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PubMed2005

Visualization methods for statistical analysis of microarray clusters.

BACKGROUND: The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gold-standard. Appropriate data visualization tools can aid this analysis process, but existing visualization methods do not specifically address this issue. RESULTS: We present several visualization techniques that incorporate meaningful statistics that are noise-robust for the purpose of analyzing the results of clustering algorithms on microarray data. This includes a rank-based visualization method that is more robust to noise, a difference display method to aid assessments of cluster quality and detection of outliers, and a projection of high dimensional data into a three dimensional space in order to examine relationships between clusters. Our methods are interactive and are dynamically linked together for comprehensive analysis. Further, our approach applies to both protein and gene expression microarrays, and our architecture is scalable for use on both desktop/laptop screens and large-scale display devices. This methodology is implemented in GeneVAnD (Genomic Visual ANalysis of Datasets) and is available at http://function.princeton.edu/GeneVAnD. CONCLUSION: Incorporating relevant statistical information into data visualizations is key for analysis of large biological datasets, particularly because of high levels of noise and the lack of a gold-standard for comparisons. We developed several new visualization techniques and demonstrated their effectiveness for evaluating cluster quality and relationships between clusters.

Algorithms↗

PubMed2005

Rapid hologram updates for real-time volumetric information displays.

We have demonstrated that holograms incorporating changes in three-dimensional (3D) scenes can be recalculated in real time to present dynamic updates on information displays. This approach displays 3D information in a compatible format for fast and reliable interpretation of changes in the 3D scenes. The rapid-update algorithm has been demonstrated by real-time computation and transcription of the holograms to our digital micromirror device hologram projection system for visual validation of the reconstruction. The reported algorithm enables full parallax 1024 x 768 pixel holograms of 3D scenes to be updated at a rate of 0.8 s with a 1.8 GHz personal computer. Volumetric information displays that can enhance reliable data assimilation and decrease reaction times for applications such as air-traffic control, cockpit heads-up displays, mission crew stations, and undersea navigation can benefit from this research.

Algorithms↗

PubMed1996

[Development of a device allowing for the perfusion and preservation of rat kidneys at -4 degrees C].

OBJECTIVES: In order to prolong the cold ischaemia time and to improve the quality of donor kidneys, we have designed and developed a renal perfusion machine allowing the control of perfusion parameters (temperature, pressure, flow rate, resistance) during the various phases of a kidney perfusion and storage protocol at -4 degrees C. ANIMALS, MATERIALS AND METHODS: Twenty four rat kidneys were removed and the effects of perfusion and storage at -4 degrees C were studied using a perfusion/storage machine allowing the controlled addition of 2,3 butanediol in University of Wisconsin (UW solution). The kidneys were stored for 96 hours at -4 degrees C and were studied in terms of perfusion parameters (pressure, resistance) and according to their histological appearance. RESULTS: The machine allows controlled perfusion of a cryoprotective agent and preservation of kidneys at -4 degrees C for 96 hours. CONCLUSION: In animals, it is possible to store kidneys at a temperature of -4 degrees C for 96 hours by using a vecor solution (UW solution) and a cryoprotective agent (2,3 butanediol). The perfusion and storage of organs under these conditions must be performed by a computer-assisted machine, allowing monitoring and control of the various steps of perfusion/storage.

Animals↗

PubMed1995

A new device for measuring and recording the forces applied during laryngoscopy.

In characterising the forces exerted during laryngoscopy it is accepted that the significant force component is that which is parallel to the axis of the laryngoscope handle. This paper describes a new method of evaluating the forces exerted at laryngoscopy. A laryngoscope handle has been redesigned, incorporating a force-displacement transducer on the handle at the end opposite to where the blade is attached. The device is designed specifically to sense the axial component of force. The blade attachment block has been detached from the sleeve and connected to a steel shaft which forms the new battery compartment. This allows the axial force exerted at the blade during laryngoscopy to be transmitted along this shaft to the sensing transducer. Linear ball bearings have been introduced between the new shaft and the handle sleeve (outer casing). The rolling friction has been reduced to less than 0.1% by diamond-lapping the precision ground surface-hardened rod to produce a mirror finish. Thus, the force transmitted to the transducer is essentially constant regardless of where the load is applied along the blade. The output from the system is directly downloaded to a laptop computer and the data analysed almost instantaneously to determine the duration of laryngoscopy, the peak forces applied, the mean force with its standard deviation and graphic display of the data. Provision has been made for data entry checks, recording patient details and study data, and creating a data base for the storage and retrieval of the study details.

Adult↗

PubMed1989

[Field localization and verification system for proton beam radiotherapy in deep-seated tumors].

It has been recognized that, for precise localization and verification of radiation fields, a marking drawn on the skin surface is not entirely reliable because its position relative to bony structures or internal organs is not stationary. This is especially true when treating deep-seated tumors located below the clavicle. In proton beam radiotherapy at the University of Tsukuba, we ristrict the margins around the target volume. Therefore, special care in field localization and verification is needed, and we make it a rule to take X-ray pictures on each treatment day. To accomplish this, we have developed a localize-and-verify system by using fluoroscopic techniques and combining it with a real-time digital image processing device. This allows for the formation of a digital image of the proton field and storage it in the optic disc. By using this system as well as verification films, filed placement errors were measured in 10 patients with deep-seated tumors. Out of a total of 190 localizations, 22% exhibited a field placement error of more than 5 mm, where patient positioning and field localization were done by using skin drawings aligned with laser beams. This result strongly suggests the necessity for daily localization and verification of radiation fields, as is being done by us, for precision in the execution of proton beam radiation therapy.

Adult↗

PubMed1990

Design of the diagnostic encyclopedia workstation (DEW).

The Diagnostic Encyclopedia Workstation (DEW) contains reference knowledge for diagnostic support in pathology. Illustrations are accessible via a video disc device. DEW can hold more knowledge, pictures and case histories than books, and its information is accessible via several entries. Software for data entry has been written in MUMPS with use of the relational database toolkit AIDA, which is particularly suited for manipulation of free text. The graphical mouse-driven user interface is written in C using MetaWindows. The DEW contains 85 diagnoses in ovarian pathology, covering all frequent cases and many rarities, illustrated by approximately 3000 pictures, divided among 158 cases.

Computer Systems↗

PubMed1991

Surface and volume rendering in three-dimensional imaging: a comparison.

Many surface rendering techniques are currently available for the three-dimensional display of structure data captured by imaging devices. Comparatively fewer volume rendering techniques are also available for the same purpose. The relative performance of these two methodologies in visualization tasks has been a subject of much discussion recently. Although it is very desirable to establish, based on observer studies, objective guidelines stating the relative merits of the two methodologies even for specific situations, it is impossible to conduct meaningful observer studies that take into account the numerousness of the techniques in each methodology, and within each technique, the numerousness of the parameters and their values that control the outcome of the technique. Our aim in this article is to compare the two methodologies purely on a technical basis in an attempt to understand their common weaknesses and disparate strengths. The purpose of this article is twofold--to report a new surface rendering technique and to compare it with two volume rendering techniques reported recently in the literature. The bases of comparison are: ability to portray thin bones; clarity of portrayal of sutures, fractures, fine textures, and gyrations; smoothness of natural ridges and silhouettes; and computational time and storage requirements. We analyze the underlying algorithms to study how they behave under each of these comparative criteria. Our conclusion is that, at the current state of development, the surface method has a slight edge over the volume methods for portrayal of information of the type described above and a significant advantage considering time and storage requirements, for implementations in identical environments.

Algorithms↗

PubMed1998

Evolution of web site design: implications for medical education on the Internet.

Since its inception, the world wide web (WWW) has possessed the potential for becoming a 'watershed' medium for conveying complex, structured information across vast temporal and geographical barriers. In 1995, the MedWorld project (http:(/)/medworld.stanford.edu) was created at the Stanford University School of Medicine in an effort to innovate and explore the design process of creating WWW applications specifically for medical education. Until recently, the evolution of WWW applications has been mainly driven by technological advances in client-server technology, enabling or translating traditional modes of collaborative medical education (e.g. voice, presence, print, motion) into WWW devices and applications. Many of these applications, while technologically advanced, lack focused development of interface and interactivity design, which may enhance learning experiences. WWW applications which incorporate design innovation in parity with advances in client-server technology have been termed, 'third generation' web sites and have the potential to improve the quality of WWW applications designed for medical education. This work describes how the MedWorld project has created a 'third generation' WWW application by utilizing innovation in information, interface and interactivity design to create innovative WWW technology for the medical education arena.

Communications Media↗

PubMed2004

Wireless networking for the dental office: current wireless standards and security protocols.

Digital radiography has gained immense popularity in dentistry today in spite of the early difficulty for the profession to embrace the technology. The transition from film to digital has been happening at a faster pace in the fields of Orthodontics, Oral Surgery, Endodontics, Periodontics, and other specialties where the radiographic images (periapical, bitewing, panoramic, cephalometric, and skull radiographs) are being acquired digitally, stored within a server locally, and eventually accessed for diagnostic purposes, along with the rest of the patient data via the patient management software (PMS). A review of the literature shows the diagnostic performance of digital radiography is at least comparable to or even better than that of conventional radiography. Similarly, other digital diagnostic tools like caries detectors, cephalometric analysis software, and digital scanners were used for many years for the diagnosis and treatment planning purposes. The introduction of wireless charged-coupled device (CCD) sensors in early 2004 (Schick Technologies, Long Island City, NY) has moved digital radiography a step further into the wireless era. As with any emerging technology, there are concerns that should be looked into before adapting to the wireless environment. Foremost is the network security involved in the installation and usage of these wireless networks. This article deals with the existing standards and choices in wireless technologies that are available for implementation within a contemporary dental office. The network security protocols that protect the patient data and boost the efficiency of modern day dental clinics are enumerated.

Computer Security↗

PubMed2004

Development of an integrated automation system with a magnetic bead-mediated nucleic acid purification device for genetic analysis and gene manipulation.

We have developed an integrated automation system for genetic analysis and gene manipulation. The system, SX-8G Plus, is equipped with an 8-nozzle dispensing unit, a thermal cycler, a cooled reagent reservoir, four tip storage racks, four microplate platforms, buffer reservoirs, an agarose gel electrophoresis unit, a power supply, a pump for exchanging electrophoresis buffer, and a CCD camera. Automation of nucleic acid extraction and purification, the most difficult step in automating genetic analysis and gene manipulation, was realized using magnetic beads with Magtration Technology, which we have previously developed for automating the handling of paramagnetic beads. Using this system, we could perform the automated separation and purification of DNA fragments by agarose gel electrophoresis starting from sample loading. The system would enable the automation of almost all procedures in genetic analysis and gene manipulation.

Computers↗

PubMed1991

An investigation of the optimization of search logic for the MEDLINE database.

One of the key variables in the optimization of the retrieval process is the logic imposed on a set of query terms. If the query is small, a combinatorial algorithm can be employed to identify search expressions having an optimal logical form. An experiment is described in which this was done for queries expressed against MEDLINE, for a variety of criterion variables. The method employed is useful not only for assisting in identifying optimal logical forms, as demonstrated, but also as an experimental control device to assist investigations into the effects of varying the set, and number, of search terms. The experiment also suggests several novel properties of effective searching against MEDLINE, for example that searching with four MeSH terms is likely to be more successful than searching with a lesser number of terms, provided search logic is optimal. The latter result is, surprisingly, true for both Precision and Recall, i.e., a tradeoff between the maximally attainable values of these variables fails to hold when the number of search terms varies in this range.

Algorithms↗

PubMed2006

Long-term continuous external electrocardiographic recording: a review.

Ambulatory electrocardiographic (AECG) monitoring is an essential tool in the diagnostic evaluation of patients with cardiac arrhythmias. Recent advances in solid-state technology have improved the quality of the ECG signals and new dedicated algorithms have expanded the clinical application of software-based AECG analysis systems. These advances, in addition to the availability of inexpensive large storage capacities, and very long-term continuous high-quality AECG monitoring, have opened new potential uses for AECG. New digital recorders have the capability of multichannel simultaneous recordings (from 3 to 12 leads) and for telemetred signal transduction. These possibilities will expand the traditional uses of AECG for arrhythmia detection, as arrhythmia monitoring to assess drug and device efficacies has been further defined by new studies. The analysis of transient ST-segment deviation still remains controversial, but considerably more data are now available, especially about the prognostic value of detecting asymptomatic ischaemia. Heart rate variability analysis has shown promise for predicting mortality rates in cardiac patients at high risk. We review recent advances in this field of non-invasive cardiac testing.

Algorithms↗

PubMed1998

A method for measuring the presampled MTF of digital radiographic systems using an edge test device.

The modulation transfer function (MTF) of radiographic systems is frequently evaluated by measuring the system's line spread function (LSF) using narrow slits. The slit method requires precise fabrication and alignment of a slit and high radiation exposure. An alternative method for determining the MTF uses a sharp, attenuating edge device. We have constructed an edge device from a 250-microm-thick lead foil laminated between two thin slabs of acrylic. The device is placed near the detector and aligned with the aid of a laser beam and a holder such that a polished edge is parallel to the x-ray beam. A digital image of the edge is processed to obtain the presampled MTF. The image processing includes automated determination of the edge angle, reprojection, sub-binning, smoothing of the edge spread function (ESF), and spectral estimation. This edge method has been compared to the slit method using measurements on standard and high-resolution imaging plates of a digital storage phosphor (DSP) radiography system. The experimental results for both methods agree with a mean MTF difference of 0.008. The edge method provides a convenient measurement of the presampled MTF for digital radiographic systems with good response at low frequencies.

Computer Simulation↗

PubMed2004

Teleradiology in orthopaedics.

Teleradiology is a means of electronically transmitting radiographic image files from one location to another. Technologic advances in digital imaging, telecommunications, digital storage, and viewing technologies have made teleradiology readily available and reasonably affordable. The five components of a teleradiology system include: a sending station, a transmission network, a storage device, a viewing station and, a software package. The advantage of teleradiology is the mobility of digital images. In contrast to plain radiographs that only can be seen in one location at a time, multiple persons who are at different locations can view digital images simultaneously. When applied to orthopaedic trauma applications, when the consulting orthopaedist is at a remote location from the patient, teleradiology has been shown to improve diagnostic accuracy, disposition planning of patients from emergency departments or outlying hospitals, and planning of surgical procedures. These systems also improve the comfort level of consulting orthopaedic surgeons and potentially limit the risk of litigation for incorrect diagnosis. The quality, convenience, and effectiveness of teleradiology systems should improve as the technologies continue to mature. Having radiographic images available on handheld devices, such as cell phones, is likely to be a reality in the near future.

Computer Systems↗

PubMed1999

Full-field digital mammography designed as a complete system.

Although mammography is currently considered by many to be the best tool for the early detection of breast cancer, conventional film-screen imaging is still far from perfect. A fundamental limitation of film-screen mammography is the fact that the detection, display and storage devices are one and the same, making it impossible to separately optimize each device. In addition to a potentially equivalent or better image quality compared to the film-screen technology, full-field digital mammography (FFDM) will provide the radiologist with numerous advantages: digital image management, digital data transfer and new medical applications. Nevertheless, to fulfil the potential of digital mammography, an FFDM unit must not only provide an outstanding technology for X-ray detection, but should be designed as a complete system. Each component of the FFDM system should be designed to provide or to increase the current image quality, the current ease of use and the current throughput: the X-ray tube, the gantry, the image receptor packaging, the detector, the acquisition electronics, the softcopy review workstation, the user interface, as well as the network capabilities.

Breast Diseases↗

PubMed1991

Network system: the integrated picture archiving and communication system with the hospital information system.

We describe the outline of Hokkaido University picture archiving and communication system (HU-PACS) and its network functions. HU-PACS processes 0.5 Gbytes of images daily through 10 acquisition devices. Functional integration of hospital information system (HIS) and PACS has been implemented. The HU-PACS can access common data base with HIS. Multi-image data-base systems provide fast throughput of image retrieval. The system is composed of 4 modules: (1) 2 image data-base systems (IDS), (2) 1 image management system (IMS), (3) image display terminals (IDT), and (4) 8 image acquisition nodes interfaced to 10 modalities and 1 film scanner. These 4 modules are connected by branch and loop type local area networks (LAN). HU-PACS has functions other than basic PACS functions. Images in optical disk library (ODL) are loaded onto magnetic disks (MD) in advance according to patient booking information, the images expected to be viewed are transferred to the local storage automatically, and the desired images can be pre-downloaded into local storage by instruction through HIS terminals.

Computer Communication Networks↗

PubMed2002

Advances in modern electrocardiographic equipment for long-term ambulatory monitoring.

Electrocardiographic ambulatory "Holter" monitoring (AECG) is an essential tool in the diagnostic evaluation of patients with cardiac arrhythmias. Recent advances in digital Holter technology have improved the quality of the ECG signals and new dedicated algorithms have expanded the clinical application of software-based AECG analysis systems. Due to the availability of inexpensive large storage capacities, very long-term (weeks to months) continuous high-quality AECG monitoring will soon be available, together with devices for long-term long-distance telemetric surveillance for high-risk cardiac patients, utilizing trans-telephonic transmission of ECG data. New digital recorders will also have the capability for multichannel simultaneous recordings (currently from 3 to 8 simultaneous leads). Multichannel digital recordings will allow the recording of different biological signals by appropriate sensors, such as respiratory frequency, peripheral oxygen tension, arterial pulse pressure, EEG, and others. This will transform conventional AECG in ambulatory policardiography, allowing the comprehensive evaluation of patients with complex disorders, such as heart failure or sleep apnea syndromes. By this global approach, Holter analysis becomes a real "noninvasive electrophysiological test," to identify potential risk factors for life-threatening cardiac arrhythmias.

Arrhythmias, Cardiac↗

PubMedDate not supplied

[A computer system for the systematization of MR findings in knee joint diseases].

An inexpensive, easy-access computer-based system is proposed, which was developed for the systematization of the clinical series of knee joint disorders studied with Magnetic Resonance Imaging (MRI). The system is based upon the integration of multimedia technology and Data Base Management Systems (DBMS). The hardware configuration for this project included an Apple Macintosh workstation based on a Motorola 68040 microprocessor and a customized application developed by the authors with the 4th Dimension software. The MR images available only on film were digitized off-line with a solid-state Charge Coupled Device (CCD) scanner with back-light cover for transparency. Otherwise, MR images were acquired on-line through an Ethernet-based local area network from the MR unit or from a SparcStation-Advantage Windows workstation connected with the MR unit. Image post-processing was performed with the Adobe PhotoShop software. The system was devoted to the systematization and analysis of a clinical series of 800 MR studies of the knee. A mean of 10 significant MR images were stored for each examination with a standard image compression algorithm--the Joint Photographic Experts Group (JPEG). This permitted us to save the system's storage space and at the same time to preserve image quality for consultation and teaching purposes, not for diagnosis which is made on the backboard or on the MR unit's or Advantage Window's monitor. Finally, MR findings were indexed with a customized check-list specific for knee joint disorders. On the basis of stored and selected information, it was thus possible to carry out a statistical analysis and to make detailed reports which are useful for scientific purposes, such as the preparation of lectures and papers. Moreover, the system was very useful for patients' follow-up and for the preparation of hypermedia teaching applications on knee joint disorders which are available on the Internet at our World-Wide Web server (URL: http://mbox.unipa.it/radpa/radpa ++ +.html). In conclusion, the system is a cost-effective and user-friendly solution for the multipurpose management of radiologic series.

Humans↗