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PubMed2005

Automated Microarray Image Analysis Toolbox for MATLAB.

UNLABELLED: The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source, microarray image analysis tool that allows the user to customize analyses of microarray image sets. This tool provides several methods to identify and quantify spot statistics, as well as extensive diagnostic statistics and images to evaluate data quality and array processing. The open, modular nature of AMIA provides access to implementation details and encourages modification and extension of AMIA's capabilities. AVAILABILITY: The AMIA Toolbox is freely available at http://www.pnl.gov/statistics/amia. The AMIA Toolbox requires MATLAB 6.5 (R13) (MathWorks, Inc. Natick, MA), as well as the Statistics Toolbox 4.1 and Image Processing Toolbox 4.1 for MATLAB or more recent versions. CONTACT: amanda.white@pnl.gov

Algorithms↗

PubMed2006

Using cognitive interviews to develop surveys in diverse populations.

BACKGROUND: Conceptual equivalence of measures is essential in research that compares health across diverse racial/ethnic groups. Cognitive interviews are pretest methods to explore the conceptual equivalence of survey items. Systematic approaches for using these methods are emerging. OBJECTIVE: We describe an interaction analysis (IA) approach using qualitative data analysis software to analyze transcripts of cognitive interviews in a study to develop a survey instrument of the quality of interpersonal processes of care of diverse patients. Cognitive interviews included standard administration of the survey followed by retrospective probes for selected items. SUBJECTS: Interviews were completed with 48 Latino, black, and non-Latino white respondents 18 years of age or older with at least one doctor's visit in the past 12 months. Participants averaged 45.8 years in age (standard deviation [SD] = 18.4), 58% were women, and mean education was 14.7 years (SD = 4.0). RESULTS: Problems were identified in 126 of 159 items (79%). Behavior coding identified 32 problematic items (20%). IA of the transcript of the survey and retrospective probes identified 94 additional problematic items (59%). IA often revealed the nature of the problems, enabling decisions to modify or drop items based on respondents' comments. Behavior coding and IA identified ethnic and language similarities and differences in the use of response sets and the interpretation of items. CONCLUSIONS: IA and behavior coding of cognitive interview transcripts can identify efficiently problems with items and their source to increase the likelihood of the revised items being conceptually equivalent across ethnic groups.

Adult↗

PubMed2003

Reanalysis of clause boundaries in Japanese as a constraint-driven process.

When processing the initial segment of a sentence, readers may favor an interpretation that will turn out to be incorrect as more words are read. In these cases, a reanalysis process is necessary in order to correct the mental representation built up to that point. It has been previously proposed that readers obey a minimum change restriction, as they prefer to change the mental representation as little as possible. The present paper reports two experiments in Japanese suggesting that a minimal change restriction is unnecessary to characterize reanalysis. It is proposed instead that the present data and previous observations are more naturally explained by a constraint-driven model in which revisions are performed only when required by parsing constraints.

Adult↗

PubMed1995

Bilingual special education teachers' shifting paradigms: complex responses to educational reform.

This study examined the nature and process of change among five bilingual special education teachers as they attempted to modify existing instructional practices. Three factors affected the change process: (a) The more special education training in the teachers' background, the stronger their reductionist orientation; (b) change involves shifts in instructional practices and shifts in beliefs, and they do not automatically go hand in hand; and (c) change is most facilitated at the beginning stages of collaboration by including practicing members of the teachers' occupational community as agents of change.

Attitude↗

PubMed1997

The nature of memory processes underlying recognition judgments in the process dissociation procedure.

The hypothesis is tested that the memory processes involved in recognition judgments in the process dissociation procedure are the same as those involved in standard source-monitoring tasks. It is shown how source-monitoring response categories can be mapped onto process dissociation response categories. On the basis of this abbreviation, an experiment was conducted in which it was possible to compare, using a multinomial modeling approach, the parameters representing memory processes in the process dissociation procedure with those involved in source monitoring. For the two different encoding conditions realized, the results are compatible with the hypothesis that the same processes are involved in source monitoring and in recognition judgments in the process dissociation procedure. Implications for the interpretation of the model's parameters are discussed.

Adolescent↗

PubMed2005

Motion processing specialization in Williams syndrome.

Williams syndrome (WS) is a rare genetic disorder characterized by severe spatial deficits and relatively spared language. Although initial research suggested that WS entails a generalized motion processing deficit, later work demonstrated intact biological motion perception in people with WS, reflecting a sparing of a specific motion perception system. The present study examined whether this sparing is unique to biological motion, or extends to other motion tasks as well. WS children and adults and normal controls were tested to examine developmental changes across a variety of motion tasks. Results indicated that WS individuals performed at normal levels for motion coherence and biological motion tasks but had elevated thresholds for the 2-D form-from-motion task, a profile that extended into adulthood. These findings provide evidence that a genetic impairment can lead to a selective motion processing deficit and argue against characterizing WS as including a general motion processing impairment. The nature of the motion deficit is considered, including the implications for WS dorsal/ventral processing.

Adolescent↗

PubMed1997

Category-specific naming deficit for medical terms after dominant thalamic/capsular hemorrhage.

Postmortem, retrograde degeneration, and electrical stimulation studies have implicated the anterior pulvinar in language processing. We examined a patient who, after a hemorrhage affecting the dominant pulvinar and internal capsule, exhibited a circumscribed anomia for medical items and conditions. No other language disturbance was noted. Five category-specific word lists, matched for word frequency, were administered in a naming-to-definition format. Results indicated that the patient exhibited a significant category-specific naming deficit for medical items and conditions compared to matched control subjects. Although medical item lists were found to differ from nonmedical item lists in imageability and abstractness, B.C.'s category-specific deficit did not seem to be caused by word frequency, concept familiarity, imageability, or abstractness. Nor could the patient's performance be explained on the basis of deficits in broader semantic classifications (i.e., animate vs inanimate or man-made vs natural). The patient was unable to retrieve medical items even when given phonemic cues for those he could not name. Findings indicate that subtotal damage in the dominant pulvinar may create category-specific deficits.

Aphasia↗

PubMed2002

Similarity relations among spoken words: the special status of rimes in English.

This paper presents an analysis of the distribution of phonological similarity relations among monosyllabic spoken words in English. It differs from classical analyses of phonological neighborhood density (e.g., Luce & Pisoni, 1998) by assuming that not all phonological neighbors are equal. Rather, it is assumed that the phonological lexicon has psycholinguistic structure. Accordingly, in addition to considering the number of phonological neighbors for any given word, it becomes important to consider the nature of these neighbors. If one type of neighbor is more dominant, neighborhood density effects may reflect levels of segmental representation other than the phoneme, particularly prior to literacy. Statistical analyses of the nature of phonological neighborhoods in terms of rime neighbors (e.g., hat/cat), consonant neighbors (e.g., hat/hit), and lead neighbors (e.g., hat/ham) were thus performed for all monosyllabic words in the Celex corpus (4,086 words). Our results show that most phonological neighbors are rime neighbors (e.g., hat/cat) in English. Similar patterns were found when a corpus of words for which age-of-acquisition ratings were available was analyzed. The resultant database can be used as a tool for controlling and selecting stimuli when the role of lexical neighborhoods in phonological development and speech processing is examined.

Humans↗

PubMed1992

An evaluation of concept based latent semantic indexing for clinical information retrieval.

Latent Semantic Indexing (LSI) of surgical case report text using ICD-9-CM procedure codes and index terms was evaluated. The precision-recall performance of this two-step matrix retrieval process was compared with the SMART Document retrieval system, surface word matching, and humanly assigned procedure codes. Human coding performed best, two-step LSI did less well than surface matching or SMART. This evaluation suggests that concept-based LSI may be compromised by its two-stage nature and its dependence upon a robust term database linked to main concepts. However, the potential elegance of partial- credit concept matching merits the continued evaluation of LSI for clinical case retrieval.

Abstracting and Indexing↗

PubMed2005

Teaching and learning about culture: a European journey.

UNLABELLED: This paper explores the evolving nature of an understanding of culture through attendance on an Intensive Programme (IP) funded by ERASMUS-SOCRATES. AIMS: The purpose of this paper is to report a journey of learning about culture through attendance on a ERASMUS-SOCRATES funded Intensive Programme (IP) for nurses in Hasselt, Belgium. METHOD: This paper seeks to describe the process and experience of our involvement through an examination of the authors' participation as teachers and students. This was undertaken using serial taped group and individual interviews. The metaphor of the IP as a journey is described and used as the vehicle for data collection and analysis. FINDINGS: The key findings were the development of key themes relating to: Personal Values and Culture, Engagement and Culture, Personality and Culture and Physicality and Culture. Discussion of these findings raises issues of language and language skill, communication and listening skills, stereotyping, personal awareness, cultural awareness, sensitivity and competence. CONCLUSIONS: It is proposed that direct engagement through programmes, such as the reported IP, with other nurses and nurse educationalists in Europe is an essential part of any modern nursing curriculum and aids the development of internationalisation. Without such direct engagement there is potential for a narrower, limited view of culture and a lack of sensitivity in understanding our own and other cultures.

Cultural Diversity↗

PubMed1998

The acquisition of plural marking in English and German revisited: schemata versus rules.

This article contributes to a debate in the linguistic and psychological literature that centres around the representation of morphologically complex words in the grammar and in the lexicon. The issue is whether inflectional morphology is rule-based (i.e. symbolically represented), or whether the assumption of pattern association is more adequate to account for the facts. On the basis of the analysis of acquisitional data the article strongly argues for the latter alternative. In a classic experiment that helped shape the development of acquisition theory Berko (1958) reported substantial support for ITEM-AND-PROCESS rules in the acquisition of plural morphology in English. A large part of her results were zero responses (repetition of the stimulus). A reinterpretation of these zero responses in light of schema theory and the cue strength hypothesis shows a striking departure from randomness. Berko's subjects tended to repeat stimuli just to the extent that these already resembled a plural schema. A reinterpretation of data reported in Innes (1974) achieved compatible results. This data set is far more extensive than Berko's and is used in the present study to put the schema model to a more stringent test. A reinterpretation of a parallel experiment with German children, using the cue strength analysis of the more complex plural morphology of German yielded parallel results. Finally, natural acquisitional data obtained from seven German speaking children aged between 2;1 and 2;9 are analysed. Again, strong support is found for the schema model. It is suggested that a schema-learning mechanism may underlie the acquisition of morphology, even when the end product of the learning process involves item-and-process rules, as in the case of English plural formation. In a schema-learning model, the child builds schematic representations for possible singular and plural lexical items as whole gestalts, and attempts to map concrete forms onto these schemata in deciding whether the forms have singular or plural value.

Child↗

PubMed1993

Effects of word predictability, child development, and aging on time-gated speech recognition performance.

This study examined the interaction of acoustic-phonetic information with higher-level linguistic contextual information during the real-time speech perception process in child, young adult, and older adult listeners. Five age groups were studied: (a) young children ranging in age from 5 to 7 years, (b) older children aged 8 to 10 years, (c) young adults aged 18 to 23 years, (d) older adults aged 60 to 69 years, and (e) older adults aged 70 to 83 years. All subjects were presented with time-gated monosyllabic target words presented in sentence contexts containing contrasting levels of word predictability. Findings indicated that target word predictability influenced the timing and nature of the real-time recognition process including the listeners' use of initial word sounds. Predictability-high (PH) words were recognized earlier and with greater confidence than predictability-low (PL) words. PH recognition performance was more influenced by child development and aging than PL recognition performance. Older adult listeners required more PH-gated word stimuli to produce accurate responses than younger adults. Older children showed more effective use of PH contexts than younger children.

Acoustic Stimulation↗

PubMedDate not supplied

[The linguistic skills of infants under the age of one year].

INTRODUCTION: It is amazing how all normal children, systematically exposed to a natural language, speak using well-formed sentences by the time they are about 3 years old. This is a universally observed fact that is made possible by a series of mechanisms which mostly remain unexplained. This article reviews a series of studies concerning the linguistic capabilities of infants aged up to twelve months, which were evaluated using both behavioural and neuroimaging methods. DEVELOPMENT: Learning a language means learning its sounds, its words and its grammatical rules. During the first year of life this learning is not very apparent, since it is essentially perceptive and seems to occur without the need to make an effort. Yet, acquiring one's native language is no trivial matter because speech does not offer any known physical evidence that systematically indicates the occurrence of sounds, words and/or grammatical rules. A human being starts to process speech just a few hours after birth; nevertheless, this early sensitivity is not enough to 'know' a particular language. In fact, during their early years, children will have to learn the properties that are relevant to their mother tongue, while at the same time ignoring those that are irrelevant. Processing language is accompanied by changes in brain activity which can be explored using safe neuroimaging methods, such as electroencephalogram recordings and optical topography. CONCLUSION: A deeper understanding of the cognitive and neural foundations of the early linguistic skills of children will make a significant contribution to dealing with both normal development and language disorders.

Cerebral Cortex↗

PubMed1996

Verb comprehension deficits in probable Alzheimer's disease.

Studies of lexical comprehension in probable Alzheimer's disease (pAD) have focused almost exclusively on nouns. In the following preliminary study, we examined whether lexical comprehension for verbs is also impaired in 25 pAD patients. The semantic meaning of motion verbs, cognition verbs, and perception verbs was assessed with a triadic comparison task. Structural meaning associated with these verbs was evaluated by asking the patients to judge the coherence of sentence frames that accept these verbs naturally or awkwardly. We found that pAD patients are significantly impaired at identifying semantic relations among verbs. pAD patients also encountered significantly more difficulty judging the coherence of sentences than control subjects. Correlation and regression analyses demonstrated that semantic characteristics of verbs are projected from the verb's sentence frames in control subjects, but there was minimal evidence for such a structural-semantic relationship in pAD. We consider several possible explanations for our preliminary observations of an impairment that has consequences for processing both semantic and structural aspects of verb meaning.

Aged↗

PubMed1994

Nonlinear phonology: introduction and clinical application.

The purpose of this tutorial is to introduce a recent advance in phonological theory, "nonlinear phonology," which differs fundamentally from previous theories by focusing on the hierarchical nature of relationships among phonological units. We first introduce the basic concepts and assumptions of nonlinear phonological theory and then demonstrate clinical applications of the theory for assessment and intervention. Data from a child with a severe phonological disorder are used to illustrate aspects of nonlinear theory. The data are first analyzed in terms of phonological processes in order to provide the readers with a familiar starting point for comprehension and comparison. The nonlinear frameworks are shown to provide a deeper analysis of the child's phonological system than the phonological process analyses and to lead to a more clearly defined intervention plan.

Articulation Disorders↗

PubMed1986

Informative content of narrative discourse in right-brain-damaged right-handers.

Thirty-six right-brain-damaged (RBD) right-handers and 20 controls (C) were submitted to a narrative production task using the pictorial representation of a trivial story. Each subject's narrative was analyzed, using a "propositional analysis," in order to study amount as well as nature of informative content. Results show that RBD subjects' narratives contain a smaller amount of information that did not appear to be related to a smaller amount of verbal output or to the presence of a visual neglect, that the information contained in RBD subjects' narratives appears to be a subset of that contained in C subjects' narratives, and that these results do not pertain to all C or RBD subjects, since both groups are nonhomogeneous. Even though these results are not linked to the presence of some visual neglect or visual agnosia per se, they could be, at least in part, the expression of some degree of perceptive difficulties of the iconography. However, they are also interpreted as expressing a problem with the organization of narrative discourse at levels of cognitive processing which may not be exclusive to language, but which are nonetheless essential for discourse organization.

Brain Damage, Chronic↗

PubMed1993

Early reading performance: a comparison of teacher-based and test-based assessments.

An unresolved question in early screening is whether test-based or teacher-based assessments should form the basis of the classification of children at risk of educational failure. Available structured teacher rating scales are lacking in predictive validity, and teacher predictions of students likely to experience reading difficulties have yielded disappointing true positive rates, with teachers failing to identify the majority of severely disabled readers. For this study, three educational screening instruments were developed: (a) a single teacher rating, categorizing children into three levels of reading ability (advanced, average, poor); (b) a 15-item teacher questionnaire designed to measure students' cognitive and language ability, attentional and behavioral characteristics, and academic performance; and (c) a battery of language and reading tests that are predictive of, or correlate with, reading failure. The concurrent validity of each instrument was assessed in a sample of 312 Australian schoolchildren from kindergarten, Year 1, and Year 2. Students were assessed at the end of the 1989 school year after having completed 1, 2, or 3 years of schooling. The results suggest that the nature of the skills required for success in reading changes in the first 3 years of schooling. Both teachers and tests concur more closely as children progress through the elementary years and as the risk behavior (reading) becomes more accessible to direct measurement. Carefully focused teacher rating scales may be a cost-effective means of identifying children at risk of reading failure. Improved teacher rating scales should be developed and used to assist in the early screening process.

Child↗

PubMed1996

Self-modifying systems: a model for the constructive origin of information.

The mechanisms of information processing in Turning machines and biological systems are examined from the point of view of physical sets of variables. Computation is characterized as a process, the realization of which involves a bounded set of interactions and a pre-definable set of variables in real systems. Using ideas from process philosophy, the ability of natural systems to transcend these computational modes is discussed. A class of systems, called self-modifying systems, that utilize persistent shifts in their defining interactions and variable composition is introduced. Various other ideas that lead to similarly non-computational or semi-computational scenarios (as in the case of distributed code systems) are referenced. As applications, computer models of emergent phenomena using randomly growing interaction sets as well as theoretical issues that range from the meaning of simulation to the problem of information gain in self-modifying systems are discussed.

Computer Simulation↗