Ordinary Personal Computer Research Articles

Efficient Sum-Rate Maximization for Medium-Scale MIMO AF-Relay Networks

We consider the problem of sum-rate maximization in multiple-input multiple-output (MIMO) amplify-and-forward relay networks with multi-operator. The aim is to design the MIMO relay amplification matrix (i.e., the relay beamformer) to maximize the achievable communication sum rate through the relay. The design problem for the case of single-antenna users can be cast as a non-convex optimization problem, which, in general, belongs to a class of NP-hard problems. We devise a method based on the minorization–maximization technique to obtain quality solutions to the problem. Each iteration of the proposed method consists of solving a strictly convex unconstrained quadratic program. This task can be done quite efficiently, such that the suggested algorithm can handle the beamformer design for relays with up to $\sim 70$ antennas within a few minutes on an ordinary personal computer. Such a performance lays the ground for the proposed method to be employed in medium-scale (or lower regime massive) MIMO scenarios.

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing.

Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis.

실시간 대화형 화산재 확산 예측 시스템에 의한 화산재 확산 예측

Analyzing the observational data of volcanic activities around the northern part of Korean peninsula, the odds of volcano eruption increases continuously. For example, the cumulative seismic moment and frequence observed near Mt. Baekdu show a sudden increased values. In this study, predicting the diffusion of volcanic ash for two cases were carried out by using interactive realtime simulator, which was developed during last 2 years as a research and development project. The first case is Sakurajima volcano (VEI=3) erupted in August 2013. The second case is assumed as the volcanic eruption at Mt. Baekdu (VEI=7) under landing circumstance of typhoon Maemi (August 2003) in Korean peninsula. The synoptic condition and ash diffusion for the two cases were simulated by WRF(Weather Research and Forecast) model and Lagrangian dispersion model, respectively. Comparing the simulated result of the first case (i.e., Sakurajima volcano) with satellite image, the diffusion pattern show acceptable result. The interactive realtime simulator can be available to support decision making under volcanic disaster around East Asia by predicting several days of ash dispersion within several minutes with ordinary desktop personal computer.

Engineering modelling of structural details of a bridge

This paper presents a method of engineering modelling of structural details, which enables the analysis of local static and dynamic effects in a complex structure with the use of a personal computer. An analysed structural detail, modelled with the use of shell finite elements, is mounted to a spatial truss member system. Then, on the basis of prepared computational model, a static or dynamic analysis is carried out. The proposed model allows to detect the local effects in a theoretical. Conducted analyses confirmed the correct operation of such a computational model. Hence, the method of modelling presented in this paper allows to analyse the local effects on ordinary personal computer and more importantly, the results of such calculations are available within a relatively short period of time. The calculations are carried out by analysing the local effects in a steel node of the truss railway bridge.

Two-Photon Processor and SeNeCA: a freely available software package to process data from two-photon calcium imaging at speeds down to several milliseconds per frame

Two-Photon Processor (TPP) is a versatile, ready-to-use, and freely available software package in MATLAB to process data from in vivo two-photon calcium imaging. TPP includes routines to search for cell bodies in full-frame (Search for Neural Cells Accelerated; SeNeCA) and line-scan acquisition, routines for calcium signal calculations, filtering, spike-mining, and routines to construct parametric fields. Searching for somata in artificial in vivo data, our algorithm achieved better performance than human annotators. SeNeCA copes well with uneven background brightness and in-plane motion artifacts, the major problems in simple segmentation methods. In the fast mode, artificial in vivo images with a resolution of 256 × 256 pixels containing ≈ 100 neurons can be processed at a rate up to 175 frames per second (tested on Intel i7, 8 threads, magnetic hard disk drive). This speed of a segmentation algorithm could bring new possibilities into the field of in vivo optophysiology. With such a short latency (down to 5-6 ms on an ordinary personal computer) and using some contemporary optogenetic tools, it will allow experiments in which a control program can continuously evaluate the occurrence of a particular spatial pattern of activity (a possible correlate of memory or cognition) and subsequently inhibit/stimulate the entire area of the circuit or inhibit/stimulate a different part of the neuronal system. TPP will be freely available on our public web site. Similar all-in-one and freely available software has not yet been published.

Parallelization of a hydrological model using the message passing interface

With the increasing knowledge about the natural processes, hydrological models such as the Soil and Water Assessment Tool (SWAT) are becoming larger and more complex with increasing computation time. Additionally, other procedures such as model calibration, which may require thousands of model iterations, can increase running time and thus further reduce rapid modeling and analysis. Using the widely-applied SWAT as an example, this study demonstrates how to parallelize a serial hydrological model in a Windows® environment using a parallel programing technology—Message Passing Interface (MPI). With a case study, we derived the optimal values for the two parameters (the number of processes and the corresponding percentage of work to be distributed to the master process) of the parallel SWAT (P-SWAT) on an ordinary personal computer and a work station. Our study indicates that model execution time can be reduced by 42%–70% (or a speedup of 1.74–3.36) using multiple processes (two to five) with a proper task-distribution scheme (between the master and slave processes). Although the computation time cost becomes lower with an increasing number of processes (from two to five), this enhancement becomes less due to the accompanied increase in demand for message passing procedures between the master and all slave processes. Our case study demonstrates that the P-SWAT with a five-process run may reach the maximum speedup, and the performance can be quite stable (fairly independent of a project size). Overall, the P-SWAT can help reduce the computation time substantially for an individual model run, manual and automatic calibration procedures, and optimization of best management practices. In particular, the parallelization method we used and the scheme for deriving the optimal parameters in this study can be valuable and easily applied to other hydrological or environmental models.

Three-dimensional reconstruction of paracentesis approach in transjugular intrahepatic portosystemic shunt

To establish a digital transjugular intrahepatic portosystemic shunt (TIPS) model and provide morphological data for radiological diagnosis and interventional radiology to reduce portal vein pressure, 400 serial sectional images from the internal jugular vein superior margin to the lower edge of the liver were chosen from the Chinese Visible Human dataset. Surface and volume reconstructions were performed using 3D-DOCTOR 3.5 software on an ordinary personal computer. Volume and surface renderings were employed to perform data segmentation and image edge detection for reconstruction of the internal jugular vein, brachiocephalic vein, superior vena cava, heart, inferior vena cava, hepatic vein, and portal vein for computerized 3D reconstruction of the TIPS pathway and construction of a 3D visible model of different structures along it. The model can also display pathway and distribution characteristics and interactively show the spatial structural relationships between intrahepatic venous lines from any position and angle, plus complete data acquisition for any range and angle for 3D reconstruction with stereopsis and measurements using any visualization platform. The digital reconstruction of the TIPS pathway correctly reflected the complicated anatomic structural characteristics and spatial adjacency relationships between intrahepatic venous lines, providing a reference 3D morphology for image diagnostics and interventional TIPS therapy.

Recognition of prokaryotic promoters based on a novel variable-window Z-curve method

Transcription is the first step in gene expression, and it is the step at which most of the regulation of expression occurs. Although sequenced prokaryotic genomes provide a wealth of information, transcriptional regulatory networks are still poorly understood using the available genomic information, largely because accurate prediction of promoters is difficult. To improve promoter recognition performance, a novel variable-window Z-curve method is developed to extract general features of prokaryotic promoters. The features are used for further classification by the partial least squares technique. To verify the prediction performance, the proposed method is applied to predict promoter fragments of two representative prokaryotic model organisms (Escherichia coli and Bacillus subtilis). Depending on the feature extraction and selection power of the proposed method, the promoter prediction accuracies are improved markedly over most existing approaches: for E. coli, the accuracies are 96.05% (σ70 promoters, coding negative samples), 90.44% (σ70 promoters, non-coding negative samples), 92.13% (known sigma-factor promoters, coding negative samples), 92.50% (known sigma-factor promoters, non-coding negative samples), respectively; for B. subtilis, the accuracies are 95.83% (known sigma-factor promoters, coding negative samples) and 99.09% (known sigma-factor promoters, non-coding negative samples). Additionally, being a linear technique, the computational simplicity of the proposed method makes it easy to run in a matter of minutes on ordinary personal computers or even laptops. More importantly, there is no need to optimize parameters, so it is very practical for predicting other species promoters without any prior knowledge or prior information of the statistical properties of the samples.

Software for generating gravity gradients using a geopotential model based on an irregular semivectorization algorithm

The spherical harmonic synthesis of second-order derivatives of geopotential is a task of major concern when the spatial resolution of synthesis is high and/or a high-resolution Earth's gravity model is used. Here, a computational technique is presented for such a process. The irregular semivectorization is introduced as a vectorization technique in which one loop is excluded from matrix-vector products of mathematical models in order to speed up the computation and manage the computer memory. The proposed technique has the capability of considering heights of computation points on a regular grid. MATLAB-based software is developed, which can be used for generating gravity gradients on an ordinary personal computer. The numerical results show that irregular semivectorization significantly reduces the computation time to 1 h for synthesis of these data with global coverage and resolution of 5′×5′ on an elevation model. In addition, a numerical example is presented for testing satellite gravity gradiometry data of the recent European Space Agency satellite mission, the gravity field and steady-state ocean circulation explorer (GOCE), using an Earth's gravity model.

Combining confocal laser scanning microscopy with serial section reconstruction in the study of adult neurogenesis.

Current advances in imaging techniques have extended the possibility of visualizing small structures within large volumes of both fixed and live specimens without sectioning. These techniques have contributed valuable information to study neuronal plasticity in the adult brain. However, technical limits still hamper the use of these approaches to investigate neurogenic regions located far from the ventricular surface such as parenchymal neurogenic niches, or the scattered neuroblasts induced by brain lesions. Here, we present a method to combine confocal laser scanning microscopy (CLSM) and serial section reconstruction in order to reconstruct large volumes of brain tissue at cellular resolution. In this method a series of thick sections are imaged with CLSM and the resulting stacks of images are registered and 3D reconstructed. This approach is based on existing freeware software and can be performed on ordinary laboratory personal computers. By using this technique we have investigated the morphology and spatial organization of a group of doublecortin (DCX)+ neuroblasts located in the lateral striatum of the late post-natal guinea pig. The 3D study unraveled a complex network of long and poorly ramified cell processes, often fascicled and mostly oriented along the internal capsule fiber bundles. These data support CLSM serial section reconstruction as a reliable alternative to the whole mount approaches to analyze cyto-architectural features of adult germinative niches.

Abstract P4-10-11: Nobel Approach for Breast Conserving Surgery after Primary Systemic Therapy: Real-Time Virtual Navigation

Abstract Background: Breast-conserving surgery after primary systemic therapy (PST) has become a widely acceptable procedure for locally advanced breast cancers. Sometimes it is difficult to determine the appropriate resection-line at the time of surgical operation because of tumor size reduction or indistinct boundary of the tumor. Moreover we cannot detect tumors in cases with complete response. That was why we developed a new navigation technique using real-time image reconstruction. Materials and methods: Multi-detector row computed tomography (MD-CT) has been performed for all breast cancer patients in our institute. DICOM images of MD-CT were analyzed by image processing software ‘OsiriX'. OsiriX is an open source software which anyone can download from website (http://www. osirix-viewer.com). OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images. We used 3D volume rendering images. At the time of surgery, pre-PST volume rendering images ware superimposed directly on the patients’ skin from projector which was connected to a personal computer in the operating room. Results: We could see ‘real-time’ rendering images (from skin to organ by layer to layer) on the patient's body. By using pre-PST imaging data, we could recognize precise tumor area and could perform breast conserving surgery safer and easier than before. Conclusion: Using 3D reconstruction MD-CT images which were obtained before PST, ‘real-time’ virtual navigation was helpful to determine the resection-line for clear surgical margin in breast-conserving surgery after PST. This new technique does not need some expensive equipments and easily performed by surgeon. Ordinary personal computer and projector make it possible to demonstrate a new environment in surgical operation. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-10-11.

Spatially two-dimensional mathematical model of the flow hydrodynamics in a channel filled with a net-like spacer

A spatially two-dimensional (2D) mathematical model of the flow hydrodynamics in a flat channel filled with a net-like spacer, for example, typical of the electrodialysis process, was developed and implemented. Subsequently the model was experimentally validated. The model introduced represents a novel CFD (computational fluid dynamic) approach, based on a reduction of the model dimensions from 3D to 2D. This allowed the modeling of systems of industrially relevant geometries on an ordinary personal computer. The simplification is possible because of the structure of the net-like spacer used which consists of two layers of filaments. In the individual layers the filaments are oriented identically. Due to this arrangement the model domain can be separated into two hydraulically interconnected sub-layers, which can be mathematically treated as 2D. The model presented is semiempirical. It includes two empirical coefficients representing hydraulic resistances. They reflect the resistance of spacer filaments to the flow in the normal and tangential direction. The stationary flow of incompressible liquid in the laminar flow regime was calculated. The model equations are based on Navier–Stokes and continuity equations. The pressure loss is described by anisotropic Darcy's law.

Three-dimensional reconstruction of the superior mediastinum from Chinese Visible Human Female

This research aimed to construct three-dimensional (3D) visible models of the superior mediastinum for anatomic study and surgical approaches to the superior mediastinum. Sectional images of the superior mediastinum were acquired through the Chinese Visible Human Female (VCHF) database. One hundred eighty images of the superior mediastinum were imported into Photoshop CS and the images were converted into a JPEG format. Surface and volume reconstruction were performed by 3D Doctor 3.5 and Amira 4.0 software programs on an ordinary personal computer, respectively. The surface and volume reconstruction of the superior mediastinum were successful. The surface reconstruction model allowed rotation and magnification of the superior mediastinum structures as well as displayed the contours of reconstructed structures individually or as a composite with any other selected structure. Volume reconstruction displayed abundant internal detail of reconstructed images in transverse, coronal, sagittal, and random oblique sections. Three-dimensional, visible models of the superior mediastinum based on the sectional images of VCHF can provide unique insight into the anatomy of superior mediastinum. These models provide an excellent adjunct to the anatomy curriculum in medical schools and an invaluable tool for the practicing surgeon planning an operation in this complex anatomic region.

Plant Simulation System for Developing ABWR Automatic Power Regulator System

We developed a plant simulation code system to design and verify an automatic power regulator (APR) system for an advanced boiling water reactor (ABWR). The point kinetic plant simulator AUTSIMU is an off-line and real-time online plant simulation code that can simulate the start-up process from a subcritical condition of cold water to a 100% rated power condition as well as the reactor shutdown process. The three-dimensional effect of neutron detector signals in the core was simulated by combining predetermined three-dimensional analysis and point kinetic analysis results. The AUTSIMU code was tested using ABWR start-up experimental data. The calculated results were in good agreement with the measured ones. Less than one minute was needed in the off-line mode to simulate a ten-hour transient with an ordinary personal computer. We confirmed that simple AUTSIMU models could effectively simulate ABWR start-up behaviors. The APR hardware was effectively verified in the online mode through factory tests before being shipped to the nuclear site.

Web-Based Virtual Microscopy for Parasitology: A Novel Tool for Education and Quality Assurance

BackgroundThe basis for correctly assessing the burden of parasitic infections and the effects of interventions relies on a somewhat shaky foundation as long as we do not know how reliable the reported laboratory findings are. Thus virtual microscopy, successfully introduced as a histopathology tool, has been adapted for medical parasitology.Methodology/Principal FindingsSpecimens containing parasites in tissues, stools, and blood have been digitized and made accessible as a “webmicroscope for parasitology” (WMP) on the Internet (http://www.webmicroscope.net/parasitology).These digitized specimens can be viewed (“navigated” both in the x-axis and the y-axis) at the desired magnification by an unrestricted number of individuals simultaneously. For virtual microscopy of specimens containing stool parasites, it was necessary to develop the technique further in order to enable navigation in the z plane (i.e., “focusing”). Specimens were therefore scanned and photographed in two or more focal planes. The resulting digitized specimens consist of stacks of laterally “stiched” individual images covering the entire area of the sample photographed at high magnification. The digitized image information (∼10 GB uncompressed data per specimen) is accessible at data transfer speeds from 2 to 10 Mb/s via a network of five image servers located in different parts of Europe. Image streaming and rapid data transfer to an ordinary personal computer makes web-based virtual microscopy similar to conventional microscopy.Conclusion/SignificanceThe potential of this novel technique in the field of medical parasitology to share identical parasitological specimens means that we can provide a “gold standard”, which can overcome several problems encountered in quality control of diagnostic parasitology. Thus, the WMP may have an impact on the reliability of data, which constitute the basis for our understanding of the vast problem of neglected tropical diseases. The WMP can be used also in the absence of a fast Internet communication. An ordinary PC, or even a laptop, may function as a local image server, e.g., in health centers in tropical endemic areas.

Color image based sorter for separating red and white wheat

A simple imaging system was developed to inspect and sort wheat samples and other grains at mod- erate feed-rates (30 kernels/s or 3.5 kg wheat/h). A single camera captured color images of three sides of each kernel by using mirrors, and the images were processed using a personal computer (PC). Real time image acquisition and processing was enabled on an ordinary PC under Windows XP operating system using the IEEE 1394 data transfer protocol, DirectX application software, and dual-core computer processor. Image acquisition and transfer to the PC required approximately 17 ms per kernel, and an additional 1.5 ms was required for image processing. After classification, the computer could output a signal from the parallel port to activate an air valve to divert (sort) kernels into a secondary container. Hard red and hard white wheat kernels were used in this study to test and demonstrate sorter capability. Simple image statistics and histograms were used as features. Discriminant analysis was per- formed with one, two, or three features to demonstrate classification improvements with increased numbers of features. The sorter was able to separate hard red kernels from hard white kernels with 95 to 99% accuracy, depending on the wheat varieties, feed-rate, and number of classification features. The system is an economical and useful instrument for sorting wheat and other grains with high accuracy.

Fast blood flow visualization of high-resolution laser speckle imaging data using graphics processing unit

Laser speckle contrast analysis (LASCA) is a non-invasive, full-field optical technique that produces two-dimensional map of blood flow in biological tissue by analyzing speckle images captured by CCD camera. Due to the heavy computation required for speckle contrast analysis, video frame rate visualization of blood flow which is essentially important for medical usage is hardly achieved for the high-resolution image data by using the CPU (Central Processing Unit) of an ordinary PC (Personal Computer). In this paper, we introduced GPU (Graphics Processing Unit) into our data processing framework of laser speckle contrast imaging to achieve fast and high-resolution blood flow visualization on PCs by exploiting the high floating-point processing power of commodity graphics hardware. By using GPU, a 12-60 fold performance enhancement is obtained in comparison to the optimized CPU implementations.

Cone Beam Computed Tomography: An Innovative Tool for Airway Assessment

Improvements in airway imaging technology provide the potential for an improved understanding of airway pathology and upper airway mechanics. We present here a preliminary report on the applicability of cone beam computed tomography technology in conjunction with multidimensional digital analysis for the purposes of clinical airway management. The use of this technology for airway imaging in anesthesiology has not been reported. Traditional skeletal and soft tissue images as well as distance and volume measurements were obtained without difficulty. Three-dimensional image reconstructions as well as "virtual laryngoscopy" were achieved with resulting excellent image quality, suggesting a broad range of possibilities for upper airway examination and analysis. A modified Muller test with volumetric rendering of the airway passages under baseline and negative pressure conditions was also performed, made possible as a result of the system's short (9 s) scanning times. We believe that cone beam computed tomography technology offers an additional dimension to airway evaluation that has considerable potential.

Fully optimized discrimination of physiological responses to auditory stimuli

The use of multivariate measurements to characterize brain activity (electrical, magnetic, optical) is widespread. The most common approaches to reduce the complexity of such observations include principal and independent component analyses (PCA and ICA), which are not well suited for discrimination tasks. We addressed two questions: first, how do the neurophysiological responses to elongated phonemes relate to tone and phoneme responses in normal children, and, second, how discriminable are these responses. We employed fully optimized linear discrimination analysis to maximally separate the multi-electrode responses to tones and phonemes, and classified the response to elongated phonemes. We find that discrimination between tones and phonemes is dependent upon responses from associative regions of the brain apparently distinct from the primary sensory cortices typically emphasized by PCA or ICA, and that the neuronal correlates corresponding to elongated phonemes are highly variable in normal children (about half respond with neural correlates of tones and half as phonemes). Our approach is made feasible by the increase in computational power of ordinary personal computers and has significant advantages for a wide range of neuronal imaging modalities.

Three-dimensional simulation of diffraction and absorption losses in all-fiber multilayer filters

A rigorous modal three-dimensional calculation method is used to analyze the diffraction and absorption losses in Fabry-Perot (FP) multilayer interferential filters between both single-mode input and output fibers. With an ordinary personal computer, this method affords accurate calculation of the absorption losses and the diffraction into the cladding modes of both fibers as well as the reflectance into the input fiber. The calculation results show that absorption losses and diffraction are troublesome for high-finesse FP filters.