Accurate sodium bisulfite sequencing in plants.

DNA cytosine methylation is a conserved epigenetic modification frequently correlating with transcriptional silencing in a wide variety of eukaryotic organisms. Sodium bisulfite treatment of DNA converts unmethylated cytosine to uracil, while 5-methylated cytosine is protected. We describe techniques that ensure reliable sequencing data following sodium bisulfite conversion and to avoid common pitfalls such as amplification of unconverted DNA and inclusion of sibling clones.

Stress reduction and bond stability during thermal annealing of tetrahedral amorphous carbon

A comprehensive study of the stress release and structural changes caused by postdeposition thermal annealing of tetrahedral amorphous carbon (ta-C) on Si has been carried out. Complete stress relief occurs at 600-700°C and is accompanied by minimal structural modifications, as indicated by electron energy loss spectroscopy, Raman spectroscopy, and optical gap measurements. Further annealing in vacuum converts sp3 sites to sp2 with a drastic change occurring after 1100°C. The field emitting behavior is substantially retained up to the complete stress relief, confirming that ta-C is a robust emitting material. © 1999 American Institute of Physics.

Improving speech transcription for Mandarin-english translation

This paper describes the development of the CU-HTK Mandarin Speech-To-Text (STT) system and assesses its performance as part of a transcription-translation pipeline which converts broadcast Mandarin audio into English text. Recent improvements to the STT system are described and these give Character Error Rate (CER) gains of 14.3% absolute for a Broadcast Conversation (BC) task and 5.1% absolute for a Broadcast News (BN) task. The output of these STT systems is then post-processed, so that it consists of sentence-like segments, and translated into English text using a Statistical Machine Translation (SMT) system. The performance of the transcription-translation pipeline is evaluated using the Translation Edit Rate (TER) and BLEU metrics. It is shown that improving both the STT system and the post-STT segmentations can lower the TER scores by up to 5.3% absolute and increase the BLEU scores by up to 2.7% absolute. © 2007 IEEE.

Picosecond pulse source for OTDM/WDM applications based on arrayed waveguide grating

A novel technique for high quality femtosecond pulse generation from a gain-switched laser diode by means of pulse compression and transformation in a compact nonlinear fiber device, based on a dispersion-imbalanced fiber loop mirror (DILM) is demonstrated. This source allows the generation of extremely high quality pulses as short as 270 fs on demand with strong suppression of pulse pedestals. Spectral filtering in arrayed waveguide grating (AWG) converts the device into a compact multiwavelength source of high-quality picosecond pulses for optical time division multiplexing/wavelength division multiplexing applications.

10-Gbits/s all-optical 3R regeneration and format conversion using a gain-switched DFB laser

A strain-compensated multiple quantum well device is used as a DFB laser, this has been optimized for low jitter gain switched operation at 10 GHz. The signal is transmitted down 80 km of standard fiber then amplified, filtered and polarization controlled before being injected into a DFB laser. The purpose of this regeneration process is to gain switch the DFB with the extracted clock signal in order to retime the converted signal. This process also simultaneously converts the input NRZ format to an output RZ data to format and results in a signal whose optical power and extinction ratio are considerably improved by the regeneration process.

The unsteady development of a turbulent wake through a downstream low-pressure turbine blade passage

This paper presents two-dimensional LDA measurements of the convection of a wake through a low-pressure (LP) turbine cascade. Previous studies have shown the wake convection to be kinematic but have not provided details of the turbulent field. The spatial resolution of these measurements has facilitated the calculation of the production of turbulent kinetic energy and this has revealed a mechanism for turbulence production as the wake converts through the bladerow. The measured ensemble-averaged velocity field confirmed the previously reported kinematics of wake convection while the measurements of the turbulence quantities showed the wake fluid to be characterised by elevated levels of turbulent kinetic energy (TKE) and to have an anisotropic structure. Based on the measured mean and turbulence quantities, the production of turbulent kinetic energy was calculated. This highlighted a TKE production mechanism that resulted in increased levels of turbulence over the rear suction surface where boundary layer transition occurs. The turbulence production mechanism within the bladerow was also observed to produce more nearly isotropic turbulence. Production occurs when the principal stresses within the wake are aligned with the mean strains. This coincides with the maximum distortion of the wake within the blade passage and provides a mechanism for the production of turbulence outside of the boundary layer.

A fully integrated 660 MHz low-swing energy-recycling DC-DC converter

A fully integrated 0.18 μm DC-DC buck converter using a low-swing "stacked driver" configuration is reported in this paper. A high switching frequency of 660 MHz reduces filter components to fit on chip, but this suffers from high switching losses. These losses are reduced using: 1) low-swing drivers; 2) supply stacking; and 3) introducing a charge transfer path to deliver excess charge from the positive metal-oxide semiconductor drive chain to the load, thereby recycling the charge. The working prototype circuit converts 2.2 to 0.75-1.0 V at 40-55 mA. Design and simulation of an improved circuit is also included that further improves the efficiency by enhancing the charge recycling path, providing automated zero voltage switching (ZVS) operation, and synchronizing the half-swing gating signals. © 2009 IEEE.

SoC energy savings = reduce+reuse+recycle: A case study using a 660MHz DC-DC converter with integrated output filter

This paper advocates 'reduce, reuse, recycle' as a complete energy savings strategy. While reduction has been common to date, there is growing need to emphasize reuse and recycling as well. We design a DC-DC buck converter to demonstrate the 3 techniques: reduce with low-swing and zero voltage switching (ZVS), reuse with supply stacking, and recycle with regulated delivery of excess energy to the output load. The efficiency gained from these 3 techniques helps offset the loss of operating drivers at very high switching frequencies which are needed to move the output filter completely on-chip. A prototype was fabricated in 0.18μm CMOS, operates at 660MHz, and converts 2.2V to 0.75-1.0V at ∼50mA.1 © 2008 IEEE.

A 660MHz ZVS DC-DC converter using gate-driver charge-recycling in 0.18μm CMOS with an integrated output filter

The design and manufacture of a prototype chip level power supply is described, with both simulated and experimental results. Of particular interest is the inclusion of a fully integrated on-chip LC filter. A high switching frequency of 660MHz and the design of a device drive circuit reduce losses by supply stacking, low-swing signaling and charge recycling. The paper demonstrates that a chip level converter operating at high frequency can be built and shows how this can be achieved, using zero voltage switching techniques similar to those commonly used in larger converters. Both simulations and experimental data from a fabricated circuit in 0.18μm CMOS are included. The circuit converts 2.2V to 0.75∼1.0V at ∼55mA. ©2008 IEEE.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Hydrogel-driven carbon nanotube microtransducers

We demonstrate the fabrication and integration of active microstructures based on composites of 3D carbon nanotube (CNT) frameworks and hydrogels. The alignment of the CNTs within the microstructures converts the isotropic expansion of the gel into a directed anisotropic motion. Actuation by a moisture-responsive gel is observed by changing the ambient humidity, and is predicted by a finite element model of the composite system. These shape changes are rapid and can be transduced electrically within a microfluidic channel, by measuring the resistance change across a CNT microstructure during expansion of the gel. Our results suggest that combinations of gels with aligned CNTs can be a platform for directing the actuation of gels and measuring their response to stimuli. © 2011 The Royal Society of Chemistry.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.