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Laboratory studies were conducted on the biodegradation of some selected lubricating oils. A standard method for determining the biodegradability of selected recalcitrant organic compounds was developed. Test results show that the species of bacteria present in the sample is an important factor affecting the biodegradation of selected lubricating oils. Results also indicate that it is difficult to degrade lubricating oils in water by using indigenous microorganisms in natural river or lake water. The study shows that up to 23% removal can be achieved biologically after 67 days of operation.

The same as in traditional surgery, surgeons in telerobotic surgery need extensive training to achieve experience and highly accurate instrument manipulation. Traditional training methods like practice in operating room have major drawbacks such as high risk and limited opportunity for which virtual reality (VR) and computer technologies can offer solutions. To accelerate the data transmission speed in our master-slave robotic simulator, GPUDirect was applied to ensure the synchronization and display rate of three computers. By using GPUDirect with InfiniBand card we realized up to 247% performance improvement in data transmission speed on NVIDIA Tesla™ products on different computers compared to that without GPUDirect, which shows that GPUDirect enables better communication between remote GPUs over InfiniBand.

Receptor interacting protein 3 (RIP3) is a protein kinase that plays a key role in programmed necrosis. Despite the importance of RIP3-dependent necrosis in many pathological processes, current knowledge on the function of RIP3 is very limited. Here we present the results of a proteome-wide analysis of RIP3-regulated phosphorylation sites using cells from wildtype (RIP3(+/+)) and RIP3 knockout (RIP3(-/-)) mice. Because the activation of RIP3 requires stimulation by certain extracellular stimuli such as ligands of death receptors or Toll-like receptors, we compared the phosphorylation sites of lipopolysaccharide (LPS)-treated peritoneal macrophages from RIP3(+/+) and RIP3(-/-) mice and the phosphorylation sites of tumor necrosis factor (TNF)-treated RIP3(+/+) and RIP3(-/-) mouse embryonic fibroblast (MEF) cells. Stable isotope labeling by amino acids in cell culture and spike-in stable isotope labeling by amino acids in cell culture were used in the analyses of the MEFs and macrophages, respectively. Proteomic analyses using stable isotope labeling by amino acids in cell culture coupled with immobilized metal affinity chromatography-hydrophilic interaction liquid chromatography fractionation and nanoLC MS/MS identified 14,057 phosphopeptides in 4306 proteins from the macrophages and 4732 phosphopeptides in 1785 proteins from the MEFs. Analysis of amino acid sequence motifs among the phosphopeptides identified a potential motif of RIP3 phosphorylation. Among the phosphopeptides identified, 73 were found exclusively in RIP3(+/+) macrophages, 121 were detected exclusively from RIP3(+/+) MEFs, 286 phosphopeptides were induced more in RIP3(+/+) macrophages than in RIP3(-/-) macrophages and 26 phosphopeptides had higher induction in RIP3(+/+) MEFs than in RIP3(-/-) cells. Many of the RIP3 regulated phosphoproteins from the macrophages and MEF cells are functionally associated with the cell cycle; the rest, however, appear to have diverse functions in that a number of metabolism related proteins were phosphorylated in macrophages and development related phosphoproteins were induced in MEFs. The results of our phosphoproteomic analysis suggest that RIP3 might function beyond necrosis and that cell type specific function of RIP3 exists.

With the advent of surgical robots, telesurgery becomes an exciting new discipline that promises to broaden the practice of expert surgeons. Accordingly surgeons need to learn more sophisticated skills for telesurgery. We proposed a master-slave surgery simulator that can teach skills in controlling telesurgery robots. The simulator consists of master-slave haptic devices and a stereoscopic display. Telesurgery is simulated in a bilateral control scheme with Position–Force control strategy. The performance of the master-slave control in undertaking free space motion is presented and the simulation of burring in spine surgery is implemented. Experiments show the following error of the telesurgery simulator is quite small and the force change during burring simulation is acceptable.

The purpose of the present study was to establish a water quality model for a river network system in Beijing‐Tianjin, China and to develop a method for estimating parameters in the established model. The Network Grid method, which was used in the study, is based on the solution of optimal problems in the entire river network system. The parameters, the decay rate of total BOD (carbonaceous and nitrogenous), K1, the re‐aeration rate, K2, the decay rate of BOD for settleable solids, K3, the DO constant rate for photosynthesis, K4, and the nitrification rate of ammonia, K5, in network models are estimated simultaneously by the Network Grid method. The comparison of results indicates that the Network Grid method is suitable for the estimation of the parameters in river network model and the concentration distribution of organic pollutants calculated by the model is in accordance with that observed in situ.

Methodology for application of a Geographical Information System (GIS) to the distribution of selected toxic chemicals in Lake Erie of the Great Lakes is proposed and described in detail in this paper. Seventeen different organic compounds were selected as toxic chemicals. An integrated analysis was conducted utilizing a GIS system — SPANS. Concentration distributions for individual organic compounds were mapped in GIS by applying the spatial interpolation of point data. An overlay map of fourteen selected toxic chemicals was produced in GIS displaying an overall concentration pattern. On this overlay map different levels of toxic chemical concentrations in Lake Erie were clearly identified taking into consideration the fourteen chemicals. The results indicated that the distributions of the selected toxic chemicals displayed higher concentration primarily in the West Basin, near the Detroit River, of the lake. Polychlorobiphenyls (PCBs) and Dieldrin which come from the sediments are the predomina...

Wide-angle images have been wisely used in many areas since they can provide much larger field-of-view (FOV) of a scene. But distortions in these images disturb users' perception and many research works have been investigated to tackle this problem. Up to now, several correction methods have been developed, such as the perspective, Mercator and stereographic projections. However, these methods tend to bend straight lines or distort the shapes of objects, and [Zorin and Barr 1995] pointed out that no global projection can preserve both straight lines and the shapes of objects. Recently, [Carroll et al. 2009] proposed a content-preserving approach to map wide-angle photographs onto image plane by computing a spatially-varying projection. Unfortunately, it required the users to draw about 20 lines on average as an initial step.

In this paper, we propose a novel algorithm for image retargeting based on adaptive scaling methods. Our algorithm starts by adaptively partitioning the input image into number of strips according to the combined saliency map, which contains both gradient information and visual saliency to measure significant regions and is also used to guide the sampling process when scaling image strips. Experimental results show that our method can achieve better results than other content-aware image retargeting operators.

In an identity-based encryption (IBE) system, a private-key generator (PKG) is assumed to be credible, which takes charge of identity authentication and private-key issuing for users. However, the reliability of IBE may be questioned since this assumption does not always hold. In this paper, we propose a new distributed private-key generation scheme with self-certified identity (SCI-DKG) which does not need any PKG. SCI-DKG takes advantage of distributed private key generation and self certification to remove PKG from IBE. Comparing with the existing IBE schemes, a user and his identity can be independently authenticated through his blind digital ID (BDID) card and identity signature. In the meanwhile, a user can extract private keys from other users' sharing packets containing secret shares, partial public parameters and BDID cards. The proposed scheme significantly extends IBE without involvement of PKGs, and provides a promising solution for applications where PKG is not always available. Theoretical analysis demonstrates that our scheme is secure and effective.

Drought is one of the most severe limitations to plant growth and productivity. Resurrection plants have evolved a unique capability to tolerate desiccation in vegetative tissues. Fern-ally Selaginella tamariscina (Beauv.) is one of the most primitive vascular resurrection plants, which can survive a desiccated state and recover when water becomes available. To better understand the mechanism of desiccation tolerance, we have applied physiological and proteomic analysis. Samples of S. tamariscina were water-deprived for up to seven days followed by 12 h of rewatering. Our results showed that endogenous abscisic acid (ABA) increased to regulate dehydration-responsive genes/proteins and physiological processes. In the course of dehydration, the contents of osmolytes represented by soluble sugars and proline were increased to maintain cell structure integrity. The activities of four antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione reductase (GR)) also increased. In contrast, both the rate of photosynthesis and the chlorophyll content decreased, and plasma membrane integrity was lost. We identified 138 desiccation-responsive two-dimensional electrophoresis (2-DE) spots, representing 103 unique proteins. Hierarchical clustering analysis revealed that 83% of the proteins were down-regulated upon dehydration. They were mainly involved in photosynthesis, carbohydrate and energy metabolism, stress and defense, protein metabolism, signaling, membrane/transport, cell structure, and cell division. The dynamic expression changes of the desiccation-responsive proteins provide strong evidence that cell structure modification, photosynthesis reduction, antioxidant system activation, and protein post-transcriptional/translational modifications are essential to the poikilochlorophyllous fern-ally S. tamariscina in response to dehydration. In addition, our comparative analysis of dehydration-responsive proteins in vegetative tissues from 19 desiccation tolerant and nontolerant plant species suggests that resurrection S. tamariscina has developed a specific desiccation tolerant mechanism. To our knowledge, this study constitutes the first detailed investigation of the protein complement in fern/fern-allies.

Lymph node involvement is the most important predictor of survival rates in patients with oral squamous cell carcinoma (OSCC). A biomarker that can indicate lymph node metastasis would be valuable to classify patients with OSCC for optimal treatment. In this study, we have performed a serum proteomic analysis of OSCC using 2-D gel electrophoresis and liquid chromatography/tandem mass spectrometry. One of the down-regulated proteins in OSCC was identified as tetranectin, which is a protein encoded by the CLEC3B gene (C-type lectin domain family 3, member B). We further tested the protein level in serum and saliva from patients with lymph-node metastatic and primary OSCC. Tetranectin was found significantly under-expressed in both serum and saliva of metastatic OSCC compared to primary OSCC. Our results suggest that serum or saliva tetranectin may serve as a potential biomarker for metastatic OSCC. Other candidate serum biomarkers for OSCC included superoxide dismutase, ficolin 2, CD-5 antigen-like protein, RalA binding protein 1, plasma retinol-binding protein and transthyretin. Their clinical utility for OSCC detection remains to be further tested in cancer patients.

In this paper, we present a novel parallel implementation of HARRIS and DOG detector on GPU for feature extractions of Patch-based Multi-View Stereo (PMVS) algorithm in image sequence. With the Compute Unified Device Architecture(CUDA)-enabled GPU, the acceleration is significant and it obtains a 34 times performance boost comparing to a CPU implementation. We adopt the hardware built-in bilinear interpolation of texture to shorten the time for image resampling while doing image transformations. While lots of time can be saved by using our improved PMVS Algorithm with GPU-based feature extraction, experimental results also show that our implementation can obtain fine details for building accurate object and scene models.

Stable isotope dilution-multiple reaction monitoring-mass spectrometry (SID-MRM-MS), which is an alternative to immunoassay methods such as ELISA and Western blotting, has been used to alleviate the bottlenecks of high-throughput verification of biomarker candidates recently. However, the inconvenience and high isotope consumption required to obtain stably labeled peptide impedes the broad application of this method. In our study, the (18)O-labeling method was introduced to generate stable isotope-labeled peptides instead of the Fmoc chemical synthesis and Qconcat recombinant protein synthesis methods. To make (18)O-labeling suitable for absolute quantification, we have added the following procedures: (1) RapiGest SF and microwave heating were added to increase the labeling efficiency; (2) trypsin was deactivated completely by chemical modification using tris(2-carboxyethyl)phosphine (TCEP) and iodoacetamide (IAA) to prevent back-exchange of (18)O to (16)O, and (3) MRM parameters were optimized to maximize specificity and better distinguish between (18)O-labeled and unlabeled peptides. As a result, the (18)O-labeled peptides can be prepared in less than 1 h with satisfactory efficiency (97%) and remained stable for 1 week, compared to traditional protocols that require 5 h for labeling with poor stability. Excellent separation of (18)O-labeled and unlabeled peptides was achieved by the MRM-MS spectrum. Finally, through the combined improvement in (18)O-labeling with multiple reaction monitoring, an absolute quantification strategy was developed to quantitatively verify hepatocellular carcinoma-related biomarker candidates, namely, vitronectin and clusterin, in undepleted serum samples. Sample preparation and capillary-HPLC analysis were optimized for high-throughput applications. The reliability of this strategy was further evaluated by method validation, with accuracy (%RE) and precision (%RSD) of less than 20% and good linearity (r(2)0.99), and clinical validation, which were consistent with previously reported results. In summary, our strategy can promote broader application of SID-MRM-MS for biomarkers from discovery to verification regarding the significant advantages of the convenient and flexible generation of internal standards, the reduction in the sample labeling steps, and the simple transition.

IntroductionGlycosylation is an important component for a number of biological processes and is perhaps the most abundant and complicated of the known post-translational modifications found on proteins.MethodsThis work combines two-dimensional (2-D) polyacrylamide gel electrophoresis and lectin blotting to map the salivary glycome and mass spectrometry to identity the proteins that are associated with the glycome map. A panel of 15 lectins that recognize six sugar-specific categories was used to visualize the type and extent of glycosylation in saliva from two healthy male individuals. Lectin blots were compared to 2-D gels stained either with Sypro Ruby (protein stain) or Pro-Q Emerald 488 (glycoprotein stain).ResultsEach lectin shows a distinct pattern, even those belonging to the same sugar-specific category. In addition, the glycosylation profiles generated from the lectin blots show that most salivary proteins are glycosylated and that the profiles are more widespread than is demonstrated by the glycoprotein-stained gel. Finally, the coreactivity between lectins was measured to determine what types of glycan structures are associated with one another and also the population variation of the lectin reactivity for 66 individuals were reported.ConclusionsThis starting 2-D gel glycosylation reference map shows that the scientifically accepted, individual oligosaccharide variability is not limited to a few large glycoproteins such as MUC5B, but are found on most members of the salivary proteome. Finally, in order to see the full range of oligosaccharide distribution, multiple reagents or lectins are needed.

A Gram-negative, chromium(VI) tolerant and reductive strain CTS-325, isolated from a Chinese chromate plant, was identified as Ochrobactrum anthropi based on its biochemical properties and 16S rDNA sequence analysis. It was able to tolerate up to 10 mmol/L Cr(VI) and completely reduce 1 mmol/L Cr(VI) to Cr(III) within 48 h. When the strain CTS-325 was induced with Cr(VI), a protein increased significantly in the whole cell proteins. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis revealed that this protein was a superoxide dismutase (SOD) homology. The measured superoxide dismutase activity was 2694 U/mg after three steps of purification. The SOD catalyzes the dismutation of the superoxide anion (O 2 ·− ) into hydrogen peroxide and molecular oxygen. This protein is considered to be one of the most important anti-oxidative enzymes for O. anthropi as it allows the bacterium to survive high oxygen stress environments, such as the environment produced during the reduction process of Cr(VI).

To accelerate the simultaneous algebraic reconstruction technique (SART) with motion compensation for speedy and quality computed tomography reconstruction by exploiting CUDA-enabled GPU.Two core techniques are proposed to fit SART into the CUDA architecture: (1) a ray-driven projection along with hardware trilinear interpolation, and (2) a voxel-driven back-projection that can avoid redundant computation by combining CUDA shared memory. We utilize the independence of each ray and voxel on both techniques to design CUDA kernel to represent a ray in the projection and a voxel in the back-projection respectively. Thus, significant parallelization and performance boost can be achieved. For motion compensation, we rectify each ray's direction during the projection and back-projection stages based on a known motion vector field.Extensive experiments demonstrate the proposed techniques can provide faster reconstruction without compromising image quality. The process rate is nearly 100 projections s (-1), and it is about 150 times faster than a CPU-based SART. The reconstructed image is compared against ground truth visually and quantitatively by peak signal-to-noise ratio (PSNR) and line profiles. We further evaluate the reconstruction quality using quantitative metrics such as signal-to-noise ratio (SNR) and mean-square-error (MSE). All these reveal that satisfactory results are achieved. The effects of major parameters such as ray sampling interval and relaxation parameter are also investigated by a series of experiments. A simulated dataset is used for testing the effectiveness of our motion compensation technique. The results demonstrate our reconstructed volume can eliminate undesirable artifacts like blurring.Our proposed method has potential to realize instantaneous presentation of 3D CT volume to physicians once the projection data are acquired.

The Active Shape Model (ASM) has been widely used to recognize and track a face from a video sequence. However, it is usually limited to frontal view or the cases of small-scale head movement, as its accuracy may greatly degrade in conditions of quick movement, large rotation and temporary occlusion. We propose an enhanced ASM and predicted Meanshift algorithm to meet these challenges, which combines the context information and predicted Meanshift to obtain multi-angle start shapes for ASM searching and the best result shape is chosen based on a matching evaluation. Extensive experiments demonstrate the flexibility and accuracy of the proposed method.

In this paper, we propose a GPU-based acceleration method to speed up volume image registration using Compute Unified Device Architecture(CUDA). A novel CUDA-based method for joint histogram computation is introduced in this paper, which is also valuable for 2D image registration and other general graphics applications. Additionally, an algorithm refinement is proposed to improve the widely used FMRIB's Linear Image Registration Tool (FLIRT). Although extra time is taken by applying that algorithm refinement, our implementation showed the ability to perform a full 12 DOF (Degrees of Freedom) registration of two brain volume images in nearly 35 seconds, which is about 10 times faster than the native FLIRT implementation.

We present a novel parallel implementation of Active Shape Model (ASM) on GPU for massive facial feature extractions in video or image sequence. With the Compute Unified Device Architecture (CUDA)-enabled GPU, the acceleration is significant and reported a 48 times performance boost comparing to a CPU implementation. We adopt the hardware built-in bilinear interpolation of texture to shorten the time for a large number of image scale transform operations. Then, a GPU-based parallel mahalanobis distance calculation is introduced in the searching process, and this enables most of the computations to be performed simultanously. As a result, we can achieve real-time performance in our video-driven 3D facial animation system.

Realistic facial animation is important in many graphics applications, like animated feature films and computer games, to enrich human computer interaction. In this paper, we propose a physically-based facial animation approach employing knowledge from the anatomy and biomechanics of human facial muscles. First, the 3D face mesh is generated automatically by commercial software and the facial skin is represented by a nonlinear mass-spring system which simulates realistic elastic dynamics of human dermis. Then, a structure skull is attached to fit the face mesh. A set of anatomically consistent facial muscles are incorporated to model the forces deforming the face mesh. Finally, we extend Waters' muscle model to improve the combination of multiple muscle actions and to generate realistic expression. Experiments show that our method is superior to the traditional geometric model and can achieve comparative results with the commercial software FaceGen.

In this paper, we apply the Compute Unified Device Architecture (CUDA) to the 3D cone-beam CT reconstruction using Simultaneous Algebraic Reconstruction Technique (SART). With the hardware acceleration, the computationally complex SART can run at speed comparable to the commonly used Filtered Back-Projection, and provide even better quality volume with less samples. The main contributions include two novel techniques to accelerate the reconstruction. We introduce a ray-driven projection along with hardware built-in trilinear interpolation, as well as a voxel-driven back-projection that can avoid redundant computation by combining CUDA shared memory. Significant performance boost is reported from experiments using our techniques. A real-time reconstruction is achieved within 3 seconds for a 128*128*128 volume from 80 128*128 projections, without compromising image quality. Our proposed method realizes the instantaneous presentation of CT volume to the physician once projection images are acquired.

Hexagonal grid is a popular and powerful network model in various networks and especially in the Mobile Ad-hoc NETworks (MANETs). To the best of our knowledge, however, there is no suitable coordinate system for the hexagonal grids. So it has been a big challenge to solve the node location problem for hexagonal grids in MANETs. In this paper, we propose an intuitive and simple two-dimensional logical coordinate system for hexagonal grids, and we propose a novel approach that maps the hexagonal grids to traditional rectangular grids based on the proposed coordinate system. Given the two-dimensional coordinate of any node in MANETs, the hexagonal grid where the node resides can be computed by the proposed approach. The location of the hexagon center can be computed easily, which is important for location-based routing protocols in MANETs.

Vessel segmentation is an essential task in many computer-aided medical systems. However, the topology complexity of vascular structures and the intensity inhomogeneity of angiogram make it a challenging problem. We propose a level set based predictor-corrector algorithm to meet these challenges. In the predictor step, the overall contour of vessel structures is delineated by piecewise constant (PC) model, which is insensitive to the initial contour and adaptive to the complex morphological variations of vessel structures. In the corrector step, the segmented results are refined by an improved local binary fitting (LBF) model, which can efficiently deal with intensity inhomogeneity in the angiogram, especially in the distal part of the vessels. Compared to original LBF model, our approach can avoid the emergence of new contour in non-vascular regions. The proposed algorithm takes both global and local information into consideration and combines the advantages of PC model and LBF model. Experimental results on MRA images demonstrate the feasibility of our algorithm.

In this paper, we propose a fast and flexible sorting algorithm with CUDA. The proposed algorithm is much more practical than the previous GPU-based sorting algorithms, as it is able to handle the sorting of elements represented by integers, floats and structures. Meanwhile, our algorithm is optimized for the modern GPU architecture to obtain high performance. We use different strategies for sorting disorderly list and nearly-sorted list to make it adaptive. Extensive experiments demon- strate our algorithm has higher performance than previous GPU-based sorting algorithms and can support real-time applications.

The development of the first Chinese ElectroMagnetic Human Model (CEMHM) in The Chinese University of Hong Kong is reported. The model can be used in any electromagnetic simulation tools to reveal more accurate and practical biological effect caused by RF radiation of a wireless device. The preliminary numerical study of SAR distribution using the CEMHM is presented. It is found that the maximum SAR value calculated using the CEMHM is below the value that is obtained using the SAM model.

With the proposed parallel marching cubes (MC) algorithm, we can naturally generate triangles in order, which facilitates the visibility-correct visualization of multiple translucent isosurfaces without performing computational expensive sorting. Upon a commodity graphics processing unit (GPU), our implementation can extract isosurfaces from a high-resolution volume and render the result in real time. The 3D volume is calculated and processed in parallel, The SIMD (Single Instructuanal Multiple Data) structure of GPU further improves the parallelism of the proposed method. The method extracts and draws triangles, from back to front, according to the viewpoint. The visibility of multi-layer translucent isosurfaces is resolved naturally. We solve three levels of order: inter-slab order (the order of slabs), intra-slab order (the order of cells within a slab), and intra-cell order (the order of triangles within a cell). The inter-slab order and intra-slab order are solved by the way similar to ldquoobject-alligned slicesrdquo. The intra-cell order is solved by generating a new traingle of the proposed parallel MC algorithm.

Multipath routing is one of the most important research directions in the area of network routing. However, it is very difficult to achieve node-disjoint multipath routing in Mobile Ad Hoc NETworks (MANETs), especially in large scale MANETs. We propose a Multiple Zones-based routing protocol (M-Zone for short) to discover node-disjoint routing paths segment-by-segment in large scale MANETs effectively. M-Zone uses a multiple zoning method based on location to guarantee that the nodes in multiple routes are different apart from the source and the destination. We propose two approaches to maintain the routes: one is local route maintenance and the other is global route maintenance. Simulation studies show that the average path length of M-Zone is close to that of GZRP, which combines the Zone Routing Protocol (ZRP) and Global Positioning System (GPS). The average packet delivery ratio of M-Zone is significantly higher than that of GZRP.

Saliva is a body fluid with important functions in oral and general health. A consortium of three research groups catalogued the proteins in human saliva collected as the ductal secretions: 1166 identifications--914 in parotid and 917 in submandibular/sublingual saliva--were made. The results showed that a high proportion of proteins that are found in plasma and/or tears are also present in saliva along with unique components. The proteins identified are involved in numerous molecular processes ranging from structural functions to enzymatic/catalytic activities. As expected, the majority mapped to the extracellular and secretory compartments. An immunoblot approach was used to validate the presence in saliva of a subset of the proteins identified by mass spectrometric approaches. These experiments focused on novel constituents and proteins for which the peptide evidence was relatively weak. Ultimately, information derived from the work reported here and related published studies can be used to translate blood-based clinical laboratory tests into a format that utilizes saliva. Additionally, a catalogue of the salivary proteome of healthy individuals allows future analyses of salivary samples from individuals with oral and systemic diseases, with the goal of identifying biomarkers with diagnostic and/or prognostic value for these conditions; another possibility is the discovery of therapeutic targets.

The advent of Visible Human Project (VHP) by the National Library of Medicine of United States in 1994 [1] has revolutionized the research in medical imaging. This was the first time true tissue color can be revealed for in depth study by all scientists and researchers worldwide. The visible human dataset has been applied to many different aspects of medicine including medical image diagnosis, anatomical education, and surgical simulation etc. Since October 2002, the Chinese Visible Human Project [2], [3] research team from The Third Military Medical University has successfully collected visible human datasets from several Chinese donors. Deploying latest processing techniques, extra-fine anatomic details, which cannot be displayed from the long ago American dataset, can now be unveiled by the Chinese visible human datasets. Together with the Visible Korean Man [4], there are totally three countries in the world has published the establishment of her own visible human data.

Proteomic analysis of human oral fluid (whole saliva) holds promise as a non-invasive method to identify biomarkers for human oral cancer, a high impact local disease in the oral cavity affecting 38,000 Americans and with 350,000 cases worldwide annually. In this study, matrix-assisted laser desorption/ionization--mass spectrometry (MALDI-MS) was used to profile oral fluid samples from oral cancer and control subjects, and 46 peptides/proteins were found at significantly different levels between the two groups. To identify a candidate protein biomarker, oral fluid samples were separated by liquid chromatography (LC) using a C4 reversed-phase column. The collected LC fractions were monitored by MALDI-MS and the fraction containing the candidate biomarker was digested for LC-MS/MS analysis to identify it. The use of nanospray MS/MS for the identification of candidate peptide biomarkers was also demonstrated. This approach can be useful for the identification of protein or peptide biomarkers following MALDI-MS or surface-enhanced laser desorption/ionization MS profiling of clinical samples. This study clearly demonstrated that oral fluid contains proteomic signatures that may serve as biomarkers for human diseases such as oral cancer. Once discovered and validated on a large and independent clinical cohort, oral fluid proteomic biomarkers may be extensively used for future disease diagnosis.

Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons comprise a large fraction of the human and mouse genomes. The mobility of these successful elements requires the protein encoded by open reading frame-1 (ORF1p), which binds single-stranded RNA with high affinity and functions as a nucleic acid chaperone. In this report, we have used limited proteolysis, filter binding, and NMR spectroscopy to characterize the global structure of ORF1p and the three-dimensional structure of a highly conserved RNA binding domain. ORF1p contains three structured regions, a coiled-coil domain, a middle domain of unknown function, and a C-terminal domain (CTD). We show that high affinity RNA binding by ORF1p requires the CTD and residues within an amino acid protease-sensitive segment that joins the CTD to the middle domain. Insights in the mechanism of RNA binding were obtained by determining the solution structure of the CTD, which is shown to adopt a novel fold consisting of a three-stranded beta sheet that is packed against three alpha-helices. An RNA binding surface on the CTD has been localized using chemical shift perturbation experiments and is proximal to residues previously shown to be essential for retrotransposition, RNA binding, and chaperone activity. A similar structure and mechanism of RNA binding is expected for all vertebrate long interspersed nuclear element-1 elements, since residues encoding the middle, protease-sensitive segment, and CTD are highly conserved.

Marching cubes has long been employed as a standard indirect volume rendering approach to extract isosurfaces from 3D volumetric data. This paper presents a GPU-friendly MC implementation. Besides the cell indexing, we propose to calculate vertex and normal interpolations by precomputing the expensive equations and looking up these values during runtime. Upon a commodity GPU, our implementation can rapidly extract isosurfaces from a high-resolution volume and render the result. With the proposed parallel marching cubes algorithm, we can naturally generate layer-structured triangles, which facilitate the visualization of multiple-layer translucent isosurfaces without performing computational expensive sorting. The algorithm extracts and draws triangles, in a layer by layer fashion, from back to front.

The research on digital visible human is of great significance and application value. The US VHP created the first digital image data set of complete human (male and female) in 1995. To promote worldwide application-oriented VHR, more visible human data sets representative of different populations of the world are in demand. The Chinese Visible Human (CVH) male (created in Oct. 2002) and female (created in Feb. 2003) project achieved greater integrity of images, easier blood vessel identification, and were free of organic lesion. The most noteworthy technical advance of CVH Project was construction of a low temperature laboratory, which contributed to prevention of small structures (including teeth, concha nasalis, and articular cartilage) from falling off of the milling surface. Thus, better integrity of images was ensured. So far, we have achieved acquisition of five CVH data sets and their volume visualization on PC. 3D reconstruction of some organs or structures has been finished. The work of segmentation of a complete data set is also under way. Although there is still a distance to go to make visible human meet the application-oriented needs in various fields, we're taking our first step toward future application by acquiring new data sets, performing segmentation and setting up a platform of computer-assisted medicine.

The success of targeting kinases in cancer with small molecule inhibitors has been tempered by the emergence of drug-resistant kinase domain mutations. In patients with chronic myeloid leukemia treated with ABL inhibitors, BCR-ABL kinase domain mutations are the principal mechanism of relapse. Certain mutations are occasionally detected before treatment, suggesting increased fitness relative to wild-type p210 BCR-ABL. We evaluated the oncogenicity of eight kinase inhibitor-resistant BCR-ABL mutants and found a spectrum of potencies greater or less than p210. Although most fitness alterations correlate with changes in kinase activity, this is not the case with the T315I BCR-ABL mutation that confers clinical resistance to all currently approved ABL kinase inhibitors. Through global phosphoproteome analysis, we identified a unique phosphosubstrate signature associated with each drug-resistant allele, including a shift in phosphorylation of two tyrosines (Tyr 253 and Tyr 257 ) in the ATP binding loop (P-loop) of BCR-ABL when Thr 315 is Ile or Ala. Mutational analysis of these tyrosines in the context of Thr 315 mutations demonstrates that the identity of the gatekeeper residue impacts oncogenicity by altered P-loop phosphorylation. Therefore, mutations that confer clinical resistance to kinase inhibitors can substantially alter kinase function and confer novel biological properties that may impact disease progression.

Glycoproteins make up a major and important part of the salivary proteome and play a vital role in maintaining the health of the oral cavity. Because changes in the physiological state of a person are reflected as changes in the glycoproteome composition, mapping the salivary glycoproteome will provide insights into various processes in the body. Salivary glycoproteins were identified by the hydrazide coupling and release method. In this approach, glycoproteins were coupled onto a hydrazide resin, the proteins were then digested and formerly N-glycosylated peptides were selectively released with the enzyme PNGase F and analyzed by LC-MS/MS. Employing this method, coupled with in-solution isoelectric focusing separation as an additional means for pre-fractionation, we identified 84 formerly N-glycosylated peptides from 45 unique N-glycoproteins. Of these, 16 glycoproteins have not been reported previously in saliva. In addition, we identified 44 new sites of N-linked glycosylation on the proteins.

Virtual reality based learning of human anatomy is feasible when a database of 3D organ models is available for the learner to explore, visualize, and dissect in virtual space interactively. In this article, we present our latest work on photorealistic virtual anatomy applications based on the Chinese Visible Human (CVH) data. We have focused on the development of state-of-the-art virtual environments that feature interactive photo-realistic visualization and dissection of virtual anatomical models constructed from ultra-high resolution CVH datasets. We also outline our latest progress in applying these highly accurate virtual and functional organ models to generate realistic look and feel to advanced surgical simulators. Clin Anat. 19:232–239, 2006. © 2006 Wiley-Liss, Inc.

In this paper, we present our application of latest information technology in assisting the Chinese acupuncture research. Having integrated the Chinese Visible Human (CVH) data, virtual reality, visualization and imaging techniques, we have constructed a 3-dimensional digital human model for acupuncture. This model integrates the meridian positioning, acupoint positioning, arbitrary cutting-plane visualization, multi-layer dissection, needle puncturing simulation, as well as the common diseases-therapy information. Our work can be widely applied to Chinese acupuncture education, clinical usage and scientific research.

Surgical training systems using virtual reality simulation techniques offer a cost-effective alternative to traditional training methods. In this sense, techniques for interactive visualization and virtual reality surgery have been one of the very important research areas. We describe various techniques we have used in developing a virtual reality system for anatomic visualization and training arthroscopic knee surgeons. Virtual models used in our systems are constructed from the Visible Human Project and Chinese Visible Human data sets. We present our various developments in segmentation, personal-computer-based real-time volume visualization, soft tissue deformation with topological change in real-time using finite element analysis, and soft tissue cutting with tactile feedback.

The bacterial actin homolog, MreB, forms helical cables within the cell that are required for maintenance of a rod shape. These helical structures are thought to be involved in the spatial organization of cell wall (peptidoglycan) synthesizing complexes of penicillin-binding proteins (PBPs). Here, we examined the role of the MreC cell shape protein in this process in Caulobacter crescentus . Subcellular fractionation experiments showed that MreC is a periplasmic protein and, as assayed by immunofluorescence microscopy, adopted helical or banded patterns along the cell length reminiscent of those formed by MreB and PBP2. The pattern of MreC and PBP2 localization remained when MreB cables were disrupted by treatment with the inhibitor A22. However, long-term absence of MreB led to cell shape changes and an eventual loss of MreC localization, suggesting that an independent structure, perhaps an intact peptidoglycan layer, contributes to the MreC localization pattern. Using affinity chromatography with MreC covalently bound to Sepharose, we isolated several PBPs from cell extracts that eluted from the column as heterogeneous complexes. In this same experiment, using mass spectrometry-based protein identification, we identified several outer membrane proteins, including TonB-dependent receptor transport proteins, that interacted with MreC. Imaging live cells containing fusions of these outer membrane proteins to green fluorescent protein showed that they adopted a subcellular localization pattern that was similar to that of MreC. These results suggest that MreC may function in the spatial organization of PBPs as well as other proteins that lie outside the cytoplasmic membrane.

Objective A 3D digitized visible model of human cerebrum was built to provide anatomical structure for making plans of cerebral surgical operation and realizing accurate simulation of cerebrum on computer. Methods Transverse sectional anatomy data of the cerebrum were chosen from the first Chinese visible human (one male and one female). Semi-automated segmentation and Photoshop software were selected to segment cerebral cortex, white matter, basal nuclei, lateral ventricle, hippocampus, etc. On personal computer, the segmented structures were reconstructed in 3D with volume rendering reconstruction and surface rendering reconstruction. Results Two accurately segmented images of the main structures of cerebrum were completed. The reconstructed structures can be displayed singly, in small groups or as a whole and can be continuously rotated in 3D space at different velocities. Conclusion Combining volume-rendering reconstruction with surface rendering reconstruction overcomes the defects of surface rendering reconstruction that lack of internal anatomical information, which provides a new method for 3D reconstruction. The reconstructed cerebrum and the main internal structures are realistic, which demonstrates the natural shape and exact position of the structures. It provides an accurate model for the automated segmentation algorithmic study and provides a digitized anatomical mode of cerebrum.

Human saliva contains a large number of proteins and peptides (salivary proteome) that help maintain homeostasis in the oral cavity. Global analysis of human salivary proteome is important for understanding oral health and disease pathogenesis. In this study, large-scale identification of salivary proteins was demonstrated by using shotgun proteomics and two-dimensinal gel electrophoresis-mass spectrometry (2-DE-MS). For the shotgun approach, whole saliva proteins were prefractionated according to molecular weight. The smallest fraction, presumably containing salivary peptides, was directly separated by capillary liquid chromatography (LC). However, the large protein fractions were digested into peptides for subsequent LC separation. Separated peptides were analyzed by on-line electrospray tandem mass spectrometry (MS/MS) using a quadrupole-time of flight mass spectrometer, and the obtained spectra were automatically processed to search human protein sequence database for protein identification. Additionally, 2-DE was used to map out the proteins in whole saliva. Protein spots 105 in number were excised and in-gel digested; and the resulting peptide fragments were measured by matrix-assisted laser desorption/ionization-mass spectrometry and sequenced by LC-MS/MS for protein identification. In total, we cataloged 309 proteins from human whole saliva by using these two proteomic approaches.

Proteome analysis of secretions from individual salivary glands is important for understanding the health of the oral cavity and pathogenesis of certain diseases. However, cross-contamination of submandibular (SM) and sublingual (SL) glandular secretions can occur. The close anatomic relationship of the SM and SL ductal orifices can lead to such contamination. Additionally, these glands may share common ducts. To insure the purity of SM/SL secretions for proteomic analysis, it is important to develop unique biomarkers which could be used to verify the integrity of the individual glandular saliva. In this study, a proteomics approach based on mass spectrometry and gel electrophoresis techniques was utilized to identify and verify a set of proteins (cystatin C, calgranulin B and MUC5B mucin), which are differentially expressed in SM/SL secretions. SM/SL fluids were obtained from nine healthy subjects. Cystatin C was found to be an SM-selective protein as it was found in all SM fluids but not detected in two SL fluids. MUC5B mucin and calgranulin B, on the other hand, were found to be SL-selective proteins. All SL samples contained MUC5B mucin, whereas MUC5B mucin was not detected in four SM samples. Eight of the SL samples contained calgranulin B; however, calgranulin B was absent in eight SM samples. This set of protein markers, especially calgranulin B, can be used to determine the purity of SM/SL samples, and therefore identify potential individuals who do not exhibit cross-contaminated SM/SL secretions, an important requirement for subsequent proteome analysis of pure SM and SL secretions.

Proteome analysis of secretions from individual salivary glands is important for understanding the health of the oral cavity and pathogenesis of certain diseases. However, cross-contamination of submandibular (SM) and sublingual (SL) glandular secretions can occur. The close anatomic relationship of the SM and SL ductal orifices can lead to such contamination. Additionally, these glands may share common ducts. To insure the purity of SM/SL secretions for proteomic analysis, it is important to develop unique biomarkers which could be used to verify the integrity of the individual glandular saliva. In this study, a proteomics approach based on mass spectrometry and gel electrophoresis techniques was utilized to identify and verify a set of proteins (cystatin C, calgranulin B and MUC5B mucin), which are differentially expressed in SM/SL secretions. SM/SL fluids were obtained from nine healthy subjects. Cystatin C was found to be an SM-selective protein as it was found in all SM fluids but not detected in two SL fluids. MUC5B mucin and calgranulin B, on the other hand, were found to be SL-selective proteins. All SL samples contained MUC5B mucin, whereas MUC5B mucin was not detected in four SM samples. Eight of the SL samples contained calgranulin B; however, calgranulin B was absent in eight SM samples. This set of protein markers, especially calgranulin B, can be used to determine the purity of SM/SL samples, and therefore identify potential individuals who do not exhibit cross-contaminated SM/SL secretions, an important requirement for subsequent proteome analysis of pure SM and SL secretions.

A method is presented for the direct relative quantitation of distinct O-linked mucin-type oligosaccharides. Mucin-type oligosaccharides are found in a host of tissues from anuran to humans. Because they are often associated with extracellular matrix, they play important roles in cell-cell recognition. Changes in glycosylation of O-linked oligosaccharides are associated with diseases such as cancer. In fertilization, they play an active role in sperm-egg recognition. We describe a method for observing changes in glycosylation of mucin-type oligosaccharides by incorporating deuterium in the release procedure. Oligosaccharides from two different sources are released separately by sodium tetrahydroborate and sodium tetradeuterioborate. The oligosaccharides are combined and separated into components by HPLC. By observing the ratio of deuterated and undeuterated species, changes in glycosylation are precisely quantified. This method is illustrated with mucin-type oligosaccharides from the egg jelly coat of the anuran Xenopus laevis.

We report the availability of a digitized Chinese male and a digitzed Chinese female typical of the population and with no obvious abnormalities. The embalming and milling procedures incorporate three technical improvements over earlier digitized cadavers. Vascular perfusion with coloured gelatin was performed to facilitate blood vessel identification. Embalmed cadavers were embedded in gelatin and cryosectioned whole so as to avoid section loss resulting from cutting the body into smaller pieces. Milling performed at -25 degrees C prevented small structures (e.g. teeth, concha nasalis and articular cartilage) from falling off from the milling surface. The male image set (.tiff images each of 36 Mb) has a section resolution of 3072 x 2048 pixels ( approximately 170 micro m, the accompanying magnetic resonance imaging and computer tomography data have a resolution of 512 x 512, i.e. approximately 440 micro m). The Chinese Visible Human male and female datasets are available at http://www.chinesevisiblehuman.com. (The male is 90.65 Gb and female 131.04 Gb). MPEG videos of direct records of real-time volume rendering are at: http://www.cse.cuhk.edu.hk/~crc

A new method for isolating ions for tandem mass spectrometry analyses in Fourier transform mass spectrometry is illustrated. The method employs an infrared laser to dissociate completely the undesired ions. The selected ions are excited to an orbit away from the degradative portion of the laser beam. Ion isolation was accomplished and tandem mass spectrometry experiments were performed on model oligosaccharides and compounds from biological samples.

This article describes the design-for-testability (DFT) methodology for an ARM powered SoC (system-on-a-chip) design which is named by Garfield and used for hand-held computing. Various test methods, including scan insertion, memory BIST (built-in self-test), boundary scan and functional test, and the strategies merging the above methods in SoC design are discussed in detail.

Mass spectrometry (MS) with electrospray ionization (ESI) has the capability to measure and detect noncovalent protein-ligand and protein-protein complexes. However, information on the sites of ligand binding is not easily obtained by the ESI-MS methodology. Electron capture dissociation (ECD) favors cleavage of covalent backbone bonds of protein molecules. We show that this characteristic of ECD translates to noncovalent protein-ligand complexes, as covalent backbone bonds of protein complexes are dissociated, but the noncovalent ligand interaction is retained. For the complex formed from 140-residue, 14.5 kDa alpha-synuclein protein, and one molecule of polycationic spermine (202 Da), ECD generates product ions that retain the protein-spermine noncovalent interaction. Spermine binding is localized to residues 106-138; the ECD data are consistent with previous solution NMR studies. Our studies suggest that ECD mass spectrometry can be used to determine directly the sites of ligand binding to protein targets.

Background Proteomic approaches based on mass spectrometry have been recently used in archaeological and art researches, generating promising results for protein identification. Little information is known about eastward spread and eastern limits of prehistoric milking in eastern Eurasia. Methodology/Principal Finding In this paper, an ancient visible food remain from Subeixi Cemeteries (cal. 500 to 300 years BC) of the Turpan Basin in Xinjiang, China, preliminarily determined containing 0.432 mg/kg cattle casein with ELISA, was analyzed by using an improved method based on liquid chromatography (LC) coupled with MALDI-TOF/TOF-MS to further identify protein origin. The specific sequence of bovine casein and the homology sequence of goat/sheep casein were identified. Conclusions/Significance The existence of milk component in ancient food implies goat/sheep and cattle milking in ancient Subeixi region, the furthest eastern location of prehistoric milking in the Old World up to date. It is envisioned that this work provides a new approach for ancient residue analysis and other archaeometry field.