PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

Evaluation of a combined wavelet and a combined principal component analysis classification system for BCG diagnostic problem

Heart disease is one of the main factor causing death in the developed countries. Over several decades, variety of electronic and computer technology have been developed to assist clinical practices for cardiac performance monitoring and heart disease diagnosis. Among these methods, Ballistocardiography (BCG) has an interesting feature that no electrodes are needed to be attached to the body during the measurement. Thus, it is provides a potential application to asses the patients heart condition in the home. In this paper, a comparison is made for two neural networks based BCG signal classification models. One system uses a principal component analysis (PCA) method, and the other a discrete wavelet transform, to reduce the input dimensionality. It is indicated that the combined wavelet transform and neural network has a more reliable performance than the combined PCA and neural network system. Moreover, the wavelet transform requires no prior knowledge of the statistical distribution of data samples and the computation complexity and training time are reduced.

Classification of jinjiang oysters Crassostrea rivularis (Gould, 1861) from China, based on morphology and phylogenetic analysis

The jinjiang oyster Crassostrea rivularis [Gould, 1861. Descriptions of Shells collected in the North Pacific Exploring Expedition under Captains Ringgold and Rodgers. Proc. Boston Soc. Nat. Hist. 8 (April) 33-40] is one of the most important and best-known oysters in China. Based on the color of its flesh, two forms of C rivularis are recognized and referred to as the "white meat" and 11 red meat" oysters. The classification of white and red forms of this species has been a subject of confusion and debate in China. To clarify the taxonomic status of the two forms of C. rivularis, we collected and analyzed oysters from five locations along China's coast using both morphological characters and DNA sequences from mitochondrial 16S rRNA and cytochrome oxidase 1, and the nuclear 28S rRNA genes. Oysters were classified as white or red forms according to their morphological characteristics and then subjected to DNA sequencing. Both morphological and DNA sequence data suggest that the red and white oysters are two separate species. Phylogenetic analysis of DNA sequences obtained in this study and existing sequences of reference species show that the red oyster is the same species as C. ariakensis Wakiya [1929. Japanese food oysters. Jpn. J. Zool. 2, 359-367.], albeit the red oysters from north and south China are genetically distinctive. The white oyster is the same species as a newly described species from Hong Kong, C. hongkongensis Lam and Morton [2003. Mitochondrial DNA and identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China. Aqua. 228, 1-13]. Although the name C. rivularis has seniority over C. ariakensis and C. hongkongensis, the original description of Ostrea rivularis by Gould [1861] does not fit shell characteristics of either the red or the white oysters. We propose that the name of C. rivularis Gould [1861] should be suspended, the red oyster should take the name C. ariakensis, and the white oyster should take the name C. hongkongensis. (C) 2004 Elsevier B.V. All rights reserved.

Classification of common oysters from North China

Oysters are commonly found on rocky shores along China's northern coast, although there is considerable confusion as to what species they are. To determine the taxonomic status of these oysters, we collected specimens from nine locations north of the Yangtze River and conducted genetic identification using DNA sequences. Fragments from three genes, mitochondrial 165 rRNA, mitochondria! cytochrome oxidase I (COI), and nuclear 285 rRNA, were sequenced in six oysters from each of the nine sites. Phylogenetic analysis of all three gene fragments clearly demonstrated that the small oysters commonly found on intertidal rocks in north China are Crassostrea gigas (Thunberg, 1793), not C. plicatula (the zhe oyster) as widely assumed. Their small size and irregular shell characteristics are reflections of the stressful intertidal environment they live in and not reliable characters for classification. Our study confirms that the oysters from Weifang, referred to as Jinjiang oysters or C. rivularis (Gould, 1861), are C. ariakensis (Wakiya, 1929). We found no evidence for the existence of C. talienwhanensis (Crosse, 1862) and other Crassostrea species in north China. Our study highlights the need for reclassifying oysters of China with molecular data.

Distance Metric Between 3D Models and 3D Images for Recognition and Classification

Similarity measurements between 3D objects and 2D images are useful for the tasks of object recognition and classification. We distinguish between two types of similarity metrics: metrics computed in image-space (image metrics) and metrics computed in transformation-space (transformation metrics). Existing methods typically use image and the nearest view of the object. Example for such a measure is the Euclidean distance between feature points in the image and corresponding points in the nearest view. (Computing this measure is equivalent to solving the exterior orientation calibration problem.) In this paper we introduce a different type of metrics: transformation metrics. These metrics penalize for the deformatoins applied to the object to produce the observed image. We present a transformation metric that optimally penalizes for "affine deformations" under weak-perspective. A closed-form solution, together with the nearest view according to this metric, are derived. The metric is shown to be equivalent to the Euclidean image metric, in the sense that they bound each other from both above and below. For Euclidean image metric we offier a sub-optimal closed-form solution and an iterative scheme to compute the exact solution.

Some Extensions of the K-Means Algorithm for Image Segmentation and Pattern Classification

In this paper we present some extensions to the k-means algorithm for vector quantization that permit its efficient use in image segmentation and pattern classification tasks. It is shown that by introducing state variables that correspond to certain statistics of the dynamic behavior of the algorithm, it is possible to find the representative centers fo the lower dimensional maniforlds that define the boundaries between classes, for clouds of multi-dimensional, mult-class data; this permits one, for example, to find class boundaries directly from sparse data (e.g., in image segmentation tasks) or to efficiently place centers for pattern classification (e.g., with local Gaussian classifiers). The same state variables can be used to define algorithms for determining adaptively the optimal number of centers for clouds of data with space-varying density. Some examples of the applicatin of these extensions are also given.

Gait Dynamics for Recognition and Classification

This paper describes a representation of the dynamics of human walking action for the purpose of person identification and classification by gait appearance. Our gait representation is based on simple features such as moments extracted from video silhouettes of human walking motion. We claim that our gait dynamics representation is rich enough for the task of recognition and classification. The use of our feature representation is demonstrated in the task of person recognition from video sequences of orthogonal views of people walking. We demonstrate the accuracy of recognition on gait video sequences collected over different days and times, and under varying lighting environments. In addition, preliminary results are shown on gender classification using our gait dynamics features.

Multiple Resolution Image Classification

Binary image classifiction is a problem that has received much attention in recent years. In this paper we evaluate a selection of popular techniques in an effort to find a feature set/ classifier combination which generalizes well to full resolution image data. We then apply that system to images at one-half through one-sixteenth resolution, and consider the corresponding error rates. In addition, we further observe generalization performance as it depends on the number of training images, and lastly, compare the system's best error rates to that of a human performing an identical classification task given teh same set of test images.

Permutation Tests for Classification

We introduce and explore an approach to estimating statistical significance of classification accuracy, which is particularly useful in scientific applications of machine learning where high dimensionality of the data and the small number of training examples render most standard convergence bounds too loose to yield a meaningful guarantee of the generalization ability of the classifier. Instead, we estimate statistical significance of the observed classification accuracy, or the likelihood of observing such accuracy by chance due to spurious correlations of the high-dimensional data patterns with the class labels in the given training set. We adopt permutation testing, a non-parametric technique previously developed in classical statistics for hypothesis testing in the generative setting (i.e., comparing two probability distributions). We demonstrate the method on real examples from neuroimaging studies and DNA microarray analysis and suggest a theoretical analysis of the procedure that relates the asymptotic behavior of the test to the existing convergence bounds.

Complex System Classification

The use of terms such as “Engineering Systems”, “System of systems” and others have been coming into greater use over the past decade to denote systems of importance but with implied higher complexity than for the term systems alone. This paper searches for a useful taxonomy or classification scheme for complex Systems. There are two aspects to this problem: 1) distinguishing between Engineering Systems (the term we use) and other Systems, and 2) differentiating among Engineering Systems. Engineering Systems are found to be differentiated from other complex systems by being human-designed and having both significant human complexity as well as significant technical complexity. As far as differentiating among various engineering systems, it is suggested that functional type is the most useful attribute for classification differentiation. Information, energy, value and mass acted upon by various processes are the foundation concepts underlying the technical types.