

Direct radiation force (DRF) and acoustic streaming provide the main influences on the behaviour of particles in aqueous suspension in an ultrasound standing wave (USW). The direct radiation force, which drives suspended particles towards and concentrates them in acoustic pressure node planes, has been applied to rapidly transfer cells in small scale analytical separators. The DRF also significantly increased the sensitivity of latex agglutination test (LAT) by concentrating the particles of an analytical sample in the pressure node positions and hence greatly increasing the antibody-antigen encounter rate. Capture of biotinylated particles and spores on a coated acoustic reflector in a quarter wavelength USW resonator was DRF-enhanced by 70- and 100-fold, respectively compared to the situation in the absence of ultrasound. Acoustic streaming has been successfully employed for mixing small analytical samples. Cavitation micro-streaming substantially enhanced, through mixing, DNA hybridization and the capture efficiency of Escherichia coli K12 on the surface of immunomagnetic beads. Acoustic streaming induced in longitudinal standing wave and flexural plate wave immuno-sensors increased the detection of antigens by a factor of five and three times, respectively. Combined DRF and acoustic streaming effects enhanced the rate of the reaction between suspended mixture of cells and retroviruses. The examples of a biochip and an ultrasonic immuno-sensor implementing the DRF and acoustic streaming effects are also described in the review.     

Aging, visual information, and adaptation to task asymmetry in bimanual force coordination

This study investigated the coordination and control strategies that the elderly adopt during a redundant finger force coordination task and how the amount of visual information regulates the coordination patterns. Three age groups (20-24, 65-69, and 75-79 yr) performed a bimanual asymmetric force task. Task asymmetry was manipulated via imposing different coefficients on the finger forces such that the weighted sum of the two index finger forces equaled the total force. The amount of visual information was manipulated by changing the visual information gain of the total force output. Two hypotheses were tested: the reduced adaptability hypothesis predicts that the elderly show less degree of force asymmetry between hands compared with young adults in the asymmetric coefficient conditions, whereas the compensatory hypothesis predicts that the elderly exhibit more asymmetric force coordination patterns with asymmetric coefficients. Under the compensatory hypothesis, two contrasting directions of force sharing strategies (i.e., more efficient coordination strategy and minimum variance strategy) are expected. A deteriorated task performance (high performance error and force variability) was found in the two elderly groups, but enhanced visual information improved the task performance in all age groups. With low visual information gain, the elderly showed reduced adaptability (i.e., less asymmetric forces between hands) to the unequal weighting coefficients, which supported the reduced adaptability hypothesis; however, the elderly revealed the same degree of adaptation as the young group under high visual gain. The findings are consistent with the notion that the age-related reorganization of force coordination and control patterns is mediated by visual information and, more generally, the interactive influence of multiple categories of constraints.     

Delayed feedback and multiple attractors in a host–parasitoid system

 Continuous-time, age structured, host–parasitoid models exhibit three types of cyclic dynamics: Lotka–Volterra-like consumer-resource cycles, discrete generation cycles, and “delayed feedback cycles” that occur if the gain to the parasitoid population (defined by the number of new female parasitoid offspring produced per host attacked) increases with the age of the host attacked. The delayed feedback comes about in the following way: an increase in the instantaneous density of searching female parasitoids increases the mortality rate on younger hosts, which reduces the density of future older and more productive hosts, and hence reduces the future per head recruitment rate of searching female parasitoids. Delayed feedback cycles have previously been found in studies that assume a step-function for the gain function. Here, we formulate a general host–parasitoid model with an arbitrary gain function, and show that stable, delayed feedback cycles are a general phenomenon, occurring with a wide range of gain functions, and strongest when the gain is an accelerating function of host age. We show by examples that locally stable, delayed feedback cycles commonly occur with parameter values that also yield a single, locally stable equilibrium, and hence their occurrence depends on initial conditions. A simplified model reveals that the mechanism responsible for the delayed feedback cycles in our host–parasitoid models is similar to that producing cycles and initial-condition-dependent dynamics in a single species model with age-dependent cannibalism. Received: 24 October 1997 / Revised version: 13 June 1998     

Duodenum electrical stimulation delays gastric emptying, reduces food intake and accelerates small bowel transit in pigs

Duodenum electrical stimulation (DES) has been shown to delay gastric emptying and reduce food intake in dogs. The aim of this study was to investigate the effects of DES on gastric emptying, small bowel transit and food intake in pigs, a large animal model of obesity. The study consisted of three experiments (gastric emptying, small bowel transit, and food intake) in pigs implanted with internal duodenal electrodes for DES and one or two duodenal cannulas for gastric emptying and small bowel transit. We found that (i) gastric emptying was dose-dependently delayed by DES of different stimulation parameters; (ii) small bowel transit was significantly accelerated with continuous DES in proximal intestine but not with intermittent DES; (iii) DES significantly reduced body weight gain with 100% duty cycle (DC), but not with DES with 40% DC. A marginal difference was noted in food intake among 100% DC session, 40% DC session, and control session. DES with long pulses energy-dependently inhibits gastric emptying in pigs. DES with appropriate parameters accelerates proximal small bowel transit in pigs. DES reduces body weight gain in obese pigs, and this therapeutic effect on obesity is mediated by inhibiting gastric emptying and food intake, and may also possibly by accelerating intestinal transit. DES may have a potential application to treat patients with obesity.     

Motor potential profile and a robust method for extracting it from time series of motor positions

Molecular motors are small, and, as a result, motor operation is dominated by high-viscous friction and large thermal fluctuations from the surrounding fluid environment. The small size has hindered, in many ways, the studies of physical mechanisms of molecular motors. For a macroscopic motor, it is possible to observe/record experimentally the internal operation details of the motor. This is not yet possible for molecular motors. The chemical reaction in a molecular motor has many occupancy states, each having a different effect on the motor motion. The overall effect of the chemical reaction on the motor motion can be characterized by the motor potential profile. The potential profile reveals how the motor force changes with position in a motor step, which may lead to insights into how the chemical reaction is coupled to force generation. In this article, we propose a mathematical formulation and a robust method for constructing motor potential profiles from time series of motor positions measured in single molecule experiments. Numerical examples based on simulated data are shown to demonstrate the method. Interestingly, it is the small size of molecular motors (negligible inertia) that makes it possible to recover the potential profile from time series of motor positions. For a macroscopic motor, the variation of driving force within a cycle is smoothed out by the large inertia.     

A model for steady isometric muscle activation

The present model of the motoneuronal (MN) pool – muscle complex (MNPMC) is deterministic and designed for steady isometric muscle activation. Time-dependent quantities are treated as time-averages. The character of the model is continuous in the sense that the motor unit (MU) population is described by a continuous density function. In contrast to most already published models, the wiring (synaptic weight) between the input fibers to the MNPMC and the MNs (about which no detailed data are known) is deduced, whereas the input–force relation is given. As suggested by experimental data, this relation is assumed to be linear during MU recruitment, but the model allows other, nonlinear relations. The input to the MN pool is defined as the number of action potentials per second in all input fibers, and the excitatory postsynaptic potential (EPSP) conductance in MNs evoked by the input is assumed to be proportional to the input. A single compartment model with a homogeneous membrane is used for a MN. The MNs start firing after passing a constant voltage threshold. The synaptic current–frequency relation is described by a linear function and the frequency–force transformation of a MU by an exponential function. The sum of the MU contraction forces is the muscle force, and the activation of the MUs obeys the size principle. The model parameters were determined a priori, i.e., the model was not used for their estimation. The analysis of the model reveals special features of the activation curve which we define as the relation between the input normalized by the threshold input of the MN pool and the force normalized by the maximal muscle force. This curve for any muscle turned out to be completely determined by the activation factor, the slope of the linear part of the activation curve (during MU recruitment). This factor determines quantitatively the relation between MU recruitment and rate modulation. This property of the model (the only known model with this property) allows a quantification of the recruitment gain (Kernell and Hultborn 1990). The interest of the activation factor is illustrated using two human muscles, namely the first dorsal interosseus muscle, a small muscle with a relatively small force at the end of recruitment, and the medial gastrocnemius muscle, a strong muscle with a relatively large force at the end of recruitment. It is concluded that the present model allows us to reproduce the main features of muscle activation in the steady state. Its analytical character facilitates a deeper understanding of these features. Received: 24 November 1997 / Accepted in revised form: 30 November 1998     

Dual-Force ISOMAP: A New Relevance Feedback Method for Medical Image Retrieval

With great potential for assisting radiological image interpretation and decision making, content-based image retrieval in the medical domain has become a hot topic in recent years. Many methods to enhance the performance of content-based medical image retrieval have been proposed, among which the relevance feedback (RF) scheme is one of the most promising. Given user feedback information, RF algorithms interactively learn a user’s preferences to bridge the “semantic gap” between low-level computerized visual features and high-level human semantic perception and thus improve retrieval performance. However, most existing RF algorithms perform in the original high-dimensional feature space and ignore the manifold structure of the low-level visual features of images. In this paper, we propose a new method, termed dual-force ISOMAP (DFISOMAP), for content-based medical image retrieval. Under the assumption that medical images lie on a low-dimensional manifold embedded in a high-dimensional ambient space, DFISOMAP operates in the following three stages. First, the geometric structure of positive examples in the learned low-dimensional embedding is preserved according to the isometric feature mapping (ISOMAP) criterion. To precisely model the geometric structure, a reconstruction error constraint is also added. Second, the average distance between positive and negative examples is maximized to separate them; this margin maximization acts as a force that pushes negative examples far away from positive examples. Finally, the similarity propagation technique is utilized to provide negative examples with another force that will pull them back into the negative sample set. We evaluate the proposed method on a subset of the IRMA medical image dataset with a RF-based medical image retrieval framework. Experimental results show that DFISOMAP outperforms popular approaches for content-based medical image retrieval in terms of accuracy and stability.     

Dynamics of Excitation and Inhibition in the Light-Adapted Limulus Eye in situ

The dynamics of spike discharge in eccentric cell axons from the in situ lateral eye of Limulus, under small sinusoidal modulation of light to which the eye is adapted, are described over two decades of light intensity and nearly three decades of frequency. Steady-state lateral inhibition coefficients, derived from the very low-frequency response, average 0.04 at three interommatidial spacings. The gain vs. frequency of a singly illuminated ommatidium is described closely from 0.004 to 0.4 cps by the linear transfer function s^0.25; this function also accounts approximately for the measured phase leads, the small signal adaptation following small step inputs, and for Pinter's (1966) earlier low-frequency generator potential data. We suggest that such dynamics could arise from a summation in the generator potential of distributed intensity-dependent relaxation processes along the dendrite and rhabdome. Analysis of the dynamic responses of an eccentric cell with and without simultaneously modulated illumination of particular neighbors indicates an effect equivalent to self-inhibition acting via a first-order low-pass filter with time constant 0.42 sec, and steady-state gain near 4.0. The corresponding filters for lateral inhibition required time constants from 0.35 to 1 sec and effective finite delay of 50–90 msec.     

Conformational stability of PrP amyloid fibrils controls their smallest possible fragment size

Fibril fragmentation is considered to be an essential step in prion replication. Recent studies have revealed a strong correlation between the incubation period to prion disease and conformational stability of synthetic prions. To gain insight into the molecular mechanism that accounts for this correlation, we proposed that the conformational stability of prion fibrils controls their intrinsic fragility or the size of the smallest possible fibrillar fragments. Using amyloid fibrils produced from full-length mammalian prion protein under three growth conditions, we found a correlation between conformational stability and the smallest possible fragment sizes. Specifically, the fibrils that were conformationally less stable were found to produce shorter pieces upon fragmentation. Site-specific denaturation experiments revealed that the fibril conformational stability was controlled by the region that acquires a cross-β-sheet structure. Using atomic force microscopy imaging, we found that fibril fragmentation occurred in both directions—perpendicular to and along the fibrillar axis. Two mechanisms of fibril fragmentation were identified: (i) fragmentation caused by small heat shock proteins, including αB-crystallin, and (ii) fragmentation due to mechanical stress arising from adhesion of the fibril to a surface. This study provides new mechanistic insight into the prion replication mechanism and offers a plausible explanation for the correlation between conformational stability of synthetic prions and incubation time to prion disease.     

Perceptions of effort and heaviness during fatigue and during the size-weight illusion

Previous work has shown that force perception and the sense of motor effort are different attributes of sensorimotor function. This study explores the hypothesis that one reason force and effort perceptions are distinct is to inform an individual of impaired motor function when muscular force lags effort. This hypothesis predicts that effort and force perceptions will dissociate when motor function is impaired by fatigue but not during the size-weight illusion. All subjects reported a distinct increase in effort when lifting a standard test weight as fatigue developed. When fatigue was sufficiently marked so that they could barely lift the test weight, they rated their effort as similar to that required to lift a maximal weight in the unfatigued state. The perceived heaviness of the test weight also increased as fatigue developed, but this fatigue-weight illusion was smaller than the increase in effort for all subjects and displayed greater variability. In contrast, both the perceived weight of a small object and the effort required to lift it increased in parallel when small and large objects were lifted sequentially. The size-weight and size-effort illusions appear to be examples of a common phenomenon in which perceptual experience is rescaled to maintain acuity under different working conditions. The fatigue-weight illusion also has the effect of increasing perceptual acuity as the subject's weight lifting range decreases due to fatigue.     

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe grisea from Horizontal Gene Transfer Hypothesis

Horizontal gene transfer (HGT) has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes (corresponding prote...     

Enhancement of rice canopy carbon gain by elevated CO(2) is sensitive to growth stage and leaf nitrogen concentration

Increasing our understanding of the factors regulating seasonal changes in rice canopy carbon gain (C(gain): daily net photosynthesis -- night respiration) under elevated CO(2) concentrations ([CO(2)]) will reduce our uncertainty in predicting future rice yields and assist in the development of adaptation strategies. In this study we measured CO(2) exchange from rice (Oryza sativa) canopies grown at c. 360 and 690 micromol mol(-1)[CO(2)] in growth chambers continuously over three growing seasons. Stimulation of C(gain) by elevated [CO(2)] was 22-79% during vegetative growth, but decreased to between -12 and 5% after the grain-filling stage, resulting in a 7-22% net enhancement for the whole season. The decreased stimulation of C(gain) resulted mainly from decreased canopy net photosynthesis and partially from increased respiration. A decrease in canopy photosynthetic capacity was noted where leaf nitrogen (N) decreased. The effect of elevated [CO(2)] on leaf area was generally small, but most dramatic under ample N conditions; this increased the stimulation of whole-season C(gain). These results suggest that a decrease in C(gain) enhancement following elevated CO(2) levels is difficult to avoid, but that careful management of nitrogen levels can alter the whole-season C(gain) enhancement.     

Computational model of E-cadherin clustering under force

E-cadherins play a critical role in the formation of cell-cell adhesions for several physiological functions, including tissue development, repair, and homeostasis. The formation of clusters of E-cadherins involves extracellular adhesive (trans-) and lateral (cis-) associations between E-cadherin ectodomains and stabilization through intracellular binding to the actomyosin cytoskeleton. This binding provides force to the adhesion and is required for mechanotransduction. However, the exact role of cytoskeletal force on the clustering of E-cadherins is not well understood. To gain insights into this mechanism, we developed a computational model based on Brownian dynamics. In the model, E-cadherins transit between structural and functional states; they are able to bind and unbind other E-cadherins on the same and/or opposite cell(s) through trans- and cis-interactions while also creating dynamic links with the actomyosin cytoskeleton. Our results show that actomyosin force governs the fraction of E-cadherins in clusters and the size and number of clusters. For low forces (below 10 pN), a large number of small E-cadherin clusters form with less than five E-cadherins each. At higher forces, the probability of forming fewer but larger clusters increases. These findings support the idea that force reinforces cell-cell adhesions, which is consistent with differences in cluster size previously observed between apical and lateral junctions of epithelial tissues.     

Isoforms Confer Characteristic Force Generation and Mechanosensation by Myosin II Filaments

Myosin II isoforms with varying mechanochemistry and filament size interact with filamentous actin (F-actin) arrays to generate contractile forces in muscle and nonmuscle cells. How myosin II force production is shaped by isoform-specific motor properties and environmental stiffness remains poorly understood. Here, we used computer simulations to analyze force production by an ensemble of myosin motors against an elastically tethered actin filament. We found that force output depends on two timescales: the duration of F-actin attachment, which varies sharply with the ensemble size, motor duty ratio, and external load; and the time to build force, which scales with the ensemble stall force, gliding speed, and environmental stiffness. Although force-dependent kinetics were not required to sense changes in stiffness, the myosin catch bond produced positive feedback between the attachment time and force to trigger switch-like transitions from transient attachments, generating small forces, to high-force-generating runs. Using parameters representative of skeletal muscle myosin, nonmuscle myosin IIB, and nonmuscle myosin IIA revealed three distinct regimes of behavior, respectively: 1) large assemblies of fast, low-duty ratio motors rapidly build stable forces over a large range of environmental stiffness; 2) ensembles of slow, high-duty ratio motors serve as high-affinity cross-links with force buildup times that exceed physiological timescales; and 3) small assemblies of low-duty ratio motors operating at intermediate speeds are poised to respond sharply to changes in mechanical context—at low force or stiffness, they serve as low-affinity cross-links, but they can transition to force production via the positive-feedback mechanism described above. Together, these results reveal how myosin isoform properties may be tuned to produce force and respond to mechanical cues in their environment.     

Modeling human postural sway using an intermittent control and hemodynamic perturbations

Ground reaction force during human quiet stance is modulated synchronously with the cardiac cycle through hemodynamics [1]. This almost periodic hemodynamic force induces a small disturbance torque to the ankle joint, which is considered as a source of endogenous perturbation that induces postural sway. Here we consider postural sway dynamics of an inverted pendulum model with an intermittent control strategy, in comparison with the traditional continuous-time feedback controller. We examine whether each control model can exhibit human-like postural sway, characterized by its power law behavior at the low frequency band 0.1–0.7 Hz, when it is weakly perturbed by periodic and/or random forcing mimicking the hemodynamic perturbation. We show that the continuous control model with typical feedback gain parameters hardly exhibits the human-like sway pattern, in contrast with the intermittent control model. Further analyses suggest that deterministic, including chaotic, slow oscillations that characterize the intermittent control strategy, together with the small hemodynamic perturbation, could be a possible mechanism for generating the postural sway.     

Are morphology–performance relationships invariant across different seasons? A test with the green anole lizard (Anolis carolinensis)

A key assumption in ecomorphological studies is that morphology–function relationships are invariant due to underlying biomechanical principles. We tested the hypothesis that morphology–performance relationships are invariant across different seasons by examining how a key performance trait, bite force, and two aspects of morphology (head shape and dewlap size) changed seasonally in the field and in the laboratory in the green anole lizard Anolis carolinensis . We found that not only did bite force change seasonally (up to 80% within the same individual), but relationships between morphology and bite force are highly plastic. Of the three traits examined (bite force, head shape, and dewlap area), only head shape did not change seasonally. We noted opposing trends for how bite force and dewlap area changed seasonally; whereas dewlap areas were large in the spring, and small in the winter, bite forces were low in the spring and high in the winter. This pattern occurred because of a tradeoff at the individual level: individuals in the spring with large dewlaps and high bite forces diminish their dewlaps (but not bite force), whereas individuals with small dewlaps and low bite forces in the spring increase their bite forces (but not dewlap size). We also show that this trend was apparent both in the field (comparing different individuals) and the laboratory (comparing the same set of individuals under standardized conditions). Finally, seasonal changes were not consistent among individuals for either bite force or dewlap area, as individuals changed seasonally in proportion to their initial state. These findings cast doubt on the widely held view of invariant morphology–performance relationships, and offer a cautionary note for eco-morphological studies.     

Paraspinal muscle reflex dynamics

Neuromuscular control of spinal stability may be represented as a control system wherein the paraspinal muscle reflex acts as feedback response to kinetic and kinematic disturbances of the trunk. The influence of preparatory muscle recruitment for the control of spinal stability has been previously examined, but there are few reported studies that characterize paraspinal reflex gain as feedback response. In the current study, the input-output dynamics of paraspinal reflexes were quantified by means of the impulse response function (IRF), with trunk perturbation force representing the input signal and EMG the output signal. Surface EMGs were collected from the trunk muscles in response to a brief anteriorly directed impact force applied to the trunk of healthy participants. Reflex behavior was measured in response to three levels of force impulse, 6.1, 9.2 and 12.0 Ns, and two different levels of external trunk flexion preload, 0 and 110 N anterior force. Reflex EMG was quantifiable in response to 91% of the perturbations. Mean reflex onset latency was 30.7+/-21.3 ms and reflex amplitude increased with perturbation amplitude. Impulse response function gain, G(IRF), was defined as the peak amplitude of the measured IRF and provided a consistent measure of response behavior. EMG reflex amplitude and G(IRF) increased with force impulse. Mean G(IRF) was 2.27+/-1.31% MVC/Ns and demonstrated declining trend with flexion preload. Results agree with a simple systems model of the neuromechanical feedback behavior. The relative contribution of the reflex dynamics to spinal stability must be investigated in future research.