MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling

Background Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm. Results After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively. Conclusions MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base

SOAR (Support Office for Aerogeophysical Research) Annual Report 1995/1996

The Support Office for Aerogeophysical Research (SOAR) was a facility of the National Science Foundation's Office of Polar Programs whose mission is to make airborne geophysical observations available to the broad research community of geology, glaciology and other sciences. The central office of the SOAR facility is located in Austin, Texas within the University of Texas Institute for Geophysics. Other institutions with significant responsibilities are the Lamont­ Doherty Earth Observatory of Columbia University and the Geophysics Branch of the U.S . Geological Survey. This report summarizes the goals and accomplishments of the SOAR facility during 1995/1996 and plans for the next year.National Science Foundation's Office of Polar ProgramsInstitute for Geophysic

A method for assessing the success and failure of community-level interventions in the presence of network diffusion, social reinforcement, and related social effects

Prevention and intervention work done within community settings often face unique analytic challenges for rigorous evaluations. Since community prevention work (often geographically isolated) cannot be controlled in the same way other prevention programs and these communities have an increased level of interpersonal interactions, rigorous evaluations are needed. Even when the `gold standard' randomized control trials are implemented within community intervention work, the threats to internal validity can be called into question given informal social spread of information in closed network settings. A new prevention evaluation method is presented here to disentangle the social influences assumed to influence prevention effects within communities. We formally introduce the method and it's utility for a suicide prevention program implemented in several Alaska Native villages. The results show promise to explore eight sociological measures of intervention effects in the face of social diffusion, social reinforcement, and direct treatment. Policy and research implication are discussed.Comment: 18 pages, 5 figure

The Orbital Period of the Be/Neutron Star Binary RX J0812.4-3114

We present the results of Rossi X-ray Timing Explorer observations of the Be star X-ray binary system RX J0812.4-3114. A light curve obtained with the RXTE All-Sky Monitor shows that the source is currently in an active state with outbursts occurring at approximately 80 day intervals. The source underwent a transition from an inactive state to this regular outburst state early in 1998. An observation of RX J0812.4-3114 was obtained with the RXTE Proportional Counter Array close to the time of a predicted maximum in March 1999 and strong pulsations were detected at a period of 31.88 seconds. This confirms the result of an earlier PCA observation by Reig & Roche which was serendipitously also obtained near the predicted maximum flux of the 80 day period and also near the start of the current active state. We interpret the periodicity in the ASM light curve as indicating the orbital period of RX J0812.4-3114 with outbursts occurring around periastron passage

Light structures phototroph, bacterial and fungal communities at the soil surface

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere

Coherent spin-current oscillations in transverse magnetic fields

We address the coherence of the dynamics of spin-currents with components transverse to an external magnetic field for the spin-1/2 Heisenberg chain. We study current autocorrelations at finite temperatures and the real-time dynamics of currents at zero temperature. Besides a coherent Larmor oscillation, we find an additional collective oscillation at higher frequencies, emerging as a coherent many-magnon effect at low temperatures. Using numerical and analytical methods, we analyze the oscillation frequency and decay time of this coherent current-mode versus temperature and magnetic field.Comment: 4 pages, 5 figures (and supplemental material: 4 pages, 6 figures

Directed diffusion of reconstituting dimers

We discuss dynamical aspects of an asymmetric version of assisted diffusion of hard core particles on a ring studied by G. I. Menon {\it et al.} in J. Stat Phys. {\bf 86}, 1237 (1997). The asymmetry brings in phenomena like kinematic waves and effects of the Kardar-Parisi-Zhang nonlinearity, which combine with the feature of strongly broken ergodicity, a characteristic of the model. A central role is played by a single nonlocal invariant, the irreducible string, whose interplay with the driven motion of reconstituting dimers, arising from the assisted hopping, determines the asymptotic dynamics and scaling regimes. These are investigated both analytically and numerically through sector-dependent mappings to the asymmetric simple exclusion process.Comment: 10 pages, 6 figures. Slight corrections, one added reference. To appear in J. Phys. Cond. Matt. (2007). Special issue on chemical kinetic

The Use of Gamma-ray Bursts as Direction and Time Markers in SETI Strategies

When transmitting a signal over a large distance it is more efficient to send a brief beamed signal than a continuous omni-directional transmission but this requires that the receiver knows where and when to look for the transmission. For SETI, the use of various natural phenomena has previously been suggested to achieve the desired synchronization. Here it is proposed that gamma-ray bursts may well the best ``synchronizers'' of all currently known phenomena due to their large intrinsic luminosities, high occurrence rate, isotropic sky distribution, large distance from the Galaxy, short duration, and easy detectability. For targeted searches, precise positions for gamma-ray bursts are required together with precise distance measurements to a target star. The required burst position determinations are now starting to be obtained, aided in large part by the discovery of optical afterglows. Good distance measurements are currently available from Hipparcos and even better measurements should be provided by spacecraft now being developed. For non-targeted searches, positional accuracies simply better than a detector's field of view may suffice but the time delay between the detection of a gamma-ray burst and the reception of the transmitted signal cannot be predicted in an obvious way.Comment: 8 pages, accepted for publication in PAS

Pore-blockade Times for Field-Driven Polymer Translocation

We study pore blockade times for a translocating polymer of length $N$, driven by a field $E$ across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical interactions. We find that the typical time the pore remains blocked during a translocation event scales as $\sim N^{(1+2\nu)/(1+\nu)}/E$, where $\nu\simeq0.588$ is the Flory exponent for the polymer. In line with our previous work, we show that this scaling behaviour stems from the polymer dynamics at the immediate vicinity of the pore -- in particular, the memory effects in the polymer chain tension imbalance across the pore. This result, along with the numerical results by several other groups, violates the lower bound $\sim N^{1+\nu}/E$ suggested earlier in the literature. We discuss why this lower bound is incorrect and show, based on conservation of energy, that the correct lower bound for the pore-blockade time for field-driven translocation is given by $\eta N^{2\nu}/E$, where $\eta$ is the viscosity of the medium surrounding the polymer.Comment: 14 pages, 6 figures, slightly shorter than the previous version; to appear in J. Phys.: Cond. Ma