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At least 397 records · Page 22Linked to original sources

PubMed2006

Visual setup of logical models of signaling and regulatory networks with ProMoT.

BACKGROUND: The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networks using this formalism. Even though there is a large number of tools to set up models describing biological networks using a biochemical (kinetic) formalism, however, they do not support logical models. RESULTS: Herein we present a flexible framework for setting up large logical models in a visual manner with the software tool ProMoT. An easily extendible library, ProMoT's inherent modularity and object-oriented concept as well as adaptive visualization techniques provide a versatile environment. Both the graphical and the textual description of the logical model can be exported to different formats. CONCLUSION: New features of ProMoT facilitate an efficient set-up of large Boolean models of biochemical interaction networks. The modeling environment is flexible; it can easily be adapted to specific requirements, and new extensions can be introduced. ProMoT is freely available from http://www.mpi-magdeburg.mpg.de/projects/promot/.

Animals↗

PubMed1991

Evaluation of a parallel implementation of the learning portion of the backward error propagation neural network: experiments in artifact identification.

Various methods have been proposed in an attempt to solve problems in artifact and/or alarm identification including expert systems, statistical signal processing techniques, and artificial neural networks (ANN). ANNs consist of a large number of simple processing units connected by weighted links. To develop truly robust ANNs, investigators are required to train their networks on huge training data sets, requiring enormous computing power. We implemented a parallel version of the backward error propagation neural network training algorithm in the widely portable parallel programming language C-Linda. A maximum speedup of 4.06 was obtained with six processors. This speedup represents a reduction in total run-time from approximately 6.4 hours to 1.5 hours. We conclude that use of the master-worker model of parallel computation is an excellent method for obtaining speedups in the backward error propagation neural network training algorithm.

Algorithms↗

PubMed2003

August Knoblauch and amusia: a nineteenth-century cognitive model of music.

Early models of human cognition can be traced to nineteenth-century investigations of brain and behavior. Influential neurologists such as Wernicke, Kussmaul, and Lichtheim constructed diagrammatic models to illustrate current theories of cognition. Language was the most commonly studied cognitive function during this time; however, investigators also studied other cognitive functions, such as music and visual processing. While a number of nineteenth-century neurologists made observations about music abilities in aphasic patients, August Knoblauch, a German physician and anatomist, was the first to propose a diagrammatic model of music (1888/1890). He described a detailed cognitive model of music processing, hypothesized the existence of nine disorders of music production and perception, and coined the term "amusia." Knoblauch's model is the earliest cognitive model of music and is largely unrecognized as an important part of the history of neurology, neuropsychology, and music cognition.

Agnosia↗

PubMed2006

Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.

A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra interrnode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.

Algorithms↗

PubMed2005

CoaSim: a flexible environment for simulating genetic data under coalescent models.

BACKGROUND: Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these. RESULTS: We have created the CoaSim application as a flexible environment for Monte Carlo simulation of various types of genetic data under equilibrium and non-equilibrium coalescent processes for a variety of applications. Interaction with the tool is through the Guile version of the Scheme scripting language. Scheme scripts for many standard and advanced applications are provided and these can easily be modified by the user for a much wider range of applications. A graphical user interface with less functionality and flexibility is also included. It is primarily intended as an exploratory and educational tool CONCLUSION: CoaSim is a powerful tool because of its flexibility and ease of use. This is illustrated through very varied uses of the application, e.g. evaluation of association mapping methods, parametric bootstrapping, and design and choice of markers for specific questions.

Case-Control Studies↗

PubMed2002

Auditory processing deficits in reading disabled adults.

The nature of the auditory processing deficit of disabled readers is still an unresolved issue. The quest for a fundamental, nonlinguistic, perceptual impairment has been dominated by the hypothesis that the difficulty lies in processing sequences of stimuli at presentation rates of tens of milliseconds. The present study examined this hypothesis using tasks that require processing of a wide range of stimulus time constants. About a third of the sampled population of disabled readers (classified as "poor auditory processors") had difficulties in most of the tasks tested: detection of frequency differences, detection of tones in narrowband noise, detection of amplitude modulation, detection of the direction of sound sources moving in virtual space, and perception of the lateralized position of tones based on their interaural phase differences. Nevertheless, across-channel integration was intact in these poor auditory processors since comodulation masking release was not reduced. Furthermore, phase locking was presumably intact since binaural masking level differences were normal. In a further examination of temporal processing, participants were asked to discriminate two tones at various intervals where the frequency difference was ten times each individual's frequency just noticeable difference (JND). Under these conditions, poor auditory processors showed no specific difficulty at brief intervals, contrary to predictions under a fast temporal processing deficit assumption. The complementary subgroup of disabled readers who were not poor auditory processors showed some difficulty in this condition when compared with their direct controls. However, they had no difficulty on auditory tasks such as amplitude modulation detection, which presumably taps processing of similar time scales. These two subgroups of disabled readers had similar reading performance but those with a generally poor auditory performance scored lower on some cognitive tests. Taken together, these results suggest that a large portion of disabled readers suffer from diverse difficulties in auditory processing. No parsimonious explanation based on current models of low-level auditory processing can account simultaneously for all these results, though increased within-channel noise is consistent with the majority of the deficits found in the subgroup of poorer auditory processors.

Adult↗

PubMed2005

Access to care and children's primary care experiences: results from a prospective cohort study.

OBJECTIVE: To examine whether and how different kinds of access to care (financial, potential, and realized) predict parent-report child primary care experiences in an urban community sample. DATA SOURCES/STUDY SETTING: A prospective cohort study was performed. Baseline survey data were collected (67 percent response rate) from 3,406 parents of kindergarten through sixth grade students in a large urban school district in California during the 1999-2000 school year. A 1-year survey (80.4 percent response rate) resulted in a final sample of 2,738. STUDY DESIGN: Data were analyzed using multiple regression models with robust estimation. The dependent variable was Time 2 parent reports of primary care experiences, assessed via the Parents' Perceptions of Primary Care (P3C) measure. The independent variables were financial access (insurance status), potential access (presence of a regular source of care), and realized access (foregone care), controlling for child and family characteristics (race/ethnicity, parent's language, mother's education level, and child chronic health condition status) and baseline P3C scores. DATA COLLECTION: Data were collected by mail, telephone, and in person in English, Spanish, Vietnamese, and Tagalog. PRINCIPAL FINDINGS: Controlling for baseline P3C scores and child and family characteristics, having no health insurance at both baseline and Time 2 was associated with a 6.2-point lower Time 2 P3C score, relative to having had health insurance at both time points. Having a regular provider at Time 2 (either always having had one or gaining one during the year) was associated with, on average, a 10-point higher Time 2 P3C score, compared to children without a regular provider (either never having had one or losing one during the year). Episodes of foregone care during the year were associated with 10.7 points lower Time 2 P3C scores, relative to children whose parents did not report foregone care. Similar relationships were found between all three measures of access to care and each of the sub-domain measures of primary care experience. CONCLUSIONS: Financial, potential, and realized access to care are associated prospectively with the full range of primary care experiences--comprehensiveness, communication, coordination, and contextual knowledge--beyond continuity and accessibility. Access to a regular source of care and to needed care are each associated with larger effects on primary care experiences than is the presence of health insurance. Gaining insurance or a regular source of care results in primary care experiences similar to always having had these, while losing a regular source of care has a more immediate effect than losing insurance on primary care experiences.

Child↗

PubMed2002

[Neurophysiology of inspiration: a chapter of the relations between since and literature around 1900].

How does the literary inspiration phenomenon find an explanation around 1900? As an unexpected glimpse of imagination, is inspiration opposed to the idea of making? Does the individual attend as a passive spectator the work of his motive system or is he its master? Can we suppose that the opposition between automatic and self-willed language is legitimate? By investigating models of physiological psychology, which are focused on the brain and the nervous system, we will try to answer these questions. And by reading some doctor's, neurologist's and philosopher's writings, we will go in search of a concrete representation of the literary inspiration phenomenon. Indeed, if inspiration is a process which results from an organic motive combination, as several scientists seem to consider, it should be visible enough to have its own physiological model. We shall nevertheless see that the investigation of these models reveals interests which largely overstep the bounds of science. Thus, between rigour and dreaming, illness and health, neurological physiology and creation, we realise that the literary inspiration phenomenon does not find its place among the positive facts.

Authorship↗

PubMed1996

Low birth weight and neurocognitive status at six years of age.

We examined the relationship between low birth weight (LBW) (< or = 2500 g) and specific neurocognitive abilities at 6 years of age in a large-scale nonconcurrent prospective study. In 1990-1992, we randomly selected and evaluated LBW and normal birth weight (NBW) children from the 1983-1985 newborn lists of two major hospitals in southeast Michigan, one serving an urban and the other a suburban population. LBW children (n = 473) scored significantly lower than NBW children (n = 350) on tests measuring language, spatial, fine motor, tactile, and attention abilities, controlling for population site, race, maternal IQ, and education. Gradient relationships were observed across levels of LBW with language, spatial, tactile, and attention tests. Exploratory analysis, using general additive models, revealed that test performance varied within birth weight levels and that performance continued to improve with increased birth weight well above 3000 g. Follow-up assessments as the children mature will shed light on the persistence of these associations and their implications for learning disorders.

Attention↗

PubMed2000

A model of outcomes research: spinal cord injury.

OBJECTIVE: To use spinal cord injury (SCI) care and research as a paradigm to illustrate how the principles and practices of outcomes research have been and can be applied to the sequelae of a specific disability. DATA SOURCES: Review of data sources and literature pertaining to outcomes of SCI. STUDY SELECTION: English language literature, health status and health services research agencies, academic and governmental research, and surveillance settings. DATA EXTRACTION: A critical review of measures that have been and may be used to measure the outcomes of SCI. Special attention was paid to data sources; the need for methodologic accommodations: the research balance between generic and condition-specific methods; and the measurement outcomes that are highly relevant to people with SCIs. DATA SYNTHESIS: There is a substantial research record related to the natural history, rehabilitation, survival, and long-term social reintegration of people with SCI, but relatively less addressing widely used generic health outcomes. CONCLUSION: Contemporary outcomes research is relevant to people with SCI and those who provide treatment. One area of special attention is the occurrence of secondary conditions. To a large extent, SCI outcomes research can use conventional methods and generic instruments. There also is a need to modify research methods and to refine and apply some measures specific to people with SCI.

Activities of Daily Living↗

PubMed2002

Effect of Spanish interpretation method on patient satisfaction in an urban walk-in clinic.

OBJECTIVE: To examine the effect of Spanish interpretation method on satisfaction with care. DESIGN: Self-administered post-visit questionnaire. SETTING: Urban, university-affiliated walk-in clinic. PARTICIPANTS: Adult, English- and Spanish-speaking patients presenting for acute care of non-emergent medical problems. MEASUREMENTS AND MAIN RESULTS: Satisfaction with overall clinic visit and with 7 provider characteristics was evaluated by multiple logistic regression, controlling for age, gender, ethnicity, education, insurance status, having a routine source of medical care, and baseline health. "Language-concordant" patients, defined as Spanish-speaking patients seen by Spanish-speaking providers and English-speaking patients, and patients using AT&T telephone interpreters reported identical overall visit satisfaction (77%; P = .57), while those using family or ad hoc interpreters were significantly less satisfied (54% and 49%; P < .01 and P = .007, respectively). AT&T interpreter use and language concordance also yielded similar satisfaction rates for provider characteristics (P > .2 for all values). Compared to language-concordant patients, patients who had family members interpret were less satisfied with provider listening (62% vs 85%; P = .003), discussion of sensitive issues (60% vs 76%; P = .02), and manner (62% vs 89%; P = .005). Patients who used ad hoc interpreters were less satisfied with provider skills (60% vs 83%; P = .02), manner (71% vs 89%; P = .02), listening (54% vs 85%; P = .002), explanations (57% vs 84%; P = .02), answers (57% vs 84%; P = .05), and support (63% vs 84%; P = .02). CONCLUSIONS: Spanish-speaking patients using AT&T telephone interpretation are as satisfied with care as those seeing language-concordant providers, while patients using family or ad hoc interpreters are less satisfied. Clinics serving a large population of Spanish-speaking patients can enhance patient satisfaction by avoiding the use of untrained interpreters, such as family or ad hoc interpreters.

Adolescent↗

PubMed1983

Clinical inferences and decisions--I. Diagnosis and Bayes' theorem.

Clinical decisions are based upon inferences derived from test evidence where data is collected as a means of hypothesis testing. In medicine, the initial expectation of a clinical state is rarely expressed in the classical scientific language of a null hypothesis where alternative outcomes are assumed to be equally probable, because clinical experience reinforces the maxim that common events occur commonly. The collection of test evidence in clinical practice, therefore, is directed towards overturning prior likelihoods for a clinically pathological state which are far from mere chance expectations. The extent to which any test evidence can modify such prior expectations not only depends on its relevance to the clinical state in question (i.e. the hypothesis) but also is largely influenced by the inherent error rates in the test itself. Clinical decision models should reflect these facts. Using examples from the field of ophthalmology, this paper presents a normative model using Bayes' theorem of conditional probabilities which provides a rational framework upon which to base or appraise clinical decisions. Parts II and III of the series will expand this clinical application of decision theory to show how it may be used in the absence of hard test evidence and also where a different emphasis or utility may be placed on false positive or false negative errors.

Bayes Theorem↗

PubMedDate not supplied

[Neuropsychological deficits in hydrocephalus associated spina bifida].

INTRODUCTION. The term spina bifida is used to describe a large number of abnormalities in which the common denominator is incomplete posterior fusion of the vertebral arches. DEVELOPMENT. Spina bifida, as a congenital alteration affecting closure of the neural tube frequently appears in relation to hydrocephaly. The object of this article is to review the neuropsychological alterations which occur in hydrocephaly, with special reference to hydrocephaly linked to spina bifida. The authors suggest consideration of these alterations in view of the new models of cognitive neuropsychology. The commonest alterations are those affecting visual-perceptive and visual-constructive function, working memory, pragmatic use of language and executive functions.

Humans↗

PubMed1994

The role of the UMLS in 'storing' and 'sharing' across systems.

We will argue that 'sharing', 're-use', 're-purposing', and 'addition' of health care information is difficult, intrinsically; that the best way to overcome the difficulty is to start doing it, as soon as possible, and that the UMLS Knowledge Sources provide the best place to start. We recommend that the UMLS be used as a default source of biomedical concept names and relationships, as a comprehensive, data-based, 'reference model', and as an example of a large, ecumenical, evolving, continuously updated source of re-usable health care information.

Computer User Training↗

PubMed2005

Closure procedures for monotone bi-factorial dose-response designs.

Two goals of multiple-dose factorial trials are (i) demonstrating improved effectiveness of a fixed combination over each of its components as well as (ii) identifying a safe and effective dose range. The authors address both goals though with focus on the second by closure procedures that guarantee strong control of the familywise error rate. Two different families of null hypotheses are investigated for bi-factorial dose-response designs that are monotone with respect to the matrix partial order. One is suitable to find the minimum effective dose(s) and the other one is large enough to identify the highest effective dose step(s). Likelihood ratio tests and appropriate multiple contrast tests are applied to an unbalanced clinical trial example taken from Hung (2000, Statistics in Medicine 19, 2079-2087). Full computer code written in the R language is available from the Internet.

Antihypertensive Agents↗

PubMed2005

Electronically signed documents in health care--analysis and assessment of data formats and transformation.

OBJECTIVES: Our objectives were to analyze and assess data formats for their suitability for conclusive and secure long-term archiving and to develop a concept for legally secure transformation of electronically signed documents that are not available in data formats appropriate for long-term archiving. METHODS: On the basis of literature review and Internet searches we developed general evaluation criteria to assess data formats with regard to their suitability for conclusive and secure long-term archiving. The assessment of data formats refers to format specifications and available literature. For the analyses of the transformation of signed documents we analyzed legal requirements on the basis of laws and ordinances as well as technical requirements by means of literature reviews, Internet searches and technical specifications. RESULTS: The following evaluation criteria are suited for this kind of assessment of data formats: transparency and standardization, stability, presentation and security. According to our assessment the following data formats are most suitable for conclusive and secure long-term archiving: PDF for formatted and unstructured text documents, XML for markup languages, TIFF for images in general, DICOM for medical images and S/MIME for the storage of e-mail. To transform electronically signed documents we propose an elementary procedure and universal basic model in form of an XML schema definition that includes the necessary legal and technical information. CONCLUSIONS: If electronic documents are to replace paper-based documents in patient records, they have to conform to the criteria for secure long-term archiving. The analyzed data formats are to be extended by mechanisms to guarantee the long-term security of electronic signatures. To transform large quantities of documents in a legally secure way, our basic model has to be extended for automated procedures.

Archives↗

PubMed1995

Familial sinistrality: the utility of calculating exact genotype probabilities for individuals.

Measures of familial sinistrality are frequently used in neuropsychological research. However they suffer from the problem that they are essentially a global measure of phenotypes in the family, whereas they are interpreted as an indicator of the genotype of the individual concerned. In this paper it is shown how to calculate a precise probabilistic estimate of a proband's genotype, given a particular genetic model of handedness, using all of the information available in a family tree. Example calculations are provided for a range of families with one or two sinistral relatives. Genotype probabilities are also calculated for a large population data set (the National Childhood Encephalopathy Study) and it is shown that familial sinistrality does not account for all of the variability present in the genotype probabilities, and that genotype probabilities provide an additional prediction of individual sinistrality after taking familial sinistrality into account, whereas all of the information in familial sinistrality is accounted for by the genotype probabilities. Finally it is shown how genotype probabilities can be used to assess whether there is heterozygote advantage for a characteristic, and using this method it is suggested that there is no support for heterozygotes having higher intellectual ability than homozygotes.

Family↗

PubMed2005

Competitive hybridization kinetics reveals unexpected behavior patterns.

Although the kinetics of hybridization between a soluble polynucleotide and an immobilized complementary sequence have been studied by others, it is almost universally assumed that the interaction between each probe/target pair can be treated as a separate event. This simplifies the mathematics considerably, but it can give a false picture of the extent of hybridization that one achieves at equilibrium as well as the relative quantities of each hybridized pair during the approach to equilibrium. Here we solve the relevant kinetics equations simultaneously using Mathematica as a simulation language. Among the interesting results of this study are that, for certain circumstances, the relative ratio of incorrect to correct hybrids can change dramatically with time; that the relative abundances of two pairs are not what one would expect based on their equilibrium dissociation constants; that the volume of a wash solution after hybridization can have a large effect on results; and the fact that a short wash is typically better than a long one. We show that an optimum wash time exists for a given set of conditions. In addition, the ratio of soluble to insoluble (spotted) molecules can influence results substantially. Finally, the true levels of rare transcripts can be masked by the presence of highly abundant ones. Code is supplied to enable others to study conditions beyond those presented in this article.

Base Composition↗