Scintillation particle detection based on microfluidics

A novel type of particle detector based on scintillation, with precise spatial resolution and high radiation hardness, is being studied. It consists of a single microfluidic channel filled with a liquid scintillator and is designed to define an array of scintillating waveguides each independently coupled to a photodetector. Prototype detectors built using an SU-8 epoxy resin have been tested with electrons from a radioactive source. The experimental results show a light yield compatible with the theoretical expectations and confirm the validity of the approach

Modeling DNA-binding of Escherichia coli σ70 exhibits a characteristic energy landscape around strong promoters

We present a computational model of DNA-binding by σ70 in Escherichia coli which allows us to extract the functional characteristics of the wider promoter environment. Our model is based on a measure for the binding energy of σ70 to the DNA, which is derived from promoter strength data and used to build up a non-standard weight matrix. Opposed to conventional approaches, we apply the matrix to the environment of 3765 known promoters and consider the average matrix scores to extract the common features. In addition to the expected minimum of the average binding energy at the exact promoter site, we detect two minima shortly upstream and downstream of the promoter. These are likely to occur due to correlation between the two binding sites of σ70. Moreover, we observe a characteristic energy landscape in the 500 bp surrounding the transcription start sites, which is more pronounced in groups of strong promoters than in groups of weak promoters. Our subsequent analysis suggests that the characteristic energy landscape is more likely an influence on target search by the RNA polymerase than a result of nucleotide biases in transcription factor binding sites

Local conservation scores without a priori assumptions on neutral substitution rates

<p>Abstract</p> <p>Background</p> <p>Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed that about half of the experimentally verified functional elements found in non-coding DNA were classified as unconstrained by computational predictions. Following this observation, it has been hypothesized that this may be partly explained by biased estimates on neutral evolutionary rates used by existing sequence conservation metrics. All methods we are aware of rely on a comparison with the neutral rate and conservation is estimated by measuring the deviation of a particular genomic region from this rate. Consequently, it is a reasonable assumption that inaccurate neutral rate estimates may lead to biased conservation and constraint estimates.</p> <p>Results</p> <p>We propose a conservation signal that is produced by local Maximum Likelihood estimation of evolutionary parameters using an optimized sliding window and present a Kullback-Leibler projection that allows multiple different estimated parameters to be transformed into a conservation measure. This conservation measure does not rely on assumptions about neutral evolutionary substitution rates and little a priori assumptions on the properties of the conserved regions are imposed. We show the accuracy of our approach (KuLCons) on synthetic data and compare it to the scores generated by state-of-the-art methods (phastCons, GERP, SCONE) in an ENCODE region. We find that KuLCons is most often in agreement with the conservation/constraint signatures detected by GERP and SCONE while qualitatively very different patterns from phastCons are observed. Opposed to standard methods KuLCons can be extended to more complex evolutionary models, e.g. taking insertion and deletion events into account and corresponding results show that scores obtained under this model can diverge significantly from scores using the simpler model.</p> <p>Conclusion</p> <p>Our results suggest that discriminating among the different degrees of conservation is possible without making assumptions about neutral rates. We find, however, that it cannot be expected to discover considerably different constraint regions than GERP and SCONE. Consequently, we conclude that the reported discrepancies between experimentally verified functional and computationally identified constraint elements are likely not to be explained by biased neutral rate estimates.</p

Iterative Network and Channel Decoding for the Two-Way Relay Channel

Abstract — We introduce an extension of the relay channel that we call two-way relay channel. The two-way relay channel consists of two users which want to communicate to each other with the help of one relay. We consider the time-division twoway relay channel without power control, where the broadcast channels are orthogonalized in time and where the two users and the relay use the same transmission power. We describe a joint network-channel coding method for this channel model, where channel codes are used at both users and a network code is used at the relay. The channel code of one user and the network code form a distributed turbo code which we call turbo network code and which can be iteratively decoded at the other user. Moreover, we conjecture closed expressions for lower bounds for the channel capacities of the time-division relay and twoway relay channel without power control and deliver simulation results of the proposed turbo network code. I

Iterative Source-Channel Decoding based on a Trellis representation for Variable

Abstract -A new trellis representation for variable length codes (VLC) is proposed which allows soft-in/soft-out decoding of these codes. Applying the BCJR-algorithm on this trellis either symbol-level or bit-level reliability information for the variable length coded sequence can be obtained. By using this softin/soft-out VLC decoder for iterative (&quot;turbo&quot;) decoding of a serially concatenated scheme consisting of an outer variable length code and an inner convolutional code separated by an interleaver significant gains can be yielded compared to a instantaneously decoded variable length c6de of the same overall source and channel code rate