777 research outputs found
Evolving Robots on Easy Mode: Towards a Variable Complexity Controller for Quadrupeds
The complexity of a legged robot's environment or task can inform how
specialised its gait must be to ensure success. Evolving specialised robotic
gaits demands many evaluations - acceptable for computer simulations, but not
for physical robots. For some tasks, a more general gait, with lower
optimization costs, could be satisfactory. In this paper, we introduce a new
type of gait controller where complexity can be set by a single parameter,
using a dynamic genotype-phenotype mapping. Low controller complexity leads to
conservative gaits, while higher complexity allows more sophistication and high
performance for demanding tasks, at the cost of optimization effort. We
investigate the new controller on a virtual robot in simulations and do
preliminary testing on a real-world robot. We show that having variable
complexity allows us to adapt to different optimization budgets. With a high
evaluation budget in simulation, a complex controller performs best. Moreover,
real-world evolution with a limited evaluation budget indicates that a lower
gait complexity is preferable for a relatively simple environment.Comment: Accepted to EvoApplications1
Extreme genetic fragility of the HIV-1 capsid
Genetic robustness, or fragility, is defined as the ability, or lack thereof, of a biological entity to maintain function in the face of mutations. Viruses that replicate via RNA intermediates exhibit high mutation rates, and robustness should be particularly advantageous to them. The capsid (CA) domain of the HIV-1 Gag protein is under strong pressure to conserve functional roles in viral assembly, maturation, uncoating, and nuclear import. However, CA is also under strong immunological pressure to diversify. Therefore, it would be particularly advantageous for CA to evolve genetic robustness. To measure the genetic robustness of HIV-1 CA, we generated a library of single amino acid substitution mutants, encompassing almost half the residues in CA. Strikingly, we found HIV-1 CA to be the most genetically fragile protein that has been analyzed using such an approach, with 70% of mutations yielding replication-defective viruses. Although CA participates in several steps in HIV-1 replication, analysis of conditionally (temperature sensitive) and constitutively non-viable mutants revealed that the biological basis for its genetic fragility was primarily the need to coordinate the accurate and efficient assembly of mature virions. All mutations that exist in naturally occurring HIV-1 subtype B populations at a frequency >3%, and were also present in the mutant library, had fitness levels that were >40% of WT. However, a substantial fraction of mutations with high fitness did not occur in natural populations, suggesting another form of selection pressure limiting variation in vivo. Additionally, known protective CTL epitopes occurred preferentially in domains of the HIV-1 CA that were even more genetically fragile than HIV-1 CA as a whole. The extreme genetic fragility of HIV-1 CA may be one reason why cell-mediated immune responses to Gag correlate with better prognosis in HIV-1 infection, and suggests that CA is a good target for therapy and vaccination strategies
Display of probability densities for data from a continuous distribution
Based on cumulative distribution functions, Fourier series expansion and
Kolmogorov tests, we present a simple method to display probability densities
for data drawn from a continuous distribution. It is often more efficient than
using histograms.Comment: 5 pages, 4 figures, presented at Computer Simulation Studies XXIV,
Athens, GA, 201
Two-Particle-Self-Consistent Approach for the Hubbard Model
Even at weak to intermediate coupling, the Hubbard model poses a formidable
challenge. In two dimensions in particular, standard methods such as the Random
Phase Approximation are no longer valid since they predict a finite temperature
antiferromagnetic phase transition prohibited by the Mermin-Wagner theorem. The
Two-Particle-Self-Consistent (TPSC) approach satisfies that theorem as well as
particle conservation, the Pauli principle, the local moment and local charge
sum rules. The self-energy formula does not assume a Migdal theorem. There is
consistency between one- and two-particle quantities. Internal accuracy checks
allow one to test the limits of validity of TPSC. Here I present a pedagogical
review of TPSC along with a short summary of existing results and two case
studies: a) the opening of a pseudogap in two dimensions when the correlation
length is larger than the thermal de Broglie wavelength, and b) the conditions
for the appearance of d-wave superconductivity in the two-dimensional Hubbard
model.Comment: Chapter in "Theoretical methods for Strongly Correlated Systems",
Edited by A. Avella and F. Mancini, Springer Verlag, (2011) 55 pages.
Misprint in Eq.(23) corrected (thanks D. Bergeron
Comparative Genomics of 2009 Seasonal Plague (Yersinia pestis) in New Mexico
Plague disease caused by the Gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19th century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen
The Impact of Duty Hours on Resident Self Reports of Errors
BACKGROUND: Resident duty hour limitations aim, in part, to reduce medical errors. Residents’ perceptions of the impact of duty hours on errors are unknown. OBJECTIVE: To determine residents’ self-reported contributing factors, frequency, and impact of hours worked on suboptimal care practices and medical errors. DESIGN: Cross-sectional survey. SUBJECTS: 164 Internal Medicine Residents at the University of California, San Francisco. MEASUREMENTS AND RESULTS: Residents were asked to report the frequency and contributing factors of suboptimal care practices and medical errors, and how duty hours impacted these practices and aspects of resident work-life. One hundred twenty-five residents (76%) responded. The most common suboptimal care practices were working while impaired by fatigue and forgetting to transmit information during sign-out. In multivariable models, residents who felt overwhelmed with work (p = 0.02) and who reported spending >50% of their time in nonphysician tasks (p = 0.002) were more likely to report suboptimal care practices. Residents reported work-stress (a composite of fatigue, excessive workload, distractions, stress, and inadequate time) as the most frequent contributing factor to medical errors. In multivariable models, only engaging in suboptimal practices was associated with self-report of higher risk for medical errors (p < 0.001); working more than 80 hours per week was not associated with suboptimal care or errors. CONCLUSION: Our findings suggest that administrative load and work stressors are more closely associated with resident reports of medical errors than the number of hours work. Efforts to reduce resident duty hours may also need to address the nature of residents’ work to reduce errors
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