Proteomic analysis of a noninvasive human model of acute inflammation and its resolution:the twenty-one day gingivitis model

The 21-day experimental gingivitis model, an established noninvasive model of inflammation in response to increasing bacterial accumulation in humans, is designed to enable the study of both the induction and resolution of inflammation. Here, we have analyzed gingival crevicular fluid, an oral fluid comprising a serum transudate and tissue exudates, by LC-MS/MS using Fourier transform ion cyclotron resonance mass spectrometry and iTRAQ isobaric mass tags, to establish meta-proteomic profiles of inflammation-induced changes in proteins in healthy young volunteers. Across the course of experimentally induced gingivitis, we identified 16 bacterial and 186 human proteins. Although abundances of the bacterial proteins identified did not vary temporally, Fusobacterium outer membrane proteins were detected. Fusobacterium species have previously been associated with periodontal health or disease. The human proteins identified spanned a wide range of compartments (both extracellular and intracellular) and functions, including serum proteins, proteins displaying antibacterial properties, and proteins with functions associated with cellular transcription, DNA binding, the cytoskeleton, cell adhesion, and cilia. PolySNAP3 clustering software was used in a multilayered analytical approach. Clusters of proteins that associated with changes to the clinical parameters included neuronal and synapse associated proteins.

Exploring ant-based algorithms for gene expression data analysis

Objective: Recently, much research has been proposed using nature inspired algorithms to perform complex machine learning tasks. Ant colony optimization (ACO) is one such algorithm based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper investigates ant-based algorithms for gene expression data clustering and associative classification. Methods and material: An ant-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms are proposed for gene expression data analysis. The proposed algorithms make use of the natural behavior of ants such as cooperation and adaptation to allow for a flexible robust search for a good candidate solution. Results: Ant-C has been tested on the three datasets selected from the Stanford Genomic Resource Database and achieved relatively high accuracy compared to other classical clustering methods. Ant-ARM has been tested on the acute lymphoblastic leukemia (ALL)/acute myeloid leukemia (AML) dataset and generated about 30 classification rules with high accuracy. Conclusions: Ant-C can generate optimal number of clusters without incorporating any other algorithms such as K-means or agglomerative hierarchical clustering. For associative classification, while a few of the well-known algorithms such as Apriori, FP-growth and Magnum Opus are unable to mine any association rules from the ALL/AML dataset within a reasonable period of time, Ant-ARM is able to extract associative classification rules.

Clustering web documents using hierarchical representation with multi-granularity

Web document cluster analysis plays an important role in information retrieval by organizing large amounts of documents into a small number of meaningful clusters. Traditional web document clustering is based on the Vector Space Model (VSM), which takes into account only two-level (document and term) knowledge granularity but ignores the bridging paragraph granularity. However, this two-level granularity may lead to unsatisfactory clustering results with “false correlation”. In order to deal with the problem, a Hierarchical Representation Model with Multi-granularity (HRMM), which consists of five-layer representation of data and a twophase clustering process is proposed based on granular computing and article structure theory. To deal with the zero-valued similarity problemresulted from the sparse term-paragraphmatrix, an ontology based strategy and a tolerance-rough-set based strategy are introduced into HRMM. By using granular computing, structural knowledge hidden in documents can be more efficiently and effectively captured in HRMM and thus web document clusters with higher quality can be generated. Extensive experiments show that HRMM, HRMM with tolerancerough-set strategy, and HRMM with ontology all outperform VSM and a representative non VSM-based algorithm, WFP, significantly in terms of the F-Score.

Clustering algorithm based on minimal path loss ratio for vehicular communication

Emerging vehicular comfort applications pose a host of completely new set of requirements such as maintaining end-to-end connectivity, packet routing, and reliable communication for internet access while on the move. One of the biggest challenges is to provide good quality of service (QoS) such as low packet delay while coping with the fast topological changes. In this paper, we propose a clustering algorithm based on minimal path loss ratio (MPLR) which should help in spectrum efficiency and reduce data congestion in the network. The vehicular nodes which experience minimal path loss are selected as the cluster heads. The performance of the MPLR clustering algorithm is calculated by rate of change of cluster heads, average number of clusters and average cluster size. Vehicular traffic models derived from the Traffic Wales data are fed as input to the motorway simulator. A mathematical analysis for the rate of change of cluster head is derived which validates the MPLR algorithm and is compared with the simulated results. The mathematical and simulated results are in good agreement indicating the stability of the algorithm and the accuracy of the simulator. The MPLR system is also compared with V2R system with MPLR system performing better. © 2013 IEEE.

Some clarifications on the DEA clustering approach

This paper clarifies the role of alternative optimal solutions in the clustering of multidimensional observations using data envelopment analysis (DEA). The paper shows that alternative optimal solutions corresponding to several units produce different groups with different sizes and different decision making units (DMUs) at each class. This implies that a specific DMU may be grouped into different clusters when the corresponding DEA model has multiple optimal solutions. © 2011 Elsevier B.V. All rights reserved.

A multiple pheromone ant clustering algorithm

Ant colony optimisation algorithms model the way ants use pheromones for marking paths to important locations in their environment. Pheromone traces are picked up, followed, and reinforced by other ants but also evaporate over time. Optimal paths attract more pheromone and less useful paths fade away. The main innovation of the proposed Multiple Pheromone Ant Clustering Algorithm (MPACA) is to mark objects using many pheromones, one for each value of each attribute describing the objects in multidimensional space. Every object has one or more ants assigned to each attribute value and the ants then try to find other objects with matching values, depositing pheromone traces that link them. Encounters between ants are used to determine when ants should combine their features to look for conjunctions and whether they should belong to the same colony. This paper explains the algorithm and explores its potential effectiveness for cluster analysis. © 2014 Springer International Publishing Switzerland.

The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods

Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties into several smaller, more meaningful groups. Two commonly used clustering techniques are introduced in the following section: principal component analysis (PCA) and hierarchical clustering. PCA calculates the variance between variables and groups them into a few uncorrelated groups or principal components (PCs) that are orthogonal to each other. Hierarchical clustering is carried out by separating data into many clusters and merging similar clusters together. Here, we use an example of human leukocyte antigen (HLA) supertype classification to demonstrate the usage of the two methods. Two programs, Generating Optimal Linear Partial Least Square Estimations (GOLPE) and Sybyl, are used for PCA and hierarchical clustering, respectively. However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R.

Clustering algorithm based on minimal path loss ratio for vehicular communication

Emerging vehicular comfort applications pose a host of completely new set of requirements such as maintaining end-to-end connectivity, packet routing, and reliable communication for internet access while on the move. One of the biggest challenges is to provide good quality of service (QoS) such as low packet delay while coping with the fast topological changes. In this paper, we propose a clustering algorithm based on minimal path loss ratio (MPLR) which should help in spectrum efficiency and reduce data congestion in the network. The vehicular nodes which experience minimal path loss are selected as the cluster heads. The performance of the MPLR clustering algorithm is calculated by rate of change of cluster heads, average number of clusters and average cluster size. Vehicular traffic models derived from the Traffic Wales data are fed as input to the motorway simulator. A mathematical analysis for the rate of change of cluster head is derived which validates the MPLR algorithm and is compared with the simulated results. The mathematical and simulated results are in good agreement indicating the stability of the algorithm and the accuracy of the simulator. The MPLR system is also compared with V2R system with MPLR system performing better. © 2013 IEEE.

Reliability of vegetation community information derived using decorana ordination and fuzzy c-means clustering

Descriptions of vegetation communities are often based on vague semantic terms describing species presence and dominance. For this reason, some researchers advocate the use of fuzzy sets in the statistical classification of plant species data into communities. In this study, spatially referenced vegetation abundance values collected from Greek phrygana were analysed by ordination (DECORANA), and classified on the resulting axes using fuzzy c-means to yield a point data-set representing local memberships in characteristic plant communities. The fuzzy clusters matched vegetation communities noted in the field, which tended to grade into one another, rather than occupying discrete patches. The fuzzy set representation of the community exploited the strengths of detrended correspondence analysis while retaining richer information than a TWINSPAN classification of the same data. Thus, in the absence of phytosociological benchmarks, meaningful and manageable habitat information could be derived from complex, multivariate species data. We also analysed the influence of the reliability of different surveyors' field observations by multiple sampling at a selected sample location. We show that the impact of surveyor error was more severe in the Boolean than the fuzzy classification. © 2007 Springer.

Influence of birth cohort on age of onset cluster analysis in bipolar I disorder

PURPOSE: Two common approaches to identify subgroups of patients with bipolar disorder are clustering methodology (mixture analysis) based on the age of onset, and a birth cohort analysis. This study investigates if a birth cohort effect will influence the results of clustering on the age of onset, using a large, international database. METHODS: The database includes 4037 patients with a diagnosis of bipolar I disorder, previously collected at 36 collection sites in 23 countries. Generalized estimating equations (GEE) were used to adjust the data for country median age, and in some models, birth cohort. Model-based clustering (mixture analysis) was then performed on the age of onset data using the residuals. Clinical variables in subgroups were compared. RESULTS: There was a strong birth cohort effect. Without adjusting for the birth cohort, three subgroups were found by clustering. After adjusting for the birth cohort or when considering only those born after 1959, two subgroups were found. With results of either two or three subgroups, the youngest subgroup was more likely to have a family history of mood disorders and a first episode with depressed polarity. However, without adjusting for birth cohort (three subgroups), family history and polarity of the first episode could not be distinguished between the middle and oldest subgroups. CONCLUSION: These results using international data confirm prior findings using single country data, that there are subgroups of bipolar I disorder based on the age of onset, and that there is a birth cohort effect. Including the birth cohort adjustment altered the number and characteristics of subgroups detected when clustering by age of onset. Further investigation is needed to determine if combining both approaches will identify subgroups that are more useful for research.

The New Software Package for Dynamic Hierarchical Clustering for Circles Types of Shapes

In data mining, efforts have focused on finding methods for efficient and effective cluster analysis in large databases. Active themes of research focus on the scalability of clustering methods, the effectiveness of methods for clustering complex shapes and types of data, high-dimensional clustering techniques, and methods for clustering mixed numerical and categorical data in large databases. One of the most accuracy approach based on dynamic modeling of cluster similarity is called Chameleon. In this paper we present a modified hierarchical clustering algorithm that used the main idea of Chameleon and the effectiveness of suggested approach will be demonstrated by the experimental results.

Using the Agglomerative Method of Hierarchical Clustering as a Data Mining Tool in Capital Market

The purpose of this paper is to explain the notion of clustering and a concrete clustering method- agglomerative hierarchical clustering algorithm. It shows how a data mining method like clustering can be applied to the analysis of stocks, traded on the Bulgarian Stock Exchange in order to identify similar temporal behavior of the traded stocks. This problem is solved with the aid of a data mining tool that is called XLMiner™ for Microsoft Excel Office.

Correlating liposomal adjuvant characteristics to in-vivo cell-mediated immunity using a novel Mycobacterium tuberculosis fusion protein:a multivariate analysis study

Objective In this study, we have used a chemometrics-based method to correlate key liposomal adjuvant attributes with in-vivo immune responses based on multivariate analysis. Methods The liposomal adjuvant composed of the cationic lipid dimethyldioctadecylammonium bromide (DDA) and trehalose 6,6-dibehenate (TDB) was modified with 1,2-distearoyl-sn-glycero-3-phosphocholine at a range of mol% ratios, and the main liposomal characteristics (liposome size and zeta potential) was measured along with their immunological performance as an adjuvant for the novel, postexposure fusion tuberculosis vaccine, Ag85B-ESAT-6-Rv2660c (H56 vaccine). Partial least square regression analysis was applied to correlate and cluster liposomal adjuvants particle characteristics with in-vivo derived immunological performances (IgG, IgG1, IgG2b, spleen proliferation, IL-2, IL-5, IL-6, IL-10, IFN-γ). Key findings While a range of factors varied in the formulations, decreasing the 1,2-distearoyl-sn-glycero-3-phosphocholine content (and subsequent zeta potential) together built the strongest variables in the model. Enhanced DDA and TDB content (and subsequent zeta potential) stimulated a response skewed towards a cell mediated immunity, with the model identifying correlations with IFN-γ, IL-2 and IL-6. Conclusion This study demonstrates the application of chemometrics-based correlations and clustering, which can inform liposomal adjuvant design.

Data Flow Analysis and the Linear Programming Model

* The research is supported partly by INTAS: 04-77-7173 project, http://www.intas.be

Evolutionary Clustering of Complex Systems and Processes

In a paper the method of complex systems and processes clustering based use of genetic algorithm is offered. The aspects of its realization and shaping of fitness-function are considered. The solution of clustering task of Ukraine areas on socio-economic indexes is represented and comparative analysis with outcomes of classical methods is realized.