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At least 487 records · Page 27Linked to original sources

Segmentation of breast tumor in three-dimensional ultrasound images using three-dimensional discrete active contour model.

In this paper, we apply the three-dimensional (3-D) active contour model to a 3-D ultrasonic data file for segmenting of the breast tumor. The 3-D ultrasonic file is composed of a series of two-dimensional (2-D) images. Most of traditional techniques of 2-D image segmentation will not use the information between adjacent images. To suit the property of the 3-D data, we introduce the concept of the 3-D stick, the 3-D morphologic process and the 3-D active contour model. The 3-D stick can get over the problem that the ultrasonic image is full of speckle noise and highlight the edge information in images. The 3-D morphologic process helps to determine the contour of the tumor and the resulting contour can be regarded as the initial contour of the active contour model. Finally, the 3-D active contour model will make the initial contour approach to the real contour of the tumor. However, there is emphasis on these 3-D techniques that they do not consist of a series of 2-D techniques. When they work, they will consider the horizontal, vertical and depth directions at the same time. The use of these 3-D techniques not only segments the 3-D shape but also obtains the volume of the tumor. The volume of the tumor calculated by the proposed method will be compared with the volume calculated by the VOCAL software with the physician's manually drawn shape and it shows that the performance of our method is satisfactory.

Breast Neoplasms↗

Testosterone use in men and its effects on bone health. A systematic review and meta-analysis of randomized placebo-controlled trials.

CONTEXT: Androgen-deficient men are at increased risk of osteoporosis. The extent to which testosterone can prevent and treat osteoporosis in men remains unclear. OBJECTIVE AND DESIGN: We performed a systematic review and meta-analysis of randomized placebo-controlled trials in men to estimate the effect of testosterone use on bone health outcomes. DATA SOURCES: The review encompassed librarian-designed search strategies using MEDLINE (1966 to March 2005), EMBASE (1988 to March 2005), and Cochrane CENTRAL (inception to March 2005); a review of reference lists from included studies; and content expert files. DATA COLLECTION: Independently and in duplicate, we assessed the methodological quality of the eligible trials and collected data on bone mineral density and bone fractures at the longest point of complete follow-up. DATA SYNTHESIS: We included eight trials enrolling 365 patients. Two trials followed patients for more than 1 yr. Meta-analysis of these trials showed that, compared with placebo, im testosterone was associated with an 8% (95% confidence interval, 4%, 13%) gain in lumbar bone mineral density and transdermal testosterone had no significant impact. Testosterone use was associated with a nonsignificant 4% (95% confidence interval, -2%, 9%) gain in femoral neck bone mineral density with unexplained differences in results across trials (26% of these differences were not explained by chance alone). No trials measured or reported the effect of testosterone on fractures. CONCLUSIONS: Intramuscular testosterone moderately increased lumbar bone density in men; the results on femoral neck bone density are inconclusive. Without bone fracture data, the available trials offer weak and indirect inferences about the clinical efficacy of testosterone on osteoporosis prevention and treatment in men.

Bone Density↗

Mental health supplement to the Ontario Health Survey: methodology.

OBJECTIVE: To describe the methodology of a province-wide, cross-sectional, epidemiologic study of psychiatric disorder among those aged 15 years and over living in household dwellings in Ontario. METHOD: Respondents for the survey were drawn from households (N = 13002) participating in a province-wide health survey. One person per household was selected, and 9953 (76.5%) participated. RESULTS: Participants and nonparticipants were similar to each other. An extensive array of data, including measures of psychiatric disorder classified using a revised version of the Composite International Diagnostic Interview (CIDI), are available for all respondents. CONCLUSIONS: The Ontario Health Supplement is contained in a public-use data file at the Ontario Ministry of Health and is available to investigators for study. A strong survey design, careful measurement, and acceptable levels of response provide the rationale for our inviting researchers to access and use the Ontario Health Supplement data base.

Adolescent↗

Survey highlights trends in managing Medicare drug costs.

Data File: Before you assume risk for your Medicare risk plan's pharmacy benefit, you ought to understand what the benefit is, how it works, and how much it's likely to cost you. Find out the latest trends and benchmark data in managed Medicare pharmacy from a recent survey.

Aged↗

Senior-age population growth may redefine 'frail elderly'.

Data File: A key to future success in Medicare risk may be how well you manage your frail elderly members who have multiple health problems and chronic conditions. While they may just be a handful of patients in your panel now, data from the U.S. Census Bureau show their numbers are growing.

Aged↗

AAQUANT: a computer program for quantitative amino acid analysis of proteins and peptides.

Quantitative amino acid analysis is an important tool used in the characterization and structural determination of peptides and proteins. A new computer program, AAQUANT, has been developed specifically to aid researchers in analyzing amino acid composition data. AAQUANT calculates amino acid recoveries, including 95% confidence intervals, following acid hydrolysis of peptides and proteins, and also includes useful routines to locate regions of a specified amino acid composition in known protein sequences, compute amino acid composition reports of known protein sequences, generate proteolytic digestion maps of proteins, and create and edit protein sequence data files. This report describes the AAQUANT routines, and demonstrates the use of the program.

Amino Acid Sequence↗

SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project.

The multidisciplinary UCSF Pharmacogenetics of Membrane Transporters project seeks to systematically identify sequence variants in transporters and to determine the functional significance of these variants through evaluation of relevant cellular and clinical phenotypes. The project is structured around four interacting cores: genomics, cellular phenotyping, clinical phenotyping, and bioinformatics. The bioinformatics core is responsible for collecting, storing, and analyzing the information obtained by the other cores and for presenting the results, in particular, for the genomic data. Most of this process is automated using locally developed software written in Python, an open source language well suited for rapid, modular development that meets requirements that are themselves constantly evolving. Here we present the details of transforming ABI trace file data into useful information for project investigators and a description of the types of data analysis and display that we have developed.

Amino Acid Sequence↗

Anemia in pregnancy and race in the United States: blacks at risk.

OBJECTIVES: This study's objectives were to determine the national prevalence of anemia in pregnancy (AIP) in the United States, compare racial differences in the prevalence, compare the AIP risk factor profiles between non-Hispanic whites and non-Hispanic blacks, and to analyze the associations between AIP and some maternal and fetal/neonatal complications between whites and blacks. METHODS: The data used were from the United States natality data files (1995 through 2000), which included 23,654,695 live births. All mothers diagnosed with AIP, defined as hemoglobin-concentration < 10 g/dl, were included. The cohorts were analyzed in two groups. The "whole group" (WG) comprised all women in the data set who had anemia status reported. The "low-risk group" (LRG) comprised women with low-risk factors for AIP. Race was determined by mothers' skin colors and racial self-identifications. Logistic regression was used to explore associations between race and AIP while controlling for other covariates. RESULTS: The national prevalence of AIP among the general population was 21.55/1,000 among the WG and 11.51/1,000 among the LRG. Among the WG, the prevalence of AIP was two times higher among non-Hispanic blacks (35.38/1,000) than among non-Hispanic whites (18.02/1,000). Among the LRG, the prevalence was 1.94 times higher among non-Hispanic blacks (20.44/1,000) than among non-Hispanic whites (10.63/1,000). The other risk factor profiles for AIP were similar among the races. Many serious maternal and fetal/neonatal complications occurred more frequently among anemic patients when compared with non-anemic patients. CONCLUSIONS: The results of this study showed that black race was significantly associated with higher risk of AIP. The other risk factor profiles of AIP were significantly similar between whites and blacks. This study also confirmed that AIP was significantly associated with some serious maternal and fetal/neonatal complications. The findings of this study indicate that race is an important risk factor of AIP.

Anemia↗

A multichannel electronic monitor of acoustic behaviors, and software to parse individual channels.

We designed an electronic device to monitor calling behavior in male crickets. The device and its associated software can record to disk the activity of as many as 16 individuals simultaneously. The data recorded contain detailed information about the temporal structure of each individual's calls. The temporal resolution achieved with an ordinary PC is good enough to detect and record the occurrence of every pulse of sound from each cricket. The resulting data files are efficient and compact, and so the system is appropriate for experiments lasting many days.

Acoustics↗

Automated data collection and processing for a cycle ergometer.

A system is described for collection and processing of data from a cycle ergometer. Cycle pedals, specially made to withstand the extremely high forces exerted during maximal power cycling, contain transducers to measure pedal angle relative to the crank and foot forces both perpendicular and parallel to the pedal surface. An additional transducer monitors crank position. Output signals are conditioned, amplified, digitized by a 12-bit analog-to-digital converter, fed into a computer at 100 Hz/channel, and mathematically smoothed to attenuate noise. For each sample interval, foot force components perpendicular and parallel to the crank arm are calculated. Power generated on each crank revolution is determined from transducer information. Computer graphics display pedaling parameters vs. crank angle in both rectangular and circular format. Data files containing variables descriptive of pedaling force curves are produced to enable computerized statistical analysis of cycling performance.

Computer Graphics↗

Authentication and management of radiologic reports: value of a computer workstation integrated with a radiology information system.

An increasing number of radiology departments are using computers to facilitate management of radiologic information. Transcription, storage, and printing of radiologic reports are among the primary functions of a radiology information system. Consequently, manual signature of radiologic reports is being replaced by on-line electronic authentication. However, the utilities provided on most radiology information systems to review, edit, and otherwise manipulate radiologic reports are relatively crude compared with commercial word-processing and data-base management software available for personal computers. We have developed a personal computer software system that is integrated with our existing radiology information system; expedites the radiologist's task of reviewing, editing, and authenticating (i.e., signing) radiologic reports; provides a teaching file data base on the workstation into which radiologic reports and patients' demographics can be instantly transferred; and provides a similar data base to facilitate follow-up on those examinations deemed appropriate for quality-assurance procedures. These features improve the radiologist's efficiency and increase his or her willingness to more fully exploit the intended purposes of a radiology information system.

Humans↗

A new combined integral-light and slit-scan data analysis system (DAS) for flow cytometry.

Flow cytometry using list mode parameters such as fluorescence emission, light scatter and size on one hand and different slit-scan parameters on the other hand needs a fast, flexible, efficient and easy-to-use data analysis software. A new software package (data analysis system, DAS) has been developed that integrates data analysis for conventional (integral-light) flow cytometry and for slit-scan flow cytometry. The requirements, design and some examples are discussed and an implementation for IBM-compatible computers is presented. Special attention is directed to the handling of different data types from one-parameter histograms to multiparameter slit-scan data files. The package can be used as an interpreting programming language or as an interactive menu-driven command line interpreter with a large number of graphic, mathematical and statistical functions. DAS is not limited to use in flow cytometry only, but multidimensional data analysis, from astronomy to economics, can be done as well.

Data Display↗

The National Survey of Children's Health: a new data resource.

CONTEXT: Federal and state maternal and child health programs are responsible for promoting and improving the health and well-being of children. To support achievement of this goal, the federal Maternal and Child Health Bureau (MCHB) in partnership with the National Center for Health Statistics (NCHS), Centers for Disease Control and Prevention has developed a new survey that will provide uniform national and state data on the health and well-being of children, as well as the characteristics of their families and neighborhoods. PURPOSE: The National Survey of Children's Health was designed to produce reliable and representative state- and national-level estimates for Healthy People 2010 national prevention objectives, for each state's Title V needs assessment, and for Title V program planning and evaluation. In addition, it will provide a new data resource for researchers, advocacy groups, and other interested parties. It is anticipated that this survey will be repeated periodically, making trend analysis possible. METHODS: This survey was conducted using the State and Local Area Integrated Telephone Survey (SLAITS) mechanism, which shares the random-digit-dial sampling frame of the National Immunization Survey (sponsored by the National Immunization Program and NCHS). Using the SLAITS platform, interviews on approximately 2000 children were conducted in each state and the District of Columbia. The parent or guardian most knowledgeable about the child completed a battery of questions on health and development, health insurance coverage, access to care, utilization of health care services, presence of a medical home, family functioning, parental health, and neighborhood characteristics. Data collection began in January 2003 and continued through April 2004. Summary reports and electronic data files will be available to the public by early 2005. CONCLUSION: This is the second state and national survey jointly completed by MCHB and NCHS. It is designed to complement the 2001 National Survey of Children with Special Health Care Needs by providing data on the health of the general child population.

Centers for Disease Control and Prevention, U.S.↗

Comparison of x-ray cross sections for diagnostic and therapeutic medical physics.

The purpose of this technical report is to make available an up-to-date source of attenuation coefficient data to the medical physics community, and to compare these data with other more familiar sources. Data files from Lawrence Livermore National Laboratory (in Livermore, CA) were truncated to match the needs of the medical physics community, and an interpolation routine was written to calculate a continuous set of cross sections spanning energies from 1 keV to 50 MeV. Coefficient data are available for elements Z = 1 through Z = 100. Values for mass attenuation coefficients, mass-energy-transfer coefficients, and mass-energy absorption coefficients are produced by a single computer subroutine. In addition to total interaction cross sections, the cross sections for photoelectric, Rayleigh, Compton, pair, and some triplet interactions are also produced by this single program. The coefficients were compared to the 1970 data of Storm and Israel over the energy interval from 1 to 1000 keV; for elements 10, 20, 30, 40, 50, 60, 70, and 80, the average positive difference between the Storm and Israel coefficients and the coefficients reported here are 1.4%, 2.7%, and 2.6%, for the mass attenuation, mass energy-transfer, and mass-energy absorption coefficients, respectively. The 1969 data compilation of mass attenuation coefficients from McMaster et al. were also compared with the newer LLNL data. Over the energy region from 10 keV to 1000 keV, and from elements Z = 1 to Z = 82 (inclusive), the overall average difference was 1.53% (sigma = 0.85%). While the overall average difference was small, there was larger variation (> 5%) between cross sections for some elements. In addition to coefficient data, other useful data such as the density, atomic weight, K, L1, L2, L3, M, and N edges, and numerous characteristic emission energies are output by the program, depending on a single input variable. The computer source code, written in C, can be accessed and downloaded from the World Wide Web at: http:@www.aip.org/epaps/epaps.html [E-MPHSA-23-1977].

Biophysical Phenomena↗

Microprocessors as intelligent front-end devices for medical-information systems.

Computer technology has produced increasingly powerful systems whose miniaturization has spawned the term microprocessor. The role of microcomputers is optimal if they are linked to larger systems in a distributed, hierarchical network with each element performing those functions for which it is best suited. Obstacles to the development of such a network include incompatibilities in operating systems, application languages, file structures, and communication protocols. Some attempts to address these problems are briefly reviewed. Given the availability on an effective distributed hierarchy of computers, the microprocessor can be useful in a number of functions requiring rapid response and limited access to large, central data files. Examples of such activities in the medical-information environment included program development and testing, forms entry, and text-management systems. With adequate attention to the systems support as well as the development of effective application techniques, the role of microprocessor-based intelligent terminals will inevitably expand rapidly in coming years.

Computers↗

Umbilical artery catheters in the newborn: effects of position of the catheter tip.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: To determine whether the position of the tip of an umbilical arterial catheter influences the frequency of ischemic events, aortic thrombosis, intraventricular hemorrhage, mortality or necrotising enterocolitis in newborn infants. SEARCH STRATEGY: Randomized and quasi randomized controlled trials of umbilical catheterization use were obtained from the following sources: 1. Effective Care of the Newborn Infant, edited by JC Sinclair and MB Bracken. 2. Medline Search using Melvyl Medline Plus and the keyword headings 'Umbilic#', 'Catheter#' and subject heading 'Infant, Newborn' 3. Search of personal data files SELECTION CRITERIA: Randomized trials in newborn infants of any birthweight or gestation. Comparison of high catheter placement with the tip above the diaphragm to a lower position just above the aortic bifurcation. Clinically important end points such as ischemic events or aortic thrombosis. DATA COLLECTION AND ANALYSIS: Five randomized controlled trials and one alternate assignment study had sufficiently detailed data to allow interpretation. MAIN RESULTS: High placed umbilical artery catheters are associated with a lower incidence of clinical vascular complications, without an increase in any adverse sequelae. Intraventricular hemorrhage rates, death and necrotising enterocolitis are not more frequent with high compared to low catheters. REVIEWER'S CONCLUSIONS: There appears to be no evidence to support the use of low placed umbilical artery catheters. High catheters should be used exclusively.

Catheterization↗

A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via Internet.

Proteome analysis by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry, in combination with protein chemical methods, is a powerful approach for the analysis of the protein composition of complex biological samples. Data organization is imperative for efficient handling of the vast amount of information generated. Thus we have constructed a 2-D PAGE database to store and compare protein patterns of cell-associated and culture-supernatant proteins of different mycobacterial strains. In accordance with the guidelines for federated 2-DE databases, we developed a program that generates a dynamic 2-D PAGE database for the World-Wide-Web to organise and publish, via the internet, our results from proteome analysis of different Mycobacterium tuberculosis as well as Mycobacterium bovis BCG strains. The uniform resource locator for the database is http://www.mpiib-berlin.mpg.de/2D-PAGE and can be read with a Java compatible browser. The interactive hypertext markup language documents displayed are generated dynamically in each individual session from a rational data file, a 2-D gel image file and a map file describing the protein spots as polygons. The program consists of common gateway interface scripts written in PERL, minimizing the administrative workload of the database. Furthermore, the database facilitates not only interactive use, but also worldwide active participation of other scientific groups with their own data, requiring only minimal computer hardware and knowledge of information technology.

Bacterial Proteins↗

Querying the public databases for sequences using complex keywords contained in the feature lines.

BACKGROUND: High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords. RESULTS: We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use. CONCLUSION: Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs.

Database Management Systems↗