4,040 research outputs found
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High-order, linearly stable, partitioned solvers for general multiphysics problems based on implicit–explicit Runge–Kutta schemes
This work introduces a general framework for constructing high-order, linearly stable, partitioned solvers for multiphysics problems from a monolithic implicit–explicit Runge–Kutta (IMEX-RK) discretization of the semi-discrete equations. The generic multiphysics problem is modeled as a system of n systems of partial differential equations where the ith subsystem is coupled to the other subsystems through a coupling term that can depend on the state of all the other subsystems. This coupled system of partial differential equations reduces to a coupled system of ordinary differential equations via the method of lines where an appropriate spatial discretization is applied to each subsystem. The coupled system of ordinary differential equations is taken as a monolithic system and discretized using an IMEX-RK discretization with a specific implicit–explicit decomposition that introduces the concept of a predictor for the coupling term. We propose four coupling predictors that enable the monolithic system to be solved in a partitioned manner, i.e., subsystem-by-subsystem, and preserve the IMEX-RK structure and therefore the design order of accuracy of the monolithic scheme. The four partitioned solvers that result from these predictors are high-order accurate, allow for maximum re-use of existing single-physics software, and two of the four solvers allow the subsystems to be solved in parallel at a given stage and time step. We also analyze the stability of a coupled, linear model problem with a specific coupling structure and show that one of the partitioned solvers achieves unconditional linear stability for this problem, while the others are unconditionally stable only for certain values of the coupling strength. We demonstrate the performance of the proposed partitioned solvers on several classes of multiphysics problems including a simple linear system of ODEs, advection–diffusion–reaction systems, fluid–structure interaction problems, and particle-laden flows, where we verify the design order of the IMEX schemes and study various stability properties
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Observations of total RONO2 over the boreal forest: NO x sinks and HNO3 sources
In contrast with the textbook view of remote chemistry where HNO 3 formation is the primary sink of nitrogen oxides, recent theoretical analyses show that formation of RONO2 (ΣANs) from isoprene and other terpene precursors is the primary net chemical loss of nitrogen oxides over the remote continents where the concentration of nitrogen oxides is low. This then increases the prominence of questions concerning the chemical lifetime and ultimate fate of ΣANs. We present observations of nitrogen oxides and organic molecules collected over the Canadian boreal forest during the summer which show that ΣANs account for ∼20% of total oxidized nitrogen and that their instantaneous production rate is larger than that of HNO3. This confirms the primary role of reactions producing ΣANs as a control over the lifetime of NOx (NOx =NO+NO2) in remote, continental environments. However, HNO 3 is generally present in larger concentrations than ΣANs indicating that the atmospheric lifetime of ΣANs is shorter than the HNO3 lifetime. We in-vestigate a range of proposed loss mechanisms that would explain the inferred lifetime of ΣANs finding that in combination with deposition, two processes are consistent with the observations: (1) rapid ozonolysis of isoprene nitrates where at least ∼40% of the ozonolysis producs t ts release NOx from the carbon backbone and/or (2) hydrolysis of particulate organic nitrates with HNO3 as a product. Implications of these ideas for our understanding of NOx and NOy budget in remote and rural locations are discussed. © Author(s) 2013
Antibacterial Metabolites Obtained from Fermentation of Peanut and Cowpea by Lactobacillus spp
Lactic acid bacteria elective habitat is food matrix, where they
release encrypted metabolites from several parent proteins as a result
of their proteolytic activity in the matrix. These metabolites when
decrypted confer different bioactive activity thus improving public
health. This study was aimed at producing peptide containing
metabolites with antibacterial efficacy from defatted cowpea and peanut
using Lactobacillus spp. Lactobacillus spp. isolated from spoilt
yoghurt were identified using culture dependent and independent method.
The isolates were screened for proteolytic ability on skimmed milk
agar. The selected isolate with highest proteolytic activity was used
for metabolites production through fermentation of defatted cowpea and
peanut at 37 oC for 72 h. Parameters analyzed during fermentation were
pH, Lactobacillus count, protease activity, peptide concentration and
antibacterial activity. The crude peptides produced were assayed for
antibacterial activity against bacteria isolated from spoilt meat. From
the identified Lactobacillus spp., L. plantarum CAU4347 had the
highest proteolytic activity with clear zone of 24.50 \ub1 0.707 mm.
During fermentation the highest and lowest Lactobacillus counts were
from cowpea and peanut media with values 294.2 \ub1 0.21
7107
and 0.60 \ub1 0.4
7107 cfu/ml respectively. Cowpea medium
inoculated with L. plantarum CAU4347, had the highest peptide
concentration of 79.92 \ub1 0.01 \u3bcg/ml. Consequently, peanut
medium showed higher antibacterial activity of 18 mm against
Escherichia coli . This result finding suggests that encrypted peptide
metabolites from cowpea and peanut flour can confer antibacterial
activity against meat spoilage bacteria thus could be utilized as a
potential bio-preservative
Applying TADF Emitters in Bioimaging and Sensing—A Novel Approach Using Liposomes for Encapsulation and Cellular Uptake
A new method for facilitating the delivery, uptake and intracellular localisation of thermally activated delayed fluorescence (TADF) complexes was developed. First, confinement of TADF complexes in liposomes was demonstrated, which were subsequently used as the delivery vehicle for cellular uptake. Confocal fluorescence microscopy showed TADF complexes subsequently localise in the cytoplasm of HepG2 cells. The procedures developed in this work included the removal of molecular oxygen in the liposome preparation without disrupting the liposome structures. Time-resolved fluorescence microscopy (point scanning) showed initial prompt fluorescence followed by a weak, but detectable, delayed fluorescence component for liposomal TADF internalised in HepG2 cells. By demonstrating that it is possible to deliver un-functionalised and/or unshielded TADF complexes, a sensing function for TADFs, such as molecular oxygen, can be envisaged
An inhibitory pull-push circuit in frontal cortex.
Push-pull is a canonical computation of excitatory cortical circuits. By contrast, we identify a pull-push inhibitory circuit in frontal cortex that originates in vasoactive intestinal polypeptide (VIP)-expressing interneurons. During arousal, VIP cells rapidly and directly inhibit pyramidal neurons; VIP cells also indirectly excite these pyramidal neurons via parallel disinhibition. Thus, arousal exerts a feedback pull-push influence on excitatory neurons-an inversion of the canonical push-pull of feedforward input
A reverse engineering approach to the suppression of citation biases reveals universal properties of citation distributions
The large amount of information contained in bibliographic databases has
recently boosted the use of citations, and other indicators based on citation
numbers, as tools for the quantitative assessment of scientific research.
Citations counts are often interpreted as proxies for the scientific influence
of papers, journals, scholars, and institutions. However, a rigorous and
scientifically grounded methodology for a correct use of citation counts is
still missing. In particular, cross-disciplinary comparisons in terms of raw
citation counts systematically favors scientific disciplines with higher
citation and publication rates. Here we perform an exhaustive study of the
citation patterns of millions of papers, and derive a simple transformation of
citation counts able to suppress the disproportionate citation counts among
scientific domains. We find that the transformation is well described by a
power-law function, and that the parameter values of the transformation are
typical features of each scientific discipline. Universal properties of
citation patterns descend therefore from the fact that citation distributions
for papers in a specific field are all part of the same family of univariate
distributions.Comment: 9 pages, 6 figures. Supporting information files available at
http://filrad.homelinux.or
Increasing confidence and changing behaviors in primary care providers engaged in genetic counselling.
BackgroundScreening and counseling for genetic conditions is an increasingly important part of primary care practice, particularly given the paucity of genetic counselors in the United States. However, primary care physicians (PCPs) often have an inadequate understanding of evidence-based screening; communication approaches that encourage shared decision-making; ethical, legal, and social implication (ELSI) issues related to screening for genetic mutations; and the basics of clinical genetics. This study explored whether an interactive, web-based genetics curriculum directed at PCPs in non-academic primary care settings was superior at changing practice knowledge, attitudes, and behaviors when compared to a traditional educational approach, particularly when discussing common genetic conditions.MethodsOne hundred twenty one PCPs in California and Pennsylvania physician practices were randomized to either an Intervention Group (IG) or Control Group (CG). IG physicians completed a 6 h interactive web-based curriculum covering communication skills, basics of genetic testing, risk assessment, ELSI issues and practice behaviors. CG physicians were provided with a traditional approach to Continuing Medical Education (CME) (clinical review articles) offering equivalent information.ResultsPCPs in the Intervention Group showed greater increases in knowledge compared to the Control Group. Intervention PCPs were also more satisfied with the educational materials, and more confident in their genetics knowledge and skills compared to those receiving traditional CME materials. Intervention PCPs felt that the web-based curriculum covered medical management, genetics, and ELSI issues significantly better than did the Control Group, and in comparison with traditional curricula. The Intervention Group felt the online tools offered several advantages, and engaged in better shared decision making with standardized patients, however, there was no difference in behavior change between groups with regard to increases in ELSI discussions between PCPs and patients.ConclusionWhile our intervention was deemed more enjoyable, demonstrated significant factual learning and retention, and increased shared decision making practices, there were few differences in behavior changes around ELSI discussions. Unfortunately, barriers to implementing behavior change in clinical genetics is not unique to our intervention. Perhaps the missing element is that busy physicians need systems-level support to engage in meaningful discussions around genetics issues. The next step in promoting active engagement between doctors and patients may be to put into place the tools needed for PCPs to easily access the materials they need at the point-of-care to engage in joint discussions around clinical genetics
Beyond Gross-Pitaevskii Mean Field Theory
A large number of effects related to the phenomenon of Bose-Einstein
Condensation (BEC) can be understood in terms of lowest order mean field
theory, whereby the entire system is assumed to be condensed, with thermal and
quantum fluctuations completely ignored. Such a treatment leads to the
Gross-Pitaevskii Equation (GPE) used extensively throughout this book. Although
this theory works remarkably well for a broad range of experimental parameters,
a more complete treatment is required for understanding various experiments,
including experiments with solitons and vortices. Such treatments should
include the dynamical coupling of the condensate to the thermal cloud, the
effect of dimensionality, the role of quantum fluctuations, and should also
describe the critical regime, including the process of condensate formation.
The aim of this Chapter is to give a brief but insightful overview of various
recent theories, which extend beyond the GPE. To keep the discussion brief,
only the main notions and conclusions will be presented. This Chapter
generalizes the presentation of Chapter 1, by explicitly maintaining
fluctuations around the condensate order parameter. While the theoretical
arguments outlined here are generic, the emphasis is on approaches suitable for
describing single weakly-interacting atomic Bose gases in harmonic traps.
Interesting effects arising when condensates are trapped in double-well
potentials and optical lattices, as well as the cases of spinor condensates,
and atomic-molecular coupling, along with the modified or alternative theories
needed to describe them, will not be covered here.Comment: Review Article (19 Pages) - To appear in 'Emergent Nonlinear
Phenomena in Bose-Einstein Condensates: Theory and Experiment', Edited by
P.G. Kevrekidis, D.J. Frantzeskakis and R. Carretero-Gonzalez (Springer
Verlag
One year follow-up of patients with refractory angina pectoris treated with enhanced external counterpulsation
BACKGROUND: Enhanced external counterpulsation (EECP) is a non-invasive technique that has been shown to be effective in reducing both angina and myocardial ischemia in patients not responding to medical therapy and without revascularization alternatives. The aim of the present study was to assess the long-term outcome of EECP treatment at a Scandinavian centre, in relieving angina in patients with chronic refractory angina pectoris. METHODS: 55 patients were treated with EECP. Canadian cardiovascular society (CCS) class, antianginal medication and adverse clinical events were collected prior to EECP, at the end of the treatment, and at six and 12 months after EECP treatment. Clinical signs and symptoms were recorded. RESULTS: EECP treatment significantly improved the CCS class in 79 ± 6% of the patients with chronic angina pectoris (p < 0.001). The reduction in CCS angina class was seen in patients with CCS class III and IV and persisted 12 months after EECP treatment. There was no significant relief in angina in patients with CCS class II prior to EECP treatment. 73 ± 7% of the patients with a reduction in CCS class after EECP treatment improved one CCS class, and 22 ± 7% of the patients improved two CCS classes. The improvement of two CCS classes could progress over a six months period and tended to be more prominent in patients with CCS class IV. In accordance with the reduction in CCS classes there was a significant decrease in the weekly nitroglycerin usage (p < 0.05). CONCLUSION: The results from the present study show that EECP is a safe treatment for highly symptomatic patients with refractory angina. The beneficial effects were sustained during a 12-months follow-up period
Listen to genes : dealing with microarray data in the frequency domain
Background: We present a novel and systematic approach to analyze temporal microarray data. The approach includes
normalization, clustering and network analysis of genes.
Methodology: Genes are normalized using an error model based uniform normalization method aimed at identifying and
estimating the sources of variations. The model minimizes the correlation among error terms across replicates. The
normalized gene expressions are then clustered in terms of their power spectrum density. The method of complex Granger
causality is introduced to reveal interactions between sets of genes. Complex Granger causality along with partial Granger
causality is applied in both time and frequency domains to selected as well as all the genes to reveal the interesting
networks of interactions. The approach is successfully applied to Arabidopsis leaf microarray data generated from 31,000
genes observed over 22 time points over 22 days. Three circuits: a circadian gene circuit, an ethylene circuit and a new
global circuit showing a hierarchical structure to determine the initiators of leaf senescence are analyzed in detail.
Conclusions: We use a totally data-driven approach to form biological hypothesis. Clustering using the power-spectrum
analysis helps us identify genes of potential interest. Their dynamics can be captured accurately in the time and frequency
domain using the methods of complex and partial Granger causality. With the rise in availability of temporal microarray
data, such methods can be useful tools in uncovering the hidden biological interactions. We show our method in a step by
step manner with help of toy models as well as a real biological dataset. We also analyse three distinct gene circuits of
potential interest to Arabidopsis researchers
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