A temporal switch model for estimating transcriptional activity in gene expression

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation

The 2p yields 1s pionic transition

Pion-atomic transitions, perturbation theory, S waves, and P wave

The 5g yields 4f pionic transition in Th 232 and U 238

X ray energy measurements in 5g yields 4f pionic transitions of Th-232 and U-23

Speckle visibility spectroscopy and variable granular fluidization

We introduce a dynamic light scattering technique capable of resolving motion that changes systematically, and rapidly, with time. It is based on the visibility of a speckle pattern for a given exposure duration. Applying this to a vibrated layer of glass beads, we measure the granular temperature and its variation with phase in the oscillation cycle. We observe several transitions involving jammed states, where the grains are at rest during some portion of the cycle. We also observe a two-step decay of the temperature on approach to jamming.Comment: 4 pages, 4 figures, experimen

Microwave radiometric studies and ground truth measurements of the NASA/USGS Southern California test site

The field measurement program conducted at the NASA/USGS Southern California Test Site is discussed. Ground truth data and multifrequency microwave brightness data were acquired by a mobile field laboratory operating in conjunction with airborne instruments. The ground based investigations were performed at a number of locales representing a variety of terrains including open desert, cultivated fields, barren fields, portions of the San Andreas Fault Zone, and the Salton Sea. The measurements acquired ground truth data and microwave brightness data at wavelengths of 0.8 cm, 2.2 cm, and 21 cm

Shocks in supersonic sand

We measure time-averaged velocity, density, and temperature fields for steady granular flow past a wedge and calculate a speed of granular pressure disturbances (sound speed) equal to 10% of the flow speed. The flow is supersonic, forming shocks nearly identical to those in a supersonic gas. Molecular dynamics simulations of Newton's laws and Monte Carlo simulations of the Boltzmann equation yield fields in quantitative agreement with experiment. A numerical solution of Navier-Stokes-like equations agrees with a molecular dynamics simulation for experimental conditions excluding wall friction.Comment: 4 pages, 5 figure

Low-speed inducers for cryogenic upper-stage engines

Two-phase, low-speed hydrogen and oxygen inducers driven by electric motors and applicable to the tug engine were designed and constructed. The oxygen inducer was tested in liquid and two-phase oxygen. Its head and flow performance were approximately as designed, and it was able to accelerate to full speed in 3 seconds and produce its design flow and head. The analysis of the two-phase data indicated that the inducer was able to pump with vapor volume fractions in excess of 60 percent. The pump met all of its requirements (duration of runs and number of starts) to demonstrate its mechanical integrity

Laser ablated high T(sub c) superconducting thin YBa2Cu3O(7-x) films on substrates suitable for microwave applications

The development of high temperature superconducting YBa2Cu3O(7-x) thin films on substrates suitable for microwave applications is of great interest for evaluating their applications for space radar, communication, and sensor systems. Thin films of YBa2Cu3O(7-x) were formed on SrTiO3, ZrO2, MgO, and LaAlO3 substrates by laser ablation. The wavelength used was 248 nm from a KrF excimer laser. During deposition the films were heated to 600 C in a flowing oxygen environment, and required no post annealing. The low substrate temperature during deposition with no post annealing gave films which were smooth, which had their c-axis aligned to the substrates, and which had grains ranging from 0.2 to 0.5 microns in size. The films being c-axis aligned gave excellent surface resistance at 35 GHz which was lower than that of copper at 77 K. At present, LaAlO3 substrates with a dielectric constant of 22, appears suitable as a substrate for microwave and electronic applications. The films were characterized by resistance-temperature measurements, scanning electron microscopy, and x ray diffraction. The highest critical transition temperatures (T sub c) are above 89 K for films on SrTiO3 and LaAlO3, above 88 K for ZrO2, and above 86 K for MgO. The critical current density (J sub c) of the films on SrTiO3 is above 2 x 10(exp 6) amperes/sq cm at 77 K. The T(sub c) and J(sub c) are reported as a function of laser power, composition of the substrate, and temperature of the substrate during deposition

Universal velocity distributions in an experimental granular fluid

We present experimental results on the velocity statistics of a uniformly heated granular fluid, in a quasi-2D configuration. We find the base state, as measured by the single particle velocity distribution $f(c)$, to be universal over a wide range of filling fractions and only weakly dependent on all other system parameters. There is a consistent overpopulation in the distribution's tails, which scale as $f\propto\exp(\mathrm{const.}\times c^{-3/2})$. More importantly, the high probability central region of $f(c)$, at low velocities, deviates from a Maxwell-Boltzmann by a second order Sonine polynomial with a single adjustable parameter, in agreement with recent theoretical analysis of inelastic hard spheres driven by a stochastic thermostat. To our knowledge, this is the first time that Sonine deviations have been measured in an experimental system.Comment: 13 pages, 15 figures, with minor corrections, submitted to Phys. Rev.

Genetic diversity at the FMR1 locus in the Indonesian population

We report an analysis of allelic diversity at short tandem repeat polymorphisms within the fragile XA locus in 1069 male volunteers from twelve Indonesian sub-populations. An odd numbered allele of DXS548 was found at high frequency in all Indonesian populations. Greater allelic diversity was identified at the loci under study than has been previously reported for an Asian population. These differences distinguish the Indonesian population from all previously reported Asian, European and African populations. A high frequency of small premutation alleles, 4/120 (3.3%, 95% CI 0.9–8.3%), was identified in the Moluccan population of Hiri Island