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Concept: Type theory

173

Cholinergic urticaria (CU) has clinically characteristic features, and has been frequently described in the literature. However, despite its comparatively old history, the pathogenesis and classification remains to be clarified. CU patients are occasionally complicated by anhidrosis and/or hypohidrosis. This reduced-sweat type should be included in the classification because the therapeutic approaches are different from the ordinary CU. It is also well-known that autologous sweat is involved in the occurrence of CU. More than half of CU patients may have sweat hypersensitivity. We attempt to classify CU and address the underlying mechanisms of CU based on the published data and our findings. The first step for classification of CU seems to discriminate the presence or absence of hypersensitivity to autologous sweat. The second step is proposed to determine whether the patients can sweat normally or not. With these data, the patients could be categorized into three subtypes: (1) CU with sweat hypersensitivity; (2) CU with acquired anhidrosis and/or hypohidrosis; (3) idiopathic CU. The pathogenesis of each subtype is also discussed in this review.

Concepts: Medical terms, Perspiration, Hyperhidrosis, Type theory, Polymorphism in object-oriented programming, Subtype polymorphism, Cholinergic urticaria

169

The identification and surveillance of patients with preneoplastic lesions at high risk of progressing to gastric cancer (GC) represents the most effective way of reducing the burden of GC. The incomplete type of intestinal metaplasia (IM) could be considered as the best candidate for surveillance. However, the usefulness of subtyping of IM has been considered by some authors as limited and inconsistent. A search was carried out to identify all cross-sectional (n= 14) and follow-up (n= 10) studies that assessed the risk of GC among subjects with different types of IM. Out of the 14 cross-sectional studies, 13 reported that the prevalence of incomplete IM was statistically significantly higher in GC than in other gastric lesions. Out of the 10 follow-up studies, 6 found a statistically significant association between incomplete IM and subsequent GC risk. The relative risks of GC were from 4 to 11-fold higher for the presence of incomplete type in comparison to complete type or in comparison to the absence of incomplete type, among the studies that reported the magnitude of the risk. According to this comprehensive review, most of the scientific evidence supports the utility of subtyping IM as a predictor of GC risk. Recognizing its usefulness by gastroenterologists should encourage pathologists to subtype IM. © 2012 Wiley Periodicals, Inc.

Concepts: Scientific method, Epidemiology, Decision theory, First-order logic, Risk aversion, Type theory, Polymorphism in object-oriented programming, Subtype polymorphism

26

Sanfilippo syndrome (mucopolysaccharidosis type III; MPS III) is an inherited monogenic lysosomal storage disorder divided into subtypes A, B, C and D. Each subtype is characterized by deficiency of a different enzyme participating in metabolism of heparan sulphate. The resultant accumulation of this substrate in bodily tissues causes various malfunctions of organs, ultimately leading to premature death. Eighty-four, 24 and 5 death certificates of patients with Sanfilippo syndrome types A, B and C, respectively, were obtained from the Society of Mucopolysaccharide Diseases (UK) to better understand the natural course of these conditions, covering the years 1977-2007.

Concepts: Death, Lysosomal storage disease, Heparan sulfate, Heparin, Mucopolysaccharidosis, Lysosomal storage diseases, Sanfilippo syndrome, Type theory

21

Malignant mesothelioma (MM) has distinct histological subtypes (epithelioid, sarcomatoid and biphasic) with variable behaviour and prognoses. It is well recognised that survival time varies with the histological subtype of MM. It is not known, however, if asbestos exposure characteristics (type of asbestos, degree of exposure) are associated with different histological subtypes.

Concepts: Cancer, Mesothelioma, Asbestos, Type theory, Polymorphism in object-oriented programming, Data types, Asbestos and the law, Wittenoom, Western Australia

20

Technological advances enable the cost-effective acquisition of Multi-Modal Data Sets (MMDS) composed of measurements for multiple, high-dimensional data types obtained from a common set of bio-samples. The joint analysis of the data matrices associated with the different data types of a MMDS should provide a more focused view of the biology underlying complex diseases such as cancer that would not be apparent from the analysis of a single data type alone. As multi-modal data rapidly accumulate in research laboratories and public databases such as The Cancer Genome Atlas (TCGA), the translation of such data into clinically actionable knowledge has been slowed by the lack of computational tools capable of analyzing MMDSs. Here, we describe the Joint Analysis of Many Matrices by ITeration (JAMMIT) algorithm that jointly analyzes the data matrices of a MMDS using sparse matrix approximations of rank-1.

Concepts: Cancer, Sparse matrix, Computational complexity theory, Type theory, Type system, The Cancer Genome Atlas, Data types, Data type

19

Williams and Bargh (2008) reported an experiment in which participants were simply asked to plot a single pair of points on a piece of graph paper, with the coordinates provided by the experimenter specifying a pair of points that lay at one of three different distances (close, intermediate, or far, relative to the range available on the graph paper). The participants who had graphed a more distant pair reported themselves as being significantly less close to members of their own family than did those who had plotted a more closely-situated pair. In another experiment, people’s estimates of the caloric content of different foods were reportedly altered by the same type of spatial distance priming. Direct replications of both results were attempted, with precautions to ensure that the experimenter did not know what condition the participant was assigned to. The results showed no hint of the priming effects reported by Williams and Bargh (2008).

Concepts: Function, Participation, Food, Experiment, Distance, Analytic geometry, Plot, Type theory

8

This study investigated whether close friends affect each other’s fear responses (fear beliefs and avoidance) when they discuss fear-related issues together. Children (N = 242) aged 7-10 years were first presented with ambiguous and threatening information about two novel animals respectively, after which their fear responses towards each animal were assessed (T1). Next, dyads of close friends had a discussion about their feelings regarding the animals, and their fear responses were measured again (T2). Results showed that children influenced each other’s cognitions following the discussion; from T1 to T2 their fear responses became more similar and close friends' fear responses at T1 significantly predicted children’s fear responses at T2. Gender pair type predicted change in children’s fear responses over time. Children in boy-boy pairs showed a significant increase in fear responses following the discussion; their fear level became more in line with that of other gender pairs at T2, while those in girl-girl pairs showed a significant decrease in their fear beliefs, at least when threatening information was given. Differences in anxiety level between close friends did not affect change in fear responses over time. Altogether, the results indicate that children may affect each other’s fears.

Concepts: Anxiety, The Animals, Anxiety disorder, Fear, Social anxiety, Paranoia, Emotions, Type theory

7

Natural killer (NK)/T-cell lymphomas are a rare and distinct subtype of non-Hodgkin’s lymphomas. NK/T-cell lymphomas are predominantly extranodal and most of these are nasal type, often localized to the upper aerodigestive tract. Because extranodal NK/T-cell lymphomas (ENKL) are rare malignancies, randomized trials comparing different regimens have not been conducted to date and standard therapy has not yet been established for these patients. These NCCN Guidelines Insights discuss the recommendations for the diagnosis and management of patients with ENKL as outlined in the NCCN Guidelines for T-Cell Lymphomas.

Concepts: Cancer, Types of cancer, Lymphoma, Hematological malignancy, Non-Hodgkin lymphoma, Type theory, T-cell lymphoma

3

The current study examined the prevalence and subtypes of Mild Cognitive Impairment (MCI) in an Australian sample of people with Parkinson’s Disease (PD). Seventy participants with PD completed neuropsychological assessments of their cognitive performance, using MDS Task Force Level II diagnostic criteria for PD-MCI. A cut-off score of less than one standard deviation (SD) below normative data determined impaired performance on a neuropsychological test. Of 70 participants, 45 (64%) met Level II diagnostic criteria for PD-MCI. Among those with PD-MCI, 42 (93%) were identified as having multiple domain impairment (28 as amnestic multiple domain and 14 as nonamnestic multiple domain). Single domain impairment was less frequent (2 amnestic/1 nonamnestic). Significant differences were found between the PD-MCI and Normal Cognition groups, across all cognitive domains. Multiple domain cognitive impairment was more frequent than single domain impairment in an Australian sample of people with PD. However, PD-MCI is heterogeneous and current prevalence and subtyping statistics may be an artifact of variable application methods of the criteria (e.g., cut off scores and number of tests). Future longitudinal studies refining the criteria will assist with subtyping the progression of PD-MCI, while identifying individuals who may benefit from pharmacological and nonpharmacological interventions.

Concepts: Psychology, Epidemiology, Neurocognitive, Cognitive psychology, Cognition, Standard deviation, Neuropsychological assessment, Type theory

2

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a ‘model system’ to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [∼42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters (∼0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more ‘biologically-realistic’ models is likely to be critical for efforts to reconstruct the tree of life.

Concepts: Scientific method, Bird, Phylogenetic nomenclature, Phylogenetics, Cladistics, Type theory, Type system, Data type