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PubMed1981

Sensorimotor functioning and prelinguistic communication of severely and profoundly retarded individuals.

The prelinguistic, nonverbal communicative behavior of 40 institutionalized severely and profoundly retarded children and adolescents functioning at various stages of Piaget's sensorimotor period was examined. Five scales of the Uzgiris and Hunt (1975) sensorimotor assessment were used to determine general level of sensorimotor functioning. A standard set of communication elicitation tasks was employed to examine the gestures used to communicate in both imperative and declarative contexts. More competent sensorimotor performance was associated with higher frequency of more sophisticated and symbolic forms of gestural communication, and subjects generally used more complex gestures to communicate in the imperative than in the declarative tasks. Applicability of the results to the design of future language-intervention programs and their implications for general theory concerning the relations between language and cognition and between normal and atypical development were discussed.

Adolescent↗
PubMed2004

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.

SUMMARY: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. AVAILABILITY: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/.

Abstracting and Indexing↗
PubMed2005

PSE: a tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords.

BACKGROUND: MEDLINE/PubMed (hereinafter called PubMed) is one of the most important literature databases for the biological and medical sciences, but it is impossible to read all related records due to the sheer size of the repository. We usually have to repeatedly enter keywords in a trial-and-error manner to extract useful records. Software which can reduce such a laborious task is therefore required. RESULTS: We developed a web-based software, the PubMed Sentence Extractor (PSE), which parses large number of PubMed abstracts, extracts and displays the co-occurrence sentences of gene names and other keywords, and some information from EntrezGene records. The result links to whole abstracts and other resources such as the Online Mendelian Inheritance in Men and Reference Sequence. While PSE executes at the sentence-level when evaluating the existence of keywords, the popular PubMed operates at the record-level. Therefore, the relationship between the two keywords, a gene name and a common word, is more accurately captured by PSE than PubMed. In addition, PSE shows the list of keywords and considers the synonyms and variations on gene names. Through these functions, PSE would reduce the task of searching through records for gene information. CONCLUSION: We developed PSE in order to extract useful records efficiently from PubMed. This system has four advantages over a simple PubMed search; the reduction in the amount of collected literatures, the showing of keyword lists, the consideration for synonyms and variations on gene names, and the links to external databases. We believe PSE is helpful in collecting necessary literatures efficiently in order to find research targets. PSE is freely available under the GPL licence as additional files to this manuscript.

Abstracting and Indexing↗
PubMed2005

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.

BACKGROUND: Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. RESULTS: Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. CONCLUSIONS: The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.

Computational Biology↗
PubMed2002

An English-language clinic-based literacy program is effective for a multilingual population.

OBJECTIVE: To assess the effectiveness of a clinic-based pediatric literacy intervention on a multilingual population. BACKGROUND: Clinic-based literacy interventions are effective among English- and Spanish-speaking children. No data exist for multilingual populations. SETTING: Pediatric clinic in an urban county hospital. Design/Methods. Reading practices of 2 cross-sectional groups were assessed by standardized interview before and after the intervention. The intervention consisted of waiting-room volunteers reading to children, literacy counseling, and gift of a children's book at each well-child visit from 6 months to 5 years. Outcomes were assessed separately for primary English-speaking and primary non-English-speaking families. RESULTS: The baseline (N=85) and postintervention (N=95) groups were similar with respect to child age and sex, parental education, and length of time in the United States. Fourteen languages were represented in total, the most common being English (41%), Somali (28%), Spanish (9%), Vietnamese (7%), Oromo (3%), and Tigrinyan (3%). Compared with baseline, postintervention respondents were more likely to report reading as a favorite activity for the child (10% vs 25%) and parent (18% vs 40%), to read to their child before bed at least weekly (45% vs 71%), and to possess over 10 children's books at home (49% vs 63%). Among English-speaking families (N=30 baseline, N=40 postintervention), weekly bedtime reading increased (63% to 93%), reading as child's favorite activity increased (7% vs 30%), and reading as the parent's favorite activity to do with child increased (33% vs 58%). The proportion of English-speaking families possessing over 10 books at home and those reading with their children at least weekly showed no difference between the baseline and postintervention groups. Among non-English-speaking families (N=55 baseline, N=55 postintervention), weekly bedtime reading increased (36% vs 56%), reading as the parent's favorite activity increased (11% vs 27%), and the number of families to possess >10 children's books in the home increased (31% vs 49%). Reading as child's favorite activity (13% vs 24%) and weekly book sharing (60% vs 76%) showed nonsignificant trends between the non-English-speaking baseline and postintervention groups. CONCLUSIONS: This clinic-based literacy intervention influences home literacy behavior in this multiethnic setting, in both English-speaking and non-English-speaking families. Although efforts should be made to make such programs more appropriate for linguistic minorities, non-English-speaking families do stand to benefit from English-language-oriented programs. literacy, Reach Out and Read, pediatrics, reading, child development.

Child, Preschool↗
PubMed1989

Language skills of children with different preschool experiences.

This study examined the language at age 5 of socioeconomically disadvantaged children who had been randomly assigned at birth to a language-enriched day care program with a parent education component, a parent education program without a language-enriched day care, or no treatment. The interventions were administered between the ages of 3 months to 5 years. Language measures, reflecting children's ability to manipulate topics, as well as their structural complexity, semantic diversity, and general talkativeness were examined. The results showed that the disadvantaged children who attended the language-enriched day care program with the parent education component used a significantly greater proportion of high quality topic manipulation skills and less low quality topic manipulation skills during conversation than did children in the other two groups. The day care effect on high quality topic manipulation was present even after adjusting for children's intelligence and for the amount of community day care experience of the children in the parent education alone and control groups. No significant treatment differences were found for structural, semantic, and talkativeness measures. Implications of the result for early language intervention are discussed.

Child Day Care Centers↗
PubMed2005

Wildfire: distributed, Grid-enabled workflow construction and execution.

BACKGROUND: We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers. RESULTS: We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids. CONCLUSION: Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

Algorithms↗
PubMed1989

Adolescent language as affectively coded behavior: findings of an observational research project.

This study aims to formulate a minimal typology of the speech-programming categories of adolescent language. In all, thirty-six adolescents (ages 13 to 18) living in the city of Toronto were recorded both in spontaneous conversational settings and in formal interview sessions. The ensuing analysis of these recordings led to the postulation of three basic categories: emotive, connotative, and socially coded language programming. These categories can be seen to provide a framework within which to conduct more specific kinds of research on adolescent language.

Adolescent↗
PubMed2004

Numeric and symbolic knowledge representation of cerebral cortex anatomy: methods and preliminary results.

The human cerebral cortex anatomy describes the brain organization at the scale of gyri and sulci. It is used as landmarks for neurosurgery as well as localization support for functional data analysis or inter-subject data comparison. Existing models of the cortex anatomy either rely on image labeling but fail to represent variability and structural properties or rely on a conceptual model but miss the inner 3D nature and relations of anatomical structures. This study was therefore conducted to propose a model of sulco-gyral anatomy for the healthy human brain. We hypothesized that both numeric knowledge (i.e., image-based) and symbolic knowledge (i.e., concept-based) have to be represented and coordinated. In addition, the representation of this knowledge should be application-independent in order to be usable in various contexts. Therefore, we devised a symbolic model describing specialization, composition and spatial organization of cortical anatomical structures. We also collected numeric knowledge such as 3D models of shape and shape variation about cortical anatomical structures. For each numeric piece of knowledge, a companion file describes the concept it refers to and the nature of the relationship. Demonstration software performs a mapping between the numeric and the symbolic aspects for browsing the knowledge base.

Cerebral Cortex↗
PubMed1993

PALM--a pattern language for molecular biology.

This paper presents a new pattern language, PALM, for describing patterns in molecular biology sequences. The language is intended for representing knowledge about such patterns in a declarative, clear and concise way. It is also shown that its expressive power enables the definition of any regular or context free language, and also higher languages in the Chomsky hierarchy by parameter attachment, variables and procedural attachment. It is also possible to define approximate patterns. The language is rigorously defined, and several examples of its use and expressive power are given.

DNA-Directed DNA Polymerase↗
PubMed2000

SIMPSON: a general simulation program for solid-state NMR spectroscopy.

A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tcl scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basically, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple 1D experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at http://nmr.imsb.au.dk. The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments.

Algorithms↗
PubMed1980

Computer software.

While many nurses are aware that the term "software" denotes the programs of instructions by which the computer operates, most of us could probably benefit by knowing more about software basics--what constitutes a program, what constitutes a system, what distinguishes various types of systems, and levels of computer language, and so forth. Few of us are familiar with the types of computer languages in use today. Fewer still realize that the type of language used to program a system has a significant effect on the resources needed to develop and maintain application programs; that specific languages are best used for specific types of applications; or that the amount of flexibility inherent in a specific system depends largely on the language used to program it. This article attempts to inform nurses at the decision-making level about the characteristics of computer software and their implications as criteria for selecting software systems that perform the required functions as efficiently and economically as possible.

Computers↗
PubMed1980

Speech therapy after total laryngectomy and esophageal replacement in a preschool patient: a case study.

This case study reports the development of a speech and language therapy program for a preschool boy laryngectomized at age two and three-quarters. Etiology was attributed to the accidental ingestion of lye, which caused severe burns and subsequent damage to both the larynx and esophagus. During the 20-month hospital stay, colon transplantation to the pharynx and laryngectomy were performed and a speech therapy program was initiated. The speech pathologist worked closely with the patient by stimulating his speech and language, developing his articulation skills, and finally providing him with a means of using expressive speech via an electrolarynx designed for him. In addition to the case study, this report reviews the different methods of alaryngeal speech, and suggests the need for further research in developing these methods as viable alternatives for the young laryngectomized child.

Child, Preschool↗
PubMed2001

Simple recurrent networks learn context-free and context-sensitive languages by counting.

It has been shown that if a recurrent neural network (RNN) learns to process a regular language, one can extract a finite-state machine (FSM) by treating regions of phase-space as FSM states. However, it has also been shown that one can construct an RNN to implement Turing machines by using RNN dynamics as counters. But how does a network learn languages that require counting? Rodriguez, Wiles, and Elman (1999) showed that a simple recurrent network (SRN) can learn to process a simple context-free language (CFL) by counting up and down. This article extends that to show a range of language tasks in which an SRN develops solutions that not only count but also copy and store counting information. In one case, the network stores information like an explicit storage mechanism. In other cases, the network stores information more indirectly in trajectories that are sensitive to slight displacements that depend on context. In this sense, an SRN can learn analog computation as a set of interdependent counters. This demonstrates how SRNs may be an alternative psychological model of language or sequence processing.

Models, Neurological↗