bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying operons and untranslated regions of transcripts
using Escherichia coli RNA expression analysis
Authors: Tjaden Brian , Haynor David R. , Stolyar Sergey , Rosenow Carsten , Kolker Eugene
Published: May 2011

Microarrays traditionally have been used to assay the transcript expression of coding regions of genes. Here, we use Escherichia coli oligonucleotide microarrays to assay transcript expression of both open reading frames (ORFs) and intergenic regions. We then use hidden Markov models to analyse this expression data and estimate transcription boundaries of genes. This approach allows us to identify 5′ untranslated regions (5′ UTRs) of transcripts as well as genes that are likely to be operon members. The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5′ UTR results accurately coincide with experimentally verified promoter regions for most genes.

Contact: tjaden@cs.washington.edu

Keywords: untranslated regions; operons; intergenic; microarrays; Escherichia coli.

*To whom correspondence should be addressed.
Detecting recombination with MCMC
Authors: Husmeier Dirk , McGuire Gráinne
Published: May 2011

Motivation: We present a statistical method for detecting recombination, whose objective is to accurately locate the recombinant breakpoints in DNA sequence alignments of small numbers of taxa (4 or 5). Our approach explicitly models the sequence of phylogenetic tree topologies along a multiple sequence alignment. Inference under this model is done in a Bayesian way, using Markov chain Monte Carlo (MCMC). The algorithm returns the site-dependent posterior probability of each tree topology, which is used for detecting recombinant regions and locating their breakpoints.

Results: The method was tested on a synthetic and three real DNA sequence alignments, where it was found to outperform the established detection methods PLATO, RECPARS, and TOPAL.

Availability: The algorithm has been implemented in the C++ program package BARCE, which is freely available from http://www.bioss.sari.ac.uk/~dirk/my_software

Contact: dirk@bioss.ac.uk

Keywords: phylogenetic trees; DNA sequence alignments; recombination; hidden Markov models; Gibbs sampling; Markov chain Monte Carlo.
Finding composite regulatory patterns in DNA sequences
Authors: Eskin Eleazar , Pevzner Pavel A.
Published: May 2011

Pattern discovery in unaligned DNA sequences is a fundamental problem in computational biology with important applications in finding regulatory signals. Current approaches to pattern discovery focus on monad patterns that correspond to relatively short contiguous strings. However, many of the actual regulatory signals are composite patterns that are groups of monad patterns that occur near each other. A difficulty in discovering composite patterns is that one or both of the component monad patterns in the group may be ‘too weak’. Since the traditional monad-based motif finding algorithms usually output one (or a few) high scoring patterns, they often fail to find composite regulatory signals consisting of weak monad parts. In this paper, we present a MITRA (MIsmatch TRee Algorithm) approach for discovering composite signals. We demonstrate that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data.

Availability: MITRA is available at http://www.cs.columbia.edu/compbio/mitra/

Contact: eeskin@cs.columbia.edu

Keywords: regulatory motif finding; pattern finding; dyad motifs.
The POPPs: clustering and searching using peptide probability
profiles
Authors: Wise Michael J.
Published: May 2011

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically ‘unusual’ in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins.

Availability: Contact the author.

Contact: mw263@cam.ac.uk

Keywords: protein clustering; clustering algorithms; protein search; peptide composition; Pfam; late embryogenesis abundant proteins.
A sequence-profile-based HMM for predicting and
discriminating β barrel membrane proteins
Authors: Martelli Pier Luigi , Fariselli Piero , Krogh Anders , Casadio Rita
Published: May 2011

Motivation: Membrane proteins are an abundant and functionally relevant subset of proteins that putatively include from about 15 up to 30% of the proteome of organisms fully sequenced. These estimates are mainly computed on the basis of sequence comparison and membrane protein prediction. It is therefore urgent to develop methods capable of selecting membrane proteins especially in the case of outer membrane proteins, barely taken into consideration when proteome wide analysis is performed. This will also help protein annotation when no homologous sequence is found in the database. Outer membrane proteins solved so far at atomic resolution interact with the external membrane of bacteria with a characteristic β barrel structure comprising different even numbers of β strands (β barrel membrane proteins). In this they differ from the membrane proteins of the cytoplasmic membrane endowed with alpha helix bundles (all alpha membrane proteins) and need specialised predictors.

Results: We develop a HMM model, which can predict the topology of β barrel membrane proteins using, as input, evolutionary information. The model is cyclic with 6 types of states: two for the β strand transmembrane core, one for the β strand cap on either side of the membrane, one for the inner loop, one for the outer loop and one for the globular domain state in the middle of each loop. The development of a specific input for HMM based on multiple sequence alignment is novel. The accuracy per residue of the model is 83% when a jack knife procedure is adopted. With a model optimisation method using a dynamic programming algorithm seven topological models out of the twelve proteins included in the testing set are also correctly predicted. When used as a discriminator, the model is rather selective. At a fixed probability value, it retains 84% of a non-redundant set comprising 145 sequences of well-annotated outer membrane proteins. Concomitantly, it correctly rejects 90% of a set of globular proteins including about 1200 chains with low sequence identity (<30%) and 90% of a set of all alpha membrane proteins, including 188 chains.

Availability:The program will be available on request from the authors.

Contact: gigi@lipid.biocomp.unibo.ithttp://www.biocomp.unibo.it

Keywords: β barrel membrane proteins; HMM; genome analysis; protein structure prediction; outer membrane protein topology.

3Present address: Bioinformatics Centre, University of Copenhagen, DK-2100 Copenhagen, Denmark

*To whom correspondence should be addressed.
Variance stabilization applied to microarray data calibration
and to the quantification of differential expression
Authors: Huber Wolfgang , von Heydebreck Anja , Sültmann Holger , Poustka Annemarie , Vingron Martin
Published: May 2011

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In particular, we derive a transformation h for intensity measurements, and a difference statistic Δh whose variance is approximately constant along the whole intensity range. This forms a basis for statistical inference from microarray data, and provides a rational data pre-processing strategy for multivariate analyses. For the transformation h, the parametric form h(x)=arsinh(a+bx) is derived from a model of the variance-versus-mean dependence for microarray intensity data, using the method of variance stabilizing transformations. For large intensities, h coincides with the logarithmic transformation, and Δh with the log-ratio. The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation. We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays.

Availability: Software is freely available for academic use as an R package at http://www.dkfz.de/abt0840/whuber

Contact: w.huber@dkfz.de
Contextual alignment of biological sequences (Extended abstract)
Authors: Gambin Anna , Lasota Sławomir , Szklarczyk Radosław , Tiuryn Jerzy , Tyszkiewicz Jerzy
Published: May 2011

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

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

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

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

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

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

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

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

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

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
Special situations
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter explores special situations in dialysis, including dialysis in the elderly, assisted PD, managing diabetic patients on dialysis, surgery in dialysis patients, myeloma and renal failure, pain management in end-stage kidney disease (ESKD), difficulty of pain management in renal patients, managing pain, analgesic drugs, pain at the end of life, pregnancy in dialysis patients, travelling and holidays, plasmapheresis, immunoadsorption techniques, and indications for immunoadsorption.
Complications of ESKD: infection
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses infection as a complication of end-stage kidney disease (ESKD), including infection risk in dialysis patients, non-access-related infections in dialysis patients, tuberculosis, resistant organisms (MRSA, VISA, VRSA, VRE, and others), and viral infections(HBV, HCV viral infections, and HIV).
Symptoms related to ESKD
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses symptoms related to end-stage kidney disease (ESKD), including fatigue/lack of energy, pruritus/dry skin, pain, sleep disorders, restless leg syndrome (RLS), anorexia, constipation, nausea and vomiting, cramps, and fluid overload and oedema.
Death in dialysis patients
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses survival rates in dialysis patients, as well as causes of death, cardiac arrest during dialysis, end of life issues, palliative care and management of symptoms, withdrawal of dialysis, and quality of death.
Thinking about psychiatry
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Symptoms of psychiatric illness
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Bipolar illness
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Eating and impulse-control disorders
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Sleep disorders
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Personality disorders
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Old age psychiatry
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Therapeutic issues
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Useful resources
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Orange Rust Effects on Leaf Photosynthesis and Related Characters of Sugarcane
Authors: Zhao Duli , Glynn Neil C. , Glaz Barry , Comstock Jack C. , Sood Sushma
Published: May 2011

Orange rust of sugarcane (Saccharum spp. hybrids), caused by Puccinia kuehnii, is a relatively new disease in the Western Hemisphere that substantially reduces yields in susceptible sugarcane genotypes. The objective of this study was to determine the physiological mechanisms of orange rust–induced reductions in sugarcane growth and yield by quantifying effects of the disease on leaf SPAD index (an indication of leaf chlorophyll content), net photosynthetic rate, dark respiration, maximum quantum yield of CO2 assimilation, carbon fixation efficiency, and the relationships between these leaf photosynthetic components and rust disease ratings. Plants growing in pots were inoculated with the orange rust pathogen using a leaf whorl inoculation method. A disease rating was assigned using a scale from 0 to 4 with intervals of 0.5. At disease ratings ≥2, the rust-infected leaf portion of inoculated plants showed significant reductions in SPAD index, maximum quantum yield, carbon fixation efficiency, stomatal conductance, leaf transpiration rate, and net photosynthetic rate; but the rusted portion of the infected leaves had increased intercellular CO2 concentration and leaf dark respiration rate. Although leaf SPAD index, photosynthetic rate, stomatal conductance, and transpiration rate at the rust-infected portion decreased linearly with increased rust rating, the effect of orange rust on photosynthetic rate was much greater than that on stomatal conductance and transpiration. Unlike earlier reports on other crops, reduction in leaf photosynthesis by orange rust under low light was greater than that under high light conditions. These results help improve the understanding of orange rust etiology and physiological bases of sugarcane yield loss caused by orange rust.
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

Insect 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.
The role of information sharing in trade credit distribution: evidence from Thailand
Authors: Zhang Rongrong
Published: May 2011

Prior research has shown that information sharing among lenders facilitates bank credit allocation and reduces default rates. We examine the role of information sharing in trade credit allocation using a sample of publicly traded firms in Thailand over the 1994–2005 period. Taking the establishment of a private credit bureau in 1999 as signalling improvement in information sharing among lenders, we obtain three main results in the improved information sharing period: (1) Thai firms have become less dependent on supplier credit; (2) financially constrained firms redistribute more funds via trade credit; and (3) the relationships between the use of trade credit and firm‐specific factors such as liquidity, free cash flow, tangible assets, interest cost ratio, and firm size weaken as information sharing improves. Our results are consistent with the view that better information sharing facilitates credit allocation. Hence, policies aiming at facilitating information exchange among financial intermediaries should be supported. We also find support for the view that bank credit substitutes for trade credit. This substitution lowers firms' cost of capital, given that trade credit is assumed to be more costly than bank loans.
HOW THE PAST DEPENDS ON THE FUTURE
Authors: Hazlett Allan
Published: May 2011

It 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

In 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
CO‐EVOLVING: JUDAISM AND BIOLOGY
Authors: Artson Bradley Shavit
Published: May 2011

Abstract. Biology has been able to systematize and order its vast information through the theory of evolution, offering the possibility of a more engaged dialogue and possible integration with religious insights and emotions. Using Judaism as a focus, this essay examines ways that contemporary evolutionary theory offers room for balancing freedom and constraint, serendipity and intentionality in ways fruitful to Jewish thought and expression. This essay then looks at a productive integration of Judaism and biology in the examples of co‐evolution, environmental ethics, the place of humans within nature, the relationship of mind and brains, and the ways that individual and group identity blur.
MUSLIM HERMENEUTICS AND ARABIC VIEWS OF EVOLUTION
Authors: Elshakry Marwa
Published: May 2011

Abstract. Over the last century and a half, discussions of Darwin in Arabic have involved a complex intertwining of sources of authority. This paper reads one of the earliest Muslim responses to modern evolution against those in more recent times to show how questions of epistemology and exegesis have been critically revisited. This involved, on the one hand, the resuscitation of long‐standing debates over claims regarding the nature of evidence, certainty, and doubt, and on the other, arguments about the use (and limits) of reason in relation to scripture. Categories of knowledge and belief, alongside methods of scriptural hermeneutics, were repositioned in the process, transforming the meaning and discursive reach of the former as much as the latter. Indeed, this paper argues that the long‐run engagement with Darwin in Arabic led to the mutual transformation of both “science” and “religion,” whether as objects of knowledge (and belief) or as general discursive formations.
EMERGING IN THE IMAGE OF GOD TO KNOW GOOD AND EVIL
Authors: Roberts Jason P.
Published: May 2011

Abstract. Found in the Primeval History in Genesis, the biblical concepts of the “image of God” and the “knowledge of good and evil” remain integral to Christian anthropology, especially with regard to the theologoumena of “fall” and “original sin.” All of these symbols are remained important and appropriate descriptors of the human condition, provided that contemporary academic theological anthropology engages in constructive dialogue with the natural and social sciences. Using Paul Ricoeur's notion of “second naïveté experience,” I illustrate the hermeneutical significance of contemporary bio‐cultural or socio‐biological evolutionary theory for reformulating these concepts of Christian anthropology today.
THE PLACEBO EFFECT: WHAT'S INTERESTING FOR SCHOLARS OF RELIGION?
Authors: Harrington Anne
Published: May 2011

Abstract. The placebo effect these days is no longer merely the insubstantial, subjective response that some patients have to a sham treatment, like a sugar pill. It has been reconceived as a powerful mind‐body phenomenon. Because of this, it has also emerged as a complex reference point in a number of high‐stakes conversations about the metaphysical significance of experiences of religious healing, the possible health benefits of being religious, and the feasibility of using double‐blind placebo‐controlled trials to investigate the efficacy of prayer. In each of these conversations, the placebo effect is always pointing toward some larger issue, serving some larger agenda. The agendas, though, tend to pull in different directions, leading to a situation that feels at once fractured and stalemated. This essay reviews the main areas of interest, and proposes some specific issues where humanistic scholars of religion in particular might be able to introduce constructive and creative new perspectives.
Habitat partitioning among sympatric wintering Common Eiders Somateria mollissima and King Eiders Somateria spectabilis
Authors: BUSTNES JAN OVE , LØNNE OLE JØRGEN
Published: May 2011

We studied the distribution of sympatric wintering Common Elders Somateria mollissima and King Eiders Somateria spectabilis in northern Norway in relation to the water depth and substrate type. The Common Eider selected water shallower than 10 m, mainly over kelp beds and sand/rock habitats. At the darkest time of the year, Common Elders also fed much more than expected over urchin barrens. In contrast, the King Eider usually dived deeper than 20 m, and when they arrived in December, King Eiders fed especially in areas which were dominated by cobbles. Later in the season, they dispersed into areas with other substrates but still preferred deep water. The segregation between the two species was significant both for depth and substrate type, but depth was the most important factor. The change in the use of various substrate types throughout the winter was also significantly different between the two species, thus very little interspecific competition seemed to occur.
INFORMAL SECTOR ENTERPRISES: SOME MEASUREMENT ISSUES
Authors: JOSHI KAUSHAL , AMORANTO GLENITA , HASAN RANA
Published: May 2011

In this paper, we examine the differences in the measures of: (i) profits of an enterprise obtained from a detailed set of questions on incomes and expenses of the enterprise, versus profits obtained through a single direct question; and (ii) gross value added (GVA) obtained using the production approach as the difference between output and intermediate consumption from a detailed set of questions on incomes and expenses, versus GVA using the income approach by asking a few questions on factor incomes, and a single direct question on profits. We use data from the 56th round survey of unorganized manufacturing conducted by the National Sample Survey Organization of India during the period July 2000–June 2001. We also examine if the differences vary with the characteristics of the enterprises, and suggest further empirical research to develop suitable tools for providing accurate measurements of informal sector enterprises.
THE INFORMAL SECTOR: AN EQUILIBRIUM MODEL AND SOME EMPIRICAL EVIDENCE FROM BRAZIL
Authors: DE PAULA ÁUREO , SCHEINKMAN JOSÉ A.
Published: May 2011

We test implications of a simple equilibrium model of informality using a survey of 48,000+ small firms in Brazil. In the model, agents' ability to manage production differs and informal firms face a higher cost of capital and limitation on size, although these informal firms avoid tax payments. As a result, informal firms are managed by less able entrepreneurs, are smaller, and employ a lower capital–labor ratio. The model predicts that the interaction of an index of observable inputs to entrepreneurial ability and formality is positively correlated with firm size, which we verify in the data. Using the model, we estimate that informal firms in our dataset faced at least 1.3 times the cost of capital of formal firms.
HOW DOES DECENTRALIZED MINIMUM WAGE SETTING AFFECT EMPLOYMENT AND INFORMALITY? THE CASE OF INDONESIA
Authors: COMOLA MARGHERITA , DE MELLO LUIZ
Published: May 2011

The Indonesian labor market is characterized by widespread and growing informality (defined as non‐salaried work). To what extent can the growth in informality be attributed to a sharp increase in the real value of the minimum wage since 2001, when minimum‐wage setting was decentralized to the provincial governments? To answer this and related questions we use survey data on the labor market, on household income and expenditure, and on the industrial sector to construct a district‐level dataset spanning the period 1996 to 2004. The effects of changes in the minimum wage on unemployment, formal‐sector employment, and the incidence of informality in urban areas are estimated by fixed effects with a seemingly unrelated regression estimator. We find that an increase in the ratio of the minimum to the mean wage is associated with a net increase in employment: a rise in informal‐sector employment more than compensates for job losses in the formal sector.
EARNINGS STRUCTURES, INFORMAL EMPLOYMENT, AND SELF‐EMPLOYMENT: NEW EVIDENCE FROM BRAZIL, MEXICO, AND SOUTH AFRICA
Authors: BARGAIN OLIVIER , KWENDA PRUDENCE
Published: May 2011

We estimate the conditional earnings gap between formal and informal sectors, distinguishing between salary and self‐employed workers. Rich panel datasets for Brazil, Mexico, and South Africa are assembled to define informality in a comparable way and to control for (time‐invariant) unobserved heterogeneity. Estimations are conducted at different points of the conditional earnings distributions. Interesting results emerge. First, informal salary workers are systematically underpaid compared to their formal sector counterparts, in all countries and at almost all conditional quantiles. Yet penalties are very moderate in Brazil and Mexico while more substantial in South Africa, a country where legal advantages in formal employment are effective. Second, informal self‐employment contributes to a more dispersed earnings distribution in all three countries. International comparisons reveal a continuum of situations reflecting historical and legal differences across countries, from very large self‐employment penalties in South Africa to significant conditional earnings premia in Mexico.
THE LIGHTHOUSE EFFECT AND BEYOND
Authors: BOERI TITO , GARIBALDI PIETRO , RIBEIRO MARTA
Published: May 2011

A large body of empirical literature indicates that, contrary to predictions from economic theory, wages in the informal sector increase after a minimum wage hike. This phenomenon was so far explained as a byproduct of a signal (a lighthouse) conveyed by statutory minima to wage setting in the informal sector. A simple matching model shows that an increase in wages in the informal sector may also be induced by significant sorting and composition effects between the formal and the shadow sectors in the aftermath of the increase in the minimum wage. Using data on Brazil, we find that sorting accounts for at least one third of the increase in average wages in the informal sector after a minimum wage hike. This contribution of endogenous sorting to wage dynamics in the informal sector is also increasing over time.
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.
Secondary renal tubular acidosis in a Hereford calf
Authors: Hardefeldt Laura Y. , Poulsen Keith P. , Darien Benjamin J.
Published: May 2011

Abstract:A 3‐month‐old Hereford heifer calf was presented for lethargy. Blood gas analysis and plasma biochemical testing revealed severe metabolic acidosis, azotemia, hyponatremia, hyperchloremia, and normal anion gap. Results of a urinalysis were consistent with acute tubular necrosis with inadequate acidification of urine based on the degree of acidemia.Salmonella entericaserovaragonawas cultured from both urine and feces. The calf was treated with intravenous polyionic fluids, bicarbonate, and antimicrobials. Acidosis and azotemia resolved, and 4 months following initial presentation the heifer was clinically normal.