A unifying approach for haplotype analysis of quantitative traits in family-based association studies: Testing and estimating gene-environment interactions with complex exposure variables

We propose robust and e±cient tests and estimators for gene-environment/gene-drug interactions in family-based association studies. The methodology is designed for studies in which haplotypes, quantitative pheno- types and complex exposure/treatment variables are analyzed. Using causal inference methodology, we derive family-based association tests and estimators for the genetic main effects and the interactions. The tests and estimators are robust against population admixture and strati¯cation without requiring adjustment for confounding variables. We illustrate the practical relevance of our approach by an application to a COPD study. The data analysis suggests a gene-environment interaction between a SNP in the Serpine gene and smok- ing status/pack years of smoking that reduces the FEV1 volume by about 0.02 liter per pack year of smoking. Simulation studies show that the pro- posed methodology is su±ciently powered for realistic sample sizes and that it provides valid tests and effect size estimators in the presence of admixture and stratification.

Parent – environmental interactions shape acoustic signatures in tree swallows: a cross-fostering experiment.

Acoustic signatures are common components of avian vocalizations and are important for the recognition of individuals and groups. The proximate mechanisms by which these signatures develop are poorly understood, however. The development of acoustic signatures in nestling birds is of particular interest, because high rates of extra-pair paternity or egg dumping can cause nestlings to be unrelated to at least one of the adults that are caring for them. In such cases, nestlings might conceal their genetic origins, by developing acoustic signatures through environmental rather than genetic mechanisms. In a cross-fostering experiment with tree swallows Tachycineta bicolor, we investigated whether brood signatures of nestlings that were about to fledge were attributable to their genetic/maternal origins or to their rearing environment. We found that the calls of cross-fostered nestlings did not vary based on their genetic/maternal origin, but did show some variation based on their rearing environment. Control nestlings that were not swapped, however, showed stronger brood signatures than either experimental group, suggesting that acoustic signatures develop through an interaction between rearing environment and genetic/maternal effects.

MS 066 Guide to the Howard B. Hamilton, MD, papers; 1945-1997

The Howard B. Hamilton, MD, papers, MS 66, includes material from 1945-1997 related to the Atomic Bomb Casualty Commission (ABCC) and the Radiation Effects Research Foundation (RERF). Hamilton was the Chief of Clinical Laboratories for the Atomic Bomb Casualty Commission from 1956 until its dissolution in 1975. He served in the same capacity for the Radiation Effects Research Foundation, which succeeded the ABCC, until 1984. This collection encompasses this period of time in Dr. Hamilton's career, as well as his related scholarly work after his retirement from RERF. Dr. Hamilton donated his collection of letters, reprints, newspaper articles, photographs, memos, and ephemera to the John P. McGovern Historical Collections and Research Center between 1985 and 2002. The collection is in good condition and consists of 3.75 cubic feet (10 boxes).

Seawater carbonate chemistry and length, weight, survival rate, metabolic rate of coral reef fish Amphiprion melanopus in a laboratory experiment

Carbon dioxide concentrations in the surface ocean are increasing owing to rising CO2 concentrations in the atmosphere. Higher CO2 levels are predicted to affect essential physiological processes of many aquatic organisms, leading to widespread impacts on marine diversity and ecosystem function, especially when combined with the effects of global warming. Yet the ability for marine species to adjust to increasing CO2 levels over many generations is an unresolved issue. Here we show that ocean conditions projected for the end of the century (approximately 1,000 µatm CO2 and a temperature rise of 1.5-3.0 °C) cause an increase in metabolic rate and decreases in length, weight, condition and survival of juvenile fish. However, these effects are absent or reversed when parents also experience high CO2 concentrations. Our results show that non-genetic parental effects can dramatically alter the response of marine organisms to increasing CO2 and demonstrate that some species have more capacity to acclimate to ocean acidification than previously thought.

Self-reference Scrubber for TMR Systems Based on Xilinx Virtex FPGAs

SRAM-based FPGAs are sensitive to radiation effects. Soft errors can appear and accumulate, potentially defeating mitigation strategies deployed at the Application Layer. Therefore, Configuration Memory scrubbing is required to improve radiation tolerance of such FPGAs in space applications. Virtex FPGAs allow runtime scrubbing by means of dynamic partial reconfiguration. Even with scrubbing, intra-FPGA TMR systems are subjected to common-mode errors affecting more than one design domain. This is solved in inter-FPGA TMR systems at the expense of a higher cost, power and mass. In this context, a self-reference scrubber for device-level TMR system based on Xilinx Virtex FPGAs is presented. This scrubber allows for a fast SEU/MBU detection and correction by peer frame comparison without needing to access a golden configuration memory

Crack mechanical failure in lithium niobate crystal under ion irradiation; novel simulation by extended finite elements

Swift heavy ion irradiation (ions with mass heavier than 15 and energy exceeding MeV/amu) transfer their energy mainly to the electronic system with small momentum transfer per collision. Therefore, they produce linear regions (columnar nano-tracks) around the straight ion trajectory, with marked modifications with respect to the virgin material, e.g., phase transition, amorphization, compaction, changes in physical or chemical properties. In the case of crystalline materials the most distinctive feature of swift heavy ion irradiation is the production of amorphous tracks embedded in the crystal. Lithium niobate is a relevant optical material that presents birefringence due to its anysotropic trigonal structure. The amorphous phase is certainly isotropic. In addition, its refractive index exhibits high contrast with those of the crystalline phase. This allows one to fabricate waveguides by swift ion irradiation with important technological relevance. From the mechanical point of view, the inclusion of an amorphous nano-track (with a density 15% lower than that of the crystal) leads to the generation of important stress/strain fields around the track. Eventually these fields are the origin of crack formation with fatal consequences for the integrity of the samples and the viability of the method for nano-track formation. For certain crystal cuts (X and Y), these fields are clearly anisotropic due to the crystal anisotropy. We have used finite element methods to calculate the stress/strain fields that appear around the ion-generated amorphous nano-tracks for a variety of ion energies and doses. A very remarkable feature for X cut-samples is that the maximum shear stress appears on preferential planes that form +/-45º with respect to the crystallographic planes. This leads to the generation of oriented surface cracks when the dose increases. The growth of the cracks along the anisotropic crystal has been studied by means of novel extended finite element methods, which include cracks as discontinuities. In this way we can study how the length and depth of a crack evolves as function of the ion dose. In this work we will show how the simulations compare with experiments and their application in materials modification by ion irradiation.

MMonCa: A flexible and powerful new Kinetic Monte Carlo simulator

Kinetic Monte Carlo (KMC) is a widely used technique to simulate the evolution of radiation damage inside solids. Despite de fact that this technique was developed several decades ago, there is not an established and easy to access simulating tool for researchers interested in this field, unlike in the case of molecular dynamics or density functional theory calculations. In fact, scientists must develop their own tools or use unmaintained ones in order to perform these types of simulations. To fulfil this need, we have developed MMonCa, the Modular Monte Carlo simulator. MMonCa has been developed using professional C++ programming techniques and has been built on top of an interpreted language to allow having a powerful yet flexible, robust but customizable and easy to access modern simulator. Both non lattice and Lattice KMC modules have been developed. We will present in this conference, for the first time, the MMonCa simulator. Along with other (more detailed) contributions in this meeting, the versatility of MMonCa to study a number of problems in different materials (particularly, Fe and W) subject to a wide range of conditions will be shown. Regarding KMC simulations, we have studied neutron-generated cascade evolution in Fe (as a model material). Starting with a Frenkel pair distribution we have followed the defect evolution up to 450 K. Comparison with previous simulations and experiments shows excellent agreement. Furthermore, we have studied a more complex system (He-irradiated W:C) using a previous parametrization [1]. He-irradiation at 4 K followed by isochronal annealing steps up to 500 K has been simulated with MMonCa. The He energy was 400 eV or 3 keV. In the first case, no damage is associated to the He implantation, whereas in the second one, a significant Frenkel pair concentration (evolving into complex clusters) is associated to the He ions. We have been able to explain He desorption both in the absence and in the presence of Frenkel pairs and we have also applied MMonCa to high He doses and fluxes at elevated temperatures. He migration and trapping dominate the kinetics of He desorption. These processes will be discussed and compared to experimental results. [1] C.S. Becquart et al. J. Nucl. Mater. 403 (2010) 75

Effect of ion flux on helium retention in helium-irradiated tungsten

Helium retention in irradiated tungsten leads to swelling, pore formation, sample exfoliation and embrittlement with deleterious consequences in many applications. In particular, the use of tungsten in future nuclear fusion plants is proposed due to its good refractory properties. However, serious concerns about tungsten survivability stems from the fact that it must withstand severe irradiation conditions. In magnetic fusion as well as in inertial fusion (particularly with direct drive targets), tungsten components will be exposed to low and high energy ion (helium) irradiation, respectively. A common feature is that the most detrimental situations will take place in pulsed mode, i.e., high flux irradiation. There is increasing evidence on a correlation between a high helium flux and an enhancement of detrimental effects on tungsten. Nevertheless, the nature of these effects is not well understood due to the subtleties imposed by the exact temperature profile evolution, ion energy, pulse duration, existence of impurities and simultaneous irradiation with other species. Physically based Kinetic Monte Carlo is the technique of choice to simulate the evolution of radiation-induced damage inside solids in large temporal and space scales. We have used the recently developed code MMonCa (Modular Monte Carlo simulator), presented in this conference for the first time, to study He retention (and in general defect evolution) in tungsten samples irradiated with high intensity helium pulses. The code simulates the interactions among a large variety of defects and impurities (He and C) during the irradiation stage and the subsequent annealing steps. In addition, it allows us to vary the sample temperature to follow the severe thermo-mechanical effects of the pulses. In this work we will describe the helium kinetics for different irradiation conditions. A competition is established between fast helium cluster migration and trapping at large defects, being the temperature a determinant factor. In fact, high temperatures (induced by the pulses) are responsible for large vacancy cluster formation and subsequent additional trapping with respect to low flux irradiation.

Electrodynamic tether at Jupiter 2. Tour missions after capture

Three separate scenarios of an electrodynamic tether mission at Jupiter following capture of a spacecraft (SC) into an equatorial, highly elliptical orbit around the planet, with perijove at about 1.5 times the Jovian radius, are discussed. Repeated application of Lorentz drag on the spinning tether, at the perijove vicinity, can progressively lower the apojove. One mission involves the tethered-SC rapidly and frequently visiting Galilean moons; elliptical orbits with apojove down at the Ganymede, Europa, and Io orbits are in 2:5, 4:9, and 1:2 resonances with the respective moons. About 20 slow flybys of Io would take place before the accumulated radiation dose exceeds 3 Mrad (Si) at 10 mm Al shield thickness, with a total duration of 5 months after capture (4 months for lowering the apojove to Io and one month for the flybys). The respective number of flybys for Ganymede would be 10 with a total duration of about 9 months. An alternative mission would have the SC acquire a low circular orbit around Jupiter, below the radiation belts, and manoeuvre to get an optimal altitude, with no major radiation effects, in less than 5 months after capture. In a third mission, repeated thrusting at the apojove vicinity, once down at the Io torus, would raise the perijove itself to the torus to acquire a low circular orbit around Io in about 4 months, for a total of 8 months after capture; this corresponds, however, to over 100 apojove passes with an accumulated dose, of about 8.5 Mrad (Si), that poses a critical issue.

Design techniques for xilinx virtex FPGA configuration memory scrubbers

SRAM-based FPGAs are in-field reconfigurable an unlimited number of times. This characteristic, together with their high performance and high logic density, proves to be very convenient for a number of ground and space level applications. One drawback of this technology is that it is susceptible to ionizing radiation, and this sensitivity increases with technology scaling. This is a first order concern for applications in harsh radiation environments, and starts to be a concern for high reliability ground applications. Several techniques exist for coping with radiation effects at user application. In order to be effective they need to be complemented with configuration memory scrubbing, which allows error mitigation and prevents failures due to error accumulation. Depending on the radiation environment and on the system dependability requirements, the configuration scrubber design can become more or less complex. This paper classifies and presents current and novel design methodologies and architectures for SRAM-based FPGAs, and in particular for Xilinx Virtex-4QV/5QV, configuration memory scrubbers.

Deriva genética de caracteres quantitativos em milho

A obtenção de genótipos superiores no melhoramento de plantas depende da existência de variabilidade genética. A existência de coleções de germoplasma representativas e a utilização de um tamanho adequado de amostra são fundamentais para a preservação das frequências alélicas e genotípicas, diminuindo a perda de variabilidade genética e postergando o aparecimento dos efeitos da deriva genética. Assim, teve-se como objetivo avaliar os efeitos da deriva genética em caracteres quantitativos em subpopulações de milho. Este estudo foi realizado a partir das populações originais BR-105 e BR-106, das quais 10 subpopulações foram obtidas em cada um dos cinco ciclos sucessivos de amostragem com tamanho efetivo reduzido, totalizando 50 subpopulações para cada população original, as quais foram posteriormente autofecundadas, gerando um nível a mais de endogamia. Os tratamentos foram constituídos de 10 amostras da população original sem autofecundação, 10 amostras com autofecundação, 50 subpopulações obtidas da população original e 50 subpopulações autofecundadas, totalizando 120 tratamentos para cada população, avaliados separadamente. Utilizou-se o delineamento em blocos casualizados no esquema de parcelas subdivididas em faixas hierárquico, em quatro ambientes com duas repetições por ambiente. Os caracteres avaliados foram produção de grãos (PG), prolificidade (PROL), comprimento e diâmetro de espigas (CE e DE), número de fileiras por espiga (NFE), número de grãos por fileira (NGF), altura de planta e espiga (AP e AE), florescimento masculino e feminino (FM e FF) e número de ramificações do pendão (NRP). Foram estimados os efeitos da deriva genética entre as médias das subpopulações nos dois níveis de endogamia e os efeitos da depressão por endogamia nas subpopulações dentro dos ciclos. Posteriormente, realizaram-se análises de regressão linear para as subpopulações nos dois níveis de endogamia, separadamente, e em conjunto. Foi verificada uma grande variação nas médias das subpopulações ao longo dos ciclos, indicando que a deriva genética causou diferenciação entre as mesmas e que estas se diferenciaram das populações originais. Detectaram-se efeitos significativos da deriva genética nas populações não autofecundadas para todos os caracteres avaliados, em maior número para PG, já que este caráter é mais sensível à deriva genética por possuir maior grau de dominância que os demais. Houve diminuição no número de estimativas de deriva significativas para as populações autofecundadas, incluindo mudanças na magnitude e no sinal das mesmas em relação às populações não autofecundadas. Para as estimativas de depressão por endogamia, os caracteres PG, NGF, FM e FF apresentaram maior quantidade de estimativas significativas que os demais. Para a maioria dos caracteres, a regressão linear explicou a maior parte da variação encontrada com o aumento dos coeficientes de endogamia. As populações BR-105 e BR-106, por terem estruturas genéticas distintas, apresentaram performances diferentes quanto aos efeitos da deriva genética. Enfim, como a deriva genética interfere na integridade genética das populações, torna-se importante considerar seus efeitos na coleta e manutenção dos bancos de germoplasma e nas populações utilizadas no melhoramento genético de plantas.

A Hardware-Software Approach for On-Line Soft Error Mitigation in Interrupt-Driven Applications

Integrity assurance of configuration data has a significant impact on microcontroller-based systems reliability. This is especially true when running applications driven by events which behavior is tightly coupled to this kind of data. This work proposes a new hybrid technique that combines hardware and software resources for detecting and recovering soft-errors in system configuration data. Our approach is based on the utilization of a common built-in microcontroller resource (timer) that works jointly with a software-based technique, which is responsible to periodically refresh the configuration data. The experiments demonstrate that non-destructive single event effects can be effectively mitigated with reduced overheads. Results show an important increase in fault coverage for SEUs and SETs, about one order of magnitude.

Annual report of the Division of Life Sciences /

Mode of access: Internet.