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At least 415 records · Page 23Linked to original sources
PubMed2003

Additional, physically ordered markers increase linkage signal for bipolar disorder on chromosome 18q22.

BACKGROUND: We recently reported evidence of linkage of bipolar disorder to chromosome 18q, with a paternal logarithm of odds (LOD) score of 4.67 (p =.004) in a clinically defined subset of families. Like other linkage studies, we had to rely on imprecise genetic maps to establish the marker order. Here, we test for linkage in the same sample with a denser set of markers, now physically ordered according to the draft sequence of the human genome. METHODS: Families were ascertained through probands with bipolar I disorder and diagnosed with reliable methods. Genotypes were generated for 12 microsatellite markers within an 11-centimorgan (cM) region of chromosome 18q22. Multipoint affected sib-pair linkage analysis was performed in a set of 16 nuclear families. RESULTS: The additional markers significantly increased the total genetic information extracted from our sample. We also observed an increase in the LOD score (to 5.42, p =.0066) and linkage resolution. The approximate 1-LOD support interval is now 9 male cM. CONCLUSIONS: The results strengthen our previous findings and further define a region suitable for genetic fine-mapping analysis on chromosome 18q. Our data suggest that a dense set of markers, when physically ordered, can increase the informational value of genetic linkage signals.

Adult↗
PubMed1993

Assessment of sexual mixing patterns.

The manner in which people with varying partner change rates choose their partners may have important implications for the future of the AIDS epidemic. A relatively rapid but small epidemic can be expected if sexual mixing patterns are highly assortative so that those with high partner change rates nearly always choose partners with similar rates. Direct estimation of sexual mixing is exceedingly difficult. On the other hand, information on the way people mix is implicitly contained in the epidemiology of other sexually transmitted diseases (STDs). If mixing is highly assortative, one might expect gonorrhea to be largely confined to a small subsection of the population who would frequently contract the disease repeatedly. In this paper a model of gonorrhea transmission in which partner change rates and preference are dealt with as continuous variables is used to extract information on mixing from data on an Australian heterosexual population. It was found that in this population mixing is not far from random with respect to partner change rates.

Algorithms↗
PubMed2005

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.

We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with other reduced dimensionality approaches, HIFI-NMR collects n-dimensional data as a set of two-dimensional (2D) planes. The HIFI-NMR algorithm incorporates several innovative features. (1) Following the initial collection of two orthogonal 2D planes, tilted planes are selected adaptively, one-by-one. (2) Spectral space is analyzed in a rigorous statistical manner. (3) An online algorithm maintains a model that provides a probabilistic representation of the three-dimensional (3D) peak positions, derives the optimal angle for the next plane to be collected, and stops data collection when the addition of another plane would not improve the data model. (4) A robust statistical algorithm extracts information from the plane projections and is used to drive data collection. (5) Peak lists with associated probabilities are generated directly, without total reconstruction of the 3D spectrum; these are ready for use in subsequent assignment or structure determination steps. As a proof of principle, we have tested the approach with 3D triple-resonance experiments of the kind used to assign protein backbone and side-chain resonances. Peaks extracted automatically by HIFI-NMR, for both small and larger proteins, included approximately 98% of real peaks obtained from control experiments in which data were collected by conventional 3D methods. HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR.

Animals↗
PubMed1995

A class of parametrically excited calcium oscillation detectors.

Intracellular Ca2+ oscillations are often a response to external signals such as hormones. Changes in the external signal can alter the frequency, amplitude, or form of the oscillations suggesting that information is encoded in the pattern of Ca2+ oscillations. How might a cell decode this signal? We show that an excitable system whose kinetic parameters are modulated by the Ca2+ concentration can function as a Ca2+ oscillation detector. Such systems have the following properties: (1) They are more sensitive to an oscillatory than to a steady Ca2+ signal. (2) Their response is largely independent of the signal amplitude. (3) They can extract information from a noisy signal. (4) Unlike other frequency sensitive detectors, they have a flat frequency response. These properties make a Ca(2+)-sensitive excitable system nearly ideal for detecting and decoding Ca2+ oscillations. We suggest that Ca2+ oscillations, in concert with these detectors, can act as cellular timekeepers to coordinate related biochemical reactions and enhance their overall efficiency.

Animals↗
PubMed2005

BioCreAtIvE task 1A: gene mention finding evaluation.

BACKGROUND: The biological research literature is a major repository of knowledge. As the amount of literature increases, it will get harder to find the information of interest on a particular topic. There has been an increasing amount of work on text mining this literature, but comparing this work is hard because of a lack of standards for making comparisons. To address this, we worked with colleagues at the Protein Design Group, CNB-CSIC, Madrid to develop BioCreAtIvE (Critical Assessment for Information Extraction in Biology), an open common evaluation of systems on a number of biological text mining tasks. We report here on task 1A, which deals with finding mentions of genes and related entities in text. "Finding mentions" is a basic task, which can be used as a building block for other text mining tasks. The task makes use of data and evaluation software provided by the (US) National Center for Biotechnology Information (NCBI). RESULTS: 15 teams took part in task 1A. A number of teams achieved scores over 80% F-measure (balanced precision and recall). The teams that tried to use their task 1A systems to help on other BioCreAtIvE tasks reported mixed results. CONCLUSION: The 80% plus F-measure results are good, but still somewhat lag the best scores achieved in some other domains such as newswire, due in part to the complexity and length of gene names, compared to person or organization names in newswire.

Computational Biology↗
PubMed2005

Natural-like function in artificial WW domains.

Protein sequences evolve through random mutagenesis with selection for optimal fitness. Cooperative folding into a stable tertiary structure is one aspect of fitness, but evolutionary selection ultimately operates on function, not on structure. In the accompanying paper, we proposed a model for the evolutionary constraint on a small protein interaction module (the WW domain) through application of the SCA, a statistical analysis of multiple sequence alignments. Construction of artificial protein sequences directed only by the SCA showed that the information extracted by this analysis is sufficient to engineer the WW fold at atomic resolution. Here, we demonstrate that these artificial WW sequences function like their natural counterparts, showing class-specific recognition of proline-containing target peptides. Consistent with SCA predictions, a distributed network of residues mediates functional specificity in WW domains. The ability to recapitulate natural-like function in designed sequences shows that a relatively small quantity of sequence information is sufficient to specify the global energetics of amino acid interactions.

Amino Acid Sequence↗
PubMedDate not supplied

Monitoring maternity services by postal questionnaire: congruity between mothers' reports and their obstetric records.

The validity of information obtained from women about the medical aspects of their childbearing experiences has been assessed by comparing the responses of 223 mothers on a postal questionnaire with information extracted from their medical records. When discrepancies between the two sources were found, it was not assumed that the hospital records were correct. Instead, attempts were made to ascertain why the data might be inconsistent by re-checking the records and by contacting the mothers again. There appeared to be five main reasons for discrepancies: mothers' limited knowledge or understanding of certain procedures; problems of interpretation and definition; occasionally inaccurate or missing information in the medical records; under-reporting of sensitive information by mothers and, finally, questions which were misunderstood or misinterpreted by the mothers. For most items, however, good agreement between the mothers and hospitals was obtained, and the results indicate that valid information over a range of events can be obtained using postal surveys of mothers.

England↗
PubMed1995

Development of motion perception in early infancy.

This article summarizes some research on the development of motion perception in early infancy. The sensitivity for slow and rapid motion was studied with 1-month-old and 3-month-old babies. The findings suggest that there are different developmental courses for the detection of slow and rapid motion. The ability to detect very slow motion seems to improve gradually with age whereas the sensitivity for very rapid motion seems to be at a level comparable to adults soon after birth. Three-month-old babies do use kinetic visual information in order to perceive object boundaries and form. After having seen a form visible only when moving they are able to "identify" the same form when seeing it under static conditions. Infants and young children do use kinetic visual information for recognizing figures that are never completely in sight only if they have been familiarized with the fully visible form first. Even 4-year-olds have difficulties in perceiving the full form of a figure that moves behind a slit in an opaque occluding surface if there is no familiarity or "priming" with the global form first. In conclusion, infants are able to detect visual motion very early in life and do extract information which leads to the perception of form. However, this ability may be limited to events with uninterrupted, continuous movement of visible elements.

Age Factors↗
PubMed1991

An interactive race model of divided attention.

Two classes of models have been proposed to explain how redundant information extracted from separate sources comes to activate a single response. Each provides a fundamentally different account of why responses to redundant signals are typically faster than those to either signal alone (the redundant-signals effect). Independent race models assume that a race occurs between perceptual codes on independent channels and that only the winner activates the response. Coactivation models assume that there is some form of energy or activation-strength summation, with information being pooled across channels prior to decision. An intermediate class of models is introduced and a specific exemplar, the interactive race model, is tested in a series of redundant-target detection experiments. In particular, we examine the effects on performance of two types of contingency that have previously been overlooked as sources of task-relevant information. The results reveal that response times are significantly influenced by both interstimulus and stimulus-response contingencies. The interactive race model provides a natural account of these findings as well as several otherwise puzzling results in the divided-attention literature.

Adult↗
PubMed1996

Kinship and familiarity as factors affecting social transfer of food preferences in adult Mongolian gerbils (Meriones unguiculatus).

Experiments were carried out with Mongolian gerbils (Meriones unguiculatus) to assess whether a socially mediated acquisition of diet selection exists in this species. Results showed that a gerbil was influenced in its diet choices by information extracted during a brief period of interaction with a familiar conspecific that had recently eaten a novel food. Data revealed that the acquisition of a food preference from a conspecific depends on the existence of a social bond between the interacting gerbils. Either genetic relatedness (being brother or sister raised in different litters) or familiarity (being bred in the same litter or being member of a reproductive pair) is necessary for the transfer of information. Unfamiliar and unrelated observer gerbils did not selectively choose their demonstrator's food.

Age Factors↗
PubMed2004

The reporting of theoretical health risks by the media: Canadian newspaper reporting of potential blood transmission of Creutzfeldt-Jakob disease.

BACKGROUND: The media play an important role at the interface of science and policy by communicating scientific information to the public and policy makers. In issues of theoretical risk, in which there is scientific uncertainty, the media's role as disseminators of information is particularly important due to the potential to influence public perception of the severity of the risk. In this article we describe how the Canadian print media reported the theoretical risk of blood transmission of Creutzfeldt-Jakob disease (CJD). METHODS: We searched 3 newspaper databases for articles published by 6 major Canadian daily newspapers between January 1990 and December 1999. We identified all articles relating to blood transmission of CJD. In duplicate we extracted information from the articles and entered the information into a qualitative software program. We compared the observations obtained from this content analysis with information obtained from a previous policy analysis examining the Canadian blood system's decision-making concerning the potential transfusion transmission of CJD. RESULTS: Our search identified 245 relevant articles. We observed that newspapers in one instance accelerated a policy decision, which had important resource and health implication, by communicating information on risk to the public. We also observed that newspapers primarily relied upon expert opinion (47 articles) as opposed to published medical evidence (28 articles) when communicating risk information. Journalists we interviewed described the challenges of balancing their responsibility to raise awareness of potential health threats with not unnecessarily arousing fear amongst the public. CONCLUSIONS: Based on our findings we recommend that journalists report information from both expert opinion sources and from published studies when communicating information on risk. We also recommend researchers work more closely with journalists to assist them in identifying and appraising relevant scientific information on risk.

Bibliometrics↗
PubMed1998

Substance abuse in children: prediction, protection, and prevention.

OBJECTIVE: To review the latest studies on risk and protective factors for the development of substance abuse and the effectiveness of prevention interventions for the pediatric population. DATA SOURCES: Multiple bibliographic databases, including MEDLINE and ERIC, were used to develop a comprehensive review of the literature on substance abuse prevention during the last 10 years. Selected indexing terms included substance abuse prevention, risk factors, and protective factors. Research monographs from the National Institute on Drug Abuse and the Center for Substance Abuse Prevention were used, along with information from authors of prevention curricula. STUDY SELECTION: Study populations included children from birth through adolescence who were enrolled in controlled, prospective, and/or longitudinal studies of either protective or risk factors for the development of substance abuse or response to substance abuse prevention programs. Studies of adult patients that investigated predisposing risk factors for substance abuse (eg, genetic implications) were also used. Care was taken to ensure studies included children from diverse racial and social backgrounds. DATA EXTRACTION: Information was abstracted and summarized from peer-reviewed publications. Controlled random-designed studies were used to determine prevention program efficacy. DATA SYNTHESIS: Main results of the review are summarized in a qualitative format. CONCLUSIONS: Factors that contribute to the emergence of substance abuse in the pediatric population are multifactorial. Behavioral, emotional, and environmental factors that place children at risk for the development of substance abuse may be remediated through prevention and intervention programs that use research-based, comprehensive, culturally relevant, social resistance skills training and normative education in an active school-based learning format.

Adolescent↗
PubMed1993

Time course of object identification: evidence for a global-to-local contingency.

A time course contingency is the modification of later phases of object recognition contingent upon stimulus information extracted earlier in processing. It can increase the efficiency of later processing and reduce computational burdens. This idea was instantiated within a global-to-local model and supported in 4 integration priming experiments, in which primes and target objects were presented briefly and then masked. In Experiment 1-3, global and coarse-grained common-feature primes presented early in processing facilitated discriminations between similarly shaped objects, even though they provided no discrimination-relevant information. In Experiment 4, global primes were more effective than local primes early in processing, whereas local primes were more effective than global primes late in processing.

Adult↗
PubMed2006

TreeDyn: towards dynamic graphics and annotations for analyses of trees.

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

Computer Graphics↗
PubMed1998

Prediction of villages at risk for filariasis transmission in the Nile Delta using remote sensing and geographic information system technologies.

Remote sensing and geographic information system (GIS) technologies were used to discriminate between 130 villages, in the Nile Delta, at high and low risk for filariasis, as defined by microfilarial prevalence. Landsat Thematic Mapper (TM) data were digitally processed to generate a map of landcover as well as spectral indices such as NDVI and moisture index. A Tasseled Cap transformation was also carried out on the TM data which produced three more indices: brightness, greenness and wetness. GIS functions were used to extract information on landcover and spectral indices within one km buffers around the study villages. The relationship between satellite data and prevalence was investigated using discriminant analysis. The analysis indicated that the most important landscape elements associated with prevalence were water and marginal vegetation, while wetness and moisture index were the most important indices. Discriminant functions generated for these variables were able to correctly predict 80% and 74% of high and low prevalence villages, respectively, with an overall accuracy of 77%. The present approach provides a promising tool for regional filariasis surveillance and helps direct control efforts.

Animals↗
PubMed2002

TAIR: a resource for integrated Arabidopsis data.

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.

Arabidopsis↗
PubMed1988

Perception of dynamic information in static handwritten forms.

Handwriting recognition presents a problem for most theories of letter perception. How do people accurately discriminate letters given the variability in handwritten forms? We propose that perceivers detect and capitalize on information relating to production inherent in the static trace of the handwritten letter. In an "implicit detection" task, subjects' ability to detect stroke direction in a series of handwritten characters was found to be influenced by the particular drawing method used to generate the stimuli. Similar results were obtained in an "explicit detection" task in which the subjects were asked to speculate on the drawing method used to generate the samples. Our findings suggest that perceivers are able to extract information relating to production from the static trace. We propose that they can then use this information in conjunction with their knowledge of a common production process, shared by both producers and perceivers, to aid character recognition.

Form Perception↗
PubMed2006

Text mining and its potential applications in systems biology.

With biomedical literature increasing at a rate of several thousand papers per week, it is impossible to keep abreast of all developments; therefore, automated means to manage the information overload are required. Text mining techniques, which involve the processes of information retrieval, information extraction and data mining, provide a means of solving this. By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models.

Artificial Intelligence↗