An efficient system to generate monoclonal antibodies against membrane-associated proteins by immunisation with antigen-expressing mammalian cells

ABSTRACT: BACKGROUND: The generation of monoclonal antibodies specific for protein antigens usually depends on purified recombinant protein for both immunisation and hybridoma screening. Purification of recombinant protein in sufficient yield and purity is a tedious undertaking and can be demanding especially in the case of membrane proteins. Furthermore, antibodies generated against a purified recombinant protein are frequently incapable of binding to the endogenous protein in its native context. RESULTS: We describe a strategy to generate monoclonal antibodies against membrane or membrane-associated proteins that completely bypasses any need for purified recombinant antigen. This approach utilises stably transfected mammalian cells expressing recombinant antigens on their cell surface for immunisation of mice. The transfected cells are also used for measuring seroconversion, hybridoma selection and antibody characterisation. By presenting the antigen in its native conformation for immunisation and hybridoma selection, this procedure promotes the generation of antibodies capable of binding to the endogenous protein. In the present study, we applied this approach successfully for three predicted GPI-anchored proteins of the malaria parasite Plasmodium falciparum. CONCLUSIONS: The described entirely cell-based technology is a fast and efficient approach for obtaining antibodies reactive with endogenous cell-surface proteins in their native conformatio

Microarchitectural Low-Power Design Techniques for Embedded Microprocessors

With the omnipresence of embedded processing in all forms of electronics today, there is a strong trend towards wireless, battery-powered, portable embedded systems which have to operate under stringent energy constraints. Consequently, low power consumption and high energy efficiency have emerged as the two key criteria for embedded microprocessor design. In this thesis we present a range of microarchitectural low-power design techniques which enable the increase of performance for embedded microprocessors and/or the reduction of energy consumption, e.g., through voltage scaling. In the context of cryptographic applications, we explore the effectiveness of instruction set extensions (ISEs) for a range of different cryptographic hash functions (SHA-3 candidates) on a 16-bit microcontroller architecture (PIC24). Specifically, we demonstrate the effectiveness of light-weight ISEs based on lookup table integration and microcoded instructions using finite state machines for operand and address generation. On-node processing in autonomous wireless sensor node devices requires deeply embedded cores with extremely low power consumption. To address this need, we present TamaRISC, a custom-designed ISA with a corresponding ultra-low-power microarchitecture implementation. The TamaRISC architecture is employed in conjunction with an ISE and standard cell memories to design a sub-threshold capable processor system targeted at compressed sensing applications. We furthermore employ TamaRISC in a hybrid SIMD/MIMD multi-core architecture targeted at moderate to high processing requirements (> 1 MOPS). A range of different microarchitectural techniques for efficient memory organization are presented. Specifically, we introduce a configurable data memory mapping technique for private and shared access, as well as instruction broadcast together with synchronized code execution based on checkpointing. We then study an inherent suboptimality due to the worst-case design principle in synchronous circuits, and introduce the concept of dynamic timing margins. We show that dynamic timing margins exist in microprocessor circuits, and that these margins are to a large extent state-dependent and that they are correlated to the sequences of instruction types which are executed within the processor pipeline. To perform this analysis we propose a circuit/processor characterization flow and tool called dynamic timing analysis. Moreover, this flow is employed in order to devise a high-level instruction set simulation environment for impact-evaluation of timing errors on application performance. The presented approach improves the state of the art significantly in terms of simulation accuracy through the use of statistical fault injection. The dynamic timing margins in microprocessors are then systematically exploited for throughput improvements or energy reductions via our proposed instruction-based dynamic clock adjustment (DCA) technique. To this end, we introduce a 6-stage 32-bit microprocessor with cycle-by-cycle DCA. Besides a comprehensive design flow and simulation environment for evaluation of the DCA approach, we additionally present a silicon prototype of a DCA-enabled OpenRISC microarchitecture fabricated in 28 nm FD-SOI CMOS. The test chip includes a suitable clock generation unit which allows for cycle-by-cycle DCA over a wide range with fine granularity at frequencies exceeding 1 GHz. Measurement results of speedups and power reductions are provided

Application-Specific Processor Design for Low-Complexity & Low-Power Embedded Systems

PhD Forum: Presentation & Poster Sessio

Track loading limits and cross-acceptance of vehicle approvals

The requirements for track loading limits are one of the main barriers to simple cross-acceptance of vehicles where rolling stock that is already operating successfully in one (or more) networks has to be retested before it can be approved for operation on another network. DynoTRAIN Work Package 4 studied this area in order to determine whether the additional requirements were justified, or if the process could be made much cheaper and simpler without increasing the risk of track deterioration for the networks. The review of national requirements identified modified criteria and limit values for track forces in some member states; however, these can be obtained from additional analysis of the normal test results with no new tests required. The influence of design rail inclination has also been found not to be significant, provided a realistic range of wheel–rail contact conditions are included in the tests. For line speeds greater than or equal to 160 km/h, the current standards for track construction across the member states appear to be similar. On lower speed lines in some countries, a ‘weaker’ track condition may require a lower limit on one of the vehicle assessment parameters. Track dynamics modelling has shown that the vehicle assessment parameters used in international standards are suitable for use in cross-acceptance for track forces. The use of multiple regression analysis allows the estimated maximum value for relevant parameters to be evaluated for different target conditions and then compared with the appropriate limit value, or with values for existing, comparable vehicles. Guidance has also been provided on the relevant parameters to consider when developing operating controls for different types of track deterioration

Investigating the Potential of Custom Instruction Set Extensions for SHA-3 Candidates on a 16-bit Microcontroller Architecture

In this paper, we investigate the benefit of instruction set extensions for software implementations of all five SHA-3 candidates. To this end, we start from optimized assembly code for a common 16-bit microcontroller instruction set architecture. By themselves, these implementations provide reference for complexity of the algorithms on 16-bit architectures, commonly used in embedded systems. For each algorithm, we then propose suitable instruction set extensions and implement the modified processor core. We assess the gains in throughput, memory consumption, and the area overhead. Our results show that with less than 10% additional area, it is possible to increase the execution speed on average by almost 40%, while reducing memory requirements on average by more than 40%. In particular, the Grostl algorithm, which was one of the slowest algorithms in previous reference implementations, ends up being the fastest implementation by some margin, once minor (but dedicated) instruction set extensions are taken into account

A Wireless Body Sensor Network For Activity Monitoring With Low Transmission Overhead

Activity recognition has been a research field of high interest over the last years, and it finds application in the medical domain, as well as personal healthcare monitoring during daily home- and sports-activities. With the aim of producing minimum discomfort while performing supervision of subjects, miniaturized networks of low-power wireless nodes are typically deployed on the body to gather and transmit physiological data, thus forming a Wireless Body Sensor Network (WBSN). In this work, we propose a WBSN for online activity monitoring, which combines the sensing capabilities of wearable nodes and the high computational resources of modern smartphones. The proposed solution provides different tradeoffs between classification accuracy and energy consumption, thanks to different workloads assigned to the nodes and to the mobile phone in different network configurations. In particular, our WBSN is able to achieve very high activity recognition accuracies (up to 97.2%) on multiple subjects, while significantly reducing the sampling frequency and the volume of transmitted data with respect to other state-of-the art solutions

A Targeted Genetic Association Study of Epithelial Ovarian Cancer Susceptibility

BACKGROUND: Genome-wide association studies have identified several common susceptibility alleles for epithelial ovarian cancer (EOC). To further understand EOC susceptibility, we examined previously ungenotyped candidate variants, including uncommon variants and those residing within known susceptibility loci. RESULTS: At nine of eleven previously published EOC susceptibility regions (2q31, 3q25, 5p15, 8q21, 8q24, 10p12, 17q12, 17q21.31, and 19p13), novel variants were identified that were more strongly associated with risk than previously reported variants. Beyond known susceptibility regions, no variants were found to be associated with EOC risk at genome-wide statistical significance (p \u3c5x10(-8)), nor were any significant after Bonferroni correction for 17,000 variants (p\u3c 3x10-6). METHODS: A customized genotyping array was used to assess over 17,000 variants in coding, non-coding, regulatory, and known susceptibility regions in 4,973 EOC cases and 5,640 controls from 13 independent studies. Susceptibility for EOC overall and for select histotypes was evaluated using logistic regression adjusted for age, study site, and population substructure. CONCLUSION: Given the novel variants identified within the 2q31, 3q25, 5p15, 8q21, 8q24, 10p12, 17q12, 17q21.31, and 19p13 regions, larger follow-up genotyping studies, using imputation where necessary, are needed for fine-mapping and confirmation of low frequency variants that fall below statistical significance

DynOR: A 32-bit Microprocessor in 28 nm FD-SOI with Cycle-By-Cycle Dynamic Clock Adjustment

This paper presents DynOR, a 32-bit 6-stage OpenRISC microprocessor with dynamic clock adjustment. To alleviate the issue of unused dynamic timing margins, the clock period of the processor is adjusted on a cycle-by-cycle level, based on the instruction types currently in flight in the pipeline. To this end, we employ a custom designed clock generation unit, capable of immediate glitch-free adjustments of the clock period over a wide range with fine granularity. Our chip measurements in 28nm FD-SOI technology show that DynOR provides an average speedup of 19% in program execution over a wide range of operating conditions, with a peak speedup for certain applications of up to 41%. Furthermore, this speedup can be traded off against energy, to reduce the chip power consumption for a typical die by up to 15%, compared to a static clocking scheme based on worst case excitation

TamaRISC-CS: An Ultra-Low-Power Application-Specific Processor for Compressed Sensing

Compressed sensing (CS) is a universal technique for the compression of sparse signals. CS has been widely used in sensing platforms where portable, autonomous devices have to operate for long periods of time with limited energy resources. Therefore, an ultra-low-power (ULP) CS implementation is vital for these kind of energy-limited systems. Sub-threshold (sub-VT ) operation is commonly used for ULP computing, and can also be combined with CS. However, most established CS implementations can achieve either no or very limited benefit from sub-VT operation. Therefore, we propose a sub-VT application-specific instruction-set processor (ASIP), exploiting the specific operations of CS. Our results show that the proposed ASIP accomplishes 62x speed-up and 11.6x power savings with respect to an established CS implementation running on the baseline low-power processor

1 Mbps coherent one-way QKD with dense wavelength division multiplexing and hardware key distillation

We present the latest results obtained with a quantum cryptography prototype based on a coherent-one way quantum key distribution (QKD) scheme. To support its continuous high rate secret key generation we developed different low-noise single photon detectors for telecom wavelength based on a sine gating and low-pass-filtering technique, as well as a negative feedback APD in an active hold-off circuit. A newly developed hardware distillation engine allows for continuous operation of secret key distribution up to 1 Mbps. We also present results of our system in a DWDM (dense wavelength-division multiplexing) configuration where only one single fiber is needed to interconnect Alice’ and Bob’s systems. The final prototype is fully compatible to serve a high-speed encryption device developed in parallel which provides encrypted communication of up to 100 Gbps