The combinatorics of transcriptional regulation

The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their internal and external environment. At the transcriptional level, binding of transcription factors (TFs) in the vicinity of promoters can modulate the rate at which transcripts are produced, and as such play an important role in gene regulation. TFs with regulatory action at multiple promoters is the rule rather than the exception, with examples ranging from TFs like the cAMP receptor protein (CRP) in E. coli that regulates hundreds of different genes, to situations involving multiple copies of the same gene, such as on plasmids, or viral DNA. When the number of TFs heavily exceeds the number of binding sites, TF binding to each promoter can be regarded as independent. However, when the number of TF molecules is comparable to the number of binding sites, TF titration will result in coupling ("entanglement") between transcription of different genes. The last few decades have seen rapid advances in our ability to quantitatively measure such effects, which calls for biophysical models to explain these data. Here we develop a statistical mechanical model which takes the TF titration effect into account and use it to predict both the level of gene expression and the resulting correlation in transcription rates for a general set of promoters. To test these predictions experimentally, we create genetic constructs with known TF copy number, binding site affinities, and gene copy number; hence avoiding the need to use free fit parameters. Our results clearly prove the TF titration effect and that the statistical mechanical model can accurately predict the fold change in gene expression for the studied cases. We also generalize these experimental efforts to cover systems with multiple different genes, using the method of mRNA fluorescence in situ hybridization (FISH). Interestingly, we can use the TF titration affect as a tool to measure the plasmid copy number at different points in the cell cycle, as well as the plasmid copy number variance. Finally, we investigate the strategies of transcriptional regulation used in a real organism by analyzing the thousands of known regulatory interactions in E. coli. We introduce a "random promoter architecture model" to identify overrepresented regulatory strategies, such as TF pairs which coregulate the same genes more frequently than would be expected by chance, indicating a related biological function. Furthermore, we investigate whether promoter architecture has a systematic effect on gene expression by linking the regulatory data of E. coli to genome-wide expression censuses.

Optimum linear coding for additive noise systems using information feedback

The feedback coding problem for Gaussian systems in which the noise is neither white nor statistically independent between channels is formulated in terms of arbitrary linear codes at the transmitter and at the receiver. This new formulation is used to determine a number of feedback communication systems. In particular, the optimum linear code that satisfies an average power constraint on the transmitted signals is derived for a system with noiseless feedback and forward noise of arbitrary covariance. The noisy feedback problem is considered and signal sets for the forward and feedback channels are obtained with an average power constraint on each. The general formulation and results are valid for non-Gaussian systems in which the second order statistics are known, the results being applicable to the determination of error bounds via the Chebychev inequality.

Model-based approaches to handling additive noise in reverberant environments

Model-based approaches to handle additive and convolutional noise have been extensively investigated and used. However, the application of these schemes to handling reverberant noise has received less attention. This paper examines the extension of two standard additive/convolutional noise approaches to handling reverberant noise. The first is an extension of vector Taylor series (VTS) compensation, reverberant VTS, where a mismatch function including reverberant noise is used. The second scheme modifies constrained MLLR to allow a wide-span of frames to be taken into account and projected into the required dimensionality. To allow additive noise to be handled, both these schemes are combined with standard VTS. The approaches are evaluated and compared on two tasks, MC-WSJ-AV, and a reverberant simulated version of AURORA-4. © 2011 IEEE.

Additive Gaussian processes

We introduce a Gaussian process model of functions which are additive. An additive function is one which decomposes into a sum of low-dimensional functions, each depending on only a subset of the input variables. Additive GPs generalize both Generalized Additive Models, and the standard GP models which use squared-exponential kernels. Hyperparameter learning in this model can be seen as Bayesian Hierarchical Kernel Learning (HKL). We introduce an expressive but tractable parameterization of the kernel function, which allows efficient evaluation of all input interaction terms, whose number is exponential in the input dimension. The additional structure discoverable by this model results in increased interpretability, as well as state-of-the-art predictive power in regression tasks.

The foundations of a new approach to additive manufacturing: Characteristics of free space metal deposition

In this paper, we report on the realisation of a free space deposition process (FSD). For the first time the use of a moving support structure to deposit tracks of metal starting from a substrate and extending into free space is characterised. The ability to write metal shapes in free space has wide ranging applications in additive manufacturing and rapid prototyping where the tracks can be layered to build overhanging features without the use of fixed support structures (such as is used in selective laser melting (SLM) and stereo lithography (SLA)). We demonstrate and perform a preliminary characterisation of the process in which a soldering iron was used to deposit lead free solder tracks. The factors affecting the stability of tracks and the effect of operating parameters, temperature, velocity, initial track starting diameter and starting volume were measured. A series of 10 tracks at each setting were compared with a control group of tracks; the track width, taper and variation between tracks were compared. Notable results in free space track deposition were that the initial track diameter and volume affected the repeatability and quality of tracks. The standard deviation of mean track width of tracks from the constrained initial diameter group were half that of the unconstrained group. The amount of material fed to the soldering iron before commencing deposition affected the taper of tracks. At an initial volume of 7 mm3 and an initial track diameter of 0.8 mm, none of the ten tracks deposited broke or showed taper > ∼1°. The maximum deposition velocity for free space track deposition using lead-free solder was limited to 1.5 mm s-1. © 2011 Elsevier B.V. All rights reserved.

Electronic device with self-aligned electrodes fabricated using additive liquid deposition

The invention provides a multilayer electronic device having electrodes, formed on a laterally extending first layer, the lateral position of each of at least two adjacent electrodes being defined by a channel in the first layer. Each channel is adjacent a deposition region, the material which forms each electrode substantially covering the deposition region to form a continuous conductive structure.