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At least 433 records · Page 24Linked to original sources

PubMed1999

Promoter2.0: for the recognition of PolII promoter sequences.

MOTIVATION: A new approach to the prediction of eukaryotic PolII promoters from DNA sequence takes advantage of a combination of elements similar to neural networks and genetic algorithms to recognize a set of discrete subpatterns with variable separation as one pattern: a promoter. The neural networks use as input a small window of DNA sequence, as well as the output of other neural networks. Through the use of genetic algorithms, the weights in the neural networks are optimized to discriminate maximally between promoters and non-promoters. RESULTS: After several thousand generations of optimization, the algorithm was able to discriminate between vertebrate promoter and non-promoter sequences in a test set with a correlation coefficient of 0.63. In addition, all five known transcription start sites on the plus strand of the complete adenovirus genome were within 161 bp of 35 predicted transcription start sites. On standardized test sets consisting of human genomic DNA, the performance of Promoter2.0 compares well with other software developed for the same purpose. AVAILABILITY: Promoter2.0 is available as a Web server at http://www.cbs.dtu. dk/services/promoter/

Algorithms↗

PubMedDate not supplied

Middle-latency auditory-evoked potential in acepromazine-sedated dogs.

The middle-latency auditory-evoked potential (MLAEP) has been investigated as means of monitoring anesthesia in dogs. The goals of this study were to develop a technique to record MLAEPs in awake dogs and to determine the effects of sedation. The MLAEP was recorded in 12 dogs with and without sedation with acepromazine. Three needle electrodes were inserted SC. Click stimuli were delivered biaurally. Signal acquisition, averaging, and analysis were performed by software developed in-house. Signals were recorded for 128 milliseconds, and the responses to 1,024 stimuli were averaged. The waveforms from 10 recordings were averaged, and the amplitudes and latencies of peaks that could be consistently identified were measured. Data measured were compared by means of a paired 2-sided Student's t-test. Interpretable MLAEPs were recorded in 10 of the 12 dogs. Three peaks were consistently identified (Pa, Nb, and Pb). The latencies of these peaks were significantly (P = .032, .035, and .028, respectively) shorter in awake (mean +/- SD milliseconds) (Pa = 18.85 +/- 1.36, Nb = 30.50 +/- 3.55, and Pb = 47.70 +/- 5.53) than in sedated (Pa = 22.40 +/- 3.88, Nb = 35.75 +/- 6.77, and Pb = 55.30 +/- 10.55) dogs. The Pb amplitude was not significantly different (2.51 +/- 1.30 microV awake and 2.19 +/- 1.10 microV sedated). This study demonstrates that acepromazine sedation causes changes in MLAEP.

Acepromazine↗

PubMed1999

JADE: computerization of a structured interview for childhood psychiatric diagnosis.

JADE is a new, computerized structured interview system to design, administer, and report results of the National Institute of Health's Diagnostic Interview Schedule for Children (NIMH-DISC). It has been developed under the auspices of the DISC Group at the Division of Child and Adolescent Psychiatry at Columbia University/New York State Psychiatric Institute. The development of JADE is based on extensive experience in the use of the DISC and with several previous computerized versions. It illustrates the importance to program design of consultation with those experienced in research and clinical application of the system and of the early adoption of a mature software development strategy.

Child↗

PubMed2006

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies.

BACKGROUND: High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option.GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. RESULTS: MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. CONCLUSION: MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.

Cloning, Molecular↗

PubMed2001

Digital radiography and film scanners: automating the transition to filmless radiology.

To facilitate the integration of digital radiography (DR) and legacy film/screen technology, we have devised a methodology for film digitization that optimizes workflow and integrates well with the picture archiving and communication system (PACS). This work was performed at Mercy Medical Center (Cedar Rapids, IA) using a film digitizer with built-in Digital Imaging and Communications in Medicine (DICOM) communication. The radiology department at Mercy has one DR system and three separate film/screen systems. The DR system software suite features DICOM Modality Worklist capability to provide complete radiology information system (RIS) integration functionality. This provides for patient demographic information to be automatically downloaded from the RIS worklist to populate the DICOM image header. Likewise, we have taken advantage of the film scanner's DICOM capability to develop software linking it with the hospital RIS. This capability provides a worklist downloading functionality equivalent to that of the DR. Patient demographics can then be rapidly downloaded as each film is digitized. The worklist capability of the scanner is essential in several respects. First, it guarantees that patient demographic information is completely accurate and, therefore, that the digitized x-ray image will be merged with the correct patient file in the PACS. Additionally, high film scanner throughput is achieved, guaranteeing that all inpatient-digitized films are as readily available on the PACS as their DR image counterparts. The digitized images have proven to be of diagnostic quality on the typical 1K by 1K PACS workstation. Also, as patients are admitted to the hospital, prior films from the radiology archive are digitized to form a readily available patient history for in-house physicians. Over time, we are building archival patient histories of soft-copy images that will enable increased availability of patient x-rays to both in-hospital and outside referring physicians, especially as more internet-viewing software becomes available to the out-of-hospital medical community. Finally, the results of this study show that high-throughput RIS integration of film scanning equipment is a key component to making a graceful transition to the filmless hospital as more DR systems are installed.

Humans↗

PubMed1981

EPA health and environmental effects data analysis system.

This paper discusses the development of a system to organize, store, retrieve, and correlate data pertaining to chemicals and their biological and environmental effects. The particular problems of data identification, acquisition, classification, and automation are discussed in relation to existing data sources and methods of data collection and analysis. The problems of computer software development are also addressed, and a design overview of the system is presented.

Animals↗

PubMed2004

Formation flying design and applications in weak stability boundary regions.

Weak stability regions serve as superior locations for interferomertric scientific investigations. These regions are often selected to minimize environmental disturbances and maximize observation efficiency. Designs of formations in these regions are becoming ever more challenging as more complex missions are envisioned. The development of algorithms to enable the capability for formation design must be further enabled to incorporate better understanding of weak stability boundary solution space. This development will improve the efficiency and expand the capabilities of current approaches. The Goddard Space Flight Center (GSFC) is currently supporting multiple formation missions in weak stability boundary regions. This end-to-end support consists of mission operations, trajectory design, and control. It also includes both algorithm and software development. The Constellation-X, Maxim, and Stellar Imager missions are examples of the use of improved numeric methods to attain constrained formation geometries and control their dynamical evolution. This paper presents a survey of formation missions in the weak stability boundary regions and a brief description of formation design using numerical and dynamical techniques.

Journal Article↗

PubMed1995

PLACO: a cooperative architecture for managing workflow in CCU.

Computer-Supported Cooperative Work (CSCW) is a multi-disciplinary research theme involving software developers, computer scientists, as well as psychologists and sociologists. CSCW is devoted to the analysis of interactions among humans when performing their work in a collaborative way. The main application fields are work organization, healthcare, education and training. The term of Groupware, as defined by C.A. Ellis, refers to software that assists groups of people in communicating, in collaborating and in coordinating their activities. Our objective is to study software architectures allowing task coordination and conflict management between participants within a distributed environment, in particular medical units. We do not aim to produce a practical system suitable for near-term deployment in the Critical Care Unit (CCU), but rather a "proof of concept", an experimental system that performs and coordinates a range of intelligent planning tasks in CCU activities. The emphasis will be put especially on asynchronous cooperation since the work of physicians and nurses is discontinuous.

Communication↗

PubMed1996

Radiology systems architecture.

This article focuses on the software requirements for enterprise integration in radiology. The needs of a future radiology systems architecture are examined, both at a concrete functional level and at an abstract system-properties level. A component-based approach to software development is described and is validated in the context of each of the abstract system requirements for future radiology computing environments.

Computer Systems↗

PubMed2002

[Stressor and stress reduction strategies for computer software engineers].

First, in this article we discuss 10 significant occupational stressors for computer software engineers, based on the review of the scientific literature on their stress and mental health. The stressors include 1) quantitative work overload, 2) time pressure, 3) qualitative work load, 4) speed and diffusion of technological innovation, and technological divergence, 5) low discretional power, 6) underdeveloped career pattern, 7) low earnings/reward from jobs, 8) difficulties in managing a project team for software development and establishing support system, 9) difficulties in customer relations, and 10) personality characteristics. In addition, we delineate their working and organizational conditions that cause such occupational stressors in order to find strategies to reduce those stressors in their workplaces. Finally, we suggest three stressor and stress reduction strategies for software engineers.

Humans↗

PubMed1983

A system for the analysis of long-term electrocardiographic studies in clinical research and training.

A computer system has been developed for the analysis of data from long-term electrocardiographic studies in the context of an institution committed to clinical research and training. The major characteristics required of such a system are intelligence, flexibility, friendliness, and maintainability. These attributes are achieved by a user interface which consists of menus and interactive graphics, and by the use of highly modular software developed in a high-level programming language. The system has been used in studies of the effects of drugs on cardiac arrhythmias and has been easy to learn and convenient to use.

Academies and Institutes↗

PubMedDate not supplied

Motorized head impulse stimulator to determine angular horizontal vestibulo-ocular reflex.

The objective of the current study was to develop a computer-controlled mechanical system for the generation of impulsive head rotations to measure eye movements induced by angular horizontal vestibulo-ocular reflex. This is a clinical eye movement test recently introduced for the usage of otoneurological balance laboratories. We built the system and modified our prior computer software developed for other types of eye movement tests. Motor controlled stimulation has fulfilled the requirement of more uniform and constant acceleration stimulation than obtained with manually administrated impulses. After having executed preliminary experiments at our balance laboratory we found the system to be efficient, reliable and secure.

Acceleration↗

PubMed2006

Markers improve clustering of CGH data.

MOTIVATION: We consider the problem of clustering a population of Comparative Genomic Hybridization (CGH) data samples using similarity based clustering methods. A key requirement for clustering is to avoid using the noisy aberrations in the CGH samples. RESULTS: We develop a dynamic programming algorithm to identify a small set of important genomic intervals called markers. The advantage of using these markers is that the potentially noisy genomic intervals are excluded during the clustering process. We also develop two clustering strategies using these markers. The first one, prototype-based approach, maximizes the support for the markers. The second one, similarity-based approach, develops a new similarity measure called RSim and refines clusters with the aim of maximizing the RSim measure between the samples in the same cluster. Our results demonstrate that the markers we found represent the aberration patterns of cancer types well and they improve the quality of clustering significantly. AVAILABILITY: All software developed in this paper and all the datasets used are available from the authors upon request.

Biomarkers, Tumor↗

PubMed1990

Photoresistive measurement of the Pavlovian conditioned eyelid response in human subjects.

An inexpensive technique is described for measuring eyelid closure during classical (Pavlovian) conditioning experiments. This technique employs a Coulbourn Instruments Co. densitometric device that focuses a beam of infrared light on the cornea. Reflection of the light is interrupted by the eyelids when they are closed, which is sensed by an infrared detector. The latter causes a voltage change to occur, which can then be measured in a variety of ways. Details of both the hardware required and software developed for this purpose are described.

Arousal↗

PubMed2005

Measurement of masticatory movement by a new jaw tracking system using a home digital camcorder.

The aim of this study was to confirm the precision of our simple and inexpensive jaw tracking system which combined the use of a digital camcorder and a motion capture software developed lately. A marker was attached to the mandibular incisors of the subject, and a mirror was assembled beside the subject's face to detect antero-posterior movement during chewing. Jaw movements, including the mirror images, were recorded by a digital camcorder. The movements were traced by a motion capture software and translated into 3D data using original handmade software. To confirm the beneficial performance of our system in measuring masticatory movement, the masticatory movements of five subjects were simultaneously recorded together with a conventional jaw tracking system. Trajectories obtained from both systems were similar, and the correlation coefficient values by simple regression analysis between both trajectories were 0.9 or higher for all subjects. It was confirmed that our system could record masticatory movement with sufficient precision equivalent to that of a conventional jaw tracking system.

Adult↗

PubMed1997

Experiences with DCE: the pro7 communication server based on OSF-DCE functionality.

The pro7-communication server is a new approach to manage communication between different applications on different hardware platforms in a hospital environment. The most important features are the use of OSF/DCE for realising remote procedure calls between different platforms, the use of an SQL-92 compatible relational database and the design of a new software development tool (called protocol definition language compiler) for describing the interface of a new application, which is to integrate in a hospital environment.

Computer Communication Networks↗

PubMed1997

Developing sexual health software incorporating user feedback: a British experience.

This article describes an interactive prototyping model for development of four computer software modules for British youth on sexual issues. An iterative cycle of development, user review and feedback, and subsequent modification and retesting was used with approximately 150 young adults, with particular attention to presentation style, screen design, usability, relevance of material, enjoyment, and learning. The software was designed to be realistically accommodated in school settings, to be used as a reference tool by students working alone or in a group teaching situation. Feedback from youth and adults attests to the feasibility of development, implementation, and instructional usefulness. Interactive prototyping proved essential in the face of skepticism from teachers concerning young people's information needs and acceptance of a computerized educational approach.

Adolescent↗

PubMed2003

Video recording system for the measurement of eyelid movements during classical conditioning of the eyeblink response in the rabbit.

Classical conditioning of the eyeblink response in the rabbit is a popular model for studying the neural substrates of associative learning. Most of the common eyeblink recording techniques require invasive procedures. To perform experiments in intact animals, a non-invasive, high-speed video recording system was developed to measure eyeblink responses of rabbits during classical conditioning experiments. Besides being non-invasive, this method does not require excessive restraint of the animal. The PC-based system combines a Pulnix video camera with National Instruments video capture and timing hardware to control the experiment and acquire images of the peri-ocular region. The software developed for controlling these experiments also detects the eyeblink by measuring the movement of the upper and lower eyelids, the area of the exposed surface of the eye, and head movements in the sagittal plane. The time resolution of this relatively inexpensive system is 8.33 ms, and at a working distance of 0.8 m, it can detect movements as small as 0.11 mm.

Animals↗