Validation of nonlinear PCA

Linear principal component analysis (PCA) can be extended to a nonlinear PCA by using artificial neural networks. But the benefit of curved components requires a careful control of the model complexity. Moreover, standard techniques for model selection, including cross-validation and more generally the use of an independent test set, fail when applied to nonlinear PCA because of its inherent unsupervised characteristics. This paper presents a new approach for validating the complexity of nonlinear PCA models by using the error in missing data estimation as a criterion for model selection. It is motivated by the idea that only the model of optimal complexity is able to predict missing values with the highest accuracy. While standard test set validation usually favours over-fitted nonlinear PCA models, the proposed model validation approach correctly selects the optimal model complexity.Comment: 12 pages, 5 figure

Organism-sediment interactions govern post-hypoxia recovery of ecosystem functioning

Hypoxia represents one of the major causes of biodiversity and ecosystem functioning loss for coastal waters. Since eutrophication-induced hypoxic events are becoming increasingly frequent and intense, understanding the response of ecosystems to hypoxia is of primary importance to understand and predict the stability of ecosystem functioning. Such ecological stability may greatly depend on the recovery patterns of communities and the return time of the system properties associated to these patterns. Here, we have examined how the reassembly of a benthic community contributed to the recovery of ecosystem functioning following experimentally-induced hypoxia in a tidal flat. We demonstrate that organism-sediment interactions that depend on organism size and relate to mobility traits and sediment reworking capacities are generally more important than recovering species richness to set the return time of the measured sediment processes and properties. Specifically, increasing macrofauna bioturbation potential during community reassembly significantly contributed to the recovery of sediment processes and properties such as denitrification, bedload sediment transport, primary production and deep pore water ammonium concentration. Such bioturbation potential was due to the replacement of the small-sized organisms that recolonised at early stages by large-sized bioturbating organisms, which had a disproportionately stronger influence on sediment. This study suggests that the complete recovery of organism-sediment interactions is a necessary condition for ecosystem functioning recovery, and that such process requires long periods after disturbance due to the slow growth of juveniles into adult stages involved in these interactions. Consequently, repeated episodes of disturbance at intervals smaller than the time needed for the system to fully recover organism-sediment interactions may greatly impair the resilience of ecosystem functioning.

Does the level of expressed emotion (LEE) questionnaire have the same factor structure for adolescents as it has for adults?

Background The level of expressed emotion (LEE) is a four-factor questionnaire that measures expressed emotion (EE) as perceived by the recipient. These factors are: perceived lack of emotional support, perceived intrusiveness, perceived irritation, and perceive criticism. The four factors of the LEE has previously been found to be related to psychological disorders and has good psychometric properties for adults. However, it has not previously been studied in adolescent populations. Methods A total of 311 adolescents participated in this study. Using structural equation modeling, confirmatory factor analyses were conducted to examine if the LEE also had the same four-factor structure for adolescents as it does for adults. Results The confirmatory factor analyses demonstrated that the LEE's four-factor structure also applied to adolescents. The internal consistency of the scales were good and all the inter-correlations between the scales were significant. Additionally, the factors were significantly correlated to adolescent depressive and anxiety symptom score dimensions. Conclusion These findings seem to indicate that the LEE may be a good instrument in the measurement of adolescents perceived EE

Dental management considerations for the patient with an acquired coagulopathy. Part 1: Coagulopathies from systemic disease

Current teaching suggests that many patients are at risk for prolonged bleeding during and following invasive dental procedures, due to an acquired coagulopathy from systemic disease and/or from medications. However, treatment standards for these patients often are the result of long-standing dogma with little or no scientific basis. The medical history is critical for the identification of patients potentially at risk for prolonged bleeding from dental treatment. Some time-honoured laboratory tests have little or no use in community dental practice. Loss of functioning hepatic, renal, or bone marrow tissue predisposes to acquired coagulopathies through different mechanisms, but the relationship to oral haemostasis is poorly understood. Given the lack of established, science-based standards, proper dental management requires an understanding of certain principles of pathophysiology for these medical conditions and a few standard laboratory tests. Making changes in anticoagulant drug regimens are often unwarranted and/or expensive, and can put patients at far greater risk for morbidity and mortality than the unlikely outcome of postoperative bleeding. It should be recognised that prolonged bleeding is a rare event following invasive dental procedures, and therefore the vast majority of patients with suspected acquired coagulopathies are best managed in the community practice setting

A UMLS-based spell checker for natural language processing in vaccine safety

BACKGROUND: The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. METHODS: We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. RESULTS: We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74–75), 100% (95% CI: 100–100), and 47% (95% CI: 46%–48%), respectively. CONCLUSION: We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest

Candidate target genes for loss of heterozygosity on human chromosome 17q21

Loss of heterozygosity (LOH) on chromosome 17q21 has been detected in 30% of primary human breast tumours. The smallest common region deleted occurred in an interval between the D17S746 and D17S846 polymorphic sequences tagged sites that are located on two recombinant PI-bacteriophage clones of chromosome 17q21: 122F4 and 50H1, respectively. To identify the target gene for LOH, we defined a map of this chromosomal region. We found the following genes: JUP, FK506BP10, SC65, Gastrin (GAS) and HAP1. Of the genes that have been identified in this study, only JUP is located between D17S746 and D17S846. This was of interest since earlier studies have shown that JUP expression is altered in breast, lung and thyroid tumours as well as cell lines having LOH in chromosome 17q21. However, no mutations were detected in JUP using single-strand conformation polymorphism analysis of primary breast tumour DNAs having LOH at 17q21. We could find no evidence that the transcription promoter for JUP is methylated in tumour DNAs having LOH at 17q21. We suspect that the target gene for LOH in primary human breast tumours on chromosome 17q21 is either JUP and results in a haploinsufficiency for expression or may be an unidentified gene located in the interval between D17S846 and JUP. © 2004 Cancer Research UK

Anthropometry and body composition in ethnic Japanese and Caucasian adolescent girls: Considerations on ethnicity and menarche

Objective: This study aimed to compare the various anthropometric and body composition parameters based on the ethnicity and the absence or presence of menarche.Design: A cross-sectional study with incomplete sampling, using the subject as the evaluation unit.Subjects: the final sample of 550 subjects was composed of 122 Japanese and 179 Caucasian premenarcheal adolescents, and 72 Japanese and 177 Caucasian postmenarcheal adolescents.Methods: the variables of body composition were measured through the following methods: bioelectrical impedance analysis, near-infrared interactance (NIR), Slaughter cutaneous skinfold equations and body mass index. Weight, height and sitting height were also evaluated.Results: the Japanese pre- and postmenarcheal girls presented lower weight and height values when compared with the Caucasian girls. in general, the Japanese premenarcheal girls presented less fat and fat-free mass than the premenarcheal Caucasian girls. This fact was demonstrated through NIR results. Conversely, the Japanese postmenarcheal adolescents accumulated more fat than their Caucasian counterparts. However, significant differences were solely encountered in the values of cutaneous skinfold percent body fat. With regard to menarche, it was verified that, regardless of ethnicity, all the anthropometric and body composition variables reached higher values among postmenarcheal adolescents when compared with premenarcheal adolescents.Conclusion: Different results of weight and height between the ethnic groups may bring back the discussion concerning separate growth curves for different ethnic groups. the results of the body composition analysis indicated high adiposity levels among postmenarcheal adolescents.Universidade Federal de São Paulo, Escola Paulista Med, Dept Postgrad Nutr, BR-04020060 São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Prevent Med, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Postgrad Nutr, BR-04020060 São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Prevent Med, São Paulo, BrazilWeb of Scienc

Forces exerted during exercises by patients with adolescent idiopathic scoliosis wearing fiberglass braces

OBJECTIVE: To quantify and compare the forces exerted by scoliosis patients in fiberglass braces during exercises usually prescribed in departments where casts are made. The exercises are intended to increase corrective forces, activate muscles, stimulate ventilation and help the patient psychologically. SETTING: Outpatient care. PATIENTS: 17 consecutive adolescent patients wearing fiberglass brace for idiopathic scoliosis. INTERVENTIONS: Exercises (kyphotization, rotation, "escape from the pad") in different positions (sitting, supine, on all fours). MAIN OUTCOME MEASURE: Pressure detected by the F-Socket System between the rib hump and the pad of the brace. RESULTS: In static and dynamic conditions, the position adopted did not alter the total pressure exerted by the brace, although the part of the sensor stimulated did vary. Kyphotization and rotation exercises produced a significant increase of pressure (+ 58.9% and +29.8%, respectively); however, the "escape from the pad" exercise, despite its name, did not produce any significant variation of pressure. CONCLUSION: Exercises in the brace allow adjunctive forces to be applied on soft tissues and through them, presumably on the spine. Different exercises can be chosen to obtain different actions. Physical exercises and sporting activities are useful in mechanical terms, although other important actions should not be overlooked

Men and Women Exhibit a Differential Bias for Processing Movement versus Objects

Sex differences in many spatial and verbal tasks appear to reflect an inherent low-level processing bias for movement in males and objects in females. We explored this potential movement/object bias in men and women using a computer task that measured targeting performance and/or color recognition. The targeting task showed a ball moving vertically towards a horizontal line. Before reaching the line, the ball disappeared behind a masking screen, requiring the participant to imagine the movement vector and identify the intersection point. For the color recognition task, the ball briefly changed color before disappearing beneath the mask and participants were required only to identify the color shade. Results showed that targeting accuracy for slow and fast moving balls was significantly better in males compared to females. No sex difference was observed for color shade recognition. We also studied a third, dual attention task comprised of the first two, where the moving ball briefly changed color randomly just before passing beneath the masking screen. When the ball changed color, participants were required only to identify the color shade. If the ball didn't change color, participants estimated the intersection point. Participants in this dual attention condition were first tested with the targeting and color tasks alone and showed results that were similar to the previous groups tested on a single task. However, under the dual attention condition, male accuracy in targeting, as well as color shade recognition, declined significantly compared to their performance when the tasks were tested alone. No significant changes were found in female performance. Finally, reaction times for targeting and color choices in both sexes correlated highly with ball speed, but not accuracy. Overall, these results provide evidence of a sex-related bias in processing objects versus movement, which may reflect sex differences in bottom up versus top-down analytical strategies

Ice sheets as a missing source of silica to the polar oceans

Ice sheets play a more important role in the global silicon cycle than previously appreciated. Input of dissolved and amorphous particulate silica into natural waters stimulates the growth of diatoms. Here we measure dissolved and amorphous silica in Greenland Ice Sheet meltwaters and icebergs, demonstrating the potential for high ice sheet export. Our dissolved and amorphous silica flux is 0.20 (0.06-0.79) Tmol year(-1), ∼50% of the input from Arctic rivers. Amorphous silica comprises >95% of this flux and is highly soluble in sea water, as indicated by a significant increase in dissolved silica across a fjord salinity gradient. Retreating palaeo ice sheets were therefore likely responsible for high dissolved and amorphous silica fluxes into the ocean during the last deglaciation, reaching values of ∼5.5 Tmol year(-1), similar to the estimated export from palaeo rivers. These elevated silica fluxes may explain high diatom productivity observed during the last glacial-interglacial period