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PubMed1990

SPLICE, a computer program for automated extraction of information from GenBank sequence entries.

SPLICE, a software tool for the extraction of sequences from files in GenBank tape format, has been developed. The program can analyze the features table in this format and use any of the information provided to write the corresponding sequences into a standard sequence file format suitable for use with sequence analysis programs. Sequences that are present as several subsequent fragments in a single GenBank file, such as those encoding a peptide, can be spliced together by the program. Further, sequences that are present in more than one Genbank file, such as an exon which spans several different files, can also be spliced into one sequence. SPLICE runs under the MS/DOS and Unix operating systems, can be called as a sub-process by other programs and can process batches of files.

Animals↗
PubMed2001

Microarrays: handling the deluge of data and extracting reliable information.

Application of powerful, high-throughput genomics technologies is becoming more common and these technologies are evolving at a rapid pace. Genomics facilities are being established in major research institutions to produce inexpensive, customized cDNA microarrays that are accessible to researchers in a broad range of fields. These high-throughput platforms have generated a massive onslaught of data, which threatens to overwhelm researchers. Although microarrays show great promise, the technology has not matured to the point of consistently generating robust and reliable data when used in the average laboratory. This article addresses several aspects related to the handling of the deluge of microarray data and extracting reliable information from these data. We review the essential elements of data acquisition, data processing and data analysis, and briefly discuss issues related to the quality, validation and storage of data. Our goal is to point out some of the problems that must be overcome before this promising technology can achieve its full potential.

DNA, Complementary↗
PubMed1991

Duration of visible persistence in relation to stimulus complexity.

Visible persistence refers to the phenomenal impression that a stimulus is still present after its offset. A dispute exists whether visible persistence is due to temporal sluggishness in the visual pathway (neural hypothesis) or whether it is a byproduct of information-extraction processes under cognitive control (process hypothesis). This was investigated by manipulating stimulus complexity in five temporal integration experiments and one recognition memory experiment. According to the process hypothesis, complex stimuli should persist longer than simple stimuli because they require more information extraction. This prediction was not confirmed; in all six experiments, complexity was found to have no reliable effect on the duration of visible persistence. By contrast, and in accordance with earlier findings, complexity was shown to have a significant effect on a short-lived, nonvisible form of memory known as schematic persistenc. This pattern of results supports two major conclusions: First, that the effects of complexity reported in earlier research were probably on schematic--rather than visible--persistence; and second, that visible persistence must be regarded as a residual neural trace of an extinguished stimulus, rather than as a byproduct of information-extraction processes.

Adult↗
PubMed2003

On the intersubject generalization ability in extracting kinematic information from afferent nervous signals.

In the recent past, many efforts have been carried out in order to evaluate the feasibility of implementing closed-loop controlled neuroprostheses based on the processing of sensory electroneurographic (ENG) signals. The success of these techniques mostly relies on the development of processing algorithms capable of extracting the necessary kinematic information from these signals. Soft-computing algorithms can be very useful when dealing with the complexity of the neuromuscular system because of their generalization ability and model-free structure. In this paper, these techniques were used to extract angular position information from the ENG signals recorded from muscle afferents in animal model using cuff electrodes. Specifically, a genetic algorithm-based dynamic nonsingleton fuzzy logic system (named GA-DNSFLS) was developed and tested on different types of angular trajectories (characterized by small or large angular excursions). In particular, two different Takagi-Sugeno-Kang (TSK)-like structures were used in the consequent part of the neuro-fuzzy model in order to verify which one could improve the generalization abilities (intrasubject and intersubject). The results showed that the GA-DNSFLS was able to reconstruct the trajectories giving interesting results in terms of correlation between the actual and the predicted trajectories for small excursion movements during intrasubject and intersubject tests. Particularly, one of the TSK models showed better results in terms of intersubject generalization. The simulations conducted with the large excursion movements led in some cases to interesting results but further experiments are necessary in order to analyze this point more in deep.

Action Potentials↗
PubMed2003

FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes.

FIE2 (5' end Information Extraction v2) is a web-based program for easy identification and extraction of nucleotide sequence around the start of genes (promoter region) and their translation initiation site (TIS). Using information provided by the National Center for Biotechnology Information's (NCBI's) LocusLink, FIE2 identifies the 5'-most end of a gene on its respective chromosome based on alignment of a selected set of mRNAs representative of the gene. FIE2 then uses currently available human genome sequence information to extract the desired sequences. The accuracy of the information extracted is therefore limited by the accuracy and completeness of the sequence annotation and sequence alignment provided by LocusLink. In addition, multiple TIS positions are also occasionally presented, for example, as a result of multiple alignments of transcript variants. One of the key criteria of FIE2 is that it should extract only the correct information or attempt no extraction at all. To date, the authors are not aware of any publicly available web-based tool that uses the human genomic sequence to extract pertinent promoter- and TIS-region information in this fashion. FIE2 is freely available at http://sdmc.lit.org.sg/FIE2.0.

Base Sequence↗
PubMed2006

Improvement of statistical potentials and threading score functions using information maximization.

We show that statistical potentials and threading score functions, derived from finite data sets, are informatic functions, and that their performance depends on the manner in which data are classified and compressed. The choice of sequence and structural parameters affects estimates of the conditional probabilities P(C|S), the quantification of the effect of sequence S on conformation C, and determines the amount of information extracted from the data set, as measured by information gain. The mathematical link between information gain and mean conformational energy, established in this work using the local backbone potential as model, demonstrates that manipulation of descriptive parameters also alters the "energy" values assigned to native conformation and to decoy structures in the test pool, and consequently, the performance of such statistical potential functions in fold recognition exercises. We show that sequence and structural partitions that maximize information gain also minimize the mean energy of the ensemble of native conformations. Moreover, we establish an informatic basis for the placement of the native score within an energy spectrum given by the decoy pool in a threading exercise. We discover that, among all informatic quantities, information gain is the best predictor of threading success, even better than the standard Z-score. Consequently, the choices of sequence and structural descriptors, extent of compression, and levels of discretization that maximize information gain must also produce the best potential functions. Strategies to optimize these parameters with respect to information extraction are therefore relevant to building better statistical potentials. Last, we demonstrate that the backbone torsion potential, defined by the trimer sequence, can be an effective tool in greatly reducing the set of possible conformations from a vast decoy pool.

Amino Acid Sequence↗
PubMed1998

Multipoint genetic mapping of quantitative trait loci using a variable number of sibs per family.

We present a multipoint algorithm to map quantitative trait loci (QTLs) using families from outbred populations with a variable number of sibs. The algorithm uses information from all markers on a chromosome simultaneously to extract information of QTL segregation. A previous multipoint method (Kruglyak & Lander (1995) American Journal of Human Genetics 57, 439-454) extracts information using a hidden Markov model. However, this method is restricted to small families (< 10 sibs). We present an approximate hidden Markov model approach that can handle large sibships while retaining similar efficiency to the previous method. Computer simulations support the notion that data sampled from a small number of large families provide more power than data obtained from a large number of small families, under the constraint that the total number of individuals for the two schemes is the same. This is further reflected in simulations with variable family sizes, where variance in family size improves the statistical power of QTL detection relative to a constant size control.

Chromosome Mapping↗
PubMed2000

Early use of inhaled corticosteroids in the emergency department treatment of acute asthma.

BACKGROUND: Systemic corticosteroids therapy is central to the management of acute asthma The use of inhaled steroids may also be beneficial in this setting. OBJECTIVES: To determine the benefit of ICS for the treatment of patients with acute asthma managed in the emergency department (ED). SEARCH STRATEGY: Randomised controlled trials (RCTs) were identified from the Cochrane Airways Review Group register. Bibliographies from included studies, known reviews, and texts also were searched. SELECTION CRITERIA: Only RCTs or quasi-randomised trials were eligible for inclusion. Studies were included if patients presented with acute asthma to the ED or its equivalent, and were treated with ICS or placebo, in addition to standard therapy. Two reviewers independently selected potentially relevant articles, and then independently selected articles for inclusion. Methodological quality was independently assessed by two reviewers. DATA COLLECTION AND ANALYSIS: Data were extracted independently by two reviewers if the authors were unable to verify the validity of extracted information. Missing data were obtained from the authors or calculated from other data presented in the paper. MAIN RESULTS: Seven trials were selected for inclusion, but data were not available for one of them. In the six usable rials, (4 adult, 2 paediatric), a total of 352 patients were studied (179 ICS, 173 non-ICS treated). Patients treated with ICS were less likely to be admitted to hospital (OR: 0.30; 95% CI: 0.16, 0.57). This benefit was confined to patients not receiving concomitant systemic steroids. Such patients showed the same, but non-significant, trend towards reduced admissions compared to placebo treatment (OR 0.46; 95% CI: 0. 19, 1.11). In children, ICS appeared to be at least as effective as systemic steroids (OR 0.5; 95% CI: 0.24, 1.06). Patients receiving ICS demonstrated small, significant improvements in peak expiratory flows (PEFR WMD: 7%; 95% CI: 3, 13) and forced expiratory volumes (FEV-FEV1 WMD: 5.0%; 95% CI: 0.4, 9.7). The treatment was well tolerated, with few reported adverse side effects. REVIEWER'S CONCLUSIONS: Inhaled steroids reduced admission rates in patients with acute asthma who were not receiving concomitant systemic steroids. In children, inhaled steroids appear to be at least as effective as systemic steroids. Further research is needed to clarify the effect of ICS when used in addition to systemic corticosteroids, and to determine the optimal dose, agent, and frequency of ICS administration.

Acute Disease↗
PubMed2001

What's left if the Jabberwock gets the semantics? An ERP investigation into semantic and syntactic processes during auditory sentence comprehension.

This study examined auditory ERP responses to syntactic phrase structure violations occurring either in sentences containing regular words or in sentences in which content words had been replaced by pseudowords while retaining morphological markers (so-called jabberwocky sentences). Syntactic violations were found to elicit an early anterior negativity followed by a P600 for both types of sentences, suggesting that the syntactic processes in question are independent of the presence of lexical-semantic information. In syntactically correct sentences, content words in regular sentences elicited an N400 component while their pseudoword place-holders in jabberwocky sentences did not. By contrast, in syntactically incorrect sentences neither sentence type showed an N400 for the word creating the syntactic violation, indicating that the detection of a syntactic error at an early stage blocks semantic integration processes in regular sentences. We discuss these results and findings from related studies in the light of a timing hypothesis of syntactic and semantic information processing and propose that syntactic information extracted particularly early can affect semantic processes while syntactic information extracted relatively late cannot.

Adult↗
PubMed1998

Skin biopsy techniques for the internist.

OBJECTIVE: To review three commonly performed skin biopsy procedures: shave, punch, and excision. DATA SOURCES: English-language articles identified through a MEDLINE search (1966-1997) using the MeSH headings skin and biopsy, major dermatology and primary care textbooks, and cross-references. STUDY SELECTION: Articles that reviewed the indications, contraindications, choice of procedure, surgical technique, specimen handling, and wound care. DATA EXTRACTION: Information was manually extracted from all selected articles and texts; emphasis was placed on information relevant to internal medicine physicians who want to learn skin biopsy techniques. DATA SYNTHESIS: Shave biopsies require the least experience and time but are limited to superficial, nonpigmented lesions. Punch biopsies are simple to perform, have few complications, and if small, can heal without suturing. Closing the wound with unbraided nylon on a C-17 needle will enhance the cosmetic result but requires more expertise and time. Elliptical excisions are ideal for removing large or deep lesions, provide abundant material for many studies, and can be curative for a number of conditions, but require the greatest amount of time, expertise, and office resources. Elliptical excisions can be closed with unbraided nylon using a CE-3 or FS-3 needle in thick skin or a P-3 needle on the face. All specimens should be submitted in a labeled container with a brief clinical description and working diagnosis. CONCLUSIONS: Skin biopsies are an essential technique in the management of skin diseases and can enhance the dermatologic care rendered by internists.

Biopsy↗
PubMed2000

Cranberries for preventing urinary tract infections.

BACKGROUND: Cranberries (particularly in the form of cranberry juice) have been used widely for several decades for the prevention and treatment of urinary tract infections. The aim of this review is to assess the effectiveness of cranberries in preventing such infections. OBJECTIVES: To assess the effectiveness of cranberry juice and other cranberry products in preventing urinary tract infections in susceptible populations. SEARCH STRATEGY: Electronic databases and the Internet were searched using English and non English language terms; companies involved with the promotion and distribution of cranberry preparations were contacted; reference lists of review articles and relevant trials were searched. SELECTION CRITERIA: All randomised or quasi randomised controlled trials of cranberry juice/products for the prevention of urinary tract infections in susceptible populations. Trials of men, women or children were included. DATA COLLECTION AND ANALYSIS: Reviewers RJ and LM independently assessed and extracted information using specially designed data extraction forms. For each included trial, information was collected on methods of the trial, participants, interventions and outcomes. We were unable to perform statistical analysis due to the nature of the data available for review. MAIN RESULTS: Four trials met the inclusion criteria (three cross-over, one parallel group). Three compared the effectiveness of cranberry juice versus placebo juice or water and one compared the effectiveness of cranberry capsules versus placebo. Two further trials were excluded. The outcomes of interest were number of urinary tract infections in each group (symptomatic and asymptomatic), side effects and adherence to therapy. Data from three out of the four trials indicated that cranberries were effective for at least one of the outcomes of interest. The quality of the four included trials was poor, however, and thus the reliability of the results must be questionable. REVIEWER'S CONCLUSIONS: The small number of poor quality trials gives no reliable evidence of the effectiveness of cranberry juice and other cranberry products. The large number of dropouts/withdrawals from the trials indicates that cranberry juice may not be acceptable over long periods of time. Other cranberry products such as cranberry capsules may be more acceptable. On the basis of the available evidence, cranberry juice cannot be recommended for the prevention of urinary tract infections in susceptible populations. Further properly designed trials with relevant outcomes are needed.

Beverages↗
PubMed1998

Medical language processing applied to extract clinical information from Dutch medical documents.

In this paper, we want to show how an existing morpho-syntactic analyser for Dutch (Dutch Medical Language Processor--DMLP) has been extended in order to produce output that is compatible with the language independent modules of the LSP-MLP system (Linguistic String Project--Medical Language Processor) of the New York University. The former can focus on idiosyncrasies for Dutch and take advantage of the language independent developments of the latter. This general strategy will be illustrated by a practical application, namely the extraction of clinical information from Dutch patient discharge summaries. Such an application can be of use for education, research and quality control purposes in a hospital environment.

Humans↗
PubMed2004

Information and aggression in fishes.

Aggressive interactions between fishes commonly take place in a social environment in which uninvolved individuals (bystanders) have an opportunity to gather information about interactants. Signals frequently used during such interactions are designed to transmit information about resource-holding power and/or intention. They are generally related to the level of escalation reached and the eventual outcome of a fight. We consider here the information available in signaling and nonsignaling aspects of aggressive interactions. We focus, in particular, on information available to bystanders. We summarize evidence that bystanders alter their behavior toward interactants on the basis of information acquired while bystanding, and we discuss the sources of information that may result in this change of behavior. In particular, we distinguish eavesdropping (i.e., extracting information from signaling interactions) as a subset of bystanding (i.e., extracting information from all available sources). We conclude that considerations of aggressive strategies should include potential costs and benefits resulting from wider social contexts in which aggression occurs.

Adaptation, Psychological↗
PubMed2005

Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes.

MOTIVATION: The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method. RESULTS: To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes. AVAILABILITY: The ACS program is available upon request from the authors.

Artificial Intelligence↗
PubMed1999

Exploring the dense mapping of a region of potential linkage in complex disease: an example in multiple sclerosis.

In 1996 we reported the results of a genome screen in multiple sclerosis, in which potential linkage was identified in a total of twenty regions, including the centromeric region of chromosome 5. In order to investigate the efficiency of typing dense arrays of markers in regions of potential linkage, we have typed an additional nineteen microsatellite markers from this chromosome 5 region (D5S623 - D5S428) in the same sibling pair families. The mean additional information extracted per marker typed declined with increasing map density, while inaccuracies in the mapping and the density of genotyping errors increased. Our empirical results suggest that, in linkage-based experiments, there is a limit to the benefits that are gained from typing additional markers in the same families. Increasing map density up to the 2.5-5 cM level efficiently extracts valuable extra information; however, beyond this level efficiency declines while the confounding effects of mapping and genotyping errors accumulate. We, therefore, recommend that extra markers typed in linkage studies be limited to this level of resolution. Mapping regions beyond this density should only be initiated when searching for linkage disequilibrium.

Chromosome Mapping↗
PubMed2006

Role of geographic information system (GIS) in watershed simulation by WinVAST model.

The uncertainty of modeling input will increase the simulation error, and this situation always happens in a model without user-friendly interface. WinVAST model, developed by the University of Virginia in 2003, treats an entire multi-catchment by a tree-view structure. Its extra computer programs can connect geographic information system (GIS). Model users can prepare all the necessary information in ArcGIS. Extracting information from GIS interface can not only decrease the inconvenience of data input, but also lower the uncertainty due to data preparation. The Daiyuku Creek and Qupoliao Creek in the Fei-tsui reservoir watershed in Northern Taiwan provided the setting for the case study reported herein. The required information, including slope, stream length, subbasin area, soil type and land-use condition, for WinVAST model should be prepared in a Microsoft Access database, which is the project file of WinVAST with extension mdb. In ArcGIS interface, when the soil layer, land-use layer, and Digital Elevation Model (DEM) map are prepared, all the watershed information can be created as well. This study compared the simulation results from automatically generated input and manual input. The results show that the relative simulation error resulting from the rough process of data input can be around 30% in runoff simulation, and even reach 70% in non-point source pollution (NPSP) simulation. It could conclude that GIS technology is significant for predicting watershed responses by WinVAST model, because it can efficiently reduce the uncertainty induced by input errors.

Computer Simulation↗
PubMed1985

Identification of best electrocardiographic leads for diagnosing myocardial infarction by statistical analysis of body surface potential maps.

This study describes a practical approach for the extraction of diagnostic information from body surface potential maps. Body surface potential map data from 361 subjects were used to identify optimal subsets of leads and features to distinguish 184 normal subjects from 177 patients with myocardial infarction (MI). Multivariate analysis was performed on 120-lead data, using as features instantaneous voltage measurements on time-normalized QRS and STT waveforms. Several areas on the map, most of which were located outside the precordial region, contained leads with important discriminant features; 2 of the 3 limb leads (aVR and aVF) also exhibited high diagnostic capability. A total of 6 features (mostly STT measurements) from 3 locations accounted for a specificity of 95% and a sensitivity of 95%; these were the right subclavicular area, the left posterior axillary region and the left leg. As a comparison, the same number of features from the standard 12-lead electrocardiogram yielded a sensitivity of 88% for a specificity of 95%. To investigate the repeatability of the results, the entire population was separated into a training set (100 normal subjects and 100 patients with MI) and a testing set (84 normal subjects and 77 patients with MI); computing a discriminant function on the training set and applying it to the testing set only moderately deteriorated the diagnostic classification. It is concluded that this approach achieves efficient information extraction from body surface potential maps for improved diagnostic classification.

Adult↗
PubMed2005

Finding the fittest fold: using the evolutionary record to design new proteins.

For many years, the holy grail of protein engineering has been the design of artificial amino acid sequences that fold into stable proteins with desired functions. In the current issue of Nature, two papers from the Ranganathan group (Russ et al., 2005; Socolich et al., 2005) report remarkable success in the design of artificial WW domains. Their method, termed statistical coupling analysis (Lockless and Ranganathan, 1999), does not use structural or physicochemical information but instead extracts information about essential patterns of amino acids from the evolutionary record.

Amino Acid Sequence↗