Effects of Epistasis and Pleiotropy on Fitness Landscapes

The factors that influence genetic architecture shape the structure of the fitness landscape, and therefore play a large role in the evolutionary dynamics. Here the NK model is used to investigate how epistasis and pleiotropy -- key components of genetic architecture -- affect the structure of the fitness landscape, and how they affect the ability of evolving populations to adapt despite the difficulty of crossing valleys present in rugged landscapes. Populations are seen to make use of epistatic interactions and pleiotropy to attain higher fitness, and are not inhibited by the fact that valleys have to be crossed to reach peaks of higher fitness.Comment: 10 pages, 6 figures. To appear in "Origin of Life and Evolutionary Mechanisms" (P. Pontarotti, ed.). Evolutionary Biology: 16th Meeting 2012, Springer-Verla

Synthesis of nanostructures in nanowires using sequential catalyst reactions.

Nanowire growth by the vapour-liquid-solid (VLS) process enables a high level of control over nanowire composition, diameter, growth direction, branching and kinking, periodic twinning, and crystal structure. The tremendous impact of VLS-grown nanowires is due to this structural versatility, generating applications ranging from solid-state lighting and single-photon sources to thermoelectric devices. Here, we show that the morphology of these nanostructures can be further tailored by using the liquid droplets that catalyse nanowire growth as a 'mixing bowl', in which growth materials are sequentially supplied to nucleate new phases. Growing within the liquid, these phases adopt the shape of faceted nanocrystals that are then incorporated into the nanowires by further growth. We demonstrate this concept by epitaxially incorporating metal-silicide nanocrystals into Si nanowires with defect-free interfaces, and discuss how this process can be generalized to create complex nanowire-based heterostructures.Supported by the National Science Foundation under Grants No. DMR-0606395 and 0907483 (YCC), ERC Grant 279342: InSituNANO (FP, SH), the National Science Council of Taiwan under Grant No. NSC-101-2112-M-009-021-MY3 (YCC), the Center for Interdisciplinary Science under the MOE-ATU project for NCTU (YCC) and the Center for Functional Nanomaterials, Brookhaven National Laboratory, which is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under contract DE-AC02-98CH10886 (DZ and EAS).This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nmat435

Effects of built environment on walking among Hong Kong older adults

published_or_final_versio

Election turnout statistics in many countries: similarities, differences, and a diffusive field model for decision-making

We study in details the turnout rate statistics for 77 elections in 11 different countries. We show that the empirical results established in a previous paper for French elections appear to hold much more generally. We find in particular that the spatial correlation of turnout rates decay logarithmically with distance in all cases. This result is quantitatively reproduced by a decision model that assumes that each voter makes his mind as a result of three influence terms: one totally idiosyncratic component, one city-specific term with short-ranged fluctuations in space, and one long-ranged correlated field which propagates diffusively in space. A detailed analysis reveals several interesting features: for example, different countries have different degrees of local heterogeneities and seem to be characterized by a different propensity for individuals to conform to the cultural norm. We furthermore find clear signs of herding (i.e. strongly correlated decisions at the individual level) in some countries, but not in others.Comment: 15 pages, 9 figures, 7 table

Microstructure of non-polar GaN on LiGaO2 grown by plasma-assisted MBE

We have investigated the structure of non-polar GaN, both on the M - and A-plane, grown on LiGaO2 by plasma-assisted molecular beam epitaxy. The epitaxial relationship and the microstructure of the GaN films are investigated by transmission electron microscopy (TEM). The already reported epi-taxial relationship and for M -plane GaN is confirmed. The main defects are threading dislocations and stacking faults in both samples. For the M -plane sample, the density of threading dislocations is around 1 × 1011 cm-2 and the stacking fault density amounts to approximately 2 × 105 cm-1. In the A-plane sample, a threading dislocation density in the same order was found, while the stacking fault density is much lower than in the M -plane sample

Adolescent survey non-response and later risk of death. A prospective cohort study of 78 609 persons with 11-year follow-up

<p>Abstract</p> <p>Background</p> <p>Non-response in survey studies is a growing problem and, being usually selective, it leads to under- or overestimation of health outcomes in the follow-up. We followed both respondents and non-respondents by registry linkage to determine whether there is a risk of death, related to non-response at baseline.</p> <p>Methods</p> <p>Sample data of biennial surveys to 12-18-year-old Finns in 1979–1997 were linked with national death registry up to 2001. The number of respondents was 62 528 (79.6%) and non-respondents 16 081 (20.4%). The average follow-up was 11.1 years, totalling 876 400 person-years. The risk of death between non-respondents and respondents was estimated by hazard ratios (HR).</p> <p>Results</p> <p>The number of deaths per 100 000 person-years were 229 in non-respondents and 447 in respondents (HR 2.0, 95% CI: 1.5–2.6). The hazard ratios of death were for intoxication 3.2 (95% CI: 1.9–5.4), for disease 3.1 (95% CI: 2.2–4.1), for violence-related injury 2.0 (95% CI: 1.5–2.6) and for unintentional injury 1.8 (95% CI: 1.3–2.4) in non-respondents vs. respondents. The association between non-response and death increased with age at baseline, and the increase persisted after the age of 25.</p> <p>Conclusion</p> <p>Our study demonstrated significantly increased rates of death among adolescent non-respondents in a follow-up. The highest hazard ratios were seen in disease- and violence-related deaths. The death rate varied between respondents and non-respondents by death type. Increased rates of death persisted beyond the age of 25.</p

The impact of SARS on hospital performance

© 2008 Chu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

A genetic approach for building different alphabets for peptide and protein classification

<p>Abstract</p> <p>Background</p> <p>In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using features extracted by different reduced alphabets. Each alphabet is constructed by a Genetic Algorithm whose objective function is the maximization of the area under the ROC-curve obtained in several classification problems.</p> <p>Results</p> <p>The new approach has been tested in three peptide classification problems: HIV-protease, recognition of T-cell epitopes and prediction of peptides that bind human leukocyte antigens. The tests demonstrate that the idea of training a pool classifiers by reduced alphabets, created using a Genetic Algorithm, allows an improvement over other state-of-the-art feature extraction methods.</p> <p>Conclusion</p> <p>The validity of the novel strategy for creating reduced alphabets is demonstrated by the performance improvement obtained by the proposed approach with respect to other reduced alphabets-based methods in the tested problems.</p

Calpain 3 Is a Rapid-Action, Unidirectional Proteolytic Switch Central to Muscle Remodeling

Calpain 3 (CAPN3) is a cysteine protease that when mutated causes Limb Girdle Muscular Dystrophy 2A. It is thereby the only described Calpain family member that genetically causes a disease. Due to its inherent instability little is known of its substrates or its mechanism of activity and pathogenicity. In this investigation we define a primary sequence motif underlying CAPN3 substrate cleavage. This motif can transform non-related proteins into substrates, and identifies >300 new putative CAPN3 targets. Bioinformatic analyses of these targets demonstrate a critical role in muscle cytoskeletal remodeling and identify novel CAPN3 functions. Among the new CAPN3 substrates are three E3 SUMO ligases of the Protein Inhibitor of Activated Stats (PIAS) family. CAPN3 can cleave PIAS proteins and negatively regulates PIAS3 sumoylase activity. Consequently, SUMO2 is deregulated in patient muscle tissue. Our study thus uncovers unexpected crosstalk between CAPN3 proteolysis and protein sumoylation, with strong implications for muscle remodeling