Biomedical subjects

Bing Wu

Publications and source records attributed to Bing Wu.

18 recordsLinked to original sources

PubMed2006

Utility of multidetector CT in the diagnosis of gastric bare area invasion by proximal gastric carcinoma.

PURPOSE: To investigate the utility of multidetector CT (MDCT) in the diagnosis of gastric bare area (GBA) invasion by proximal gastric carcinoma (PGC). METHODS: Sixty-eight consecutive patients with biopsy-proven PGC underwent MDCT scan prior to gastrectomy. We evaluated the CT images separately for the site, size, depth, lymph node, and enhancement characteristic of each case. Each postsurgical stomach specimen was axially sectioned and comparison was made to determine the correlation between the CT findings and the pathological examination of each tumor bearing slice. RESULTS: The sensitivity for detecting GBA involvement in patients with PGC was 84%. MDCT correctly identified 32 of 38 patients with GBA invasion and 10/13 (77%) tumors with metastatic lymph node greater than 5 mm in GBA or subphrenic retroperitoneal space. 33/36 (92%) patients with tumor extension within the edge of the gastric wall and 28/32 (88%) patients with tumor infiltration into subphrenic fat were correctly identified. MDCT correctly predicted the infiltration of tumor into the diaphragm in all 14 patients and identified 6/11 (55%) patients with gastrophrenic ligament invasion. CONCLUSION: MDCT may be of value in assessing the important radiological characteristics of GBA invasion in patients with PGC.

Adult↗

PubMed2006

Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database.

Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid (http://www.biosimgrid.org) database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely acetylcholinesterase, outer-membrane phospholipase A, outer-membrane protease T, and PagP (an outer-membrane enzyme which transfers a palmitate chain from a phospholipid to lipid A). A set of 17 simulations were analyzed corresponding to a total of approximately 0.1 micros simulation time. A simple metric for active-site integrity was used to demonstrate the existence of clusters of dynamic conformational behaviour of the active sites. Small (i.e. within a cluster) fluctuations appear to be related to the function of an enzymatically active site. Larger fluctuations (i.e. between clusters) correlate with transitions between catalytically active and inactive states. Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods.

Acetylcholinesterase↗

PubMed2006

Design of an inductively decoupled microstrip array at 9.4 T.

By independent control of the phases and amplitudes of its elements, the microstrip transmission-line array can mitigate sample-induced RF non-uniformities, and has been widely used as the transceiver in parallel imaging applications. One major challenge in implementing the microstrip array is the reduction of mutual coupling among individual elements. The low-input impedance preamplifier is commonly used for the decoupling purpose. However, it is impractical in the transceiver array design. Although interconnecting capacitors can be utilized to reduce the mutual coupling, they only efficiently work for the neighbor elements. In addition, this approach is impractical at fields higher than 300 MHz, in which the required decoupling capacitance is commonly less than 0.5 pF. We propose a novel decoupling approach by using decoupling inductors in this study. Due to the fact that the decoupling inductance is independent of the resonant frequency, the microstrip arrays can be well decoupled at ultra-high fields. To verify the proposed approach, an eight-channel microstrip array is fabricated and tested at 9.4 T. For this prototype, couplings between elements are significantly reduced by using the interconnecting inductors. The phantom experiment shows that the inductively decoupled microstrip array has good parallel imaging performance.

Equipment Design↗

PubMed2006

Biodegradation of p-nitrophenol by aerobic granules in a sequencing batch reactor.

In this study, aerobic granules to treat wastewater containing p-nitrophenol (PNP) were successfully developed in a sequencing batch reactor (SBR) using activated sludge as inoculum. A key step was the conditioning of the activated sludge seed to enrich for biomass with improved settleability and higher PNP degradation activity by implementing progressive decreases in settling time and stepwise increases in PNP concentration. The aerobic granules were cultivated at a PNP loading rate of 0.6 kg/ m3 x day, with glucose to boost the growth of PNP-degrading biomass. The granules had a clearly defined shape and appearance, settled significantly faster than activated sludge, and were capable of nearly complete PNP removal. The granules had specific PNP degradation rates that increased with PNP concentration from 0 to 40.1 mg of PNP/L, peaked at 19.3 mg of PNP/(g of VSS) x h (VSS = volatile suspended solids), and declined with further increases in PNP concentration as substrate inhibition effects became significant. Batch incubation experiments show that the PNP-degrading granules could also degrade other phenolic compounds, such as hydroquinone, p-nitrocatechol, phenol, 2,4-dichlorophenol, and 2,6-dichlorophenol. The PNP-degrading granules contained diverse microbial morphotypes, and PNP-degrading bacteria accounted for 49% of the total culturable heterotrophic bacteria. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments showed a gradual temporal shift in microbial community succession as the granules developed from the activated sludge seed. Specific oxygen utilization rates at 100 mg/L PNP were found to increase with the evolution of smaller granules to large granules, suggesting that the granulation process can enhance metabolic efficiency toward biodegradation of PNP. The results in this study demonstrate that it is possible to use aerobic granules for PNP biodegradation and broadens the benefits of using the SBR to target treatment of toxic and recalcitrant organic compounds.

Aerobiosis↗

PubMed2006

Perceptual space in the dark affected by the intrinsic bias of the visual system.

Correct judgment of egocentric/absolute distance in the intermediate distance range requires both the angular declination below the horizon and ground-surface information being represented accurately. This requirement can be met in the light environment but not in the dark, where the ground surface is invisible and hence cannot be represented accurately. We previously showed that a target in the dark is judged at the intersection of the projection line from the eye to the target that defines the angular declination below the horizon and an implicit surface. The implicit surface can be approximated as a slant surface with its far end slanted toward the frontoparallel plane. We hypothesize that the implicit slant surface reflects the intrinsic bias of the visual system and helps to define the perceptual space. Accordingly, we conducted two experiments in the dark to further elucidate the characteristics of the implicit slant surface. In the first experiment we measured the egocentric location of a dimly lit target on, or above, the ground, using the blind-walking-gesturing paradigm. Our results reveal that the judged target locations could be fitted by a line (surface), which indicates an intrinsic bias with a geographical slant of about 12.4 degrees. In the second experiment, with an exocentric/relative-distance task, we measured the judged ratio of aspect ratio of a fluorescent L-shaped target. Using trigonometric analysis, we found that the judged ratio of aspect ratio can be accounted for by assuming that the L-shaped target was perceived on an implicit slant surface with an average geographical slant of 14.4 degrees. That the data from the two experiments with different tasks can be fitted by implicit slant surfaces suggests that the intrinsic bias has a role in determining perceived space in the dark. The possible contribution of the intrinsic bias to representing the ground surface and its impact on space perception in the light environment are also discussed.

Cues↗

PubMed2005

Grid computing and biomolecular simulation.

Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

Biopolymers↗

PubMed2005

Laser needle guide for the sonic flashlight.

We have extended the real-time tomographic reflection display of the Sonic Flashlight to a laser guidance system that aims to improve safety and accuracy of needle insertion, especially for deep procedures. This guidance system is fundamentally different from others currently available. Two low-intensity lasers are mounted on opposite sides of a needle aimed parallel to the needle. The needle is placed against a notch in the Sonic Flashlight mirror such that the laser beams reflect off the mirror to create bright red spots on the flat panel display. Due to diffuse reflection from these spots, the virtual image created by the flat panel display contains the spots, identifying the projected destination of the needle at its actual location in the tissue. We have implemented our design and validated its performance, identifying several areas for potential improvement.

Equipment Design↗

PubMed2005

Tailored utilization of acquired k-space points for GRAPPA reconstruction.

The generalized auto-calibrating partially parallel acquisition (GRAPPA) is an auto-calibrating parallel imaging technique which incorporates multiple blocks of data to derive the missing signals. In the original GRAPPA reconstruction algorithm only the data points in phase encoding direction are incorporated to reconstruct missing points in k-space. It has been recognized that this scheme can be extended so that data points in readout direction are also utilized and the points are selected based on a k-space locality criterion. In this study, an automatic subset selection strategy is proposed which can provide a tailored selection of source points for reconstruction. This novel approach extracts a subset of signal points corresponding to the most linearly independent base vectors in the coefficient matrix of fit, effectively preventing incorporating redundant signals which only bring noise into reconstruction with little contribution to the exactness of fit. Also, subset selection in this way has a regularization effect since the vectors corresponding to the smallest singular values are eliminated and consequently the condition of the reconstruction is improved. Phantom and in vivo MRI experiments demonstrate that this subset selection strategy can effectively improve SNR and reduce residual artifacts for GRAPPA reconstruction.

Algorithms↗

PubMed2004

Paradoxical effects of statins on aortic valve myofibroblasts and osteoblasts: implications for end-stage valvular heart disease.

OBJECTIVES: We evaluated the effects of statins on aortic valve myofibroblasts (AVMFs) and osteoblast calcification in vitro. METHODS AND RESULTS: Cultured porcine AVMFs and M2-10B4 cells were treated with simvastatin and pravastatin. Mevalonate, a 3-hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) reductase metabolite, was added in parallel experiments. Manumycin A, which inhibits protein prenylation, was added to cultures in the absence of statins. Calcification was assessed by counting the number of calcific nodules formed and measuring alkaline phosphatase activity (APA). Statins inhibited calcific nodule formation (P<0.01) and APA (P<0.01) in AVMFs. Mevalonate reversed the statin effect on nodule formation (P<0.05) and APA (P<0.01). Manumycin A had no effect on either parameter. M2-10B4 cells treated with simvastatin formed more calcific nodules compared with controls (P<0.01), although pravastatin had no effect. Both statins, however, resulted in increased APA in M2-10B4 cells (P<0.01). Mevalonate had no impact on nodule numbers or APA in M2-10B4 cells. CONCLUSIONS: Statins inhibit calcification in AVMFs by inhibiting the cholesterol biosynthetic pathway, independent of protein prenylation, but paradoxically stimulate bone cell calcification. Because 15% of patients with end-stage valvular heart disease exhibit mature bone in their aortic valves, statins may differentially regulate calcification within a valve, limiting dystrophic calcification but promoting ossification of formed bone.

Animals↗

PubMed2004

Effects of selenium on peripheral blood mononuclear cell membrane fluidity, interleukin-2 production and interleukin-2 receptor expression in patients with chronic hepatitis.

AIM: To study the effect of selenium on peripheral blood mononuclear cell (PBMC) membrane fluidity and immune function in patients with chronic hepatitis. METHODS: PBMCs were pretreated with selenium (1.156x10(-7) mol/L) for 6 h in vitro or extracted directly from patients after administration of selenium-yeast continuously for 8-12 wk (200 microg/d), and then exposed to Con-A for 48 h. The membrane fluidity, interleukin-2 (IL-2) production and interleukin-2 receptor (IL-2R) expression in PBMCs and malondialdehyde (MDA) concentration in medium and lipid peroxide (LPO) in plasma were determined. RESULTS: The PBMC membrane fluidity, IL-2 production and IL-2R expression in patients with chronic hepatitis were significantly lower than those in healthy blood donators (particle adhesive degree R, 0.17+/-0.01 vs 0.14+/-0.01, P<0.01; IL-2, 40.26+/-9.55 vs 72.96+/-11.36, P<0.01; IL-2R, 31.05+/-5.09 vs 60.58+/-10.56, P<0.01), and the MDA concentration in medium in patients with chronic hepatitis was significantly higher than that in healthy blood donators (1.44+/-0.08 vs 0.93+/-0.08, P<0.01). Both in vitro and in vivo administration of selenium could reverse the above parameters. CONCLUSION: Supplement of selenium can suppress lipid peroxidation, and improve PBMC membrane fluidity and immune function in patients with chronic hepatitis.

Adult↗

PubMed2004

BioSimGrid: towards a worldwide repository for biomolecular simulations.

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

Acetylcholinesterase↗

PubMed2004

Perceiving distance accurately by a directional process of integrating ground information.

By itself, the absolute distance of an object cannot be accurately judged beyond 2-3 m (refs 1-3). Yet, when it is viewed with reference to a flat terrain, humans accurately judge the absolute distance of the object up to 20 m, an ability that is important for various actions. Here we provide evidence that this is accomplished by integrating local patches of ground information into a global surface reference frame. We first show that restricting an observer's visual field of view to the local ground area around the target leads to distance underestimation, indicating that a relatively wide expanse of the ground surface is required for accurate distance judgement. Second, as proof of surface integration, we show that even with the restricted view, the observer can accurately judge absolute distance by scanning local patches of the ground surface, bit by bit, from near to far, but not in the reverse direction. This finding also reveals that the surface integration process uses the near-ground-surface information as a foundation for surface representation, and extrapolation to the far ground surface around the target for accurate absolute distance computation.

Darkness↗

PubMed2004

Judging egocentric distance on the ground: occlusion and surface integration.

On the basis of the finding that a common and homogeneous ground surface is vital for accurate egocentric distance judgments (Sinai et al, 1998 Nature 395 497-500), we propose a sequential-surface-integration-process (SSIP) hypothesis to elucidate how the visual system constructs a representation of the ground-surface in the intermediate distance range. According to the SSIP hypothesis, a near ground-surface representation is formed from near depth cues, and is utilized as an anchor to integrate the more distant surfaces by using texture-gradient information as the depth cue. The SSIP hypothesis provides an explanation for the finding that egocentric distance judgment is underestimated when a texture boundary exists on the ground surface that commonly supports the observer and target. We tested the prediction that the fidelity of the visually represented ground-surface reference frame depends on how the visual system selects the surface information for integration. Specifically, if information is selected along a direct route between the observer and target where the ground surface is disrupted by an occluding object, the ground surface will be inaccurately represented. In experiments 1-3 we used a perceptual task and two different visually directed tasks to show that this leads to egocentric distance underestimation. Judgment is accurate however, when the observer selects the continuous ground information bypassing the occluding object (indirect route), as found in experiments 4 and 5 with a visually directed task. Altogether, our findings provide support for the SSIP hypothesis and reveal, surprisingly, that the phenomenal visual space is not unique but depends on how optic information is selected.

Analysis of Variance↗

PubMed2004

Categorization of dysmotility in patients with chronic constipation and its significance for management.

BACKGROUND: Chronic constipation is a common gastrointestinal symptom with different patterns of dysmotility for which there is not one simple and effective diagnostic method for categorization. The present study assessed the diagnostic method used in patients with chronic constipation and its significance for clinical management. METHODS: The study group comprised 210 consecutive patients with chronic constipation who underwent history, digital anorectal examination (DARE), gastrointestinal transit test (GITT) and anorectal manometry (ARM) to determine the pattern of dysmotility. Symptoms and the examinations were summarized for establishing the diagnostic method and evaluation of the role of the examinations. RESULTS: Outlet obstructive constipation (OOC), slow transit constipation (STC) and mixed constipation (MC) accounted for 50.8%, 10.2% and 39.0% of cases, respectively. The stool was harder in STC or MC than in OOC (P = 0.036). The presence of a paradoxical inverse contraction of anal sphincter when straining to defecate during DARE or ARM was significant for the diagnosis of OOC (P < 0.001). The distribution of the residual markers on abdominal plain film after 48 h GITT was significant for the diagnosis of STC (P < 0.001). The sensitivity of DARE, GITT and ARM was 82.5%, 89.1% and 94.4%, and specificity was 95.2%, 87.9% and 82.6%, respectively. Clinical management was modified in 69.5% of patients after categorizing the constipation pattern. CONCLUSIONS: The symptoms, DARE, GITT and ARM are effective methods of evaluating the dysmotility patterns in patients with chronic constipation. DARE and ARM could improve the diagnostic rate of OOC, and GITT assists in diagnosis of STC. Proper categorization of the dysmotility pattern is important for the clinical management of chronic constipation.

Adolescent↗

PubMed2004

[The effect of electroacupuncture on the weakening of CPP of morphine dependence rats and the mechanism therein involved].

OBJECTIVE: To address the research questions whether electroacupuncture can weaken the CPP of morphine dependence rats and whether the neurobiological mechanism for control of anxiety is related to the transcription of DBI mRNA. METHODS: Twenty-four SD rats were randomly divided into the control group, electroacupuncture group and morphine group. After the CPP model was constructed. The time of CPP was examined on the 5th and 10th day as the interventional electroacupuncture was instituted. The total RNA was extracted from the brain of sacrificed rat and was defected by use of RT-PCR. RESULTS: The CPP time of the electroacupuncture group was significantly decreased on the 5th and 10th day after abstinence (P<0.05). The transcription of the DBI mRNA of the electroacupuncture group was obviously lower than that of the morphine group (P<0.05), and there was no difference between the electroacupuncture group and control group. CONCLUSION: Electroacupuncture can weaken the CPP of the morphine dependence rats, and the neurobiological mechanism may be related to the electroacupuncture-induced transcription of DBI mRNA.

Animals↗

PubMed2002

Hairpin versus extended DNA binding of a substituted beta-alanine linked polyamide.

A series of alpha-substituted beta-alanine (beta) linked polyamides (DbaPyPyPy-beta*-PyPyPy) were prepared and examined. This resulted in the observation that while most substituents disrupt DNA binding, (R)-alpha-methoxy-beta-alanine (beta((R)-OMe)) maintains strong binding affinity and preferentially adopts a hairpin versus extended binding mode, providing an alternative hairpin linker to gamma-aminobutyric acid (gamma). A generalized variant of a fluorescent intercalator displacement assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding site size was developed to distinguish between the extended binding of the parent beta-alanine 1 (DbaPyPyPy-beta-PyPyPy) and the hairpin binding of 3 (DbaPyPyPy-beta((R)-OMe)-PyPyPy).

Alanine↗

PubMed2002

The effect of C-terminal helix stabilization on specific DNA binding by monomeric GCN4 peptides.

DNA binding by a 29-residue, monomeric, GCN4 basic region peptide, GCN4br, as well as by peptide br-C, a monomeric basic-region analogue that is helix stabilized at its C-terminal end by a Lys25. Asp29 side-chain lactam-bridged alanine-rich sequence, was studied at 25 C in an aqueous buffer containing 100 mm NaCl. Mixing of both peptides with duplex DNA containing the cAMP-responsive element (CRE) was accompanied by significant helix stabilization in the peptides, whereas mixing of the peptides with duplex DNA containing a scrambled CRE site was not. Peptide NBD-br-C was synthesized as a fluorescent probe to evaluate these peptide-DNA interactions further. Quantitative analysis of the fluorescence quenching of peptide NBD-br-C by CRE half-site DNA indicated the formation of a 1:1 complex with a dissociation constant of 1.41 +/- 0.22 microm. Competitive displacement fluorescence assays of CRE half-site binding gave dissociation constants of 0.65 +/- 0.09 microm for peptide br-C and 3.9 +/- 0.5 microM for GCN4br, which corresponds to a free energy difference of 1.1 kcal/mol that is attributed to the helix stabilization achieved in peptide br-C. This result indicates that helix initiation by the alpha-helical leucine zipper dimerization motif in native bzip proteins, such as GCN4, contributes significantly to the affinity of basic region peptides for their recognition sites on DNA. Our fluorescence assay should also prove useful for determining dissociation constants for CRE binding by other GCN4 basic region analogues under equilibrium conditions and physiological salt concentrations.

Circular Dichroism↗

PubMedDate not supplied

Psychophysical evaluation of in-situ ultrasound visualization.

We present a novel psychophysical method for evaluating ultrasonography based on Real-Time Tomographic Reflection (RTTR), in comparison to Conventional Ultrasound (CUS). The method measures the user's perception of the location of an ultrasound-imaged target independently from assessing the action employed to reach it. Three experiments were conducted with the Sonic Flashlight (SF), an RTTR device, and CUS. The first two experiments determined subjects' perception of target location with a triangulation-by-pointing task. Depth perception with the SF was comparable to direct vision, while CUS caused considerable underestimation of target depth. Binocular depth information in the SF was shown to significantly contribute to its superiority. The third experiment tested subjects in an ultrasound-guided needle insertion task. Because the SF provides visualization of the target at its actual location, subjects performed insertions faster and more accurately by using the SF rather than CUS. Furthermore, the trajectory analysis showed that insertions with the SF generally went directly to the target along the desired path, while CUS often led to a large deviation from the correct path consistent with the observed underestimation of target depth. These findings lend great promise to the use of RTTR-based imaging in clinical practice and provide precise means of assessing efficacy.

Biopsy, Needle↗