CONTEST : a Controllable Test Matrix Toolbox for MATLAB

Large, sparse networks that describe complex interactions are a common feature across a number of disciplines, giving rise to many challenging matrix computational tasks. Several random graph models have been proposed that capture key properties of real-life networks. These models provide realistic, parametrized matrices for testing linear system and eigenvalue solvers. CONTEST (CONtrollable TEST matrices) is a random network toolbox for MATLAB that implements nine models. The models produce unweighted directed or undirected graphs; that is, symmetric or unsymmetric matrices with elements equal to zero or one. They have one or more parameters that affect features such as sparsity and characteristic pathlength and all can be of arbitrary dimension. Utility functions are supplied for rewiring, adding extra shortcuts and subsampling in order to create further classes of networks. Other utilities convert the adjacency matrices into real-valued coefficient matrices for naturally arising computational tasks that reduce to sparse linear system and eigenvalue problems

On Bogovski\u{\i} and regularized Poincar\'e integral operators for de Rham complexes on Lipschitz domains

We study integral operators related to a regularized version of the classical Poincar\'e path integral and the adjoint class generalizing Bogovski\u{\i}'s integral operator, acting on differential forms in $R^n$. We prove that these operators are pseudodifferential operators of order -1. The Poincar\'e-type operators map polynomials to polynomials and can have applications in finite element analysis. For a domain starlike with respect to a ball, the special support properties of the operators imply regularity for the de Rham complex without boundary conditions (using Poincar\'e-type operators) and with full Dirichlet boundary conditions (using Bogovski\u{\i}-type operators). For bounded Lipschitz domains, the same regularity results hold, and in addition we show that the cohomology spaces can always be represented by $C^\infty$ functions.Comment: 23 page

Climatology of Short-Period Gravity Waves Observed over Northern Australia during the Darwin Area Wave Experiment (DAWEX) and their Dominant Source Regions

The Darwin Area Wave Experiment (DAWEX) was designed to investigate the generation and propagation of gravity waves from intense regions of localized convection that occur regularly over northern Australia (in the vicinity of Darwin) during the premonsoon period. This multinational program was conducted during the austral spring 2001 using a range of coordinated optical, radar, and in situ balloon measurements. As part of this program, all-sky image observations of short-period gravity wave events in the near infrared OH nightglow emission (altitude ~87 km) were made from two well-separated sites in northern Australia: Wyndham (15.5ºS, 128.1ºE) and Katherine (14.5ºS, 132.3ºE), over a 10-day period during November 2001. A total of 25 extensive wave events were observed during this period, from which the dominant horizontal wave characteristics were determined to be: wavelength 25–35 km and observed phase speed 27–75 m/s, yielding observed periods from 7 to 14 min, consistent with previous measurements at other low-latitude sites. A key finding of this study was a marked anisotropy in the wave propagation headings, with over 3/4 of the events exhibiting a strong southward component of motion and a clear preference for wave progression over the azimuthal range SE to SSW. Although this range encompasses gravity waves originating locally from the Darwin area, the majority of the wave events exhibited propagation headings consistent with more distant sources located to the north and northwest of Australia. Assuming deep convection was the dominant mechanism for the waves, the strong asymmetry in their velocity distribution appears to result from a combination of nonuniformity in the geographic occurrence of thunderstorms coupled together with significant wind filtering effects at the source altitude and within the middle atmosphere. These results are consistent with long-range, short-period wave propagation (most probably in the form of ducted waves) possibly from intense convective regions located ~1000 km to the north over the Indonesian Island chain

On the Nature of Singularities in Plane Symmetric Scalar Field Cosmologies

The nature of the initial singularity in spatially compact plane symmetric scalar field cosmologies is investigated. It is shown that this singularity is crushing and velocity dominated and that the Kretschmann scalar diverges uniformly as it is approached. The last fact means in particular that a maximal globally hyperbolic spacetime in this class cannot be extended towards the past through a Cauchy horizon. A subclass of these spacetimes is identified for which the singularity is isotropic.Comment: 7 pages, MPA-AR-94-

Transcription factor expression levels and environmental signals constrain transcription factor innovation

Evolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Transcription factors can gain or lose connections to target genes, resulting in novel regulatory responses and phenotypes. However the frequency of functional adaptation varies between different regulators, even when they are closely related. To identify factors influencing propensity for innovation, we utilise a Pseudomonas fluorescens SBW25 strain rendered incapable of flagellar mediated motility in soft-agar plates via deletion of the flagellar master regulator (fleQ). This bacterium can evolve to rescue flagellar motility via gene regulatory network rewiring of an alternative transcription factor to rescue activity of FleQ. Previously, we have identified two members (out of 22) of the RpoN-dependent enhancer binding protein (RpoN-EBP) family of transcription factors (NtrC and PFLU1132) that are capable of innovating in this way. These two transcription factors rescue motility repeatably and reliably in a strict hierarchy – with NtrC the only route in a ∆fleQ background, and PFLU1132 the only route in a ∆fleQ∆ntrC background. However, why other members in the same transcription factor family have not been observed to rescue flagellar activity is unclear. Previous work shows that protein homology cannot explain this pattern within the protein family (RpoN-EBPs), and mutations in strains that rescued motility suggested high levels of transcription factor expression and activation drive innovation. We predict that mutations that increase expression of the transcription factor are vital to unlock evolutionary potential for innovation. Here, we construct titratable expression mutant lines for 11 of the RpoN-EBPs in P. fluorescens. We show that in five additional RpoN-EBPs (FleR, HbcR, GcsR, DctD, AauR and PFLU2209), high expression levels result in different mutations conferring motility rescue, suggesting alternative rewiring pathways. Our results indicate that expression levels (and not protein homology) of RpoN-EBPs are a key constraining factor in determining evolutionary potential for innovation. This suggests that transcription factors that can achieve high expression through few mutational changes, or transcription factors that are active in the selective environment, are more likely to innovate and contribute to adaptive gene regulatory network evolution

Can springs cut canyons into rock?

Amphitheater-headed valleys on Earth and Mars are often assumed to result from erosion by emerging spring water (i.e., seepage erosion or groundwater sapping) rather than by surface runoff. The origin of such valleys has implications for landscape evolution on Earth and the hydrologic cycle and associated potential for life on other planets. In this paper we explore the evidence for seepage erosion in bedrock to address whether valley morphology can be used as a diagnostic indicator of seepage erosion. Seepage erosion is an important process in loose sediment where hydraulic forces cause grain detachment, often resulting in amphitheater-headed valleys. However, the extension of these processes to resistant rock is uncertain. In sedimentary rocks, groundwater might control the shape and rate of valley formation. It is possible, however, that seepage plays only a secondary role to runoff processes. This seems likely in basaltic valleys on Earth, where little evidence exists for seepage erosion. Since the ability of seepage to erode bedrock valleys remains unclear and because many amphitheater-headed valleys were probably carved by other processes, seepage erosion should not be inferred based solely on valley form

An assessment of the Hua Oranga outcome instrument and comparison to other outcome measures in an intervention study with Maori and Pacific people following stroke

The Hua Oranga instrument, developed for Maori people with mental illness, showed good responsiveness and adequate psychometric properties in Maori and Pacific people after stroke. Its simplicity, relative brevity, minimal cost and adequate psychometric properties should favour its use in future studies with both Maori and Pacific people. Suggestions are made for refinements to the measure. These should be tested in a new population before Hua Oranga is recommended for general use in a clinical setting. Abstract Aim Health outcomes research for Maori has been hampered by the lack of adequately validated instruments that directly address outcomes of importance to Maori, framed by a Maori perspective of health. Hua Oranga is an outcome instrument developed for Maori with mental illness that uses a holistic view of Maori health to determine improvements in physical, mental, spiritual and family domains of health. Basic psychometric work for Hua Oranga is lacking. We sought to explore the psychometric properties of the instrument and compare its responsiveness alongside other, more established tools in an intervention study involving Maori and Pacific people following acute stroke. Method Randomised 2x2 controlled trial of Maori and Pacific people following acute stroke with two interventions aimed at facilitating self-directed rehabilitation, and with follow-up at 12 months after randomisation. Primary outcome measures were the Physical Component Summary (PCS) and Mental Component Summary (MCS) of the Short Form 36 (SF36) at 12 months. Hua Oranga was used as a secondary outcome measure for participants at 12 months and for carers and whanau (extended family). Psychometric properties of Hua Oranga were explored using plots and correlation coefficients, principal factors analysis and scree plots. Results 172 participants were randomised, of whom 139 (80.8%) completed follow-up. Of these, 135 (97%) completed the Hua Oranga and 117 (84.2%) completed the PCS and MCS of the SF36. Eighty-nine carers completed the Hua Oranga. Total Hua Oranga scores and PCS improved significantly for one intervention group but not the other. Total Hua Oranga scores for carers improved significantly for both interventions. Total Hua Oranga score correlated moderately with the PCS (correlation coefficient 0.55, p<0.001). Factor analysis suggested that Hua Oranga measures two and not four factors; one 'physical-mental' and one 'spiritual-family'. Conclusion The Hua Oranga instrument, developed for Maori people with mental illness, showed good responsiveness and adequate psychometric properties in Maori and Pacific people after stroke. Its simplicity, relative brevity, minimal cost and adequate psychometric properties should favour its use in future studies with both Maori and Pacific people. Suggestions are made for refinements to the measure. These should be tested in a new population before Hua Oranga is recommended for general use in a clinical setting

Genetic Evidence for Modifying Oceanic Boundaries Relative to Fiji

We present the most comprehensive genetic characterization to date of five Fijian island populations: Viti Levu, Vanua Levu, Kadavu, the Lau Islands, and Rotuma, including non-recombinant Y (NRY) chromosome and mitochondrial DNA (mtDNA) haplotypes and haplogroups. As a whole, Fijians are genetically intermediate between Melanesians and Polynesians, but the individual Fijian island populations exhibit significant genetic structure reflecting different settlement experiences in which the Rotumans and the Lau Islanders were more influenced by Polynesians, and the other Fijian island populations were more influenced by Melanesians. In particular, Rotuman and Lau Islander NRY chromosomal and mtDNA haplogroup frequencies and Rotuman mtDNA hypervariable segment 1 (HVS1) region haplotypes more closely resemble those of Polynesians, while genetic markers of the other populations more closely resemble those of the Near Oceanic Melanesians. Our findings provide genetic evidence supportive of modifying regional boundaries relative to Fiji, as has been suggested by others based on a variety of non-genetic evidence. Specifically, for the traditional Melanesia/Polynesia/Micronesia scheme, our findings support moving the Melanesia-Polynesia boundary so as to include Rotuma and the Lau Islands in Polynesia. For the newer Near/Remote Oceania scheme, our findings support keeping Rotuma and the Lau Islands in Remote Oceania and locating the other Fijian island populations in an intermediate or “Central Oceania” region to better reflect the great diversity of Oceania

Images of survival, stories of destruction: Nuclear war on British screens from 1945 to the early 1960s

This article discusses a range of depictions and discussions of nuclear war, which appeared on British screens in the first half of the Cold War, in order to understand the changing way nuclear weapons were viewed within British culture. Using such screened images to understand how nuclear war was constructed and represented within British culture, the article argues that the hydrogen bomb, not the atomic bomb, was the true harbinger of the nuclear revolution that transformed cultural understandings of warfare and destruction. Although the atomic bomb created a great deal of anxiety within British popular culture, representations of atomic attack elided atomic destruction with that experienced in 1939-45, emphasising the 'survivability' of atomic war. In the thermonuclear era, the Second World War could not undertake the same symbolic work. The image of the city-destroying bomb was an imaginative as well as technological step-change. Screened representations stressed that a thermonuclear war would literally end the world. As such, they preceded, and indeed provided the cultural climate for, the rise of the Campaign for Nuclear Disarmament (CND). The Campaign exploited and further popularised this idea of the apocalyptic nuclear war as a key aspect of its political and moral standpoint. The article concludes, however, that the cultural hegemony of this vision of nuclear war equally helped underpin notions of nuclear deterrence. The basic assumptions about the nature of nuclear war constructed and circulated on British screens therefore formed part of CND's 'cultural' victory but the article also explains why this did not translate into the political realm. © Edinburgh University Press

Multiwavelength Observations of the Second Largest Known FR II Radio Galaxy, NVSS 2146+82

We present multi-frequency VLA, multicolor CCD imaging, optical spectroscopy, and ROSAT HRI observations of the giant FR II radio galaxy NVSS 2146+82. This galaxy, which was discovered by the NRAO VLA Sky Survey (NVSS), has an angular extent of nearly 20' from lobe to lobe. The radio structure is normal for an FR II source except for its large size and regions in the lobes with unusually flat radio spectra. Our spectroscopy indicates that the optical counterpart of the radio core is at a redshift of z=0.145, so the linear size of the radio structure is ~4 h_50^-1 Mpc. This object is therefore the second largest FR II known (3C 236 is ~6 h_50^-1 Mpc). Optical imaging of the field surrounding the host galaxy reveals an excess number of candidate galaxy cluster members above the number typically found in the field surrounding a giant radio galaxy. WIYN HYDRA spectra of a sample of the candidate cluster members reveal that six share the same redshift as NVSS 2146+82, indicating the presence of at least a ``rich group'' containing the FR II host galaxy. ROSAT HRI observations of NVSS 2146+82 place upper limits on the X-ray flux of 1.33 x 10^-13 ergs cm^-2 s^-1 for any hot IGM and 3.52 x 10^-14 ergs cm^-2 s^-1 for an X-ray AGN, thereby limiting any X-ray emission at the distance of the radio galaxy to that typical of a poor group or weak AGN. Several other giant radio galaxies have been found in regions with overdensities of nearby galaxies, and a separate study has shown that groups containing FR IIs are underluminous in X-rays compared to groups without radio sources. We speculate that the presence of the host galaxy in an optically rich group of galaxies that is underluminous in X-rays may be related to the giant radio galaxy phenomenon.Comment: 46 pages, 15 figures, AASTeX aaspp4 style, accepted for publication in A