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Neural networks in clinical medicine.

Neural networks are parallel, distributed, adaptive information-processing systems that develop their functionality in response to exposure to information. This paper is a tutorial for researchers intending to use neural nets for medical decision-making applications. It includes detailed discussion of the issues particularly relevant to medical data as well as wider issues relevant to any neural net application. The article is restricted to back-propagation learning in multilayer perceptrons, as this is the neural net model most widely used in medical applications.

Algorithms↗

The prevalence of mental disorders in the elderly in Edmonton: a community survey using GMS-AGECAT. Geriatric Mental State-Automated Geriatric Examination for Computer Assisted Taxonomy.

OBJECTIVE: To estimate the current prevalence rate of Geriatric Mental State-Automated Geriatric Examination for Computer Assisted Taxonomy (GMS-AGECAT) disorders in the elderly population in Edmonton, Alberta. To compare the prevalence rate of GMS-AGECAT depression with the prevalence rate of Diagnostic Interview Schedule-Diagnostic and Statistical Manual of Mental Disorders (DIS-DSM-III) major depression based on an earlier survey in Edmonton. METHOD: A sample of 1119 community residents age 65 years and over was selected using the provincial health insurance database. Data on mental disorders were collected using the Geriatric Mental State questionnaire, and diagnoses were made with the Automated Geriatric Examination for Computer Assisted Taxonomy computer program. Prevalence rates, standard errors, and logistic regression coefficients were estimated using software designed to analyze survey data. RESULTS: The prevalence rates of GMS-AGECAT depression and organic disorder were 11.2% and 2.9% respectively. For depression there was a statistically significant difference in the prevalence rates for males (7.3%) and females (14.1%) (P = 0.003), and for organic disorder there was a statistically significant increasing trend across age-groups for females (P < 0.0001). The prevalence rate of GMS-AGECAT depression in Edmonton is comparable to rates reported from several European studies but is much higher than the 6-month prevalence rate of DIS-DSM-III major depression of 1.2% based on an earlier Edmonton survey. CONCLUSIONS: GMS-AGECAT depression is a depressive syndrome that has a larger prevalence rate than DIS-DSM-III major depression. Community surveys that measure only the prevalence rate of DSM-III major depression may be missing clinically significant cases of geriatric depression.

Aged↗

Scintigraphic measurement of tracheal mucus velocity in vivo.

Mucociliary clearance (MCC) is an important mechanism for removing inhaled particles, secretions and cellular debris from the respiratory tract. Here, a direct measurement of tracheal mucus velocity (TMV) for assessment of MCC, suitable for clinical and research use, is reported, and a comparison is made of TMV in normal subjects and patients with chronic obstructive pulmonary disease (COPD). A 0.1-mL bolus of radiolabelled (2-5 MBq), technetium-labelled macroaggregated human albumin (99mTc MAA) was injected through the cricothyroid membrane into the trachea of 20 young (< 50 yrs) and 12 older (> 50 yrs) normal subjects and 34 patients with COPD. Repeat studies were carried out in 13 normal subjects and 16 COPD patients. Movement of the bolus in the trachea was recorded (15 min) using a gamma camera interfaced to a computer. Data were analysed using specifically designed software. The test was well tolerated by subjects and patients, and no significant adverse events were reported. No significant differences were observed between data recorded from different regions of the bolus (leading edge, peak, trailing edge) by analysis of variance (ANOVA). Bland-Altman plots of the repeat studies indicated that data were more variable in normal subjects (coefficient of repeatability (COR) 10.3 mm.min-1) than in COPD patients (COR 5.5 mm.min-1). TMV (mean +/- SD) in young normal subjects (n = 20) was 10.7 +/- 3.5 mm.min-1. TMV was reduced in older normal subjects (n = 12; 6.5 +/- 2.6 mm.min-1) and further reduced in COPD (n = 34; 2.1 +/- 2.7 mm.min-1). In conclusion, this technique can be used to measure tracheal mucus velocity rapidly and safely in healthy subjects and patients with respiratory tract disease. This study has confirmed that tracheal mucus velocity declines with age and is further impaired in patients with chronic obstructive pulmonary disease.

Adult↗

Acoustic analysis of snoring before and after palatal surgery.

To investigate the effectiveness of palatal surgery for nonapnoeic snoring, 35 patients were block randomised to undergo one of two different palatoplasty procedures. Patients were admitted pre-operatively for audio recording of snoring sound and video recording of sleeping position, and between 1.0 and 4.1 months (mean 2.5) and between 5.9 and 17.5 months (mean 9.7) post-operatively. Sound files, comprising the inspiratory sound of the first 100 snores whilst sleeping in a supine position, were analysed using specifically designed software. Snore duration (s), loudness (dBA), periodicity (%) and energy ratios for the frequency bands 0-200 Hz, 0-250 Hz and 0-400 Hz were calculated. Subjective outcomes were noted. Operation type, body mass index, age, peak nasal inspiratory flow rate, Epworth sleep score and alcohol intake were considered as confounding variables. No patient was cured from snoring. Paired t-test analysis demonstrated statistically significant changes between pre- and early post-operative recordings for snore periodicity and energy ratios in the frequency ranges 0-200 Hz, 0-250 Hz and 0-400 Hz. In conclusion, only the 0-250-Hz energy ratio measurements maintained a statistically significant improvement at the time of the late post-operative recording, despite an obvious drift back to pre-operative levels. No confounding variables were identified. The subjective and objective results correlated poorly. Post-operative changes in the acoustic parameters of snoring sound, following palatal surgery, are demonstrable but short-lived.

Acoustics↗

CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes.

BACKGROUND: Improvements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining. RESULTS: CoreGenes is a global JAVA-based interactive data mining tool that identifies and catalogs a "core" set of genes from two to five small whole genomes simultaneously. CoreGenes performs hierarchical and iterative BLASTP analyses using one genome as a reference and another as a query. Subsequent query genomes are compared against each newly generated "consensus." These iterations lead to a matrix comprising related genes from this set of genomes, e. g., viruses, mitochondria and chloroplasts. Currently the software is limited to small genomes on the order of 330 kilobases or less. CONCLUSION: A computational tool CoreGenes has been developed to analyze small whole genomes globally. BLAST score-related and putatively essential "core" gene data are displayed as a table with links to GenBank for further data on the genes of interest. This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes or http://www.bif.atcc.org/CoreGenes.

Algorithms↗

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

BACKGROUND: The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. RESULTS: The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs) of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with <8 sequences gave 91.4% accuracy, significantly better than CLUSTALW (88.9%) and all other methods considered here. The complete suite is available from http://www.compbio.dundee.ac.uk. CONCLUSIONS: The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5% with 52.5% accuracy for alignments in the 0-10 percentage identity range. This suggests that further improvements in accuracy will be possible in the future.

Amino Acid Sequence↗

Tools for loading MEDLINE into a local relational database.

BACKGROUND: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. RESULTS: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. CONCLUSIONS: Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.

Database Management Systems↗

CisOrtho: a program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting.

BACKGROUND: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. RESULTS: We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. CONCLUSIONS: CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription factor targets.

Animals↗

Considerations when using the significance analysis of microarrays (SAM) algorithm.

BACKGROUND: Users of microarray technology typically strive to use universally acceptable data analysis strategies to determine significant expression changes in their experiments. One of the most frequently utilised methods for gene expression data analysis is SAM (significance analysis of microarrays). The impact of selection thresholds, on the output from SAM, may critically alter the conclusion of a study, yet this consideration has not been systematically evaluated in any publication. RESULTS: We have examined the effect of discrete data selection criteria (qualification criteria for inclusion) and response thresholds (out-put filtering) on the number of significant genes reported by SAM. The use of a reduced data set by applying arbitrary restrictions vis-à-vis abundance calls (e.g. from D-chip) or application of the fold change (FC) option within SAM (named the FC hurdle hereafter), can substantially alter the significant gene list when running SAM in Microsoft Excel. We determined that for a given final FC criteria (e.g. 1.5 fold change) the FC hurdle applied within Microsoft Excel SAM alters the number of reported genes above the final FC criteria. The reason is that the FC hurdle changes the composition of the control data set, such that a different significance level (q-value) is obtained for any given gene. This effect can be so large that it changes subsequent post hoc analysis interpretation, such as ontology overrepresentation analysis. CONCLUSION: Our results argue for caution when using SAM. All data sets analysed with SAM could be reanalysed taking into account the potential impact of the use of arbitrary thresholds to trim data sets before significance testing.

Adult↗

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

BACKGROUND: Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. RESULTS: We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. CONCLUSION: Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

Algorithms↗

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

BACKGROUND: We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. RESULTS: In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. CONCLUSION: On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

Algorithms↗

GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.

BACKGROUND: Macrophages play an integral role in the host immune system, bridging innate and adaptive immunity. As such, they are finely attuned to extracellular and intracellular stimuli and respond by rapidly initiating multiple signalling cascades with diverse effector functions. The macrophage cell is therefore an experimentally and clinically amenable biological system for the mapping of biological pathways. The goal of the macrophage expression atlas is to systematically investigate the pathway biology and interaction network of macrophages challenged with a variety of insults, in particular via infection and activation with key inflammatory mediators. As an important first step towards this we present a single searchable database resource containing high-throughput macrophage gene expression studies. DESCRIPTION: The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for gene expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX-MEA follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the searching of expression data from different microarray experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the research community. CONCLUSION: GPX-MEA is the first example of a quality scored gene expression database focussed on a macrophage cellular system that allows efficient identification of transcriptional patterns. The resource will provide novel insights into the phenotypic response of macrophages to a variety of benign, inflammatory, and pathogen insults. GPX-MEA is available through the GPX website at http://www.gti.ed.ac.uk/GPX.

Animals↗

Effects of contrast material on computed tomographic measurements of lung volumes in patients with acute lung injury.

BACKGROUND: Intravenous injection of contrast material is routinely performed in order to differentiate nonaerated lung parenchyma from pleural effusion in critically ill patients undergoing thoracic computed tomography (CT). The aim of the present study was to evaluate the effects of contrast material on CT measurement of lung volumes in 14 patients with acute lung injury. METHOD: A spiral thoracic CT scan, consisting of contiguous axial sections of 10 mm thickness, was performed from the apex to the diaphragm at end-expiration both before and 30 s (group 1; n = 7) or 15 min (group 2; n = 7) after injection of 80 ml contrast material. Volumes of gas and tissue, and volumic distribution of CT attenuations were measured before and after injection using specially designed software (Lungview; Institut National des Télécommunications, Evry, France). The maximal artifactual increase in lung tissue resulting from a hypothetical leakage within the lung of the 80 ml contrast material was calculated. RESULTS: Injection of contrast material significantly increased the apparent volume of lung tissue by 83 +/- 57 ml in group 1 and 102 +/- 80 ml in group 2, whereas the corresponding maximal artifactual increases in lung tissue were 42 +/- 52 ml and 31 +/- 18 ml. CONCLUSION: Because systematic injection of contrast material increases the amount of extravascular lung water in patients with acute lung injury, it seems prudent to avoid this procedure in critically ill patients undergoing a thoracic CT scan and to reserve its use for specific indications.

Adult↗

Establishment of the Brazilian telehealth network for paediatric oncology.

A telemedicine network has been established in Brazil to support distance medical practice in paediatric oncology. ONCONET comprises a national network of universities, research institutes and medical institutions. The system is Web-based and hosted on a high-performance computing infrastructure based on clusters of computers. It is based on open-source software, designed to provide high performance, fault tolerance and high availability. The ONCONET began operation in 2004. Currently, 30 hospitals affiliated to the Brazilian Society for Paediatric Oncology are users of the ONCONET. Six hospitals are connected by broadband access through the National Education and Research Network and 24 by conventional Internet access. The Multimedia Patients Registry also became operational in 2004, and its database contains information on 3,200 patients from the 30 hospitals. The technological platform was notable for its low production cost. It thus appears to be a sustainable solution to the problem of delivering continuing medical education in a large country with widely dispersed health professionals.

Brazil↗

Review article: some cost-benefit considerations for PACS: a radiological perspective.

Some cost-benefit considerations for a picture archiving and communication system (PACS) are discussed in relation to a hospital-wide PACS. The acquisition of plain radiography by phosphor f2p4ing plate technology (currently state of the art computed radiography), the soft copy display of the clinical history and radiological reports in association with the corresponding images, and the retrieval and simultaneous display of past with current images, are all considered to be integral to a true PACS. Cost-benefit considerations for a PACS extend far beyond the purely economic issues. More important and far reaching consequences relate to efficient data management provided by a PACS properly interfaced to hospital and radiological information systems. The hardware required to install and operate a hospital-wide PACS is now ubiquitously available and its performance has been amply demonstrated by a number of filmless hospitals. Software design and implementation is now the outstanding consideration determining the clinical and, in particular, the radiological benefit of a PACS.

Cost-Benefit Analysis↗

Virtual reality for simulation of radiographic projections: validation of projection geometry.

OBJECTIVE: To develop a software for virtual reality (VR) simulation of X-ray images based on perspective projections through a patient model derived from data from a CT examination and to evaluate the accuracy in the projection geometry obtained by the software. METHODS: A VR software was developed on a personal computer, with models of a patient, an X-ray machine and a detector. The model of the patient was derived from data from a CT examination of a dry skull. Simulated radiographic images of the patient model could be rendered as perspective projections based on the relative positions between the models. The projection geometry of the software was validated by developing an artificial CT data set containing high attenuation points as objects to be imaged. The accuracy in projection geometry was evaluated in a systematic way. The distances between two dots, representing the projected test points in the simulated radiographic images, were measured. They were compared with theoretical calculations of the corresponding distances using traditional mathematical tools. RESULTS: The difference between the simulated and calculated projected distances never exceeded 0.5 mm. The error in simulated projected distances was in most cases within 1%. No systematic errors were revealed. CONCLUSION: The software, developed for personal computers, can produce simulated X-ray images with high geometric accuracy based on perspective projections through a CT data set. The software can be used for simulation of radiographic examinations.

Computer Simulation↗

Perceptibility curve test for conventional and colour-coded radiographs.

OBJECTIVE: A colour scale has been developed as a complement to the grey scale in radiographs. The aim of the present study was to compare colour-coded with conventional black-and-white radiographs in terms of the perceptibility curve test. MATERIALS AND METHODS: Twelve digital radiographs were exposed on a test object from low to high exposures and recorded using the DIXI system (Planmeca Oy, Helsinki, Finland). An aluminium test object was used containing ten object details in the form of holes with depths ranging from 0.03 mm to 0.30 mm in steps of 0.03+/-0.01 mm. The new colour scale was used to transform the conventional black-and-white radiographs into colour radiographs by specially designed software. Ten observers were asked to analyse four sets of radiographs, i.e. colour-coded and black-and-white radiographs, and reversed colour-coded and reversed black-and-white radiographs. The object detail having the lowest perceptible contrast in each radiograph was registered for each observer. Perceptibility curves were plotted based on the mean value of observer data. RESULTS: Results from the perceptibility curve test showed that the information in colour-coded radiographs was at least as good as that in black-and-white radiographs. In fact, in the lower exposure range, colour-coded radiographs exhibited better perception than conventional black-and-white radiographs. CONCLUSION: Radiographs that are colour-coded with the applied colour scale may be used as an alternative to conventional black-and-white radiographs.

Absorptiometry, Photon↗

Software for automated application of a reference-based method for a posteriori determination of the effective radiographic imaging geometry.

OBJECTIVES: Presentation and validation of software developed for automated and accurate application of a reference-based algorithm (reference sphere method: RSM) inferring the effective imaging geometry from quantitative radiographic image analysis. METHODS: The software uses modern pattern recognition and computer vision algorithms adapted for the particular application of automated detection of the reference sphere shadows (ellipses) with subpixel accuracy. It applies the RSM algorithm to the shadows detected, thereby providing three-dimensional Cartesian coordinates of the spheres. If the three sphere centres do not lie on one line, they uniquely determine the imaging geometry. Accuracy of the computed coordinates is investigated in a set of 28 charge-coupled device (CCD)-based radiographs of two human mandible segments produced on an optical bench. Each specimen contained three reference spheres (two different radii r1=1.5 mm, r2=2.5 mm). True sphere coordinates were assessed with a manually operated calliper. Software accuracy was investigated for a weighted and unweighted algebraic ellipse-fitting algorithm. RESULTS: The critical depth- (z-) coordinates revealed mean absolute errors ranging between 1.1+/-0.7 mm (unweighted version; r=2.5 mm) and 1.4+/-1.4 mm (weighted version, r=2.5 mm), corresponding to mean relative errors between 5% and 6%. Outliers resulted from complete circular dense structure superimposition and one obviously deformed reference sphere. CONCLUSIONS: The software provides information fundamentally important for the image formation and geometric image registration, which is a crucial step for three-dimensional reconstruction from > or =2 two-dimensional views.

Algorithms↗