Clustering gene expression data using graph separators

Recent work has used graphs to modelize expression data from microarray experiments, in view of partitioning the genes into clusters. In this paper, we introduce the use of a decomposition by clique separators. Our aim is to improve the classical clustering methods in two ways: first we want to allow an overlap between clusters, as this seems biologically sound, and second we want to be guided by the structure of the graph to define the number of clusters. We test this approach with a well-known yeast database (Saccharomyces cerevisiae). Our results are good, as the expression profiles of the clusters we find are very coherent. Moreover, we are able to organize into another graph the clusters we find, and order them in a fashion which turns out to respect the chronological order defined by the the sporulation process.

Hub-based simulation and graphics hardware accelerated visualization for nanotechnology applications

The Network for Computational Nanotechnology (NCN) has developed a science gateway at nanoHUB.org for nanotechnology education and research. Remote users can browse through online seminars and courses, and launch sophisticated nanotechnology simulation tools, all within their web browser. Simulations are supported by a middleware that can route complex jobs to grid supercomputing resources. But what is truly unique about the middleware is the way that it uses hardware accelerated graphics to support both problem setup and result visualization. This paper describes the design and integration of a remote visualization framework into the nanoHUB for interactive visual analytics of nanotechnology simulations. Our services flexibly handle a variety of nanoscience simulations, render them utilizing graphics hardware acceleration in a scalable manner, and deliver them seamlessly through the middleware to the user. Rendering is done only on-demand, as needed, so each graphics hardware unit can simultaneously support many user sessions. Additionally, a novel node distribution scheme further improves our system's scalability. Our approach is not only efficient but also cost-effective. Only a half-dozen render nodes are anticipated to support hundreds of active tool sessions on the nanoHUB. Moreover, this architecture and visual analytics environment provides capabilities that can serve many areas of scientific simulation and analysis beyond nanotechnology with its ability to interactively analyze and visualize multivariate scalar and vector fields.

Motion compensation in digital subtraction angiography using graphics hardware

An inherent disadvantage of digital subtraction angiography (DSA) is its sensitivity to patient motion which causes artifacts in the subtraction images. These artifacts could often reduce the diagnostic value of this technique. Automated, fast and accurate motion compensation is therefore required. To cope with this requirement, we first examine a method explicitly designed to detect local motions in DSA. Then, we implement a motion compensation algorithm by means of block matching on modern graphics hardware. Both methods search for maximal local similarity by evaluating a histogram-based measure. In this context, we are the first who have mapped an optimizing search strategy on graphics hardware while paralleling block matching. Moreover, we provide an innovative method for creating histograms on graphics hardware with vertex texturing and frame buffer blending. It turns out that both methods can effectively correct the artifacts in most case, as the hardware implementation of block matching performs much faster: the displacements of two 1024 x 1024 images can be calculated at 3 frames/s with integer precision or 2 frames/s with sub-pixel precision. Preliminary clinical evaluation indicates that the computation with integer precision could already be sufficient.

Fast and reliable collision culling using graphics hardware

We present a reliable culling algorithm that enables fast and accurate collision detection between triangulated models in a complex environment. Our algorithm performs fast visibility queries on the GPUs for eliminating a subset of primitives that are not in close proximity. In order to overcome the accuracy problems caused by the limited viewport resolution, we compute the Minkowski sum of each primitive with a sphere and perform reliable 2.5D overlap tests between the primitives. We are able to achieve more effective collision culling as compared to prior object-space culling algorithms. We integrate our culling algorithm with CULLIDE [1] and use it to perform reliable GPU-based collision queries at interactive rates on all types of models, including nonmanifold geometry, deformable models, and breaking objects.

Blood pressure and arterial stiffness: A comparison of two devices for measuring augmentation index and pulse wave velocity

Augmentationindex (AIx) and Pulse Wave Velocity (PWV) give much more information on the function of the arterial tree than that obtained by blood pressure recordings. The rediscovered value of arterial stiffness measured by means of AIx or PWV is now proven as an independent cardiovascular risk factor and helps to differentiate patients at risk and their cardiovascular treatment offer. In the last decade, the methods to measure and to calculate AIx and PWV have become increasingly simple. But as the different methods use different strategies for measuring and calculating these parameters, the results concerning the same term vary, depending on the device used. We undertook nearly simultaneous recordings of AIx in 400 and of PWV in 100 treated hypertensive patients with the very new TensioClinic device developed by M. Illyés, and compared those data with measurements obtained by the SphygmoCor device. The absolute values of m (mean) and SD (standard deviation) of AIx were when TensioClinic was used m: -6.2 % +/- SD:37.9 % and by SphygmoCor m: 26,2 % +/- SD: 11,8 %. The differences were caused by the different methods. As both devices measure the same quality of vascular function, the results correlate closely with a correlation coefficient r = 0.77. In PWV the results of Aortic PWV measured by TensioClinic were m: 9.1 +/- SD: 1.8m/sec and of brachial PWV measured by SphygmoCor: 8.4 +/- SD: 1.5 m/sec. As in AIx, these results were also different, but in contrast to AIx they did not correlate (r = -0.04) because PWV depend on the artery and its physical characteristics, and we

The use of virtual environments for percentage view analysis

It is recognised that Visual Impact Assessment (VIA), unlike many other aspects of Environmental Impact Assessments (EIA), relies less upon measurement than upon experience and judgement. Hence, it is necessary for a more structured and consistent approach towards VIA, reducing the amount of bias and subjectivity. For proposed developments, there are very few quantitative techniques for the evaluation of visibility, and these existing methods can be highly inaccurate and time consuming. Percentage view changes are one of the few quantitative techniques, and the use of computer technology can reduce the inaccuracy and the time spent evaluating the visibility of either existing or proposed developments. For over 10 years, research work undertaken by the authors at the University of Nottingham has employed Computer Graphics (CG) and Virtual Reality (VR) in civilian and industrial contexts for environmental planning, design visualisation, accident reconstruction, risk analysis, data visualisation and training simulators. This paper describes a method to quantitatively assess the visual impact of proposed developments on the landscape using CG techniques. This method allows the determination of accurate percentage view changes with the use of a computer-generated model of the environment and the application of specialist software that has been developed at the University of Nottingham. The principles are easy to understand and therefore planners, authorisation agencies and members of the public can use and understand the results. A case study is shown to demonstrate the application and the capabilities of the technology.

Effect of dynamic display and speed of display movement on reading Chinese text presented on a small screen

Automatic dynamic displays, e.g., scrolling displays, are frequently used to present text information on small screens. This study examined the effects of three dynamic displays [leading, scrolling, and rapid serial visual presentation (RSVP)] and three presentations speeds [171, 250, and 305 wpm (words per minute)] on subjects' reading comprehension for different types of small screens for laptops, personal digital assistants (PDAs), and mobile phones. 12 college students who were native speakers of Chinese (4 men and 8 women between the ages of 19 and 36 years) participated. Scores for reading comprehension indicated (1) for laptops, both leading displays and RSVP, at speeds of about 250 wpm, comprehension was highest; (2) for PDAs and mobile phones, scrolling displays and RSVP, speeds of about 305 wpm were more suitable for presenting information in Chinese text; (3) consequently, RSVP appeared to be the most viable dynamic display on small screens and led to the highest reading comprehension for these Chinese readers.

Monitoring of symptoms and interventions associated with multiple sclerosis

We have utilized the Structured Data Entry approach to build a prototype interface for the recording of personalized symptoms associated with Multiple Sclerosis (MS). The software provides both graphical input and output, to facilitate efficient data entry and monitoring. Graphical input is transformed to textual information, which is stored in a database in a hierarchical tree structure. Pain management in MS may be achieved by careful monitoring of the symptom in response to treatment. Pain location is selected on a body image and severity and other attributes represented using a graphical visual analog scale, leading to more convenient input and a less ambiguous coding than is achievable with narrative text alone. The Internet can be used to record and provide access to clinical data, assisting the citizen by providing a healthcare professional partnership approach to care. This approach could provide an objective means of monitoring symptoms and hence provide a more personalized approach to MS management.

Specificity of computerized physician order entry has a significant effect on the efficiency of workflow for critically ill patients

BACKGROUND

Critically ill patients require rapid care, yet they are also at risk for morbidity from the potential complications of that care. Computerized physician order entry (CPOE) is advocated as a tool to reduce medical errors, improve the efficiency of healthcare delivery, and improve outcomes. Little is known regarding the essential attributes of CPOE in the intensive care unit (ICU).

OBJECTIVE

To assess the effect of CPOE on ICU patient care.

DESIGN

Retrospective before and after cohort study.

SETTING

An academic ICU.

PATIENTS

Patients admitted to the ICU during use of the initial CPOE application and those admitted after its modification.

INTERVENTIONS

Comprehensive order interface redesign improving clarity, specificity, and efficiency.

MEASUREMENTS

Orders for complex ICU care were compared between the two groups. In addition, the use of higher-efficiency CPOE order paths was tracked.

RESULTS

Patients treated with both the initial and modified CPOE system were similar for all measured characteristics. With the modified CPOE system, there were significant reductions in orders for vasoactive infusions, sedative infusions, and ventilator management. There was also a significant increase in orders executed through ICU-specific order sets after system modifications.

LIMITATIONS

This retrospective study cannot assess issues related to learner expertise and is meant to only suggest the importance of developing CPOE systems that are appropriate for specialty care environments.

CONCLUSION

Appropriate CPOE applications can improve the efficiency of care for critically ill patients. The workflow requirements of individual units must be analyzed before technologies like CPOE can be properly developed and implemented.

Quantitative evaluation of axial wall taper in prepared artificial teeth

The purpose of this study was to quantitatively evaluate the axial wall taper of prepared artificial teeth using a non-contact three-dimensional shape measuring system. A total of 54 artificial teeth prepared by pre-clinical dental students for complete cast restorations were evaluated. For quantitative analysis, five cross sections were computer-graphically placed perpendicularly to the z-axis. The surface coordinate values (x, y, z) of each cross section were converted into polar coordinate values (r, theta), which were then graphically rendered to a two-dimensional plane. At four points, each 90 degrees from the distal center point of the cross section, the axial wall taper was quantitatively calculated using a formula based on the differences in radius between the highest and lowest positions of the cross sections of the prepared tooth. The average calculated taper was 5.8 degrees in the distal region, 21.7 degrees in the buccal region, 14.9 degrees in the mesial region and 12.5 degrees in the lingual region. These results suggest that the axial wall taper of prepared teeth can be quantitatively evaluated using this measuring system.

Inadequacy of Standard Screen Resolution for Localization of Seizures Recorded from Intracranial Electrodes

Seizures recorded during long-term monitoring with implanted intracranial electrodes are typically interpreted by visual inspection alone by using digital display systems. When high-frequency activity is digitized and displayed on a typical monitor, it is altered in ways that are not always appreciated and that may have an impact on the intracranial EEG (ICEEG) interpretation. We describe a case of a neocortical-onset seizure in which false localization occurred with a 12-s per screen display. Because frequencies in excess of 100 Hz are not uncommon in neocortical seizures, at most 4 to 5 s of EEG, depending on the screen resolution, data-sampling rate, and other factors, should be displayed at one time during visual interpretation to localize the seizure onset. Alternatively, spectral analysis should be performed on recordings of neocortical seizures to detect high-frequency activity that may be missed on visual inspection.

A vision research apparatus for broad luminance range displays

Lightness, the perceived gray shade of a surface, and the perception of self-luminous surfaces--that is, surfaces that appear to glow--have most often been studied with paper displays and computer-generated stimuli presented on CRT monitors. Although both methods are often effective, experiments that require a wide range of luminance values in the same display are often difficult to conduct with paper and computer displays alone. Also, color mode appearance is often an issue when surface color perception is the topic of research; CRT monitors are essentially light sources themselves and often appear in the luminous mode of color appearance. Here, we describe an apparatus in which the target is an undetected aperture whose luminance is adjustable. Whereas a typical CRT monitor offers a luminance range of about 100:1, much broader luminance ranges are possible with the described apparatus. Unlike a CRT monitor, the stimulus background will always appear in the surface mode of color perception, and the target(s) can appear as either surface colors or luminous colors. Apparatus modifications are possible, including the addition of a stereoscope or an embedded CRT for creating an adjustable region that is computer controlled.

Antastgenauigkeit von Orientierungspunkten bei navigierter Implantation von Knieendoprothesen

AIMS

Cinematic and pointing procedures are used for non-image based navigated implantation during total knee replacement. Pointing procedures require an exact knowledge of the landmarks. In this anatomical study, landmarks are defined and repeatedly referenced. Precision and reproducibility are evaluated by means of an inter- and an intra-observer study. The axes of the femur and tibia are calculated using the landmarks.

MATERIAL AND METHODS

The specific landmarks of 30 femurs and 27 tibias were palpated by three surgeons and digitised by means of a photogrammetric system, as used intra-operatively. The recorded data were statistically evaluated.

RESULTS

The specific landmarks can be referenced with great precision. The vectors that influence the implant position show a mean femoral deviation of 0.9 mm and a mean tibial deviation of 1.0 mm. The repeating accuracy of every observer was 1.5 mm femoral and 1.0 mm tibial. The calculated long axes at the femur and tibia thus reach a precision of 0.1 degrees (min.-max.: 0-0.9 degrees) at the femur and 0.2 degrees (.0-1.1 degrees) at the tibia. The short axes at the distal femur and proximal tibia exhibit an average deviation of from 0.7 degrees to 1.9 degrees (0-11.3 degrees).

CONCLUSION

Long axes (mechanical axes) can be determined exactly but the precision of the short axes (rotational axes) is unsatisfactory, although palpation of landmarks was accurate. Therefore, palpation of more than one rotational axis at the femur and tibia is mandatory and should be visualized on the monitor during surgery.

The pedigree tool: Web‐based visualization of a family tree

We describe the development of a novel tool that facilitates the design and visualization of pedigrees using a special Internet application. The tool is programmed in Java, using a PHP script as an interface. This web-based tool is used to generate, edit, and/or view pedigrees. The advantage of our novel tool is that it is based on a notation that allows the representation of any given number of generations, family members per generation, and multiple clinical or genetic features of an individual family member. In addition, the notation allows us to minimize the storage space by 100% to 500% and to standardize the presentation of family trees and segregation analysis for inheritance of mendelian disorders or even complex traits. This pedigree tool has been implemented with a database of thyroid-stimulating hormone receptor (TSHR) mutations (http://www.uni-leipzig.de/innere/tshr/).

Genauigkeit eines bildfreien Navigationssystemes für die Hüftpfannenimplantation – eine anatomische Studie / Accuracy of an Image-free Cup Navigation System – an Anatomical Study

The position of the acetabular cup is of decisive importance for the function of a total hip replacement (THR). Using the conventional surgical technique, correct placement of the cup often fails due to a lack of information about pelvic tilt. With CT-based and fluoroscopically-assisted navigation procedures the accuracy of implantation has been significantly improved. However, additional radiation exposure, high cost and the increased time requirement have hampered the acceptance of these techniques. The present anatomical study evaluates the accuracy of an alternative procedure--image-free navigation. This method requires little extra effort, does not substantially delay surgery, and needs no additional imaging. Press-fit cups were implanted in 10 human cadaveric hips with the help of the image-free navigation system, and the position of the cups was checked intraoperatively with a CT-based navigation system and postoperatively by computed tomography. All cups were implanted within the targeted safe zone with an average inclination of 44 degrees (range 40 degrees-48 degrees, SABW 2.7 degrees) and an average anteversion of 18 degrees (range 12-24 degrees, SABW 4.1 degrees). Analysis of accuracy of the image-free navigation software revealed only a small, clinically tolerable deviation in cup anteversion and cup inclination in comparison with the CT-based navigation system and the post operative CT scans. The evaluated image-free navigation system appears to be a practicable and reliable alternative to the computer-assisted implantation of acetabular cups in total hip arthroplasty.

Engineering the next generation of large-area displays: prospects and pitfalls

Considerable effort is currently expounded on the development and improvement of the myriad display technologies that have come to the market place. In this paper, several key questions are addressed in the development of the future generation of large-area field-emission-based displays based on semiconducting amorphous carbon thin films and carbon nanotubes (CNTs). The development of carbon-based cathodes has to date proceeded along empirical lines, with attempts to correlate the variation of field-emission characteristics with changes in deposition or post-deposition processing parameters, often without a full explanation being forthcoming. In addition, there have been incidents of incorrect interpretation of some of the results, due to a lack of appreciation of the significant differences between the different types of amorphous carbon film that exist. It is only recently that a fuller understanding of the different electron-emission mechanisms has begun to emerge through an understanding of the roles played by the electrical and structural inhomogeneity at nanometre level. This 'intrinsic dielectric inhomogeneity' is shown to possess some remarkable electronic properties, which also have important consequences for extrinsic inhomogeneous nanometre systems such as CNT and CNT-polymer-composite-based displays. The future outlook for broad-area displays based on amorphous carbon and CNTs is also addressed.

A Magnet-Friendly Virtual Reality Fiberoptic Image Delivery System

A custom display was built into the MR radiofrequency headcoil to project high-resolution, wide field-of-view stereographic images. Advanced stimulus presentation technologies such as the one described could potentially contribute to a better understanding of the relation between what people are thinking or experiencing, and their associated patterns of brain activity (www.vrpain.com).

Genome-wide prediction, display and refinement of binding sites with information theory-based models

BACKGROUND

We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices.

RESULTS

Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4-6 hours for transcription factor binding sites and 10-19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths.

CONCLUSIONS

Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXRalpha, AHR and NF-kappaB p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. Comparisons of genome scans with the original and refined PXR/RXRalpha information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites.

Inexpensive ethography using digital video

We describe an inexpensive method for digital video recording of behavioral experiments and present a simple, freely-redistributable software tool enabling ethographic analysis of these recordings via classification of video frames into user-defined categories. While high-end commercial solutions already exist for these purposes, we focus on minimizing equipment expenses and complexity for research projects or undergraduate laboratory courses employing compatible behavioral paradigms.