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PubMed2006

Supporting the SBML layout extension.

MOTIVATION: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted format. SUMMARY: Two modules, SBMLSupportLayout and SBWAutoLayout, support reading, creating, manipulating and writing layout information for biochemical models. SBMLSupportLayout can read, update, add and render model layout information. SBWAutoLayout can automatically layout models, graphically manipulate model layout and generate layout information for models without layout information. AVAILABILITY: SBMLSupportLayout and SBWAutoLayout are distributed with the Systems Biology Workbench (SBW), which can be downloaded from http://www.sys-bio.org. Additionally, their visualization and layout capabilities are available online at http://www.sys-bio.org/Layout. Both modules run on Win32, Linux and the Mac OS X version is forthcoming.

Algorithms↗

PubMed1987

Evaluation of multiple component relaxation training with developmentally disabled persons.

Prior studies evaluating the response of developmentally disabled persons to relaxation training procedures are largely limited to case study reports. Most often relaxation training procedures are vaguely described in these studies, and limited outcome measures are employed. In the present comparative group outcome study a specific progressive muscle relaxation training procedure was combined with auditory electromyographic (EMG) biofeedback, modeling, and reinforcement procedures in an attempt to teach relaxation skills to mentally retarded persons (N = 32) who functioned in the profound to mild range. The procedure was effective in reducing experimental group subjects' EMG levels, F (1,28) = 6.39, p less than .05, and activity level as measured with an interval recording behavior rating procedure, F (1,28) = 58.05, p less than .05. No effect was found on peripheral skin temperature. Additionally, no significant difference between the response of low functioning and high functioning subjects was seen indicating that intellectual level and adaptive behavior level failed to predict success in treatment. Scoring on a simple behavioral assessment designed to measure receptive language skills and modeling abilities thought to relate to relaxation training success also failed to correlate with outcome measures. The need to develop other predictors of relaxation training success with a mentally retarded population is discussed.

Adult↗

PubMed1998

Conceptual integration of information databases into an Intranet.

Large information systems handle massive volume of data stored in heterogeneous sources of information. Each server has its own model of concepts representation with regard to its aims. One of the main problems encountered by end-users when accessing different servers is to match their own viewpoint on biomedical concepts with their various representations that are made in the database servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet, and to propose a method to realize it. Moreover, this method provides designers of web sites with a powerful tool to manage them on the basis of an ontology of the biomedical domain. This method is based on the knowledge sources provided by the Unified Medical Language System project of the U.S. National Library of Medicine and exploits intensively the conceptual graphs theory.

Computer Communication Networks↗

PubMed2001

Visual and visuospatial development in young children with Williams syndrome.

This study investigated the relation between sensory visual problems and the severity of visuospatial difficulties in a large group of young children with Williams' syndrome (WS). A questionnaire describing visual and associated problems was completed by the families of 108 children with WS and detailed follow-up assessments were conducted, including visual, spatial, motor, visuocognitive, and linguistic tests of 73 of these children (mean age 7 years 3 months; 40 males, 73 females). Children with WS showed a much higher incidence of common paediatric sensory vision problems (strabismus, visual acuity loss, amblyopia, reduced stereopsis) than normally developing children. It was found that delays with respect to age normative values increased with age on all tests. No significant correlation was found between the presence of a visual deficit and the severity of the visuospatial problems, suggesting that the difficulties children with WS have in understanding spatial arrangements are not simply a result of their earlier sensory visual problems. Results confirm the dissociation between visuospatial and language abilities in children with WS, and support the neurobiological model of a split between ventral and dorsal stream processing of visual information with a generalized deficit in dorsal stream processing in young children with WS.

Amblyopia↗

PubMed1996

Temporal processing asymmetries between the cerebral hemispheres: evidence and implications.

This paper reviews a large body of research which has investigated the capacities of the cerebral hemispheres to process temporal information. This research includes clinical, non-clinical, and electrophysiological experimentation. On the whole, the research supports the notion of a left hemisphere advantage for temporal resolution. The existence of such an asymmetry demonstrates that cerebral lateralisation is not limited to the higher-order functions such as language. The capacity for the resolution of fine temporal events appears to play an important role in other left hemisphere functions which require a rapid sequential processor. The functions that are facilitated by such a processor include verbal, textual, and fine movement skills. The co-development of these functions with an efficient temporal processor can be accounted for with reference to a number of evolutionary scenarios. Physiological evidence favours a temporal processing mechanism located within the left temporal cortex. The function of this mechanism may be described in terms of intermittency or travelling moment models of temporal processing. The travelling moment model provides the most plausible account of the asymmetry.

Journal Article↗

PubMed1990

An object oriented user interface for analysis of biological data.

In a previous paper we described a self-documented file and a collection of general purpose programs or tools that facilitates the management and analysis of biological data. The tools can be specified in a pipeline to accomplish a specific analysis task. However, we found that it was difficult for investigators to learn the UNIX command language for specifying pipelines, specify selection tasks through a command language, and visualize the data as they were transformed and rearranged. To alleviate these problems we developed an object-oriented user interface for the pipeline programs. The system consists of four major programs for visualization: Vedit, Vgraf, Vscan, and V spread. Vedit is a simple text editor, Vgraf is a flexible graphics program, Vscan facilitates scanning graphically through large files, and Vspread provides spreadsheet-like capabilities. To demonstrate how the visualization programs are used together to accomplish the needed analysis we describe two case studies and then discuss how well the system accomplished the goals of visualization, short learning curve, and user adaptability.

Biology↗

PubMed2005

The importance of modality specificity in diagnosing central auditory processing disorder.

PURPOSE: This article argues for the use of modality specificity as a unifying framework by which to conceptualize and diagnose central auditory processing disorder (CAPD). The intent is to generate dialogue and critical discussion in this area of study. METHOD: Research in the cognitive, behavioral, and neural sciences that relates to the concept of modality specificity was reviewed and synthesized. RESULTS: Modality specificity has a long history as an organizing construct within a diverse collection of mainstream scientific disciplines. The principle of modality specificity was contrasted with the unimodal inclusive framework, which holds that auditory tests alone are sufficient to make the CAPD diagnosis. Evidence from a large body of data demonstrated that the unimodal framework was unable to delineate modality-specific processes from more generalized dysfunction; it lacked discriminant validity and resulted in an incomplete assessment. Consequently, any hypothetical model resulting from incomplete assessments or potential therapies that are based on indeterminate diagnoses are themselves questionable, and caution should be used in their application. CONCLUSIONS: Improving specificity of diagnosis is an imperative core issue to the area of CAPD. Without specificity, the concept has little explanatory power. Because of serious flaws in concept and design, the unimodal inclusive framework should be abandoned in favor of a more valid approach that uses modality specificity.

Brain↗

PubMed1994

Educational interpreting and teacher preparation. An interdisciplinary model.

Educational interpreting remains the fastest growing area in the field of interpreting largely due to the Individual with Disabilities Education Act and the Americans with Disabilities Act. The United States Department of Education, Personal Preparation and Special Topics, has awarded grants to a number of organizations, agencies, colleges and universities to establish preparation programs for educational interpreters. This article describes how resources, namely the curriculum, extant in a teacher preparation program in deafness are used in establishing a four year preparation program for educational interpreters leading to a Bachelor of Science degree. The interdisciplinary model outlined follows the curriculum recommendations of the Council on Education of the Deaf/Registry of Interpreters for the Deaf Ad Hoc Committee for Educational Interpreting.

Curriculum↗

PubMed2004

Bariatric surgery: a systematic review and meta-analysis.

CONTEXT: About 5% of the US population is morbidly obese. This disease remains largely refractory to diet and drug therapy, but generally responds well to bariatric surgery. OBJECTIVE: To determine the impact of bariatric surgery on weight loss, operative mortality outcome, and 4 obesity comorbidities (diabetes, hyperlipidemia, hypertension, and obstructive sleep apnea). DATA SOURCES AND STUDY SELECTION: Electronic literature search of MEDLINE, Current Contents, and the Cochrane Library databases plus manual reference checks of all articles on bariatric surgery published in the English language between 1990 and 2003. Two levels of screening were used on 2738 citations. DATA EXTRACTION: A total of 136 fully extracted studies, which included 91 overlapping patient populations (kin studies), were included for a total of 22,094 patients. Nineteen percent of the patients were men and 72.6% were women, with a mean age of 39 years (range, 16-64 years). Sex was not reported for 1537 patients (8%). The baseline mean body mass index for 16 944 patients was 46.9 (range, 32.3-68.8). DATA SYNTHESIS: A random effects model was used in the meta-analysis. The mean (95% confidence interval) percentage of excess weight loss was 61.2% (58.1%-64.4%) for all patients; 47.5% (40.7%-54.2%) for patients who underwent gastric banding; 61.6% (56.7%-66.5%), gastric bypass; 68.2% (61.5%-74.8%), gastroplasty; and 70.1% (66.3%-73.9%), biliopancreatic diversion or duodenal switch. Operative mortality (< or =30 days) in the extracted studies was 0.1% for the purely restrictive procedures, 0.5% for gastric bypass, and 1.1% for biliopancreatic diversion or duodenal switch. Diabetes was completely resolved in 76.8% of patients and resolved or improved in 86.0%. Hyperlipidemia improved in 70% or more of patients. Hypertension was resolved in 61.7% of patients and resolved or improved in 78.5%. Obstructive sleep apnea was resolved in 85.7% of patients and was resolved or improved in 83.6% of patients. CONCLUSIONS: Effective weight loss was achieved in morbidly obese patients after undergoing bariatric surgery. A substantial majority of patients with diabetes, hyperlipidemia, hypertension, and obstructive sleep apnea experienced complete resolution or improvement.

Adolescent↗

PubMed1993

NONMEM version III implementation on a VAX 9000: a DCL procedure for single-step execution and the unrealized advantage of a vectorizing FORTRAN compiler.

There is great interest within the FDA, academia, and the pharmaceutical industry to provide more detailed information about the time course of drug concentration and effect in subjects receiving a drug as part of their overall therapy. Advocates of this effort expect the eventual goal of these endeavors to provide labeling which reflects the experience of drug administration to the entire population of potential recipients. The set of techniques which have been thus far applied to this task has been defined as population approach methodologies. While a consensus view on the usefulness of these techniques is not likely to be formed in the near future, most pharmaceutical companies or individuals who provide kinetic/dynamic support for drug development programs are investigating population approach methods. A major setback in this investigation has been the shortage of computational tools to analyze population data. One such algorithm, NONMEM, supplied by the NONMEM Project Group of the University of California, San Francisco has been widely used and remains the most accessible computational tool to date. The program is distributed to users as FORTRAN 77 source code with instructions for platform customization. Given the memory and compiler requirements of this algorithm and the intensive matrix manipulation required for run convergence and parameter estimation, this program's performance is largely determined by the platform and the FORTRAN compiler used to create the NONMEM executable. Benchmark testing on a VAX 9000 with Digital's FORTRAN (v. 1.2) compiler suggests that this is an acceptable platform. Due to excessive branching within the loops of the NONMEM source code, the vector processing capabilities of the KV900-AA vector processor actually decrease performance. A DCL procedure is given to provide single step execution of this algorithm.

Algorithms↗

PubMed1994

Limitations of angiography for analyzing coronary atherosclerosis progression or regression.

PURPOSE: To analyze the utility and limitations of serial coronary angiography for determining atherosclerosis progression and regression. DATA SOURCES: A MEDLINE search of the English-language literature (1966 to January 1994) using the keywords atherosclerosis regression, atherosclerosis progression, lipid reduction therapy, and coronary angiography. STUDY SELECTION: Selected articles on the effects of cholesterol reduction and lifestyle modification on angiographic coronary artery disease, on the animal models of atherosclerosis progression and regression, and on the limitations of coronary angiography. DATA EXTRACTION: Independent extraction by two authors. RESULTS: Although several studies have reported that the rate of atherosclerosis progression, defined by serial coronary angiography, can be reduced and that luminal diameter can be improved somewhat by aggressive lipid modification, the reported changes are small (0.3 mm or 10% change) and have required a prolonged study duration (range, 1 to 10 years). More importantly, angiography simply does not measure atherosclerosis and cannot assess lesion composition. Angiography also underestimates the extent of atherosclerosis, especially in angiographically normal segments. In addition, difficulties with data acquisition, such as substantial variabilities in serial measurements of percent diameter stenosis and minimal luminal diameters, require large sample sizes to show statistically significant regression, even with computerized quantification. CONCLUSIONS: Given its current limitations, serial coronary angiography is not a satisfactory means of detecting atherosclerosis progression or regression.

Anticholesteremic Agents↗

PubMed2000

Lupus erythematosus and nutrition: a review of the literature.

The purpose of this review was to search the scientific literature for dietary compounds that alleviate or exacerbate symptoms of lupus erythematosus (LE) in both animal and human models. A detailed literature review was undertaken to find articles showing a relationship between LE and nutrition by using MEDLINE/INDEX MEDICUS (1950-March 2000) for English-language articles, followed by cross-referencing. Aggravating substances appear to include excess calories, excess protein, high fat (especially saturated and omega-6 polyunsaturated fatty acids), zinc, iron, and L-canavanine found in alfalfa tablets. Possible beneficial dietary compounds include vitamin E, vitamin A (beta-carotene), selenium, fish oils (omega-3 polyunsaturated fatty acids), evening primrose oil, flaxseed, a plant herb (Tripterygium wilfordii), dehydroepiandrosterone, and calcium plus vitamin D (if taking corticosteroids). Some people with systemic LE placed on food allergy elimination diets reported improvement in their LE symptoms; however, this may be related to a decrease of other substances in the diet. Also, although no direct evidence was reported on the beneficial effects of either bromelain or a vegetarian diet (possibly allowing fish), it is suggested that they might be beneficial. Limitations to this research are that the findings are based on relatively few studies, many of which were without control groups or extrapolated from animal models. No large-scale studies have been performed with LE patients to substantiate the benefit, if any, of these individual dietary interventions, and if they were conducted, the remission and exacerbation pattern of LE may interfere with elucidating their effectiveness. Also, dietary changes should not be attempted without a physician's approval/monitoring.

Animals↗

PubMed2004

Environmental and individual influences on Australian young adults' likelihood of attending university: a follow-up study.

In this longitudinal study, which is a follow-up analysis of a previous investigation (K. Marjoribanks, 2002a), the author examined environmental and individual influences on the likelihood of Australian young adults attending university. Participants were 5,181 Anglo-Australian (parents born in Australia, English was the language of the family), 460 Asian, 699 English (parents born in England), 746 European, and 163 Middle Eastern students (M age = 14.7 years, when the study began). The analyses indicated that Asian, European, and Middle Eastern young adults were more likely to attend university than were young adults from Anglo-Australian and English families, and young women had higher odds of attending university than did young men. Family social status variations in the likelihood of university attendance could be explained by differences in individual characteristics and proximal learning environments. Adolescents' individual characteristics and proximal learning environments combined to have a large independent association with the decision to attend university.

Adolescent↗

PubMed2001

[Measuring fatigue of cancer patients in the German-speaking region: development of the Fatigue Assessment Questionnaire].

UNLABELLED: Fatigue is recognised as one of the most frequent and distressing symptoms of patients with cancer. Whilst causal relationships mainly remain unclear, researchers meanwhile acknowledge its multidimensional nature. Causes and manifestations are complex and multifaceted and therefore, measurement in the past has been difficult. In recent years, some instruments have been developed in the English language. It is the aim of this article to describe the development of a new fatigue measurement instrument in the German language, the Fatigue Assessment Questionnaire. The following steps are described: 1. Concept analysis, 2. Identification of measurement criteria, 3. Comparison of these criteria with those described in the literature available, 4. Construction of a measurement scale, 5. Testing the new instrument, 6. Use of the instrument in a large study population. Steps 5 and 6 primarily deal with validity and reliability testing while step 6 also tests the hypothesis that patients with some types and stages of cancer suffer more from distressing fatigue than patients with other types and stages. CONCLUSION: Validity of the measurement items in the Fatigue Assessment Questionnaire was supported by the fact that they were derived from qualitative interviews with cancer patients. The first test with 77 cancer patients and 77 healthy individuals led to small adaptations and the following study, including 592 cancer patients, supported the reliability and validity of the Fatigue Assessment Questionnaire. It was able to distinguish between different populations. Factor analyses supported the earlier generated model of physical, affective and cognitive fatigue. Internal consistency of the questionnaire was supported by the Alpha Coefficient 0.90 (Cronbach). A difference was found in physical tiredness for patients with different types of cancer (p = 0.008) but this was not the case for affective and cognitive tiredness. More fatigue feelings were experienced by cancer patients with advanced disease than by patients in remission and this was true for physical fatigue (p = 0.0001), affective fatigue (p = 0.01), cognitive fatigue (p = 0.02) as well as for fatigue intensity (p = 0.0001) and distress (p = 0.0001). This group of patients also experienced significantly higher levels of depression and anxiety (p = 0.0001). The Fatigue Assessment Questionnaire, developed in the German speaking part of Switzerland, can be used for further activities in the field of quality of life and nursing care in oncology. The instrument and a proposed scoring system are published as an addendum to this article.

Adolescent↗

PubMed1998

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.

MOTIVATION: Although a large amount of information on the structure, function and properties of biomolecules is becoming available, it is difficult to understand the relationship between them. Thus, we have attempted to create an integrated relational database, search and visualization tool, 3DinSight, to help researchers to gain insight into their relationship. RESULTS: We have gathered data on the structure, function and properties of biomolecules, and implemented them into a relational database system. The structural data contain several subset data such as protein homologues, protein-DNA complex, in order to enable searching within a specific class of data. The functional data include motif sequence and mutation data of proteins. Also, various amino acid properties are implemented as a relational table. The World Wide Web (WWW) interfaces enable users to carry out various kinds of searches among these data. The locations of motif sequences and mutations are automatically mapped on the structure, and visualized in three-dimensional (3D) space by interactive viewers, VRML (Virtual Reality Modeling Language) and RasMol. In the case of VRML, the mapped 3D objects are hyper-linked to the corresponding document data. Also, amino acid properties, linked with structure, functional and mutation sites, can be displayed as graph plots. AVAILABILITY: 3DinSight is freely accessible through the Internet (http://www.rtc.riken.go.jp/3DinSight.h tml). CONTACT: sarai@rtc.riken.go.jp

Computer Communication Networks↗

PubMed1998

Developmental screening scores among preschool-aged children: the roles of poverty and child health.

OBJECTIVES: To investigate, using a nationally representative sample of preschool-aged children, the relationship among poverty history, child health, and risk of an abnormal developmental screening score. METHODS: Data were derived from the 1988 National Maternal and Infant Health Survey and 1991 Longitudinal Follow-up. Family income in the child's prenatal year and at 2 years old defined a poverty history for each child. Multivariate logistic regression was used to estimate the effects of poverty history on risk of an abnormal screening score or delays in large-motor, personal-social, or language subscales. RESULTS: Poor and near-poor children were 1.6 to 2.0 times as likely as nonpoor children to be classified as abnormal, even when maternal and household characteristics and the child's health history were taken into account. Preterm birth, chronic illness, dearth of reading materials in the home, and maternal depression were also associated with elevated risks of abnormal scores. CONCLUSIONS: Poverty is the largest single predictor of an abnormal developmental screening score. The implications of inadequate medical care among poor children for the interpretation of individual screening scores and for amelioration of problems are also discussed.

Child Health Services↗

PubMed1996

Optometric record keeping in a comprehensive health care environment.

Optometric records which have evolved in private practice must be reconsidered when included in a comprehensive care environment. These hospital, health maintenance organization (HMO), preferred provider organization, and similarly linked systems require a higher degree of communication among specialties than do self-standing practices. Furthermore, the administrative requirements of such a system require more standardization, cost sensitivity, medicolegal compliance, and other elements pecular to a comprehensive facility. The expended scope of care provided by optometrists within a hospital requires familiarity with a new range of procedures, languages, and reports. Information from laboratories, radiology, and other areas must be incorporated into the optometric record. Continuity of care is more complex. Opportunities for strong interprofessional synergies within the organization arise directly from proactivity in optometric record keeping. New legal hot spots arise from questions of records ownership, access, and privacy. Billing procedures are becoming extremely important, with significant effects on quality assurance audits, coding, doctor "profiling" against fraud, and abuse; these priorities can interfere with clinical priorities. Driven primarily by the concerns and resources of large third-party payers, technology is making rapid changes in the form of optometric record keeping in comprehensive systems. Electronic data management will change the face of medical records, although administrative data will be digitized much more quickly than clinical notes. Comprehensive care environments will be the "test beds" for these technologies. Optometry is in a good position to show its contribution to the health care team through leadership in the implementation of new record keeping models.

Comprehensive Health Care↗

PubMed1999

XINPUT: a program to edit "DOSRZ" input files.

The DOSRZ user code, which is part of the EGS4 standard distribution, is widely used in medical physics for the calculation of dose deposition in cylindrical geometries. The code provides the use of advanced Monte-Carlo techniques (PRESTA) and variance reduction methods. In the case of complex cylinder geometries the input of coordinates and radii is not only tedious but also prone to a high error rate. Coordinates are to be stated in absolute numbers. A change of one number, e.g., the slab thickness, requires the change of all subsequent numbers. Furthermore, parameters are only stated as numbers with no indication of their meaning. Obviously, there is a need for a user interface to facilitate the input for DOSRZ and to largely reduce the possibility for errors. We, therefore, wrote a graphical user interface (GUI) consisting of an input mask, a coordinate input interpreter, and a two-dimensional and/or pseudo-three-dimensional display section. The GUI is based on the scripting language Tcl/Tk, which runs under various platforms such as UNIX (LINUX), w95, and WIN NT. It consists of a main window which provides common-style menus and buttons to navigate through the edit dialog boxes. The most important tools are the region input, which enables the user to create the simulation geometry, and the graphics section where the scaled output can be displayed. Different media are shown in different colors which are user defined. Furthermore, the program contains some tools to reduce the probability of an erroneous input in the EGS4 input file. Since Tcl/Tk is a modern scripting language, it offers advanced tools to create the GUI and to "glue" different applications to it. XINPUT may also be considered as a model program for the development of a more general interface to other input areas of the EGS4 simulation code.

Computer Simulation↗