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Phylogenetic analysis using parsimony and likelihood methods.

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were allowed to differ between nucleotides or across sites, the probability that MP recovers the true topology, and especially its performance relative to that of the likelihood method, generally deteriorates. As the complexity of the process of nucleotide substitution in real sequences is well recognized, the likelihood method appears preferable to parsimony. However, the development of a statistical methodology for the efficient estimation of the tree topology remains a difficult open problem.

Animals↗

Essentialism, word use, and concepts.

The essentialist approach to word meaning has been used to undermine the fundamental assumptions of the cognitive psychology of concepts. Essentialism assumes that a word refers to a natural kind category in virtue of category members possessing essential properties. In support of this thesis, Kripke and Putnam deploy various intuitions concerning word use under circumstances in which discoveries about natural kinds are made. Although some studies employing counterfactual discoveries and related transformations appear to vindicate essentialism, we argue that the intuitions have not been investigated exhaustively. In particular, we argue that discoveries concerning the essential properties of whole categories (rather than simply of particular category members) are critical to the essentialist intuitions. The studies reported here examine such discovery contexts, and demonstrate that words and concepts are not used in accordance with essentialism. The results are, however, consistent with "representational change" views of concepts, which are broadly Fregean in their motivation. We conclude that since essentialism is not vindicated by ordinary word use, it fails to undermine the cognitive psychology of concepts.

Adult↗

Category essence or essentially pragmatic? Creator's intention in naming and what's really what.

Daily experience is filled with objects that have been created by humans to serve specific purposes. For such objects, the very act of creation may be a key element of how people understand them. But exactly how does creator's intention matter? We evaluated its contribution to two forms of categorization: the name selected for an artifact, and intuitions about what an artifact "really" is. To contrast the possibility that intention serves as an essence (Bloom, P. (1996). Intention, history, and artifact concepts. Cognition, 60, 1-29; Bloom, P. (1998). Theories of artifact categorization. Cognition, 66, 87-93.) determining an artifact's name with the possibility that it matters through its relevance to discourse goals, participants in three experiments read scenarios about people interacting with an artifact and then judged the suitability of different names for it. The intention of the creator was of differing degrees of relevance to the communication, and the relevance of other aspects of the entity varied in a complementary fashion. We found that name selection was altered by the communicative goals of a situation, and name choice was most consistent with creator's intention when the situation made intention relevant to achieving those goals. In a fourth experiment, we used the same scenarios to test the possibility that intention serves as an essence determining intuitions about what an object "really" is. The impact of creator's intention was modulated by the discourse context. These findings suggest that creator's intention influences both name choice and intuitions about what something "really" is by virtue of its impact on how communicative goals are best realized.

Humans↗

Clinical education and clinical evaluation of respiratory therapy students.

Different blends of knowledge, decision making, problem solving,professional behaviors, values, and technical skills are necessary in the changing health care environments in which respiratory therapists practice. Frequently, novice students are expected to perform quickly and efficiently,and it may be forgotten that students are still learning and mastering the foundation pieces of practice. Clinical educators take on the responsibility of student development in addition to overseeing patient care. Normally,these volunteer instructors are role models for respiratory therapy students. The characteristic of initiative when demonstrated by a beginning student is attractive to the clinical instructor, promotes sharing of experiences, and may evolve into a mentor-protege relationship. Some clinical instructors may be underprepared to teach and are uncomfortable with student evaluation. Respiratory therapy facilities in conjunction with academic institutions may consider sponsoring ongoing programs for clinical teachers. Teaching and learning in the clinical environment is more than demonstration of skills and knowledge. Furthermore, it can be debated whether the memorization of facts or of the steps of a skill is more valuable than competency in problem solving, clinical reasoning, or information retrieval. New knowledge is built within a context and is further integrated when grounded by experience. Development of "prediction in practice" or the anticipation of the next necessary actions may be worth integrating into the instructional toolbox. Intuition has been defined as an "understanding without a rationale". This definition separates intuition from rational decision making and presents intuition as a type of innate ability. Reflection when guided by clinical instructors can help deepen critical thinking, as will Socratic questioning on a regular basis. Most clinical staff can agree on the performance of an incompetent student, but discrimination of the levels of competence is more challenging. Observations allow the assessor to obtain the data necessary to evaluate performance, followed by assessment, which denotes a judgment made on the basis of an observation of events. Performance assessment should have stability and consistency, measure what is intended to be measured, and truly determine competence. In contrast, reflective analysis has been shown to be successful for clinical evaluation, thus departing from strict competency and product-based assessment. Students yearn to become clinically knowledgeable, and their enthusiasm should be fostered. An interest in clinical practice is the primary reason individuals enroll in respiratory therapy education programs. Educators,managers, and staff should assure that students experience an appropriate, rich, and diverse clinical curriculum that with practice develops clinical judgment, reasoning, and reflection on practice.

Allied Health Personnel↗

Simple but predictive protein models.

The traditional approach to computational biophysics studies of molecular systems is brute force molecular dynamics simulations under the conditions of interest. The disadvantages of this approach are that the time and length scales that are accessible to computer simulations often do not reach biologically relevant scales. An alternative approach, which we call intuitive modeling, is hypothesis-driven and based on tailoring simplified protein models to the systems of interest. Using intuitive modeling, the length and time scales that can be achieved using simplified protein models exceed those of traditional molecular-dynamic simulations. Here, we describe several recent studies that signify the predictive power of simplified protein models within the intuitive-modeling approach.

Computer Simulation↗

Computer-assisted telemanipulation: an enabling technology for endoscopic coronary artery bypass.

BACKGROUND: The ultimate objective of minimally invasive coronary artery bypass grafting is to perform the anastomosis totally endoscopically. In this feasibility study, we examined the potential of performing coronary artery bypass grafting with the use of computer-assisted telemanipulation technology. METHODS: Intuitive Telemanipulation Technology (Intuitive Surgical, Mountain View, CA) was used to perform an arterial graft to left anterior descending coronary artery anastomosis in an ex vivo on-bench swine heart model. The degree of difficulty in performing the anastomosis, intraoperative events, duration of the anastomosis, and its quality were determined. RESULTS: Anastomosis was performed with relative facility, in a range of 10.7 to 17.4 minutes (mean +/- standard deviation, 14.6 +/- 2.6 minutes). All anastomoses were patent and of good quality except one, which had 30% narrowing of its heel. CONCLUSIONS: We conclude that Intuitive Telemanipulation Technology may in the future permit the performance of quality totally endoscopic coronary artery anastomosis with facility and acceptable time.

Anastomosis, Surgical↗

Common errors of reasoning in child protection work.

OBJECTIVE: Repeated public inquiries into child abuse tragedies in Britain demonstrate the level of public concern about the services designed to protect children. These inquiries identify faults in professionals' practice but the similarities in their findings indicate that they are having insufficient impact on improving practice. This study is based on the hypothesis that the recurrent errors may be explicable as examples of the typical errors of human reasoning identified by psychological research. METHODS: The sample comprised all child abuse inquiry reports published in Britain between 1973 and 1994 (45 in total). Using a content analysis and a framework derived from psychological research on reasoning, a study was made of the reasoning of the professionals involved and the findings of the inquiries. RESULTS: It was found that professionals based assessments of risk on a narrow range of evidence. It was biased towards the information readily available to them, overlooking significant data known to other professionals. The range was also biased towards the more memorable data, that is, towards evidence that was vivid, concrete, arousing emotion and either the first or last information received. The evidence was also often faulty, due, in the main, to biased or dishonest reporting or errors in communication. A critical attitude to evidence was found to correlate with whether or not the new information supported the existing view of the family. A major problem was that professionals were slow to revise their judgements despite a mounting body of evidence against them. CONCLUSIONS: Errors in professional reasoning in child protection work are not random but predictable on the basis of research on how people intuitively simplify reasoning processes in making complex judgements. These errors can be reduced if people are aware of them and strive consciously to avoid them. Aids to reasoning need to be developed that recognize the central role of intuitive reasoning but offer methods for checking intuitive judgements more rigorously and systematically.

Child↗

Multidisciplinary modelling of biomedical systems.

This paper describes general principles and example results of a new software tool being developed for physiologically-based modelling of biomedical systems within a multidisciplinary framework. The aim is to overcome some limitations of currently available software designed either for general purpose or for highly specialised modelling applications. In fact, general purpose tools usually impose explicit coding of mathematical model equations or non-intuitive system representations, whereas specialised software use domain-specific notations that allow efficient and convenient model building only for special classes of systems. The aim of the present study is to pursue intuitive representation of various, possibly interacting, types of biological systems described as interconnected physical components, such as mass and energy storage elements, active and passive transport or biochemical transformations. The presented software generates automatically the mathematical model equations that can be coded in different formats. This allows interoperability with other existing software, e.g. for numerical simulation, symbolic analysis or text processing. A multi-domain structural language has been defined for an intuitive, hierarchical and self-explanatory specification of physiological models. The proposed strategies may become useful for dissemination and integration of multidisciplinary modelling knowledge.

Computational Biology↗

Moral heuristics.

With respect to questions of fact, people use heuristics--mental short-cuts, or rules of thumb, that generally work well, but that also lead to systematic errors. People use moral heuristics too--moral short-cuts, or rules of thumb, that lead to mistaken and even absurd moral judgments. These judgments are highly relevant not only to morality, but to law and politics as well. examples are given from a number of domains, including risk regulation, punishment, reproduction and sexuality, and the act/omission distinction. in all of these contexts, rapid, intuitive judgments make a great deal of sense, but sometimes produce moral mistakes that are replicated in law and policy. One implication is that moral assessments ought not to be made by appealing to intuitions about exotic cases and problems; those intuitions are particularly unlikely to be reliable. Another implication is that some deeply held moral judgments are unsound if they are products of moral heuristics. The idea of error-prone heuristics is especially controversial in the moral domain, where agreement on the correct answer may be hard to elicit; but in many contexts, heuristics are at work and they do real damage. Moral framing effects, including those in the context of obligations to future generations, are also discussed.

Decision Making↗

Both coloured overlays and coloured lenses can improve reading fluency, but their optimal chromaticities differ.

Some individuals read more fluently when the text is coloured: i.e., when coloured sheets of plastic (overlays) are placed upon the page, or when coloured lenses are worn. Overlays provide a surface colour whereas lenses mimic a change in the colour of a light source. The neural mechanisms that underlie colour constancy ensure that the chromaticity of overlays and lenses is processed differently by the visual system. We investigated (1) the relationship between the optimal colours of overlays and lenses, and (2) how reading rate is affected by a particular colour in overlays and lenses. In 100 patients we noted (1) the overlay(s) chosen from among the 29 combinations of the 10 IOO Intuitive Overlays which sample chromaticity systematically and (2) the chromaticity co-ordinates of the lenses subsequently chosen using the intuitive Colorimeter, a device providing a light source that can be adjusted in hue, saturation and luminance independently. The relationship between the chromaticities of the overlays and the lenses showed considerable variation. In a second study, patients attending the Specific Learning Difficulties clinic at the Institute of Optometry, London, were given overlays to use for two months. Seventeen who derived benefit were examined using the Intuitive Colorimeter. Patients were asked to read aloud randomly ordered common words (Wilkins Rate of Reading Test): (1) with no colour, (2) with the chosen overlay, (3) with lenses matching the chosen overlay and (4) with lenses matching the Colorimeter setting. The aids increased reading rate significantly only in conditions (2) and (4). There was no significant improvement when lenses matching the overlay colour were used, and under this condition the reading rate was significantly poorer than in conditions (2) and (4). The colour of a lens will improve reading only if it is selected under conditions that mimic a change in the colour of a light source: coloured overlays give no clinically reliable guide to optimal lens colour.

Color↗

Killing, letting die, and withdrawing aid.

One of the aims of this article is to contribute to the identification of the empirical criteria governing the use of the concepts of killing and letting die. I will not attempt a comprehensive analysis of the concepts but will limit the inquiry to certain problematic cases -- namely, cases involving the removal or withdrawal of life-supporting aid or protection. The analysis of these cases will, however, shed light on the criteria for distinguishing killing and letting die in other cases as well. My overall aims in the article are partly constructive and partly skeptical. I hope to advance our understanding of the nature of the distinction between killing and letting die. This, I believe, will enable us to defend the moral relevance of the distinction against certain objections -- in particular, objections that claim that the distinction fails to coincide with commonsense moral intuitions. Yet I will suggest that, as we get clearer about the nature of the distinction and the sources of its intuitive appeal, it may seem that the intuitions it supports are not so well grounded as one could wish.

Abortion, Induced↗

Underlying personality differences between alcohol/substance-use disorder patients with and without an affective disorder.

The Myers-Briggs Type Indicator (MBTI), a popular personality test, was used to profile the personalities of in-patient alcoholics/substance-use disorder patients who had, and those who did not have, a concurrent affective disorder diagnosis. The MBTI divides individuals into eight categories: Extroverts and Introverts, Sensors and Intuitives, Thinkers and Feelers, and Judgers and Perceivers. Alcohol/substance-use disorder patients with no affective disorder differed from a normative population only in being significantly more often Sensing and significantly less often Intuitive single-factor types. The Extroverted/Sensing/ Feeling/Judging four-factor type was also significantly over-represented in this group, compared to a normative population. In contrast, mood-disordered alcohol/substance-use disorder patients were significantly more often Introverted, Sensing, Feeling, and Perceiving and significantly less often Extroverted, Intuitive, Thinking, and Judging single-factor types. They were also significantly more often Introverted/Sensing/ Feeling/Perceiving and Introverted/Intuitive/Feeling/Perceiving four-factor types. 'Pure' alcohol/ substance-use disorder patients differed from alcohol/substance-use disorder patients with a mood disorder in that they were significantly more often Extroverted and Thinking and significantly less often Introverted and Feeling single-factor types; and significantly less often were an Introverted/Sensing/ Feeling/Perceiving four-factor type. The above results may have psychogenetic, diagnostic, and psychotherapeutic implications.

Adult↗

Asymmetric stratification. An outline for an efficient method for controlling confounding in cohort studies.

Confounding is usually controlled by either cross-stratification or multivariate modeling. The first approach is simple and intuitive, but it is not practical for controlling many factors. The second approach, although less intuitive, may provide a more efficient means for controlling many confounders, but its ability to control confounding depends on the appropriateness of the chosen model. Hybrid methods based on a multivariate confounder score or a propensity score combine the favorable characteristics of both methods and may be better suited for controlling many confounders. However, the resulting strata are defined by subranges of a multivariate model, and, therefore, may possess little intrinsic meaning. The authors propose the principle of asymmetric stratification to control efficiently a number of confounders in cohort studies while retaining the intuitive appeal and general framework of cross-stratification. The proposed method resembles a propensity score analysis but does not use a multivariate model to define the strata. Instead, strata are defined by the categories of only a subset of the original potential confounders. The authors also demonstrate how our proposed method can be implemented by an application of classification and regression trees (CART) (recursive partitioning), as outlined by Breiman et al. (Classification and Regression Trees. Belmont, CA: Wadsworth, 1984). Computer simulations and an actual example suggest that the proposed method is a potentially simpler alternative to the standard propensity score analysis. Specific recommendations on how the proposed method can be improved are also presented.

Aged↗

Reliability and validity of scores from the index of learning styles.

BACKGROUND: No medical education studies have investigated the validity of scores from Felder's Index of Learning Styles (ILS). This study evaluated the reliability of ILS scores, and compared them with scores from Pelley's Learning Styles Type Indicator (LSTI). METHOD: Internal medicine residents completed the ILS twice and the LSTI once. RESULTS: A total of 138 residents consented. Cronbach's alpha and test-retest correlation for ILS scores were 0.61 and 0.75 (active-reflective dimension), 0.78 and 0.81 (sensing-intuitive), 0.70 and 0.60 (visual-verbal), and 0.67 and 0.81 (sequential-global). The multitrait-multimethod matrix provided evidence of convergence and discrimination for scores from the active-reflective and sensing-intuitive dimensions of the ILS and LSTI. Cronbach's alpha for LSTI scores ranged from 0.19 to 0.69. CONCLUSIONS: These data support the reliability and validity of scores from the ILS active-reflective and sensing-intuitive dimensions.

Female↗

Validity of index of learning styles scores: multitrait-multimethod comparison with three cognitive/learning style instruments.

Cognitive and learning styles research is limited by the lack of evidence supporting valid interpretations of style assessment scores. We sought evidence to support the validity of scores from 4 instruments: the Index of Learning Styles (ILS); the Learning Style Inventory (LSI); the Cognitive Styles Analysis (CSA), and the Learning Style Type Indicator (LSTI). The ILS assesses 4 domains: sensing-intuitive (SensInt), active-reflective (ActRefl), sequential-global (SeqGlob) and visual-verbal (VisVerb), each of which parallel a similar domain in at least 1 of the other instruments. We administered the ILS, LSI and CSA to family medicine and internal medicine residents and Year 1 and 3 medical students and applied the multitrait-multimethod matrix to evaluate convergence and discrimination. After 3 months participants repeated the ILS and completed the LSTI. A total of 89 residents and medical students participated. Multitrait-multimethod analysis showed evidence of both convergence and discrimination for ActRefl (ILS, LSI and LSTI) and SensInt (ILS and LSTI) scores. ILS SeqGlob and SensInt scores showed unanticipated correlation. No other domains met the criteria for convergence or discrimination. Test-retest reliabilities for ILS scores were 0.856 for SensInt, 0.809 for ActRefl, 0.703 for SeqGlob and 0.684 for VisVerb. Cronbach's alpha values were > or = 0.810 for LSI and 0.237-0.758 for LSTI. At least 9 participants misinterpreted the LSI instructions. These data support the validity of ILS active-reflective and sensing-intuitive scores, LSI active-reflective scores and LSTI sensing-intuitive scores for determining learning styles in this population. Cognitive style and learning style scores may not be interchangeable, even for constructs with similar definitions.

Adult↗

Cochlear orientation and dimensions of the facial recess in cochlear implantation.

OBJECTIVE: To study the dimensions of the facial recess and the spatial relationship between the facial recess and the cochlea, using CT scanning in cochlear implantees. METHOD: In 29 cochlear implantees, preoperative CT scans of the temporal bone were compared with findings done at surgery. The dimensions of the facial recess and the relationship between the facial recess and the cochlea were both measured on a viewing station and classified on printed films by 3 blinded and independent reviewers. RESULTS: No significant relations could be found between either intuitive classification of facial recess width or electrode array insertion feasibility and the measurements with the viewing station. The 3 reviewers had large interobserver variability. In 5 cases, neither intuitive review of the CT scans nor viewing station measurements could predict any of the problems encountered during surgery. CONCLUSION: Our findings show that intuitive review was not reliable in classifying facial recess width. Viewing station measurements, in classifying the spatial relation between the facial recess and the cochlear basal turn, need a more detailed review in terms of the relationship with the operation direction and the orientation of the basal turn of the cochlea. Advanced imaging techniques, specifically multislice CT, might improve the diagnostic capabilities.

Chorda Tympani Nerve↗

Hyperspace geography: visualizing fitness landscapes beyond 4D.

Human perception is finely tuned to extract structure about the 4D world of time and space as well as properties such as color and texture. Developing intuitions about spatial structure beyond 4D requires exploiting other perceptual and cognitive abilities. One of the most natural ways to explore complex spaces is for a user to actively navigate through them, using local explorations and global summaries to develop intuitions about structure, and then testing the developing ideas by further exploration. This article provides a brief overview of a technique for visualizing surfaces defined over moderate-dimensional binary spaces, by recursively unfolding them onto a 2D hypergraph. We briefly summarize the uses of a freely available Web-based visualization tool, Hyperspace Graph Paper (HSGP), for exploring fitness landscapes and search algorithms in evolutionary computation. HSGP provides a way for a user to actively explore a landscape, from simple tasks such as mapping the neighborhood structure of different points, to seeing global properties such as the size and distribution of basins of attraction or how different search algorithms interact with landscape structure. It has been most useful for exploring recursive and repetitive landscapes, and its strength is that it allows intuitions to be developed through active navigation by the user, and exploits the visual system's ability to detect pattern and texture. The technique is most effective when applied to continuous functions over Boolean variables using 4 to 16 dimensions.

Algorithms↗

Studies of Jungian typology: III. Personality and marriage.

Jung's theory of psychological types provided the conceptual framework for a study of personality characteristics implicated in marital relationships. Partners in 20 couples completed the Myers-Briggs Type Indicator and a series of open-ended questions describing their marital relationships. As predicted, (a) type similarity was more characteristic than type dissimilarity, particularly on sensation-intuition and thinking-feeling preferences, (b) sensation-intuition preferences were reflected in perceptions of qualities valued in self and spouse, (c) thinking-feeling preferences were significantly related to reported satisfaction in marriage, and (d) intuitives were more open to changes in the relationship than were sensing types. Marital problems were highly diverse, and were not related in any clear way to type patterns in individuals or dyads.

Journal Article↗