Context-free and context-sensitive dynamics in recurrent neural networks

Continuous-valued recurrent neural networks can learn mechanisms for processing context-free languages. The dynamics of such networks is usually based on damped oscillation around fixed points in state space and requires that the dynamical components are arranged in certain ways. It is shown that qualitatively similar dynamics with similar constraints hold for a(n)b(n)c(n), a context-sensitive language. The additional difficulty with a(n)b(n)c(n), compared with the context-free language a(n)b(n), consists of 'counting up' and 'counting down' letters simultaneously. The network solution is to oscillate in two principal dimensions, one for counting up and one for counting down. This study focuses on the dynamics employed by the sequential cascaded network, in contrast to the simple recurrent network, and the use of backpropagation through time. Found solutions generalize well beyond training data, however, learning is not reliable. The contribution of this study lies in demonstrating how the dynamics in recurrent neural networks that process context-free languages can also be employed in processing some context-sensitive languages (traditionally thought of as requiring additional computation resources). This continuity of mechanism between language classes contributes to our understanding of neural networks in modelling language learning and processing.

Free energy approximations in simple lattice proteins

This work addresses the question of whether it is possible to define simple pairwise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how reliable it could possibly be. In a two-dimensional, infinite lattice model system one can calculate exact free energies by exhaustive enumeration. A series of approximations were fitted to exact results to assess the feasibility and utility of pairwise free energy terms. Approximating the true free energy with pairwise interactions gives a poor fit with little transferability between systems of different size. Adding extra artificial terms to the approximation yields better fits, but does not improve the ability to generalize from one system size to another. Furthermore, one cannot distinguish folding from nonfolding sequences via the approximated free energies. Most usefully, the methodology shows how one can assess the utility of various terms in lattice protein/polymer models. (C) 2001 American Institute of Physics.

A method for the design of MRI radiofrequency coils based on triangular and pulse basis functions

This paper presents a numerical technique for the design of an RF coil for asymmetric magnetic resonance imaging (MRI) systems. The formulation is based on an inverse approach where the cylindrical surface currents are expressed in terms of a combination of sub-domain basis functions: triangular and pulse functions. With the homogeneous transverse magnetic field specified in a spherical region, a functional method is applied to obtain the unknown current coefficients. The current distribution is then transformed to a conductor pattern by use of a stream function technique. Preliminary MR images acquired using a prototype RF coil are presented and validate the design method. (C) 2002 Elsevier Science B.V. All rights reserved.

In situ measures of spawning synchrony and fertilization success in an intertidal, free-spawning invertebrate

The rocky intertidal zone has the potential to be one of the harshest environments for free-spawning organisms, but empirical data on fertilization success are scarce. Here, I report on an intertidal, solitary ascidian, Pyura stolonifera, which was observed to spawn at low tide. At a scale likely to be most important to gametes (metres, duration of tide), approximately 30% of individuals in the population were spawning synchronously. Spawned gametes remained in a viscous matrix and this appeared to minimise their dilution. Fertilization success varied greatly among individuals (0 to 92%) and was related to the distance to the nearest neighbouring spawner. Occasional wave wash facilitated the movement of sperm between spawners. Fertilization success in some individuals was limited by the scarcity of sperm whilst the experimental addition of sperm did not increase success in others.

Sources of variation in larval quality for free-spawning marine invertebrates: Egg size and the local sperm environment

There has been growing interest in the effects of variation in larval quality on the post-larval performance of adult marine invertebrates. Variation in egg/larval size is an obvious source of variation in larval quality but sources of variation have received little attention. For broadcast spawners, larval size may vary according to the local sperm environment but the generality of this result is unclear. Here, we show that, for a solitary ascidian, a polychaete and an echinoid, larval size is affected by the concentration of sperm present during fertilization. Larvae that are produced at high sperm concentrations are smaller than larvae that are produced from eggs exposed to low sperm concentrations. We also show that for three ascidians and an asteroid, egg size increases with maternal body size. These differences in larval size are likely to affect larval and subsequent adult performance in the field. Given that sperm concentrations in the field can fluctuate widely, it is likely that larval quality in free-spawning marine invertebrates will also vary widely.

The early sperm gets the good egg: mating order effects in free spawners

Mating order can have important consequences for the fertilization success of males whose ejaculates compete to fertilize a clutch of eggs. Despite an excellent body of literature on mating-order effects in many animals, they have rarely been considered in marine free-spawning invertebrates, where both sexes release gametes into the water column. In this study, we show that in such organisms, mating order can have profound repercussions for male reproductive success. Using in vitro fertilization for two species of sea urchin we found that the 'fertilization history' of a clutch of eggs strongly influenced the size distribution of unfertilized eggs, and consequently the likelihood that they will be fertilized. Males that had first access to a batch of eggs enjoyed elevated fertilization success because they had privileged access to the largest and therefore most readily fertilizable eggs within a clutch. By contrast, when a male's sperm were exposed to a batch of unfertilized eggs left over from a previous mating event, fertilization rates were reduced, owing to smaller eggs remaining in egg clutches previously exposed to sperm. Because of this size-dependent fertilization, the fertilization history of eggs also strongly influenced the size distribution of offspring, with first-spawning males producing larger, and therefore fitter, offspring. These findings suggest that when there is variation in egg size, mating order will influence not only the quantity but also the quality of offspring sired by competing males.

Electrochemical oxidation of synthetic tannery wastewater in chloride-free aqueous media

The electrochemical treatment of a synthetic tannery wastewater, prepared with several compounds used by finishing tanneries, was studied in chloride-free media. Boron-doped diamond (Si/BDD), antimony-doped tin dioxide (Ti/SnO(2)-Sb), and iridium-antimony-doped tin dioxide (Ti/SnO(2)-Sb-Ir)were evaluated as anode. The influence of pH and current density on the treatment was assessed by means of the parameters used to measure the level of organic contaminants in the wastewater; i.e., total phenols, chemical oxygen demand (COD), total organic carbon (TOC), and absorbance. Results showed that faster decrease in these parameters occurred when the Si/BDD anode was used. Good results were obtained with the Ti/SnO(2)-Sb anode, but its complete deactivation was reached after 4h of electrolysis at 25 mA cm(-2), indicating that the service life of this electrode is short. The Ti/SnO(2)-Sb-Ir anode is chemically and electrochemically more stable than the Ti/SnO(2)-Sb anode, but it is not suitable for the electrochemical treatment under the studied conditions. No significant changes were observed for electrolyses performed at different pH conditions with Si/BDD, and this electrode led to almost complete mineralization after 4 h of electrolysis at 100mAcm(-2). The increase in current density resulted in faster wastewater oxidation, with lower current efficiency and higher energy consumption. Si/BBD proved to be the best electrodic material for the direct electrooxidation of tannery wastewaters. (C) 2010 Elsevier B.V. All rights reserved.

The benefits of polyandry in the free-spawning polychaete Galeolaria caespitosa

In many species, females are thought to benefit from polyandry due to the reduced risks of fertilization by genetically incompatible sperm. However, few studies that have reported such benefits have directly attributed variation in female reproductive success to the interacting effects of males and females at fertilization. In this paper, we determine whether male x female interactions influence fertilization in vitro in the free-spawning, sessile polychaete Galeolaria caespitosa. Furthermore, we determined whether polyandry results in direct fertilization benefits for females by experimentally manipulating the number of males contributing towards staged spawning events. To test for male x female interaction effects we performed an initial experiment that crossed seven males with six females (in all 42 combinations), enabling us to assess fertilization rates for each specific male-female pairing and attribute variation in fertilization success to males, females and their interaction. This initial experiment revealed a strong interaction between males and females at fertilization, confirming that certain male-female combinations were more compatible than others. A second experiment tested the hypothesis that polyandry enhances female reproductive success by exposing each female's eggs to either a single male's sperm (monandry) or the sperm from three males simultaneously (polyandry). We performed this second experiment at two ecologically relevant sperm concentrations. This latter experiment revealed a strong fertilization benefit of polyandry, independent of the effects of sperm concentration (which were also significant). We suggest that these direct fertilization gains arising from polyandry will constitute an important source of selection on females to mate multiply in nature.

The crystal structure of free human hypoxanthineguanine phosphoribosyltransferase reveals extensive conformational plasticity throughout the catalytic cycle

Human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) catalyses the synthesis of the purine nucleoside monophosphates, IMP and GMP, by the addition of a 6-oxopurine base, either hypoxanthine or guanine, to the 1-beta-position of 5-phospho-U-D-ribosyl-1-pyrophosphate (PRib-PP). The mechanism is sequential, with PRib-PP binding to the free enzyme prior to the base. After the covalent reaction, pyrophosphate is released followed by the nucleoside monophosphate. A number of snapshots of the structure of this enzyme along the reaction pathway have been captured. These include the structure in the presence of the inactive purine base analogue, 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and PRib-PP. Mg2+, and in complex with IMP or GMP. The third structure is that of the immucillinHP.Mg2+.PPi complex, a transition-state analogue. Here, the first crystal structure of free human HGPRT is reported to 1.9 angstrom resolution, showing that significant conformational changes have to occur for the substrate(s) to bind and for catalysis to proceed. Included in these changes are relative movement of subunits within the tetramer, rotation and extension of an active-site alpha-helix (D137-D153), reorientation of key active-site residues K68, D137 and K165, and the rearrangement of three active-site loops (100-128, 165-173 and 186-196). Toxoplasina gondii HGXPRT is the only other 6-oxopurine phosphoribosyltransferase structure solved in the absence of ligands. Comparison of this structure with human HGPRT reveals significant differences in the two active sites, including the structure of the flexible loop containing K68 (human) or K79 (T gondii). (c) 2005 Elsevier Ltd. All rights reserved.

Physiologic parameters that affect pulse transit time difference between the upper and lower limbs in children

Pulse wave velocity (PWV) is a known parameter that is related to arterial distensibility. However, its potential is hampered by the absence of appropriate techniques to estimate it noninvasively. PWV can be used as an assessment of increased arterial stiffness that is linked to systolic hypertension, excess cardiovascular morbidity and mortality.(1,2)