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Perceptual "read-out" of conjoined direction and disparity maps in extrastriate area MT.

Cortical neurons are frequently tuned to several stimulus dimensions, and many cortical areas contain intercalated maps of multiple variables. Relatively little is known about how information is "read out" of these multidimensional maps. For example, how does an organism extract information relevant to the task at hand from neurons that are also tuned to other, irrelevant stimulus dimensions? We addressed this question by employing microstimulation techniques to examine the contribution of disparity-tuned neurons in the middle temporal (MT) visual area to performance on a direction discrimination task. Most MT neurons are tuned to both binocular disparity and the direction of stimulus motion, and MT contains topographic maps of both parameters. We assessed the effect of microstimulation on direction judgments after first characterizing the disparity tuning of each stimulation site. Although the disparity of the stimulus was irrelevant to the required task, we found that microstimulation effects were strongly modulated by the disparity tuning of the stimulated neurons. For two of three monkeys, microstimulation of nondisparity-selective sites produced large biases in direction judgments, whereas stimulation of disparity-selective sites had little or no effect. The binocular disparity was optimized for each stimulation site, and our result could not be explained by variations in direction tuning, response strength, or any other tuning property that we examined. When microstimulation of a disparity-tuned site did affect direction judgments, the effects tended to be stronger at the preferred disparity of a stimulation site than at the nonpreferred disparity, indicating that monkeys can selectively monitor direction columns that are best tuned to an appropriate conjunction of parameters. We conclude that the contribution of neurons to behavior can depend strongly upon tuning to stimulus dimensions that appear to be irrelevant to the current task, and we suggest that these findings are best explained in terms of the strategy used by animals to perform the task.

Animals↗

Leukotriene-receptor antagonists and 5-lipoxygenase inhibitors in asthma.

OBJECTIVE: To familiarize readers with a potentially new class of compounds for treating asthma. Background information on leukotrienes is provided in addition to an in-depth review of pertinent clinical trials. DATA SOURCES: Information was obtained from controlled clinical trials, abstracts, and review articles identified through a MEDLINE search of English-language articles. STUDY SELECTION: Emphasis was placed on early clinical trials that showed some benefit with these compounds as well as more recent studies using newer agents that produced more promising results. DATA EXTRACTION: Information regarding leukotriene biochemistry was extracted from basic science research and data from human studies were evaluated by the authors according to patient selection, study design, methodology, and therapeutic response. DATA SYNTHESIS: Leukotrienes have a pathophysiologic role in asthma. Two distinct but pharmacologically similar classes of leukotriene inhibitors are currently being clinically evaluated. These are leukotriene receptor antagonists and 5-lipoxygenase inhibitors. Early clinical trials with these agents yielded unfavorable results primarily because of lack of drug potency and selectivity, poor patient tolerance, and possibly the route of administration. Subsequent studies with more potent and selective agents have further implicated leukotrienes as biochemical mediators in asthma and, consequently, have shown promising clinical outcomes with respect to pulmonary function testing and patient tolerance. CONCLUSIONS: Advancements in the pathogenesis of asthma are beginning to define a role for the leukotrienes. Although more studies are needed to assess the efficacy of leukotriene inhibitors, recent clinical trials using leukotriene-receptor antagonists and 5-lipoxygenase inhibitors indicate a potential for the expansion of therapeutic regimens currently used in the treatment of asthma.

Arachidonate 5-Lipoxygenase↗

Aggregating automatically extracted regulatory pathway relations.

Automatic tools to extract information from biomedical texts are needed to help researchers leverage the vast and increasing body of biomedical literature. While several biomedical relation extraction systems have been created and tested, little work has been done to meaningfully organize the extracted relations. Organizational processes should consolidate multiple references to the same objects over various levels of granularity, connect those references to other resources, and capture contextual information. We propose a feature decomposition approach to relation aggregation to support a five-level aggregation framework. Our BioAggregate tagger uses this approach to identify key features in extracted relation name strings. We show encouraging feature assignment accuracy and report substantial consolidation in a network of extracted relations.

Artificial Intelligence↗

Use of toxicological information in drug design.

This paper is an extension of the keynote address and another talk at the Symposium on the Use of Toxiciological Information in Drug Design. The symposium was organized by American Chemical Society's Chemical Information Division at the 220th National Meeting of the American Chemical Society in Washington, DC, August 20-24, 2000. We outline an approach for meeting the scientific information needs of the U.S. Food and Drug Administration (FDA). Ready access to scientific information is critical to support safety-related regulatory decisions and is especially valuable in situations where available experimental information from in vivo/in vitro studies are inadequate or unavailable. This approach also has applications for lead selection in drug discovery. A pilot electronic toxicology/safety knowledge base and computational toxicology initiative is underway in the FDA Center for Drug Evaluation and Research (CDER) that may be a prototype for an FDA knowledge base. The objectives of this effort are: (i) to strengthen and broaden the scientific basis of regulatory decisions, (ii) to provide the Agency with an electronic scientific institutional memory, (iii) to create a scientific resource for regulatory and applied research, and (iv) to establish an internal Web-based support service that can provide decision support information for regulators that will facilitate the review process and improve consistency and uniformity. An essential component of this scientific knowledge base is the creation of a comprehensive electronic inventory of CDER-regulated substances that permit identification of clusters of substances having similar chemical, pharmacological or toxicological activities, and molecular structure/substructures. Furthermore, the inventory acts as a pointer and link to other databases and critical non-clinical and clinical pharmacology/toxicology studies and reviews in FDA archives. Clusters of related substances are identified through the use of: (i) an extensive index of alternative names for each substance, (ii) a molecular structure key field consisting of a rudimentary or core structure represented as an ISIS.mol-file, (iii) global search terms (molecular group, chemical class, clinical indication, or pharmacologic activity), and (iv) molecular clustering using structure/sub-structure similarity indices. The information contained in a toxicology knowledge database has limited value unless means are available to extract information, identify relationships, and create and test hypotheses. One such means is computational toxicology, also called in silico toxicology, ComTox, or e-TOX. Computational toxicology is the application of computer technology and information processing (informatics) to analyze, model, and estimate chemical toxicity based upon structure activity relationships (SAR). A computational toxicology software package, MCASE, has been evaluated and successfully improved by CDER through the incorporation of data from FDA archives and concomitant alterations of the logic used in the interpretation of the results to reflect the data analysis and hazard identification practices and priorities of the Center. Our modifications and uses of the MCASE program are discussed in detail.

Databases, Factual↗

Within-ear and across-ear interference in a dichotic cocktail party listening task: effects of masker uncertainty.

Increases in masker variability have been shown to increase the effects of informational masking in non-speech listening tasks, but relatively little is known about the influence that masker uncertainty has on the informational components of speech-on-speech masking. In this experiment, listeners were asked to extract information from a target phrase that was presented in their right ear while ignoring masking phrases that were presented in the same ear as the target phrase and in the ear opposite the target phrase. The level of masker uncertainty was varied by holding constant or "freezing" the talkers speaking the masking phrases, the semantic content used in the masking phrases, or both the talkers and the semantic content in the masking phrases within each block of 120 trials. The results showed that freezing the semantic content of the masking phrase in the target ear was the only reduction in masker uncertainty that ever resulted in a significant improvement in performance. Providing feedback after each trial improved performance overall, but did not prevent the listeners from making incorrect responses that matched the content of the frozen target-ear masking phrase. However, removing the target-ear contents corresponding to the masking phrase from the response set resulted in a dramatic improvement in performance. This suggests that the listeners were generally able to understand both of the phrases presented to the target ear, and that their incorrect responses in the task were almost entirely a result of their inability to determine which words were spoken by the target talker.

Adult↗

A criterion-shift model for enhanced discriminability in perceptual identification: a note on the counter model.

The original version of the counter model for perceptual identification (Ratcliff & McKoon, 1997) assumed that word frequency and prior study act solely to bias the identification process (i.e., subjects have a tendency to prefer high-frequency and studied low-frequency words, irrespective of the presented word). In a recent study, using a two-alternative forced-choice paradigm, we showed an enhanced discriminability effect for high-frequency and studied low-frequency words (Wagenmakers, Zeelenberg, & Raaijmakers, 2000). These results have led to a fundamental modification of the counter model: Prior study and high frequency not only result in bias, but presumably also result in a higher rate of feature extraction (i.e., better perception). We demonstrate that a criterion-shift model, assuming limited perceptual information extracted from the flash as well as a reduced distance to an identification threshold for high-frequency and studied low-frequency words, can also account for enhanced discriminability.

Cues↗

Melanoma incidence and trends in the Nelson-Marlborough area of New Zealand.

AIMS: To determine the recent incidence of melanoma in the Nelson-Marlborough area of New Zealand and to compare this with a formerly determined incidence from the same area and with published incidences and trends elsewhere in New Zealand and Queensland. METHODS: All histopathology reports for the region were examined retrospectively each four weeks and relevant information extracted. In cases of doubt, pathologists were consulted and cases reviewed. Population, demographic and weather information was obtained from statistical records. RESULTS: These showed a doubling of the incidence since the previous survey with a reduction in female incidence. There was marked reduction in the incidence in the age groups 20-39 with an increase in those over 60 years. The number of superficial more easily cured lesions were almost doubled with marked reduction in the more sinister thicker and nodular lesions. CONCLUSIONS: The incidence of melanoma in the region is increasing at a rate comparable with other areas but with significant reductions in the incidence of thicker and more advanced melanoma as well as a decreased incidence in those under 40 years of age. The incidence in Nelson-Marlborough still remains very high but is slightly less than that shown for the Tauranga district over a similar period.

Adult↗

Learning statistical models for annotating proteins with function information using biomedical text.

BACKGROUND: The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein with codes from the Gene Ontology (GO) using the text of an article from the biomedical literature as evidence. METHODS: Our system relies on simple statistical analyses of the full text article provided. We learn n-gram models for each GO code using statistical methods and use these models to hypothesize annotations. We also learn a set of Naïve Bayes models that identify textual clues of possible connections between the given protein and a hypothesized annotation. These models are used to filter and rank the predictions of the n-gram models. RESULTS: We report experiments evaluating the utility of various components of our system on a set of data held out during development, and experiments evaluating the utility of external data sources that we used to learn our models. Finally, we report our evaluation results from the BioCreative organizers. CONCLUSION: We observe that, on the test data, our system performs quite well relative to the other systems submitted to the evaluation. From other experiments on the held-out data, we observe that (i) the Naïve Bayes models were effective in filtering and ranking the initially hypothesized annotations, and (ii) our learned models were significantly more accurate when external data sources were used during learning.

Bayes Theorem↗

The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text.

Interpretation of semantic propositions in free-text documents such as MEDLINE citations would provide valuable support for biomedical applications, and several approaches to semantic interpretation are being pursued in the biomedical informatics community. In this paper, we describe a methodology for interpreting linguistic structures that encode hypernymic propositions, in which a more specific concept is in a taxonomic relationship with a more general concept. In order to effectively process these constructions, we exploit underspecified syntactic analysis and structured domain knowledge from the Unified Medical Language System (UMLS). After introducing the syntactic processing on which our system depends, we focus on the UMLS knowledge that supports interpretation of hypernymic propositions. We first use semantic groups from the Semantic Network to ensure that the two concepts involved are compatible; hierarchical information in the Metathesaurus then determines which concept is more general and which more specific. A preliminary evaluation of a sample based on the semantic group Chemicals and Drugs provides 83% precision. An error analysis was conducted and potential solutions to the problems encountered are presented. The research discussed here serves as a paradigm for investigating the interaction between domain knowledge and linguistic structure in natural language processing, and could also make a contribution to research on automatic processing of discourse structure. Additional implications of the system we present include its integration in advanced semantic interpretation processors for biomedical text and its use for information extraction in specific domains. The approach has the potential to support a range of applications, including information retrieval and ontology engineering.

Abstracting and Indexing↗

Safeguarding the confidentiality of automated medical information.

BACKGROUND: Information about encounters between patients and physicians, nurses, and other caregivers is recorded on paper and in computer databases. Caregivers are expected to respect the confidential nature of patient information. Yet quality management programs, for example, entail systematic, efficient collection of information extracted from patient case files. Compiling "report cards" on managed care networks necessitates access to aggregated information on episodes of care and their outcomes. Regional provider networks; the development of comprehensive computerized patient records; and the dependence of health care reform on large-scale, highly distributed databases make the patient record even more vulnerable. Each organization must assess whether its protection of patients' privacy is sufficient. AN INFORMATION SECURITY PROGRAM: A logical first step in devising such a program is to establish the necessary policies, which are prerequisites to the proper development of computer systems. A policy should address such issues as the authorized access needs to sensitive information and limitations concerning secondary use; the application of technical, procedural, physical, and personnel safeguards; and the dissemination of information. Information managers should seek opportunities to install commercially secure products that meet their security requirements. CONCLUSIONS: Top management, information systems planners, and quality improvement leaders must jointly determine policies that satisfy the duty to preserve patients' confidentiality, foster the most effective use of information in the patient record, and avoid overly restrictive policies that would impede total quality management.

Computer Security↗

Cytomegalovirus prophylaxis and treatment following bone marrow transplantation.

OBJECTIVE: To provide an overview of the role of cytomegalovirus (CMV) in the bone marrow transplant (BMT) population and update the current methods of prevention and treatment of CMV infection and disease, with emphasis on CMV interstitial pneumonia (CMV-IP). DATA SOURCES: The current medical literature, including abstracts presented at recent national and international meetings, is reviewed. References were identified by searching the MEDLINE database from January 1988 through June 1994. The reference lists of the published studies and reviews obtained from the initial literature search were reviewed as well. STUDY SELECTION: Data regarding the epidemiology of CMV, the risk factor associated with CMV infection and disease, as well as data on the prevention and the treatment of CMV infection and disease in the BMT population are cited. Specific attention was focused on randomized, placebo-controlled studies pertaining to the prevention of CMV infection and disease in CMV-immunoglobulin G positive recipients undergoing allogeneic BMT. Information from nonrandomized, placebo-controlled studies was included in the absence of stronger data. DATA EXTRACTION: Information contributing to CMV in the BMT population was reviewed. Data supporting and disputing specific preventive and treatment modalities are presented. DATA SYNTHESIS: The incidence of CMV seropositivity in the general population is high and while BMT becomes a widely accepted treatment modality, CMV reactivation and subsequent disease, especially CMV-IP, becomes a significant prognostic factor of morbidity and mortality. Even though antiviral agents such as ganciclovir and foscarnet can inhibit the viral replication in vivo, they have not been able to treat CMV-IP effectively. It has been suggested that CMV-IP is an immunopathologic process that can cause irreversible damage, hence, the low efficacy of antiviral therapy and the associated high mortality. Immunomodulating agents such as intravenous immune globulin and cytomegalovirus hyperimmune globulin can increase the efficacy of antivirals in the treatment of CMV-IP. This further supports the postulated immunopathologic process of this disease. The lack of understanding of the pathophysiology of the disease compromised the efforts of treatment and led to the development of preventive interventions with antiviral and immunomodulatory regimens that resulted in a significantly lower incidence of infection and disease. As a result of current data, the Eastern Cooperative Oncology Group has published guidelines for the prevention and treatment of CMV infection and disease. CONCLUSIONS: The prognosis of CMV disease in the BMT recipients has improved as a result of a wide variety of modifications in the management of BMT recipients. These include an increased understanding of the risk factors associated with CMV infection, routine screening for CMV replication and excretion, and more effective prophylactic regimens. Still, more than half of the patients who develop pneumonia will die, indicating that more studies are needed to increase the understanding of the pathophysiology and refine the preventive and therapeutic regimens against CMV.

Antiviral Agents↗

Epilepsy monitoring and advice recorded: general practitioners' views, current practice and patients' preferences.

BACKGROUND: Epilepsy is a common condition that is managed at the interface between primary and secondary care. AIM: A study aimed to describe general practitioners' criteria for aspects of optimal epilepsy care and their estimates of current levels of care achieved; to compare these estimates with clinical data extracted from their patients' medical records; and to compare general practitioners' estimates and recorded data with information provided by the patients themselves. METHOD: Thirty seven general practitioners from six practices in the south Thames region were sent a questionnaire enquiring about current practice with regard to general practitioner and specialist monitoring of patients with epilepsy and provision of advice, and about their criteria for the optimum levels of aspects of epilepsy care. Of patients aged over 15 years in the study practices, 0.6% were found to have active epilepsy; 283 of these 326 patients were sent a questionnaire enquiring about their epilepsy, the service and advice provided, and whether they required more information. Responses to the general practitioners' questionnaire and to the patients' questionnaire were compared and also compared with information extracted from the patients' medical records. RESULTS: Ninety five per cent of the general practitioners responded. Of 255 patient questionnaires (90%) returned, 251 could be analysed. Of 247 patients, 168 (68%) reported having had no seizure in the previous six months. Forty of 241 patients (17%) had a regular arrangement to see their general practitioner regarding their epilepsy. Of 191 patients who expressed a preference, 116 (61%) reported preferring to receive their epilepsy care mainly from their general practitioner. General practitioners reported that ideally patients should be monitored in primary care every six months (the median recorded frequency was 14 months) and that there should be a record of advice given to all patients on driving, adverse effects of antiepileptic drugs, and self-help groups. Advice was recorded in patients' records as having been given on driving (46% of records), adverse effects of antiepileptic drugs (9%), and self-help groups (3%); 82 of 237 patients (35%) reported not receiving enough advice. CONCLUSION: Patients generally preferred to receive their epilepsy care in general practice. Monitoring and provision of advice were less than optimal from both the general practitioners' and the patients' point of view. New resources and skills will be necessary to bridge this perceived gap. Specially trained nurses may have a role in this monitoring and advice provision.

Adolescent↗

Perceptual parsing of acoustic consequences of velum lowering from information for vowels.

Three experiments were designed to investigate how listeners to coarticulated speech use the acoustic speech signal during a vowel to extract information about a forthcoming oral or nasal consonant. A first experiment showed that listeners use evidence of nasalization in a vowel as information for a forthcoming nasal consonant. A second and third experiment attempted to distinguish two accounts of their ability to do so. According to one account, listeners hear nasalization in the vowel as such and use it to predict that a forthcoming nasal consonant is nasal. According to a second, they perceive speech gestures and hear nasalization in the acoustic domain of a vowel as the onset of a nasal consonant. Therefore, they parse nasal information from a vowel and hear the vowel as oral. In Experiment 2, evidence in favor of the parsing hypothesis was found. Experiment 3 showed, however, that parsing is incomplete.

Female↗

Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences.

The Olfactory Receptor Database (ORDB; http://senselab.med.yale.edu/senselab/ordb) is a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. To deal with the very large OR gene family, we have constructed an algorithm that automatically downloads sequences from web sources such as GenBank and SWISS-PROT into the database. The algorithm uses hypertext markup language (HTML) parsing techniques that extract information relevant to ORDB. The information is then correlated with the metadata in the ORDB knowledge base to encode the unstructured text extracted into the structured format compliant with the database architecture, entity attribute value with classes and relationship (EAV/CR), which supports the SenseLab project as a whole. Three population methods: batch, automatic and semi-automatic population are discussed. The data is imported into the database using extensible markup language (XML).

Algorithms↗

Neural network technique for detecting emergency states in neurosurgical patients.

The problem of reliable detection of life-threatening situations in the neurosurgical patient undergoing treatment in the ICU is still far from reaching a satisfactory solution, although several methods of clinical and instrumental evaluation have recently been developed for the early detection of oncoming signs of danger. Continuous monitoring of intracranial pressure (ICP) provides neurosurgeons with valuable information about the current condition of the patient. However, it is increasingly felt that traditional methods of extracting information from the ICP signal have reached their natural limits, mostly because of difficulties in fitting the appropriate mathematical model to this non-linear and non-stationary process. Successful implementations of artificial neural networks in many medical tasks have encouraged the application of this method of ICP processing. Two problems are considered: the prediction of trends in ICP, and recognition of the configuration of unfavourable symptoms likely to signal danger for the neurosurgical patient. The construction of neural network predictors of ICP trends is based on wavelet pre-processing of the original signal. The approach to the second task involves pre-processing of the ICP with spectral and statistical methods and classification of the extracted features of the current signal on an arbitrarily selected scale of danger.

Brain Diseases↗

Aids and services for disabled people-getting the message across.

Information about aids and services for disabled people has two primary target audiences - the administrators and the disabled recipients - and their needs and problems are different. The administrators experience problems with the diversity and poor quality of information available to them, making it difficult for them to keep up-to-date in all relevant areas without becoming massively overloaded. The disabled themselves suffer from problems related to the whole information dissemination system. They are often referred from one agency to another and are frequently required to extract information rather than having it freely volunteered. Their decreased functional ability, mobility, motivation and sometimes educational level compound this problem so that many disabled people frequently fail to find out about their entitlements. Two areas of information availability causing great problems to both groups are those of aids and financial assistance. Aids supplied to disabled people in their own homes are currently much underused and the take-up rate for financial benefits is frequently quite low. Some solutions to these problems include improvements in the quality of information available to both groups by ensuring more appropriate form and content, communication medium and distribution points. The recognition that most people prefer to ask for information rather than seek it out from written sources is important since the provision of a 'named' person employed by Local Authorities in this capacity would contribute greatly to the improved dissemination of information.

Journal Article↗

Information structure and the relative efficacy of tables and graphs.

Users and system designers often prefer to display information with graphs rather than with tables. However, empirical studies that compared task performance with the two display types frequently revealed either an advantage of tables over graphs or no differences between the displays. This apparent contradiction may result from previous studies in which the importance of the structure that usually exists in displayed information is overlooked. We predict that graphic displays will have an advantage over tables when the displayed information has structure and when this structure is relevant for the task. These conditions generally exist in the actual use of information displays, but have seldom been assessed in experiments. In the present study participants in an experiment performed an information extraction task and a prediction task with unstructured or structured data and with different levels of prior information about the structure. The results showed that the information structure and prior knowledge about the existence of structure affected the advantage of graphic displays over tables when task performance depended on the use of structure. Existing approaches to the study of displays were analyzed in view of these findings. Actual or potential applications of this research include the development of better displays for process control and decision support and better operator training programs.

Analysis of Variance↗

Epidural blood patching for preventing and treating post-dural puncture headache.

BACKGROUND: Dural puncture is a common procedure, but leakage of CSF from the resulting dural defect may cause postural headache after the procedure, and this can be disabling. Injecting an epidural blood patch around the site of the defect may stop this leakage, and so may have a role in preventing or treating post dural puncture headache. OBJECTIVES: To assess the possible benefits and harms of epidural blood patching in both the prevention and the treatment of post-dural puncture headache. SEARCH STRATEGY: We searched the Cochrane Controlled Trials Register (Cochrane Library, Issue 4, 2000), MEDLINE (January 1994 to December 1998), and EMBASE (January 1980 to December 1998). We also searched the reference lists of relevant articles identified electronically, and asked both the authors of all included trials and colleagues with an interest in this area to let us know of any other potentially relevant studies not already identified. Date of last search: December 2000. SELECTION CRITERIA: We sought all properly randomised, unconfounded trials that compared epidural blood patch versus no epidural blood patch in the prevention or treatment of post-dural puncture headache among all types of patients undergoing dural puncture for any reason. The primary outcome of effectiveness was postural headache. DATA COLLECTION AND ANALYSIS: One reviewer extracted details of trial methodology and outcome data from the reports of all trials considered eligible for inclusion. We invited the authors of all such trials both to check the information extracted and to provide any details that were unavailable in the published reports. Intention-to-treat analyses were performed using the Peto O-E method. Information about adverse effects (post-dural puncture backache, epidural infection and lower limb paraesthesia) was also extracted. MAIN RESULTS: Three trials (77 patients) were eligible for inclusion. Methodological details were generally incomplete. Although the results of our analyses suggested that both prophylactic and therapeutic epidural blood patching may be of benefit, the very small numbers of patients and outcome events, as well as uncertainties about trial methodology, precluded reliable assessments of the potential benefits and harms of this intervention. REVIEWER'S CONCLUSIONS: Further, adequately powered, randomised trials (including at least a few hundred patients) are required before reliable conclusions can be drawn about the role of epidural blood patching in the prevention and treatment of post-dural puncture headache.

Blood Patch, Epidural↗