Evolution of robustness in digital organisms

We study the evolution of robustness in digital organisms adapting to a high mutation rate. As genomes adjust to the harsh mutational environment, the mean effect of single Imitations decreases, up until the point where a sizable fraction (up to 30% in many cases) of the Imitations are neutral. We correlate the changes in robustness along the line of descent to changes in directional epistasis, and find that increased robustness is achieved by moving from antagonistic epistasis between mutations towards codes where mutations are, on average, independent. We interpret this recoding as a breakup of linkage between vital sections of the genome, up to the point where instructions are maximally independent of each other. While such a recoding often requires sacrificing some replication speed, it is the best strategy for withstanding high rates of mutation

The White Dwarf -- White Dwarf galactic background in the LISA data

LISA (Laser Interferometer Space Antenna) is a proposed space mission, which will use coherent laser beams exchanged between three remote spacecraft to detect and study low-frequency cosmic gravitational radiation. In the low-part of its frequency band, the LISA strain sensitivity will be dominated by the incoherent superposition of hundreds of millions of gravitational wave signals radiated by inspiraling white-dwarf binaries present in our own galaxy. In order to estimate the magnitude of the LISA response to this background, we have simulated a synthesized population that recently appeared in the literature. We find the amplitude of the galactic white-dwarf binary background in the LISA data to be modulated in time, reaching a minimum equal to about twice that of the LISA noise for a period of about two months around the time when the Sun-LISA direction is roughly oriented towards the Autumn equinox. Since the galactic white-dwarfs background will be observed by LISA not as a stationary but rather as a cyclostationary random process with a period of one year, we summarize the theory of cyclostationary random processes, present the corresponding generalized spectral method needed to characterize such process, and make a comparison between our analytic results and those obtained by applying our method to the simulated data. We find that, by measuring the generalized spectral components of the white-dwarf background, LISA will be able to infer properties of the distribution of the white-dwarfs binary systems present in our Galaxy.Comment: 36 pages, 15 figure

Neural Prediction Errors Reveal a Risk-Sensitive Reinforcement-Learning Process in the Human Brain

Humans and animals are exquisitely, though idiosyncratically, sensitive to risk or variance in the outcomes of their actions. Economic, psychological, and neural aspects of this are well studied when information about risk is provided explicitly. However, we must normally learn about outcomes from experience, through trial and error. Traditional models of such reinforcement learning focus on learning about the mean reward value of cues and ignore higher order moments such as variance. We used fMRI to test whether the neural correlates of human reinforcement learning are sensitive to experienced risk. Our analysis focused on anatomically delineated regions of a priori interest in the nucleus accumbens, where blood oxygenation level-dependent (BOLD) signals have been suggested as correlating with quantities derived from reinforcement learning. We first provide unbiased evidence that the raw BOLD signal in these regions corresponds closely to a reward prediction error. We then derive from this signal the learned values of cues that predict rewards of equal mean but different variance and show that these values are indeed modulated by experienced risk. Moreover, a close neurometric–psychometric coupling exists between the fluctuations of the experience-based evaluations of risky options that we measured neurally and the fluctuations in behavioral risk aversion. This suggests that risk sensitivity is integral to human learning, illuminating economic models of choice, neuroscientific models of affective learning, and the workings of the underlying neural mechanisms

Simulating Responses of Gravitational-Wave Instrumentation

Synthetic LISA is a computer program for simulating the responses of the instrumentation of the NASA/ESA Laser Interferometer Space Antenna (LISA) mission, the purpose of which is to detect and study gravitational waves. Synthetic LISA generates synthetic time series of the LISA fundamental noises, as filtered through all the time-delay-interferometry (TDI) observables. (TDI is a method of canceling phase noise in temporally varying unequal-arm interferometers.) Synthetic LISA provides a streamlined module to compute the TDI responses to gravitational waves, according to a full model of TDI (including the motion of the LISA array and the temporal and directional dependence of the arm lengths). Synthetic LISA is written in the C++ programming language as a modular package that accommodates the addition of code for specific gravitational wave sources or for new noise models. In addition, time series for waves and noises can be easily loaded from disk storage or electronic memory. The package includes a Python-language interface for easy, interactive steering and scripting. Through Python, Synthetic LISA can read and write data files in Flexible Image Transport System (FITS), which is a commonly used astronomical data format

Numerical Investigation of Spinal Neuron Facilitation with Multi-electrode Epidural Stimulation

Approximately 1,275,000 people in the US have a spinal cord injury severe enough to cause some paralysis of the arms and/or legs. Epidural stimulation using implanted multi-electrode stimulating arrays over the lumbosacral spinal cord has recently shown promise in assisting individuals with severe spinal cord injuries to stand, walk, and even facilitate voluntary movement. Both animal model and human studies have shown that sub-threshold facilitation of motor recovery gives the best results. The underlying neural mechanisms by which sub-threshold epidural stimulation leads to motor recovery are incompletely known. This thesis uses computational methods to study the facilitation effect. A neuron is facilitated if a sub-threshold synaptic input can cause a neuronal output under the influence of a stimulating electric field. The analysis in this thesis is based on a computational model of the epidural spinal stimulation process in the rat spinal cord. This model includes a time-domain finite element simulation (using COMSOL®) of the various tissues in the spinal cord with the appropriate anisotropic and frequency-dependent complex relative permittivities. The voltages obtained from the finite element simulations were used as the extracellular voltage in NEURON simulations. A population of neurons were simulated under a wide variety of conditions. These simulations highlight the effect of neuron orientation, location, and synaptic timing as key parameters which influence facilitation. This study indicates that regions of the spinal cord that have previously been ignored may be actively involved in motor recovery. These results may also enable the design of specialized epidural electrode arrays and the design of new stimulation protocols.</p

Axel: A Minimalist Tethered Rover for Exploration of Extreme Planetary Terrains

Recent scientific findings suggest that some of the most interesting sites for future exploration of planetary surfaces lie in terrains that are currently inaccessible to conventional robotic rovers. To provide robust and flexible access to these terrains, we have been developing Axel, the robotic rover. Axel is a lightweight two-wheeled vehicle that can access steep terrains and negotiate relatively large obstacles because of its actively managed tether and novel wheel design. This article reviews the Axel system and focuses on those system components that affect Axel's steep terrain mobility. Experimental demonstrations of Axel on sloped and rocky terrains are presented

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles

Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest. The profile hidden Markov model (HMM) framework enables the construction of very useful probabilistic models for protein families that allow for accurate modeling of position specific matches, insertions, and deletions. We present a novel homology detection algorithm that integrates banded Viterbi algorithm for profile HMM parsing with an iterative simultaneous alignment and assembly computational framework. The algorithm searches a given profile HMM of a protein family against a database of fragmentary MG/MT sequencing data and simultaneously assembles complete or near-complete gene and protein sequences of the protein family. The resulting program, HMM-GRASPx, demonstrates superior performance in aligning and assembling homologs when benchmarked on both simulated marine MG and real human saliva MG datasets. On real supragingival plaque and stool MG datasets that were generated from healthy individuals, HMM-GRASPx accurately estimates the abundances of the antimicrobial resistance (AMR) gene families and enables accurate characterization of the resistome profiles of these microbial communities. For real human oral microbiome MT datasets, using the HMM-GRASPx estimated transcript abundances significantly improves detection of differentially expressed (DE) genes. Finally, HMM-GRASPx was used to reconstruct comprehensive sets of complete or near-complete protein and nucleotide sequences for the query protein families. HMM-GRASPx is freely available online from http://sourceforge.net/projects/hmm-graspx

Simulation of the White Dwarf -- White Dwarf galactic background in the LISA data

LISA (Laser Interferometer Space Antenna) is a proposed space mission, which will use coherent laser beams exchanged between three remote spacecraft to detect and study low-frequency cosmic gravitational radiation. In the low-part of its frequency band, the LISA strain sensitivity will be dominated by the incoherent superposition of hundreds of millions of gravitational wave signals radiated by inspiraling white-dwarf binaries present in our own galaxy. In order to estimate the magnitude of the LISA response to this background, we have simulated a synthesized population that recently appeared in the literature. We find the amplitude of the galactic white-dwarf binary background in the LISA data to be modulated in time, reaching a minimum equal to about twice that of the LISA noise for a period of about two months around the time when the Sun-LISA direction is roughly oriented towards the Autumn equinox. Since the galactic white-dwarfs background will be observed by LISA not as a stationary but rather as a cyclostationary random process with a period of one year, we summarize the theory of cyclostationary random processes and present the corresponding generalized spectral method needed to characterize such process. We find that, by measuring the generalized spectral components of the white-dwarf background, LISA will be able to infer properties of the distribution of the white-dwarfs binary systems present in our Galaxy.Comment: 14 pages and 6 figures. Submitted to Classical and Quantum Gravity (Proceedings of GWDAW9