1,607 research outputs found
A study of genetic association with electrophysiological measures related to alcoholism: GAW14 data
Recently, alcohol-related traits have been shown to have a genetic component. Here, we study the association of specific genetic measures in one of the three sets of electrophysiological measures in families with alcoholism distributed as part of the Genetic Analysis Workshop 14 data, the NTTH (non-target case of Visual Oddball experiment for 4 electrode placements) phenotypes: ntth1, ntth2, ntth3, and ntth4. We focused on the analysis of the 786 Affymetrix markers on chromosome 4. Our desire was to find at least a partial answer to the question of whether ntth1, ntth2, ntth3, and ntth4 are separately or jointly genetically controlled, so we studied the principal components that explain most of the covariation of the four quantitative traits. The first principal component, which explains 70% of the covariation, showed association but not genetic linkage to two markers: tsc0272102 and tsc0560854. On the other hand, ntth1 appeared to be the trait driving the variation in the second principal component, which showed association and genetic linkage at markers in four regions: tsc0045058, tsc1213381, tsc0055068, and tsc0051777 at map distances 53.26, 85.42, 89.31, and 172.86, respectively. These results show that the partial answer to our starting question for this brief analysis is that the NTTH phenotypes are not jointly genetically controlled. The component ntth1 displays marked genetic linkage
Investigating a Science Gateway for an Agent-Based Simulation Application Using REPAST
The benefits of using e-Infrastructure environments,
such as cloud, grid, and high performance computing, for
performing scientific experiments could be quite significant. In
particular, modeling and simulation, which can serve as a key
decision making and system analysis tool, could benefit immensely
from such environments ranging from issues of how a community
of practice could access a simulation to how it could be run
quickly. However, the access and use of these e-Infrastructure
environments may present a completely different set of challenges,
most especially for non-ICT users. Science Gateways (SG), which
are digital interfaces to advanced technologies, can be used to
overcome the challenges of running many simulations on e-
Infrastructures in a reasonable amount of time. In this work,
we developed a SG, based on the Liferay portal framework and
the Catania grid and cloud engine. We show how an Agent-
Based infection simulation, which has been implemented using the
Recursive Porous Agent Simulation Toolkit (REPAST) Simphony,
can be ported to a Science Gateway and deployed on distributed
computing infrastructures. This demonstration illustrates how
this technology can be used easily to allow multiple users across
the world to access a simulation and to execute their applications
in an e-Infrastructures environment.Special thanks go to the team at the University of Catania
for their support and the provision of the infrastructures that
enable the execution of our ABMS application jobs. This work
was part-funded by the H2020 project Energising Scientific
Endeavour through Science Gateways and e-Infrastructures in
Africa (Sci-GaIA) (project number 654237)
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A Practical Application of Low Voltage DC Distribution Network Within Buildings
Science & Technolog
Fourier Magnetic Imaging with Nanoscale Resolution and Compressed Sensing Speed-up using Electronic Spins in Diamond
Optically-detected magnetic resonance using Nitrogen Vacancy (NV) color
centres in diamond is a leading modality for nanoscale magnetic field imaging,
as it provides single electron spin sensitivity, three-dimensional resolution
better than 1 nm, and applicability to a wide range of physical and biological
samples under ambient conditions. To date, however, NV-diamond magnetic imaging
has been performed using real space techniques, which are either limited by
optical diffraction to 250 nm resolution or require slow, point-by-point
scanning for nanoscale resolution, e.g., using an atomic force microscope,
magnetic tip, or super-resolution optical imaging. Here we introduce an
alternative technique of Fourier magnetic imaging using NV-diamond. In analogy
with conventional magnetic resonance imaging (MRI), we employ pulsed magnetic
field gradients to phase-encode spatial information on NV electronic spins in
wavenumber or k-space followed by a fast Fourier transform to yield real-space
images with nanoscale resolution, wide field-of-view (FOV), and compressed
sensing speed-up.Comment: 31 pages, 10 figure
The stress-responsive Hsp90 chaperone is required for the production of the genotoxin colibactin and the siderophore yersiniabactin by Escherichia coli
The genotoxin colibactin synthesized by Escherichia coli is a secondary metabolite belonging to the chemical family of hybrid polyketide/non-ribosomal peptide compounds. It is produced by a complex biosynthetic assembly line encoded by the pks pathogenicity island. The presence of this large cluster of genes in the E. coli genome is invariably associated with the High-Pathogenicity Island, encoding the siderophore yersiniabactin that belongs to the same chemical family as colibactin. The E. coli heat shock protein HtpG (Hsp90Ec) is the bacterial homolog of the eukaryotic molecular chaperone Hsp90 involved in the protection of cellular proteins against a variety of environmental stresses. In contrast to the eukaryotic Hsp90, the functions and client proteins of Hsp90Ec are poorly known. Here, we demonstrated that production of colibactin and yersiniabactin is abolished in the absence of Hsp90Ec We further characterized an interplay between the Hsp90Ec molecular chaperone and the ClpQ protease involved in colibactin and yersiniabactin synthesis. Finally, we demonstrated that Hsp90Ec is required for the full in vivo virulence of extraintestinal pathogenic E. coli This is the first report highlighting the role of heat shock protein Hps90Ec in the production of two secondary metabolites involved in E. coli virulence
Challenges of Loss to Follow-up in Tuberculosis Research.
In studies evaluating methods for diagnosing tuberculosis (TB), follow-up to verify the presence or absence of active TB is crucial and high dropout rates may significantly affect the validity of the results. In a study assessing the diagnostic performance of the QuantiFERON®-TB Gold In-Tube test in TB suspect children in Tanzania, factors influencing patient adherence to attend follow-up examinations and reasons for not attending were examined. In 160 children who attended and 102 children who did not attend scheduled 2-month follow-up baseline health characteristics, demographic data and risk factors for not attending follow-up were determined. Qualitative interviews were used to understand patient and caretakers reasons for not returning for scheduled follow-up. Being treated for active tb in the dots program (OR: 4.14; 95% CI:1.99-8.62;p-value<0.001) and receiving money for the bus fare (OR:129; 95% CI 16->100;P-value<0.001) were positive predictors for attending follow-up at 2 months, and 21/85(25%) of children not attending scheduled follow-up had died. Interviews revealed that limited financial resources, i.e. lack of money for transportation and poor communication, were related to non-adherence. Patients lost to follow-up is a potential problem for TB research. Receiving money for transportation to the hospital and communication is crucial for adherence to follow-up conducted at a study facility. Strategies to ensure follow-up should be part of any study protocol
Second trimester inflammatory and metabolic markers in women delivering preterm with and without preeclampsia.
ObjectiveInflammatory and metabolic pathways are implicated in preterm birth and preeclampsia. However, studies rarely compare second trimester inflammatory and metabolic markers between women who deliver preterm with and without preeclampsia.Study designA sample of 129 women (43 with preeclampsia) with preterm delivery was obtained from an existing population-based birth cohort. Banked second trimester serum samples were assayed for 267 inflammatory and metabolic markers. Backwards-stepwise logistic regression models were used to calculate odds ratios.ResultsHigher 5-α-pregnan-3β,20α-diol disulfate, and lower 1-linoleoylglycerophosphoethanolamine and octadecanedioate, predicted increased odds of preeclampsia.ConclusionsAmong women with preterm births, those who developed preeclampsia differed with respect metabolic markers. These findings point to potential etiologic underpinnings for preeclampsia as a precursor to preterm birth
The contribution of statistical physics to evolutionary biology
Evolutionary biology shares many concepts with statistical physics: both deal
with populations, whether of molecules or organisms, and both seek to simplify
evolution in very many dimensions. Often, methodologies have undergone parallel
and independent development, as with stochastic methods in population genetics.
We discuss aspects of population genetics that have embraced methods from
physics: amongst others, non-equilibrium statistical mechanics, travelling
waves, and Monte-Carlo methods have been used to study polygenic evolution,
rates of adaptation, and range expansions. These applications indicate that
evolutionary biology can further benefit from interactions with other areas of
statistical physics, for example, by following the distribution of paths taken
by a population through time.Comment: 18 pages, 3 figures, glossary. Accepted in Trend in Ecology and
Evolution (to appear in print in August 2011
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