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PubMed2005

GeneSeer: a sage for gene names and genomic resources.

BACKGROUND: Independent identification of genes in different organisms and assays has led to a multitude of names for each gene. This balkanization makes it difficult to use gene names to locate genomic resources, homologs in other species and relevant publications. METHODS: We solve the naming problem by collecting data from a variety of sources and building a name-translation database. We have also built a table of homologs across several model organisms: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae, S. pombe and A. thaliana. This allows GeneSeer to draw phylogenetic trees and identify the closest homologs. This, in turn, allows the use of names from one species to identify homologous genes in another species. A website http://geneseer.cshl.org/ is connected to the database to allow user-friendly access to our tools and external genomic resources using familiar gene names. CONCLUSION: GeneSeer allows access to gene information through common names and can map sequences to names. GeneSeer also allows identification of homologs and paralogs for a given gene. A variety of genomic data such as sequences, SNPs, splice variants, expression patterns and others can be accessed through the GeneSeer interface. It is freely available over the web http://geneseer.cshl.org/ and can be incorporated in other tools through an http-based software interface described on the website. It is currently used as the search engine in the RNAi codex resource, which is a portal for short hairpin RNA (shRNA) gene-silencing constructs.

Alternative Splicing↗
PubMed2006

Using geographic information systems to identify prospective marketing areas for a special library.

BACKGROUND: The Center for Disability Resources (CDR) Library is the largest collection of its kind in the Southeastern United States, consisting of over 5,200 books, videos/DVDs, brochures, and audiotapes covering a variety of disability-related topics, from autism to transition resources. The purpose of the library is to support the information needs of families, faculty, students, staff, and other professionals in South Carolina working with individuals with disabilities. The CDR Library is funded on a yearly basis; therefore, maintaining high usage is crucial. A variety of promotional efforts have been used to attract new patrons to the library. Anyone in South Carolina can check out materials from the library, and most of the patrons use the library remotely by requesting materials, which are then mailed to them. The goal of this project was to identify areas of low geographic usage as a means of identifying locations for future library marketing efforts. METHODS: Nearly four years worth of library statistics were compiled in a spreadsheet that provided information per county on the number of checkouts, the number of renewals, and the population. Five maps were created using ArcView GIS software to create visual representations of patron checkout and renewal behavior per county. RESULTS: Out of the 46 counties in South Carolina, eight counties never checked out materials from the library. As expected urban areas and counties near the library's physical location have high usage totals. CONCLUSION: The visual representation of the data made identification of low usage regions easier than using a standalone database with no visual-spatial component. The low usage counties will be the focus of future Center for Disability Resources Library marketing efforts. Due to the impressive visual-spatial representations created with Geographic Information Systems, which more efficiently communicate information than stand-alone database information can, librarians may benefit from the software's use as a supplemental tool for tracking library usage and planning promotional efforts.

Journal Article↗
PubMed2004

Multislice CT urography: state of the art.

Recent improvements in helical CT hardware and software have provided imagers with the tools to obtain an increasingly large number of very thin axial images. As a result, a number of new applications for multislice CT have recently been developed, one of which is CT urography. The motivation for performing CT urography is the desire to create a single imaging test that can completely assess the kidneys and urinary tract for urolithiasis, renal masses and mucosal abnormalities of the renal collecting system, ureters and bladder. Although the preferred technique for performing multislice CT urography has not yet been determined and results are preliminary, early indications suggest that this examination can detect even subtle benign and malignant urothelial abnormalities and that it has the potential to completely replace excretory urography within the next several years. An important limitation of multislice CT urography is increased patient radiation exposure encountered when some of the more thorough recommended techniques are utilized.

Contrast Media↗
PubMed1998

Portable productivity at the point of care.

Managed care is motivating providers to explore ways to reduce costs by improving performance at the point of care. One increasingly popular tool: portable and wireless computers and software to help capture clinical data.

Cost Control↗
PubMed1998

Methods of evaluation in outcomes research.

UNLABELLED: This activity is designed for pharmacists, physicians, physician assistants, nurses, and other healthcare team members; payers for health services; and healthcare executives. GOAL: To provide basic information on the methods used and computer software available for evaluating invariant factorial structures, such as those found in health status measurement tools. OBJECTIVES: 1. Discuss why comparison of mean scores may not be appropriate when interpreting humanistic outcomes results. 2. Identify alternative methods for evaluating data from health status measurement tools, such as the SF-36. 3. Define validity, reliability, and structure. 4. Understand the value of structural equation modeling when using health status measurement tools, such as the SF-36. 5. Describe the statistical software used to perform structural equation modeling.

Data Interpretation, Statistical↗
PubMed2002

[Three-dimensional imaging and cephalometry of cranio-facial asymmetry].

The 75th meeting of the French Orthodontics Society will be held in Biarritz May 8-9-10-11 2002. The main topic for discussion will be: "facial asymmetry". During the meeting, authors will present study of facial asymmetries using a new innovative three-dimensional cephalometry. The method combines CT scans data, anatomical landmarks and mathematical tools to create, using the "Cepha" software, a 3D model of the human face. Balance and symmetry of the model are stable enough to define normality for each individual even with different ethnic and cultural origins. Unbalance and asymmetry characterize pathologies. Follow up shape and size of models allows growth prediction and modeling. The model is in the process of becoming the indispensable reference for all those who are interested in studying the human face: Orthodontics, Surgery, Anatomy, Anthropology, Plastic surgery, Forensic Medicine.

Cephalometry↗
PubMedDate not supplied

Automated testing of arrhythmia monitors using annotated databases.

Arrhythmia-algorithm performance is typically tested using the AHA and MIT/BIH databases. The tools for this test are simulation software programs. While these simulations provide rapid results, they neglect hardware and software effects in the monitor. To provide a more accurate measure of performance in the actual monitor, a system has been developed for automated arrhythmia testing. The testing system incorporates an IBM-compatible personal computer, a digital-to-analog converter, an RS232 board, a patient-simulator interface to the monitor, and a multi-tasking software package for data conversion and communication with the monitor. This system "plays" patient data files into the monitor and saves beat classifications in detection files. Tests were performed using the MIT/BIH and AHA databases. Statistics were generated by comparing the detection files with the annotation files. These statistics were marginally different from those that resulted from the simulation. Differences were then examined. As expected, the differences were related to monitor hardware effects.

Algorithms↗
PubMed1992

Positron emission tomography in clinical practice.

Positron emission tomography (PET) has been considered a research tool; however, advances in hardware and software, along with availability of small medical cyclotrons, make clinical metabolic imaging feasible. There is accumulating data, especially in the areas of neurology and cardiology, to support its use in the appropriate clinical setting and patient population.

Adult↗
PubMed2003

Engineering requirements for a haptic simulator for knee arthroscopy training.

This paper describes the initial development of an innovative haptic device that will be integrated into an existing virtual reality training system for knee arthroscopy. The resulting system will be called WISHKATS (Warwick, Imperial, Sheffield Knee Arthroscopy Training System). This haptic device will enable the trainee to feel realistic forces on the probing tool and will work together with software, which will simulate tissue deformation. The proposed haptic system is a compact, multi-degree of freedom, motorised mechanism with force sensors, and will be used to simulate the diagnostic aspects of knee arthroscopy. There are a number of problems associated with the development of a suitable haptic system and this paper explores the engineering requirements of such a device.

Arthroscopy↗
PubMed2004

[The ultrastructure study of membrane surface of the bone marrow CD34+ cells with the atomic force microscope].

Human CD34(+) hematopoietic cells, a distinctive cell population containing hematopoietic stem/progenitor cells (HSPC), have the capability to highly self-renewal, differentiation into all lineages of committed progenitor cells and reconstitution of both long-term hematopoiesis and immunefunctions after transplantation. CD34(+) hematopoietic cells from bone marrow (BM) recently have been employed for treating neoplastic and genetic disorders. This study was aimed to investigate membrane surface ultrastructures of bone marrow CD34(+) cell from mormal persons and leukemia patients and to compare their morphologic differences by using atomic force microscope (AFM). BM was collected from 5 normal donors and 6 leukaemia patients. All samples were layered on Ficoll-Paque gradients (specific gravity 1.077 g/ml) to separate the mononuclear cells. After that CD34(+) cells were purified by immuno-magnetic bead separation and evaluated with a FACS Calibur, these cells were detected by AFM of tapping mode inair. At lest 20 cells per samples were observed. The results showed that most of CD34(+) hematopoietic cells were like circle plate, the diameter was 10 - 14 microm. The surface of CD34(+) hematopoietic cell membrane was comparatively complex. The surface of CD34(+) hematopoietic cell membrane appeared as granular, with packed particles. With the region analysis function of IP2.1 software, the region of 2 microm x 2 microm was selected and four parameters of the surface (maximum peak-to-valley distance, average roughness, root-mean-squared roughness and mean height) were measured. Values of the 4 parameters showed that the characteristic parameters of CD34(+) HSPC from leukaemia were higher than that from normal person. It is concluded that AFM has specific advantages in analyzing cell membrane in the nanometer level and can gain more information. With the help of analysis software, AFM can be a helpful tool for fast leukaemic diagnosis and CD34(+) hematopoietic cells selection.

Antigens, CD34↗
PubMed2005

[Long-term effect of stapes surgery on tympanosclerosis].

OBJECTIVE: To study the long-term effect of stapes surgery on tympanosclerosis and its influence factors. METHODS: The effect of stapes surgery on tympanosclerosis was retrospectively summed up in 119 patients (149 ears) in General Hospital of people's Liberation Army from April 1984 to March 2002. The Stata 7.0 software was used as a statistical tool. RESULTS: The average of hearing threshold (hearing level) of air conduction was (50.7 +/- 12.1) dB before operation, and the hearing loss was mostly on low frequency. Following-up the half-year post-operation, the average of hearing threshold of air conduction was (25.6 +/- 15.2) dB. The total successful rate of post-operation half year, 1 year, 2 and 5 years were 50.3%, 45.8%, 41.3% and 34.5%, respectively. Comparing the different operation methods, stapedotomy (piston technique) owned the best effect on hearing recovery (62.5%), then was stapedectomy (43.1%), but the last one was stapediolysis (30.8%). There was significant difference effect among three different operation methods (P < 0.05). The average of hearing threshold of air conduction was steadily within the first five-years following-up (Ridit analysis, P > 0.05), but obviously increased more than 5 years after operation (Ridit analysis, P < 0.05). The influence factors to successful rate were the following-up time post-operation, pathological changes of stapes, operative methods, and complications during operation, respectively. CONCLUSION: Stapes surgery is the effective method to treat tympanosclerosis, but the long-term effect is not good enough as expectation. It is important to select proper operation methods for better hearing results.

Adolescent↗
PubMed2005

Enabling on-demand real-time functional MRI analysis using grid technology.

OBJECTIVES: The analysis of brain imaging data such as functional MRI often requires considerable computing resources, which in most cases are not readily available in many medical imaging facilities. This lack of computing power makes it difficult for researchers and medical practitioners alike to perform on-site analysis of the generated data. This paper presents a system that is capable of analyzing functional MRI data in real time with results available within seconds after data acquisition. METHODS: The system employs remote computational servers to provide the necessary computing power. System integration is accomplished by an accompanying software package, which includes fMRI analysis tools, data transfer routines, and an easy-to-use graphical user interface. The remote analysis is transparent to the user as if all computations are performed locally. RESULTS: The use of PC clusters in the analysis of fMRI data significantly improved the performance of the system. Simulation runs fully achieved real-time performance with a total processing time of 1.089 s per image volume (64 x 64 x 30 in size), much less than the per volume acquisition time set to 3.0 s. CONCLUSIONS: The results show the feasibility of using remote computational resources to enable on-demand real-time fMRI capabilities to imaging sites. It also offers the possibility of doing more intensive analysis even if the imaging site doesn't have the necessary computing resources.

Brain↗
PubMed2005

Planning, modelling and assessing source control concepts on catchment scale.

Today's water management practice was identified often not to be consistently structured. Usually the decision space is not clearly depicted and then systematically explored. Often stakeholders are involved too late and many objectives are neglected. An adaptive DSS is being developed to help overcoming these problems. Core of the DSS is a "decision matrix", which has been implemented as a web based application (www.wsm300.de). The management objectives are represented by the indicators labelling the rows. They will be the result of a discussion of the objectives and problems in the specific sub-basin, which is supported by the catalogue of indicators. The columns of the matrix are specified by the scenarios whose development is supported by the database of measures and a Geographical Information System (GIS). The matrix, once the labels are defined, serves as a plot for the planning process, defining clearly which objectives have to be considered and which indicator-values have to be calculated. The DSS further includes a concept and tools for the combination of existing software components and supports the processing of model-outputs to indicator-values. Filled with the indicator-values the matrix allows a comparison of the scenarios and provides a good base for a decision. Multi-criteria decision aid methods can (if desired) further help to find the optimal scenario and to mediate between stakeholders. Finding the optimal scenario will likely be an iterative process.

Databases, Factual↗
PubMed1989

Computer-aided design in wheelchair seating.

This paper describes the integration of computer-aided design (CAD) with the design and fabrication of wheelchair seats. The use of CAD during the design phase permits personal seating for adult and pediatric clientele through a series of standard manufactured seating components. The advent of CAD has permitted the creation of databases of detailed 3-D wheelchair structures that are commercially available, in addition to most standard modular seating components. Direct on-screen manipulation of these components on any selected wheelchair structure is through user-friendly software. When using CAD, structural and physical limitations can be foreseen and taken into consideration during the routine initial fitting on an adjustable simulation fitting chair. The end product is a dimensioned drawing of the seating arrangement as it is positioned in the wheelchair structure. The seating components are manufactured from this drawing. The CAD system permits seating specialists to simulate a client's seating arrangement on the wheelchair in order to determine a functional position before the fabrication phase. Essentially, the CAD software is used as a simulation tool for creating functional seating units. It is also a design tool that allows access through a database to dimensional information about commercial seating products and seating products developed through the use of the CAD system.

Computer Graphics↗
PubMed1994

Computer-based patient record: the essential data set approach.

The clamor for data to study the impact of care, to evaluate clinical performance and justify resource utilization is increasing. The data in demand normally should exist in the record of a clinical encounter. Advances in information technology and software techniques have provided us with tools to develop and implement computer-based patient record systems. The issues that constrain development are integral issues of clinical medicine, such as the variability in medical data, specialized practice of medicine, and differing demands of the numerous end-users of a medical record. This paper describes an approach to develop a computer-based patient record. The focus is on identification of the essential data set by infological data modeling and its implementation in a commercially available package for a physician's office.

Computer Systems↗
PubMed1993

[Auto-training in radiology: the FORUM project applied to MRI of the uterus].

We describe the FORUM project which is a computer-assisted learning tool written with hypertext and hypermedia software emphasizing student interaction. This project is designed to allow the user to teach himself uterine Magnetic Resonance Imaging, which is a rapidly expanding technique with a wealth of specific findings. The program is currently available for Apple personal computers and is intended for beginners or confirmed radiologists and gynaecologists.

Computer User Training↗