Expression Templates Research Articles

A sequential expression system for high‐throughput functional genomic analysis

A method employing sequential rounds of cell-free protein synthesis (CFPS) was developed to identify gene products influencing the complex metabolic systems that result in protein accumulation and folding in vitro. The first round of CFPS creates an array of cell extracts individually enriched with a single gene product expressed in-parallel from linear DNA expression templates (ETs). The cell extract is engineered to enhance template stability and to provide reaction conditions conducive for general protein activation. Following first-round expression, linear templates are selectively degraded and a plasmid template for a reporter enzyme is added to initiate a subsequent round of protein expression. Reporter concentration and activity identify first-round gene products that affect amino acid and nucleic acid stability, energy supply, protein expression, stability, and activation. This sequential CFPS system provides a unique format for the functional genomic identification of broadly diverse metabolic activities.

Rapid Expression of Functional Genomic Libraries

Genomic-scale analysis of protein function is currently limited by the ability to rapidly express the enormous diversity of protein targets in their active form. We describe a method to construct transcriptionally active expression templates (ETs) in parallel using a single PCR step wherein the overlap-extension reaction for addition of transcription regulatory elements is separated from the amplification of the full-length product by using a GC-rich single primer. Over 90% of 55 diverse genomic targets were extended with T7 regulatory elements to form ETs in high yield and purity. The unpurified ETs directed protein expression using a cell-free protein synthesis (CFPS) system supplemented with cofactors and metal ions to activate a variety of enzymes. Higher activities were obtained in the modified CFPS reactions compared to standard reaction conditions. Protein purification was avoided because the expressed enzyme activity was significantly greater than the background activity associated with the cell extract. These improvements in the parallel synthesis of linear ETs combined with enhanced in vitro enzyme activation help to make CFPS systems more attractive platforms for high-throughput evaluation of protein function.

A Domain Specific Embedded Language in C++ for Automatic Differentiation, Projection, Integration and Variational Formulations

In this article, we present a domain specific embedded language in C++ that can be used in various contexts such as numerical projection onto a functional space, numerical integration, variational formulations and automatic differentiation. Albeit these tools operate in different ways, the language overcomes this difficulty by decoupling expression constructions from evaluation. The language is implemented using expression templates and meta‐programming techniques and uses various Boost libraries. The language is exercised on a number of non‐trivial examples and a benchmark presents the performance behavior on a few test problems.

A massively parallel particle-in-cell code for the simulation of field-emitter based electron sources

For the realistic simulation of electron sources using field emitter arrays, the sub-micron resolution required for the emitters leads to simulation models not suitable for current serial codes. Thus, a parallel high-performance 3D Particle-In-Cell code, called Capone, has been implemented in C++ using the POOMA II framework on the Linux platform. Sophisticated C++ expression templates techniques deliver Fortran performance combined with high-level programming and development comfort. For the computation of external fields, matching parallel field solvers are in development with the electrostatic one being completed. The Maxwell field solver is based on the Finite Integration Algorithm on a non-uniform rectilinear grid. Anisotropic ε and μ constants and perfect electric/magnetic materials stored in triangulated grid cells are supported as well as open, electric and magnetic boundary conditions. Self-consistent macro-particle pushing is accomplished by integrating the classical relativistic equations of motion in combination with charge-conserving current scattering onto the computational grid. Parallelization is performed by partitioning the calculation domain into patches associated to individual processors. Fields are statically distributed while Particles are concurrently distributed to processors according to their position to allow fast local interpolation.

RNA interference targeting leptin gene effect on hepatic stellate cells

To construct the specific siRNA expression vectors and investigate their effect on leptin and collagen I in HSC, which provide a new approach to the prevent and treat hepatic fibrosis. The five siRNAs against leptin gene were transcript synthesized intracellularly by expression templates of plasmid vector psiRNA-hH1neo. The recombinant leptin siRNA plasmid vectors could express in eukaryocyte, and then to evaluate them by using enzyme cutting and sequencing. The recombinant plasmids were transfected into HSCs using Lipofectamine methods respectively. The cells were selected after growing in DMEM containing 300 microg/mL G418 for about 4 weeks. Gene expression of leptin and collagen I were showed by Western blot analysis and reverse transcription polymerase chain reaction (RT-PCR). Identification by enzyme cutting and sequencing showed that the leptin siRNA expression vectors were constructed successfully, and leptin siRNA could inhibit the leptin and collagen I gene expression effectively. It was concluded that RNA interference-mediated silencing of leptin gene diminished leptin and collagen I gene expression in HSCs. Furthermore, attenuated the extracellular matrix over-deposition at the same time. Leptin gene is ideal targets of gene therapy for liver fibrosis.

The abstract vector processor

The abstract vector processing unit (VPU) is a virtual VPU that represents a set of real VPUs. It has an idealised instruction set and constraints common to the VPUs that it represents. Together, the idealised instruction set and common constraints allow programs to be portable and to perform efficiently on the real VPUs being represented. The abstract VPU is suitable for programmers who want the performance advantages of using the VPU directly, without being restricted to a particular VPU. An abstract VPU implementation, Vector Virtual Machine (VVM), is presented in this paper. VVM is designed to represent desktop VPUs, such as AltiVec, and to support the creation of a generic, vectorised, machine-vision library. Constraints common to desktop VPUs that VVM are short vectors, fixed vector sizes, and fast access to aligned memory addresses only. To support the creation of a generic, vectorised, machine-vision library, VVM has traits, templated vectors, constant scalar count vectors, and uses consistent functions for scalars and vectors where possible. Because VVM has constant scalar count, each VVM vector can consist of more than one scalar or VPU vector. Since the cost of type conversions is large for VPU programs, VVM only supports explicit type conversions. Ideally, an abstract VPU should have no overheads; that is be zero-cost. Function overloading and expression templates were tested to investigate the possibility of creating a zero-cost implementation of VVM using only Standard C++ and Apple's GCC 3.1 20021003 compiler. Results show that in this environment, zero-cost can be achieved only when processing VVM vectors that contain a single scalar or VPU vector. For expressions involving one to five additions, function overloading was at worst 3.6% slower than hand-coded programs when processing VVM vectors with one scalar or VPU vector. Unfortunately, for VVM vectors with four VPU vectors, function overloading was at worst 23.0% slower. For the same kind of expressions, the expression templates implementation was up to 888.3% slower. It was comparable to hand-coded programs only for expressions involving only one addition between VVM vectors that contain four VPU vectors. When a VPU is available, only char VVM vectors will consist of one VPU vector. In scalar mode, all VVM vectors will consist of one scalar. Thus, with Apple GCC 3.1 20031003, a VVM implementation based on function overloading has minimal overheads only for applications where most operations involve char types. This implementation's performance is adequate for creating a generic, vectorised, machine-vision library because most image processing operations operate on char types.

Comparing and combining a semantic tagger and a statistical tool for MWE extraction

Automatic extraction of multiword expressions (MWEs) presents a tough challenge for the NLP community and corpus linguistics. Indeed, although numerous knowledge-based symbolic approaches and statistically driven algorithms have been proposed, efficient MWE extraction still remains an unsolved issue. In this paper, we evaluate the Lancaster UCREL Semantic Analysis System (henceforth USAS (Rayson, P., Archer, D., Piao, S., McEnery, T., 2004. The UCREL semantic analysis system. In: Proceedings of the LREC-04 Workshop, Beyond Named Entity Recognition Semantic labelling for NLP tasks, Lisbon, Portugal. pp. 7–12)) for MWE extraction, and explore the possibility of improving USAS by incorporating a statistical algorithm. Developed at Lancaster University, the USAS system automatically annotates English corpora with semantic category information. Employing a large-scale semantically classified multi-word expression template database, the system is also capable of detecting many multiword expressions, as well as assigning semantic field information to the MWEs extracted. Whilst USAS therefore offers a unique tool for MWE extraction, allowing us to both extract and semantically classify MWEs, it can sometimes suffer from low recall. Consequently, we have been comparing USAS, which employs a symbolic approach, to a statistical tool, which is based on collocational information, in order to determine the pros and cons of these different tools, and more importantly, to examine the possibility of improving MWE extraction by combining them. As we report in this paper, we have found a highly complementary relation between the different tools: USAS missed many domain-specific MWEs (law/court terms in this case), and the statistical tool missed many commonly used MWEs that occur in low frequencies (lower than three in this case). Due to their complementary relation, we are proposing that MWE coverage can be significantly increased by combining a lexicon-based symbolic approach and a collocation-based statistical approach.

A new look at expression templates for maxtrix computation

We reinterpret the expression templates for matrix computation put forward by other authors in light of functional programming ideas. Existing expression template libraries frequently focus on componentwise operations such as addition at the expense of matrix multiplication. The ideas presented are implemented in a C++ library called LLANO (Lazy Linear Algebraic Numerical Objects).

Expression templates for partial differential equations

The implementation of numerical algorithms for solving partial differential equations costs a lot of time and the optimization of such codes is difficult. These problems can be reduced by expression templates for partial differential equations. Using this concept, one can implement numerical algorithms for PDE’s in a language which is close to the mathematical language. Expression templates give the compiler global informations on an expression such that the optimization of the code can be left to the compiler. Numerical results for the Stokes operator on general domains in 3D are presented.

Automatic differentiation in C++ using expression templates and. application to a flow control problem

This work deals with an implementation of automatic differentiation of C++ computer programs in forward mode using operator overloading and expression templates. We report on the efficiency of such implementation and its obvious advantage : the ability to perform sensitivity analysis without touching the source of the computer program by simply adding a library to it. We apply this tool to a flow control problem : minimize the drag of a cylinder, in subsonic unsteady turbulent flow, by controlling the boundary condition of the cylinder.

Left hemisphere representations of emotional facial expressions

Researchers have suggested that the right hemisphere is superior at processing emotional facial expressions because it contains stored perceptual ‘templates’ of facial expressions. We tested each hemisphere of a split-brain patient on two tasks involving emotional facial expressions. Both hemispheres performed equally well and significantly above chance matching facial expressions with emotion words. The subject's right hemisphere consistently performed well judging whether two facial expressions were the same or different. His left hemisphere performed poorly on this discrimination task at first, but showed a sharp improvement when the instructions were changed slightly, emphasizing verbal labels for the facial expressions. Results suggest that ‘facial expression templates’ may not be stored only on the right.

Processing determinants required for in vitro cleavage of the poliovirus P1 precursor to capsid proteins.

We generated defined alterations in poliovirus protein-processing substrates and assayed the effects of these alterations with an in vitro expression system. A complete cDNA copy of the poliovirus genome was inserted into a bacteriophage T7 transcription vector. Using this expression template, we produced RNA transcripts containing defined regions of the poliovirus capsid precursor polypeptide (P1) and RNA transcripts containing mutations in the P1 and P2 regions. In vitro translation of P1-derived transcripts allowed us to characterize the 3C-mediated cleavage of P1 to capsid proteins. We demonstrated that, for either posttranslational or cotranslational cleavage at any of the Q-G amino acid pairs within P1, almost the entire P1 precursor is required. We also demonstrated that minimal sequences 3' to the 2A coding sequence are required to generate active 2A proteinase in vitro and that two specific four-amino-acid insertions in protein 2C do not alter 2A- or 3C-mediated processing of the poliovirus polyprotein. In addition, we demonstrated that substantial deletion of P1 sequences does not alter 2A-mediated cleavage of the Y-G site at the P1-P2 junction. These results allowed us to compare the P1 sequences required for 2A- versus 3C-mediated processing of the capsid precursor, and we discuss these results in the context of the three-dimensional structure of the capsid proteins.