bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contextual alignment of biological sequences (Extended abstract)
Authors: Gambin Anna , Lasota Sławomir , Szklarczyk Radosław , Tiuryn Jerzy , Tyszkiewicz Jerzy 
Published: May 2011

Abstract
We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.
Contact: jty@mimuw.edu.pl
Biological information: making it accessible and
integrated (and trying to make sense of it)
Authors: Hubbard Tim 
Published: May 2011

Abstract
The availability of the genome sequences of human and mouse, human sequence variation data and other large genetic data sets will lead to a revolution in understanding of the human machine and the treatment of its diseases. The success of the international genome sequencing consortiums shows what can be achieved by well coordinated large scale public domain projects and the benefits of data access to all. It is already clear that the availability of this sequence is having a huge impact on research worldwide.
Complete genome sequences provide a framework to pull all biological data together such that each piece has the potential to say something about biology as a whole. Biology is too complex for any organisation to have a monopoly of ideas or data, so the collection, analysis and access to this data can be contributed to by research institutes around the world. However, although it is possible for all this data to be accessible to all through the internet, the more organisations provide data or analysis separately, the harder it becomes for anyone to collect and integrate the results. To address these problems of intergration of data, open standards for biological data exchange, such as the‘ Distributed Annotation System’ (DAS) are being developed and bioinformatics (Dowell et al., 2001) as a whole is now being strongly driven by the open source software (OSS) model for collaborative software development (Hubbard and Birney, 1999). The leading provider of human genome annotation, the Ensembl project (http://www.ensembl.org), is entirely an OSS project and has been widely adopted by academic and commerical organisations alike (Hubbard et al., 2002).
Accurate automatic annotation of features such as genes in vertebrate genomes currently relies on supporting evidence in the form of homologies to mRNAs, ESTs or protein. However, it appears that sufficient high quality experimentally curated annotation now exists to be used as a substrate for machine learning algorithms to create effective models of biological signal sequences (Down and Hubbard, 2002). Is there hope for ab initio prediction methods after all?
An automatic block and spot indexing with k-nearest neighbors graph
for microarray image analysis
Authors: Jung Ho-Youl , Cho Hwan-Gue 
Published: May 2011

Abstract
Motivation: In this paper, we propose a fully automatic block and spot indexing algorithm for microarray image analysis. A microarray is a device which enables a parallel experiment of ten to hundreds of thousands of test genes in order to measure gene expression. Due to this huge size of experimental data, automated image analysis is gaining importance in microarray image processing systems. Currently, most of the automated microarray image processing systems require manual block indexing and, in some cases, spot indexing. If the microarray image is large and contains a lot of noise, it is very troublesome work. In this paper, we show it is possible to locate the addresses of blocks and spots by applying the Nearest Neighbors Graph Model. Also, we propose an analytic model for the feasibility of block addressing. Our analytic model is validated by a large body of experimental results.
Results: We demonstrate the features of automatic block detection, automatic spot addressing, and correction of the distortion and skewedness of each microarray image.
Contact: hyjung@pearl.cs.pusan.ac.kr
Comparative genomics of microbial pathogens and symbionts
Authors: Andersson Siv G.E. , Alsmark Cecilia , Canbäck Björn , Davids Wagied , Frank Carolin , Karlberg Olof , Klasson Lisa , Antoine-Legault Boris , Mira Alex , Tamas Ivica 
Published: May 2011

Abstract
We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and Buchnera. Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.
Stochastic roadmap simulation for the study of
ligand-protein interactions
Authors: Apaydın Mehmet Serkan , Guestrin Carlos E. , Varma Chris , Brutlag Douglas L. , Latombe Jean-Claude 
Published: May 2011

Abstract
Understanding the dynamics of ligand-protein interactions is indispensable in the design of novel therapeutic agents. In this paper, we establish the use of Stochastic Roadmap Simulation (SRS) for the study of ligand-protein interactions through two studies. In our first study, we measure the effects of mutations on the catalytic site of a protein, a process called computational mutagenesis. In our second study, we focus on distinguishing the catalytic site from other putative binding sites. SRS compactly represents many Monte Carlo (MC) simulation paths in a compact graph structure, or roadmap. Furthermore, SRS allows us to analyze all the paths in this roadmap simultaneously. In our application of SRS to the domain of ligand-protein interactions, we consider a new parameter called escape time, the expected number of MC simulation steps required for the ligand to escape from the ‘funnel of attraction‘ of the binding site, as a metric for analyzing such interactions. Although computing escape times would probably be infeasible with MC simulation, these computations can be performed very efficiently with SRS. Our results for six mutant complexes for the first study and seven ligand-protein complexes for the second study, are very promising: In particular, the first results agree well with the biological interpretation of the mutations, while the second results show that escape time is a good metric to distinguish the catalytic site for five out of seven complexes.
Contact: apaydin@cs.stanford.eduguestrin@cs.stanford.edulatombe@cs.stanford.eduvarma@cs.stanford.edubrutlag@stanford.edu
Building an automated classification of DNA-binding protein domains
Authors: Ponomarenko Julia V. , Bourne Philip E. , Shindyalov Ilya N. 
Published: May 2011

Abstract
Intensive growth in 3D structure data on DNA-protein complexes as reflected in the Protein Data Bank (PDB) demands new approaches to the annotation and characterization of these data and will lead to a new understanding of critical biological processes involving these data. These data and those from other protein structure classifications will become increasingly important for the modeling of complete proteomes. We propose a fully automated classification of DNA-binding protein domains based on existing 3D-structures from the PDB. The classification, by domain, relies on the Protein Domain Parser (PDP) and the Combinatorial Extension (CE) algorithm for structural alignment. The approach involves the analysis of 3D-interaction patterns in DNA-protein interfaces, assignment of structural domains interacting with DNA, clustering of domains based on structural similarity and DNA-interacting patterns. Comparison with existing resources on describing structural and functional classifications of DNA-binding proteins was used to validate and improve the approach proposed here. In the course of our study we defined a set of criteria and heuristics allowing us to automatically build a biologically meaningful classification and define classes of functionally related protein domains. It was shown that taking into consideration interactions between protein domains and DNA considerably improves the classification accuracy. Our approach provides a high-throughput and up-to-date annotation of DNA-binding protein families which can be found at http://spdc.sdsc.edu.
Contact: shindyal@sdsc.edu
*To whom correspondence should be addressed.
Application of metabolomics to plant genotype
discrimination using statistics and machine
learning
Authors: Taylor Janet , King Ross D. , Altmann Thomas , Fiehn Oliver 
Published: May 2011

Abstract
Motivation: Metabolomics is a post genomic technology which seeks to provide a comprehensive profile of all the metabolites present in a biological sample. This complements the mRNA profiles provided by microarrays, and the protein profiles provided by proteomics. To test the power of metabolome analysis we selected the problem of discrimating between related genotypes of Arabidopsis. Specifically, the problem tackled was to discrimate between two background genotypes (Col0 and C24) and, more significantly, the offspring produced by the crossbreeding of these two lines, the progeny (whose genotypes would differ only in their maternally inherited mitichondia and chloroplasts).
Overview: A gas chromotography—mass spectrometry (GCMS) profiling protocol was used to identify 433 metabolites in the samples. The metabolomic profiles were compared using descriptive statistics which indicated that key primary metabolites vary more than other metabolites. We then applied neural networks to discriminate between the genotypes. This showed clearly that the two background lines can be discrimated between each other and their progeny, and indicated that the two progeny lines can also be discriminated. We applied Euclidean hierarchical and Principal Component Analysis (PCA) to help understand the basis of genotype discrimination. PCA indicated that malic acid and citrate are the two most important metabolites for discriminating between the background lines, and glucose and fructose are two most important metabolites for discriminating between the crosses. These results are consistant with genotype differences in mitochondia and chloroplasts.
Keywords: Metabolome, Arabidopsis, Clustering
Contact: jat@aber.ac.uk
Modeling splicing sites with pairwise correlations
Authors: Arita Masanori , Tsuda Koji , Asai Kiyoshi 
Published: May 2011

Abstract
Motivation: A new method for finding subtle patterns in sequences is introduced. It approximates the multiple correlations among residuals with pair-wise correlations, with the learning cost O(m2n) where n is the number of training sequences, each of length m. The method suits to model splicing sites in human DNA, which are reported to have higher-order dependencies.
Results: By computational experiments, the prediction accuracy of our model was shown to surpass that of previously reported Markov models for the prediction of acceptor sites in human.
Availability: The C++ source code is available on request from the authors.
Contact: m-arita@aist.go.jp
Common intervals and sorting by reversals: a marriage of necessity
Authors: Bergeron A. , Heber S. , Stoye J. 
Published: May 2011

Abstract
This paper revisits the problem of sorting by reversals with tools developed in the context of detecting common intervals. Mixing the two approaches yields new definitions and algorithms for the reversal distance computations, that apply directly on the original permutation.
Traditional constructions such as recasting the signed permutation as a positive permutation, or traversing the overlap graph to analyze its connected components, are replaced by elementary definitions in terms of intervals of the permutation. This yields simple linear time algorithms that identify the essential features in a single pass over the permutation and use only simple data structures like arrays and stacks.
Contact: stoye@TechFak.Uni-Bielefeld.DE
Annotating regulatory DNA based on man-mouse genomic comparison
Authors: Dieterich Christoph , Cusack Brian , Wang Haiyan , Rateitschak Katja , Krause Antje , Vingron Martin 
Published: May 2011

Abstract
Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such conserved elements from upstream regions of orthologous gene pairs from man and mouse. We focus on orthologous genes in order to maximize our chances to find functionally similar regulatory elements. The identification of conserved elements is effected using the Waterman–Eggert local suboptimal alignment algorithm. We have modified an implementation of this algorithm such that it integrates the determination of statistical significance for the local suboptimal alignments. This has the effect of outputting a dynamically determined number of suboptimal alignments that are deemed statistically significant. Comparison with experimentally determined annotation shows a striking enrichement of regulatory sites among the conserved regions. Furthermore, the conserved regions tend to cover the promotor region described in the EPD database.
Contact: martin.vingron@molgen.mpg.de
First Report of Aster Yellows (16SrI-B) Associated with Potatoes in Alaska
Authors: McBeath J. H. , Laski P. J. , Cheng M. 
Published: May 2011

During a disease survey conducted in 2009 in Alaska, one potato plant (Solanum tuberosum) with symptoms characteristic of aster yellows, such as apical leaves rolling inward, leaves turning yellow or purple, and presence of aerial tubers, was found in a commercial field. Total DNA was extracted from leaves, stems, and roots of the symptomatic and symptomless plants with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA) according to the instructions of the manufacturer. A nested PCR was carried out with the first round primer pair P1/P7 followed by second round primer pair R16F2n/R16R2 (1,3). An approximate 1.2-kb PCR product was amplified from the symptomatic plant, but not symptomless plants. The PCR products from R16F2n/R16R2 were digested using restriction enzymes AluI, BfaI, BstUI, HhaI, HpaI, KpnI, MseI, and RsaI. The restriction fragment length polymorphism (RFLP) patterns were compared with those from known phytoplasma strains (1) and they matched the patterns for aster yellows subgroup B (16SrI-B). After P1/P7 amplification, the nested PCR product of primer pair P1A/16S-SR (2) was purified with a MiniElute Gel Extraction kit (Qiagen), sequenced by GENEWIZ (South Plainfield, NJ), and the sequence data analyzed by iPhyClassifier software (4). The results indicated that the sequence (GenBank Accession No. HQ599231) had 99.65% similarity to ‘Candidatus Phytoplasma asteris’ reference strain (GenBank Accession No. M30790). The RFLP similarity was identical (coefficient 1.00) to the reference pattern of 16Sr group I, subgroup B (GenBank Accession No. NC 005303). To our knowledge, this is the first report on the molecular identification of aster yellows phytoplasma associated with potatoes in Alaska. The source of the phytoplasma and pathway of disease transmission is currently under investigation. References: (1) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (2) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Absence of Nepotism in Genetically Heterogeneous Colonies of a Clonal Ant
Authors: Kellner Katrin , Heinze Jürgen 
Published: May 2011

AbstractInsect societies are normally closed entities from which alien individuals are excluded. The occasional fusion of unrelated colonies of the thelytokous ant Platythyrea punctata is therefore puzzling, because it strongly intensifies competition among nestmates for the replacement of an old reproductive. Most colonies of P. punctata have only one or few reproductives, which produce female offspring from unfertilized eggs, and therefore have a clonal structure. Fusion leads to multi‐clone colonies. We compared the occurrence of dominance and policing behavior between single‐ and double‐clone colonies. We find that the frequency of aggression is higher in double‐clone colonies, but that individuals do not preferentially direct attacks toward non‐clonemates. This matches observations in other species that social insects perceive genetic homogeneity but are not capable of reliable discrimination among nestmates of different degree of relatedness.
HOW THE PAST DEPENDS ON THE FUTURE
Authors: Hazlett Allan 
Published: May 2011

AbstractIt is often said that, according to common sense, there is a fundamental asymmetry between the past and future; namely, that the past is closed and the future is open. Eternalism in the ontology of time is often seen as conflicting with common sense on this point. Here I argue against the claim that common sense is committed to this fundamental asymmetry between the past and the future, on the grounds that facts about the past often depend on facts about the future.1
WHAT IS IT TO COMMIT SUICIDE?
Authors: Hill Daniel J. 
Published: May 2011

AbstractIn this article I defend a new definition of what it is to commit suicide:
(D) A commits suicide by performing an act x if and only if A intends that he or she kill himself or herself by performing x (under the description ‘I kill myself’), and this intention is fully satisfied.
The definition has some surprising implications: various real‐life examples often referred to as ‘suicides’ (e.g. ‘suicide bombers’) may well turn out not to be suicides after all.1
Direct colloid osmometry in healthy New World camelids
Authors: Quesada Rolando J. , Gorman Maria Elena , Cebra Christopher K. , Verdugo Claudio , Mosley Craig A. 
Published: May 2011

Background:Direct colloid osmometry provides an objective assessment of the oncotic effects of crystalloid or colloidal fluid therapy, which is especially useful in monitoring fluid therapy of critically ill camelids due to their tendency toward nonspecific hypoproteinemia with increased risk of developing edema and ascites.Objectives:The aims of this study were to measure colloid osmotic pressure (COP) of alpacas and llamas, determine its correlation with concentrations of total protein (TP) and total solids (TS), as well as both albumin (A) and globulin (G) concentrations in the same model (A+G), and evaluate the effects of sample type and storage conditions on COP.Methods:Blood was collected from clinically healthy alpacas (n=23) and llamas (n=22) into heparin tubes. COP of fresh whole blood (COPFB) and plasma (COPFP) was determined using a membrane osmometer. For 20 alpacas, COP of refrigerated whole blood (COPRB) and frozen plasma (COPFrP) was also measured. Correlations between COPFBand TS, TP, and A+G concentrations were assessed by simple and multiple regression analysis to model potential predictors.Results:Median COPFBfrom alpacas (24.6 mmHg, range 19.3–28.1) was not significantly different from that of llamas (25.3 mmHg, range 22.5–33.7). Sample type or storage conditions did not affect COP. Measured COP had a strong positive linear correlation with TS, TP, and A+G concentrations in alpacas (r2=.7, .74, and .88, respectively). In llamas, COP correlated best with TS concentration (r2=.59), whereas correlation with TP and A+G concentrations was poor (r2=.19 and .25, respectively).Conclusion:COP can be measured using heparinized whole blood or plasma, either fresh or stored. Direct measurement is recommended whenever quantitative knowledge of COP is required in clinical or research setting. Further studies are needed to verify if the poor association of COP with TP found in this study can be generalized to llamas.
One‐stage prothrombin time, activated partial thromboplastin time, thrombin time, fibrin degradation product concentration, and antithrombin activity in healthy adult alpacas
Authors: House Amanda M. , Barton Michelle H. , Williamson Lisa H. 
Published: May 2011

Background:Alpacas are increasingly presented to veterinarians for evaluation and care. Reports of alpaca reference intervals for one‐stage prothrombin time (PT), activated partial thromboplastin time (aPTT), thrombin time (TT), concentration of fibrin degradation products (FDP), and antithrombin (AT) activities are scarce or nonexistent.Objective:The aim of this study was to determine values for blood coagulation times (PT, aPTT, and TT), FDP concentrations, and AT activities in healthy adult alpacas.Methods:Of blood samples collected from 35 clinically healthy adult alpacas via jugular venipuncture and placed into sodium citrate and FDP tubes, 29 samples were assayable for coagulation testing. PT, aPTT, and TT were determined by physical (mechanical) clot detection; AT activity was determined using a thrombin‐specific chromogenic substrate end‐point assay; and FDP concentrations were determined by the slide agglutination method.Results:Median values and ranges (minimum–maximum) were determined for PT (8.7 seconds, 6.6–11.2 seconds), aPTT (17.3 seconds, 11.9–22.5 seconds), TT (10.2 seconds, 5.4–16.0 seconds), and AT activity (123.3%, 104.8–144.2%). The mean concentration of FDP was <8 μg/mL.Conclusion:These values for coagulation times, FDP concentration, and AT activity will provide a useful starting point in the diagnostic evaluation of ill adult alpacas.