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PubMed2005

Gene/protein name recognition based on support vector machine using dictionary as features.

BACKGROUND: Automated information extraction from biomedical literature is important because a vast amount of biomedical literature has been published. Recognition of the biomedical named entities is the first step in information extraction. We developed an automated recognition system based on the SVM algorithm and evaluated it in Task 1.A of BioCreAtIvE, a competition for automated gene/protein name recognition. RESULTS: In the work presented here, our recognition system uses the feature set of the word, the part-of-speech (POS), the orthography, the prefix, the suffix, and the preceding class. We call these features "internal resource features", i.e., features that can be found in the training data. Additionally, we consider the features of matching against dictionaries to be external resource features. We investigated and evaluated the effect of these features as well as the effect of tuning the parameters of the SVM algorithm. We found that the dictionary matching features contributed slightly to the improvement in the performance of the f-score. We attribute this to the possibility that the dictionary matching features might overlap with other features in the current multiple feature setting. CONCLUSION: During SVM learning, each feature alone had a marginally positive effect on system performance. This supports the fact that the SVM algorithm is robust on the high dimensionality of the feature vector space and means that feature selection is not required.

Algorithms↗
PubMed2006

Various criteria in the evaluation of biomedical named entity recognition.

BACKGROUND: Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most frequently used for training and testing biomedical named entity recognition (Bio-NER) systems. JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance. This paper details these differences and describes alternative criteria. We then examine the impact of different criteria and annotation schemes on system performance by retesting systems participated in the above two tasks. RESULTS: To analyze the difference between JNLPBA's and BioCreAtIvE's evaluation, we conduct Experiment 1 to evaluate the top four JNLPBA systems using BioCreAtIvE's classification scheme. We then compare them with the top four BioCreAtIvE systems. Among them, three systems participated in both tasks, and each has an F-score lower on JNLPBA than on BioCreAtIvE. In Experiment 2, we apply hypothesis testing and correlation coefficient to find alternatives to BioCreAtIvE's evaluation scheme. It shows that right-match and left-match criteria have no significant difference with BioCreAtIvE. In Experiment 3, we propose a customized relaxed-match criterion that uses right match and merges JNLPBA's five NE classes into two, which achieves an F-score of 81.5%. In Experiment 4, we evaluate a range of five matching criteria from loose to strict on the top JNLPBA system and examine the percentage of false negatives. Our experiment gives the relative change in precision, recall and F-score as matching criteria are relaxed. CONCLUSION: In many applications, biomedical NEs could have several acceptable tags, which might just differ in their left or right boundaries. However, most corpora annotate only one of them. In our experiment, we found that right match and left match can be appropriate alternatives to JNLPBA and BioCreAtIvE's matching criteria. In addition, our relaxed-match criterion demonstrates that users can define their own relaxed criteria that correspond more realistically to their application requirements.

Algorithms↗
PubMed2006

Color naming deficits and attention-deficit/hyperactivity disorder: a retinal dopaminergic hypothesis.

BACKGROUND: Individuals with Attention-Deficit/Hyperactive Disorder (ADHD) have unexplained difficulties on tasks requiring speeded processing of colored stimuli. Color vision mechanisms, particularly short-wavelength (blue-yellow) pathways, are highly sensitive to various diseases, toxins and drugs that alter dopaminergic neurotransmission. Thus, slow color processing might reflect subtle impairments in the perceptual encoding stage of stimulus color, which arise from hypodopaminergic functioning. PRESENTATION OF HYPOTHESES: 1) Color perception of blue-yellow (but not red-green) stimuli is impaired in ADHD as a result of deficient retinal dopamine; 2) Impairments in the blue-yellow color mechanism in ADHD contribute to poor performance on speeded color naming tasks that include a substantial proportion of blue-yellow stimuli; and 3) Methylphenidate increases central dopamine and is also believed to increase retinal dopamine, thereby normalizing blue-yellow color perception, which in turn improves performance on the speeded color naming tasks. TESTING THE HYPOTHESIS: Requires three approaches, including:1) direct assessment of color perception in individuals with ADHD to determine whether blue-yellow color perception is selectively impaired; 2) determination of relationship between performance on neuropsychological tasks requiring speeded color processing and color perception; and 3) randomized, controlled pharmacological intervention with stimulant medication to examine the effects of enhancing central dopamine on color perception and task performance IMPLICATIONS OF HYPOTHESIS: If substantiated, the findings of color perception problems would necessitate a re-consideration of current neuropsychological models of attention-deficit/hyperactivity disorder, guide psycho-education, academic instruction, and require consideration of stimulus color in many of the widely used neuropsychological tests.

Journal Article↗
PubMed2005

Assessing executive dysfunction in girls with fragile X or Turner syndrome using the Contingency Naming Test (CNT).

The aim of this study was to examine executive function (EF) skills in girls with fragile X or Turner syndrome, using the Contingency Naming Test (CNT). The CNT is a Stroop-like task involving a 1- or 2-attribute contingency rule. We predicted that girls with fragile X would make errors reflecting poor cognitive flexibility and working memory limitations. We predicted that girls with Turner syndrome would have sufficient cognitive flexibility to perform the CNT accurately, but would have difficulty with verbal inhibition and would thus make more self-corrections than girls in a comparison group. The hypotheses were partially supported: relative to their Full Scale IQ-matched comparison group, girls with fragile X or Turner syndrome were slower on the warm-up naming task; girls with fragile X made more errors on the 1-attribute task, and girls with Turner syndrome were less efficient on both the 1- and 2-attribute tasks, without making more self-corrections. These results support previous findings of executive dysfunction associated with fragile X or Turner syndrome. The results suggest that both low IQ and fragile X status contribute to working memory limitations in girls with fragile X and that EF inefficiency in girls with Turner syndrome is due to both working memory limitations and slower response times.

Child↗
PubMed2006

Naming speed and visual search deficits in readers with disabilities: evidence from an orthographically regular language (Italian).

The study examined rapid automatized naming (RAN) in 42 children with reading disabilities and 101 control children-all native speakers of Italian, a language with shallow orthography. Third-, 5th- and 6th-grade children were given a RAN test that required rapid naming of color, object, or digit matrices. A visual search test using the same stimulus material (but not requiring a verbal response) and an oral articulation test were also given. Readers with disabilities performed worse than controls on the RAN test. This effect was larger in higher grades than in lower ones. Readers with disabilities were also slower than controls in performing the visual search test. The pattern of results for the RAN test held constant when the visual search performance was partialed out by covariance analysis, indicating the independence of the 2 deficits. The 2 groups did not differ for articulation rate. Finally, analysis of the pattern of intercorrelations indicated that reading speed was most clearly related to RAN, particularly in the group with reading disabilities. The results extend observations of RAN effects on reading deficits to Italian, an orthographically shallow language.

Attention↗
PubMed1977

Alexia without agraphia, hemianopia, or color-naming defect: a disconnection syndrome.

A patient with alexia without agraphia, hemianopia, or color-naming defect was found at operation to have a meningioma arising from the tentorium cerebelli that compressed the inferior aspect of the left temporal-occipital junction. It is presumed to have involved only the left ventral visual association cortex and its inferior outflow tracts to the angular gyrus. The input from the right occipital area also was disconnected from the visual language verbal association area by involvement of the ventral outflow of the splenium of the corpus callosum. Preservation of color naming and matching suggests that these functions are dependent on the integrity of more dorsal occipital association systems.

Brain Neoplasms↗
PubMed1993

How hard-of-hearing and deaf children learn their names.

Data from a qualitative study on the literacy development of preschool hard-of-hearing and deaf children were analyzed to discover how the children learned to read, write, and spell or fingerspell their names. The research was conducted for 9 months in two preschool classes for hard-of-hearing and deaf children. Four hard-of-hearing and three deaf children participated. Data sources included extensive descriptive and interpretive field notes on classroom observations of the children, and drawing and writing samples from the children. Analysis revealed that the children learned that names are powerful expressions of identity through teacher demonstrations, immersion in a literacy-rich environment, and numerous opportunities to explore written language.

Child, Preschool↗
PubMed1999

L-NAME, a nitric oxide synthase inhibitor, modulates cholinergic antinociception.

Systemic administration of sumatriptan and buspirone (20 mg/kg: 5-HT1A agonists) produced antinociception against acetic acid-induced writhing. The antinociceptive effect was potentiated by cholinomimetic physostigmine (0.05 mg/kg i.p.) and blocked by the muscarinic antagonist atropine (5 mg/kg i.p.). Naloxone, an opiate antagonist, failed to reverse the sumatriptan- or buspirone-induced antinociception, but pindolol (10 mg/kg), a nonselective 5-HT1A antagonist, blocked this response. Sumatriptan- or buspirone-induced antinociception was significantly potentiated by L-NAME (a nitric oxide [NO] synthase inhibitor) although L-NAME (20 mg/kg) given alone had no effect on the nociceptive threshold. Recent studies have suggested that the L-arginine/NO/cGMP pathway is involved in the modulation of pain perception. The present results suggest that NO may play a role in cholinergic antinociception-mediated 5-HT1A receptor stimulation and that NO exerts an inhibitory action on cholinergic analgesia.

Acetic Acid↗
PubMed2006

L-NAME prevents anxiety-like and depression-like behavior in rats exposed to restraint stress.

Stressful life events contribute to the development of many neuropsychiatric disorders including depression and anxiety. Animal studies based on the relationship of stress and depression or anxiety are scarce and controversial. Moreover, neither the neurobiological basis of anxiety and depression nor the mechanisms responsible for neurochemical regulation by stressful stimuli are well understood. This study was designed to investigate the possible contribution of both acute (2 h) and chronic (2 h X 15 d) restraint stress in the generation of anxiety and depression, and also to find out whether nitric oxide (NO) has a modulatory role in these behavioral reactions. Elevated plus-maze and forced swimming test (FST) were chosen for assessment of anxiety and depression, respectively, and N(G)-nitro L-arginine methyl ester (L-NAME, 10 mg/kg), a NO synthase (NOS) inhibitor, and L-arginine (50 mg/kg), a NO precursor, were used to evaluate the role of nitrergic system in restraint exposed rats. The results showed that acute and chronic stress caused depression-like and anxiety-like behaviors in rats and the acute inhibition of NOS by L-NAME prevented these acute and chronic stress-induced anxiogenesis and depression. These data lead to the conclusion that stress and NO seem to be involved in the generation of anxiety and depression.

Acute Disease↗
PubMed2006

Naming and counting disorders (conditions) included in newborn screening panels.

The rapid introduction of new technologies for newborn screening is affecting decisions about the disorders (conditions) that are required or offered as an option through public and private newborn screening. An American College of Medical Genetics report to the Health Resources and Services Administration summarized an extensive effort by a group of experts, with diverse expertise within the newborn screening system, to determine a process for selecting a uniform panel of newborn screening disorders. The expert panel did not propose a mechanism for counting or naming conditions. Differences in the nomenclature used to identify disorders have resulted in difficulties in developing a consensus listing and counting scheme for the disorders in the recommended uniform panel. We suggest a system of nomenclature that correlates the screening panel of disorders recommended in the American College of Medical Genetics report with the screening analyte and accepted standardized nomenclature. This nomenclature system is proposed to remove ambiguity and to increase national uniformity in naming and counting screening disorders.

Consensus↗
PubMed2003

A program to convert patients from trade-name to generic clozapine.

In spring 2000, the Missouri Department of Mental Health mandated that its psychiatric inpatient facilities convert patients from trade-name to generic clozapine. The pharmacy department at our facility was encouraged to develop a conversion program to oversee and assess the efficacy and tolerability of the change. A protocol to monitor the conversion of patients to generic clozapine hospitalwide was developed. The primary objective was to determine whether therapeutic response and level of tolerability were the same with generic versus trade-name clozapine. The secondary objective was to determine whether changes in monitoring white blood cell and absolute neutrophil counts were necessary after conversion. Our results showed that most patients did not experience changes greater than a mean of 5 points in their scores on the Brief Psychiatric Rating Scale (BPRS). However, a statistically significant difference was seen in 22 patients who had a mean reduction or an increase of less than 5 points (p=0.0139) in BPRS scores compared with two patients who had a mean increase greater than 5 points. Assessment of percentage change in BPRS scores indicated that 14 (58%) converted patients had a 1-50% decrease in mean BPRS scores, and 10 (42%) had a 1-40% increase. However, of those with a mean BPRS increase, five (50%) had an increase of 10% or less. Our clozapine conversion program resulted in the successful conversion of all 24 patients.

Adult↗
PubMed1995

Differential vocalization in budgerigars: towards an experimental analysis of naming.

In Experiment 1, 3 budgerigars (Melopsittacus undulatus) were trained with food reinforcement to make low- or high-frequency calls in response to different color stimuli, C1 and C2 (a color-naming task), using a gradual response-differentiation procedure and an automatic call-recognition system. Thus, a call within a certain frequency band was reinforced in the presence of C1 ("C1 call"), and a call within a different band was reinforced in the presence of C2 ("C2 call"). In Experiment 2, all 3 budgerigars were trained in a form-to-color matching-to-sample task, alternating trial by trial with either the color-naming task (2 birds) or an identity color matching-to-sample task (1 bird). Sample stimuli for the new matching-to-sample task were forms (F1 or F2) and comparisons were the same two colors (C1 and C2). Given Sample F1 or F2, birds had to make a call to produce Comparison Pair C1 and C2. With F1 as the sample, a peck on C1 was reinforced; with F2 as the sample, a peck on C2 was reinforced. Although no particular call was specified in the presence of F1 and F2, 2 birds made the C1 call in the presence of F1 and the C2 call in the presence of F2. In Experiment 3, the bird that failed to match form and color calls in Experiment 2 and another bird were first trained in a color-to-form matching-to-sample task: C1 to F3 and C2 to F4. In this task, to produce the comparison pair of forms, a high call (or low for the other bird) was required in the presence of C1, and a low call (or high) was required in the presence of C2. Both birds were then trained with an identity matching-to-sample task in which sample and comparison stimuli were the same two forms, F3 and F4. Trials on the identity task alternated with the color-to-form trials. Although no particular call was required in the presence of Samples F3 and F4, both birds came to make the C1 call in the presence of F3 and the C2 call in the presence of F4. Our technique promises to be useful for the study of emergent vocal relations in budgerigars and other animals.

Animals↗
PubMed2005

Naming and categorization in young children: III. Vocal tact training and transfer of function.

Following pretraining with everyday objects, 10 children aged from 1 to 4 years were given common vocal tact training with a set of three pairs of arbitrary stimuli of differing shapes; Set 1. Nine children learned to tact one stimulus as "zog" and the other as "vek" in each pair, and all passed subsequent pairwise tests for the corresponding listener behavior to each listener stimulus (i.e., /zog/ and /vek/, respectively). The children were next trained to clap to one stimulus of Pair 1 and wave to the other, and all then showed name-consistent transfer of these behaviors to the stimuli of Pair 2 and Pair 3. Seven children also were given a test of listener responding to experimenter-modeled clap and wave gestures, respectively, which they all passed. Four of the children next participated in a category match-to-sample test for the Set 1 stimuli; all 4 passed. For each pair of two additional six-stimuli sets, Set 2 and Set 3, 3 children were trained to wave to one stimulus and to clap to the other. For each set, all 3 children showed perfect transfer of the vocal tacts trained to Set 1, and of listener behavior both to the auditory stimuli /zog/ and /vek/ and to experimenter-modeled clap and wave gestures. They also sorted the stimuli perfectly in category match-to-sample tests for Set 2, Sets 1 and 2 combined, Set 3, and Sets 1, 2, and 3 combined. The results show that even in very young children, naming is a powerful means of generating new category relations among as many as 18 arbitrary stimuli.

Child Language↗
PubMed2003

Generic clozapine: a cost-saving alternative to brand name clozapine?

As a consequence of its prevalence, early onset and chronicity, schizophrenia imposes clinical and economic impediments to healthcare practitioners and society alike. Among the many antipsychotics available to treat the symptoms of this devastating illness, clozapine has emerged and differentiated itself from the others as the agent most efficacious for the treatment of refractory patients. Since the patent for Clozaril (Novartis) expired in 1998, three manufacturers of generic clozapine have submitted abbreviated new drug applications to the US FDA for review and approval to market a generic clozapine product. In each case, the US FDA deemed the generic formulations to be bioequivalent to the brand name Clozaril. Apart from case reports, industry-sponsored studies have been conducted comparing Clozaril with two generic formulations. In one case, a generic formulation of clozapine manufactured by Creighton Products Corporation (formerly a subsidiary [generic house] of Sandoz Pharmaceuticals) was found to be bioequivalent to Clozaril. On the other hand, studies (sponsored by Novartis) have challenged the bioequivalence, therapeutic equivalence and interchangeability between Clozaril and a generic formulation manufactured by Zenith Goldline Pharmaceuticals (now IVAX Corporation). The IVAX Corporation-sponsored studies refuted these claims citing data from two patient registry database studies and one small clinical trial. Apart from a single in-house bioequivalence study, no further investigations have been conducted with a third generic formulation manufactured by Mylan Pharmaceutical. Although the clinical significance of the above discrepancy is obvious, what is less than obvious is the pharmacoeconomic implications that arises from this debate. Clearly, if the brand name and generic formulations are 'truly' bioequivalent, then the cost savings realised would be the difference in acquisition cost. On the other hand, if the various formulations are not bioequivalent, then the economic benefits of a lower-priced generic formulation may be compromised. In the worst-case scenario, if a patient decompensates as a result of switching from Clozaril to a generic formulation, the added direct costs (i.e. hospitalisation) and indirect cost (i.e. lost productivity) will most certainly offset any cost savings resulting from the use of a generic formulation. Until further studies have been conducted, we suggest that patients who are treatment refractory and stabilised on Clozaril are not switched to a generic formulation. On the other hand, if a patient is stabilised on Clozaril and not treatment refractory, then cautious switching to a generic formulation may be reasonable. Finally, initiating a generic formulation in a 'clozapine-naïve' individual would be appropriate. The cost implications related to these recommendations will depend on the success or failure of treatment.

Antipsychotic Agents↗
PubMed2005

Evaluating current deficit theories of poor reading: role of phonological processing, naming speed, balance automaticity, rapid verbal perception and working memory.

To clarify the nature of cognitive deficits experienced by poor readers, 9-10-yr.-old poor readers were matched against 9 chronological age and 9 younger reading age-matched controls screened and selected from regular classrooms. Poor readers performed significantly more poorly than chronological age-matched peers on digit naming speed, spoonerisms, and nonsense word reading. Poor readers were also significantly poorer than reading age-matched controls on nonword reading but were significantly better than reading age-matched controls on postural stability. Analyses of effect sizes were consistent with these findings, showing strong effects for digit naming speed, spoonerisms, and nonword reading. However, effect size analysis also suggested that poor readers experienced moderate difficulties with balance automatisation but did not show verbal speech perception deficits relative to either control

Child↗
PubMed1983

Numbers of word associations to color patches and color names differ across two opponent pairs.

68 female undergraduate students completed word-association and semantic-differential tasks in response to stimuli which were patches or names of eight colors. The number of word associations for the group viewing color patches differed from that of the group responding to color names on the basis of four colors forming two of the three opponent pairs of the opponent-process theory of color vision.

Adult↗
PubMed1986

Naming reaction times to tachistoscopically presented pictures: some evidence of right hemisphere encoding.

The present study measured naming reaction times by normal subjects to unilaterally presented picture stimuli. Significant differences in picture-naming reaction time did not exist between left and right visual-field stimulations. The right hemisphere in the intact brain is capable of generating a verbal label for pictured stimuli. A psychological model suggests that a possible processing synergy between the two hemispheres may be tied to spatial processing and elementary linguistics.

Cerebral Cortex↗