Turning down the lamp: Software specialisation for the cloud

© USENIX Workshop on Hot Topics in Cloud Computing, HotCloud 2010.All right reserved. The wide availability of cloud computing offers an unprecedented opportunity to rethink how we construct applications. The cloud is currently mostly used to package up existing software stacks and operating systems (e.g. LAMP) for scaling out websites. We instead view the cloud as a stable hardware platform, and present a programming framework which permits applications to be constructed to run directly on top of it without intervening software layers. Our prototype (dubbed Mirage) is unashamedly academic; it extends the Objective Caml language with storage extensions and a custom run-time to emit binaries that execute as a guest operating system under Xen. Mirage applications exhibit significant performance speedups for I/O and memory handling versus the same code running under Linux/Xen. Our results can be generalised to offer insight into improving more commonly used languages such as PHP, Python and Ruby, and we discuss lessons learnt and future directions

The DNA damage checkpoint pathway promotes extensive resection and nucleotide synthesis to facilitate homologous recombination repair and genome stability in fission yeast.

DNA double-strand breaks (DSBs) can cause chromosomal rearrangements and extensive loss of heterozygosity (LOH), hallmarks of cancer cells. Yet, how such events are normally suppressed is unclear. Here we identify roles for the DNA damage checkpoint pathway in facilitating homologous recombination (HR) repair and suppressing extensive LOH and chromosomal rearrangements in response to a DSB. Accordingly, deletion of Rad3(ATR), Rad26ATRIP, Crb2(53BP1) or Cdc25 overexpression leads to reduced HR and increased break-induced chromosome loss and rearrangements. We find the DNA damage checkpoint pathway facilitates HR, in part, by promoting break-induced Cdt2-dependent nucleotide synthesis. We also identify additional roles for Rad17, the 9-1-1 complex and Chk1 activation in facilitating break-induced extensive resection and chromosome loss, thereby suppressing extensive LOH. Loss of Rad17 or the 9-1-1 complex results in a striking increase in break-induced isochromosome formation and very low levels of chromosome loss, suggesting the 9-1-1 complex acts as a nuclease processivity factor to facilitate extensive resection. Further, our data suggest redundant roles for Rad3ATR and Exo1 in facilitating extensive resection. We propose that the DNA damage checkpoint pathway coordinates resection and nucleotide synthesis, thereby promoting efficient HR repair and genome stability

Lattice Model of Sweeping Interface for Drying Process in Water-Granule Mixture

Based on the invasion percolation model, a lattice model for the sweeping interface dynamics is constructed to describe the pattern forming process by a sweeping interface upon drying the water-granule mixture. The model is shown to produce labyrinthine patterns similar to those found in the experiment[Yamazaki and Mizuguchi, J. Phys. Soc. Jpn. \textbf{69} (2000) 2387]. Upon changing the initial granular density, resulting patterns undergo the percolation transition, but estimated critical exponents are different from those of the conventional percolation. Loopless structure of clusters in the patterns produced by the sweeping dynamics seems to influence the nature of the transition.Comment: 6 pages, 7 figure

Identifying runoff sources across scales in Amazon watersheds: an LBA synthesis effort.

Abstract ID: 54

Ground-state properties of rutile: electron-correlation effects

Electron-correlation effects on cohesive energy, lattice constant and bulk compressibility of rutile are calculated using an ab-initio scheme. A competition between the two groups of partially covalent Ti-O bonds is the reason that the correlation energy does not change linearly with deviations from the equilibrium geometry, but is dominated by quadratic terms instead. As a consequence, the Hartree-Fock lattice constants are close to the experimental ones, while the compressibility is strongly renormalized by electronic correlations.Comment: 1 figure to appear in Phys. Rev.

Social support for and through exercise and sport in a sample of men with serious mental illness.

Social support is important for people experiencing serious mental illness and is also important during the initiation and maintenance of exercise. In this article we draw on interpretive research into the experiences of 11 men with serious mental illness to explore four dimensions of social support both for and through exercise. Our findings suggest that informational, tangible, esteem, and emotional support were both provided for and given by participants through exercise. We conclude that experiences of both receiving and giving diverse forms of support in this way are significant for some people living with and recovering from serious mental illness

Sympathoinhibition and vasodilation contribute to the acute hypotensive response of the superoxide dismutase mimic, MnTnBuOE-2-PyP5+, in hypertensive animals

The pathogenesis of hypertension has been linked to excessive levels of reactive oxygen species (ROS), particularly superoxide (O2•−), in multiple tissues and organ systems. Overexpression of superoxide dismutase (SOD) to scavenge O2•− has been shown to decrease blood pressure in hypertensive animals. We have previously shown that MnTnBuOE-2-PyP5+ (BuOE), a manganese porphyrin SOD mimic currently in clinical trials as a normal tissue protector for cancer patients undergoing radiation therapy, can scavenge O2•− and acutely decrease normotensive blood pressures. Herein, we hypothesized that BuOE decreases hypertensive blood pressures. Using angiotensin II (AngII)-hypertensive mice, we demonstrate that BuOE administered both intraperitoneally and intravenously (IV) acutely decreases elevated blood pressure. Further investigation using renal sympathetic nerve recordings in spontaneously hypertensive rats (SHRs) reveals that immediately following IV injection of BuOE, blood pressure and renal sympathetic nerve activity (RSNA) decrease. BuOE also induces dose-dependent vasodilation of femoral arteries from AngII-hypertensive mice, a response that is mediated, at least in part, by nitric oxide, as demonstrated by ex vivo video myography. We confirmed this vasodilation in vivo using doppler imaging of the superior mesenteric artery in AngII-hypertensive mice. Together, these data demonstrate that BuOE acutely decreases RSNA and induces vasodilation, which likely contribute to its ability to rapidly decrease hypertensive blood pressure

Correlation effects in MgO and CaO: Cohesive energies and lattice constants

A recently proposed computational scheme based on local increments has been applied to the calculation of correlation contributions to the cohesive energy of the CaO crystal. Using ab-initio quantum chemical methods for evaluating individual increments, we obtain 80% of the difference between the experimental and Hartree-Fock cohesive energies. Lattice constants corrected for correlation effects deviate by less than 1% from experimental values, in the case of MgO and CaO.Comment: LaTeX, 4 figure

Self-assembly of Microcapsules via Colloidal Bond Hybridization and Anisotropy

Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures. Mutually attractive nanoparticles that are deformable due to flexible surface groups, for example, may spontaneously order themselves into strings, sheets and large vesicles. Furthermore, anisotropic colloids with attractive patches can self-assemble into open lattices and colloidal equivalents of molecules and micelles. However, model systems that combine mutual attraction, anisotropy, and deformability have---to the best of our knowledge---not been realized. Here, we synthesize colloidal particles that combine these three characteristics and obtain self-assembled microcapsules. We propose that mutual attraction and deformability induce directional interactions via colloidal bond hybridization. Our particles contain both mutually attractive and repulsive surface groups that are flexible. Analogous to the simplest chemical bond, where two isotropic orbitals hybridize into the molecular orbital of H2, these flexible groups redistribute upon binding. Via colloidal bond hybridization, isotropic spheres self-assemble into planar monolayers, while anisotropic snowman-like particles self-assemble into hollow monolayer microcapsules. A modest change of the building blocks thus results in a significant leap in the complexity of the self-assembled structures. In other words, these relatively simple building blocks self-assemble into dramatically more complex structures than similar particles that are isotropic or non-deformable

Generations of interdisciplinarity in bioinformatics

Bioinformatics, a specialism propelled into relevance by the Human Genome Project and the subsequent -omic turn in the life science, is an interdisciplinary field of research. Qualitative work on the disciplinary identities of bioinformaticians has revealed the tensions involved in work in this “borderland.” As part of our ongoing work on the emergence of bioinformatics, between 2010 and 2011, we conducted a survey of United Kingdom-based academic bioinformaticians. Building on insights drawn from our fieldwork over the past decade, we present results from this survey relevant to a discussion of disciplinary generation and stabilization. Not only is there evidence of an attitudinal divide between the different disciplinary cultures that make up bioinformatics, but there are distinctions between the forerunners, founders and the followers; as inter/disciplines mature, they face challenges that are both inter-disciplinary and inter-generational in nature