Of gene expression and cell division time: a mathematical framework for advanced differential gene expression and data analysis

Estimating fold changes of average mRNA and protein molecule counts per cell is the most common way to perform differential expression analysis. However, these gene expression data may be affected by cell division, an often-neglected phenomenon. Here, we develop a quantitative framework that links population-based mRNA and protein measurements to rates of gene expression in single cells undergoing cell division. The equations we derive are easy-to-use and widely robust against biological variability. They integrate multiple "omics" data into a coherent, quantitative description of single-cell gene expression and improve analysis when comparing systems or states with different cell division times. We explore these ideas in the context of resting versus activated B cells. Analyzing differences in protein synthesis rates enables to account for differences in cell division times. We demonstrate that this improves the resolution and hit rate of differential gene expression analysis when compared to analyzing population protein abundances alone

Patterns of convection in rotating spherical shells

Patterns of convection in internally heated, self-gravitating rotating spherical fluid shells are investigated through numerical simulations. While turbulent states are of primary interest in planetary and stellar applications the present paper emphasizes more regular dynamical features at Rayleigh numbers not far above threshold which are similar to those which might be observed in laboratory or space experiments. Amplitude vacillations and spatial modulations of convection columns are common features at moderate and large Prandtl numbers. In the low Prandtl number regime equatorially attached convection evolves differently with increasing Rayleigh number and exhibits an early transition into a chaotic state. Relationships of the dynamical features to coherent structures in fully turbulent convection states are emphasized

Presence of asthma risk factors and environmental exposures related to upper respiratory infection-triggered wheezing in middle school-age children.

Viral respiratory infections and exposure to environmental constituents such as tobacco smoke are known or suspected to trigger wheezing/asthma exacerbations in children. However, few population-based data exist that examine the relationship between wheezing triggered by viral respiratory infections and environmental exposures. In this investigation we used population-based data to evaluate differences in exposures between symptomatic middle school-age children who did and did not report wheezing triggered by viral respiratory infections. As part of the North Carolina School Asthma Survey (NCSAS), a 66-question data instrument was used to collect information from children enrolled in North Carolina public middle schools during the 1999-2000 school year. Associations between exposures and upper respiratory infection-triggered wheezing (URI-TW) among symptomatic children were examined using adjusted prevalence odds ratios (PORs). Video methods developed for the International Study of Asthma and Allergies in Childhood were used to assess wheezing. Among the 33,534 NCSAS symptomatic participants, positive associations were observed between most exposures and URI-TW. Reported presence of all allergy variables (PORs ranging from 2.11 to 2.45) was more strongly associated with URI-TW than either smoking or other exposures. Presence of URI-TW was higher at increasing levels of tobacco smoke exposure, but no apparent dose-response effect was observed for other indoor air pollutants. URI-TW in middle school children is most associated with reported allergen sensitivity, relative to other asthma risk factors and environmental exposures. Data from this investigation may be useful in developing assessment, screening, and targeting strategies to improve asthma and wheezing management in children

Continuum-type stability balloon in oscillated granular layers

The stability of convection rolls in a fluid heated from below is limited by secondary instabilities, including the skew-varicose and crossroll instabilities. We observe a stability boundary defined by the same instabilities in stripe patterns in a vertically oscillated granular layer. Molecular dynamics simulations show that the mechanism of the skew-varicose instability in granular patterns is similar to that in convection. These results suggest that pattern formation in granular media can be described by continuum models analogous to those used in fluid systems.Comment: 4 pages, 6 ps figs, submitted to PR

Intermittent magnetic field excitation by a turbulent flow of liquid sodium

The magnetic field measured in the Madison Dynamo Experiment shows intermittent periods of growth when an axial magnetic field is applied. The geometry of the intermittent field is consistent with the fastest growing magnetic eigenmode predicted by kinematic dynamo theory using a laminar model of the mean flow. Though the eigenmodes of the mean flow are decaying, it is postulated that turbulent fluctuations of the velocity field change the flow geometry such that the eigenmode growth rate is temporarily positive. Therefore, it is expected that a characteristic of the onset of a turbulent dynamo is magnetic intermittency.Comment: 5 pages, 7 figure

Hysteresis phenomenon in turbulent convection

Coherent large-scale circulations of turbulent thermal convection in air have been studied experimentally in a rectangular box heated from below and cooled from above using Particle Image Velocimetry. The hysteresis phenomenon in turbulent convection was found by varying the temperature difference between the bottom and the top walls of the chamber (the Rayleigh number was changed within the range of $10^7 - 10^8$). The hysteresis loop comprises the one-cell and two-cells flow patterns while the aspect ratio is kept constant ($A=2 - 2.23$). We found that the change of the sign of the degree of the anisotropy of turbulence was accompanied by the change of the flow pattern. The developed theory of coherent structures in turbulent convection (Elperin et al. 2002; 2005) is in agreement with the experimental observations. The observed coherent structures are superimposed on a small-scale turbulent convection. The redistribution of the turbulent heat flux plays a crucial role in the formation of coherent large-scale circulations in turbulent convection.Comment: 10 pages, 9 figures, REVTEX4, Experiments in Fluids, 2006, in pres

Autonomous on-board data processing and instrument calibration software for the SO/PHI

The extension of on-board data processing capabilities is an attractive option to reduce telemetry for scientific instruments on deep space missions. The challenges that this presents, however, require a comprehensive software system, which operates on the limited resources a data processing unit in space allows. We implemented such a system for the Polarimetric and Helioseismic Imager (PHI) on-board the Solar Orbiter (SO) spacecraft. It ensures autonomous operation to handle long command-response times, easy changing of the processes after new lessons have been learned and meticulous book-keeping of all operations to ensure scientific accuracy. This contribution presents the requirements and main aspects of the software implementation, followed by an example of a task implemented in the software frame, and results from running it on SO/PHI. The presented example shows that the different parts of the software framework work well together, and that the system processes data as we expect. The flexibility of the framework makes it possible to use it as a baseline for future applications with similar needs and limitations as SO/PHI.Comment: Conference: SPIE Astronomical Telescopes + Instrumentatio, Software and Cyberinfrastructure for Astronomy

Convection in nanofluids with a particle-concentration-dependent thermal conductivity

Thermal convection in nanofluids is investigated by means of a continuum model for binary-fluid mixtures, with a thermal conductivity depending on the local concentration of colloidal particles. The applied temperature difference between the upper and the lower boundary leads via the Soret effect to a variation of the colloid concentration and therefore to a spatially varying heat conductivity. An increasing difference between the heat conductivity of the mixture near the colder and the warmer boundary results in a shift of the onset of convection to higher values of the Rayleigh number for positive values of the separation ratio psi>0 and to smaller values in the range psi<0. Beyond some critical difference of the thermal conductivity between the two boundaries, we find an oscillatory onset of convection not only for psi<0, but also within a finite range of psi>0. This range can be extended by increasing the difference in the thermal conductivity and it is bounded by two codimension-2 bifurcations.Comment: 13 pages, 11 figures; submitted to Physical Review

Wave function mapping in graphene quantum dots with soft confinement

Using low-temperature scanning tunneling spectroscopy, we map the local density of states (LDOS) of graphene quantum dots supported on Ir(111). Due to a band gap in the projected Ir band structure around the graphene K point, the electronic properties of the QDs are dominantly graphene-like. Indeed, we compare the results favorably with tight binding calculations on the honeycomb lattice based on parameters derived from density functional theory. We find that the interaction with the substrate near the edge of the island gradually opens a gap in the Dirac cone, which implies soft-wall confinement. Interestingly, this confinement results in highly symmetric wave functions. Further influences of the substrate are given by the known moir{\'e} potential and a 10% penetration of an Ir surface resonanceComment: 7 pages, 11 figures, DFT calculations directly showing the origin of soft confinment, correct identification of the state penetrating from Ir(111) into graphen