378 research outputs found
Role models for complex networks
We present a framework for automatically decomposing ("block-modeling") the
functional classes of agents within a complex network. These classes are
represented by the nodes of an image graph ("block model") depicting the main
patterns of connectivity and thus functional roles in the network. Using a
first principles approach, we derive a measure for the fit of a network to any
given image graph allowing objective hypothesis testing. From the properties of
an optimal fit, we derive how to find the best fitting image graph directly
from the network and present a criterion to avoid overfitting. The method can
handle both two-mode and one-mode data, directed and undirected as well as
weighted networks and allows for different types of links to be dealt with
simultaneously. It is non-parametric and computationally efficient. The
concepts of structural equivalence and modularity are found as special cases of
our approach. We apply our method to the world trade network and analyze the
roles individual countries play in the global economy
On the Origin of S0 Galaxies
I will review the basic properties of S0 galaxies in the local Universe in
relation to both elliptical and spiral galaxies, their neighbours on the Hubble
sequence, and also in relation to dwarf spheroidal (dSph) galaxies. This will
include colours, luminosities, spectral features, information about the age and
metallicity composition of their stellar populations and globular clusters,
about their ISM content, as well as kinematic signatures and their implications
for central black hole masses and past interaction events, and the number
ratios of S0s to other galaxy types in relation to environmental galaxy
density. I will point out some caveats as to their morphological discrimination
against other classes of galaxies, discuss the role of dust and the wavelength
dependence of bulge/disk light ratios. These effects are of importance for
investigations into the redshift evolution of S0 galaxies -- both as individual
objects and as a population. The various formation and transformation scenarios
for S0 and dSph galaxies will be presented and confronted with the available
observations.Comment: Invited Review, 18 pages, ``BARS 2004'' Conference, South Africa,
June 2004, eds.: K. C. Freeman, D. L. Block, I. Puerari, R. Groess, Kluwer,
in pres
Folding of the apolipoprotein A1 driven by the salt concentration as a possible mechanism to improve cholesterol trapping
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution
at increasing ionic strength is studied using atomically detailed molecular
dynamics simulations. We calculate various structural properties to
characterize the conformation of the protein, such as the radius of gyration,
the radial distribution function and the end to end distance. Additionally we
report information using tools specifically tailored for the characterization
of proteins, such as the mean smallest distance matrix and the Ramachandran
plot. We find that two qualitatively different configurations of this protein
are preferred, one where the protein is extended, and one where it forms loops
or closed structures. It is argued that the latter promote the association of
the protein with cholesterol and other fatty acids.Comment: 14 pages, 6 figures. To appear in "Selected Topics of Computational
and Experimental Fluid Mechanics", Springer, J. Klapp, G. Ru\'iz, A. Medina,
A. L\'opez & L. Di G. Sigalotti (eds.), 201
A population-based case-control study of Selective Serotonin Reuptake Inhibitors (SSRIs) and breast cancer: The impact of duration of use, cumulative dose and latency
Quality of Data Entry Using Single Entry, Double Entry and Automated Forms ProcessingâAn Example Based on a Study of Patient-Reported Outcomes
Background: The clinical and scientific usage of patient-reported outcome measures is increasing in the health services. Often paper forms are used. Manual double entry of data is defined as the definitive gold standard for transferring data to an electronic format, but the process is laborious. Automated forms processing may be an alternative, but further validation is warranted. Methods: 200 patients were randomly selected from a cohort of 5777 patients who had previously answered two different questionnaires. The questionnaires were scanned using an automated forms processing technique, as well as processed by single and double manual data entry, using the EpiData Entry data entry program. The main outcome measure was the proportion of correctly entered numbers at question, form and study level. Results: Manual double-key data entry (error proportion per 1000 fields = 0.046 (95 % CI: 0.001â0.258)) performed better than single-key data entry (error proportion per 1000 fields = 0.370 (95 % CI: 0.160â0.729), (p = 0.020)). There was no statistical difference between Optical Mark Recognition (error proportion per 1000 fields = 0.046 (95 % CI: 0.001â0.258)) and double-key data entry (p = 1.000). With the Intelligent Character Recognition method, there was no statistical difference compared to single-key data entry (error proportion per 1000 fields = 6.734 (95 % CI: 0.817â24.113), (p = 0.656)), as well as double-key data entry (error proportion per 1000 fields = 3.367 (95 % CI: 0.085â18.616)), (p = 0.319))
Observed and predicted risk of breast cancer death in randomized trials on breast cancer screening
BACKGROUND: The role of breast screening in breast cancer mortality declines is debated. Screening impacts cancer mortality through decreasing the number of advanced cancers with poor diagnosis, while cancer treatment works through decreasing the case-fatality rate. Hence, reductions in cancer death rates thanks to screening should directly reflect reductions in advanced cancer rates. We verified whether in breast screening trials, the observed reductions in the risk of breast cancer death could be predicted from reductions of advanced breast cancer rates. PATIENTS AND METHODS: The Greater New York Health Insurance Plan trial (HIP) is the only breast screening trial that reported stage-specific cancer fatality for the screening and for the control group separately. The Swedish Two-County trial (TCT)) reported size-specific fatalities for cancer patients in both screening and control groups. We computed predicted numbers of breast cancer deaths, from which we calculated predicted relative risks (RR) and (95% confidence intervals). The Age trial in England performed its own calculations of predicted relative risk. RESULTS: The observed and predicted RR of breast cancer death were 0.72 (0.56-0.94) and 0.98 (0.77-1.24) in the HIP trial, and 0.79 (0.78-1.01) and 0.90 (0.80-1.01) in the Age trial. In the TCT, the observed RR was 0.73 (0.62-0.87), while the predicted RR was 0.89 (0.75-1.05) if overdiagnosis was assumed to be negligible and 0.83 (0.70-0.97) if extra cancers were excluded. CONCLUSIONS: In breast screening trials, factors other than screening have contributed to reductions in the risk of breast cancer death most probably by reducing the fatality of advanced cancers in screening groups. These factors were the better management of breast cancer patients and the underreporting of breast cancer as the underlying cause of death. Breast screening trials should publish stage-specific fatalities observed in each group
Multiple Routes and Milestones in the Folding of HIVâ1 Protease Monomer
Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIVâ1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIVâ1 protease
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
A roadmap for the Human Developmental Cell Atlas
The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human Cell Atlas, aims to create a comprehensive reference map of cells during development. This will be critical to understanding normal organogenesis, the effect of mutations, environmental factors and infectious agents on human development, congenital and childhood disorders, and the cellular basis of ageing, cancer and regenerative medicine. Here we outline the HDCA initiative and the challenges of mapping and modelling human development using state-of-the-art technologies to create a reference atlas across gestation. Similar to the Human Genome Project, the HDCA will integrate the output from a growing community of scientists who are mapping human development into a unified atlas. We describe the early milestones that have been achieved and the use of human stem-cell-derived cultures, organoids and animal models to inform the HDCA, especially for prenatal tissues that are hard to acquire. Finally, we provide a roadmap towards a complete atlas of human development
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