610 research outputs found
Application of Markov Stability for graph-based clustering on protein-protein interaction networks
Protein-Protein interaction networks are one of the most well-explored and documented parts of the interactome, as such, they have had a variety of databases and analyses developed for them, in order to harness this highly useful abstraction of very complex systems. Community detection is a popular analysis for many datasets which can be abstracted onto graphs and otherwise is a concept still performed on non-graph-based datasets through clustering methods. Community detection can also be performed at varying scales through the introduction of artificial time parameters, which in this case is a result of the use of a measure called Markov Stability. Markov Stability is also used as a measure to define a good graph partition but optimizing by having it be the objective function of the Louvain algorithm. In this study, we implement a framework for multiscale community detection governed by Markov stability, which has been previously used in other studies and apply this framework to an example protein-protein network of the proteins related to the 20 most frequently mutated human cancer genes from the STRING database. The results of this application are then explored and we show that due to the underlying properties of the example, robust partitions are obtained across varying Markov times
Metal concentrations in seaweeds from KwaZulu-Natal, South Africa - a first report
A survey of concentrations of selected metals in some common seaweeds from the KwaZulu-Natal coast was conducted. Samples of 40 seaweeds were collected from Palm Beach, Isipingo Beach and Mission Rocks and analysed for metals by X-ray fluorescence. High metal concentrations were found in a number of the seaweeds examined, Stypocaulon funiculare (Phaeophyta) and Osmundaria serrata (Rhodophyta) showed high levels of a wide range of metals and are recommended for further study as indicator species for metals in the marine environment of the KwaZulu-Natal coast
On the GRAS status of seaweeds. I. Observations on the association between antibacterial activity of ethanolic extracts and metal levels present in selected seaweeds.
The relationship between antibacterial activity and levels of 24 metals in 19 selected southern African seaweeds was examined. The antibacterial activity of ethanolic extracts of these seaweeds was assessed by agar diffusion against selected Gram positive and Gram negative test bacteria. Metal levels associated with seaweeds were determined using X-ray fluorescence (XRF) analysis. Extracts of the Phaeophyta exhibited the highest level of antibacterial activity, followed by the Rhodophyta and then the Chlorophyta, in decreasing order. Metal levels, however, were highest in the examples studied from the Rhodophyta and then the Phaeophyta and Chlorophyta, in decreasing order. There was no relationship between the observed antibacterial activity of the crude extracts tested and the levels of metals occurring in their tissues. Thus the antimicrobial activity of extracts from the seaweeds tested should also be generally recognised as safe (GRAS)
Application of Markov Stability for graph-based clustering on protein-protein interaction networks
Protein-Protein interaction networks are one of the most well-explored and documented parts of the interactome, as such, they have had a variety of databases and analyses developed for them, in order to harness this highly useful abstraction of very complex systems. Community detection is a popular analysis for many datasets which can be abstracted onto graphs and otherwise is a concept still performed on non-graph-based datasets through clustering methods. Community detection can also be performed at varying scales through the introduction of artificial time parameters, which in this case is a result of the use of a measure called Markov Stability. Markov Stability is also used as a measure to define a good graph partition but optimizing by having it be the objective function of the Louvain algorithm. In this study, we implement a framework for multiscale community detection governed by Markov stability, which has been previously used in other studies and apply this framework to an example protein-protein network of the proteins related to the 20 most frequently mutated human cancer genes from the STRING database. The results of this application are then explored and we show that due to the underlying properties of the example, robust partitions are obtained across varying Markov times
BantuWeb: A Digital Library for Resource Scarce South African Languages
South Africa is a linguistically diverse country: it is a home to 11 official languages of which nine, excluding English and Afrikaans, are Resource Scarce Languages (RSLs). Accordingly, many South Africans struggle to access information written in their native languages on the Web. Unfortunately, lack of access to information hinders social economic growth. This paper proposes a Web based digital library to act as a central repository for content written in these languages that is crawled from the Web, and generated or contributed by a community of users. Gamification features have been incorporated into the digital library to motivate users to contribute content to strengthen the collection of resources and to increase community participation. Specifically, the paper: (i) proposes a ranking algorithm, smart interleaving, to aggregate and rank multilingual search results effectively from collections of varying size; and (ii) investigates which gamification features, among leaderboard, notifications, virtual points and level, motivate users to contribute content in the context of South African RSLs. The results show that users were motivated to contribute more content to reach the next level than improving their leaderboard ranking or virtual points. Further, the overall results on merging and ranking multilingual search results show no significant improvement in using smart interleaving
An asymptotic form of the reciprocity theorem with applications in x-ray scattering
The emission of electromagnetic waves from a source within or near a
non-trivial medium (with or without boundaries, crystalline or amorphous, with
inhomogeneities, absorption and so on) is sometimes studied using the
reciprocity principle. This is a variation of the method of Green's functions.
If one is only interested in the asymptotic radiation fields the generality of
these methods may actually be a shortcoming: obtaining expressions valid for
the uninteresting near fields is not just a wasted effort but may be
prohibitively difficult. In this work we obtain a modified form the reciprocity
principle which gives the asymptotic radiation field directly. The method may
be used to obtain the radiation from a prescribed source, and also to study
scattering problems. To illustrate the power of the method we study a few
pedagogical examples and then, as a more challenging application we tackle two
related problems. We calculate the specular reflection of x rays by a rough
surface and by a smoothly graded surface taking polarization effects into
account. In conventional treatments of reflection x rays are treated as scalar
waves, polarization effects are neglected. This is a good approximation at
grazing incidence but becomes increasingly questionable for soft x rays and UV
at higher incidence angles.
PACs: 61.10.Dp, 61.10.Kw, 03.50.DeComment: 19 pages, 4 figure
Summer effects on body mass index (BMI) gain and growth patterns of American Indian children from kindergarten to first grade: a prospective study
<p>Abstract</p> <p>Background</p> <p>Overweight and obesity are highly prevalent among American Indian children, especially those living on reservations. There is little scientific evidence about the effects of summer vacation on obesity development in children. The purpose of this study was to investigate the effects of summer vacation between kindergarten and first grade on growth in height, weight, and body mass index (BMI) for a sample of American Indian children.</p> <p>Methods</p> <p>Children had their height and weight measured in four rounds of data collection (yielded three intervals: kindergarten, summer vacation, and first grade) as part of a school-based obesity prevention trial (Bright Start) in a Northern Plains Indian Reservation. Demographic variables were collected at baseline from parent surveys. Growth velocities (Z-score units/year) for BMI, weight, and height were estimated and compared for each interval using generalized linear mixed models.</p> <p>Results</p> <p>The children were taller and heavier than median of same age counterparts. Height Z-scores were positively associated with increasing weight status category. The mean weight velocity during summer was significantly less than during the school year. More rapid growth velocity in height during summer than during school year was observed. Obese children gained less adjusted-BMI in the first grade after gaining more than their counterparts during the previous two intervals. No statistically significant interval effects were found for height and BMI velocities.</p> <p>Conclusions</p> <p>There was no indication of a significant summer effect on children's BMI. Rather than seasonal or school-related patterns, the predominant pattern indicated by weight-Z and BMI-Z velocities might be related to age or maturation.</p> <p>Trial registration</p> <p>Bright Start: Obesity Prevention in American Indian Children Clinical Trial Govt ID# <a href="http://www.clinicaltrials.gov/ct2/show/NCT00123032">NCT00123032</a></p
Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV
The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration
Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector
The inclusive and dijet production cross-sections have been measured for jets
containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass
energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The
measurements use data corresponding to an integrated luminosity of 34 pb^-1.
The b-jets are identified using either a lifetime-based method, where secondary
decay vertices of b-hadrons in jets are reconstructed using information from
the tracking detectors, or a muon-based method where the presence of a muon is
used to identify semileptonic decays of b-hadrons inside jets. The inclusive
b-jet cross-section is measured as a function of transverse momentum in the
range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet
cross-section is measured as a function of the dijet invariant mass in the
range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets
and the angular variable chi in two dijet mass regions. The results are
compared with next-to-leading-order QCD predictions. Good agreement is observed
between the measured cross-sections and the predictions obtained using POWHEG +
Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet
cross-section. However, it does not reproduce the measured inclusive
cross-section well, particularly for central b-jets with large transverse
momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final
version published in European Physical Journal
Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC
Measurements of inclusive jet suppression in heavy ion collisions at the LHC
provide direct sensitivity to the physics of jet quenching. In a sample of
lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated
luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with
a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the
transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the
anti-kt algorithm with values for the distance parameter that determines the
nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of
the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp.
Jet production is found to be suppressed by approximately a factor of two in
the 10% most central collisions relative to peripheral collisions. Rcp varies
smoothly with centrality as characterized by the number of participating
nucleons. The observed suppression is only weakly dependent on jet radius and
transverse momentum. These results provide the first direct measurement of
inclusive jet suppression in heavy ion collisions and complement previous
measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables,
submitted to Physics Letters B. All figures including auxiliary figures are
available at
http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02
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