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PubMedDate not supplied

Vibrotactile stimulation system to treat apnea of prematurity.

We modified a system that uses vibrotactile stimulation (VTS) to treat apnea (a cessation of respiration) in neonates in order to make the system more portable and easier to use by clinicians and nurses. The biomedical engineering department at Hartford Hospital (Hartford, CT) together with the Neonatology Division at the Connecticut Children's Medical Center (CCMC) (Hartford, CT) has been involved in developing the VTS system. Clinical trails were conducted in the neonatal intensive care unit of CCMC, and further preliminary data were collected. The main components of the system are a Tacaid vibrotactile stimulator (Audiological Engineering, Somerville, MA), a neonatal physiological monitor (Model 511; CAS Medical Inc, Branford, CT), a laptop computer running Windows 95 by Microsoft, National Instruments' data acquisition cards DAQCard-1200 and DAQCard-5102, and a software application developed by Premise Development Corporation, Hartford, CT. Heart rate, oxygen saturation, pulse, thoracic impedance, nasal airflow, and electrocardiogram are recorded from the monitor to the laptop. Whenever an apneic spell is detected, the nurse has the option of triggering a 3-second, 10-V, 250-Hz square-wave pulse to the transducer. The vibrotactile transducer is placed noninvasively with tape on the infant's thorax. This stimulus should arouse the infant and end the apneic event. To facilitate clinical study, the system provides voice and visual prompts for the clinician and nurses. Preliminary data continue to support both the safety and efficacy of the VTS.

Apnea↗

PubMed2005

htSNPer1.0: software for haplotype block partition and htSNPs selection.

BACKGROUND: There is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection. RESULTS: A heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm. CONCLUSION: htSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.

Algorithms↗

PubMed1996

An automated system for bedside verification of the match between patient identification and blood unit identification.

BACKGROUND: The administration of blood to the wrong patient remains the leading cause of acute hemolytic transfusion reactions and subsequent death. A process control system for blood administration was developed that verifies, at the bedside, the match between barcoded patient identification and blood unit identification. STUDY DESIGN AND METHODS: The system is composed of 1) a portable bedside scanner that reads barcoded patient identification and blood unit identification, 2) a host computer system capable of accepting transfusion data from the bedside scanner, 3) printed documentation of the transfusion episode, and 4) audit trail monitoring of whether all steps in the automated patient and blood unit identification process have been performed. Software design, development, and validation protocols followed industry standards. RESULTS: A pilot study was performed over a 2-month period evaluating the blood administration process using the computerized bedside transfusion identification system prototype for transfusions in 39 oncology patients. CONCLUSION: This system controls the blood administration process and includes bedside verification of the match between patient identification and blood unit identification.

Blood Transfusion↗

PubMed2006

Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry.

An efficient method was developed for toxicological drug screening in urine by liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry. The method relies on a large target database of exact monoisotopic masses representing the elemental formulae of reference drugs and their metabolites. Mass spectral identification is based on matching measured accurate mass and isotopic pattern (SigmaFit) of a sample component with those in the database. Data post-processing software was developed for automated reporting of findings in an easily interpretable form. The mean and median of SigmaFit for true-positive findings were 0.0066 and 0.0051, respectively. The mean and median of mass error absolute values for true-positive findings were 2.51 and 2.17 ppm, respectively, corresponding to 0.65 and 0.60 mTh. For routine screening practice, a SigmaFit tolerance of 0.03 and a mass tolerance of 10 ppm were chosen. Ion abundance differences from urine extracts did not affect the accuracy of the automatically acquired SigmaFit or mass values. The results show that isotopic pattern matching by SigmaFit is a powerful means of identification in addition to accurate mass measurement.

Algorithms↗

PubMed1986

Use of computerized information systems in U.S. health maintenance organizations and hospitals.

A comparison was made between the use of data processing in hospitals and Health Maintenance Organizations (HMOs). Findings indicate that the HMO and hospital data processing markets are currently quite distinct. As expected, the functions automated reflect the uses of the different care delivery systems. The hardware and software vendors to these markets are also different. A high percentage (50%) of HMOs are using software they developed in-house. In this respect, current HMO data processing is similar to the hospitals of a decade ago. The hospital market (for hardware and total systems) is highly concentrated. A few firms have a combined market share of over 50% and there are a large number of firms with very small shares. In the HMO market, there is a high concentration ratio for hardware but not for software or systems. HMOs and hospitals are almost uniformly satisfied with their hardware. Satisfaction with most applications is between 80 and 90% but there is a need, at least within HMOs, for improvements in support of the software supplied.

Data Collection↗

PubMed2004

Thallium SPECT-based stereotactic targeting for brain tumor biopsies. A technical note.

MR or CT images acquired under stereotactic conditions are often used to plan and guide brain tumor biopsies. The objective of this study was to design and test a methodology to increase target selection reliability by acquiring stereotactic 201Tl-SPECT data and by integrating them into the surgical planning. The three-headed Philips gamma camera system (Prism 3000) was adapted to stereotactic acquisitions (patient pallet, headholder). A software was developed for the stereotactic target determination based on SPECT images (pixel with the highest metabolic activity inside the tumor). The whole system accuracy was tested with the Elekta phantom adapted to SPECT imaging. The methodology was applied to one brain tumor biopsy. Comparison of the specific phantom coordinates evaluated in SPECT with the theoretical ones did not reveal any significant difference. In this way, our methodology including our homemade software (identification of the stereotactic frame, determination of the pixel with highest metabolic activity within the tumor in the stereotactic coordinate system) was validated. No significant geometric deformations were detected. Clinical feasibility was confirmed in 1 patient with a brain glioma. This study illustrates the feasibility and the accuracy of SPECT acquisitions with the stereotactic Leksell G-frame. The clinical relevance of this methodology is under evaluation. This definition of the target, based on the point with the highest metabolic activity within the tumor, might lead to improved diagnosis in biopsies and patient management. Furthermore, it might prepare the future for therapy aimed at delivering a therapeutic agent within a tumor.

Biopsy↗

PubMed2004

Handling multiple testing while interpreting microarrays with the Gene Ontology Database.

BACKGROUND: The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally. RESULTS: We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database. CONCLUSIONS: We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.

Animals↗

PubMed1989

Computerized schedules--one solution to variable workstyles.

A computerized scheduling program was developed to provide hospital anaesthetic coverage and yet still satisfy the complex workstyles of 30 anaesthetists. Hospital commitments required ten anaesthetists available each weekday and four each weekend day for after-hours coverage of the intensive care units and operating rooms. The workstyles included part-time arrangements, limited calls by some individuals, and calls restricted to certain anaesthetists with specific areas of expertise. Rules were defined to limit the proximity of late calls to avoid fatigue and computer software was developed. For each scheduling period, the program assists in making daily call assignments based on each anaesthetist's availability and a priority ranking system. It is flexible enough to allow personal preferences. The number and distribution of all calls scheduled are counted. When the assignments are completed, differences are reconciled. For two years, this program has proved superior to previous manual systems for scheduling this group of anaesthetists with variable workstyles.

Anesthesia Department, Hospital↗

PubMed1984

[Use of computers in forensic toxicology analysis].

For more than 10 years the analytical data gathered on nearly 600 drugs and other potentially poisonous substances that came up in our own investigations, as well as the pertinent bibliography, were stored in card indexes and lists. For immediate and fast recall via terminal we now store this cumulative data collection on magnetic tapes or disks in our clinic host computer. Extensive software was developed in FORTRAN compiler language to achieve rapid coordination of the data measured to that stored and consequently permit positive identification of unknown substances. The data obtained by different analytical methods such as TLC, GC, ultraviolet and infrared spectra, or HPLC can be evaluated by selective or sequential procedures using variable tolerances. That is also possible to enlarge and complete these data files in an easy manner using the same software.

Computers↗

PubMed2005

Anterior chamber width measurement by high-speed optical coherence tomography.

OBJECTIVE: To measure anterior chamber (AC) width and other dimensions relevant to the sizing of phakic intraocular lenses (IOLs) with a high-speed optical coherence tomography (OCT) system. DESIGN: Cross-sectional observational study. PARTICIPANTS: Both eyes of 20 normal volunteers. METHODS: A novel high-speed (4000 axial scans/second) OCT prototype was developed for anterior segment scanning. The system uses long wavelength (1310 nm) for deeper angle penetration, rectangular scanning for undistorted imaging, and short image acquisition time (0.125 seconds) to reduce motion error. Three horizontal cross-sectional OCT images (15.5 mm wide and 6 mm deep) of the anterior segment were obtained from each eye with real-time image display to guide centration on the corneal apex. Image processing software was developed to correct for image warping resulting from index transitions. Anterior chamber dimensions were measured using computer calipers by 3 expert raters (ophthalmologists). Analysis of variance was used to determine interrater, interimage, right versus left eye, and intersubject standard deviation (SD) of OCT measurements. MAIN OUTCOME MEASURES: Anterior chamber width (recess to recess), AC depth, and crystalline lens vault as measured by OCT; external white-to-white (WTW) corneal diameter (CD) as measured by Holladay-Godwin gauge. RESULTS: The mean AC width was 12.53+/-0.47 mm (intereye SD), and the mean corneal diameter was 11.78+/-0.57 mm. Optical coherence tomography measurement of AC width has good repeatability from image to image (SD, 0.134 mm), but there was significant difference between raters (SD, 0.215 mm). Estimation of AC width from WTW CD by linear regression was relatively inaccurate (residual SD, 0.41 mm). The mean AC depth was 2.99+/-0.323 mm (intereye SD), with repeatability of less than 0.001 mm (interimage SD), and the mean crystalline lens vault was 0.39+/-0.27 mm with 0.023 mm repeatability. CONCLUSIONS: Reproducible OCT AC biometry was demonstrated using a high-speed OCT prototype. Further improvement in reproducibility may be achieved by automating the measurements with a computer. Direct OCT AC width measurement may improve sizing of angle-supported AC IOLs over conventional estimation by WTW CD. The measurement of AC depth and lens vault also may be useful for other types of phakic AC IOLs.

Adult↗

PubMed2005

In vitro analysis of the cement mantle of femoral hip implants: development and validation of a CT-scan based measurement tool.

We developed, validated and assessed inter- and intraobserver reliability of a CT-scan based measurement tool to evaluate morphological characteristics of the bone-cement-stem complex of hip implants in cadaver femurs. Two different models were investigated: the stem-cavity model using a double tapered polished femoral-stem that is removed after cement curing and the plastic-replica model using a stereolithographic stem replica that is left in place during CT-scanning. Software was developed to segment and analyze connective CT-images and identify the contours of bone, cement, and stem based on their respective gray values. Volume parameters (whole specimen, cement, stem, air contents of bone and cement), concentricity parameters (distances between centroids of stem and cement, cement and bone, stem and bone), contact surfaces (bone/air and cement/bone) and bone cement mantle thickness parameters were calculated. A three-dimensional protocol was developed to evaluate the minimal mantle thickness out of the CT-plane. The average accuracy for surfaces within CT-images was 7.47 mm2 (1.80%), for bone and cement mantle thickness it was 0.51 mm (9.39%), for distances between centroids it was 0.38 mm (18.5%) and contours: 0.27 mm (2.57%). The intra- and interobserver reliability of air content in bone and cement was sub-optimal (intraclass-correlation coefficient (ICC) as low as 0.54 with an average ICC of 0.85). All other variables were reliable (ICC>0.81, average ICC: 0.96). This in vitro technique can assess characteristics of cement mantles produced by different cementing techniques, stem types or centralizers.

Arthroplasty, Replacement, Hip↗

PubMed2005

Development and applications of a software for Functional Image Registration (FIRE).

Image registration with anatomical modalities, such as CT and MRI, facilitates the anatomical identification and localization in the interpretation of nuclear medicine images that lack anatomical information. The implementation of Functional Image Registration (FIRE), an operating system (OS) and platform independent multimodal image registration software is reported. In order to register the images without an operator's interaction, several automatic algorithms were implemented. These include principal axes matching and maximization of the mutual information methods. The user interface was designed to support the manual registration of the images. Fused images were composed by overlaying one image with the other one transparently, in which the opacity of the overlaid image was interactively controlled. FIRE was successfully applied to many clinical cases for which automatic and/or manual registration was required. An OS and platform independent program for image registration developed in this study will be useful for the clinical application of image registration techniques.

Algorithms↗

PubMed2005

Randomized algorithms for motif detection.

MOTIVATION: Motif detection for DNA sequences has many important applications in biological studies, e.g. locating binding sites regulatory signals, designing genetic probes etc. In this paper, we propose a randomized algorithm, design an improved EM algorithm and combine them to form a software tool. RESULTS: (1) We design a randomized algorithm for consensus pattern problem. We can show that with high probability, our randomized algorithm finds a pattern in polynomial time with cost error at most x l for each string, where l is the length of the motif and can be any positive number given by the user. (2) We design an improved EM algorithm that outperforms the original EM algorithm. (3) We develop a software tool, MotifDetector, that uses our randomized algorithm to find good seeds and uses the improved EM algorithm to do local search. We compare MotifDetector with Buhler and Tompa's PROJECTION which is considered to be the best known software for motif detection. Simulations show that MotifDetector is slower than PROJECTION when the pattern length is relatively small, and outperforms PROJECTION when the pattern length becomes large. AVAILABILITY: It is available for free at http://www.cs.cityu.edu.hk/~lwang/software/motif/index.html, subject to copyright restrictions.

Algorithms↗

PubMed1986

Cephalometry with a video display computer.

A new technique to develop cephalometric analyses for orthodontic problems is illustrated. A digital analyzer of images is employed in our laboratory, and this allows us to get the X-ray picture digitized and displayed on both a black and white and a colour TV screen. All the cephalometric points are selected by an operator who watches a coloured cross which can be moved on the colour TV screen by means of a keyboard. A suitable software was developed to calculate linear and angular measurements. The cephalometric coloured lines appear at the top of the X-ray image and the data are displayed on a monitor, from which a print-out is obtained. Such a technique has some advantages: the X-ray image can be processed before the cephalometric analysis to enhance details, thus making the analysis more accurate; the cephalometric lines can be seen on the X-ray image displayed on the colour TV screen and can be photographed or stored on floppy or rigid disc.

Cephalometry↗

PubMed2006

Development and evaluation of different methods to assess download and display time of image web systems.

OBJECTIVES: The aim of this study was to develop and verify different methods of measuring time-to-display (TTD) for radiological images with image web systems (IWS). The process should be automatable in order to repeatedly perform a large number of measurements without human interaction. MATERIALS AND METHODS: Three methods were defined and compared with respect to usability, stability, and quality of results. Method 1 was based on Windows 2000 Performance Monitor, whereas method 2 employed phototransistors taped to the screen and connected to a separate PC. A software tool developed for method 3, which used Windows application programming interface (API) function, calls to read the color code assigned to specific pixels on the screen. RESULTS: Method 3 proved to be the most reliable and easy to automate. The accuracy is practically equivalent to method 2, but it proved to be far more automatable. Method 1 produced the largest mean error, was easily disturbed, but was also easy to set up and provided additional insights into the system's architecture especially if combined with method 3. CONCLUSIONS: To measure the performance of image distribution systems, any of these methods can be used, but method 3 proved to be superior.

Data Compression↗

PubMed2004

Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays.

We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted oligomers. It incorporates a novel use of position-specific scoring matrices, for the sensitive and specific identification of secondary binding sites anywhere in the target sequence. Using accelerated hardware is faster and more efficient than the traditional pairwise alignments used in most oligo-design software. Osprey consists of a module for target site selection based on user input, novel utilities for dealing with problematic sequences such as repeats, and a common code base for the identification of optimal oligonucleotides from the target list. Overall, these improvements provide a program that, without major increases in run time, reflects current DNA thermodynamics models, improves specificity and reduces the user's data preprocessing and parameterization requirements. Using a TimeLogic hardware accelerator, we report up to 50-fold reduction in search time versus a linear search strategy. Target sites may be derived from computer analysis of DNA sequence assemblies in the case of sequencing efforts, or genome or EST analysis in the case of microarray development in both prokaryotes and eukaryotes.

Binding Sites↗

PubMed2004

HEART: an automated beat-to-beat cardiovascular analysis package using Matlab.

A computer program is described for beat-to-beat analysis of cardiovascular parameters from high-fidelity pressure and flow waveforms. The Hemodynamic Estimation and Analysis Research Tool (HEART) is a post-processing analysis software package developed in Matlab that enables scientists and clinicians to document, load, view, calibrate, and analyze experimental data that have been digitally saved in ascii or binary format. Analysis routines include traditional hemodynamic parameter estimates as well as more sophisticated analyses such as lumped arterial model parameter estimation and vascular impedance frequency spectra. Cardiovascular parameter values of all analyzed beats can be viewed and statistically analyzed. An attractive feature of the HEART program is the ability to analyze data with visual quality assurance throughout the process, thus establishing a framework toward which Good Laboratory Practice (GLP) compliance can be obtained. Additionally, the development of HEART on the Matlab platform provides users with the flexibility to adapt or create study specific analysis files according to their specific needs.

Algorithms↗

PubMed2005

Digital chat reference in health science libraries: challenges in initiating a new service.

Digital reference service adds a valuable new dimension to health science reference services, but the road to implementation can present questions that require carefully considered decisions. This article incorporates suggestions from the published literature, provides tips from interviews with practicing academic health science librarians, and reports on data from students' exploration of academic health science library Web sites' digital reference services. The goal of this study is to provide guidelines to plan new services, assess user needs, and select software, and to showcase potential benefits of collaboration and proactive and user-friendly marketing. In addition, tips for successful operation and evaluation of services are discussed.

Computer Communication Networks↗