The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies

The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20 330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28 064 new domains have been assigned since our NAR 2007 database publication (CATH version 3.0). The CATH website has been completely redesigned and includes more comprehensive documentation. We have revisited the CATH architecture level as part of the development of a `Protein Chart` and present information on the population of each architecture. The CATHEDRAL structure comparison algorithm has been improved and used to characterize structural diversity in CATH superfamilies and structural overlaps between superfamilies. Although the majority of superfamilies in CATH are not structurally diverse and do not overlap significantly with other superfamilies, similar to 4% of superfamilies are very diverse and these are the superfamilies that are most highly populated in both the PDB and in the genomes. Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website.

The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups

Bothropasin is a 48 kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys(189) is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from I`ll SVMPs. The ECD motif is stabilized by the Cys(117)_Cys(310) disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu(276) of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other Pill SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other Pill members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain. (C) 2008 Elsevier Ltd. All rights reserved.

A novel MAP-MRF approach for multispectral image contextual classification using combination of suboptimal iterative algorithms

In this paper we present a novel approach for multispectral image contextual classification by combining iterative combinatorial optimization algorithms. The pixel-wise decision rule is defined using a Bayesian approach to combine two MRF models: a Gaussian Markov Random Field (GMRF) for the observations (likelihood) and a Potts model for the a priori knowledge, to regularize the solution in the presence of noisy data. Hence, the classification problem is stated according to a Maximum a Posteriori (MAP) framework. In order to approximate the MAP solution we apply several combinatorial optimization methods using multiple simultaneous initializations, making the solution less sensitive to the initial conditions and reducing both computational cost and time in comparison to Simulated Annealing, often unfeasible in many real image processing applications. Markov Random Field model parameters are estimated by Maximum Pseudo-Likelihood (MPL) approach, avoiding manual adjustments in the choice of the regularization parameters. Asymptotic evaluations assess the accuracy of the proposed parameter estimation procedure. To test and evaluate the proposed classification method, we adopt metrics for quantitative performance assessment (Cohen`s Kappa coefficient), allowing a robust and accurate statistical analysis. The obtained results clearly show that combining sub-optimal contextual algorithms significantly improves the classification performance, indicating the effectiveness of the proposed methodology. (C) 2010 Elsevier B.V. All rights reserved.

The classification and the conjugacy classes of the finite subgroups of the sphere braid groups

Let n >= 3. We classify the finite groups which are realised as subgroups of the sphere braid group B(n)(S(2)). Such groups must be of cohomological period 2 or 4. Depending on the value of n, we show that the following are the maximal finite subgroups of B(n)(S(2)): Z(2(n-1)); the dicyclic groups of order 4n and 4(n - 2); the binary tetrahedral group T*; the binary octahedral group O*; and the binary icosahedral group I(*). We give geometric as well as some explicit algebraic constructions of these groups in B(n)(S(2)) and determine the number of conjugacy classes of such finite subgroups. We also reprove Murasugi`s classification of the torsion elements of B(n)(S(2)) and explain how the finite subgroups of B(n)(S(2)) are related to this classification, as well as to the lower central and derived series of B(n)(S(2)).

CLASSIFICATION OF SUBALGEBRAS OF THE CAYLEY ALGEBRA OVER A FINITE FIELD

We classify all unital subalgebras of the Cayley algebra O(q) over the finite field F(q), q = p(n). We obtain the number of subalgebras of each type and prove that all isomorphic subalgebras are conjugate with respect to the automorphism group of O(q). We also determine the structure of the Moufang loops associated with each subalgebra of O(q).

Classification of the virtually cyclic subgroups of the pure braid groups of the projective plane

We classify the ( finite and infinite) virtually cyclic subgroups of the pure braid groups P(n)(RP(2)) of the projective plane. The maximal finite subgroups of P(n)(RP(2)) are isomorphic to the quaternion group of order 8 if n = 3, and to Z(4) if n >= 4. Further, for all n >= 3, the following groups are, up to isomorphism, the infinite virtually cyclic subgroups of P(n)(RP(2)): Z, Z(2) x Z and the amalgamated product Z(4)*(Z2)Z(4).

Enhanced classification of Chagas serologic results and epidemiologic characteristics of seropositive donors at three large blood centers in Brazil

BACKGROUND: A major problem in Chagas disease donor screening is the high frequency of samples with inconclusive results. The objective of this study was to describe patterns of serologic results among donors to the three Brazilian REDS-II blood centers and correlate with epidemiologic characteristics. STUDY DESIGN AND METHODS: The centers screened donor samples with one Trypanosoma cruzi lysate enzyme immunoassay (EIA). EIA-reactive samples were tested with a second lysate EIA, a recombinant-antigen based EIA, and an immunfluorescence assay. Based on the serologic results, samples were classified as confirmed positive (CP), probable positive (PP), possible other parasitic infection (POPI), and false positive (FP). RESULTS: In 2007 to 2008, a total of 877 of 615,433 donations were discarded due to Chagas assay reactivity. The prevalences (95% confidence intervals [CIs]) among first-time donors for CP, PP, POPI, and FP patterns were 114 (99-129), 26 (19-34), 10 (5-14), and 96 (82-110) per 100,000 donations, respectively. CP and PP had similar patterns of prevalence when analyzed by age, sex, education, and location, suggesting that PP cases represent true T. cruzi infections; in contrast the demographics of donors with POPI were distinct and likely unrelated to Chagas disease. No CP cases were detected among 218,514 repeat donors followed for a total of 718,187 person-years. CONCLUSION: We have proposed a classification algorithm that may have practical importance for donor counseling and epidemiologic analyses of T. cruzi-seroreactive donors. The absence of incident T. cruzi infections is reassuring with respect to risk of window phase infections within Brazil and travel-related infections in nonendemic countries such as the United States.

Comparison for three Classification Techniques

In this paper we show the results of a comparison simulation study for three classification techniques: Multinomial Logistic Regression (MLR), No Metric Discriminant Analysis (NDA) and Linear Discriminant Analysis (LDA). The measure used to compare the performance of the three techniques was the Error Classification Rate (ECR). We found that MLR and LDA techniques have similar performance and that they are better than DNA when the population multivariate distribution is Normal or Logit-Normal. For the case of log-normal and Sinh(-1)-normal multivariate distributions we found that MLR had the better performance.

Multivariate Analysis for the Classification Differentiation of Brazilian Sugarcane Spirits by Analysis of Organic and Inorganic Compounds

Brazilian sugarcane spirits were analyzed to elucidate similarities and dissimilarities by principal component analysis. Nine aldehydes, six alcohols, and six metal cations were identified and quantified. Isobutanol (LD 202.9 mu gL-1), butiraldehyde (0.08-0.5 mu gL-1), ethanol (39-47% v/v), and copper (371-6068 mu gL-1) showed marked similarities, but the concentration levels of n-butanol (1.6-7.3 mu gL-1), sec-butanol (LD 89 mu gL-1), formaldehyde (0.1-0.74 mu gL-1), valeraldehyde (0.04-0.31 mu gL-1), iron (8.6-139.1 mu gL-1), and magnesium (LD 1149 mu gL-1) exhibited differences from samples.

Use of Metals and Anion Species with Chemometrics Tools for Classification of Unprocessed and Processed Coconut Waters

Coconut water is a natural isotonic, nutritive, and low-caloric drink. Preservation process is necessary to increase its shelf life outside the fruit and to improve commercialization. However, the influence of the conservation processes, antioxidant addition, maturation time, and soil where coconut is cultivated on the chemical composition of coconut water has had few arguments and studies. For these reasons, an evaluation of coconut waters (unprocessed and processed) was carried out using Ca, Cu, Fe, K, Mg, Mn, Na, Zn, chloride, sulfate, phosphate, malate, and ascorbate concentrations and chemometric tools. The quantitative determinations were performed by electrothermal atomic absorption spectrometry, inductively coupled plasma optical emission spectrometry, and capillary electrophoresis. The results showed that Ca, K, and Zn concentrations did not present significant alterations between the samples. The ranges of Cu, Fe, Mg, Mn, PO (4) (3-) , and SO (4) (2-) concentrations were as follows: Cu (3.1-120 A mu g L(-1)), Fe (60-330 A mu g L(-1)), Mg (48-123 mg L(-1)), Mn (0.4-4.0 mg L(-1)), PO (4) (3-) (55-212 mg L(-1)), and SO (4) (2-) (19-136 mg L(-1)). The principal component analysis (PCA) and hierarchical cluster analysis (HCA) were applied to differentiate unprocessed and processed samples. Multivariated analysis (PCA and HCA) were compared through one-way analysis of variance with Tukey-Kramer multiple comparisons test, and p values less than 0.05 were considered to be significant.

Machine vision for the automatic classification of images acquired from Non-destructive tests

This project is based on Artificial Intelligence (A.I) and Digital Image processing (I.P) for automatic condition monitoring of sleepers in the railway track. Rail inspection is a very important task in railway maintenance for traffic safety issues and in preventing dangerous situations. Monitoring railway track infrastructure is an important aspect in which the periodical inspection of rail rolling plane is required.Up to the present days the inspection of the railroad is operated manually by trained personnel. A human operator walks along the railway track searching for sleeper anomalies. This monitoring way is not more acceptable for its slowness and subjectivity. Hence, it is desired to automate such intuitive human skills for the development of more robust and reliable testing methods. Images of wooden sleepers have been used as data for my project. The aim of this project is to present a vision based technique for inspecting railway sleepers (wooden planks under the railway track) by automatic interpretation of Non Destructive Test (NDT) data using A.I. techniques in determining the results of inspection.

Nonstationary feature extraction techniques for automatic classification of impact acoustic signals

Condition monitoring of wooden railway sleepers applications are generallycarried out by visual inspection and if necessary some impact acoustic examination iscarried out intuitively by skilled personnel. In this work, a pattern recognition solutionhas been proposed to automate the process for the achievement of robust results. Thestudy presents a comparison of several pattern recognition techniques together withvarious nonstationary feature extraction techniques for classification of impactacoustic emissions. Pattern classifiers such as multilayer perceptron, learning cectorquantization and gaussian mixture models, are combined with nonstationary featureextraction techniques such as Short Time Fourier Transform, Continuous WaveletTransform, Discrete Wavelet Transform and Wigner-Ville Distribution. Due to thepresence of several different feature extraction and classification technqies, datafusion has been investigated. Data fusion in the current case has mainly beeninvestigated on two levels, feature level and classifier level respectively. Fusion at thefeature level demonstrated best results with an overall accuracy of 82% whencompared to the human operator.

Filmljudets funktioner i krigsfilm : En audio-visuell analys av Apocalypse Now och Saving Private Ryan

I denna uppsats har filmljudet i krigsfilmerna Apocalypse Now och Saving Private Ryan undersökts. Detta har gjorts för att försöka bidra med ökad förståelse för filmljudets användningsområde och funktioner, främst för filmerna i fråga, men även för krigsfilm rent generellt. Filmljud i denna kontext omfattar allt det ljud som finns i film, men utesluter dock all ickediegetisk musik. Båda filmerna har undersökts genom en audio-visuell analys. En sådan analys görs genom att detaljgranska båda filmernas ljud- och bildinnehåll var för sig, för att slutligen undersöka samma filmsekvens som helhet då ljudet och bilden satts ihop igen. Den audio-visuella analysmetod som nyttjats i uppsatsen är Michel Chions metod, Masking. De 30 minuter film som analyserades placerades sedan i olika filmljudzoner, där respektive filmljudzons ljudinnehåll bland annat visade vilka främsta huvudfunktioner somfilmljudet hade i dessa filmer. Dessa funktioner är till för att bibehålla åskådarens fokus och intresse, att skapa närhet till rollkaraktärerna, samt att tillföra en hög känsla av realism och närvaro. Intentionerna med filmljudet verkade vara att flytta åskådaren in i filmens verklighet, att låta åskådaren bli ett med filmen. Att återspegla denna känsla av realism, närvaro, fokus samt intresse, visade sig också vara de intentioner som funnits redan i de båda filmernas förproduktionsstadier. Detta bevisar att de lyckats åstadkomma det de eftersträvat. Men om filmljudet använts på samma sätt eller innehar samma funktioner i krigsfilm rent genrellt går inte att säga.I have for this bachelor’s thesis examined the movie sound of the classic warfare movies Apocalypse Now and Saving Private Ryan. This is an attempt to contribute to a more profound comprehension of the appliance and importance of movie sound. In this context movie sound implies all kinds of sounds within the movies, accept from non-diegetic music. These two movies have been examined by an audio-visual analysis. It's done by auditing the sound and picture content separately, and then combined to audit the same sequence as a whole. Michel Chion, which is the founder of this analysis, calls this method Masking. The sound in this 30 minute sequence was then divided into different zones, where every zone represented a certain main function. These functions are provided to create a stronger connection to the characters, sustain the viewers interest and bring a sense of realism and presence. It seems though the intention with the movies sound is to bring the viewers to the scene in hand, and let it become their reality. To mirror this sense of realism, presence, focus and interest, proves to be the intention from an early stage of the production. This bachelor’s thesis demonstrates a success in their endeavours. Although it can’t confirm whether the movie sound have been utilized in the same manner or if they posess the same functions to warefare movies in general.

Filmljudets funktioner i dramafilm : En audio-visuell analys av filmen The King's Speech

Johansson, Fredrik (2012). Filmljudets funktioner i dramafilm – En audio-visuell analys av filmen The King´s Speech. Examensuppsats inom Ljudproduktion, Högskolan Dalarna, Akademin för språk och medier, Falun. I denna uppsats undersöktes filmljudet i dramafilmen The King´s Speech. Detta för att ta reda på vilka funktioner filmljudet fyller i de valda sekvenserna ur nämnda film, samt hur ljudet är placerat i filmens flerkanalsmix. Filmen granskades med hjälp av en audio-visuell analys. Denna metod går ut på att ljudet och bilden undersöks separat, för att sedan åter kombineras och analyseras som helhet. Den audio-visuella analysmetod som använts kommer från ljudteoretikern Michel Chion, och kallas Masking. Resultatet av den audio-visuella analysen pekade mot att ljudets huvudsakliga funktioner var att skapa en realistisk skildring av karaktärer och omgivningar, skapa en känsla av närvaro, samt att skapa och bibehålla olika perspektiv i den narrativa världen. Den stora majoriteten av ljud visade sig vara placerade i centerkanalen, medan främst ickediegetisk musik och ambiensljud var placerade i front- och surroundkanalerna. Detta kanalanvändande tycktes gynna de funna funktionerna, främst genom att bidra till känslan av närvaro och realism, genom att omsluta filmpubliken med ambienta ljud.

Game Audio in Audio Games : Towards a Theory on the Roles and Functions of Sound in Audio Games

For the past few decades, researchers have increased our understanding of how sound functions within various audio–visual media formats. With a different focus in mind, this study aims to identify the roles and functions of sound in relation to the game form Audio Games, in order to explore the potential of sound when acting as an autonomous narrative form. Because this is still a relatively unexplored research field, the main purpose of this study is to help establish a theoretical ground and stimulate further research within the field of audio games. By adopting an interdisciplinary approach to the topic, this research relies on theoretical studies, examinations of audio games and contact with the audio game community. In order to reveal the roles of sound, the gathered data is analyzed according to both a contextual and a functional perspective. The research shows that a distinction between the terms ‘function’ and ‘role’ is important when analyzing sound in digital games. The analysis therefore results in the identification of two analytical levels that help define the functions and roles of an entity within a social context, named the Functional and the Interfunctional levels. In addition to successfully identifying three main roles of sound within audio games—each describing the relationship between sound and the entities game system, player and virtual environment—many other issues are also addressed. Consequently, and in accordance with its purpose, this study provides a broad foundation for further research of sound in both audio games and video games.