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PubMed2005

Yet another application of the Monte Carlo method for modeling in the field of biomedicine.

By means of Monte Carlo simulations performed in the C programming language, an example of scientific programming for the generation of pseudorandom numbers relevant to both teaching and research in the field of biomedicine is presented. The relatively simple algorithm proposed makes possible the statistical analysis of sequences of random numbers. The following three generators of pseudorandom numbers were used: the rand function contained in the stdlib.h library of the C programming language, Marsaglia's generator, and a chaotic function. The statistical properties of the sequences generated were compared, identical parameter values being adopted for this purpose. The properties of two estimators in finite samples of the pseudorandom numbers were also evaluated and, under suitable conditions, both the maximum-likelihood and method of moments proved to be good estimators. The findings demonstrated that the proposed algorithm appears to be suitable for the analysis of data from random experiments, indicating that it has a large variety of possible applications in the clinical practice.

Algorithms↗

PubMed2004

Implicit and explicit processing of kanji and kana words and non-words studied with fMRI.

Using functional magnetic resonance imaging (fMRI), we investigated the implicit language processing of kanji and kana words (i.e., hiragana transcriptions of normally written kanji words) and non-words. Twelve right-handed native Japanese speakers performed size judgments for character stimuli (implicit language task for linguistic stimuli), size judgments for scrambled-character stimuli (implicit language task for non-linguistic stimuli), and lexical decisions (explicit language task). The size judgments for scrambled-kanji stimuli and scrambled-kana stimuli produced activations on the bilateral lingual gyri (BA 18), the bilateral occipitotemporal regions (BA 19/37), and the bilateral superior and inferior parietal cortices (BA 7/40). Interestingly, besides these areas, activations of the left inferior frontal region (Broca's area, BA 44/45) and the left posterior inferior temporal cortex (PITC, BA 37), which have been considered as language areas, were additionally activated during size judgment for kanji character stimuli. Size judgment for kana character stimuli also activated Broca's area, the left PITC, and the left supramarginal gyrus (SMG, BA 40). The activations of these language areas were replicated in the lexical decisions for both kanji and kana. These findings suggest that language processing of both kanji and kana scripts is obligatory to literate Japanese subjects. Moreover, comparison between the scrambled kanji and the scrambled kana showed no activation in the language areas, while greater activation in the bilateral fusiform gyri (left-side predominant) was found in kanji vs. kana comparison during the size judgment and the lexical decision. Kana minus kanji activated the left SMG during the size judgment, and Broca's area and the left middle/superior temporal junction during the lexical decision. These results probably reflect that in implicit or explicit reading of kanji words and kana words (i.e., hiragana transcriptions of kanji words), although using largely overlapping cortical regions, there are still some differences. Kanji reading may involve more heavily visual orthographic retrieval and lexical-semantic system through the ventral route, while kana transcriptions of kanji words require phonological recoding to gain semantic access through the dorsal route.

Adult↗

PubMed2004

Managing large online classes across multiple locations.

We now have many different ways of delivering educational offerings, hopefully tailored to the educational environments and student characteristics. Programs vary based on country of origin and delivery location, organisational structures, development and delivery technologies, and the business arrangements made between providers and agents/students. At Central Queensland University (CQU) we deliver the same courses domestically and internationally, often with more than 1000 students per offering, several times per year across 14 campuses located thousands of kilometers apart using face-to-face and/or virtual mode. The students are a mix of Australian distance and on campus plus international on campus. This chapter builds on the CQU experience managing these large classes, particularly within the Faculty of Informatics and Communication, using an evolving mix of technologies. The economic realities of tertiary education require providers to focus on servicing international markets, including an emphasis on student preferences for language of instruction, preferred location (campus or distance delivery) and mode of instruction. Educational delivery requires development and delivery teamwork, maintenance of consistency (quality) in terms of offerings and assessment, appropriate use of technology and cultural awareness.

Curriculum↗

PubMed2005

A horse named 'Twilight Sleep': the language of obstetric anaesthesia in 20th century Britain.

Historians of medicine frequently marginalize or completely ignore the importance of linguistics in the development and dissemination of medical theories and clinical techniques, both in professional culture and in society at large. This is particularly true in the history of pain relief in labour, despite the significant role played by popular attitudes to birth and pain relief in the development of clinical services. This paper uses a simple form of citation analysis to examine shifts in the usage of terms related to regional nerve block techniques in The Lancet and The Times from 1900 to 1999. Graphical representations of these data are used to relate changes in the incidence of citations to key events in the 20th century history of obstetric anaesthesia in Britain. A study of the rise and fall of 'twilight sleep' in the early part of the century is used to demonstrate the advantages and disadvantages associated with this approach to medical history. Conclusions from this analysis are used to suggest (tentative) models for the acceptance and diffusion of medical words in professional and popular vocabularies.

Anesthesia, Obstetrical↗

PubMed2001

The declarative/procedural model of lexicon and grammar.

Our use of language depends upon two capacities: a mental lexicon of memorized words and a mental grammar of rules that underlie the sequential and hierarchical composition of lexical forms into predictably structured larger words, phrases, and sentences. The declarative/procedural model posits that the lexicon/grammar distinction in language is tied to the distinction between two well-studied brain memory systems. On this view, the memorization and use of at least simple words (those with noncompositional, that is, arbitrary form-meaning pairings) depends upon an associative memory of distributed representations that is subserved by temporal-lobe circuits previously implicated in the learning and use of fact and event knowledge. This "declarative memory" system appears to be specialized for learning arbitrarily related information (i.e., for associative binding). In contrast, the acquisition and use of grammatical rules that underlie symbol manipulation is subserved by frontal/basal-ganglia circuits previously implicated in the implicit (nonconscious) learning and expression of motor and cognitive "skills" and "habits" (e.g., from simple motor acts to skilled game playing). This "procedural" system may be specialized for computing sequences. This novel view of lexicon and grammar offers an alternative to the two main competing theoretical frameworks. It shares the perspective of traditional dual-mechanism theories in positing that the mental lexicon and a symbol-manipulating mental grammar are subserved by distinct computational components that may be linked to distinct brain structures. However, it diverges from these theories where they assume components dedicated to each of the two language capacities (that is, domain-specific) and in their common assumption that lexical memory is a rote list of items. Conversely, while it shares with single-mechanism theories the perspective that the two capacities are subserved by domain-independent computational mechanisms, it diverges from them where they link both capacities to a single associative memory system with broad anatomic distribution. The declarative/procedural model, but neither traditional dual- nor single-mechanism models, predicts double dissociations between lexicon and grammar, with associations among associative memory properties, memorized words and facts, and temporal-lobe structures, and among symbol-manipulation properties, grammatical rule products, motor skills, and frontal/basal-ganglia structures. In order to contrast lexicon and grammar while holding other factors constant, we have focused our investigations of the declarative/procedural model on morphologically complex word forms. Morphological transformations that are (largely) unproductive (e.g., in go-went, solemn-solemnity) are hypothesized to depend upon declarative memory. These have been contrasted with morphological transformations that are fully productive (e.g., in walk-walked, happy-happiness), whose computation is posited to be solely dependent upon grammatical rules subserved by the procedural system. Here evidence is presented from studies that use a range of psycholinguistic and neurolinguistic approaches with children and adults. It is argued that converging evidence from these studies supports the declarative/procedural model of lexicon and grammar.

Aphasia↗

PubMed2005

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.

SUMMARY: Efficient RNA sequence manipulations (such as multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures similar to those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information. Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S has been implemented using the Java language and has been developed and tested under UNIX systems, such as Linux and MacOSX. AVAILABILITY: S2S is available at http://bioinformatics.org/S2S/.

Algorithms↗

PubMed1993

Varieties of developmental dyslexia.

This paper reviews and evaluates the evidence for the existence of distinct varieties of developmental dyslexia, analogous to those found in the acquired dyslexic population. Models of the normal adult reading process and of the development of reading in children are used to provide a framework for considering the issues. Data from a large-sample study of the reading patterns of developmental dyslexics are then reported. The lexical and sublexical reading skills of 56 developmental dyslexics were assessed through close comparison with the skills of 56 normally developing readers. The results indicate that there are at least two varieties of developmental dyslexia, the first of which is characterised by a specific difficulty using the lexical procedure, and the second by a difficulty using the sublexical procedure. These subtypes are apparently not rare, but are relatively prevalent in the developmental dyslexic population. The results of a second experiment, which suggest that neither of these reading patterns can be accounted for in terms of a general language disorder, are then reported.

Age Factors↗

PubMedDate not supplied

Value of XML in the implementation of clinical practice guidelines--the issue of content retrieval and presentation.

The purpose of guidelines in clinical practice is to improve the effectiveness and efficiency of clinical care. It is known that nationally or internationally produced guidelines which, in particular, do not involve medical processes at the time of consultation, do not take local factors into account, and have no consistent implementation strategy, have limited impact in changing either the behaviour of physicians, or patterns of care. The literature provides evidence for the effectiveness of computerization of CPGs for increasing compliance and improving patient outcomes. Probably the most effective concepts are knowledge-based functions for decision support or monitoring that are integrated in clinical information systems. This approach is mostly restricted by the effort required for development and maintenance of the information systems and the limited number of implemented medical rules. Most of the guidelines are text-based, and are primarily published in medical journals and posted on the internet. However, internet-published guidelines have little impact on the behaviour of physicians. It can be difficult and time-consuming to browse the internet to find (a) the correct guidelines to an existing diagnosis and (b) and adequate recommendation for a specific clinical problem. Our objective is to provide a web-based guideline service that takes as input clinical data on a particular patient and returns as output a customizable set of recommendations regarding diagnosis and treatment. Information in healthcare is to a very large extent transmitted and stored as unstructured or slightly structured text such as discharge letters, reports, forms, etc. The same applies for facilities containing medical information resources for clinical purposes and research such as text books, articles, guidelines, etc. Physicians are used to obtaining information from text-based sources. Since most guidelines are text-based, it would be practical to use a document-based solution that preserves the original cohesiveness. The lack of structure limits the automatic identification and extraction of the information contained in these resources. For this reason, we have chosen a document-based approach using eXtensible Markup Language (XML) with its schema definition and related technologies. XML empowers the applications for in-context searching. In addition it allows the same content to be represented in different ways. Our XML reference clinical data model for guidelines has been realized with the XML schema definition. The schema is used for structuring new text-based guidelines and updating existing documents. It is also used to establish search strategies on the document base. We hypothesize that enabling the physicians to query the available CPGs easily, and to get access to selected and specific information at the point of care will foster increased use. Based on current evidence we are confident that it will have substantial impact on the care provided, and will improve health outcomes.

Computer Systems↗

PubMed2006

Solving structures of protein complexes by molecular replacement with Phaser.

Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ;tree search with pruning' approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ;automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

Algorithms↗

PubMed2005

The acquisition of allophonic rules: statistical learning with linguistic constraints.

Phonological rules relate surface phonetic word forms to abstract underlying forms that are stored in the lexicon. Infants must thus acquire these rules in order to infer the abstract representation of words. We implement a statistical learning algorithm for the acquisition of one type of rule, namely allophony, which introduces context-sensitive phonetic variants of phonemes. This algorithm is based on the observation that different realizations of a single phoneme typically do not appear in the same contexts (ideally, they have complementary distributions). In particular, it measures the discrepancies in context probabilities for each pair of phonetic segments. In Experiment 1, we test the algorithm's performances on a pseudo-language and show that it is robust to statistical noise due to sampling and coding errors, and to non-systematic rule application. In Experiment 2, we show that a natural corpus of semiphonetically transcribed child-directed speech in French presents a very large number of near-complementary distributions that do not correspond to existing allophonic rules. These spurious allophonic rules can be eliminated by a linguistically motivated filtering mechanism based on a phonetic representation of segments. We discuss the role of a priori linguistic knowledge in the statistical learning of phonology.

Humans↗

PubMed2004

Self-concept and self-efficacy: a test of the internal/external frame of reference model and predictions of subsequent motivation and achievement.

We examined how final grades in mathematics and verbal arts in the first year of high school (Grade 11) were predicted in a Norwegian population by sex, previous grades in middle school (Grade 10), self-concept, self-efficacy at a domain-specific level, and intrinsic motivation. Direct and indirect relations were examined by means of a series of regression analyses. Participants were 483 students from six Norwegian high schools. End of term grades in high school correlated positively with grades in middle school in both mathematics (r = .62) and verbal arts (r = .55). The relation between grades at the two points of time was to a large extent mediated through mathematics, verbal self-concept, and self-efficacy. Intrinsic motivation also correlated positively with subsequent achievement (r = .63 and .42 in mathematics and verbal arts, respectively). However, intrinsic motivation had little predictive value for subsequent grades over and above the prediction made by self-concept and self-efficacy. Thus, self-concept and self-efficacy were the strongest predictors of subsequent grades. Predictions from the Internal/External frame of reference model were supported for self-concept but not for domain-specific self-efficacy.

Adolescent↗

PubMedDate not supplied

Cost of hospital care for elderly at risk of falling.

The variables that relate to cost of hospital care for a large sample of elderly patients at risk for falling are examined. The chief predictors of cost of hospitalization were medical, pharmacy, and nursing interventions. Use of nursing interventions, on average, raised the median hospital cost less than use of medical or pharmacy interventions. Using a standardized nursing language with the hospital's information system can provide nurses with information that demonstrates the cost effectiveness of their interventions.

Accidental Falls↗

PubMed2004

How the brain processes causal inferences in text.

Theoretical models of text processing, such as the construction-integration framework, pose fundamental questions about causal inference making that are not easily addressed by behavioral studies. In particular, a common result is that causal relatedness has a different effect on text reading times than on memory for the text: Whereas reading times increase linearly as causal relatedness decreases, memory for the text is best for events that are related by a moderate degree of causal relatedness and is poorer for events with low and high relatedness. Our functional magnetic resonance imaging study of the processing of two-sentence passages that varied in their degree of causal relatedness suggests that the inference process can be analyzed into two components, generation and integration, that are subserved by two large-scale cortical networks (a reasoning system in dorsolateral prefrontal cortex and the right-hemisphere language areas). These two cortical networks, which are distinguishable from the classical left-hemisphere language areas, approximately correspond to the two functional relations observed in the behavioral results.

Brain↗

PubMed2006

Knowledge discovery in nursing minimum data set using data mining.

PURPOSE: The purposes of this study were to apply data mining tool to nursing specific knowledge discovery process and to identify the utilization of data mining skill for clinical decision making. METHODS: Data mining based on rough set model was conducted on a large clinical data set containing NMDS elements. Randomized 1,000 patient data were selected from year 1998 database which had at least one of the five most frequently used nursing diagnoses. Patient characteristics and care service characteristics including nursing diagnoses, interventions and outcomes were analyzed to derive the meaningful decision rules. RESULTS: Number of comorbidity, marital status, nursing diagnosis related to risk for infection and nursing intervention related to infection protection, and discharge status were the predictors that could determine the length of stay. Four variables (age, impaired skin integrity, pain, and discharge status) were identified as valuable predictors for nursing outcome, relieved pain. Five variables (age, pain, potential for infection, marital status, and primary disease) were identified as important predictors for mortality. CONCLUSIONS: This study demonstrated the utilization of data mining method through a large data set with standardized language format to identify the contribution of nursing care to patient's health.

Adult↗

PubMed1996

Scalable and expressive medical terminologies.

The K-Rep system, based on description logic, is used to represent and reason with large and expressive controlled medical terminologies. Expressive concept descriptions incorporate semantically precise definitions composed using logical operators, together with important non-semantic information such as synonyms and codes. Examples are drawn from our experience with K-Rep in modeling the InterMed laboratory terminology and also developing a large clinical terminology now in production use at Kaiser-Permanente. System-level scalability of performance is achieved through an object-oriented database system which efficiently maps persistent memory to virtual memory. Equally important is conceptual scalability-the ability to support collaborative development, organization, and visualization of a substantial terminology as it evolves over time. K-Rep addresses this need by logically completing concept definitions and automatically classifying concepts in a taxonomy via subsumption inferences. The K-Rep system includes a general-purpose GUI environment for terminology development and browsing, a custom interface for formulary term maintenance, a C+2 application program interface, and a distributed client-server mode which provides lightweight clients with efficient run-time access to K-Rep by means of a scripting language.

Artificial Intelligence↗

PubMed2006

Characteristics of Project Liberty clients that predicted referrals to intensive mental health services.

OBJECTIVE: The authors describe characteristics of Project Liberty crisis counseling recipients that predicted referral to more intensive professional mental health treatments over the two-year period after the terrorist attacks on the World Trade Center. METHODS: Random-effects ordinal regression models were applied to data from 684,500 logs of Project Liberty service encounters for individual counseling sessions. RESULTS: Overall, about 9 percent of individual counseling visits ended with a referral to professional mental health services. Individuals needing intensive mental health treatment continued to enter Project Liberty for two years after the World Trade Center attacks. The strongest predictor of referral was having reactions to the attack that fell into a greater number of the four domains assessed-behavioral, emotional, physical, or cognitive domains. Individuals with reactions in four domains were most likely to be referred. Those who had greater attack-related exposure were also more likely to be referred. CONCLUSIONS: It is important to provide long-term access to brief counseling and triage services and to target these interventions specifically to individuals displaying greater distress or impairment and having more traumatic exposure.

Affective Symptoms↗

PubMed2025

Genomic and Developmental Models to Predict Cognitive and Adaptive Outcomes in Autistic Children.

IMPORTANCE: Although early signs of autism are often observed between 18 and 36 months of age, there is considerable uncertainty regarding future development. Clinicians lack predictive tools to identify those who will later be diagnosed with co-occurring intellectual disability (ID). OBJECTIVE: To predict ID in children diagnosed with autism. DESIGN, SETTING, AND PARTICIPANTS: This prognostic study involved the development and validation of models integrating genetic variants and developmental milestones to predict ID. Models were trained, cross-validated, and tested for generalizability across 3 autism cohorts: Simons Foundation Powering Autism Research (SPARK), Simons Simplex Collection, and MSSNG. Autistic participants were assessed older than 6 years of age for ID. Study data were analyzed from January 2023 to July 2024. EXPOSURES: Ages at attaining early developmental milestones, occurrence of language regression, polygenic scores for cognitive ability and autism, rare copy number variants, de novo loss-of-function and missense variants impacting constrained genes. MAIN OUTCOMES AND MEASURES: The out-of-sample performance of predictive models was assessed using the area under the receiver operating characteristic curve (AUROC), positive predictive values (PPVs), and negative predictive values (NPVs). RESULTS: A total of 5633 autistic participants (4574 male [81.2%]) were included in this analysis. On average, participants were diagnosed with autism at 4 (IQR, 3-7) years of age and assessed for ID at 11 (8-14) years of age, with 1159 participants (20.6%) being diagnosed with ID. The model integrating all predictors yielded an AUROC of 0.653 (95% CI, 0.625-0.681), and this predictive performance was cross-validated and generalized across cohorts. This modest performance reflected that only a subset of individuals carried large-effect variants, high polygenic scores, or presented delayed milestones. However, combinations of genetic variants that are typically not considered clinically relevant by diagnostic laboratories achieved PPVs of 55% and correctly identified 10% of individuals developing ID. The addition of polygenic scores to developmental milestones specifically improved NPVs rather than PPVs. Notably, the ability to stratify ID probabilities using genetic variants was up to 2-fold higher in individuals with delayed milestones compared with those with typical development. CONCLUSIONS AND RELEVANCE: Results of this prognostic study suggest that the growing number of neurodevelopmental condition-associated variants cannot, in most cases, be used alone for predicting ID. However, models combining different classes of variants with developmental milestones provide clinically relevant individual-level predictions that could be useful for targeting early interventions.

Humans↗

PubMed2006

Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection.

In recent years, the study of immune response behaviour through mathematical and computational models has attracted considerable efforts. The dynamics of key cell types, and their interactions, has been a primary focus in terms of building a picture of how the immune system responds to a threat. Discrete methods, based on lattice Monte-Carlo (MC) models, with their flexibility and relative simplicity have previously been used to model the immune system behaviour. However, due to speed and memory constraints, large-scale simulations cannot be done on a single computer. Key issues in the reduction of simulation time are code optimisation and code parallelisation. In this paper, optimisation and parallelisation solutions are discussed, with reference to existing MC simulation code for dynamics of HIV infection.

Antibodies, Viral↗