Adaptive clutter filter design for micro-ultrasound color flow imaging of small blood vessels

In micro-ultrasound, which uses imaging frequencies above 20 MHz, obtainingcolor flow images (CFI) of small blood vessels using is not a trivial taskbecause it is more challenging to suppress tissue clutter properly given thestronger blood signal power at high imaging frequencies and the slow bloodvelocity inside the microcirculation. To improve clutter suppression inmicro-ultrasound CFI, this paper presents an adaptive clutter filtering approachthat is based on a two-stage eigen-analysis of slow-time ensemblecharacteristics. The approach first identifies tissue pixels in the imaging viewby examining whether high-frequency contents are absent in the principalslow-time eigen-components for each pixel as computed from single-ensembleeigen-decomposition. It then computes the filtered slow-time ensemble for eachpixel by finding the least-squares projection residual between the pixel'sslow-time ensemble and the clutter eigen-components estimated from amulti-ensemble eigen-decomposition of tissue slow-time ensembles within aspatial window. In this filtering approach, the clutter eigen-components arechosen based on whether their mean frequency lies within a spectral band. Toanalyze the efficacy of the proposed adaptive filter, both in-vitro experimentsand Field II simulations were carried out. For the experiments, raw CFI datawere acquired using a 64-element, 33 MHz linear array prototype (pulse duration:2 cycles, PRF: 1 kHz, transmit focus: 8mm, F-number: 5). Their imaging viewcorresponded to the cross-section of a 0.9mm-diameter tube that was placed ontop of an unsuspended table where ambient vibrations may appear; flow velocity(5, 7, 10, 15 mm/s) within the tube was controlled using a syringe pump. For thesimulations, raw CFI data was computed for both plug and parabolic flowprofiles, and tissue motion was modeled as 0.5 mm/s sinusoidal vibrations. Forall flow velocities tested in our in-vitro study, the proposed adaptive filterimproved the flow detection sensitivity as compared to existing ones. In theslow-flow case (5 mm/s), we observed over 70% increase in flow detectionsensitivity (assuming a 5% false alarm rate). This effectively reduced flashingartifacts in the resulting CFIs and gave a more consistent visualization of theflow tube. © 2010 IEEE.published_or_final_versionThe 2010 IEEE International Ultrasonics Symposium, San Diego, CA.,, 11-14 October 2010. In Proceedings of IEEE IUS, 2010, p. 1206-120

Design of a programmable micro-ultrasound research platform

To foster innovative uses of micro-ultrasound in biomedicine, it is beneficial to develop flexible research-purpose systems that allow researchers to easily reconfigure its system-level operations such as transmit firing sequence and receive processing. In this paper, we present the development of a programmable micro-ultrasound research platform that is capable of realizing various micro-imaging algorithms. The research platform comprises a linear-array-based scanning front-end and a PC-based data processing back-end, which employs a graphical processing unit (GPU) as the processor core. The front-end operations can be configured from the PC via the parallel port and the two blocks are synchronized by an external clock. Acquired data from the front-end is first digitized and relayed to the PC through an data acquisition card (200 MHz, 14-bit). They are then transferred to the GPU (GTX 275) in which the image formation is carried out via multi-thread processing. Results are displayed on-screen in real-time and can be saved to the PC's hard disk for offline analysis. Through a module-based programming approach, this platform can facilitate realization of custom-designed imaging algorithms developed by researchers. In this work, B-mode imaging and adaptive color flow imaging have been implemented as demonstrations of the research platform's programmability. The performance results show that real-time processing frame rates can be achieved for both imaging modes. © 2010 IEEE.published_or_final_versionThe 2010 IEEE International Ultrasonics Symposium, San Diego, CA., 11-14 October 2010. In Proceedings of IEEE IUS, 2010, p. 1980-198

Sample entropy analysis of EEG signals via artificial neural networks to model patients' consciousness level based on anesthesiologists experience.

Electroencephalogram (EEG) signals, as it can express the human brain's activities and reflect awareness, have been widely used in many research and medical equipment to build a noninvasive monitoring index to the depth of anesthesia (DOA). Bispectral (BIS) index monitor is one of the famous and important indicators for anesthesiologists primarily using EEG signals when assessing the DOA. In this study, an attempt is made to build a new indicator using EEG signals to provide a more valuable reference to the DOA for clinical researchers. The EEG signals are collected from patients under anesthetic surgery which are filtered using multivariate empirical mode decomposition (MEMD) method and analyzed using sample entropy (SampEn) analysis. The calculated signals from SampEn are utilized to train an artificial neural network (ANN) model through using expert assessment of consciousness level (EACL) which is assessed by experienced anesthesiologists as the target to train, validate, and test the ANN. The results that are achieved using the proposed system are compared to BIS index. The proposed system results show that it is not only having similar characteristic to BIS index but also more close to experienced anesthesiologists which illustrates the consciousness level and reflects the DOA successfully.This research is supported by the Center forDynamical Biomarkers and Translational Medicine, National Central University, Taiwan, which is sponsored by Ministry of Science and Technology (Grant no. MOST103-2911-I-008-001). Also, it is supported by National Chung-Shan Institute of Science & Technology in Taiwan (Grant nos. CSIST-095-V301 and CSIST-095-V302)

Promotor hypermethylation of the CpG Islands of human Ras Association Domain Family 1A gene (RASSF1A) in adenocarcinoma of lung in Hong Kong Chinese - a comparison between smokers and non-smokers

published_or_final_versio

Measuring the functional sequence complexity of proteins

<p>Abstract</p> <p>Background</p> <p>Abel and Trevors have delineated three aspects of sequence complexity, Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC) observed in biosequences such as proteins. In this paper, we provide a method to measure functional sequence complexity.</p> <p>Methods and Results</p> <p>We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families. Considerations were made in determining how the measure can be used to correlate functionality when relating to the whole molecule and sub-molecule. In the experiment, we show that when the proposed measure is applied to the aligned protein sequences of ubiquitin, 6 of the 7 highest value sites correlate with the binding domain.</p> <p>Conclusion</p> <p>For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins.</p

Genetic polymorphisms of DNA double strand break gene Ku70 and gastric cancer in Taiwan

<p>Abstract</p> <p>Background and aim</p> <p>The DNA repair gene <it>Ku70</it>, an important member of non-homologous end-joining repair system, is thought to play an important role in the repairing of DNA double strand breaks. It is known that defects in double strand break repair capacity can lead to irreversible genomic instability. However, the polymorphic variants of <it>Ku70</it>, have never been reported about their association with gastric cancer susceptibility.</p> <p>Methods</p> <p>In this hospital-based case-control study, the associations of <it>Ku70 </it>promoter T-991C (rs5751129), promoter G-57C (rs2267437), promoter A-31G (rs132770), and intron 3 (rs132774) polymorphisms with gastric cancer risk in a Taiwanese population were investigated. In total, 136 patients with gastric cancer and 560 age- and gender-matched healthy controls recruited from the China Medical Hospital in Taiwan were genotyped.</p> <p>Results</p> <p>As for <it>Ku70 </it>promoter T-991C, the ORs after adjusted by age and gender of the people carrying TC and CC genotypes were 2.41 (95% CI = 1.53-3.88) and 3.21 (95% CI = 0.96-9.41) respectively, compared to those carrying TT wild-type genotype. The <it>P </it>for trend was significant (<it>P </it>< 0.0001). In the dominant model (TC plus CC versus TT), the association between <it>Ku70 </it>promoter T-991C polymorphism and the risk for gastric cancer was also significant (adjusted OR = 2.48, 95% CI = 1.74-3.92). When stratified by age and gender, the association was restricted to those at the age of 55 or elder of age (TC vs TT: adjusted OR = 2.52, 95% CI = 1.37-4.68, <it>P </it>= 0.0139) and male (TC vs TT: adjusted OR = 2.58, 95% CI = 1.33-4.47, <it>P </it>= 0.0085). As for the other three polymorphisms, there was no difference between both groups in the distributions of their genotype frequencies.</p> <p>Conclusion</p> <p>In conclusion, the <it>Ku70 </it>promoter T-991C (rs5751129), but not the <it>Ku70 </it>promoter C-57G (rs2267437), promoter A-31G (rs132770) or intron 3 (rs132774), is associated with gastric cancer susceptibility. This polymorphism may be a novel useful marker for gastric carcinogenesis.</p

Imbibition in Disordered Media

The physics of liquids in porous media gives rise to many interesting phenomena, including imbibition where a viscous fluid displaces a less viscous one. Here we discuss the theoretical and experimental progress made in recent years in this field. The emphasis is on an interfacial description, akin to the focus of a statistical physics approach. Coarse-grained equations of motion have been recently presented in the literature. These contain terms that take into account the pertinent features of imbibition: non-locality and the quenched noise that arises from the random environment, fluctuations of the fluid flow and capillary forces. The theoretical progress has highlighted the presence of intrinsic length-scales that invalidate scale invariance often assumed to be present in kinetic roughening processes such as that of a two-phase boundary in liquid penetration. Another important fact is that the macroscopic fluid flow, the kinetic roughening properties, and the effective noise in the problem are all coupled. Many possible deviations from simple scaling behaviour exist, and we outline the experimental evidence. Finally, prospects for further work, both theoretical and experimental, are discussed.Comment: Review article, to appear in Advances in Physics, 53 pages LaTe

Circuit dissection of the role of somatostatin in itch and pain

Stimuli that elicit itch are detected by sensory neurons that innervate the skin. This information is processed by the spinal cord; however, the way in which this occurs is still poorly understood. Here we investigated the neuronal pathways for itch neurotransmission, particularly the contribution of the neuropeptide somatostatin. We find that in the periphery, somatostatin is exclusively expressed in Nppb+ neurons, and we demonstrate that Nppb+somatostatin+ cells function as pruriceptors. Employing chemogenetics, pharmacology and cell-specific ablation methods, we demonstrate that somatostatin potentiates itch by inhibiting inhibitory dynorphin neurons, which results in disinhibition of GRPR+ neurons. Furthermore, elimination of somatostatin from primary afferents and/or from spinal interneurons demonstrates differential involvement of the peptide released from these sources in itch and pain. Our results define the neural circuit underlying somatostatin-induced itch and characterize a contrasting antinociceptive role for the peptide

Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Diethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure

The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including [DEP − H]−, [DEP + H]+, [DEP + Na]+, and [DEP − H + 2Na]+ are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) with an electrospray ionization (ESI) source, and theoretical electronic structure calculations. Measured IRMPD spectra are compared to linear IR spectra calculated at the B3LYP/6-31G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral complexes are also performed. These experiments and calculations suggest that specific geometric changes occur upon the binding of protons and/or sodium cations, including changes correlating to nucleic acid backbone geometry, specifically P–O bond lengths and ∠OPO bond angles. Information from these observations may be used to gain insight into the structures of more complex systems, such as nucleotides and solvated nucleic acids

Mutations in Arabidopsis YCF20-like genes affect thermal dissipation of excess absorbed light energy

Plants dissipate excess absorbed light energy as heat to protect themselves from photo-oxidative stress. The Arabidopsis thaliananpq6 mutant affected in thermal dissipation was identified by its partial defect in the induction of nonphotochemical quenching of chlorophyll fluorescence (NPQ) by excess light. Positional cloning revealed that npq6 contains a frameshift mutation caused by a single base-pair deletion in the At5g43050 gene, which encodes a member of the hypothetical chloroplast open reading frame 20 (YCF20) family of proteins with unknown function(s). The YCF20 protein family is mostly conserved in oxygenic photosynthetic organisms including cyanobacteria, eukaryotic algae, and plants. Amino acid sequence comparison identified two other genes in Arabidopsis that encode similar proteins to NPQ6: At1g65420 and At3g56830. These three Arabidopsis proteins have functional chloroplast-targeting transit peptides. Using reverse genetics, a mutant with a T-DNA insertion within the At1g65420 gene was identified and shown to exhibit a low NPQ phenotype similar to that of npq6; therefore, At1g65420 was named NPQ7. In contrast, a knockdown mutant in the At3g56830 gene with lower transcript levels showed wild-type levels of NPQ. The npq6 npq7 double mutant had an additive NPQ defect, indicating that the YCF20 family members in Arabidopsis have overlapping functions affecting thermal dissipation