Picosecond fiber optical parametric oscillator with 500 nm tuning range using dispersion-shifted fiber

We demonstrate a picosecond fiber optical parametric oscillator with a tuning range of 500 nm pumped by a relatively low-cost intensity-modulated pump. Pulses with pulsewidth from 7 ps to 17 ps are generated. © 2010 Optical Society of America.published_or_final_versionThe 2010 Conference on Optical Fiber Communication (OFC), collocated National Fiber Optic Engineers Conference (OFC/NFOEC), San Diego, CA., 21-25 March 2010. In Proceedings of OFC/NFOEC, 2010, p. 1-

A simple 10-GHz picosecond pulse source based on fiber optical parametric oscillator

We demonstrate a simple fully fiber-integrated picosecond optical parametric oscillator based on high-nonlinear dispersion-shifted fiber. High quality picosecond pulses are generated with a 40-nm tuning range. © 2009 IEEE.published_or_final_versio

HaploShare: identification of extended haplotypes shared by cases and evaluation against controls

Recent founder mutations may play important roles in complex diseases and Mendelian disorders. Detecting shared haplotypes that are identical by descent (IBD) could facilitate discovery of these mutations. Several programs address this, but are usually limited to detecting pair-wise shared haplotypes and not providing a comparison of cases and controls. We present a novel algorithm and software package, HaploShare, which detects extended haplotypes that are shared by multiple individuals, and allows comparisons between cases and controls. Testing on simulated and real cases demonstrated significant improvements in detection power and reduction of false positive rate by HaploShare relative to other programs.published_or_final_versio

Subpicosecond fiber optical parametric chirped pulse amplifier based on highly-nonlinear fiber

We experimentally demonstrate a fiber optical parametric chirped pulse amplifier. A 750-fs signal is stretched to 40 ps, amplified with a gain of 30 dB through parametric process and then compressed to 808 fs. 2010 Optical Society of America. © 2010 IEEE.published_or_final_versionThe 2010 Conference on Lasers and Electro-Optics (CLEO) and Quantum Electronics and Laser Science Conference (QELS), San Josa, CA., 16-21 May 2010. In Proceedings of the CLEO/QELS, 2010, p. 1-

Intelligent spider for Internet searching

As World Wide Web (WWW) based Internet services become more popular, information overload also becomes a pressing research problem. Difficulties with searching on the Internet get worse as the amount of information that is available increases. A scalable approach to support Internet search is critical to the success of Internet services and other current or future national information infrastructure (NII) applications. A new approach to build an intelligent personal spider (agent), which is based on automatic textual analysis of Internet documents, is proposed. Best first search and genetic algorithm have been tested to develop the intelligent spider. These personal spiders are able to dynamically and intelligently analyze the contents of the users' selected homepages as the starting point to search for the most relevant homepages based on the links and indexing. An intelligent spider must have the capability to make adjustments according to progress of searching in order to be an intelligent agent. However, the current searching engines do not have communication between the users and the robots. The spider presented in the paper uses Java to develop the user interface such that the users can adjust the control parameters according to the progress and observe the intermediate results. The performances of the genetic algorithm based and best first search based spiders are also reported.published_or_final_versio

Wide-band generation of picosecond pulse using fiber optical parametric amplifier and oscillator

We first demonstrate a wideband generation of picosecond pulse using fiber optical parametric amplifier (FOPA). High quality pulse is generated at 85 nm away from the pump with pulsewidth narrower than that of the pump. We then explore fiber optical parametric oscillator (FOPO) configuration which has the advantage of eliminating the need of seeding laser, leading to a potentially wider wavelength tunability and flexibility. The tuning range of the FOPO is from 1511 nm to 1541 nm and from 1583 nm to 1613 nm, which is as wide as 60 nm, with wavelength span of over 100 nm. Nearly-transform-limited sub-picosecond pulses are generated by this technique. © 2009 IEEE.published_or_final_versio

Tunable repetition rate multiplier based on fiber optical parametric oscillator

We demonstrate a tunable repetition rate multiplier based on fiber optical parametric oscillator. 2-6 times repetition rate multiplication of a 10-GHz pulse source is achieved with a tuning range of 20 nm in the L-band. © 2010 IEEE.published_or_final_versionThe IEEE Photonics Society Summer Topical Meetings, Playa del Carmen, Mexico, 19-21 July 2010. In Proceedings of PHOSST, 2010, p. 133-13

HLAreporter: a tool for HLA typing from next generation sequencing data

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly developed tools such as HLAminer and PHLAT. HLAreporter can be downloaded from http://paed.hku.hk/genome/.published_or_final_versio

Wavelet domain compounding for speckle reduction in optical coherence tomography

Visibility of optical coherence tomography (OCT) images can be severely degraded by speckle noise. A computationally efficient despeckling approach that strongly reduces the speckle noise is reported. It is based on discrete wavelet transform (DWT), but eliminates the conventional process of threshold estimation. By decomposing an image into different levels, a set of sub-band images are generated, where speckle noise is additive. These sub-band images can be compounded to suppress the additive speckle noise, as DWT coefficients resulting from speckle noise tend to be approximately decorrelated. The final despeckled image is reconstructed by taking the inverse wavelet transform of the new compounded sub-band images. The performance of speckle reduction and edge preservation is controlled by a single parameter: the level of wavelet decomposition. The proposed technique is applied to intravascular OCT imaging of porcine carotid arterial wall and ophthalmic OCT images. Results demonstrate the effectiveness of this technique for speckle noise reduction and simultaneous edge preservation. The presented method is fast and easy to implement and to improve the quality of OCT images.published_or_final_versio

Widely tunable picosecond optical parametric oscillator using highly nonlinear fiber

We demonstrated a fully fiber-integrated widely tunable picosecond optical parametric oscillator based on highly nonlinear fiber. The ring cavity with a 50 m highly nonlinear fiber was synchronously pumped with a picosecond mode-locked fiber laser. The tuning range was from 1413 to 1543 nm and from 1573 to 1695 nm, which was as wide as 250 nm. A high-quality pulse was generated with a pulse width narrower than that of the pump. © 2009 Optical Society of America.published_or_final_versio