Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Genetic heterogeneity of Atlantic bluefin tuna caught in the eastern North Atlantic Ocean south of Iceland

Atlantic bluefin tuna (Thunnus thynnus) are currently managed by the member nations of the International Commission for the Conservation of Atlantic Tunas (ICCAT) as distinct western and eastern stocks, separated by the 45 degrees W meridian. Previous studies of Atlantic bluefin tuna caught in the northeast Atlantic south of Nor-way suggested mixing of putative stocks in the region, based on abrupt shifts in the size and condition of fish during the fishing season. By contrast, more recent studies south of Iceland reported only small differences in size of tuna caught at different times of the season in that area. To better understand the stock structure and composition of Atlantic bluefin tuna in the region, we Surveyed genetic variation at eight microsatellite loci for 800 Atlantic bluefin tuna collected in experimental commercial fishing operations south of Iceland during 1999 and 2002. We tested for heterogeneity between years, between seasons within a year, between two fishing areas within the region, and between sexes. Analysis of molecular variation demonstrated slight, but significant, genetic divergence between collections of fish caught early and late in the season over the two years. These results are consistent with prior observations of Atlantic bluefin tuna of different conditions entering the fishery through the season, and suggest that the northeast Atlantic fishery represents a mixed-stock fishery including animals migrating from different areas and recruited from different spawning grounds. (c) 2006 International Council for the Exploration of the Sea

Persistent Homology Over Directed Acyclic Graphs

We define persistent homology groups over any set of spaces which have inclusions defined so that the corresponding directed graph between the spaces is acyclic, as well as along any subgraph of this directed graph. This method simultaneously generalizes standard persistent homology, zigzag persistence and multidimensional persistence to arbitrary directed acyclic graphs, and it also allows the study of more general families of topological spaces or point-cloud data. We give an algorithm to compute the persistent homology groups simultaneously for all subgraphs which contain a single source and a single sink in $O(n^4)$ arithmetic operations, where $n$ is the number of vertices in the graph. We then demonstrate as an application of these tools a method to overlay two distinct filtrations of the same underlying space, which allows us to detect the most significant barcodes using considerably fewer points than standard persistence.Comment: Revised versio

Delamination growth in composite materials

The Double Cantilever Beam (DCB) and the End Notched Flexure (ENF) specimens are employed to characterize MODE I and MODE II interlaminar fracture resistance of graphite/epoxy (CYCOM 982) and graphite/PEEK (APC2) composites. Sizing of test specimen geometries to achieve crack growth in the linear elastic regime is presented. Data reduction schemes based upon beam theory are derived for the ENF specimen and include the effects of shear deformation and friction between crack surfaces on compliance, C, and strain energy release rate, G sub II. Finite element (FE) analyses of the ENF geometry including the contact problem with friction are presented to assess the accuracy of beam theory expressions for C and G sub II. Virtual crack closure techniques verify that the ENF specimen is a pure Mode II test. Beam theory expressions are shown to be conservative by 20 to 40 percent for typical unidirectional test specimen geometries. A FE parametric study investigating the influence of delamination length and depth, span, thickness and material properties on G sub II is presented. Mode I and II interlaminar fracture test results are presented. Important experimental parameters are isolated, such as precracking techniques, rate effects, and nonlinear load-deflection response. It is found that subcritical crack growth and inelastic materials behavior, responsible for the observed nonlinearities, are highly rate-dependent phenomena with high rates generally leading to linear elastic response

Current status of NLTE analysis of stellar atmospheres

Various available codes for NLTE modeling and analysis of hot star spectra are reviewed. Generalizations of standard equations of kinetic equilibrium and their consequences are discussed.Comment: in Determination of Atmospheric Parameters of B-, A-, F- and G-Type Stars, E. Niemczura et al. eds., Springer, in pres

Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae

Structure of the Afferent Terminals in Terminal Ganglion of a Cricket and Persistent Homology

We use topological data analysis to investigate the three dimensional spatial structure of the locus of afferent neuron terminals in crickets Acheta domesticus. Each afferent neuron innervates a filiform hair positioned on a cercus: a protruding appendage at the rear of the animal. The hairs transduce air motion to the neuron signal that is used by a cricket to respond to the environment. We stratify the hairs (and the corresponding afferent terminals) into classes depending on hair length, along with position. Our analysis uncovers significant structure in the relative position of these terminal classes and suggests the functional relevance of this structure. Our method is very robust to the presence of significant experimental and developmental noise. It can be used to analyze a wide range of other point cloud data sets

Multidisciplinary outpatient care program for patients with chronic low back pain: design of a randomized controlled trial and cost-effectiveness study [ISRCTN28478651]

<p>Abstract</p> <p>Background</p> <p>Chronic low back pain (LBP) is a major public and occupational health problem, which is associated with very high costs. Although medical costs for chronic LBP are high, most costs are related to productivity losses due to sick leave. In general, the prognosis for return to work (RTW) is good but a minority of patients will be absent long-term from work. Research shows that work related problems are associated with an increase in seeking medical care and sick leave. Usual medical care of patients is however, not specifically aimed at RTW.</p> <p>The objective is to present the design of a randomized controlled trial, i.e. the BRIDGE-study, evaluating the effectiveness in improving RTW and cost-effectiveness of a multidisciplinary outpatient care program situated in both primary and outpatient care setting compared with usual clinical medical care for patients with chronic LBP.</p> <p>Methods/Design</p> <p>The design is a randomized controlled trial with an economic evaluation alongside. The study population consists of patients with chronic LBP who are completely or partially sick listed and visit an outpatient clinic of one of the participating hospitals in Amsterdam (the Netherlands). Two interventions will be compared. 1. a multidisciplinary outpatient care program consisting of a workplace intervention based on participatory ergonomics, and a graded activity program using cognitive behavioural principles. 2. usual care provided by the medical specialist, the occupational physician, the patient's general practitioner and allied health professionals. The primary outcome measure is sick leave duration until full RTW. Sick leave duration is measured monthly by self-report during one year. Data on sick leave during one-year follow-up are also requested form the employers. Secondary outcome measures are pain intensity, functional status, pain coping, patient satisfaction and quality of life. Outcome measures are assessed before randomization and 3, 6, and 12 months later. All statistical analysis will be performed according to the intension-to-treat principle.</p> <p>Discussion</p> <p>Usual care of primary and outpatient health services isn't directly aimed at RTW, therefor it is desirable to look for care which is aimed at RTW. Research shows that several occupational interventions in primary care are aimed at RTW. They have shown a significant reduction of sick leave for employee with LBP. If a comparable reduction of sick leave duration of patients with chronic LBP of who attend an outpatient clinic can be achieved, such reductions will be obviously substantial for the Netherlands and will have a considerable impact.</p> <p>Trial registration</p> <p>ISRCTN28478651</p

Actin: disposition, quantities, and estimated effects on lung recoil and compliance

. ␣-Actin: disposition, quantities, and estimated effects on lung recoil and compliance. J Appl Physiol 91: [459][460][461][462][463][464][465][466][467][468][469][470][471][472][473] 2001.-We have investigated the basis and implications of pneumoconstriction by measuring disposition and quantities of ␣-smooth muscle actin in rat and guinea pig lungs and modeling its effects on lung recoil and compliance. A robust marker of contractility, ␣-smooth muscle actin appears in smooth muscle or myofibroblast-like cells in pleura, airways, blood vessels, and alveolar ductal tissues. In each site, we measured its transected area by immunofluorescent staining and frequency-modulated scanning confocal microscopy. We incorporated these data in a model of the parenchyma consisting of an extensive elastic network with embedded contractile structures. We conclude that contraction at any one of these sites alone can decrease parenchymal compliance by 20-30% during tidal breathing. This is due mostly to the stiffness of activated contractile elements undergoing passive cycling; constant muscle tension would have little effect. The magnitude of the effect corresponds with known responses of the lung to hypocapnia, consistent with a homeostatic function in which gas exchange is defended by redistributing ventilation away from overventilated units. alveolar duct; intensity-modulated multiple-wavelength scanning confocal microscopy; lung compliance; ventilationperfusion ratio; hypocapni