Astronomy in the Cloud: Using MapReduce for Image Coaddition

In the coming decade, astronomical surveys of the sky will generate tens of terabytes of images and detect hundreds of millions of sources every night. The study of these sources will involve computation challenges such as anomaly detection and classification, and moving object tracking. Since such studies benefit from the highest quality data, methods such as image coaddition (stacking) will be a critical preprocessing step prior to scientific investigation. With a requirement that these images be analyzed on a nightly basis to identify moving sources or transient objects, these data streams present many computational challenges. Given the quantity of data involved, the computational load of these problems can only be addressed by distributing the workload over a large number of nodes. However, the high data throughput demanded by these applications may present scalability challenges for certain storage architectures. One scalable data-processing method that has emerged in recent years is MapReduce, and in this paper we focus on its popular open-source implementation called Hadoop. In the Hadoop framework, the data is partitioned among storage attached directly to worker nodes, and the processing workload is scheduled in parallel on the nodes that contain the required input data. A further motivation for using Hadoop is that it allows us to exploit cloud computing resources, e.g., Amazon's EC2. We report on our experience implementing a scalable image-processing pipeline for the SDSS imaging database using Hadoop. This multi-terabyte imaging dataset provides a good testbed for algorithm development since its scope and structure approximate future surveys. First, we describe MapReduce and how we adapted image coaddition to the MapReduce framework. Then we describe a number of optimizations to our basic approach and report experimental results comparing their performance.Comment: 31 pages, 11 figures, 2 table

Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci

A loss-of-function polymorphism in the human P2X4 receptor is associated with increased pulse pressure

The P2X4 receptor is involved in endothelium-dependent changes in large arterial tone in response to shear stress and is, therefore, potentially relevant to arterial compliance and pulse pressure. Four identified nonsynonymous polymorphisms in P2RX4 were reproduced in recombinantly expressed human P2X4. Electrophysiological studies showed that one of these, the Tyr315>Cys mutation (rs28360472), significantly reduced the peak amplitude of the ATP-induced inward current to 10.9% of wild-type P2X4 receptors in transfected HEK-293 cells (10 µmol/L of ATP; n=4-8 cells; P<0.001). Concentration-response curves for ATP and the partial agonist BzATP demonstrate that the 315Cys-P2X4 mutant had an increased EC50 value for both ligands. Mutation of Tyr315>Cys likely disrupts the agonist binding site of P2X4 receptors, a finding supported by molecular modeling based on the zebrafish P2X4 receptor crystal structure. We tested inheritance of rs28360472 encoding the Tyr315>Cys mutation in P2RX4 against pulse pressure in 2874 subjects from the Victorian Family Heart Study. The minor allele frequency was 0.014 (1.4%). In a variance components analysis we found significant association with pulse pressure (P=0.023 for total association) where 1 minor allele increased pulse pressure by 2.84 mm Hg (95% CI: 0.41-5.27). This increase in pulse pressure associated with inheritance of 315Cys-P2X4 receptors might reflect reduced large arterial compliance as a result of impaired endothelium-dependent vasodilation in large arteries

Transient x-ray diffraction used to diagnose shock compressed Si crystals on the Nova laser

Transient x-ray diffraction is used to record time-resolved information about the shock compression of materials. This technique has been applied on Nova shock experiments driven using a hohlraum x-ray drive. Data were recorded from the shock release at the free surface of a Si crystal, as well as from Si at an embedded ablator/Si interface. Modeling has been done to simulate the diffraction data incorporating the strained crystal rocking curves and Bragg diffraction efficiencies. Examples of the data and post-processed simulations are presented

Mirrorless all‐optical bistability in bacteriorhodopsin

We report direct observations of all‐optical mirrorless bistability associated with saturable absorption in three kinds of bacteriorhodopsin (BR) samples: wild‐type BR in water solution and dispersed in thin films of a polymer matrix as well as water solution of the genetically engineered mutant BRD96N. The experiments are carried out with picosecond pulses at 532 nm. The values measured for the saturation intensity are explained in terms of the relaxation of the excited M state population to the B state of the BR photocycle for the three kinds of samples studied

Synthesis and Characterization of [Fe(Htrz)\u3csub\u3e2\u3c/sub\u3e(trz)](BF\u3csub\u3e4\u3c/sub\u3e)] Nanocubes

Compounds that exhibit spin-crossover (SCO) type behavior have been extensively investigated due to their ability to act as molecular switches. Depending on the coordinating ligand, in this case 1H-1,2,4-triazole, and the crystallite size of the SCO compound produced, the energy requirement for the spin state transition can vary. Here, SCO [Fe(Htrz)2(trz)](BF4)] nanoparticles were synthesized using modified reverse micelle methods. Reaction conditions and reagent ratios are strictly controlled to produce nanocubes of 40–50 nm in size. Decreases in energy requirements are seen in both thermal and magnetic transitions for the smaller sized crystallites, where, compared to bulk materials, a decrease of as much as 20 °C can be seen in low to high spin state transitions

Epistasis with HLA DR3 implicates the P2X7 receptor in the pathogenesis of primary Sjögren's syndrome

Introduction: The aim of this study was to examine the association between functional polymorphisms in the proinflammatory P2X7 receptor and the Ro/La autoantibody response in primary Sjögren's syndrome (pSS). Methods: Twelve functional P2RX7 polymorphisms were genotyped in 114 pSS patients fulfilling the Revised American-European Consensus Criteria for pSS, and 136 controls. Genotyping of the A1405G (rs2230912) polymorphism was performed on a replication cohort consisting of 281 pSS patients and 534 controls. P2X7 receptor function in lymphocytes and monocytes was assessed by measurement of ATP-induced ethidium+ uptake. Serum IL-18 levels were determined by ELISA. Results: The minor allele of P2RX7 A1405G is a tag for a common haplotype associated with gain in receptor function, as assessed by ATP-induced ethidium+ uptake. A positive association between 1405G and anti-Ro±La seropositive pSS patients was observed in Cohort 1. Although not replicated in Cohort 2, there was a consistent, significant, negative epistatic interaction effect with HLA-DR3 in seropositive pSS patients from both cohorts, thereby implicating this gain of function variant in the pathogenesis of pSS. Serum IL-18 was elevated in seropositive pSS patients, but was not influenced by P2RX7 A1405G. Conclusions: The P2RX7 1405G gain-of-function haplotype may be a risk factor for seropositive pSS in a subset of subjects who do not carry HLA risk alleles, but has no effect in subjects who do (epistasis). Potential mechanisms relate to autoantigen exposure and inflammatory cytokine expression. The observed elevation of IL-18 levels is consistent with P2X7 receptor activation in seropositive pSS patients. Collectively these findings implicate P2X7 receptor function in the pathogenesis of pSS

The influence of a Juvenile\u27s Abuse History on Support for Sex Offender Registration

We investigated whether and how a juvenile’s history of experiencing sexual abuse affects public perceptions of juvenile sex offenders in a series of 5 studies. When asked about juvenile sex offenders in an abstract manner (Studies 1 and 2), the more participants (community members and undergraduates) believed that a history of being sexually abused as a child causes later sexually abusive behavior, the less likely they were to support sex offender registration for juveniles. Yet when participants considered specific sexual offenses, a juvenile’s history of sexual abuse was not considered to be a mitigating factor. This was true when participants considered a severe sexual offense (forced rape; Study 3 and Study 4) and a case involving less severe sexual offenses (i.e., statutory rape), when a juvenile’s history of sexual abuse backfired and was used as an aggravating factor, increasing support for registering the offender (Study 3 and Study 5). Theoretical and practical implications of these results are discussed

Communicating Phylogeny: Evolutionary Tree Diagrams in Museums

Tree of life diagrams are graphic representations of phylogeny—the evolutionary history and relationships of lineages—and as such these graphics have the potential to convey key evolutionary ideas and principles to a variety of audiences. Museums play a significant role in teaching about evolution to the public, and tree graphics form a common element in many exhibits even though little is known about their impact on visitor understanding. How phylogenies are depicted and used in informal science settings impacts their accessibility and effectiveness in communicating about evolution to visitors. In this paper, we summarize the analysis of 185 tree of life graphics collected from museum exhibits at 52 institutions and highlight some potential implications of how trees are presented that may support or hinder visitors’ understanding about evolution. While further work is needed, existing learning research suggests that common elements among the diversity of museum trees such as the inclusion of anagenesis and absence of time and shared characters might represent potential barriers to visitor understanding

Fabrication and magnetic properties of Fe nanostructures in anodic alumina membrane

Several Fe nanostructures with different lengths, diameters, and separations of the constituting magnetic components have been synthesized using anodized alumina membranes (AAMs) to understand the influence of these parameters on their magnetic properties. Fe nanostructures with high crystallinity and (110) orientation were synthesized by electrodeposition at room temperature in regular AAMs and mild-hard AAM (Mi-Ha AAM). Fe nanostructures with different aspect ratios (1:1, 1:10, and 1:75) in the form of nanodots, nanorods, or nanowires were synthesized in regular AAMs with the 100 nm interpore distance. Mi-Ha AAMs with two different pore sizes (70 and 120 nm) and 250 nm interpore distances were used to investigate the effect of the interactions and of the diameter of the wires on their magnetic behavior. Nearly linear magnetization characteristics with small coercivity, observed for Fe nanowires, suggest the magnetization rotation to be the predominant magnetization process for the field applied transverse to the wires. The anisotropy of the arrays was governed by the shape anisotropy of the magnetic objects with different aspect ratios. Reduced interactions between the nanowires grown in Mi-Ha AAMs resulted in enhancement of the average anisotropy. It is believed that due to difference in spin configuration, the increased diameter of the nanowires led to reduction in the coercivity in the case of the field applied along the wires