Synchronization Landscapes in Small-World-Connected Computer Networks

Motivated by a synchronization problem in distributed computing we studied a simple growth model on regular and small-world networks, embedded in one and two-dimensions. We find that the synchronization landscape (corresponding to the progress of the individual processors) exhibits Kardar-Parisi-Zhang-like kinetic roughening on regular networks with short-range communication links. Although the processors, on average, progress at a nonzero rate, their spread (the width of the synchronization landscape) diverges with the number of nodes (desynchronized state) hindering efficient data management. When random communication links are added on top of the one and two-dimensional regular networks (resulting in a small-world network), large fluctuations in the synchronization landscape are suppressed and the width approaches a finite value in the large system-size limit (synchronized state). In the resulting synchronization scheme, the processors make close-to-uniform progress with a nonzero rate without global intervention. We obtain our results by ``simulating the simulations", based on the exact algorithmic rules, supported by coarse-grained arguments.Comment: 20 pages, 22 figure

An All-Sky 2MASS Mosaic Constructed on the TeraGrid

The Montage mosaic engine supplies on-request image mosaic services for the NVO astronomical community. A companion paper describes scientific applications of Montage. This paper describes one application in detail: the generation at SDSC of a mosaic of the 2MASS All-sky Image Atlas on the NSF TeraGrid. The goals of the project are: to provide a value-added 2MASS product that combines overlapping images to improve sensitivity; to demonstrate applicability of computing at-scale to astronomical missions and surveys, especially projects such as LSST; and to demonstrate the utility of the NVO Hyperatlas format. The numerical processing of an 8 TB, 32-bit survey to produce a 64-bit, 20 TB output atlas presented multiple scalability and operational challenges. An MPI Python module, MYMPI, was used to manage the alternately sequential and parallel steps of the Montage process. This allowed us to parallelize all steps of the mosaic process: that of many, sequential steps executing simultaneously for independent mosaics and that of a single MPI parallel job executing on many CPUs for a single mosaic. The Storage Resource Broker (SRB) was used to archive the output results in the Hyperatlas. The 2MASS mosaics are now being assessed for scientific quality. Around 130,000 CPU-hours were used to complete the mosaics. The output consists of 1734 plates spanning 6◦ for each of 3 bands. Each of the 5202 mosaics is roughly 4 GB in size, and each has been tiled into a 12×12 array of 26 MB files for ease of handling. The total size is about 20 TB in 750,000 tiles

Homozygous whole body Cbs knockout in adult mice features minimal pathology during ageing despite severe homocysteinemia

Deficiencies in Cystathionine-β-synthase (CBS) lead to hyperhomocysteinemia (HHCy), which is considered a risk factor for cardiovascular, bone and neurological disease. Moreover, CBS is important for the production of cysteine, hydrogen sulfide (H2 S) and glutathione. Studying the biological role of CBS in adult mice has been severely hampered by embryological disturbances and perinatal mortality. To overcome these issues and assess the effects of whole-body CBS deficiency in adult mice, we engineered and characterized a Cre-inducible Cbs knockout model during ageing. No perinatal mortality occurred before Cbs-/- induction at 10 weeks of age. Mice were followed until 90 weeks of age and ablation of Cbs was confirmed in liver and kidney but not in brain. Severe HHCy was observed in Cbs-/- (289 ± 58 µM) but not in Cbs+/- or control mice (<10 µM). Cbs-/- showed impaired growth, facial alopecia, endothelial dysfunction in absence of increased mortality, and signs of liver or kidney damage. CBS expression in skin localized to sebaceous glands and epidermis, suggesting local effects of Cbs-/- on alopecia. Cbs-/- showed increased markers of oxidative stress and senescence but expression of other H2 S producing enzymes (CSE and 3-MST) was not affected. CBS deficiency severely impaired H2 S production capacity in liver, but not in brain or kidney. In summary, Cbs-/- mice presented a mild phenotype without mortality despite severe HHCy. The findings demonstrate that HHCy is not directly linked to development of end organ damage

Detector Description and Performance for the First Coincidence Observations between LIGO and GEO

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial change

Subtypes of children with attention disabilities.

Subtypes of children with attentional problems were investigated using cluster analysis. Subjects were 9-year-old-elementary school children (N = 443). The test battery administered to these children comprised a comprehensive set of common attention tests, covering different aspects of attentional functioning, and a test of reading comprehension. Cluster analysis of these data yielded eight stable and reproducible clus¬ters. The test profiles of two subgroups were indicative of distinct attentional problems. One group ap¬peared deficient in speed of processing, the other in attentional control. A third subgroup showed a reading deficit. Two additional clusters had very poor and excellent performance on the whole battery, respec¬tively. Finally, three clusters were found with minor variations approximating average performance. The internal validity, that is, the adequacy and stability of the cluster solution, appeared to be reasonably good, as indicated by a variety of measures. The long-term stability over an 18-month period was also checked and found to be satisfactory

Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations

In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations. A number of important phylogenetic and general bioinformatics tools have been included in the first software release. As Armadillo is an open-source project, it allows scientists to develop their own modules as well as to integrate existing computer applications. Using our workflow platform, different complex phylogenetic tasks can be modeled and presented in a single workflow without any prior knowledge of programming techniques. The first version of Armadillo was successfully used by professors of bioinformatics at Université du Quebec à Montreal during graduate computational biology courses taught in 2010–11. The program and its source code are freely available at: <http://www.bioinfo.uqam.ca/armadillo>

Efficacy of tibolone and raloxifene for the maintenance of skeletal muscle strength, bone mineral density, balance, body composition, cognitive function, mood/depression, anxiety and quality of life/well-being in late postmenopausal women ≥ 70 years: Study design of a randomized, double-blind, double-dummy, placebo-controlled, single-center trial

<p>Abstract</p> <p>Background</p> <p>Postmenopausal women are prone to develop functional disabilities as a result of reduction in muscle strength and muscle mass caused by diminished levels of female sex hormones. While hormone replacement therapy may counteract these changes, conventional hormone replacement therapy is associated with potential harmful effects, such as an increased risk of breast cancer, and its prescription is not recommended. For this reason newer alternative drugs, such as tibolone, a synthetic steroid with estrogenic, progestogenic and androgenic activity, and raloxifene, a selective estrogen receptor modulator, may be more appropriate. This trial investigates the effect of tibolone and raloxifene on muscle strength.</p> <p>Methods</p> <p>We recruited 318 elderly women in our single-center randomized, double-blind, double-dummy, placebo-controlled trial. Participants were randomized to tibolone 1.25 mg (Org OD 14, Organon NV, the Netherlands) plus placebo, raloxifene 60 mg (Evista^®, Eli Lilly, United States) plus placebo or two placebo tablets daily for 24 months.</p> <p>The primary aim is to determine if there is a difference between tibolone and placebo or if there is a difference between raloxifene and placebo. Primary endpoints are muscle strength and bone mineral density. The secondary endpoints are postural balance, body composition, cognitive function, anxiety, mood and quality of life. The secondary aim is to determine if there is a difference between tibolone and raloxifene.</p> <p>The measure of effect is the change from the baseline visit to the visits after 3 months, 6 months, 12 months, and 24 months. A follow-up measurement is planned at 30 months to determine whether any effects are sustained after cessation of the study. By December 2007 the blind will be broken and the data analyzed.</p> <p>Trial registration number</p> <p>NTR: 1232</p