Pervasive Parallel Research Articles

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats

In wheatears and related species (‘open-habitat chats’), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species’ relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats’ plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1’300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.

Pervasive parallel and distributed computing in a liberal arts college curriculum

We present a model for incorporating parallel and distributed computing (PDC) throughout an undergraduate CS curriculum. Our curriculum is designed to introduce students early to parallel and distributed computing topics and to expose students to these topics repeatedly in the context of a wide variety of CS courses. The key to our approach is the development of a required intermediate-level course that serves as an introduction to computer systems and parallel computing. It serves as a requirement for every CS major and minor and is a prerequisite to upper-level courses that expand on parallel and distributed computing topics in different contexts. With the addition of this new course, we are able to easily make room in upper-level courses to add and expand parallel and distributed computing topics. The goal of our curricular design is to ensure that every graduating CS major has exposure to parallel and distributed computing, with both a breadth and depth of coverage. Our curriculum is particularly designed for the constraints of a small liberal arts college, however, much of its ideas and its design are applicable to any undergraduate CS curriculum.

Look up!

The "Cloud" is a wonderfully expansive phrase used to denote computation and data storage centralized in a large datacenter and elastically accessed across a network. The concept is not new; web sites and business servers have run in datacenters for a long time. These, however, were specialized applications, outside of the mainstream of desktop programs. The past few years has seen enormous change as the mainstream shifts from a single computer to mobile devices and clusters of computers. Three factors are driving this change. 1) Mobile computing, where apps run on a size- and power-constrained device and would be far less interesting without backend systems to augment computation and storage capacity. 2) Big data, which uses clusters of computers to extract valuable information from vast amounts of unstructured data. 3) Inexpensive, elastic computing, pioneered by Amazon Web Services, which enables everyone to rapidly obtain and use many servers. As a researcher from the language and compiler community, I firmly believe this sea change is at heart a programming problem. Cloud computing is far different from the environment in which most of today's languages and tools were developed, and few programmers have mastered its complexity. New challenges include pervasive parallelism, partial failure, high and variable communication latency, and replication for reliability and throughput.

Experimenting with parasail

This tutorial provides an opportunity to experiment with a new language designed to support the safe, secure, and productive development of parallel programs. ParaSail is a new language with pervasive parallelism coupled with extensive compile-time checking of annotations in the form of assertions, preconditions, postconditions, etc. ParaSail does all checking at compile time, and eliminates race conditions, null dereferences, uninitialized data access, numeric overflow, out of bounds indexing, etc. as well as statically checking the truth of all user-written assertions. After a short introduction to the language, attendees will receive a prototype ParaSail compiler and an accompanying ParaSail Virtual Machine interpreter for writing and testing ParaSail programs. The tutorial/workshop will finish with a group discussion and feedback on the experience of using this new language.

Ubiquitous Parallel Computing from Berkeley, Illinois, and Stanford

The ParLab at Berkeley, UPCRC-Illinois, and the Pervasive Parallel Laboratory at Stanford are studying how to make parallel programming succeed given industry's recent shift to multicore computing. All three centers assume that future microprocessors will have hundreds of cores and are working on applications, programming environments, and architectures that will meet this challenge. This article briefly surveys the similarities and difference in their research.

Debris Flow and Hyperconcentrated Flood‐Flow Deposits in an Alluvial Fan, Northwestern Part of the Cretaceous Yongdong Basin, Central Korea

The alluvial‐fan deposits in the Cretaceous Yongdong Basin, Korea, consist of conglomerates with a muddy or sandy matrix and sandstones with thick or thin laminations. The conglomerates and sandstones occur commonly in couplets, constituting apparently single sedimentation units. Facies transitions in the deposits can be summed up in a tripartite facies sequence: (1) a clast‐supported conglomerate with a muddy or sandy matrix and parallel clast alignment (facies A and B), (2) a matrix‐supported coarse‐tail normally graded conglomerate with random clast orientation (facies C) and thickly stratified pebbly sandstone (facies D), and (3) laminated sandstone (facies E). The clast‐supported conglomerate is interpreted as deposits of debris flows dominated by frictional grain interactions. Development of pervasive parallel clast alignment, lacking large floating clasts and inverse grading, suggests deposition via incremental aggradation rather than en masse freezing. The matrix‐supported conglomerate and thickly stratified sandstone are interpreted as deposits of dense inertia layers or traction carpets developed beneath a high‐concentration bipartite flow. The laminated sandstone indicates traction sedimentation associated with dilute flows. The facies sequence therefore suggests deposition from a composite sediment flow that comprises a preceding debris flow, a trailing watery flow, and an intermediate flow between. The intermediate flow is regarded as a hyperconcentrated flow on the basis of its bipartite nature because a hyperconcentrated suspension has a meager yield strength and is prone to be density stratified. The measured section comprises three depositional sequences, decameters thick and separated by thick mudstone beds, which could be interpreted in terms of fan evolution (progradation and retreat) under an influence of changing sediment supply from a drainage basin. Close association of sediment type with constituent facies in the three sequences suggests that composite sediment‐flow deposits are favorably developed by sand‐matrix debris flows drained from large and less rugged catchments.

Growth and Dissolution Characteristics of Dolomite Studied in Ultrathin Section: A New TEM Approach

A sample preparation technique involving ultramicrotomy is presented for the preparation of ultrathin sections of single crystals of synthetic calcite and natural dolomite cements, This technique offers certain advantages over the conventional ion-thinning technique (Wenk et al., 1983) since more material can be prepared and surveyed more quickly by transmission electron microscopy (TEM). On the other hand, the high shear strain involved in ultramicrotomy induces a nearly pervasive microcleavage parallel to {10i4} and only fragments from the original crystal are recovered. However, individual crystal fragments remain largely coherent and the nearlypervasive microcleavage highlights differences in the physical properties among different carbonate phases. TEM observations of ultrathin sections from diagenetic dolomites show that the microcleavage is not necessarily uniform through single growth sectors and reveal a pronounced domain structure. The effect of intracrystalline compositional and structural heterogeneity on the reactivity of carbonate minerals can also studied qualitatively by exposing ultrathin sections to various solutions directly on a TEM grid.

Job In Anderson's Winterset

MAXWELL ANDERSON'S Winterset has a certain unity which has often been denied the play. Once we view this drama through its most pervasive parallel, the Book of job, the unity becomes apparent. Job, the hitherto unnoticed element, is an aid toward a grasp of the playas a unified totality, providing a dominant theme and resulting in a new perspective. This unity will be found by viewing the theme not as "justice" or "love," but as the overpowering of vengeance by love, as the rejection of a lesser for a greater good. At any rate there is an interplay, and a movement from one to the other, of the two themes, justice and love. The Sacco-Vanzetti parallel points up this relationship. Scene iii of Act I moves from the puerile romanticism of an anonymous girl's seduction to an equally youthful, particularized verbal battle of cops and radicals to the ethereal first love of Mio and Miriamne and finally to the horrible, mysterious murder of Shadow. Here we have love-justice-Iove-justice developed in one scene, but the two kinds of love and the two kinds of justice are antipodal: the first two are common, worldly, particular; the last two are universal. So in this scene there is almost the admission that the play sets out to universalize the contemporary themes of romantic love and social injustice. The theme of justice has already been established in Act I: Trock has been released from prison after serving the sentence of justice, and Garth is struggling with himself to overcome his personal defeat which arose from injustice. In Scene iii the themes of love and justice are juxtaposed, and Mio reveals that the bitterness of his search for justice precludes love: he cries, "Enduring love, oh gods and worms, what mockery!" And the plot becomes twisted up in the conflict of love against justice, until it is untangled by the conquest of love.