Inherent size constraints on prokaryote gene networks due to "accelerating" growth

Networks exhibiting accelerating growth have total link numbers growing faster than linearly with network size and either reach a limit or exhibit graduated transitions from nonstationary-to-stationary statistics and from random to scale-free to regular statistics as the network size grows. However, if for any reason the network cannot tolerate such gross structural changes then accelerating networks are constrained to have sizes below some critical value. This is of interest as the regulatory gene networks of single-celled prokaryotes are characterized by an accelerating quadratic growth and are size constrained to be less than about 10,000 genes encoded in DNA sequence of less than about 10 megabases. This paper presents a probabilistic accelerating network model for prokaryotic gene regulation which closely matches observed statistics by employing two classes of network nodes (regulatory and non-regulatory) and directed links whose inbound heads are exponentially distributed over all nodes and whose outbound tails are preferentially attached to regulatory nodes and described by a scale-free distribution. This model explains the observed quadratic growth in regulator number with gene number and predicts an upper prokaryote size limit closely approximating the observed value. (c) 2005 Elsevier GmbH. All rights reserved.

Constraints on the spatiotemporal accuracy of interceptive action: effects of target size on hitting a moving object

Results of two experiments are reported that examined how people respond to rectangular targets of different sizes in simple hitting tasks. If a target moves in a straight line and a person is constrained to move along a linear track oriented perpendicular to the targetrsquos motion, then the length of the target along its direction of motion constrains the temporal accuracy and precision required to make the interception. The dimensions of the target perpendicular to its direction of motion place no constraints on performance in such a task. In contrast, if the person is not constrained to move along a straight track, the targetrsquos dimensions may constrain the spatial as well as the temporal accuracy and precision. The experiments reported here examined how people responded to targets of different vertical extent (height): the task was to strike targets that moved along a straight, horizontal path. In experiment 1 participants were constrained to move along a horizontal linear track to strike targets and so target height did not constrain performance. Target height, length and speed were co-varied. Movement time (MT) was unaffected by target height but was systematically affected by length (briefer movements to smaller targets) and speed (briefer movements to faster targets). Peak movement speed (Vmax) was influenced by all three independent variables: participants struck shorter, narrower and faster targets harder. In experiment 2, participants were constrained to move in a vertical plane normal to the targetrsquos direction of motion. In this task target height constrains the spatial accuracy required to contact the target. Three groups of eight participants struck targets of different height but of constant length and speed, hence constant temporal accuracy demand (different for each group, one group struck stationary targets = no temporal accuracy demand). On average, participants showed little or no systematic response to changes in spatial accuracy demand on any dependent measure (MT, Vmax, spatial variable error). The results are interpreted in relation to previous results on movements aimed at stationary targets in the absence of visual feedback.

Intercepting a moving target: effects of temporal precision constraints and movement amplitude

The effects of temporal precision constraints and movement amplitude on performance of an interceptive aiming task were examined. Participants were required to strike a moving target object with a 'bat' by moving the bat along a straight path (constrained by a linear slide) perpendicular to the path of the target. Temporal precision constraints were defined in terms of the time period (or window) within which contact with the target was possible. Three time windows were used (approx. 35, 50 and 65 ms) and these were achieved either by manipulating the size of the bat (experiment 1a), the size of the target (experiment 1b) or the speed of the target (experiment 2). In all experiments, movement time (MT) increased in proportion to movement amplitude but was only affected by differences in the temporal precision constraint if this was achieved by variation in the target's speed. In this case the MT was approximately inversely proportional to target speed. Peak movement speed was affected by temporal accuracy constraints in all three experiments: participants reached higher speeds when the temporal precision required was greater. These results are discussed with reference to the speed-accuracy trade-off observed for temporally constrained aiming movements. It is suggested that the MT and speed of interceptive aiming movements may be understood as responses to the spatiotemporal constraints of the task.

Improved constraints on possible variation of physical constants from HI 21-cm and molecular QSO absorption lines

Quasar (QSO) absorption spectra provide an extremely useful probe of possible cosmological variation in various physical constants. Comparison of H i 21-cm absorption with corresponding molecular (rotational) absorption spectra allows us to constrain variation in , where α is the fine-structure constant and gp is the proton g-factor. We analyse spectra of two QSOs, PKS 1413+135 and TXS 0218+357, and derive values of at absorption redshifts of and 0.6847 by simultaneous fitting of the H i 21-cm and molecular lines. We find and respectively, indicating an insignificantly smaller y in the past. We compare our results with other constraints from the same two QSOs given recently by Drinkwater et al. and Carilli et al., and with our recent optical constraints, which indicated a smaller α at higher redshifts.

Spectral properties of the tandem Jackson network, seen as a quasi-birth-and-death process

Quasi-birth-and-death (QBD) processes with infinite “phase spaces” can exhibit unusual and interesting behavior. One of the simplest examples of such a process is the two-node tandem Jackson network, with the “phase” giving the state of the first queue and the “level” giving the state of the second queue. In this paper, we undertake an extensive analysis of the properties of this QBD. In particular, we investigate the spectral properties of Neuts’s R-matrix and show that the decay rate of the stationary distribution of the “level” process is not always equal to the convergence norm of R. In fact, we show that we can obtain any decay rate from a certain range by controlling only the transition structure at level zero, which is independent of R. We also consider the sequence of tandem queues that is constructed by restricting the waiting room of the first queue to some finite capacity, and then allowing this capacity to increase to infinity. We show that the decay rates for the finite truncations converge to a value, which is not necessarily the decay rate in the infinite waiting room case. Finally, we show that the probability that the process hits level n before level 0 given that it starts in level 1 decays at a rate which is not necessarily the same as the decay rate for the stationary distribution.

Development and evaluation of neural network freeway incident detection models using field data

This paper discusses a multi-layer feedforward (MLF) neural network incident detection model that was developed and evaluated using field data. In contrast to published neural network incident detection models which relied on simulated or limited field data for model development and testing, the model described in this paper was trained and tested on a real-world data set of 100 incidents. The model uses speed, flow and occupancy data measured at dual stations, averaged across all lanes and only from time interval t. The off-line performance of the model is reported under both incident and non-incident conditions. The incident detection performance of the model is reported based on a validation-test data set of 40 incidents that were independent of the 60 incidents used for training. The false alarm rates of the model are evaluated based on non-incident data that were collected from a freeway section which was video-taped for a period of 33 days. A comparative evaluation between the neural network model and the incident detection model in operation on Melbourne's freeways is also presented. The results of the comparative performance evaluation clearly demonstrate the substantial improvement in incident detection performance obtained by the neural network model. The paper also presents additional results that demonstrate how improvements in model performance can be achieved using variable decision thresholds. Finally, the model's fault-tolerance under conditions of corrupt or missing data is investigated and the impact of loop detector failure/malfunction on the performance of the trained model is evaluated and discussed. The results presented in this paper provide a comprehensive evaluation of the developed model and confirm that neural network models can provide fast and reliable incident detection on freeways. (C) 1997 Elsevier Science Ltd. All rights reserved.

Capillary network models for transport in packed beds: Considerations of pore aspect ratio

The conventional analysis for the estimation of the tortuosity factor for transport in porous media is modified here to account for the effect of pore aspect ratio. Structural models of the porous medium are also constructed for calculating the aspect ratio as a function of porosity. Comparison of the model predictions with the extensive data of Currie (1960) for the effective diffusivity of hydrogen in packed beds shows good agreement with a network model of randomly oriented intersecting pores for porosities upto about 50 percent, which is the region of practical interest. The predictions based on this network model are also found to be in better agreement with the data of Currie than earlier expressions developed for unconsolidated and grainy media.

Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Modeling the fluid-flow-induced stress and collapse in a dendritic network

An analytical approach to the stress development in the coherent dendritic network during solidification is proposed. Under the assumption that stresses are developed in the network as a result of the friction resisting shrinkage-induced interdendritic fluid flow, the model predicts the stresses in the solid. The calculations reflect the expected effects of postponed dendrite coherency, slower solidification conditions, and variations of eutectic volume fraction and shrinkage. Comparing the calculated stresses to the measured shear strength of equiaxed mushy zones shows that it is possible for the stresses to exceed the strength, thereby resulting in reorientation or collapse of the dendritic network.

Sedimentologic, petrographic, and sulfur isotope constraints on fine-grained pyrite formation at Mount Isa Mine and environs, Northwest Queensland, Australia

Fine-grained pyrite is the earliest generation of pyrite and the most abundant sulfide within the Urquhart Shale at Mount Isa, northwest Queensland. The pyrite is intimately interbanded with ore-grade Pb-Zn miner alization at the Mount Isa mine but is also abundant north and south of the mine at several stratigraphic horizons within the Urquhart Shale. Detailed sedimentologic, petrographic, and sulfur isotope studies of the Urquhart Shale, mostly north of the mine, reveal that the fine-grained pyrite (delta(34)S = -3.3 to +26.3 parts per thousand) formed by thermochemical sulfate reduction during diagenesis. The sulfate source was local sulfate evaporites, pseudo morphs of which are present throughout the Urquhart Shale (i.e., gypsum, anhydrite, and barite). Deep-burial diagenetic replacement of these evaporites resulted in sulfate-bearing ground waters which migrated parallel to bedding. Fine-grained pyrite formed where these fluids infiltrated and then interacted with carbon-rich laminated siltstones. Comparison of the sulfur isotope systematics of fine-grained pyrite and spatially associated base metal sulfides from the Mount Isa Pb-Zn and Cu orebodies indicates a common sulfur source of ultimately marine origin for all sulfide types. Different sulfur isotope ratio distributions for the various sulfides are the result of contrasting formation mechanisms and/or depositional conditions rather than differing sulfur sources. The sulfur isotope systematics of the base metal and associated iron sulfide generations are consistent with mineralization by reduced hydrothermal fluids, perhaps generated by bulk reduction of evaporite-sourced sulfate-bearing waters generated deeper in the Mount Isa Group, the sedimentary sequence which contains the Urquhart Shale. The available sulfur isotope data from the Mount Isa orebodies are consistent with either a chemically and thermally zoned, evolving Cu-Pb-Zn system, or discrete Cu and Pb-Zn mineralizing events linked by a common sulfur source.

Participation in physical activities by older Australians: a review of the social psychological benefits and constraints

Participation in physical activities has been found to be an important factor in contributing to a healthy lifestyle. Research has found strong relationships between participation in regular physical activity and the prevention of disease, while its relationship to the psychological and social dimensions have been neglected. Recently however, several studies have found causal relationships between physical activity and improved mood state, reduced anxiety, reduced depression, and increased social support. Despite this, surveys indicate that participation levels in physical activities are declining among older Australians, with the exceptions of walking and gardening. This paper also examines constraints to participation in leisure programs, such as lack of time, poor health, fear of crime, the financial cost and the lack of a partner to participate with. A number of strategies have been suggested to overcome these constraints.