Statistical scene generation for polarimetric imaging systems

Little publicly available data exists for polarimetric measurements. When designing task specific polarimetric systems, the statistical properties of the task specific data becomes important. Until better polarimetric datasets are available to deduce statistics from, the statistics must be simulated to test instrument performance. Most imaged scenes have been shown to follow a power law power spectral density distribution, for both natural and city scenes. Furthermore, imaged data appears to follow a power law power spectral distribution temporally. We are interested in generating image sets which change over time, and at the same time are correlated between different components (spectral or polarimetric). In this brief communication, we present a framework and provide code to generate such data.Comment: 5 pages, 3 figures, 3 matlab function

Evolutionary rates and gene dispensability associate with replication timing in the Archaeon Sulfolobus islandicus

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog families were grouped by their consensus position and designated by their proximity to one of the three origins (O1, O2, O3). Conserved orthologs were concentrated near the origins and most variation in genome content occurred distant from the origins. Linear regressions of both synonymous and nonsynonymous substitution rates on distance from replication origins were significantly positive, the rates being greatest in the region furthest from any of the origins and slowest among genes near the origins. Genes near O1 also evolved faster than those near O2 and O3, which suggest that this origin may fire later in the cell cycle. Increased evolutionary rates and gene dispensability are strongly associated with reduced gene expression caused in part by reduced gene dosage during the cell cycle. Therefore, in this genus of Archaea as well as in many Bacteria, evolutionary rates and variation in genome content associate with replication timing

Why genes evolve faster on secondary chromosomes in bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently

The Dynamics of Presidential Legacies

It has been said that one of the few things you can’t do in life a second time is to make a first impression; however, in politics, and especially presidential politics, while it may not be possible to change that first impression, it is possible to change the public’s opinion, and how one might be perceived long after their political career is over. The 43 men who have been the U.S president have been analyzed and scrutinized throughout their lives and political careers. Prior to running for president, they establish a resume that puts them in the public eye. Later, during their campaign, the American public decides whether they have the confidence in the candidate to entrust them with the duties as president. While in office, they are evaluated daily by the press and news media along with the onslaught of polls measuring the publics’ satisfaction, or dissatisfaction, with their performance. The evaluations while in office offer them the opportunity to see how “well” they are doing, and also provide insights as to whether they may or may not be residing in the White House at the end of their first term

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence

Drop-on-demand microdroplet generation: a very stable platform for single-droplet experimentation

This paper reports the performance of drop-on-demand piezo-activated microdroplet generation investigated using microdroplet cavity enhanced fluorescence spectroscopy. Aqueous microdroplets, doped with a fluorescent dye, exhibit fluorescence spectra that are dominated by cavity resonances (termed whispering gallery modes) that, when analysed using Mie theory, allow for the determination of the radius of each microdroplet. The effect of controlled changes in the square-wave droplet generator voltage waveform on droplet size is investigated as well as the size reproducibility of successive microdroplets. Furthermore, using custom square-wave waveforms, microdroplet radii spanning ∼10 to 30 μm are produced from the same droplet dispenser. These non-standard waveforms do not sacrifice the reproducibility of microdroplet generation with \u3c1% size variation. Tuning the single square-wave pulsewidths induces predictable changes in the microdroplet radius and steps on the order of tens of nanometers are detectable. With finer voltage adjustments the microdroplet size is essentially tunable. These results confirm the extremely high stability and reproducibility of on-demand microdroplet generation and that precise size control is possible, rendering them suitable platforms for many applications in fundamental and applied research in areas including mass spectrometry, aerosol investigations and liquid-phase chemistr

Modelling Deformations in Car Crash animation

In this paper, we present a prototype of a deformation engine to efficiently model and render the damaged structure of vehicles in crash scenarios. We introduce a novel system architecture to accelerate the computation, which is traditionally an extremely expensive task. We alter a rigid body simulator to predict trajectories of cars during a collision and formulate a correction procedure to estimate the deformations of the collapsed car structures within the contact area. Non-linear deformations are solved based on the principle of energy conservation. Large plastic deformations resulting from collisions are modelled as a weighted combination of deformation examples of beams which can be produced using classical mechanics

Susceptibility of Caenorhabditis elegans to Burkholderia Infection Depends on Prior Diet and Secreted Bacterial Attractants

The nematode Caenorhabditis elegans may be killed by certain pathogenic bacteria and thus is a model organism for studying interactions between bacteria and animal hosts. However, growing nematodes on prey bacteria may influence their susceptibility to potential pathogens. A method of axenic nematode culture was developed to isolate and quantify interactions between C. elegans and potentially pathogenic strains of the Burkholderia cepacia complex. Studying these dynamics in liquid solution rather than on agar surfaces minimized nematode avoidance behavior and resolved more differences among isolates. Most isolates of B. cenocepacia, B. ambifaria and B. cepacia caused 60–80% mortality of nematodes after 7 days, whereas isolates of B. multivorans caused less mortality (<25%) and supported nematode reproduction. However, some B. cenocepacia isolates recovered from chronic infections were much less virulent (5–28% mortality). As predicted, prior diet altered the outcome of interactions between nematodes and bacteria. When given the choice between Burkholderia and E. coli as prey on agar, axenically raised nematodes initially preferred most lethal Burkholderia isolates to E. coli as a food source, but this was not the case for nematodes fed E. coli, which avoided toxic Burkholderia. This food preference was associated with the cell-free supernatant and thus secreted compounds likely mediated bacterial-nematode interactions. This model, which isolates interactions between bacteria and nematodes from the effects of prior feeding, demonstrates that bacteria can influence nematode behavior and their susceptibility to pathogens

Modulation of attention and stress with arousal: The mental and physical effects of riding a motorcycle

Existing theories suggest that moderate arousal improves selective attention, as would be expected in the context of competitive sports or sensation-seeking activities. Here we investigated how riding a motorcycle, an attention-demanding physical activity, affects sensory processing. To do so, we implemented the passive auditory oddball paradigm and measured the EEG response of participants as they rode a motorcycle, drove a car, and sat at rest. Specifically, we measured the N1 and mismatch negativity to auditory tones, as well as alpha power during periods of no tones. We investigated whether riding and driving modulated non-CNS metrics including heart rate and concentrations of the hormones epinephrine, cortisol, DHEA-S, and testosterone. While participants were riding, we found a decrease in N1 amplitude, increase in mismatch negativity, and decrease in relative alpha power, together suggesting enhancement of sensory processing and visual attention. Riding increased epinephrine levels, increased heart rate, and decreased the ratio of cortisol to DHEA-S. Together, these results suggest that riding increases focus, heightens the brain’s passive monitoring of changes in the sensory environment, and alters HPA axis response. More generally, our findings suggest that selective attention and sensory monitoring seem to be separable neural processes

Calixarene Assisted Rapid Synthesis of Silver-Graphene Nanocomposites with Enhanced Antibacterial Activity

Demonstrated herein is a single rapid approach employed for synthesis of Ag–graphene nanocomposites, with excellent antibacterial properties and low cytotoxicity, by utilizing a continuous hydrothermal flow synthesis (CHFS) process in combination with p-hexasulfonic acid calix[6]arene (SCX6) as an effective particle stabilizer. The nanocomposites showed high activity against E. coli (Gram-negative) and S. aureus (Gram-positive) bacteria. The materials were characterized using a range of techniques including transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, UV–vis spectrophotometry, FT-IR, and X-ray powder diffraction (XRD). This rapid, single step synthetic approach not only provides a facile means of enabling and controlling graphene reduction (under alkaline conditions) but also offers an optimal route for homogeneously producing and depositing highly crystalline Ag nanostructures into reduced graphene oxide substrate