Hierarchical classification of G-protein-coupled receptors with data-driven selection of attributes and classifiers

We address the important bioinformatics problem of predicting protein function from a protein's primary sequence. We consider the functional classification of G-Protein-Coupled Receptors (GPCRs), whose functions are specified in a class hierarchy. We tackle this task using a novel top-down hierarchical classification system where, for each node in the class hierarchy, the predictor attributes to be used in that node and the classifier to be applied to the selected attributes are chosen in a data-driven manner. Compared with a previous hierarchical classification system selecting classifiers only, our new system significantly reduced processing time without significantly sacrificing predictive accuracy.

On the 'classification' of neurodegenerative disorders:discrete entities, overlap or continuum?

The traditional method of classifying neurodegenerative diseases is based on the original clinico-pathological concept supported by 'consensus' criteria and data from molecular pathological studies. This review discusses first, current problems in classification resulting from the coexistence of different classificatory schemes, the presence of disease heterogeneity and multiple pathologies, the use of 'signature' brain lesions in diagnosis, and the existence of pathological processes common to different diseases. Second, three models of neurodegenerative disease are proposed: (1) that distinct diseases exist ('discrete' model), (2) that relatively distinct diseases exist but exhibit overlapping features ('overlap' model), and (3) that distinct diseases do not exist and neurodegenerative disease is a 'continuum' in which there is continuous variation in clinical/pathological features from one case to another ('continuum' model). Third, to distinguish between models, the distribution of the most important molecular 'signature' lesions across the different diseases is reviewed. Such lesions often have poor 'fidelity', i.e., they are not unique to individual disorders but are distributed across many diseases consistent with the overlap or continuum models. Fourth, the question of whether the current classificatory system should be rejected is considered and three alternatives are proposed, viz., objective classification, classification for convenience (a 'dissection'), or analysis as a continuum.

Health of entrepreneurs versus employees in a national representative sample

Prior research has found entrepreneurs to experience significantly higher job control and job demands compared with employees. This suggests that entrepreneurs have so-called active jobs and thus may benefit from positive health consequences. The present research compared entrepreneurs' health with employees' health in a national representative sample with regard to the International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) diagnoses of somatic diseases, the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) diagnoses of mental disorders, blood pressure, well-being (life-satisfaction) as well as behavioural health indicators (sick days, physician visits). Entrepreneurs showed significantly lower overall somatic and mental morbidity, lower blood pressure, lower prevalence rates of hypertension, and somatoform disorders, as well as higher well-being and more favourable behavioural health indicators. The results are discussed with regard to the active job hypothesis and recommendations for future research are provided.

Automated detection of hematological abnormalities through classification of flow cytometric data patterns

Flow Cytometry analyzers have become trusted companions due to their ability to perform fast and accurate analyses of human blood. The aim of these analyses is to determine the possible existence of abnormalities in the blood that have been correlated with serious disease states, such as infectious mononucleosis, leukemia, and various cancers. Though these analyzers provide important feedback, it is always desired to improve the accuracy of the results. This is evidenced by the occurrences of misclassifications reported by some users of these devices. It is advantageous to provide a pattern interpretation framework that is able to provide better classification ability than is currently available. Toward this end, the purpose of this dissertation was to establish a feature extraction and pattern classification framework capable of providing improved accuracy for detecting specific hematological abnormalities in flow cytometric blood data. ^ This involved extracting a unique and powerful set of shift-invariant statistical features from the multi-dimensional flow cytometry data and then using these features as inputs to a pattern classification engine composed of an artificial neural network (ANN). The contribution of this method consisted of developing a descriptor matrix that can be used to reliably assess if a donor’s blood pattern exhibits a clinically abnormal level of variant lymphocytes, which are blood cells that are potentially indicative of disorders such as leukemia and infectious mononucleosis. ^ This study showed that the set of shift-and-rotation-invariant statistical features extracted from the eigensystem of the flow cytometric data pattern performs better than other commonly-used features in this type of disease detection, exhibiting an accuracy of 80.7%, a sensitivity of 72.3%, and a specificity of 89.2%. This performance represents a major improvement for this type of hematological classifier, which has historically been plagued by poor performance, with accuracies as low as 60% in some cases. This research ultimately shows that an improved feature space was developed that can deliver improved performance for the detection of variant lymphocytes in human blood, thus providing significant utility in the realm of suspect flagging algorithms for the detection of blood-related diseases.^

The difficulty of measuring culture and diversity. Comparison of three international models of cultural measurement: FCS-2009, ESSnet-2012 and CAB-2015

The growing interest in quantifying the cultural and creative industries, visualize the economic contribution of activities related to culture demands first of all the construction of internationally comparable analysis frameworks. Currently there are three major bodies which address this issue and whose comparative study is the focus of this article: the UNESCO Framework for Cultural Statistics (FCS-2009), the European Framework for Cultural Statistics (ESSnet-Culture 2012) and the methodological resource of the “Convenio Andrés Bello” group for working with the Satellite Accounts on Culture in Ibero-America (CAB-2015). Cultural sector measurements provide the information necessary for correct planning of cultural policies which in turn leads to sustaining industries and promoting cultural diversity. The text identifies the existing differences in the three models and three levels of analysis, the sectors, the cultural activities and the criteria that each one uses in order to determine the distribution of the activities by sector. The end result leaves the impossibility of comparing cultural statistics of countries that implement different frameworks.

A Phylogenetic Classification of the Video-Game Industry’s Business Model Ecosystem

Part 8: Business Strategies Alignment

Classification of plant communities, structure and diversity of forests in Acre, Brazil.

2016

Using health-related quality of life instruments for children with long-term conditions : On the basis of a national quality registry system

Introduction: There has been a continuous development of new technologies in healthcare that are derived from national quality registries. However, this innovation needs to be translated into the workflow of healthcare delivery, to enable children with long-term conditions to get the best support possible to manage their health during everyday life. Since children living with long-term conditions experience different interference levels in their lives, healthcare professionals need to assess the impact of care on children’s day-to-day lives, as a complement to biomedical assessments. Aim: The overall aim of this thesis was to explore and describe the use of instruments about health-related quality of life (HRQOL) in outpatient care for children with long-term conditions on the basis of a national quality registry system. Methods: The research was conducted by using comparative, cross-sectional and explorative designs and data collection was performed by using different methods. The questionnaire DISABKIDS Chronic Generic Measure -37 was used as well as semi-structured interviews and video-recordings from consultations. Altogether, 156 children (8–18 years) and nine healthcare professionals participated in the studies. Children with Type 1 Diabetes (T1D) (n 131) answered the questionnaire DISABKIDS and children with rheumatic diseases, kidney diseases and T1D (n 25) were interviewed after their consultation at the outpatient clinic after the web-DISABKIDS had been used. In total, nine healthcare professionals used the HRQOL instrument as an assessment tool during the encounters which was video-recorded (n 21). Quantitative deductive content analysis was used to describe content in different HRQOL instruments. Statistical inference was used to analyse results from DISABKIDS and qualitative content analysis was used to analyse the interviews and video-recordings. Results: The findings showed that based on a biopsychosocial perspective, both generic and disease-specific instruments should be used to gain a comprehensive evaluation of the child’s HRQOL. The DISABKIDS instrument is applicable when describing different aspects of health concerning children with T1D. When DISABKIDS was used in the encounters, children expressed positive experiences about sharing their results with the healthcare professional. It was discovered that different approaches led to different outcomes for the child when the healthcare professionals were using DISABKIDS during the encounter. When an instructing approach is used, the child’s ability to learn more about their health and how to improve their health is limited. When an inviting or engaging approach is used by the professional, the child may become more involved during the conversations. Conclusions: It could be argued that instruments of HRQOL could be used as a complement to biomedical variables, to promote a biopsychosocial perspective on the child’s health. According to the children in this thesis, feedback on their results after answering to web-DISABKIDS is important, which implies that healthcare professionals need to prioritize time for discussions about results from HRQOL instruments in the encounters. If healthcare professionals involve the child in the discussion of the results of the HRQOL, misinterpreted answers could be corrected during the conversation. Concurrently, this claims that healthcare professionals invite and engage the child.

The Value Of The 2005 International Society Of Urological Pathology (isup) Modified Gleason Grading System As A Predictor Of Biochemical Recurrence After Radical Prostatectomy.

To compare time and risk to biochemical recurrence (BR) after radical prostatectomy of two chronologically different groups of patients using the standard and the modified Gleason system (MGS). Cohort 1 comprised biopsies of 197 patients graded according to the standard Gleason system (SGS) in the period 1997/2004, and cohort 2, 176 biopsies graded according to the modified system in the period 2005/2011. Time to BR was analyzed with the Kaplan-Meier product-limit analysis and prediction of shorter time to recurrence using univariate and multivariate Cox proportional hazards model. Patients in cohort 2 reflected time-related changes: striking increase in clinical stage T1c, systematic use of extended biopsies, and lower percentage of total length of cancer in millimeter in all cores. The MGS used in cohort 2 showed fewer biopsies with Gleason score ≤ 6 and more biopsies of the intermediate Gleason score 7. Time to BR using the Kaplan-Meier curves showed statistical significance using the MGS in cohort 2, but not the SGS in cohort 1. Only the MGS predicted shorter time to BR on univariate analysis and on multivariate analysis was an independent predictor. The results favor that the 2005 International Society of Urological Pathology modified system is a refinement of the Gleason grading and valuable for contemporary clinical practice.

Phylogenetics, Ancestral State Reconstruction, And A New Infrafamilial Classification Of The Pantropical Ochnaceae (medusagynaceae, Ochnaceae S.str., Quiinaceae) Based On Five Dna Regions.

Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.

Classification Of Frankfurters By Ft-raman Spectroscopy And Chemometric Methods.

Frankfurters are widely consumed all over the world, and the production requires a wide range of meat and non-meat ingredients. Due to these characteristics, frankfurters are products that can be easily adulterated with lower value meats, and the presence of undeclared species. Adulterations are often still difficult to detect, due the fact that the adulterant components are usually very similar to the authentic product. In this work, FT-Raman spectroscopy was employed as a rapid technique for assessing the quality of frankfurters. Based on information provided by the Raman spectra, a multivariate classification model was developed to identify the frankfurter type. The aim was to study three types of frankfurters (chicken, turkey and mixed meat) according to their Raman spectra, based on the fatty vibrational bands. Classification model was built using partial least square discriminant analysis (PLS-DA) and the performance model was evaluated in terms of sensitivity, specificity, accuracy, efficiency and Matthews's correlation coefficient. The PLS-DA models give sensitivity and specificity values on the test set in the ranges of 88%-100%, showing good performance of the classification models. The work shows the Raman spectroscopy with chemometric tools can be used as an analytical tool in quality control of frankfurters.

Neural networks and statistical analysis for classification of corneal videokeratography maps based on Zernike coefficients: a quantitative comparison

PURPOSE: The main goal of this study was to develop and compare two different techniques for classification of specific types of corneal shapes when Zernike coefficients are used as inputs. A feed-forward artificial Neural Network (NN) and discriminant analysis (DA) techniques were used. METHODS: The inputs both for the NN and DA were the first 15 standard Zernike coefficients for 80 previously classified corneal elevation data files from an Eyesys System 2000 Videokeratograph (VK), installed at the Departamento de Oftalmologia of the Escola Paulista de Medicina, São Paulo. The NN had 5 output neurons which were associated with 5 typical corneal shapes: keratoconus, with-the-rule astigmatism, against-the-rule astigmatism, "regular" or "normal" shape and post-PRK. RESULTS: The NN and DA responses were statistically analyzed in terms of precision ([true positive+true negative]/total number of cases). Mean overall results for all cases for the NN and DA techniques were, respectively, 94% and 84.8%. CONCLUSION: Although we used a relatively small database, results obtained in the present study indicate that Zernike polynomials as descriptors of corneal shape may be a reliable parameter as input data for diagnostic automation of VK maps, using either NN or DA.

Causas mal definidas de morte e óbitos sem assistência

OBJETIVOS: Este trabalho estuda a distribuição dos óbitos por causas mal definidas no Brasil, no ano de 2003, entre as quais identifica a proporção de mortes sem assistência. MÉTODOS: Os dados provieram do Sistema de Informações Sobre Mortalidade, coordenado pelo Ministério da Saúde. As causas mal definidas de morte compreenderam as incluídas no "Capítulo XVIII - Sintomas, sinais e achados anormais de exames clínicos e de laboratório não classificados em outra parte" da Classificação Estatística Internacional de Doenças e Problemas Relacionados à Saúde, décima revisão, capítulo este no qual a categoria R98 identificava a "morte sem assistência". RESULTADOS: No Brasil, em 2003, a causa básica de 13,3% dos óbitos foi identificada como mal definida, sendo que as proporções maiores ocorreram nas Regiões Nordeste e Norte. Do total de causas mal definidas no país, 53,3% corresponderam a mortes sem assistência, proporção esta que superou 70% nos Estados do Maranhão, Piauí, Rio Grande do Norte, Pernambuco, Bahia, Paraíba e Alagoas. CONCLUSÃO: Dada a estrutura descentralizada para o levantamento dos óbitos no país, identifica-se a maior responsabilidade dos municípios e, em seguida, dos Estados para o aprimoramento da qualidade das estatísticas de mortalidade.

O papel das Classificações da OMS - CID e CIF nas definições de deficiência e incapacidade

A Organização Mundial de Saúde tem hoje duas classificações de referência para a descrição dos estados de saúde: a Classificação Estatística Internacional de Doenças e Problemas Relacionados à Saúde, que corresponde à décima revisão da Classificação Internacional de Doenças (CID-10) e a Classificação Internacional de Funcionalidade, Incapacidade e Saúde (CIF). A utilização da CIF vem sendo aguardada com grande expectativa pelas organizações de pessoas com deficiências e instituições relacionadas. A falta de definição clara de "deficiência" ou "incapacidade" tem sido apontada como um impedimento para a promoção de saúde de pessoas com deficiência. É importante que essas definições, especialmente no âmbito legislativo e regulamentar, sejam consistentes e se fundamentem num modelo coerente sobre o processo que origina as situações de incapacidade. Este artigo tem como objetivo apresentar elementos da CID-10 e da CIF, e o papel que desempenham para definir deficiência e incapacidade. Os componentes da CIF podem contribuir para diferentes campos de aplicabilidade no que diz respeito ao entendimento das definições de deficiência ou incapacidade a partir do conceito de funcionalidade e dos fatores contextuais.