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Aim: The complications that arise when performing meta-analysis of datasets from multiple metabolomics studies are addressed with computational methods that ensure data quality, completeness of metadata and accurate interpretation across studies. Results & methodology: This paper presents an integrated system of quality control (QC) methods to assess metabolomics results by evaluating the data acquisition strategies and metabolite identification process when integrating datasets for meta-analysis. An ontology knowledge base and a rule-based system representing the experiment and chemical background information direct the processes involved in data integration and QC verification. A diabetes meta-analysis study using these QC methods finds putative biomarkers that differ between cohorts. Conclusion: The methods presented here ensure the validity of meta-analysis when integrating data from different metabolic profiling studies.

Objectives Clinical staging is widely used in medicine to map disease progression, inform prognosis, and guide treatment decisions; in psychiatry, however, staging remains a hypothetical construct. To facilitate future research in bipolar disorders (BD), a well-defined nomenclature is needed, especially since diagnosis is often imprecise with blurred boundaries, and a full understanding of pathophysiology is lacking. Methods Under the auspices of the International Society of Bipolar Disorders, a Task Force of international experts was convened to review, discuss, and integrate findings from the scientific literature relevant to the development of a consensus staging model and standardize a terminology that could be used to advance future research including staging of BD and related disorders. Results Consensus opinion and areas of uncertainty or difference were identified in regard to terms referring to staging as it may apply to BD, to at-risk status and subthreshold stages, and to various clinical stages of BD as it is currently diagnosed. Conclusion The use of a standardized nomenclature about the clinical stages of BD will facilitate communication about research on clinical and pathological components of this heterogeneous group of disorders. The concepts presented are based on current evidence, but the template provided allows for further refinements as etiological advances come to light.

Traffic flow prediction is an essential component of the intelligent transportation management system. This study applies gated recurrent neural network to predict urban traffic flow considering weather conditions. Running results show that, under the review of weather influences, their method improves predictive accuracy and also decreases the prediction error rate. To their best knowledge, this is the first time that traffic flow is predicted in urban freeways in this particular way. This study examines it with respect to extensive weather influence under gated recurrent unit-based deep learning framework.

BackgroundProtein-protein interactions(PPIs) engage in dynamic pathological and biological procedures constantly in our life. Thus, it is crucial to comprehend the PPIs thoroughly such that we are able to illuminate the disease occurrence, achieve the optimal drug-target therapeutic effect and describe the protein complex structures. However, compared to the protein sequences obtainable from various species and organisms, the number of revealed protein-protein interactions is relatively limited. To address this dilemma, lots of research endeavor have investigated in it to facilitate the discovery of novel PPIs. Among these methods, PPI prediction techniques that merely rely on protein sequence data are more widespread than other methods which require extensive biological domain knowledge.ResultsIn this paper, we propose a multi-modal deep representation learning structure by incorporating protein physicochemical features with the graph topological features from the PPI networks. Specifically, our method not only bears in mind the protein sequence information but also discerns the topological representations for each protein node in the PPI networks. In our paper, we construct a stacked auto-encoder architecture together with a continuous bag-of-words (CBOW) model based on generated metapaths to study the PPI predictions. Following by that, we utilize the supervised deep neural networks to identify the PPIs and classify the protein families. The PPI prediction accuracy for eight species ranged from 96.76% to 99.77%, which signifies that our multi-modal deep representation learning framework achieves superior performance compared to other computational methods.ConclusionTo the best of our knowledge, this is the first multi-modal deep representation learning framework for examining the PPI networks.

The extraction of logically-independent fragments out of an ontology ABox can be useful for solving the tractability problem of querying ontologies with large ABoxes. In this paper, we propose a formal definition of an ABox module, such that it guarantees complete preservation of facts about a given set of individuals, and thus can be reasoned independently w.r.t. the ontology TBox. With ABox modules of this type, isolated or distributed (parallel) ABox reasoning becomes feasible, and more efficient data retrieval from ontology ABoxes can be attained. To compute such an ABox module, we present a theoretical approach and also an approximation for SHIQ ontologies. Evaluation of the module approximation on different types of ontologies shows that, on average, extracted ABox modules are significantly smaller than the entire ABox, and the time for ontology reasoning based on ABox modules can be improved significantly.

AIM: The complications that arise when performing meta-analysis of datasets from multiple metabolomics studies are addressed with computational methods that ensure data quality, completeness of metadata and accurate interpretation across studies. RESULTS & METHODOLOGY: This paper presents an integrated system of quality control (QC) methods to assess metabolomics results by evaluating the data acquisition strategies and metabolite identification process when integrating datasets for meta-analysis. An ontology knowledge base and a rule-based system representing the experiment and chemical background information direct the processes involved in data integration and QC verification. A diabetes meta-analysis study using these QC methods finds putative biomarkers that differ between cohorts. CONCLUSION: The methods presented here ensure the validity of meta-analysis when integrating data from different metabolic profiling studies.

ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

The SPARQL LeftJoin abstract operator is not distributive over Union; this limits the algebraic manipulation of graph patterns, which in turn restricts the ability to create query plans for distributed processing or query optimization. In this paper, we present semQA, an algebraic extension for the SPARQL query language for RDF, which overcomes this issue by transforming graph patterns through the use of an idempotent disjunction operator Or as a substitute for Union. This permits the application of a set of equivalences that transform a query into distinct forms. We further present an algorithm to derive the solution set of the original query from the solution set of a query where Union has been substituted by Or. We also analyze the combined complexity of SPARQL, proving it to be NP-complete. It is also shown that the SPARQL query language is not, in the general case, fixed-parameter tractable. Experimental results are presented to validate the query evaluation methodology presented in this paper against the SPARQL standard to corroborate the complexity analysis and to illustrate the gains in processing cost reduction that can be obtained through the application of semQA.

In this paper, a new neural network model inspired by the biological immune system functions is presented. The model, termed Artificial Immune-Activated Neural Network (AIANN), extracts classification knowledge from a training data set, which is then used to classify input patterns or vectors. The AIANN is based on a neuron activation function whose behavior is conceptually modeled after the chemical bonds between the receptors and epitopes in the biological immune system. The bonding is controlled through an energy measure to ensure accurate recognition. The AIANN model was applied to the segmentation of 3-dimensional magnetic resonance imaging (MRI) data of the brain and a contextual basis was developed for the segmentation problem. Evaluation of the segmentation results was performed using both real MRI data obtained from the Center for Morphometric Analysis at Massachusetts General Hospital and simulated MRI data generated using the McGill University BrainWeb MRI simulator. Experimental results demonstrated that the AIANN model attained higher average results than those obtained using published methods for real MRI data and simulated MRI data, especially at low levels of noise.

Efficiently querying Description Logic (DL) ontologies is becoming a vital task in various data-intensive DL applications. Considered as a basic service for answering object queries over DL ontologies, instance checking can be realized by using the most specific concept (MSC) method, which converts instance checking into subsumption problems. This method, however, loses its simplicity and efficiency when applied to large and complex ontologies, as it tends to generate very large MSCs that could lead to intractable reasoning. In this paper, we propose a revision to this MSC method for DL [Formula: see text], allowing it to generate much simpler and smaller concepts that are specific enough to answer a given query. With independence between computed MSCs, scalability for query answering can also be achieved by distributing and parallelizing the computations. An empirical evaluation shows the efficacy of our revised MSC method and the significant efficiency achieved when using it for answering object queries.

Instance checking is considered a central tool for data retrieval from description logic (DL) ontologies. In this paper, we propose a revised most specific concept (MSC) method for DL $\mathcal{SHI}$, which converts instance checking into subsumption problems. This revised method can generate small concepts that are specific-enough to answer a given query, and allow reasoning to explore only a subset of the ABox data to achieve efficiency. Experiments show effectiveness of our proposed method in terms of concept size reduction and the improvement in reasoning efficiency.

Rapid developments in the Internet and multimedia applications allow us to access large amounts of image and video data. While significant progress has been made in digital data compression, content-based functionalities are still quite limited. Many existing techniques in content-based retrieval are based on global visual features extracted from the entire image. In order to provide more efficient content-based functionalities for video applications, it is necessary to extract meaningful video objects from scenes to enable object-based representation of video content. Object-based representation is also introduced by MPEG-4 to enable content-based functionality and high coding efficiency. In this paper, we propose a new algorithm that automatically extracts meaningful video objects from video sequences. The algorithm begins with the robust motion segmentation on the first two successive frames. To detect moving objects, segmented regions are grouped together according to their spatial similarity. A binary object model for each moving object is automatically derived and tracked in subsequent frames using the generalized Hausdorff distance. The object model is updated for each frame to accommodate for complex motions and shape changes of the object. Experimental results using different types of video sequences are presented to demonstrate the efficiency and accuracy of our proposed algorithm.

An algorithm is developed that detects well-localized, unfragmented, thin edges in medical images based on optimization of edge configurations using a genetic algorithm (GA). Several enhancements were added to improve the performance of the algorithm over a traditional GA. The edge map is split into connected subregions to reduce the solution space and simplify the problem. The edge-map is then optimized in parallel using incorporated genetic operators that perform transforms on edge structures. Adaptation is used to control operator probabilities based on their participation. The GA was compared to the simulated annealing (SA) approach using ideal and actual medical images from different modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound. Quantitative comparisons were provided based on the Pratt figure of merit and on the cost-function minimization. The detected edges were thin, continuous, and well localized. Most of the basic edge features were detected. Results for different medical image modalities are promising and encourage further investigation to improve the accuracy and experiment with different cost functions and genetic operators.

OBJECTIVES: To assess the effect of exposure to nitrogen oxides on peripheral blood natural killer cells. METHODS: Groups of glass craftsmen and braziers exposed to nitrogen oxides and non-exposed controls were studied. Air concentrations of nitrogen oxides were measured. Mononuclear cells isolated from peripheral blood samples were assayed for natural killer cell activity with K562 target cells in a 51Cr release assay and the percentage of natural killer cells (CD16) was measured by flow cytometry. RESULTS: Braziers were exposed to 1.2 ppm nitrogen dioxide and 8.6 ppm nitric oxide and glass craftsmen to 2.9 ppm nitrogen dioxide and 26.5 ppm nitric oxide. The natural killer cell activity of exposed workers was significantly lower than in non-exposed controls (P < 0.05 ANOVA Scheffe test). The percentage of natural killer cells in glass craftsmen was significantly greater than in controls (P < 0.05 ANOVA Scheffe test). Regression of natural killer cell activity against age, smoking habit, number of years worked and current exposure to nitrogen dioxide and nitric oxide gases was not significant. The percentage of natural killer cells was not significantly correlated with age, smoking habit, or numbers of years worked, but was significantly related to air concentrations of nitrogen dioxide (P < 0.01) and nitric oxide (P < 0.001). CONCLUSION: Natural killer cell activity and the percentage of natural killer cells in peripheral blood cells were altered in workers exposed to nitrogen oxides.

Image compression using neural networks has been attempted with some promise. Among the architectures, feedforward backpropagation networks (FFBPN) have been used in several attempts. Although it is demonstrated that using the mean quadratic error function is equivalent to applying the Karhunen-Loeve transformation method, promise still arises from directed learning possibilities, generalization abilities and performance of the network once trained. In this paper we propose an architecture and an improved training method to attempt to solve some of the shortcomings of traditional data compression systems based on feedforward neural networks trained with backpropagation-the dynamic autoassociation neural network (DANN). The successful application of neural networks to any task requires proper training of the network. In this research, this issue is taken as the main consideration in the design of DANN. We emphasize the convergence of the learning process proposed by DANN. This process provides an escape mechanism, by adding neurons in a random state, to avoid the local minima trapping seen in traditional PFBPN. Also, DANN's training algorithm constrains the error for every pattern to an allowed interval to balance the training for every pattern, thus improving the performance rates in recognition and generalization. The addition of these two mechanisms to DANN's training algorithm has the result of improving the final quality of the images processed by DANN. The results of several tasks presented to DANN-based compression are compared and contrasted with the performance of an FFBPN-based system applied to the same task. These results indicate that DANN is superior to FFBPN when applied to image compression.

In this paper we present two supervised pattern classifiers designed using Boolean neural networks. They are: 1) nearest-to-an-exemplar classifier; and 2) Boolean k-nearest neighbor classifier. The emphasis during the design of these classifiers was on simplicity, robustness, and the ease of hardware implementation. The classifiers use the idea of radius of attraction to achieve their goal. Mathematical analysis of the algorithms presented in the paper is done to prove their feasibility. Both classifiers are tested with well-known binary and continuous feature valued data sets yielding results comparable with those obtained by similar existing classifiers.

Presents a feature recognition network for pattern recognition that learns the patterns by remembering their different segments. The base algorithm for this network is a Boolean net algorithm that the authors developed during past research. Simulation results show that the network can recognize patterns after significant noise, deformation, translation and even scaling. The network is compared to existing popular networks used for the same purpose, especially the Neocognitron. The network is also analyzed as regards to interconnection complexity and information storage/retrieval. >

Objectives: To develop mechanisms to formulate queries over the semantic representation of cancer-related data services available through the cancer Biomedical Informatics Grid (caBIG). Design: The semCDI query formulation uses a view of caBIG semantic concepts, metadata, and data as an ontology, and defines a methodology to specify queries using the SPARQL query language, extended with Horn rules. semCDI enables the joining of data that represent different concepts through associations modeled as object properties, and the merging of data representing the same concept in different sources through Common Data Elements (CDE) modeled as datatype properties, using Horn rules to specify additional semantics indicating conditions for merging data. Validation: In order to validate this formulation, a prototype has been constructed, and two queries have been executed against currently available caBIG data services. Discussion: The semCDI query formulation uses the rich semantic metadata available in caBIG to build queries and integrate data from multiple sources. Its promise will be further enhanced as more data services are registered in caBIG, and as more linkages can be achieved between the knowledge contained within caBIG's NCI Thesaurus and the data contained in the Data Services. Conclusion: semCDI provides a formulation for the creation of queries on the semantic representation of caBIG. This constitutes the foundation to build a semantic data integration system for more efficient and effective querying and exploratory searching of cancer-related data.

El nefroblastoma o tumor de Wilms, es la neoplasia renal más común en niños y representa actualmente la quinta parte en tumor malignos en este grupo. Sin embargo la incidencia de dicho tumor en el adulto es mucho más rara con tan sólo menos de 250 casos reportados en la literatura. Debido a la baja frecuencia de esta patología en adultos no existe una modalidad en el tratamiento aceptada mundialmente. Actualmente las opciones terapéuticas se desprenden del National Wilms Tumor Study (NTWS). Presentamos a continuación un nuevo caso con las imágenes radiográficas, hallazgos histológicos, evolución y seguimiento.

In his comments, Guy Smith discussed three points he believes are either not correct or unclear. These points are: 1) The uniqueness of thermometer coding in the algorithm is not supported in the paper. 2) The BKNN algorithm is not equivalent to the k-nearest neighbor algorithm. 3) The relationship between examplars and classes is not clear. Following is a reply to each of the above three points