Wrapping Web Data Islands

Comisión Interministerial de Ciencia y Tecnología TIN2007-64119Junta de Andalucía P07-TIC-260

DALiuGE: A Graph Execution Framework for Harnessing the Astronomical Data Deluge

The Data Activated Liu Graph Engine - DALiuGE - is an execution framework for processing large astronomical datasets at a scale required by the Square Kilometre Array Phase 1 (SKA1). It includes an interface for expressing complex data reduction pipelines consisting of both data sets and algorithmic components and an implementation run-time to execute such pipelines on distributed resources. By mapping the logical view of a pipeline to its physical realisation, DALiuGE separates the concerns of multiple stakeholders, allowing them to collectively optimise large-scale data processing solutions in a coherent manner. The execution in DALiuGE is data-activated, where each individual data item autonomously triggers the processing on itself. Such decentralisation also makes the execution framework very scalable and flexible, supporting pipeline sizes ranging from less than ten tasks running on a laptop to tens of millions of concurrent tasks on the second fastest supercomputer in the world. DALiuGE has been used in production for reducing interferometry data sets from the Karl E. Jansky Very Large Array and the Mingantu Ultrawide Spectral Radioheliograph; and is being developed as the execution framework prototype for the Science Data Processor (SDP) consortium of the Square Kilometre Array (SKA) telescope. This paper presents a technical overview of DALiuGE and discusses case studies from the CHILES and MUSER projects that use DALiuGE to execute production pipelines. In a companion paper, we provide in-depth analysis of DALiuGE's scalability to very large numbers of tasks on two supercomputing facilities.Comment: 31 pages, 12 figures, currently under review by Astronomy and Computin

The Effect of Alien Predatory Ants (Hymenoptera: Formicidae) on Hawaiian Endemic Spiders (Araneae: Tetragnathidae)

The fauna of the Hawaiian Islands is characterized by spectacular species radiations with high levels of endemism, which is coupled with an extreme vulnerability to invasion by alien species. Of all alien invertebrate predators, ants are most notorious in their effect on native Hawaiian biota. This study examined distribution of ants in mesic and wet forests throughout the Hawaiian Islands and the extent to which they overlap the range of representatives of a lineage of endemic Hawaiian invertebrates, the genus Tetragnatha (Araneae: Tetragnathidae). Two species, Pheidole megacephala (F.) and Anoplolepis longipes (Jerdon), were implicated in the exclusion of native spiders from native and disturbed forest. One species, Solenopsis papuana Emery, showed extensive overlap in its range with that of the native spiders. However, we found a significant inverse relationship between the abundance of S. papuana in an area and the diversity of the indigenous Tetragnatha. Interactions between the spiders and the two species of ants, P. megacephala and A. longipes, were conducted in the laboratory and indicated that the spiders were very vulnerable to attack by these ants. Alien spiders appear to tolerate the presence of ants because they have either a strong exoskeleton, can appendotomize their legs, or else are capable of wrapping the ant in silk. Spiders that normally coexist with ants appear to use one or more of these methods for defense. The riparian existence of the genus Tetragnatha outside Hawaii may protect it from predation by ants. In Hawaii, where their habitat preference is no longer restricted to riparian sites, they may be extremely vulnerable to these alien predators

Software Challenges For HL-LHC Data Analysis

The high energy physics community is discussing where investment is needed to prepare software for the HL-LHC and its unprecedented challenges. The ROOT project is one of the central software players in high energy physics since decades. From its experience and expectations, the ROOT team has distilled a comprehensive set of areas that should see research and development in the context of data analysis software, for making best use of HL-LHC's physics potential. This work shows what these areas could be, why the ROOT team believes investing in them is needed, which gains are expected, and where related work is ongoing. It can serve as an indication for future research proposals and cooperations

Supergoop Dynamics

We initiate a systematic study of the dynamics of multi-particle systems with supersymmetric Van der Waals and electron-monopole type interactions. The static interaction allows a complex continuum of ground state configurations, while the Lorentz interaction tends to counteract this configurational fluidity by magnetic trapping, thus producing an exotic low temperature phase of matter aptly named supergoop. Such systems arise naturally in $\mathcal{N}=2$ gauge theories as monopole-dyon mixtures, and in string theory as collections of particles or black holes obtained by wrapping D-branes on internal space cycles. After discussing the general system and its relation to quiver quantum mechanics, we focus on the case of three particles. We give an exhaustive enumeration of the classical and quantum ground states of a probe in an arbitrary background with two fixed centers. We uncover a hidden conserved charge and show that the dynamics of the probe is classically integrable. In contrast, the dynamics of one heavy and two light particles moving on a line shows a nontrivial transition to chaos, which we exhibit by studying the Poincar\'e sections. Finally we explore the complex dynamics of a probe particle in a background with a large number of centers, observing hints of ergodicity breaking. We conclude by discussing possible implications in a holographic context.Comment: 35 pages,11 figures. v2: updated references to include a previous proof of classical integrability, exchanged a figure for a prettier versio

Diel-depth distributions of fish larvae off the Balearic Islands (western Mediterranean) under two environmental scenarios

Final workshop IDEADOS: The wrapping up of the IDEADOS project, International Workshop on Environment, Ecosystems and Demersal Resources and fisheries, 14-16 November 2012, Palma de Mallorca, SpainPeer reviewe

Are pelagic cephalopods in the Mediterranean as abundant as suggests the stomach contents of their predators?

Final workshop IDEADOS: The wrapping up of the IDEADOS project, International Workshop on Environment, Ecosystems and Demersal Resources and fisheries, 14-16 November 2012, Palma de Mallorca, SpainPeer reviewe

Production and analysis of synthetic Cascade variants

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR assoziiert) ist ein adaptives Immunsystem in Archaeen und Bakterien, das fremdes genetisches Material mit Hilfe von Ribonukleoprotein-Komplexen erkennt und zerstört. Diese Komplexe bestehen aus einer CRISPR RNA (crRNA) und Cas Proteinen. CRISPR-Cas Systeme sind in zwei Hauptklassen und mehrere Typen unterteilt, abhängig von den beteiligten Cas Proteinen. In Typ I Systemen sucht ein Komplex namens Cascade (CRISPR associated complex for antiviral defence) nach eingedrungener viraler DNA während einer Folgeinfektion und bindet die zu der eingebauten crRNA komplementäre Sequenz. Anschließend wird die Nuklease/Helikase Cas3 rekrutiert, welche die virale DNA degradiert (Interferenz). Das Typ I System wird in mehrere Subtypen unterteilt, die Unterschiede im Aufbau von Cascade vorweisen. Im Fokus dieser Arbeit steht eine minimale Cascade-Variante aus Shewanella putrefaciens CN-32. Im Vergleich zur gut untersuchten Typ I-E Cascade aus Escherichia coli fehlen in diesem Komplex zwei Untereinheiten, die gewöhnlicher Weise für die Zielerkennung benötigt werden. Dennoch ist der Komplex aktiv. Rekombinante I-Fv Cascade wurde bereits aus E. coli aufgereinigt und es war möglich, den Komplex zu modifizieren, indem das Rückgrat entweder verlängert oder verkürzt wurde. Dadurch wurden synthetische Varianten mit veränderter Protein-Stöchiometrie erzeugt. In der vorliegenden Arbeit wurde I-Fv Cascade weiter mit in vitro Methoden untersucht. So wurde die Bindung von Ziel-DNA beobachtet und die 3D Struktur zeigt, dass strukturelle Veränderungen im Komplex die fehlenden Untereinheiten ersetzen, möglicherweise um viralen Anti-CRISPR Proteinen zu entgehen. Die Nuklease/Helikase dieses Systems, Cas2/3fv, ist eine Fusion des Cas3 Proteins mit dem Interferenz-unabhängigen Protein Cas2. Ein unabhängiges Cas3fv ohne Cas2 Untereinheit wurde aufgereinigt und in vitro Assays zeigten, dass dieses Protein sowohl freie ssDNA als auch Cascadegebundene Substrate degradiert. Das komplette Cas2/3fv Protein bildet einen Komplex mit dem Protein Cas1 und zeigt eine reduzierte Aktivität gegenüber freier ssDNA, möglicherweise als Regulationsmechanismus zur Vermeidung von unspezifischer Aktivität. Weiterhin wurde ein Prozess namens „RNA wrapping“ etabliert. Synthetische Cascade-Komplexe wurden erzeugt, in denen die grundlegende RNA-Bindung des charakteristischen Cas7fv RückgratProteins auf eine ausgewählte RNA gelenkt wird. Diese spezifische Komplexbildung kann in vivo durch eine Repeat-Sequenz der crRNA stromaufwärts der Zielsequenz und durch Bindung des Cas5fv Proteins initiiert werden. Die erzeugten Komplexe beinhalten die ersten 100 nt der markierten RNA, die anschließend isoliert werden kann. Innerhalb der Komplexe ist die RNA stabilisiert und geschützt vor Degradation durch RNasen. Komplexbildung kann außerdem genutzt werden, um ReportergenTranskripte stillzulegen. Zusätzlich wurden erste Hinweise geliefert, dass das Rückgrat der synthetischen Komplexe durch Fusion mit weiteren Reporterproteinen modifiziert werden kann.CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) is an adaptive immune system of Archaea and Bacteria. It is able to target and destroy foreign genetic material with ribonucleoprotein complexes consisting of CRISPR RNAs (crRNAs) and certain Cas proteins. CRISPR-Cas systems are classified in two major classes and multiple types, according to the involved Cas proteins. In type I systems, a ribonucleoprotein complex called Cascade (CRISPR associated complex for antiviral defence) scans for invading viral DNA during a recurring infection and binds the sequence complementary to the incorporated crRNA. After target recognition, the nuclease/helicase Cas3 is recruited and subsequently destroys the viral DNA in a step termed interfere nce. Multiple subtypes of type I exist that show differences in the Cascade composition. This work focuses on a minimal Cascade variant found in Shewanella putrefaciens CN-32. In comparison to the well-studied type I-E Cascade from Escherichia coli, this complex is missing two proteins usually required for target recognition, yet it is still able to provide immunity. Recombinant I-Fv Cascade was previously purified from E. coli and it was possible to modulate the complex by extending or shortening the backbone, resulting in synthetic variants with altered protein stoichiometry. In the present study, I-Fv Cascade was further analyzed by in vitro methods. Target binding was observed and the 3D structure revealed structural variations that replace the missing subunits, potentially to evade viral anti-CRISPR proteins. The nuclease/helicase of this system, Cas2/3fv, is a fusion of the Cas3 protein with the interference-unrelated protein Cas2. A standalone Cas3fv was purified without the Cas2 domain and in vitro cleavage assays showed that Cas3fv degrades both free ssDNA as well as Cascade-bound substrates. The complete Cas2/3fv protein forms a complex with the protein Cas1 and was shown to reduce cleave of free ssDNA, potentially as a regulatory mechanism against unspecific cleavage. Furthermore, we established a process termed “RNA wrapping”. Synthetic Cascade assemblies can be created by directing the general RNA-binding ability of the characteristic Cas7fv backbone protein on an RNA of choice such as reporter gene transcripts. Specific complex formation can be initiated in vivo by including a repeat sequence from the crRNA upstream a given target sequence and binding of the Cas5fv protein. The created complexes contain the initial 100 nt of the tagged RNA which can be isolated afterwards. While incorporated in complexes, RNA is stabilized and protected from degradation by RNases. Complex formation can be used to silence reporter gene transcripts. Furthermore, we provided initial indications that the backbone of synthetic complexes can be modified by addition of reporter proteins

The Fractured Memory of a Mind’s Eye

The work I create is informed by questioning reality/identity, the fractalizing planes of existence our essence occupies, and the artifacts of memory experience navigating through space time. While existing in this realm of oversaturated media and neon glow, I question the effects of pervasive data systems overloading or programming the mental software we possess. My work includes humor as a means of exploring these conventions while also displaying psychedelic surrealist imagery to help break away from the conscious prison this existence births our concept apparatuses within