The stochastic quasi-steady-state assumption: Reducing the model but not the noise

Highly reactive species at small copy numbers play an important role in many biological reaction networks. We have described previously how these species can be removed from reaction networks using stochastic quasi-steady-state singular perturbation analysis (sQSPA). In this paper we apply sQSPA to three published biological models: the pap operon regulation, a biochemical oscillator, and an intracellular viral infection. These examples demonstrate three different potential benefits of sQSPA. First, rare state probabilities can be accurately estimated from simulation. Second, the method typically results in fewer and better scaled parameters that can be more readily estimated from experiments. Finally, the simulation time can be significantly reduced without sacrificing the accuracy of the solution

Modeling the dissipation rate in rotating turbulent flows

A variety of modifications to the modeled dissipation rate transport equation that have been proposed during the past two decades to account for rotational strains are examined. The models are subjected to two crucial test cases: the decay of isotropic turbulence in a rotating frame and homogeneous shear flow in a rotating frame. It is demonstrated that these modifications do not yield substantially improved predictions for these two test cases and in many instances give rise to unphysical behavior. An alternative proposal, based on the use of the tensor dissipation rate, is made for the development of improved models

Cosmic (super)string constraints from 21 cm radiation

We calculate the contribution of cosmic strings arising from a phase transition in the early universe, or cosmic superstrings arising from brane inflation, to the cosmic 21 cm power spectrum at redshifts z > 30. Future experiments can exploit this effect to constrain the cosmic string tension Gu and probe virtually the entire brane inflation model space allowed by current observations. Although current experiments with a collecting area of ~ 1 km^2 will not provide any useful constraints, future experiments with a collecting area of 10^4-10^6 km^2 covering the cleanest 10% of the sky can in principle constrain cosmic strings with tension Gu > 10^(-10) to 10^(-12) (superstring/phase transition mass scale >10^13 GeV).Comment: Accepted for publication in PR

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

UnlabelledPremise of the studyThe Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. •Methods and resultsWe designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. •ConclusionsThese methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families

Prevalence of tuberculosis in post-mortem studies of HIV-infected adults and children in resource-limited settings: a systematic review and meta-analysis.

OBJECTIVES: Tuberculosis (TB) is estimated to be the leading cause of HIV-related deaths globally. However, since HIV-associated TB frequently remains unascertained, we systematically reviewed autopsy studies to determine the true burden of TB at death. METHODS: We systematically searched Medline and Embase databases (to end 2013) for literature reporting on health facility-based autopsy studies of HIV-infected adults and/or children in resource-limited settings. Using forest plots and random-effects meta-analysis, we summarized the TB prevalence found at autopsy and used meta-regression to explore variables associated with autopsy TB prevalence. RESULTS: We included 36 eligible studies, reporting on 3237 autopsies. Autopsy TB prevalence was extremely heterogeneous (range 0-64.4%), but was markedly higher in adults [pooled prevalence 39.7%, 95% confidence interval (CI) 32.4-47.0%] compared to children (pooled prevalence 4.5%, 95% CI 1.7-7.4%). Post-mortem TB prevalence varied by world region, with pooled estimates in adults of 63.2% (95% CI 57.7-68.7%) in South Asia (n = 2 studies); 43.2% (95% CI 38.0-48.3) in sub-Saharan Africa (n = 9 studies); and 27.1% (95% CI 16.0-38.1%) in the Americas (n = 5 studies). Autopsy prevalence positively correlated with contemporary estimates of national TB prevalence. TB in adults was disseminated in 87.9% (82.2-93.7%) of cases and was considered the cause of death in 91.4% (95% CI 85.8-97.0%) of TB cases. Overall, TB was the cause of death in 37.2% (95% CI 25.7-48.7%) of adult HIV/AIDS-related deaths. TB remained undiagnosed at death in 45.8% (95% CI 32.6-59.1%) of TB cases. CONCLUSIONS: In resource-limited settings, TB accounts for approximately 40% of facility-based HIV/AIDS-related adult deaths. Almost half of this disease remains undiagnosed at the time of death. These findings highlight the critical need to improve the prevention, diagnosis and treatment of HIV-associated TB globally

The rigidity of crystalline color superconducting quark matter

We calculate the shear modulus of crystalline color superconducting quark matter, showing that this phase of dense, but not asymptotically dense, three-flavor quark matter responds to shear stress like a very rigid solid. To evaluate the shear modulus, we derive the low energy effective Lagrangian that describes the phonons that originate from the spontaneous breaking of translation invariance by the spatial modulation of the gap parameter $\Delta$. These massless bosons describe space- and time-dependent fluctuations of the crystal structure and are analogous to the phonons in ordinary crystals. The coefficients of the spatial derivative terms of the phonon effective Lagrangian are related to the elastic moduli of the crystal; the coefficients that encode the linear response of the crystal to a shearing stress define the shear modulus. We analyze the two particular crystal structures which are energetically favored over a wide range of densities, in each case evaluating the phonon effective action and the shear modulus up to order $\Delta^2$ in a Ginzburg-Landau expansion, finding shear moduli which are 20 to 1000 times larger than those of neutron star crusts. The crystalline color superconducting phase has long been known to be a superfluid -- by picking a phase its order parameter breaks the quark-number $U(1)_B$ symmetry spontaneously. Our results demonstrate that this superfluid phase of matter is at the same time a rigid solid. We close with a rough estimate of the pinning force on the rotational vortices which would be formed embedded within this rigid superfluid upon rotation. Our results raise the possibility that (some) pulsar glitches could originate within a quark matter core deep within a neutron star.Comment: 38 pages, 5 figures. v3. Two new paragraphs in Section V (Conclusion); some additional small changes. A paragraph discussing supercurrents added in Section I (Introduction). Version to appear in Phys. Rev.

Prevalence of overweight, obesity and thinness in 9-10 year old children in Mauritius.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.OBJECTIVE: To document the prevalence of overweight, obesity and thinness in 9-10 year old children in Mauritius. METHODS: 412 boys and 429 girls aged 9-10 years from 23 primary schools were selected using stratified cluster random sampling. All data was cross-sectional and collected via anthropometry and self-administered questionnaire. Outcome measures were BMI (kg/m2), prevalence of overweight, obesity (International Obesity Task Force definitions) and thinness (low BMI for age). Linear and logistic regression analyses, accounting for clustering at the school level, were used to assess associations between gender, ethnicity, school location, and school's academic performance (average) to each outcome measure. RESULTS: The distribution of BMI was marginally skewed with a more pronounced positive tail in the girls. Median BMI was 15.6 kg/m2 in boys and 15.4 kg/m2 in girls, respectively. In boys, prevalence of overweight was 15.8% (95% CI: 12.6, 19.6), prevalence of obesity 4.9% (95% CI: 3.2, 7.4) and prevalence of thinness 12.4% (95% CI: 9.5, 15.9). Among girls, 18.9% (95% CI: 15.5, 22.9) were overweight, 5.1% (95% CI: 3.4, 7.7) were obese and 13.1% (95% CI: 10.2, 16.6) were thin. Urban children had a slightly higher mean BMI than rural children (0.5 kg/m2, 95% CI: 0.01, 1.00) and were nearly twice as likely to be obese (6.7% vs. 4.0%; adjusted odds ratio 1.6; 95% CI: 0.9, 3.5). Creole children were less likely to be classified as thin compared to Indian children (adjusted odds ratio 0.3, 95% CI: 0.2, 0.6). CONCLUSION: Mauritius is currently in the midst of nutritional transition with both a high prevalence of overweight and thinness in children aged 9-10 years. The coexistence of children representing opposite sides of the energy balance equation presents a unique challenge for policy and interventions. Further exploration is needed to understand the specific causes of the double burden of malnutrition and to make appropriate policy recommendations

Performance of the 2007 WHO Algorithm to diagnose Smear-negative Pulmonary Tuberculosis in a HIV prevalent setting

The 2007 WHO algorithm for diagnosis of smear-negative pulmonary tuberculosis (PTB) including Mycobacterium tuberculosis (MTB) culture was evaluated in a HIV prevalent area of Kenya