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PubMed1983

Cluster analysis of the WAIS on brain-damaged patients.

In recognition of increased usage of cluster analytic techniques, the current study attempted to examine sampling bounds for tests and subjects on one cluster-analytic procedure. Specifically, the WAIS subtest scores from a heterogeneous group of subjects with CNS involvement were first, factor analyzed and then clustered by means of Ward's hierarchical procedure. This methodology had been previously applied to two different samples of aphasics and aphasia batteries. In both these aphasic studies, an underlying severity dimension of language dysfunction was found. In contrast, in the current study, salient feature groups were found. Moreover, these groups were distributed in a sequential or hierarchical model in terms of specific cognitive deficits. From these data, it is argued that two major parameters in determining the resulting cluster structures are the homogeneity/heterogeneity of the sample and test battery employed. Although such a statement is obvious, the theoretical ramifications are large, in that the cluster structure may be a function of test weighting or sample diversity, not the phenomenon of interest. However, the cluster structures found in the current study were consistent with historical models of cognitive dysfunction and also lend support to hierarchical models of sequential cognitive impairment. These findings are discussed in terms of their clinical and experimental ramifications with respect to grouping subjects in terms of WAIS profiles.

Adult↗

PubMed1996

The project ARIANE: conceptual queries to information databases.

As information databases we consider all the collections of data records indexed by key-words, stored and delivered by computer systems. In previous research works we demonstrated the interest to design a conceptual model, in the conceptual graphs formalism, and to implement a computational model for information retrieval in large information databases. These models are based on the UMLS knowledge sources. This paper reminds briefly these models and describes tests done in querying a patients database and a bibliographical database.

Databases, Bibliographic↗

PubMed2006

Variation in prescribing for anxiety and depression: a reflection of health inequalities, cultural differences or variations in access to care?

BACKGROUND: There are large variations in mental health prescribing in UK populations. However the underlying reasons for these differences, which may be related to differences in prevalence, cultural expectations or practical difficulties in access to treatment, remain uncertain. METHODS: Linear modelling was used to investigate whether population characteristics or access to primary care account for variations in mental health prescribing across 39 deprived neighbourhoods. RESULTS: The proportion of sampled respondents whose first language was not English and the ratio of general practitioners to population explained 61% of variation. Deprivation and mental health status were not significant predictors of prescribing in these relatively deprived communities. CONCLUSION: These findings suggest that mental health prescribing, within deprived areas, as well as reflecting cultural and social differences in prescribing, may also be a proxy measure of access to care.

Journal Article↗

PubMed2006

Bloch-Redfield-Wangsness theory engine implementation using symbolic processing software.

We describe a general method for the automated symbolic processing of Bloch-Redfield-Wangsness relaxation theory equations for liquid-phase spin dynamics in the algebraically challenging case of rotationally modulated interactions. The processing typically takes no more than a few seconds (on a contemporary single-processor workstation) and yields relaxation rate expressions that are completely general with respect to the spectral density functions, relative orientations, and magnitudes of the interaction tensors, with all cross-correlations accounted for. The algorithm easily deals with fully rhombic interaction tensors, and is able, with little if any modification, to treat a large variety of the relaxation mechanisms encountered in NMR, EPR, and spin dynamics in general.

Algorithms↗

PubMed1994

Users conceptual views on medical information databases.

As information databases we consider all the kinds of information repositories that are handled by computer systems. When querying very large information databases, the end-users are often faced with the problem to parse their questions efficiently into the query languages of the computer systems. Conceptual graphs were initially designed for natural language analysis and understanding. Due to their closeness to semantic networks, their expressiveness is powerful enough to be applied to knowledge representation and use by computer systems. This work demonstrates that conceptual graphs are a suitable means to model both the information in patient databases and the queries to these databases, and that operations on graphs can compute the pattern matching process needed to provide the answers. A prototype that exploits this model is presented. Experiments have been made with the material furnished by the Unified Medical Language System project (version 2, 1992) of the National Library of Medicine, USA.

Abstracting and Indexing↗

PubMed1994

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗

PubMed2000

Revisiting the concept of identifiable neurons.

Although eutely in nematodes was known, giant neurons in several taxa and unique motor neurons to leg muscles in decapod crustaceans, the idea that many animals have many identifiable neurons with relatively consistent dynamical properties and connections was only slowly established in the late 1960s and early 1970s. This has to be one of the important quiet revolutions in neurobiology. It stimulated a vast acquisition of specific information and led to some euphoria in the degree and pace of understanding activity of nervous systems and consequent behavior in terms of neuronal connections and properties. Some implications, problems and opportunities for new discovery are developed. The distribution of identifiable neurons among taxa and parts of the nervous system is not yet satisfactorily known. Their evolution may have been a case of several independent inventions. The degree of consistency has been quantified only in a few examples and the plasticity is little known. Identified neurons imply identifiable circuits but whether this extends to discrete systems, functionally definable, seems likely to have several answers in different animals or sites. Very limited attempts have been made to extend the concept to cases of two or ten or a hundred fully equivalent neurons, on all kinds of criteria. These attempts suggest a much smaller redundancy and vaster number of types of neurons than hitherto believed. Theory as well as empirical information has not yet interpreted the range of systems from those with small sets of relatively reliable neurons to those with large numbers of parallel, partially redundant units. The now classical notion of local circuits has to be extended to take account of and find roles for the plethora of integrative variables, of evidence for neural processing independent of spikes and classical synapses, of spatial configurations of terminal arbors and dendritic geometry, of modulators and transmitters, degrees of rhythmicity (regularity varying several orders of magnitude), and of synchrony. Adequate language and models need to go beyond 'circuits' in any engineering sense. Identifiable neurons can contribute to a broad spectrum of issues in neurobiology.

Animals↗

PubMed2000

Antibiotic prophylaxis for surgery for proximal femoral and other closed long bone fractures.

BACKGROUND: Antibiotic prophylaxis has been established policy for major surgical operations for many years. In fracture fixation, the effectiveness, and the duration of administration, have been a matter of debate. OBJECTIVES: To assess the effects of the prophylactic administration of antibiotics in patients undergoing surgical management of hip or other long bone fractures. SEARCH STRATEGY: We searched MEDLINE, EMBASE, Current Contents, Dissertation Abstracts, and Index to UK Theses, and bibliographies of identified articles. Trials were also obtained from the Cochrane Musculoskeletal Injuries Group trials register. Date of the most recent search: end of 1997. SELECTION CRITERIA PARTICIPANTS: Any patients with a hip or other closed long bone fracture undergoing surgery for internal fixation or replacement arthroplasty. INTERVENTIONS: Any regimen of systemic antibiotic prophylaxis administered at the time of surgery. OUTCOME MEASURES: Wound infection (deep and superficial), urinary tract infection, respiratory tract infection, adverse effects of prophylaxis, economic evaluations. DATA COLLECTION AND ANALYSIS: Both reviewers independently selected trials for inclusion, and assessed methodological quality and extracted data. Where possible, data were pooled and Peto odds ratios and absolute risk reductions, each with 95% confidence intervals, calculated. MAIN RESULTS: Twenty one randomised trials of only poor or moderate quality were included. The comparisons tested fell within six comparison groups, principally multiple dose or a single dose of antibiotic versus a placebo or no treatment. Antibiotic prophylaxis reduces wound, urinary and respiratory tract infections in patients undergoing surgery for closed fracture fixation. Economic modelling has indicated that this is a cost-effective intervention. There are limited data for the incidence of adverse effects, but as expected they appear to be more common in those receiving antibiotics. REVIEWER'S CONCLUSIONS: Antibiotic prophylaxis should be offered to those undergoing surgery for closed fracture fixation. On ethical grounds, further placebo controlled randomised trials of the effectiveness of antibiotic prophylaxis in closed fracture surgery are unlikely to be justified. Trials addressing the cost-effectiveness of different effective antibiotic regimens would need to be very large and may not be feasible.

Antibiotic Prophylaxis↗

PubMed1996

Encoding words and pictures: a positron emission tomography study.

Subjects viewed words, pictures, crosshairs, or a large X flanked by two smaller xs on either side while their brain activity was monitored using positron emission tomography (PET). When activation from the pictures, crosshairs, or Xs condition was subtracted from activation in the words condition, the left angular gyrus and Broca's area were found to be activated. In the comparison of words and pictures, additional language areas were activated. These results provide support for the classical neurological model of reading. The results also suggest that a "word form area" is near the margin of the left angular gyrus.

Adolescent↗

PubMed2004

Haplotype parsing: methods for extracting information from human genetic variations.

While the shared consensus genetic sequence of our species contains a great deal of information about our common biology, there is also much to be learned from the subtle genetic variations across our species. These variations are believed to be generally of little or no direct functional significance and predominantly reflect the chance accumulation of small genetic changes since our emergence as a species. Therefore, they carry little useful information when observed in a single individual. When tallied across a whole population though, these chance mutations can teach us a great deal about our evolutionary history and the patterns of inheritance in particular individuals. In particular, frequently observed patterns of single nucleotide polymorphisms (SNPs) in a population can identify segments of chromosome that have been passed down largely intact through long stretches of our evolution. Finding these frequently conserved chromosomal segments, or haplotypes, and developing methods to identify haplotype patterns in particular individuals, will in turn help us to identify those particular segments that carry genetic factors influencing risk for many common human diseases. To make the best use of this data, we will need to develop new models for the encoding of information in genome variations--the "language of genetic variation"--and new algorithms for fitting datasets to those models. This article surveys past work by the author and colleagues on this problem, utilising computational methods for locating frequent patterns in haploid sequence data, and "parsing" sequences so as to optimally explain them given the knowledge of the general population structure. The author's recent work in this area has been compiled into a set of computational tools available at http://www-2.cs.cmu.edu/~russells/software/hapmotif.html.

Algorithms↗

PubMed1998

Web-based segmentation and display of three-dimensional radiologic image data.

In many clinical circumstances, viewing sequential radiological image data as three-dimensional models is proving beneficial. However, designing customized computer-generated radiological models is beyond the scope of most physicians, due to specialized hardware and software requirements. We have created a simple method for Internet users to remotely construct and locally display three-dimensional radiological models using only a standard web browser. Rapid model construction is achieved by distributing the hardware intensive steps to a remote server. Once created, the model is automatically displayed on the requesting browser and is accessible to multiple geographically distributed users. Implementation of our server software on large scale systems could be of great service to the worldwide medical community.

Algorithms↗

PubMedDate not supplied

Hyperad: augmenting and visualizing free text radiology reports.

Hyperad is an automated computer system designed to extract key concepts from thoracic radiology reports and give physicians access to a large database containing the reports and key concepts. The concepts are extracted from textual documents with natural language processing techniques, then stored with the original documents in the database, which can be queried in terms of findings or associated attributes from an intuitive and easily accessible interface. The extracted concepts are represented both textually in a coded hypertext format and graphically on a coronal cross-sectional anatomy atlas, an idealized graphical model of human anatomy. To facilitate implementation, the communication protocols and standards of the World Wide Web (Web) were adopted. The reports and associated forms are encoded in standard hypertext markup language, which makes it possible to use hypermedia links to navigate the Hyperad database with any graphical Web browser. In the future, Hyperad may prove useful for other applications.

Computer Systems↗

PubMed2004

MolTalk--a programming library for protein structures and structure analysis.

BACKGROUND: Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. RESULTS: We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file header section, such as scientific organism, compound name, and EC code. CONCLUSION: MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot.2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains.3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk.4) To be used as a front end to databases, e.g. PDBChainSaw.

Artificial Intelligence↗

PubMed2003

The Newell Test for a theory of cognition.

Newell (1980; 1990) proposed that cognitive theories be developed in an effort to satisfy multiple criteria and to avoid theoretical myopia. He provided two overlapping lists of 13 criteria that the human cognitive architecture would have to satisfy in order to be functional. We have distilled these into 12 criteria: flexible behavior, real-time performance, adaptive behavior, vast knowledge base, dynamic behavior, knowledge integration, natural language, learning, development, evolution, and brain realization. There would be greater theoretical progress if we evaluated theories by a broad set of criteria such as these and attended to the weaknesses such evaluations revealed. To illustrate how theories can be evaluated we apply these criteria to both classical connectionism (McClelland & Rumelhart 1986; Rumelhart & McClelland 1986b) and the ACT-R theory (Anderson & Lebiere 1998). The strengths of classical connectionism on this test derive from its intense effort in addressing empirical phenomena in such domains as language and cognitive development. Its weaknesses derive from its failure to acknowledge a symbolic level to thought. In contrast, ACT-R includes both symbolic and sub-symbolic components. The strengths of the ACT-R theory derive from its tight integration of the symbolic component with the sub-symbolic component. Its weaknesses largely derive from its failure, as yet, to adequately engage in intensive analyses of issues related to certain criteria on Newell's list.

Adaptation, Psychological↗

PubMed2003

Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project.

BACKGROUND: Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. RESULTS: Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. CONCLUSION: An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

Algorithms↗

PubMed1999

Hierarchical subcomponents of the Big Five personality factors: a cross-language replication.

An ideal structural representation of personality attributes would include more than just broad-bandwidth factors. Specific subcomponents help define broad factors while enhancing the fidelity of the representation. There has been no consensus with regard to the necessary specific subcomponents of the Big Five. This problem was addressed by analyzing 2 representative lexical data sets, one involving English adjectives and the other involving German adjectives. Large samples (Ns of 636 and 775) were used in classifying a selection of 500 adjectives in each language by Big Five domains, and within each domain and language, the terms were factor analyzed with promax rotation. Ratings by 22 bilinguals of correspondence between the adjectives in English and German factors indicated 18 distinct content themes common to personality description in the 2 languages. The 18 subcomponents delineate necessary features of a more finely faceted measurement model for the lexical Big Five factors.

Adolescent↗

PubMed2003

Brain imaging studies of the anatomical and functional consequences of preterm birth for human brain development.

Premature birth can have devastating effects on brain development and long-term functional outcome. Rates of psychiatric illness and learning difficulties are high, and intelligence on average is lower than population means. Brain imaging studies of infants born prematurely have demonstrated reduced volumes of parietal and sensorimotor cortical gray matter regions. Studies of school-aged children have demonstrated reduced volumes of these same regions, as well as in temporal and premotor regions, in both gray and white matter. The degrees of these anatomical abnormalities have been shown to correlate with cognitive outcome and with the degree of fetal immaturity at birth. Functional imaging studies have shown that these anatomical abnormalities are associated with severe disturbances in the organization and use of neural systems subserving language, particularly for school-aged children who have low verbal IQs. Animal models suggest that hypoxia-ischemia may be responsible at least in part for some of the anatomical and functional abnormalities. Increasing evidence suggests that a host of mediators for hypoxic-ischemic insults likely contribute to the disturbances in brain development in preterm infants, including increased apoptosis, free-radical formation, glutamatergic excitotoxicity, and alterations in the expression of a large number of genes that regulate brain maturation, particularly those involved in the development of postsynaptic neurons and the stabilization of synapses. The collaboration of both basic neuroscientists and clinical researchers is needed to understand how normal brain development is derailed by preterm birth and to develop effective prevention and early interventions for these often devastating conditions.

Brain↗

PubMed2006

An existential model of oral health from evolving views on health, function and disability.

OBJECTIVE: This study explores the evolution of conceptual frameworks and models of health and disability to construct an explanatory model of oral health. RESULTS: The International Classification of Impairments, Disabilities, and Handicaps adopted by the WHO is based largely on social role theory and a utilitarian tradition portraying disablement as a negative and socially unacceptable consequence of impairment. It has been the major conceptual influence on the construction of psychometric tools for dentistry. However current views of chronic disease are refocused on the influence of coping strategies used by people to prevent or limit disability and handicap. Consequently, the WHO adopted the International Classification of Functioning, Disability and Health (ICF) as an alternative description of health and health-related states based on an existentialist view of the body, the person and society. In addition, an ethnographic exploration has identified three major domains of oral health--oral hygiene, comfort and general health--that dominate the opinions of people with oral impairments. CONCLUSIONS: Application of the framework and language of the ICF to the major domains of oral health provides the basis for a new biopsychosocial model of oral health, function and disablement.

Disability Evaluation↗