A 60 GHz wide tuning range SiGe bipolar VCO for HDMI and wireless docking applications

A wide tuning range voltage controlled oscillator (VCO) with novel architecture is proposed in this work. The entire circuit consists of a VCO core, a summing circuit, a single-ended to differential (STD) converter and a buffer amplifier. The VCO core oscillates at half the desired frequency and the second harmonic of the VCO core is extracted by the summing circuit, which is then converted to a differential pair by the STD. The entire VCO circuit operates from 58.85 to 70.85 GHz with 20% frequency tuning range. The measured VCO gain is less than 1.6 GHz/V. The measured phase noise at 3 MHz offset is less than -78 dBc/Hz across the entire tuning range. The differential phase error of the output signals is measured by down converting the VCO output signals to low gigahertz frequency using an on-chip mixer. The measured differential phase error is less than 8°. The VCO circuit, which is constructed using 0.35 µm SiGe technology, occupies 770 × 550 µm2 die area and consumes 62 mA under 3.5 V supply.

Thermal conductivity measurement of liquids in a microfluidic device

A new microfluidic-based approach to measuring liquid thermal conductivity is developed to address the requirement in many practical applications for measurements using small (microlitre) sample size and integration into a compact device. The approach also gives the possibility of high-throughput testing. A resistance heater and temperature sensor are incorporated into a glass microfluidic chip to allow transmission and detection of a planar thermal wave crossing a thin layer of the sample. The device is designed so that heat transfer is locally one-dimensional during a short initial time period. This allows the detected temperature transient to be separated into two distinct components: a short-time, purely one-dimensional part from which sample thermal conductivity can be determined and a remaining long-time part containing the effects of three-dimensionality and of the finite size of surrounding thermal reservoirs. Identification of the one-dimensional component yields a steady temperature difference from which sample thermal conductivity can be determined. Calibration is required to give correct representation of changing heater resistance, system layer thicknesses and solid material thermal conductivities with temperature. In this preliminary study, methanol/water mixtures are measured at atmospheric pressure over the temperature range 30-50A degrees C. The results show that the device has produced a measurement accuracy of within 2.5% over the range of thermal conductivity and temperature of the tests. A relation between measurement uncertainty and the geometric and thermal properties of the system is derived and this is used to identify ways that error could be further reduced.

BRCA1 transcriptionally regulates genes associated with the basal breast cancer phenotype

Background Ten to twenty per cent of breast tumours exhibit a basallike genetic profile and these tumours carry a poor prognosis. Breast tumours which contain germline mutations for BRCA1 commonly exhibit a molecular profile similar to basal breast tumours. BRCA1 is a tumour suppressor gene which is mutated in up to 5–10% of breast cancer cases and is involved in multiple cellular processes including DNA damage control, cell cycle checkpoint control, apoptosis, ubiquitination and transcriptional regulation.

Methods Microarray-based profiling was carried out using the HCC1937EV and HCC1937BR breast cancer cell lines. Basal gene and protein expression levels were analysed by qRT-PCR and western blotting. ChIP analyses were performed and demonstrated that BRCA1 regulates basal gene expression through a transcriptional mechanism involving c-myc.

Results We have previously carried out microarray-based expression profiling to examine differences in gene expression when BRCA1 is reconstituted in BRCA1 mutated HCC1937 breast cancer cells. We observed that p-cadherin and the cytokeratin 5 and cytokeratin 17 genes, which are strongly correlated with the basal phenotype, are differentially expressed when BRCA1 is reconstituted. In addition, qRT-PCR and ChIP analysis of BRCA1 reconstituted cells show that BRCA1 represses the expression of these basal genes by a transcriptional mechanism. Furthermore, abrogation of endogenous BRCA1 protein in the T47D cell line using siRNA results in reexpression of these basal genes, suggesting that BRCA1 expression levels may be important in basal gene expression. We have also demonstrated that BRCA1 is physically associated with the promoter regions of basal genes through an association with c-myc. Consequently, we have confirmed that siRNA inhibition of c-myc in T47D cells results in re-expression of these genes.

Conclusions Our results suggest that BRCA1 is involved in the transcriptional regulation of genes associated with the basal phenotype and that BRCA1 controls basal gene expression through a transcriptional mechanism involving c-myc. Further work is now concentrating on defining the relationship between BRCA1 and basal gene expression and how this may affect clinical responses to breast cancer chemotherapy.

Determination of the Physical Properties of Room Temperature Ionic Liquids Using a Love Wave Device

In this work, we have shown that a 100 MHz Love wave device can be used to determine whether room temperature ionic liquids (RTILs) are Newtonian fluids and have developed a technique that allows the determination of the density-viscosity product, rho eta of a Newtonian RTIL. In addition, a test for a Newtonian response was established by relating the phase change to insertion loss change. Five concentrations of a water-miscible RTIL and seven pure RTILs were measured. The changes in phase and insertion loss were found to vary linearly with the square root of the density-viscosity product for values up to (rho eta)(1/2) similar to 10 kg m(-2) s(-1/2). The square root of the density-viscosity product was deduced from the changes in either phase or insertion loss using glycerol as a calibration liquid. In both cases, the deduced values of rho eta agree well with those measured using viscosity and density meters. Miniaturization of the device, beyond that achievable with the lower-frequency quartz crystal microbalance approach, to measure smaller volumes is possible. The ability to fabricate Love wave and other surface acoustic wave sensors using planar metallization technologies gives potential for future integration into lab-on-a-chip analytical systems for characterizing ionic liquids.

Prediction-Based Power-Performance Adaptation of Multithreaded Scientific Codes

Computing has recently reached an inflection point with the introduction of multicore processors. On-chip thread-level parallelism is doubling approximately every other year. Concurrency lends itself naturally to allowing a program to trade performance for power savings by regulating the number of active cores; however, in several domains, users are unwilling to sacrifice performance to save power. We present a prediction model for identifying energy-efficient operating points of concurrency in well-tuned multithreaded scientific applications and a runtime system that uses live program analysis to optimize applications dynamically. We describe a dynamic phase-aware performance prediction model that combines multivariate regression techniques with runtime analysis of data collected from hardware event counters to locate optimal operating points of concurrency. Using our model, we develop a prediction-driven phase-aware runtime optimization scheme that throttles concurrency so that power consumption can be reduced and performance can be set at the knee of the scalability curve of each program phase. The use of prediction reduces the overhead of searching the optimization space while achieving near-optimal performance and power savings. A thorough evaluation of our approach shows a reduction in power consumption of 10.8 percent, simultaneous with an improvement in performance of 17.9 percent, resulting in energy savings of 26.7 percent.

Characterisation of Genome-Wide PLZF/RARA Target Genes

The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear. We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic cell line U937 conditionally expressing PLZF/RARA. By comparing bound regions found in U937 cells expressing endogenous PLZF with PLZF/RARA-induced U937 cells, we isolated specific PLZF/RARA target gene promoters. We next analysed gene expression profiles of our identified target genes in PLZF/RARA APL patients and analysed DNA sequences and epigenetic modification at PLZF/RARA binding sites. We identify 413 specific PLZF/RARA target genes including a number encoding transcription factors involved in the regulation of haematopoiesis. Among these genes, 22 were significantly down regulated in primary PLZF/RARA APL cells. In addition, repressed PLZF/RARA target genes were associated with increased levels of H3K27me3 and decreased levels of H3K9K14ac. Finally, sequence analysis of PLZF/RARA bound sequences reveals the presence of both consensus and degenerated RAREs as well as enrichment for tissue-specific transcription factor motifs, highlighting the complexity of targeting fusion protein to chromatin. Our study suggests that PLZF/RARA directly targets genes important for haematopoietic development and supports the notion that PLZF/RARA acts mainly as an epigenetic regulator of its direct target genes.

Comparison of biosensor platforms for surface plasmon resonance based detection of paralytic shellfish toxins

Paralytic shellfish poisoning (PSP) toxins are produced by certain marine dinoflagellates and may accumulate in bivalve molluscs through filter feeding. The Mouse Bioassay (MBA) is the internationally recognised reference method of analysis, but it is prone to technical difficulties and regarded with increasing disapproval due to ethical reasons. As such, alternative methods are required. A rapid surface plasmon resonance (SPR) biosensor inhibition assay was developed to detect PSP toxins in shellfish by employing a saxitoxin polyclonal antibody (R895). Using an assay developed for and validated on the Biacore Q biosensor system, this project focused on transferring the assay to a high-throughput, Biacore T100 biosensor in another laboratory. This was achieved using a prototype PSP toxin kit and recommended assay parameters based on the Biacore Q method. A monoclonal antibody (GT13A) was also assessed. Even though these two instruments are based on SPR principles, they vary widely in their mode of operation including differences in the integrated mu-fluidic cartridges, autosampler system, and sensor chip compatibilities. Shellfish samples (n = 60), extracted using a simple, rapid procedure, were analysed using each platform, and results were compared to AOAC high performance liquid chromatography (HPLC) and MBA methods. The overall agreement, based on statistical 2 x 2 comparison tables, between each method ranged from 85% to 94.4% using R895 and 77.8% to 100% using GT13A. The results demonstrated that the antibody based assays with high sensitivity and broad specificity to PSP toxins can be applied to different biosensor platforms. (C) 2011 Elsevier B.V. All rights reserved.

Paralytic shellfish poisoning (PSP) toxin binders for optical biosensor technology: problems and possibilities for the future: a review

This review examines the developments in optical biosensor technology, which uses the phenomenon of surface plasmon resonance, for the detection of paralytic shellfish poisoning (PSP) toxins. Optical biosensor technology measures the competitive biomolecular interaction of a specific biological recognition element or binder with a target toxin immobilised onto a sensor chip surface against toxin in a sample. Different binders such as receptors and antibodies previously employed in functional and immunological assays have been assessed. Highlighted are the difficulties in detecting this range of low molecular weight toxins, with analogues differing at four chemical substitution sites, using a single binder. The complications that arise with the toxicity factors of each toxin relative to the parent compound, saxitoxin, for the measurement of total toxicity relative to the mouse bioassay are also considered. For antibodies, the cross-reactivity profile does not always correlate to toxic potency, but rather to the toxin structure to which it was produced. Restrictions and availability of the toxins makes alternative chemical strategies for the synthesis of protein conjugate derivatives for antibody production a difficult task. However, when two antibodies with different cross-reactivity profiles are employed, with a toxin chip surface generic to both antibodies, it was demonstrated that the cross-reactivity profile of each could be combined into a single-assay format. Difficulties with receptors for optical biosensor analysis of low molecular weight compounds are discussed, as are the potential of alternative non-antibody-based binders for future assay development in this area.

Liquid-Liquid Flow in a Capillary Microreactor: Hydrodynamic Flow Patterns and Extraction Performance

The capillary micro reactor, with four stable operating flow patterns and a throughput range from grams per hour to kilograms per hour, presents an attractive alternative to chip-based and microstructured reactors for laboratory- and pilot-scale applications. In this article, results for the extraction of 2-butanol from toluene under different flow patterns in a water/toluene flow in long capillary microreactors are presented. The effects of the capillary length (0.4-2.2 m), flow rate (0.1-12 mL/min), and aqueous-to-organic volumetric flow ratio (0.25-9) on the slug, bubbly, parallel, and annular flow hydrodynamics were investigated. Weber-number-dependent flow maps were composed for capillary lengths of 0.4 and 2 m that were used to interpret the flow pattern formation in terms of surface tension and inertia forces. When the capillary length was decreased from 2 to 0.4 m, a transition from annular to parallel flow was observed. The capillary length had little influence on slug and bubbly flows. The flow patterns were evaluated in terms of stability, surface-to-volume ratio, throughput, and extraction efficiency. Slug and bubbly flow operations yielded 100% thermodynamic extraction efficiency, and increasing the aqueous-to-organic volumetric ratio to 9 allowed for 99% 2-butanol extraction. The parallel and annular flow operating windows were limited by the capillary length, thus yielding maximum 2-butanol extractions of 30% and 47% for parallel and annular flows, respectively.

Hydrodynamics and mixer-induced bubble formation in micro bubble columns with single and multiple-channels

A hydrodynamic characterization of an industrially used gas-liquid contacting microchannel. device is discussed, viz. the micro bubble column of IMM. Furthermore, similar characterization of a gas-liquid flow microchip of TU/e, with two tailored mixer designs, is used to solve fundamental issues on hydrodynamics, and therefore, to achieve further design and operating optimization of that chip and the IMM device. Flow pattern maps are presented in a dimensionless fashion for further predictions on new fluidic systems for optimum single-channel multiphase operation. Bubble formation was investigated in the two types of mixers and pinch-off and hydrodynamic decay mechanisms are observed. The impact of these mechanisms on bubble size, bubble size distributions, and on the corresponding flow patterns, i.e., the type of mixer design, can be decisive for the flow pattern map and thus, may be used to alter flow pattern maps. The bubble sizes and their distribution were improved for the tailored designs, i.e., smaller and more regular bubbles were generated. Finally, the impact of multi-channel distribution for gas and liquid flow is demonstrated. Intermediate flow patterns such as slug-annular flow, also found for single-phase operation, and the simultaneous coexistence of flow regimes are presented, with the latter providing evidence of flow maldistribution.

Detection of streptomycin residues in whole milk using an optical immunobiosensor

The development of an assay for the detection of streptomycin residues in pasteurized whole milk using an optical biosensor (Biacore) is reported. Streptomycin-adipic hydrazide coupled to bovine thyroglobulin was used to produce a sheep polyclonal antibody. The antibody displayed excellent cross-reactivity with dihydrostreptomycin (106%). There was no significant cross-reaction with other aminoglycosides or common antibiotics. Streptomycin was also immobilized onto a CM5 sensor chip to provide a stable, reusable surface. The developed assay permitted the direct analysis of whole milk samples (similar to3.5% fat) without prior centrifugation and defatting. Results were available in 5 min. The limit of detection of the assay was determined as 4.1 ng/mL, well below the European maximum residue limit (MRL) of 200 ng/mL. Repeatability (or coefficient of variation) between runs was determined as 3.5% (100 ng/mL; 0.5 x MRL), 5.7% (200 ng/mL; MRL), and 7.6% (400 ng/mL; 2 x MRL).

The development of a rapid immunobiosensor screening method for the detection of residues of sulphadiazine

A rapid imununoassay using an optical biosensor (BIAcore(TM)) for determining the presence of sulphadiazine (SDZ) residues in pig bile was developed. SDZ,cas immobilised onto the surface of a dextran-coated silicon chip and a solution containing SDZ antibody, sample and buffer was injected over the chip surface. The level of antibody binding to the chip was determined after 20 s and the surface of the chip was then regenerated over a 1-min period prior to another sample injection taking place. Standard curves were constructed to allow quantification of SDZ presence in sample. Concentrations ranging from 0 to 10.64 mu g ml(-1) SDZ were detected in bile samples taken from experimentally fed pigs and randomly selected pigs taken from a local slaughterhouse. These results were compared to the concentrations of SDZ detected by high-performance liquid chromatography: in associated tissues. When concentrations in bile exceeded 0.6 mu g ml(-1) SDZ, the corresponding edible tissue was above the maximum residue level (MRL), i.e. 0.1 mu g g(-1) in 13 out of 14 cases. Wizen the bile concentration was less than 0.6 mu ml(-1) the associated tissue concentrations never exceeded rite MRL. This experiment has indicated that biosensor analysis of bile is a highly effective method for detecting violative SDZ residues in meat.

On generating set index functions for randomized caches

Caches hide the growing latency of accesses to the main memory from the processor by storing the most recently used data on-chip. To limit the search time through the caches, they are organized in a direct mapped or set-associative way. Such an organization introduces many conflict misses that hamper performance. This paper studies randomizing set index functions, a technique to place the data in the cache in such a way that conflict misses are avoided. The performance of such a randomized cache strongly depends on the randomization function. This paper discusses a methodology to generate randomization functions that perform well over a broad range of benchmarks. The methodology uses profiling information to predict the conflict miss rate of randomization functions. Then, using this information, a search algorithm finds the best randomization function. Due to implementation issues, it is preferable to use a randomization function that is extremely simple and can be evaluated in little time. For these reasons, we use randomization functions where each randomized address bit is computed as the XOR of a subset of the original address bits. These functions are chosen such that they operate on as few address bits as possible and have few inputs to each XOR. This paper shows that to index a 2(m)-set cache, it suffices to randomize m+2 or m+3 address bits and to limit the number of inputs to each XOR to 2 bits to obtain the full potential of randomization. Furthermore, it is shown that the randomization function that we generate for one set of benchmarks also works well for an entirely different set of benchmarks. Using the described methodology, it is possible to reduce the implementation cost of randomization functions with only an insignificant loss in conflict reduction.

Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation

The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63.

Software-defined sphere decoding for FPGA-based MIMO detection

Sphere Decoding (SD) is a highly effective detection technique for Multiple-Input Multiple-Output (MIMO) wireless communications receivers, offering quasi-optimal accuracy with relatively low computational complexity as compared to the ideal ML detector. Despite this, the computational demands of even low-complexity SD variants, such as Fixed Complexity SD (FSD), remains such that implementation on modern software-defined network equipment is a highly challenging process, and indeed real-time solutions for MIMO systems such as 4 4 16-QAM 802.11n are unreported. This paper overcomes this barrier. By exploiting large-scale networks of fine-grained softwareprogrammable processors on Field Programmable Gate Array (FPGA), a series of unique SD implementations are presented, culminating in the only single-chip, real-time quasi-optimal SD for 44 16-QAM 802.11n MIMO. Furthermore, it demonstrates that the high performance software-defined architectures which enable these implementations exhibit cost comparable to dedicated circuit architectures.