Scalable ray tracing with multiple GPGPUs

Rapid development in the field of computer graphics over the last 40 years has brought forth different techniques to render scenes. Rasterization is today’s most widely used technique, which in its most basic form sequentially draws thousands of polygons and applies texture on them. Ray tracing is an alternative method that mimics light transport by using rays to sample a scene in memory and render the color found at each ray’s scene intersection point. Although mainstream hardware directly supports rasterization, ray tracing would be the preferred technique due to its ability to produce highly crisp and realistic graphics, if hardware were not a limitation. Making an immediate hardware transition from rasterization to ray tracing would have a severe impact on the computer graphics industry since it would require redevelopment of existing 3D graphics-employing software, so any transition to ray tracing would be gradual. Previous efforts to perform ray tracing on mainstream rasterizing hardware platforms with a single processor have performed poorly. This thesis explores how a multiple GPGPU system can be used to render scenes via ray tracing. A ray tracing engine and API groundwork was developed using NVIDIA’s CUDA (Compute Unified Device Architecture) GPGPU programming environment and was used to evaluate performance scalability across a multi-GPGPU system. This engine supports triangle, sphere, disc, rectangle, and torus rendering. It also allows independent activation of graphics features including procedural texturing, Phong illumination, reflections, translucency, and shadows. Correctness of rendered images validates the ray traced results, and timing of rendered scenes benchmarks performance. The main test scene contains all object types, has a total of 32 Abstract objects, and applies all graphics features. Ray tracing this scene using two GPGPUs outperformed the single-GPGPU and single-CPU systems, yielding respective speedups of up to 1.8 and 31.25. The results demonstrate how much potential exists in treating a modern dual-GPU architecture as a dual-GPGPU system in order to facilitate a transition from rasterization to ray tracing

Biogeographical Patterns of Herbivore Arthropods Associated with <i>Chenopodium quinoa</i> Grown along the Latitudinal Gradient of Chile

Identifying the particular guilds of herbivore arthropods that affect the production of crops is key to developing sustainable pest-management strategies; however, there is incomplete information about the identity of herbivore arthropods that could potentially damage the production of both highland and lowland quinoa landraces grown in Chile. By both reviewing the literature and conducting field collections across a large latitudinal gradient, we generated an updated list of 43 herbivore arthropods associated with quinoa production in Chile. In general, most species are polyphagous feeders, and only seven are specialists. The number and identity of species varied in relation with the latitude, such that four distinctive assemblages of herbivores were identified, each containing 32, 27, 34, and 22 species between latitudes 18–26, 26–32, 32–40, and 40–44° S, respectively. The most northern production area (18–26° S) is affected by nine unique species, including the major quinoa pest Eurysacca quinoae Povolný (Lepidoptera: Gelechiidae). Similarly, the central area (32–40° S) contains four unique species, including Eurysacca media Povolný (Lepidoptera: Gelechiidae) and Orthotylus flavosparsus (Sahlberg) (Hemiptera: Miridae). The particular species assemblages described here will help further development of local pest-management practices

Occurrence of the on-native annual Bluegrass on the Antarctic mainland and its negative effects on native plants

Few non-native species have colonized Antarctica, although increased human activity and accelerated climate change may increase their number, distributional range, and effects on native species on the continent. We searched 13 sites on the maritime Antarctic islands and 12 sites on the Antarctic Peninsula for annual bluegrass (Poa annua), a non-native flowering plant. We also evaluated the possible effects of competition between P. annua and 2 vascular plants native to Antarctica, Antarctic pearlwort (Colobanthus quitensis) and Antarctic hairgrass (Deschampsia antarctica). We grew the native species in experimental plots with and without annual bluegrass under conditions that mimicked the Antarctic environment. After 5 months, we measured photosynthetic performance on the basis of chlorophyll fluorescence and determined total biomass of both native species. We found individual specimens of annual bluegrass at 3 different sites on the Antarctic Peninsula during the 2007–2008 and 2009–2010 austral summers. The presence of bluegrass was associated with a statistically significant reduction in biomass of pearlwort and hairgrass, whereas the decrease in biomass of bluegrass was not statistically significant. Similarly, the presence of bluegrass significantly reduced the photosynthetic performance of the 2 native species. Sites where bluegrass occurred were close to major maritime routes of scientific expeditions and of tourist cruises to Antarctica. We believe that if current levels of human activity and regional warming persist, more non-native plant species are likely to colonize the Antarctic and may affect native species

Trends in Antarctic ecological research in Latin America shown by publications in international journals

Antarctica is a highly interesting region for ecologists because of its extreme climatic conditions and the uniqueness of its species. In this article, we describe the trends in Antarctic ecological research participation by Latin American countries. In a survey of articles indexed by the ISI Web of Science, we searched under the categories ‘‘Ecology,’’ ‘‘Biodiversity Conservation’’ and ‘‘Evolutionary Biology’’ and found a total of 254 research articles published by Latin American countries. We classified these articles according to the country of affiliation, kingdom of the study species, level of biological organization and environment. Our main finding is that there is a steady increase in the relative contribution of Latin American countries to Antarctic ecological research. Within each category, we found that marine studies are more common than terrestrial studies. Between the different kingdoms, most studies focus on animals and most studies use a community approach. The leading countries in terms of productivity were Argentina, Chile and Brazil, with Argentina showing the highest rate of increase.Keywords: Antarctica; Argentina; Brazil; Chile; research trends; scientific productivity(Published: 17 September 2013)Citation: Polar Research 2013, 32, 19993, http://dx.doi.org/10.3402/polar.v32i0.1999

A New Quinone-Based Inhibitor of Mitochondrial Complex I in D-Conformation, Producing Invasion Reduction and Sensitization to Venetoclax in Breast Cancer Cells

Mitochondrial Complex I plays a crucial role in the proliferation, chemoresistance, and metastasis of breast cancer (BC) cells. This highlights it as an attractive target for anti-cancer drugs. Using submitochondrial particles, we identified FRV–1, an ortho-carbonyl quinone, which inhibits NADH:duroquinone activity in D-active conformation and reduces the 3ADP state respiration dependent on Complex I, causing mitochondrial depolarization, ATP drop, increased superoxide levels, and metabolic remodeling towards glycolysis in BC cells. Introducing methyl groups at FRV–1 structure produced analogs that acted as electron acceptors at the Complex I level or increased the inhibitory effect of FCCP-stimulated oxygen consumption rate, which correlated with their redox potential, but increased toxicity on RMF-621 human breast fibroblasts was observed. FRV–1 was inactive in the naphthoquinone oxidoreductase 1 (NOQ1)-positive BC cell line, MCF7, but the sensitivity was recovered by dicoumarol, a NOQ1 inhibitor, suggesting that FRV–1 is a NOQ1 substrate. Importantly, FRV–1 selectively inhibited the proliferation, migration, and invasion of NQO1 negative BC cell, MDA-MB-231, in an OXPHOS- and ROS-dependent manner and sensitized it to the BH3 mimetic drug venetoclax. Overall, FRV–1 is a novel Complex I inhibitor in D-active conformation, blocking possibly the re-activation to A-state, producing selective anti-cancer effects in NQO1-negative BC cell lines

FR58P1a; a new uncoupler of OXPHOS that inhibits migration in triple-negative breast cancer cells via Sirt1/AMPK/β1-integrin pathway

© 2018, The Author(s).Highly malignant triple-negative breast cancer (TNBC) cells rely mostly on glycolysis to maintain cellular homeostasis; however, mitochondria are still required for migration and metastasis. Taking advantage of the metabolic flexibility of TNBC MDA-MB-231 cells to generate subpopulations with glycolytic or oxidative phenotypes, we screened phenolic compounds containing an ortho-carbonyl group with mitochondrial activity and identified a bromoalkyl-ester of hydroquinone named FR58P1a, as a mitochondrial metabolism-affecting compound that uncouples OXPHOS through a protonophoric mechanism. In contrast to well-known protonophore uncoupler FCCP, FR58P1a does not depolarize the plasma membrane and its effect on the mitochondrial membrane potential and bioenergetics is moderate suggesting a mild uncoupling of OXPHOS. FR58P1a activates AMPK in a Sirt1-dependent fashion. Although the activation of Sirt1/AMPK axis by FR58P1a has a cyto-protective role, selectively inhibit

Genome Sequencing Variations in the Octodon degus, an Unconventional Natural Model of Aging and Alzheimer's Disease.

The degu (Octodon degus) is a diurnal long-lived rodent that can spontaneously develop molecular and behavioral changes that mirror those seen in human aging. With age some degu, but not all individuals, develop cognitive decline and brain pathology like that observed in Alzheimer's disease including neuroinflammation, hyperphosphorylated tau and amyloid plaques, together with other co-morbidities associated with aging such as macular degeneration, cataracts, alterations in circadian rhythm, diabetes and atherosclerosis. Here we report the whole-genome sequencing and analysis of the degu genome, which revealed unique features and molecular adaptations consistent with aging and Alzheimer's disease. We identified single nucleotide polymorphisms in genes associated with Alzheimer's disease including a novel apolipoprotein E (Apoe) gene variant that correlated with an increase in amyloid plaques in brain and modified the in silico predicted degu APOE protein structure and functionality. The reported genome of an unconventional long-lived animal model of aging and Alzheimer's disease offers the opportunity for understanding molecular pathways involved in aging and should help advance biomedical research into treatments for Alzheimer's disease

Genome Sequencing Variations in the Octodon degus, an Unconventional Natural Model of Aging and Alzheimer's Disease

The degu (Octodon degus) is a diurnal long-lived rodent that can spontaneously develop molecular and behavioral changes that mirror those seen in human aging. With age some degu, but not all individuals, develop cognitive decline and brain pathology like that observed in Alzheimer's disease including neuroinflammation, hyperphosphorylated tau and amyloid plaques, together with other co-morbidities associated with aging such as macular degeneration, cataracts, alterations in circadian rhythm, diabetes and atherosclerosis. Here we report the whole-genome sequencing and analysis of the degu genome, which revealed unique features and molecular adaptations consistent with aging and Alzheimer's disease. We identified single nucleotide polymorphisms in genes associated with Alzheimer's disease including a novel apolipoprotein E (Apoe) gene variant that correlated with an increase in amyloid plaques in brain and modified the in silico predicted degu APOE protein structure and functionality. The reported genome of an unconventional long-lived animal model of aging and Alzheimer's disease offers the opportunity for understanding molecular pathways involved in aging and should help advance biomedical research into treatments for Alzheimer's disease

Mutation in protein disulfide isomerase A3 causes neurodevelopmental defects by disturbing endoplasmic reticulum proteostasis

Abstract Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system