Computationally-Optimized Bone Mechanical Modeling from High-Resolution Structural Images

Image-based mechanical modeling of the complex micro-structure of human bone has shown promise as a non-invasive method for characterizing bone strength and fracture risk in vivo. In particular, elastic moduli obtained from image-derived micro-finite element (μFE) simulations have been shown to correlate well with results obtained by mechanical testing of cadaveric bone. However, most existing large-scale finite-element simulation programs require significant computing resources, which hamper their use in common laboratory and clinical environments. In this work, we theoretically derive and computationally evaluate the resources needed to perform such simulations (in terms of computer memory and computation time), which are dependent on the number of finite elements in the image-derived bone model. A detailed description of our approach is provided, which is specifically optimized for μFE modeling of the complex three-dimensional architecture of trabecular bone. Our implementation includes domain decomposition for parallel computing, a novel stopping criterion, and a system for speeding up convergence by pre-iterating on coarser grids. The performance of the system is demonstrated on a dual quad-core Xeon 3.16 GHz CPUs equipped with 40 GB of RAM. Models of distal tibia derived from 3D in-vivo MR images in a patient comprising 200,000 elements required less than 30 seconds to converge (and 40 MB RAM). To illustrate the system's potential for large-scale μFE simulations, axial stiffness was estimated from high-resolution micro-CT images of a voxel array of 90 million elements comprising the human proximal femur in seven hours CPU time. In conclusion, the system described should enable image-based finite-element bone simulations in practical computation times on high-end desktop computers with applications to laboratory studies and clinical imaging

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

SMARTfarm learning hub: Next generation precision agriculture technologies for agricultural education

The industry demands on higher education agricultural students are rapidly changing. New precision agriculture technologies are revolutionizing the farming industry but the education sector is failing to keep pace. This paper reports on the development of a key resource, the SMARTfarm Learning Hub (www.smartfarmhub.com) that will increase the skill base of higher education students using a range of new agricultural technologies and innovations. The Hub is a world first; it links real industry technologies with educator resources and student learning packages. This gives higher education providers and their student’s online access to data and systems from commercial scale smart-farms across Australia and the world. The SMARTfarm Learning Hub is based around a central landing page which provides links to cloud based technologies that are running over various university properties predominantly across Australia and the globe. Participating universities have farms with a diverse range of enterprises and environmental conditions from highly productive dairy systems in Tasmania to tropical production in North Queensland and the arid rangelands of New Mexico. This is real data from real agricultural landscapes, and is matched with learning materials developed to challenge student’s critical thinking and problem solving skills. Utilization of the SMARTfarm Learning Hub is tracked using the Square Space metrics tools. The SMARTfarm Learning Hub website was launched in mid-December 2015 and since this time has reached 535 unique visitors an average of 107 per month

Conservação de sementes de ipê Conservation of "ipê" seeds

Sementes de algumas espécies de ipê foram submetidas a diferentes temperaturas de armazenamento, determinando-se a sua porcentagem de germinação a cada quarenta dias, por um período de trinta meses. Nas condições fornecidas de 10 ºC, 29 ºC e 30 ºC em embalagem hermeticamente fechada, e em saco de papel, a condições ambienteis foram avaliadas as seguintes espécies: Tabebuia avellanedae var. paulensis Tol., Tabebuia chrysotricha (Mart. ex-DC.) Standley, Tabebuia impetiginosa (Mart.) Standley, Tabebuia rosea (Bertol.) DC. e Tabebuia heptaphylla (Vell.) Tol. Dentre as condições de armazenamento, o tratamento a 10ºC em vidro hermético foi o que manteve a viabilidade da semente por maior tempo, sendo 20 &deg;C também em vidro hermético o segundo melhor resultado. A germinação das sementes armazenadas em saco de papel a temperatura ambiente foi melhor do que a das que foram armazenadas em vidro hermético a 30 &deg;C, sendo esta a pior condição de armazenagem. A comparação entre as espécies mostrou que Tabebuia heptaphylla, apresenta, além de sementes de maior longevidade, maior resistência às condições adversas de armazenamento.<br>Seeds of some species of "ipê" were stored at different temperatures and the germination percentage was determined at forty-day intervals during thirty months. Seeds were subjected to the following conditions: storage in sealed flasks at 10ºC, 20ºC and 30ºC, and in paper bags at room temperature. The following species were evaluated: Tabebuia avellanedae var. paulensis Tol., Tabebuia chrysotricha (Mart. ex DC.) Standley, Tabebuia impetiginosa (Mart.) Standley, Tabebuia rosea (Bertol.) DC. e Tabebuia heptaphylla (Vell.) Tol. Among the treatments studied, storing seeds in sealed flasks at 10&deg;C maintained seed viability for the longest period of time. The second best result was obtained when seeds were kept in sealed flasks at 20ºC. The germination of seeds stored in paper bags at room temperature was higher than that of seeds kept in sealed flasks at 30ºC which was the least favorable condition for seed storage. Among the species compared Tabebuia heptaphylla showed the highest longevity but also resisted better the adverse storage conditions