Evolution of Salmonella within Hosts

Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections

Simulation of truncated normal variables

We provide in this paper simulation algorithms for one-sided and two-sided truncated normal distributions. These algorithms are then used to simulate multivariate normal variables with restricted parameter space for any covariance structure.Comment: This 1992 paper appeared in 1995 in Statistics and Computing and the gist of it is contained in Monte Carlo Statistical Methods (2004), but I receive weekly requests for reprints so here it is

In-situ measurements of the optical absorption of dioxythiophene-based conjugated polymers

Conjugated polymers can be reversibly doped by electrochemical means. This doping introduces new sub-bandgap optical absorption bands in the polymer while decreasing the bandgap absorption. To study this behavior, we have prepared an electrochemical cell allowing measurements of the optical properties of the polymer. The cell consists of a thin polymer film deposited on gold-coated Mylar behind which is another polymer that serves as a counterelectrode. An infrared transparent window protects the upper polymer from ambient air. By adding a gel electrolyte and making electrical connections to the polymer-on-gold films, one may study electrochromism in a wide spectral range. As the cell voltage (the potential difference between the two electrodes) changes, the doping level of the conjugated polymer films is changed reversibly. Our experiments address electrochromism in poly(3,4-ethylene-dioxy-thiophene) (PEDOT) and poly(3,4-dimethyl-propylene-dioxy-thiophene) (PProDOT-Me$_2$). This closed electrochemical cell allows the study of the doping induced sub-bandgap features (polaronic and bipolaronic modes) in these easily oxidized and highly redox switchable polymers. We also study the changes in cell spectra as a function of polymer thickness and investigate strategies to obtain cleaner spectra, minimizing the contributions of water and gel electrolyte features

Genome sequence of Acetomicrobium hydrogeniformans OS1

Acetomicrobium hydrogeniformans, an obligate anaerobe of the phylum Synergistetes, was isolated from oil production water. It has the unusual ability to produce almost 4 molecules H2/molecule glucose. The draft genome of A. hydrogeniformans OS1 (DSM 22491T) is 2,123,925 bp, with 2,068 coding sequences and 60 RNA genes

Multispectral snapshot demosaicing via non-convex matrix completion

Snapshot mosaic multispectral imagery acquires an undersampled data cube by acquiring a single spectral measurement per spatial pixel. Sensors which acquire $p$ frequencies, therefore, suffer from severe $1/p$ undersampling of the full data cube. We show that the missing entries can be accurately imputed using non-convex techniques from sparse approximation and matrix completion initialised with traditional demosaicing algorithms. In particular, we observe the peak signal-to-noise ratio can typically be improved by 2 to 5 dB over current state-of-the-art methods when simulating a $p=16$ mosaic sensor measuring both high and low altitude urban and rural scenes as well as ground-based scenes.Comment: 5 pages, 2 figures, 1 tabl

Computational Methods for Structural Mechanics and Dynamics, part 1

The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling

A perpetual switching system in pulmonary capillaries

Of the 300 billion capillaries in the human lung, a small fraction meet normal oxygen requirements at rest, with the remainder forming a large reserve. The maximum oxygen demands of the acute stress response require that the reserve capillaries are rapidly recruited. To remain primed for emergencies, the normal cardiac output must be parceled throughout the capillary bed to maintain low opening pressures. The flow-distributing system requires complex switching. Because the pulmonary microcirculation contains contractile machinery, one hypothesis posits an active switching system. The opposing hypothesis is based on passive switching that requires no regulation. Both hypotheses were tested ex vivo in canine lung lobes. The lobes were perfused first with autologous blood, and capillary switching patterns were recorded by videomicroscopy. Next, the vasculature of the lobes was saline flushed, fixed by glutaraldehyde perfusion, flushed again, and then reperfused with the original, unfixed blood. Flow patterns through the same capillaries were recorded again. The 16-min-long videos were divided into 4-s increments. Each capillary segment was recorded as being perfused if at least one red blood cell crossed the entire segment. Otherwise it was recorded as unperfused. These binary measurements were made manually for each segment during every 4 s throughout the 16-min recordings of the fresh and fixed capillaries (>60,000 measurements). Unexpectedly, the switching patterns did not change after fixation. We conclude that the pulmonary capillaries can remain primed for emergencies without requiring regulation: no detectors, no feedback loops, and no effectors-a rare system in biology. NEW & NOTEWORTHY The fluctuating flow patterns of red blood cells within the pulmonary capillary networks have been assumed to be actively controlled within the pulmonary microcirculation. Here we show that the capillary flow switching patterns in the same network are the same whether the lungs are fresh or fixed. This unexpected observation can be successfully explained by a new model of pulmonary capillary flow based on chaos theory and fractal mathematics

Mini-mast CSI testbed user's guide

The Mini-Mast testbed is a 20 m generic truss highly representative of future deployable trusses for space applications. It is fully instrumented for system identification and active vibrations control experiments and is used as a ground testbed at NASA-Langley. The facility has actuators and feedback sensors linked via fiber optic cables to the Advanced Real Time Simulation (ARTS) system, where user defined control laws are incorporated into generic controls software. The object of the facility is to conduct comprehensive active vibration control experiments on a dynamically realistic large space structure. A primary goal is to understand the practical effects of simplifying theoretical assumptions. This User's Guide describes the hardware and its primary components, the dynamic characteristics of the test article, the control law implementation process, and the necessary safeguards employed to protect the test article. Suggestions for a strawman controls experiment are also included

Form factor for a family of quantum graphs: An expansion to third order

For certain types of quantum graphs we show that the random-matrix form factor can be recovered to at least third order in the scaled time $\tau$ from periodic-orbit theory. We consider the contributions from pairs of periodic orbits represented by diagrams with up to two self-intersections connected by up to four arcs and explain why all other diagrams are expected to give higher-order corrections only. For a large family of graphs with ergodic classical dynamics the diagrams that exist in the absence of time-reversal symmetry sum to zero. The mechanism for this cancellation is rather general which suggests that it may also apply at higher-orders in the expansion. This expectation is in full agreement with the fact that in this case the linear-$\tau$ contribution, the diagonal approximation, already reproduces the random-matrix form factor for $\tau<1$. For systems with time-reversal symmetry there are more diagrams which contribute at third order. We sum these contributions for quantum graphs with uniformly hyperbolic dynamics, obtaining $+2\tau^{3}$, in agreement with random-matrix theory. As in the previous calculation of the leading-order correction to the diagonal approximation we find that the third order contribution can be attributed to exceptional orbits representing the intersection of diagram classes.Comment: 23 pages (including 4 fig.) - numerous typos correcte