A Distributed Multilevel Force-directed Algorithm

The wide availability of powerful and inexpensive cloud computing services naturally motivates the study of distributed graph layout algorithms, able to scale to very large graphs. Nowadays, to process Big Data, companies are increasingly relying on PaaS infrastructures rather than buying and maintaining complex and expensive hardware. So far, only a few examples of basic force-directed algorithms that work in a distributed environment have been described. Instead, the design of a distributed multilevel force-directed algorithm is a much more challenging task, not yet addressed. We present the first multilevel force-directed algorithm based on a distributed vertex-centric paradigm, and its implementation on Giraph, a popular platform for distributed graph algorithms. Experiments show the effectiveness and the scalability of the approach. Using an inexpensive cloud computing service of Amazon, we draw graphs with ten million edges in about 60 minutes.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Islands of conformational stability for Filopodia

Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work

Airborne measurements of western U.S. wildfire emissions: Comparison with prescribed burning and air quality implications

Wildfires emit significant amounts of pollutants that degrade air quality. Plumes from three wildfires in the western U.S. were measured from aircraft during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Biomass Burning Observation Project (BBOP), both in summer 2013. This study reports an extensive set of emission factors (EFs) for over 80 gases and 5 components of submicron particulate matter (PM1) from these temperate wildfires. These include rarely, or never before, measured oxygenated volatile organic compounds and multifunctional organic nitrates. The observed EFs are compared with previous measurements of temperate wildfires, boreal forest fires, and temperate prescribed fires. The wildfires emitted high amounts of PM1 (with organic aerosol (OA) dominating the mass) with an average EF that is more than 2 times the EFs for prescribed fires. The measured EFs were used to estimate the annual wildfire emissions of carbon monoxide, nitrogen oxides, total nonmethane organic compounds, and PM1 from 11 western U.S. states. The estimated gas emissions are generally comparable with the 2011 National Emissions Inventory (NEI). However, our PM1 emission estimate (1530 ± 570 Gg yr-1) is over 3 times that of the NEI PM2.5 estimate and is also higher thanthe PM2.5 emitted from all other sources in these states in the NEI. This study indicates that the source of OA from biomass burning in the western states is significantly underestimated. In addition, our results indicate that prescribed burning may be an effective method to reduce fine particle emissions

Comparison of hospital charge prediction models for gastric cancer patients: neural network vs. decision tree models

<p>Abstract</p> <p>Background</p> <p>In recent years, artificial neural network is advocated in modeling complex multivariable relationships due to its ability of fault tolerance; while decision tree of data mining technique was recommended because of its richness of classification arithmetic rules and appeal of visibility. The aim of our research was to compare the performance of ANN and decision tree models in predicting hospital charges on gastric cancer patients.</p> <p>Methods</p> <p>Data about hospital charges on 1008 gastric cancer patients and related demographic information were collected from the First Affiliated Hospital of Anhui Medical University from 2005 to 2007 and preprocessed firstly to select pertinent input variables. Then artificial neural network (ANN) and decision tree models, using same hospital charge output variable and same input variables, were applied to compare the predictive abilities in terms of mean absolute errors and linear correlation coefficients for the training and test datasets. The transfer function in ANN model was sigmoid with 1 hidden layer and three hidden nodes.</p> <p>Results</p> <p>After preprocess of the data, 12 variables were selected and used as input variables in two types of models. For both the training dataset and the test dataset, mean absolute errors of ANN model were lower than those of decision tree model (1819.197 vs. 2782.423, 1162.279 vs. 3424.608) and linear correlation coefficients of the former model were higher than those of the latter (0.955 vs. 0.866, 0.987 vs. 0.806). The predictive ability and adaptive capacity of ANN model were better than those of decision tree model.</p> <p>Conclusion</p> <p>ANN model performed better in predicting hospital charges of gastric cancer patients of China than did decision tree model.</p

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons

Duckweed (Lemna minor) as a Model Plant System for the Study of Human Microbial Pathogenesis

BACKGROUND: Plant infection models provide certain advantages over animal models in the study of pathogenesis. However, current plant models face some limitations, e.g., plant and pathogen cannot co-culture in a contained environment. Development of such a plant model is needed to better illustrate host-pathogen interactions. METHODOLOGY/PRINCIPAL FINDINGS: We describe a novel model plant system for the study of human pathogenic bacterial infection on a large scale. This system was initiated by co-cultivation of axenic duckweed (Lemna minor) plants with pathogenic bacteria in 24-well polystyrene cell culture plate. Pathogenesis of bacteria to duckweed was demonstrated with Pseudomonas aeruginosa and Staphylococcus aureus as two model pathogens. P. aeruginosa PAO1 caused severe detriment to duckweed as judged from inhibition to frond multiplication and chlorophyll formation. Using a GFP-marked PAO1 strain, we demonstrated that bacteria colonized on both fronds and roots and formed biofilms. Virulence of PAO1 to duckweed was attenuated in its quorum sensing (QS) mutants and in recombinant strains overexpressing the QS quenching enzymes. RN4220, a virulent strain of S. aureus, caused severe toxicity to duckweed while an avirulent strain showed little effect. Using this system for antimicrobial chemical selection, green tea polyphenols exhibited inhibitory activity against S. aureus virulence. This system was further confirmed to be effective as a pathogenesis model using a number of pathogenic bacterial species. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that duckweed can be used as a fast, inexpensive and reproducible model plant system for the study of host-pathogen interactions, could serve as an alternative choice for the study of some virulence factors, and could also potentially be used in large-scale screening for the discovery of antimicrobial chemicals

Autonomy support, basic need satisfaction and the optimal functioning of adult male and female sport participants: A test of basic needs theory

Grounded in Basic Needs Theory (BNT; Ryan and Deci, American Psychologist, 55, 68–78, 2000a), the present study aimed to: (a) test a theoretically-based model of coach autonomy support, motivational processes and well-/ill being among a sample of adult sport participants, (b) discern which basic psychological need(s) mediate the link between autonomy support and well-/ill-being, and (c) explore gender invariance in the hypothesized model. Five hundred and thirty nine participants (Male = 271;Female = 268; Mage = 22.75) completed a multi-section questionnaire tapping the targeted variables. Structural Equation Modeling (SEM) analysis revealed that coach autonomy support predicted participants’ basic need satisfaction for autonomy, competence and relatedness. In turn, basic need satisfaction predicted greater subjective vitality when engaged in sport. Participants with low levels of autonomy were more susceptible to feeling emotionally and physically exhausted from their sport investment. Autonomy and competence partially mediated the path from autonomy support to subjective vitality. Lastly, the results supported partial invariance of the model with respect to gender

Evidence for solar cycles in a late Holocene speleothem record from Dongge Cave, China

The association between solar activity and Asian monsoon (AM) remains unclear. Here we evaluate the possible connection between them based on a precisely-dated, high-resolution speleothem oxygen isotope record from Dongge Cave, southwest China during the past 4.2 thousand years (ka). Without being adjusted chronologically to the solar signal, our record shows a distinct peak-to-peak correlation with cosmogenic nuclide 14C, total solar irradiance (TSI) and sunspot number (SN) at multi-decadal to centennial timescales. Further cross-wavelet analyses between our calcite δ18O and atmospheric 14C show statistically strong coherence at three typical periodicities of ~80, 200 and 340 years, suggesting important roles of solar activities in modulating AM changes at those timescales. Our result has further indicated a better correlation between our calcite δ18O record and atmospheric 14C than between our record and TSI. This better correlation may imply that the Sun–monsoon connection is dominated most likely by cosmic rays and oceanic circulation (both associated to atmospheric 14C), instead of the direct solar heating (TSI)

Mycobacterium tuberculosis acg Gene Is Required for Growth and Virulence In Vivo

Mycobacterium tuberculosis dosRS two-component regulatory system controls transcription of approximately 50 genes including hspX, acg and Rv2030c, in response to hypoxia and nitric oxide conditions and within macrophages and mice. The hspX lies between acg and Rv2030c. However, the functions of the dosR regulated genes in vitro and in vivo are largely unknown. Previously, we demonstrated that deletion of hspX gene produced a mutant which grew faster in macrophages and in mice. In this study, we attempted to determine the functions of acg and Rv2030c by gene inactivation. We demonstrate that Rv2030c is dispensable for virulence and growth. However, deletion of acg produced a mutant which is attenuated in both resting and activated macrophages and in acute and persistent murine infection models. Surprisingly, deletion of acg did not compromise the viability of the mutant to nitrosative and oxidative stresses in vitro and in vivo. In addition, when the WT and the acg mutants were treated with antibiotics such as the prodrugs nitrofurantoin and nitrofuran, the acg mutant became more sensitive than the WT strain to these drugs. This suggests that Acg may not function as a nitroreductase. These data indicate that acg encodes an essential virulence factor for M. tuberculosis and enables it to grow and survive in macrophages and in mouse organs

Improved measurement of the K+->pi+nu(nu)over-bar branching ratio

An additional event near the upper kinematic limit for K+-->pi(+)nu(nu) over bar has been observed by experiment E949 at Brookhaven National Laboratory. Combining previously reported and new data, the branching ratio is B(K+-->pi(+)nu(nu) over bar)=(1.47(-0.89)(+1.30))x10(-10) based on three events observed in the pion momentum region 211<P<229 MeV/c. At the measured central value of the branching ratio, the additional event had a signal-to-background ratio of 0.9