Hock burn: an indicator of broiler flock health.

This study aimed to identify risk factors for the prevalence of hock burn, a common disease of broiler chickens that influences the welfare and profitability of affected flocks, using hierarchical logistic regression analysis of routine flock management data. The study identified an association between hock burn and other diseases detected at slaughter and found that the management of flocks around the slaughter period was of particular importance for the control of hock burn, providing a rational basis for intervention.

[Endodontic treatment quality analysis according to the computer tomography data].

Endodontic treatment quality of different teeth groups was analysed according to computer tomography data. 1000 dental root canals of 521 teeth of 115 patients of different age groups were studied. The study results testified to low level of endodontic treatment quality. In 71.7% of cases instrumental processing and obturation of dental root canals were fulfilled inadequately. The most often mistake of endodontic treatment was insufficient root canals instrumental processing (62.8%).

Prevalence of wet litter and the associated risk factors in broiler flocks in the United Kingdom.

A postal questionnaire was sent to the managers of 857 broiler farms in the UK to determine the prevalence and risk factors for wet litter. The response rate was 75 per cent. Wet litter was reported by 75 per cent (95 per cent confidence interval [CI] 71.3 to 78.3) of the respondents in at least one flock during the year 2001 and 56.1 per cent (95 per cent CI 52.0 to 60.0) of them reported that they had an outbreak of wet litter in their most recently reared flock. Wet litter occurred more often during the winter months and farms using side ventilation systems were at an increased risk (odds ratio 1.74; 95 per cent CI 1.09 to 2.76). A multivariable analysis was carried out using two different definitions of wet litter as outcome variables - all cases of wet litter, and cases of wet litter associated with disease. Consistent risk factors for both outcomes were coccidiosis, feed equipment failures and the availability of separate farm clothing for each house. Cases of wet litter associated with disease were reported by 33.7 per cent (95 per cent CI 28.8 to 39.1) of the managers in their last flock and were associated with the use of hand sanitisers and broiler houses with walls made of concrete.

Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods.

Domain parsing, or the detection of signals of protein structural domains from sequence data, is a complex and difficult problem. If carried out reliably it would be a powerful interpretive and predictive tool for genomic and proteomic studies. We report on a novel approach to domain parsing using consensus techniques based on Hidden Markov Models (HMMs) and BLAST searches built from a training set of 1471 continuous structural domains from the Dali Domain Dictionary (DDD). Validation on an independent test sample of family-matched structural domain sequences from the Scop database yields a consensus prediction performance rate of 75.5%, well above the 58% obtained by simple agreement of methods.

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification.

A computational method has been developed for the assignment of a protein sequence to a folding class in the Structural Classification of Proteins (SCOP). This method uses global descriptors of a primary protein sequence in terms of the physical, chemical, and structural properties of the constituent amino acids. Neural networks are utilized to combine these descriptors in a way to discriminate members of a given fold from members of all other folds. An extensive testing of the method has been performed to evaluate its prediction accuracy. The method is applicable for the fold assignment of any protein sequence with or without significant sequence homology to known proteins. A WWW page for predicting protein folds is available at URL http://cbcg.lbl.gov/.

Analysis of ribosomal RNA sequences by combinatorial clustering.

We present an analysis of multi-aligned eukaryotic and procaryotic small subunit rRNA sequences using a novel segmentation and clustering procedure capable of extracting subsets of sequences that share common sequence features. This procedure consists of: i) segmentation of aligned sequences using a dynamic programming procedure, and subsequent identification of likely conserved segments; ii) for each putative conserved segment, extraction of a locall homogeneous cluster using a novel polynomial procedure; and iii) intersection of clusters associated with each conserved segment. Aside from their utilit in processing large gap-filled multi-alignments, these algorithms can be applied to a broad spectrum of rRNA analysis functions such as subalignment, phylogenetic subtree extraction and construction, and organism tree-placement, and can serve as a framework to organize sequence data in an efficient and easily searchable manner. The sequence classification we obtained using the method presented here shows a remarkable consistency with the independently constructed eukaryotic phylogenetic tree.

Assignment of folds for proteins of unknown function in three microbial genomes.

Analysis of DNA sequences of several microbial genomes has revealed that a large fraction of predicted coding regions has no known protein function. Information about the three-dimensional folds of these proteins may provide insight into their possible functions. To predict the folds for protein sequences with little or no homology to proteins of known function, we used computational neural networks trained on the database of proteins with known three-dimensional structures. Global descriptions of protein sequences based on physical and structural properties of the constituent amino acids were used as inputs for neural networks. Of the 131, 498, and 868 protein sequences of unknown function from Mycoplasma genitalium, Haemophilus influenzae, and Methanococcus jannaschii (Fleischmann et al. 1995), we have made high-confidence fold assignments for 4, 10, and 19 sequences, respectively.

Protein folding class predictor for SCOP: approach based on global descriptors.

This work demonstrates new techniques developed for the prediction of protein folding class in the context of the most comprehensive Structural Classification of Proteins (SCOP). The prediction method uses global descriptors of a protein in terms of the physical, chemical and structural properties of its constituent amino acids. Neural networks are utilized to combine these descriptors in a specific way to discriminate members of a given folding class from members of all other classes. It is shown that a specific amino acid's properties work completely differently on different folding classes. This creates the possibility of finding an individual set of descriptors that works best on a particular folding class.

Reconstruction of ancient molecular phylogeny.

Support for contradictory phylogenies is often obtained when molecular sequence data from different genes is used to reconstruct phylogenetic histories. Contradictory phylogenies can result from many data anomalies including unrecognized paralogy. Paralogy, defined as the reconstruction of a phylogenetic tree from a mixture of genes generated by duplications, has generally not been formally included in phylogenetic reconstructions. Here we undertake the task of reconstructing a single most likely evolutionary relationship among a range of taxa from a large set of apparently inconsistent gene trees. Under the assumption that differences among gene trees can be explained by gene duplications, and consequent losses, we have developed a method to obtain the global phylogeny minimizing the total number of postulated duplications and losses and to trace back such individual gene duplications to global genome duplications. We have used this method to infer the most likely phylogenetic relationship among 16 major higher eukaryotic taxa from the sequences of 53 different genes. Only five independent genome duplication events need to be postulated in order to explain the inconsistencies among these trees.

Prediction of protein folding class using global description of amino acid sequence.

We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and distribution of amino acid attributes, such as relative hydrophobicity, predicted secondary structure, and predicted solvent exposure. Cross-validation testing was performed on 15 of the largest classes. The test shows that proteins were assigned to the correct class (correct positive prediction) with an average accuracy of 71.7%, whereas the inverse prediction of proteins as not belonging to a particular class (correct negative prediction) was 90-95% accurate. When tested on 254 structures used in this study, the top two predictions contained the correct class in 91% of the cases.

Relation between protein structure, sequence homology and composition of amino acids.

A method of quantitative comparison of two classifications rules applied to protein folding problem is presented. Classification of proteins based on sequence homology and based on amino acid composition were compared and analyzed according to this approach. The coefficient of correlation between these classification methods and the procedure of estimation of robustness of the coefficient are discussed.

A biologically consistent model for comparing molecular phylogenies.

In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived.

Modeling protein cores with Markov random fields.

A mathematical formalism is introduced that has general applicability to many protein structure models used in the various approaches to the "inverse protein folding problem." The inverse nature of the problem arises from the fact that one begins with a set of assumed tertiary structures and searches for those most compatible with a new sequence, rather than attempting to predict the structure directly from the new sequence. The formalism is based on the well-known theory of Markov random fields (MRFs). Our MRF formulation provides explicit representations for the relevant amino acid position environments and the physical topologies of the structural contacts. In particular, MRF models can readily be constructed for the secondary structure packing topologies found in protein domain cores, or other structural motifs, that are anticipated to be common among large sets of both homologous and nonhomologous proteins. MRF models are probabilistic and can exploit the statistical data from the limited number of proteins having known domain structures. The MRF approach leads to a new scoring function for comparing different threadings (placements) of a sequence through different structure models. The scoring function is very important, because comparing alternative structure models with each other is a key step in the inverse folding problem. Unlike previously published scoring functions, the one derived in this paper is based on a comprehensive probabilistic formulation of the threading problem.

Efficient pattern comparative method for selecting functionally important motifs in protein sequences: application to zinc enzymes.

We have developed a pattern comparative method for identifying functionally important motifs in protein sequences. The essence of most standard pattern comparative methods is a comparison of patterns occurring in different sequences using an optimized weight matrix. In contrast, our approach is based on a measure of similarity among all the candidate motifs within the same sequence. This method may prove to be particularly efficient for proteins encoding the same biochemical function, but with different primary sequences, and when tertiary structure information from one or more sequences is available. We have applied this method to a special class of zinc-binding enzymes known as endopeptidases.

[Ranking scientific research projects based on the results of ballots in expert commissions]. / Voprosy ranzhirovaniia proektov nauchno-issledovatel'skikh rabot po resul'tatam golosovaniia v ékspertnykh komissiiakh.

A procedure for processing the secret ballot results in medical research project contests is proposed to make a generalized adjustment of research projects and their rating scales. The computing efficacy of the procedure makes it applicable in operative contest service.

[Statistical indices of 201Tl distribution in the myocardium]. / Statisticheskie pokazateli raspredeleniia 201Tl v miokarde.

A study was made of the diagnostic potentialities of a histogram analysis of scintigraphic count distribution on myocardium scans using 201Tl in 9 patients with dilated cardiomyopathy, 12 patients with coronary heart disease and 6 patients with primary pulmonary hypertension. Scans were recorded 10 min., 4 and 24 h after a single administration of 201Tl at rest in the front-forward, 45 degrees left forward oblique and left lateral projections. The heart area on a scan was marked by hand. Count distribution was represented by an intensity histogram. An array of 243 scans was processed independently by 2 operators of different professional skill. A man-machine classification procedure with algorithm teaching was implemented. The author showed a possibility of group distinction by scintillation count distribution in the heart area on myocardium scans using 201Tl, the distinguishing information being within the interval of 41-80% of maximum intensity in this area. Automatic marking of the heart area on a scan was found necessary to have an entirely automated system for distinguishing groups of examinees.