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At least 937 records · Page 52Linked to original sources
PubMed2004

ROSO: optimizing oligonucleotide probes for microarrays.

UNLABELLED: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set. AVAILABILITY: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. SUPPLEMENTARY INFORMATION: http://pbil.univ-lyon1.fr/roso

Algorithms↗
PubMed1997

Real-time multichannel computerized electrogastrograph.

The purpose of this study was to develop a real-time multichannel computerized electrogastrograph (EGG) to measure and analyze electrical signals from the human abdominal surface. A soft-contact matrix composed of 25 cutaneous electrodes is embedded evenly in a latex mat. The mat can be firmly attached to the abdominal surface by drawing a vacuum between the matrix and the stomach. Twenty-five high-amplification filter/amplifiers provide a high signal-to-noise ratio and flat amplitude response for a signal between 0.02 and 0.12 Hz (1.2-7.2 cpm). The computer program provides waveform and frequency analysis for any chosen channel and mapping analyses for all 25 channels. A two-dimensional propagation exploration program was also developed. Using four different mapping analysis program subroutines, the optimal points for analyzing the EGG signals can be reliably found and variability of these locations can be observed easily. Results show differences in the EGG mappings of normal and abnormal subjects.

Adult↗
PubMed2005

CAGER: classification analysis of gene expression regulation using multiple information sources.

BACKGROUND: Many classification approaches have been applied to analyzing transcriptional regulation of gene expressions. These methods build models that can explain a gene's expression level from the regulatory elements (features) on its promoter sequence. Different types of features, such as experimentally verified binding motifs, motifs discovered by computer programs, or transcription factor binding data measured with Chromatin Immunoprecipitation (ChIP) assays, have been used towards this goal. Each type of features has been shown successful in modeling gene transcriptional regulation under certain conditions. However, no comparison has been made to evaluate the relative merit of these features. Furthermore, most publicly available classification tools were not designed specifically for modeling transcriptional regulation, and do not allow the user to combine different types of features. RESULTS: In this study, we use a specific classification method, decision trees, to model transcriptional regulation in yeast with features based on predefined motifs, automatically identified motifs, ChlP-chip data, or their combinations. We compare the accuracies and stability of these models, and analyze their capabilities in identifying functionally related genes. Furthermore, we design and implement a user-friendly web server called CAGER (Classification Analysis of Gene Expression Regulation) that integrates several software components for automated analysis of transcriptional regulation using decision trees. Finally, we use CAGER to study the transcriptional regulation of Arabidopsis genes in response to abscisic acid, and report some interesting new results. CONCLUSION: Models built with ChlP-chip data suffer from low accuracies when the condition under which gene expressions are measured is significantly different from the condition under which the ChIP experiment is conducted. Models built with automatically identified motifs can sometimes discover new features, but their modeling accuracies may have been over-estimated in previous studies. Furthermore, models built with automatically identified motifs are not stable with respect to noises. A combination of ChlP-chip data and predefined motifs can substantially improve modeling accuracies, and is effective in identifying true regulons. The CAGER web server, which is freely available at http://cic.cs.wustl.edu/CAGER/, allows the user to select combinations of different feature types for building decision trees, and interact with the models graphically. We believe that it will be a useful tool to facilitate the discovery of gene transcriptional regulatory networks.

Algorithms↗
PubMed2003

TranSIESTA: a spice for molecular electronics.

Our recently developed method, TranSIESTA, enables modelling of molecular electronic devices under operation conditions. The method is based on density functional theory, and calculates the self-consistent electronic structure of a nanostructure coupled to three-dimensional electrodes with different electrochemical potentials. It uses a full atomistic ab initio description of both the electrodes and the nanoscale device. The calculations reveal information about the scattering states, transmission coefficients, electron current, and non-equilibrium forces in the systems. In this paper we use the method to investigate the electrical properties of three ring phenyl-ethynylene oligomers (OPE). We present results for the electrical effect of side groups and molecular conformations of the molecules. The calculations indicate that molecular switching and negative differential conductance (NDC) are related to rotations of the middle phenyl ring.

Algorithms↗
PubMedDate not supplied

A JAVA environment for medical image data analysis: initial application for brain PET quantitation.

Analysis software for medical image data tends to be expensive and usable only in a restricted environment. Therefore the aim of the current project was to implement a flexible framework for medical image processing and visualization which is portable among platforms and open to different data formats including DICOM 3.0. The software was designed as a set of tools which encapsulate specialized functionality. The tools are full stand alone applications, but they are also able to present a co-operating environment within which images and other information are communicated in real time. Currently, the emphasis is on quantitative analysis of PET data by kinetic modelling. However, general viewing capabilities are included, and the design is flexible enough that other types of processing can easily be integrated by simply plugging in Java classes. The software is successfully applied to PET data quantitation in clinical research studies and even patient studies. Portability was aimed at by encoding the programs in Java. Experience shows that the implementation of such a complex and computationally demanding Java application is feasible. Although there are major portability issues to consider, configurations can be found on which the software runs stably and at a speed comparable to C code if just-in-time compilation is available.

Brain↗
PubMed1990

PC-compatible computer-generated stimuli for video-task testing.

Whereas computer technology allows for the automation of experimentation and data collection, the process of stimulus production has remained a relatively labor-intensive process. A program for automatic computer generation of novel nonverbal stimuli is described in this paper. The program, STIMGEN, allows menu-driven control over the type and appearance of stimuli. Data are presented in which two monkeys matched to sample with high accuracy using stimuli generated with STIMGEN. These data are interpreted to support the usefulness and value of automatic stimulus generation in a variety of applications.

Animals↗
PubMed1991

Best kept secrets ... First Coast Systems, Inc. (FCS).

The FCS/APaCS system is a viable option for small-to medium-size hospitals (up to 400 beds). The table-driven system takes full advantage of IBM AS/400 computer architecture. A comprehensive application set, provided in an integrated database environment, is adaptable to multi-facility environments. Price/performance appears to be competitive. Commitment to IBM AS/400 environment assures cost-effective hardware platforms backed by IBM support and resources. As an IBM Health Industry Business Partner, FCS (and its clients) benefits from IBM's well-known commitment to quality and service. Corporate emphasis on user involvement and satisfaction, along with a commitment to quality and service for the APaCS systems, assures clients of "leading edge" capabilities in this evolutionary healthcare delivery environment. FCS/APaCS will be a strong contender in selected marketing environments.

Computers↗
PubMed1999

[A method for gait analysis--preliminary report].

A preliminary report on new method for gait evaluation is presented. Specifically designed shoes with built-in sensors allow for registration of the data during free gait on normal surface; collected data is than analyzed in PC based system. Twenty-four patients (16 females, 8 males, mean age 58 years) with hip arthritis treated at Orthopedic Department were included in this study.

Diagnosis, Computer-Assisted↗
PubMed1997

[The development of an computerized analysis system for the women pelvic cavity impedance rheogram].

This article introduces the components and functions of an computered analysis system for the women pelvic cavity impedance rheogram. It can sample the pelvic cavity impedance rheogram signal of the body double-side and the reference ECG signal. With help of manual intervence, it also can automatically recognize characteristic points of the pelvic cavity impedance rheogram and measure the parameters. It can correct the recognized characteristic points simultaneously and print the pelvic cavity impedance rheogram of the body double-side and 15 characteristic data parameters. After clinical applying, the analysis results of mors 100 patients make clear that: this system has remarkably clinical significance for diagnosis of the women pelvic cavity extravasated blood and evaluation of treating effect, so it has much better clinical applied expectation.

Equipment Design↗
PubMedDate not supplied

The design and development of a biosensor to measure the concentration of meconium in amniotic fluid.

Meconium aspiration syndrome occurs in 0.2% to 1% of all deliveries and has a mortality rate as high as 18%. The disease is responsible for 2% of all perinatal deaths. Meconium may be classified as being thick or thin, but this assessment is normally performed visually by clinicians. A "meconiumcrit" analysis has been developed to objectively define the concentration of meconium. However, this analysis does not provide real-time continuous readings. This study focused on the design and development of a sensor to provide an objective, continuous, real-time assessment of meconium thickness. Meconium has an absorption spectrum centered at 410 nm and observes Beer's law. Blue light centered at 430 nm was delivered through meconium solutions, and a photodiode translated the strength of the incoming light into a voltage. This voltage was analyzed by a microcontroller to determine the concentration of meconium.

Amniotic Fluid↗
PubMed1992

An 8086-based Holter arrhythmia monitor.

Holter monitoring is a technique which involves the use of a specialized recorder to record and analyze the ECG of an ambulatory subject for a duration up to 24 h. It is used for persons who have generally normal ECG, but who experience heart disorders under some particular stress conditions. This paper describes the design of an 8086-based Holter monitor using state-of-the-art technology. The old concept of analog signal processing and cassette recording has been replaced by digital signal processing and solid state memories. The main features of the new monitor, as compared with conventional ones, is its intelligence to detect and record arrhythmias which are of clinical importance. Emphasis was placed on miniaturization and minimization of the power consumption while designing the monitor.

Algorithms↗
PubMed2005

[An intelligent optometry system based on Client/Server Mode].

The optometry in physical examinations is conducted manually at present and this method is neither precise nor efficient. After studying the standard logarithmic visual acuity charts which is popular in our country, we have designed an optometry system based on Client/Server Computing Mode. The system's architecture and its working principle are also presented in the article.

Algorithms↗
PubMed2003

Project management system for structural and functional proteomics: Sesame.

A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.

Database Management Systems↗
PubMed1998

Computer-based quality control in high-dose chemotherapy and bone marrow transplantation.

High-dose chemotherapy with autologous and allogeneic blood stem cell transplantation has become a standard therapy for hematological malignancies and solid tumors. To ensure quality of treatment and adherence to internationally approved protocols, the use of computer systems has been introduced in some oncology centers. Most software packages cannot be used automatically by other institutions because of different treatment strategies and medications. To overcome this problem, we designed a software system based on an Oracle database, which allows the user to develop his own therapy blocks and assemble them to generate specific therapy plans. The system supports the daily work of the physicians by suggesting medications based on changes in the vital parameters or the clinical chemistry. Parameters can be given upper and lower limits whose surpassing leads to treatment suggestions by the system. All quantitative variables may be depicted in a graphical way. The system is connected to external laboratory devices. Export of data to international registries is possible. Until now, 43 patients have been transplanted with the help of this system. There is a high degree of acceptance among the nursing staff and the physicians. The system can be transferred to other centers, if the local hardware and network capacities meet the minimal requirements.

Adult↗
PubMed2006

A Web-based telemedicine system for diabetic retinopathy screening using digital fundus photography.

The purpose was to design and implement a Web-based telemedicine system for diabetic retinopathy screening using digital fundus cameras and to make the software publicly available through Open Source release. The process of retinal imaging and case reviewing was modeled to optimize workflow and implement use of computer system. The Web-based system was built on Java Servlet and Java Server Pages (JSP) technologies. Apache Tomcat was chosen as the JSP engine, while MySQL was used as the main database and Laboratory of Neuro Imaging (LONI) Image Storage Architecture, from the LONI-UCLA, as the platform for image storage. For security, all data transmissions were carried over encrypted Internet connections such as Secure Socket Layer (SSL) and HyperText Transfer Protocol over SSL (HTTPS). User logins were required and access to patient data was logged for auditing. The system was deployed at Hubert H. Humphrey Comprehensive Health Center and Martin Luther King/Drew Medical Center of Los Angeles County Department of Health Services. Within 4 months, 1500 images of more than 650 patients were taken at Humphrey's Eye Clinic and successfully transferred to King/Drew's Department of Ophthalmology. This study demonstrates an effective architecture for remote diabetic retinopathy screening.

Diabetic Retinopathy↗
PubMed1999

On-line computer system to minimize laser injuries during surgery: preliminary system layout and proposal of the key features.

The aim of this paper is to investigate some new user interface ideas and related application packages which aim to improve the degree of safety in an operating room during surgical operations in which an invasive laser beam is deployed. The overall value of the proposition is that a means is provided which ensures the successful completion of the surgical case while minimizing the risk of thermal and mechanical injuries to healthy tissues adjacent to the surgical field. According to surgeons operating with a variety of CO2 lasers available at both the National Cancer Institute in Milan, Italy, and the Sackler School of Medicine, Tel Aviv University, Israel, each laser device presents different cutting and coagulation properties. In order to identify which 'ideal' procedure might corroborate the subjective impression of each surgeon and also to provide one common tool to ensure procedures with a high level of safety, the author has worked for several months with surgeons and technicians of both Institutions to define the general design of a new on-line surgical operation planning and design system to be used during the pre-operative briefing activities and also as a consultation tool during operation. This software package will be developed and tested on both 'C' and FORTRAN compilers running on a commercially available PC which is driving a continuous wave (CW) CO2 laser device via its Instrument Bus interface. The present proposal describes the details of a software package called LCA (Laser-beam Controller and Adviser) which performs several controls in parallel on the key output parameters of a laser beam device during its utilization in delicate surgical operations. The required performances of this device needed during a given surgical operation are pre-simulated and compared against the well-known safety limits, which are stored in the computer's mass storage. If the surgeon's decision about the laser device set-up are considered to be too close to the required physiological safety limits, then the SW alerts the surgeon and proposes alternatives based on other combinations of both HW and SW configurations. An additional application of LCA uses this SW as a warning tool during the operation itself. If a wrong set-up of the laser device is accidentally used, an alarm will be generated and the laser beam automatically switched-off prior to an 'incident report' printout. The operation will continue only when the surgeon validates the choices that the SW suggests for implementation. If necessary, the surgeon can switch off the device and continue to operate it manually. In this case, the surveillance mode will be totally excluded.

Bone Cements↗