bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating functional network inference using simulations of complex
biological systems
Authors: Smith V. Anne , Jarvis Erich D. , Hartemink Alexander J.
Published: May 2011

Motivation: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. To overcome this limitation, we propose an approach to evaluate network inference algorithms according to their ability to recover a complex functional network from biologically reasonable simulated data.

Results: We designed a simulator to generate data representing a complex biological system at multiple levels of organization: behaviour, neural anatomy, brain electrophysiology, and gene expression of songbirds. About 90% of the simulated variables are unregulated by other variables in the system and are included simply as distracters. We sampled the simulated data at intervals as one would sample from a biological system in practice, and then used the sampled data to evaluate the effectiveness of an algorithm we developed for functional network inference. We found that our algorithm is highly effective at recovering the functional network structure of the simulated system—including the irrelevance of unregulated variables—from sampled data alone. To assess the reproducibility of these results, we tested our inference algorithm on 50 separately simulated sets of data and it consistently recovered almost perfectly the complex functional network structure underlying the simulated data. To our knowledge, this is the first approach for evaluating the effectiveness of functional network inference algorithms at recovering models from limited data. Our simulation approach also enables researchers a priori to design experiments and data-collection protocols that are amenable to functional network inference.

Availability: Source code and simulated data are available upon request.

Contact: amink@cs.duke.eduasmith@neuro.duke.edujarvis@neuro.duke.edu
DNA sequence and structure: direct and indirect recognition in
protein-DNA binding
Authors: Steffen N.R. , Murphy S.D. , Tolleri L. , Hatfield G.W. , Lathrop R.H.
Published: May 2011

Motivation: Direct recognition, or direct readout, of DNA bases by a DNA-binding protein involves amino acids that interact directly with features specific to each base. Experimental evidence also shows that in many cases the protein achieves partial sequence specificity by indirect recognition, i.e., by recognizing structural properties of the DNA. (1) Could threading a DNA sequence onto a crystal structure of bound DNA help explain the indirect recognition component of sequence specificity? (2) Might the resulting pure-structure computational motif manifest itself in familiar sequence-based computational motifs?

Results: The starting structure motif was a crystal structure of DNA bound to the integration host factor protein (IHF) of E. coli. IHF is known to exhibit both direct and indirect recognition of its binding sites. (1) Threading DNA sequences onto the crystal structure showed statistically significant partial separation of 60 IHF binding sites from random and intragenic sequences and was positively correlated with binding affinity. (2) The crystal structure was shown to be equivalent to a linear Markov network, and so, to a joint probability distribution over sequences, computable in linear time. It was transformed algorithmically into several common pure-sequence representations, including (a) small sets of short exact strings, (b) weight matrices, (c) consensus regular patterns, (d) multiple sequence alignments, and (e) phylogenetic trees. In all cases the pure-sequence motifs retained statistically significant partial separation of the IHF binding sites from random and intragenic sequences. Most exhibited positive correlation with binding affinity. The multiple alignment showed some conserved columns, and the phylogenetic tree partially mixed low-energy sequences with IHF binding sites but separated high-energy sequences. The conclusion is that deformation energy explains part of indirect recognition, which explains part of IHF sequence-specific binding.

Availability: Code and data on request.

Contact:Nick Steffen for code and Lorenzo Tolleri for data. nsteffen@uci.eduLorenzo_Tolleri@chiron.it

Keywords: protein-DNA binding sites; sequence motifs or patterns; indirect recognition or readout; integration host factor; IHF.
The Pathway Tools software
Authors: Karp Peter D. , Paley Suzanne , Romero Pedro
Published: May 2011

Motivation: Bioinformatics requires reusable software tools for creating model-organism databases (MODs).

Results: The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

Availability: The software is freely available to academics and is available for a fee to commercial institutions. Contact ptools-support@ai.sri.com for information on obtaining the software.

Contact: pkarp@ai.sri.com

Keywords: Bioinformatics; model organism database; genome analyses; metabolic pathways.

*To whom correspondence should be addressed.
Modelling regulatory pathways in E. coli from time
series expression profiles
Authors: Ong Irene M. , Glasner Jeremy D. , Page David
Published: May 2011

Motivation: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression profiles. Few analysis techniques, however, are well suited to modelling such time series data.

Results: We describe an approach that naturally handles time series data with the capabilities of modelling causality, feedback loops, and environmental or hidden variables using a Dynamic Bayesian network. We also present a novel way of combining prior biological knowledge and current observations to improve the quality of analysis and to model interactions between sets of genes rather than individual genes. Our approach is evaluated on time series expression data measured in response to physiological changes that affect tryptophan metabolism in E. coli. Results indicate that this approach is capable of finding correlations between sets of related genes.

Contact: ong@cs.wisc.edu

Keywords: Dynamic Bayesian networks; regulatory pathways; time series gene expression; operon model.
A tree kernel to analyse phylogenetic profiles
Authors: Vert Jean-Philippe
Published: May 2011

Motivation: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often ‘similar’ or at least ‘related’ to each other. The question we address in this paper is the following: how to measure the ‘similarity’ between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods?

Results: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles.

As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations.

Availability: All data and software used are freely and publicly available upon request.

Contact: Jean-Philippe.Vert@mines.org

Keywords: phylogenetic profile; tree; kernel; support vector machine; gene function prediction.
Beyond tandem repeats: complex pattern structures and
distant regions of similarity
Authors: Hauth Amy M. , Joseph Deborah A.
Published: May 2011

Motivation: Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of patterns and complex pattern structures. We study recognition algorithms for two complex pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs).

Results: We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data.

In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.

Availability: Algorithms can be accessed at http://www.cs.wisc.edu/areas/theory

Contact: kryder@cs.wisc.edujoseph@cs.wisc.edu

*To whom correspondence should be addressed.
Fully automated ab initio protein
structure prediction using I-SITES, HMMSTR and ROSETTA
Authors: Bystroff Christopher , Shao Yu
Published: May 2011

Motivation: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and the HMMSTR model for local structure in proteins, to form a new public server for the ab initio prediction of protein structure. The server performs several tasks in addition to tertiary structure prediction, including a database search, amino acid profile generation, fragment structure prediction, and backbone angle and secondary structure prediction. Meeting reasonable service goals required improvements in the efficiency, in particular for the ROSETTA algorithm.

Results: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment. The results for 31 of those predictions are presented here. 61% of the residues overall were found in topologically correct predictions, which are defined as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons of less than 6Å. HMMSTR 3-state secondary structure predictions were 73% correct overall. Tertiary structure predictions did not improve the accuracy of secondary structure prediction.

Availability:The server is accessible through the web at http://isites.bio.rpi.edu/hmmstr/index.html Programs are available upon requests for academics. Licensing agreements are available for commercial interests.

Supplementary information: http://isites.bio.rpi.eduhttp://predictioncenter.llnl.gov/casp4/

Contact: bystrc@rpi.edushaoy@rpi.edu

Keywords: CASP; CAFASP; protein folding; motifs; hidden Markov model; knowledge-based.

*To whom correspondence should be addressed.
Inferring sub-cellular localization through
automated lexical analysis
Authors: Nair Rajesh , Rost Burkhard
Published: May 2011

Motivation: The SWISS-PROT sequence database contains keywords of functional annotations for many proteins. In contrast, information about the sub-cellular localization is available for only a few proteins. Experts can often infer localization from keywords describing protein function. We developed LOCkey, a fully automated method for lexical analysis of SWISS-PROT keywords that assigns sub-cellular localization. With the rapid growth in sequence data, the biochemical characterisation of sequences has been falling behind. Our method may be a useful tool for supplementing functional information already automatically available.

Results: The method reached a level of more than 82% accuracy in a full cross-validation test. Due to a lack of functional annotations, we could infer localization for fewer than half of all proteins in SWISS-PROT. We applied LOCkey to annotate five entirely sequenced proteomes, namely Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Arabidopsis thaliana (plant) and a subset of all human proteins. LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes.

Availability: Annotations of localization for eukaryotes at: http://cubic.bioc.columbia.edu/services/LOCkey

Contact: nair@cubic.bioc.coplumbia.edurost@columbia.edu

Keywords: genome sequence analysis; predicting sub-cellular localization; protein function; lexical analysis.

*To whom correspondence should be addressed.
Identifying transcription factor binding sites through
Markov chain optimization
Authors: Ellrott Kyle , Yang Chuhu , Sladek Frances M. , Jiang Tao
Published: May 2011

Even though every cell in an organism contains the same genetic material, each cell does not express the same cohort of genes. Therefore, one of the major problems facing genomic research today is to determine not only which genes are differentially expressed and under what conditions, but also how the expression of those genes is regulated. The first step in determining differential gene expression is the binding of sequence-specific DNA binding proteins (i.e. transcription factors) to regulatory regions of the genes (i.e. promoters and enhancers). An important aspect to understanding how a given transcription factor functions is to know the entire gamut of binding sites and subsequently potential target genes that the factor may bind/regulate. In this study, we have developed a computer algorithm to scan genomic databases for transcription factor binding sites, based on a novel Markov chain optimization method, and used it to scan the human genome for sites that bind to hepatocyte nuclear factor 4 α (HNF4α). A list of 71 known HNF4α binding sites from the literature were used to train our Markov chain model. By looking at the window of 600 nucleotides around the transcription start site of each confirmed gene on the human genome, we identified 849 sites with varying binding potential and experimentally tested 109 of those sites for binding to HNF4α. Our results show that the program was very successful in identifying 77 new HNF4α binding sites with varying binding affinities (i.e. a 71% success rate). Therefore, this computational method for searching genomic databases for potential transcription factor binding sites is a powerful tool for investigating mechanisms of differential gene regulation.

Contact: jiang@cs.ucr.edu
Genome segmentation using piecewise constant intensity models and
reversible jump MCMC
Authors: Salmenkivi Marko , Kere Juha , Mannila Heikki
Published: May 2011

The existence of whole genome sequences makes it possible to search for global structure in the genome. We consider modeling the occurrence frequencies of discrete patterns (such as starting points of ORFs or other interesting phenomena) along the genome. We use piecewise constant intensity models with varying number of pieces, and show how a reversible jump Markov Chain Monte Carlo (RJMCMC) method can be used to obtain a posteriori distribution on the intensity of the patterns along the genome. We apply the method to modeling the occurrence of ORFs in the human genome. The results show that the chromosomes consist of 5–35 clearly distinct segments, and that the posteriori number and length of the segments shows significant variation. On the other hand, for the yeast genome the intensity of ORFs is nearly constant.

Contact: Marko.Salmenkivi@cs.helsinki.fiJuha.Kere@biosci.ki.seHeikki.Mannila@cs.helsinki.fi
The mutual information: Detecting and evaluating dependencies between
variables
Authors: Steuer R. , Kurths J. , Daub C. O. , Weise J. , Selbig J.
Published: May 2011

Motivation: Clustering co-expressed genes usually requires the definition of `distance' or `similarity' between measured datasets, the most common choices being Pearson correlation or Euclidean distance. With the size of available datasets steadily increasing, it has become feasible to consider other, more general, definitions as well. One alternative, based on information theory, is the mutual information, providing a general measure of dependencies between variables. While the use of mutual information in cluster analysis and visualization of large-scale gene expression data has been suggested previously, the earlier studies did not focus on comparing different algorithms to estimate the mutual information from finite data.

Results: Here we describe and review several approaches to estimate the mutual information from finite datasets. Our findings show that the algorithms used so far may be quite substantially improved upon. In particular when dealing with small datasets, finite sample effects and other sources of potentially misleading results have to be taken into account.

Contact: steuer@agnld.uni-potsdam.de
A new distance measure for comparing sequence profiles
based on path lengths along an entropy surface
Authors: Benson Gary
Published: May 2011

We describe a new distance measure for comparing DNA sequence profiles. For this measure, columns in a multiple alignment are treated as character frequency vectors (sum of the frequencies equal to one). The distance between two vectors is based on minimum path length along an entropy surface. Path length is estimated using a random graph generated on the entropy surface and Dijkstra's algorithm for all shortest paths to a source. We use the new distance measure to analyze similarities within familes of tandem repeats in the C. elegans genome and show that this new measure gives more accurate refinement of family relationships than a method based on comparing consensus sequences.
Comparative analysis of protein interaction networks
Authors: Bork Peer
Published: May 2011

Recent advances in proteomics and computational biology have lead to a flood of protein interaction data and resulting interaction networks (e.g. (Gavin et al., 2002)). Here I first analyse the status and quality of parts lists (genes and proteins), then comparatively assess large-scale protein interaction data (von Mering et al., 2002) and finally try to identify biological meaningful units (e.g. pathways, cellular processes) within interaction networks that are derived from the conservation of gene neighborhood (Snel et al., 2002). Possible extensions of gene neighborhood analysis to eukaryotes (von Mering and Bork, 2002) will be discussed.
Theoretical analysis of alternative splice forms using computational
methods
Authors: Boué Stéphanie , Vingron Martin , Kriventseva Evgenia , Koch Ina
Published: May 2011

Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper, we explain the approach of using the different available databases and software tools to start a large scale investigation of alternative splice forms. To collect information about alternative splicing we investigated known data in the databases using different computational methods. The investigations proceeded from the genomic sequence data to structural protein data. Then, we interpreted those data to find the relationship between alternative splice forms and protein function and structure. We found some interesting features of alternative splicing which are presented here. We discuss the results of one chosen example. They concern the coverage quality of the protein sequence of a known structure, an EST analysis, the validation of splice variants, the determination of the alternative splice type, and finally the link between alternative splicing and disease.

Contact: ina.koch@molgen.mpg.de
Feature subset selection for splice site prediction
Authors: Degroeve Sven , De Baets Bernard , Van de Peer Yves , Rouzé Pierre
Published: May 2011

Motivation: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a review and references). These algorithms need information sources or features from which the models can be computed. For splice site prediction, the features we consider in this study are the presence or absence of certain nucleotides in close proximity to the splice site. Since it is not known how many and which nucleotides are relevant for splice site prediction, the set of features is chosen large enough such that the probability that all relevant information sources are in the set is very high. Using only those features that are relevant for constructing a splice site prediction system might improve the system and might also provide us with useful biological knowledge. Using fewer features will of course also improve the prediction speed of the system.

Results: A wrapper-based feature subset selection algorithm using a support vector machine or a naive Bayes prediction method was evaluated against the traditional method for selecting features relevant for splice site prediction. Our results show that this wrapper approach selects features that improve the performance against the use of all features and against the use of the features selected by the traditional method.

Availability: The data and additional interactive graphs on the selected feature subsets are available at http://www.psb.rug.ac.be/gps

Contact: svgro@gengenp.rug.ac.beyvdp@gengenp.rug.ac.be
Haemodialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses principles of haemodialysis, factors affecting solute clearance on haemodialysis, ultrafiltration during haemodialysis, high efficiency and high flux haemodialysis, haemofiltration and haemodiafiltration, dialysers, technical specifications, dialysis membranes, biocompatibility, dialysis machines, dialysate, water purification, vascular access, evaluation prior to access surgery, formation of permanent access, stenosis and thrombosis of fistulae and grafts, screening for arteriovenous fistula/graft stenosis and thrombosis, tunnelled cuffed catheters, temporary vascular access, insertion of vascular access catheters, management of access (catheter) infections, prevention of infection of dialysis access, arteriovenous shunt (Scribner shunt), cardiopulmonary recirculation, access recirculation, complications during dialysis, hypotension from excessive ultrafiltration and other complications during dialysis, blood clotting, anticoagulation, regional anticoagulation, dialysis adequacy, residual renal function, targets for adequate dialysis, the HEMO study, increasing dialysis dose delivered, prescribing chronic haemodialysis, laboratory tests for patients on regular haemodialysis, dry weight, novel measures of dry weight, re-use of dialysers, home haemodialysis, daily haemodialysis, haemodialysis and surgery, haemodialysis in transplant recipients, haemodialysis in terminal care, and haemodialysis for non-renal disease.
Peritoneal dialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses peritoneal dialysis, including factors affecting efficiency of peritoneal dialysis, effect of dwell time on solute and fluid transfer, modes of peritoneal dialysis, continuous ambulatory peritoneal dialysis (CAPD) technique and systems, peritoneal dialysis catheters, insertion of peritoneal dialysis catheters, pre-operative preparation for peritoneal catheter insertion, peritoneal dialysis catheter insertion technique, laparoscopic peritoneal dialysis catheters, investigation and management of malfunctioning catheters, peritoneal dialysate, advantages and disadvantages of different dialysates, prescribing CAPD, adequacy of peritoneal dialysis, peritoneal equilibration tests and modelling, increasing dialysis delivered by CAPD, examples of alterations in CAPD prescription, automated peritoneal dialysis, peritoneal dialysis in anuric patients, residual renal function, causes of underdialysis, exit site infections, peritonitis, TB peritonitis, treatment of automated peritoneal dialysis peritonitis and resistant peritonitis, complications of peritonitis (encapsulating peritoneal sclerosis, hernias, fluid leaks, prolapses, and pain), pre- and post-operative assessment for peritoneal dialysis patients, peritoneal dialysis and transplantation, and transfer of PD patient to HD.
Nursing issues in peritoneal dialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses nursing issues in peritoneal dialysis, including the role of the nurse in peritoneal dialysis, nursing care of peritoneal catheters, line changes, training patients for CAPD and APD, and organizing outpatient care of peritoneal dialysis patients.
Nutrition on dialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses nutrition on dialysis, including malnutrition in end-stage kidney disease (ESKD), nutritional requirements in chronic kidney disease (pre-dialysis), dietetic treatment plan for pre-dialysis patients, assessment of nutritional status, nutritional requirements in haemodialysis and peritoneal dialysis, strategies for achieving nutritional aims, dietary problems specific to ethnic minority patients, supplemental vitamins and trace elements, use of nutritional supplements, intradialytic nutrition, carnitine and ESKD, fluid requirements in renal failure, nutrition in acute kidney injury, and routes for nutritional support in acute kidney injury.
Complications of ESKD: bone mineral disorders
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses bone mineral disordersas a complication of end-stage kidney disease (ESKD), including renal bone disease, hyperparathyroidism and hyperphosphataemia, hyperparathyroid bone disease, parathyroid hormone assays, low turnover bone disease, medical management of hyperparathyroid bone disease, maintenance of normal phosphate levels, vitamin D, paricalcitol, systemic effects of vitamin D, calcimimetics, examples of treatment plans for renal bone disease, parathyroidectomy, and calciphylaxis.
Transplantation for dialysis patients
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter explores assessment for transplant suitability, living donor transplantation, assessment of patients prior to transplantation, pre-transplant management, the transplant operation, post-transplant management, and delayed graft function.
Drug prescribing in patients on dialysis
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses drug handling in renal failure, as well as dosing of commonly used drugs (including antimicrobial drugs, antifungal drugs, antiretroviral drugs, antiviral drugs,antituberculous drugs, cardiovascular drugs, analgesics, CNS drugs, gastrointestinal drugs, and immunosuppressants). It also outlines drugs that do not require dosage alteration in CKDstage 5, haemodialysis, and continuous ambulatory peritoneal dialysis; drugs to be avoided in CKD stage 5, haemodialysis, and PD; factors affecting drug removal by continuous renalreplacement therapy; and dosing of drugs commonly used during continuousrenal replacement therapy.
Schizophrenia and related psychoses
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Anxiety and stress-related disorders
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Reproductive psychiatry, sexual dysfunction and sexuality
Authors: Semple David , Smyth Roger
Published: May 2011

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

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

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

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

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

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

Abstracts and keywords to be supplied.
Difficult and urgent situations
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
First Report of Beet severe curly top virus in Jalapeño Pepper in Chihuahua, Mexico
Authors: Robles-Hernandez L. , Gonzalez-Franco A. C. , Gill-Langarica E. M. , Sago C. , Nikolaeva O. V. , Karasev A. V.
Published: May 2011

Curly top is a serious problem in many irrigated crops in the semiarid areas in the western United States. The disease is caused by a complex of leafhopper-transmitted curtoviruses, one of which, Beet mild curly top virus (BMCTV), was previously found in chili pepper in Zacatecas and Aguascalientes, Mexico (3). During the past few years, sporadic symptoms similar to curly top disease were observed in jalapeño pepper in the south-central area of Chihuahua State. Symptomatic plants were scattered in otherwise healthy looking pepper stands and displayed stunting and yellowing. Affected leaves were brittle, showed upward curling, and a distinct green vein pattern with interveinal yellowing. In June and August of 2010, field surveys were conducted in Cordillera-Escuadra, Meoqui-Estacion Consuelo, Meoqui-Lomas del Consuelo, and Delicias-Presa Francisco I Madero. Ninety-four leaf samples were collected from symptomatic jalapeño pepper plants and subjected to ELISA and PCR testing for curly top. Of the 94 samples, 11 were found to be positive by triple-antibody sandwich-ELISA with polyclonal antibodies against curly top (2). To confirm the identification of curly top and type the specific curtovirus identified, four ELISA-positive samples were subjected to a PCR analysis using a virus-specific primer set for curtovirus typing designed by Chen et al. (1). All four samples tested produced a single 720-bp band with primers BSCTVv2688 and BGc396 (1) characteristic of the Beet severe curly top virus (BSCTV). These curly top-specific PCR amplicons were sequenced and found to be 99% similar to the BSCTV nucleotide sequence in the C1 gene region (GenBank Accession No. X97203); corresponding sequences were deposited in GenBank under Accession Nos. JF437870 to JF437873. To our knowledge, this is the first report of the curly top virus in the State of Chihuahua, demonstrating that curly top is established and common in jalapeño pepper here and will need surveillance in other vegetable crops under irrigation.

References: (1) L. F. Chen et al. Plant Dis. 94:99, 2010. (2) J. Durrin et al. Plant Dis. 94:972, 2010. (3) R. Velásquez-Valle et al. Plant Dis. 92:650, 2008.
Personality influences the neural responses to viewing facial expressions of emotion
Authors: Calder Andrew J. , Ewbank Michael , Passamonti Luca
Published: May 2011

Cognitive research has long been aware of the relationship between individual differences in personality and performance on behavioural tasks. However, within the field of cognitive neuroscience, the way in which such differences manifest at a neural level has received relatively little attention. We review recent research addressing the relationship between personality traits and the neural response to viewing facial signals of emotion. In one section, we discuss work demonstrating the relationship between anxiety and the amygdala response to facial signals of threat. A second section considers research showing that individual differences in reward drive (behavioural activation system), a trait linked to aggression, influence the neural responsivity and connectivity between brain regions implicated in aggression when viewing facial signals of anger. Finally, we address recent criticisms of the correlational approach to fMRI analyses and conclude that when used appropriately, analyses examining the relationship between personality and brain activity provide a useful tool for understanding the neural basis of facial expression processing and emotion processing in general.
High-Resolution Ground-Based GPS Measurements Show Intercampaign Bias in ICESat Elevation Data Near Summit, Greenland
Authors: Siegfried Matthew R. , Hawley Robert L. , Burkhart John F.
Published: May 2011

The Geoscience Laser Altimeter System (GLAS) aboard the National Aeronautics and Space Administration's Ice, Cloud, and land Elevation Satellite (ICESat) collected data from early 2003 to late 2009 with the specific goal of measuring ice-surface elevation changes. While the precision of GLAS instrumentation has been studied over its intended target (ice), its accuracy has only been robustly estimated using independent (terrestrial nonlaser) methods over salt flats. Here, we perform repeat high-precision Global Positioning System (GPS) surveys under four passes of ICESat track 0412 (campaigns L3I, L3J, L2D, and L2E) to compare directly GLAS elevation data footprints to a coincident GPS ground truth near Summit, Greenland. Analysis and comparison of GLAS data with GPS data show a campaign-dependent elevation bias ranging from -0.112 ±0.030 m (L3J) to 0.121 ± 0.071 m (L2E). Although uncorrected reflectance values and field observations both indicate that forward scattering of the laser signal through the atmosphere accounts for the anomalously negative L3J bias, the biases of all campaigns studied are within the instrument's goal accuracy of ±0.15 m. However, our analysis shows a campaign dependence in the bias, which may propagate through estimates of mass balance. The error introduced from intercampaign biases illustrates the importance of long-term independent validation experiments of satellite altimetry data over ice sheets.
Is There Division of Labor in Cooperative Pseudoscorpions? An Analysis of the Behavioral Repertoire of a Tropical Species
Authors: Tizo‐Pedroso Everton , Del‐Claro Kleber
Published: May 2011

Division of labor is a strategy that maximizes the foraging and reproductive success of eusocial insects. Although some arachnids exhibit colony structure and social organization similar to that of hymenopterans, temporal polyethism has only been demonstrated in few species. The social organization of cooperative pseudoscorpions Paratemnoides nidificator is similar to that of social spiders, but it involves a clear division of labor. Work allocation was experimentally investigated in colonies composed of only one developmental stage (young or adults) or by one sex (males or females), through laboratory manipulation. During 44 h of observation, more than 14 000 behavioral repetitions were quantified, distributed in 95 different types of behavioral acts, and grouped in 10 behavioral categories. The results showed that reproductive colonies of P. nidificator are maintained by gender‐ and age‐based activities. Males and non‐reproductive females performed the external cleaning of the colony and prey capture. Reproductive females take care of the juveniles and build reproductive silk chambers. Nymphs build most of the molt chambers and perform internal cleaning. In the absence of nymphs, male colonies survived 1–2 mo, while female colonies survived 3–4 mo. In nymph colonies, work is readjusted so that all maintenance tasks are executed. This is the first study clearly demonstrating division of tasks in arachnids. It suggests that specialization is an adaptative and evolutionarily old trait in this species. Unlike cooperative spiders, P. nidificator possesses physiological (e.g. reproduction, ecdysis, lifespan) and behavioral (e.g. behavioral synchrony or self‐organization) characteristics that allow task specialization.
Lack of Evidence for the Prior Residence Effect in the Allegheny Mountain Dusky Salamander (Desmognathus ochrophaeus)
Authors: Plenderleith T. Lynette , Forester Don C.
Published: May 2011

Territorial disputes are frequently settled by an advantage afforded to one of the contestants by asymmetries such as size difference, strength and motivation. Allegheny Mountain Dusky Salamanders (Desmognathus ochrophaeus) are reported to defend cover objects, a form of territorial behaviour. We conducted an experiment to determine whether or not adult salamanders of this species exhibit prior residence effect during staged encounters involving size‐matched, same sex conspecifics (i.e. does familiarity with a territory predict successful defence?). We tested 154 adult salamanders (72 female, 82 male) in reciprocal trials in which each animal acted as a resident and as an intruder. We recorded multiple agonistic behaviours including: front‐trunk raised, all‐trunk raised, nudge, bite, bite‐and‐hold and jaw‐lock. We assigned these behaviours scaled point values and calculated an index of aggression for each animal as a resident and as an intruder. We found that in same sex trials, males were significantly more aggressive than females. Although D. ochrophaeus exhibited stereotypical, agonistic behaviours similar to those reported for Plethodon, unlike Plethodon the outcomes of symmetrical social encounters were not influenced by residential status. Prior residence is documented to be a major determinant of territorial disputes among diverse animal taxa, including salamanders. However, our research suggests that the phenomenon is not universal and may depend on qualities of the microhabitat in which a species has evolved.
Effects of dietary supplementation of Chinese medicinal herbs on polymorphonuclear neutrophil immune activity and small intestinal morphology in weanling pigs
Authors: Huang C. W. , Lee T. T. , Shih Y. C. , Yu B.
Published: May 2011

The purpose of this study was to evaluate the effects of dietary Chinese medicinal herbs (CMH) supplementation composed of Panax ginseng, Dioscoreaceae opposite, Atractylodes macrocephala, Glycyrrhiza uralensis, Ziziphus jujube and Platycodon grandiflorum, on the performance, intestinal tract morphology and immune activity in weanling pigs. Two hundred and forty weaned pigs were assigned randomly to four dietary groups including the negative control (basal diet), 0.1% CMH, 0.3% CMH and 0.114% antibiotic (Chlortetracycline calcium Complex, Sulfathiazole and Procaine Penicillin G) supplementation groups for a 28‐day feeding trial. Results indicated that both CMH supplementation groups had a better gain and feed/gain than control group (CT) during the first 2 weeks of the experimental period. The 0.3% CMH had a significant decrease in the diarrhoea score in first 10 days of experimental period when compared with other groups. The CMH supplementation groups had a higher villous height, increased lactobacilli counts in digesta of ileum and decreased coliform counts in colon compared with CT. The immune activities of polymorphonuclear leucocytes (PMNs), including the respiratory burst and Salmonella‐killing ability, were significantly enhanced in CMH supplementation groups at day 7 of experiment period. The CMH and antibiotic supplementations increased the nutrient digestibility such as dietary dry matter, crude protein and gross energy in weanling pigs. In conclusion, the dietary CMH supplementation improved intestinal morphology and immune activities of PMNs, thus giving rise to nutrient digestibility and reduce diarrhoea frequency in weanling pigs.
Inflation in developing Asia: pass‐through from global food and oil price shocks
Authors: Jongwanich Juthathip , Park Donghyun
Published: May 2011

The world economy experienced a sharp spike in food and oil prices during 2007 and 2008. In light of developing Asia's dependence on imported oil and food, we can expect higher global food and oil prices to result in higher domestic consumer prices in the region. However, the actual impact of the global commodity shocks on consumer price inflation in developing Asia depends on a number of other factors, including government policy measures. The objective of this paper is to examine empirically the extent of the pass‐through of global food and oil prices to domestic consumer prices in nine countries in the region. The main empirical result is that the magnitude of the pass‐through has been limited. Government policy measures, for example, subsidies and price controls, played a role in reducing or delaying the pass‐through of oil and food price increases to domestic prices.
EUTHYPHRO AND THE GOODNESS OF GOD INCARNATE
Authors: Le Poidevin Robin
Published: May 2011

A familiar problem is here viewed from an unfamiliar angle. The familiar problem is the Euthyphro dilemma: if God wills something because it is good, then goodness is independent of God, so God becomes, morally speaking, de trop. On the other hand, if something is good because God wills it, then, given the absence of constraint on what God may will, moral truths are – counterintuitively – contingent. An examination of the kinds of necessity and possibility at work in this conundrum leads us to the most promising solution: there is a metaphysical connection between God and goodness. What he wills is an expression of his nature. But (and this is the unfamiliar angle), that solution now poses an acute problem for an understanding of the Incarnation. For if God is constitutive of goodness, and Christ is God incarnate, then Christ is constitutive of goodness. But Christ, as a human, is subject to external moral evaluation and obligation, which entails that he is not constitutive of goodness. This metaethical difficulty is not easily met by the usual strategies by which Christ is understood to have two natures. Reflection on our moral relations to our past selves, however, suggests a way forward.
JUDAISM, DARWINISM, AND THE TYPOLOGY OF SUFFERING
Authors: Cherry Shai
Published: May 2011

Abstract.  Darwinism has attracted proportionately less attention from Jewish thinkers than from Christian thinkers. One significant reason for the disparity is that the theodicies created by Jews to contend with the catastrophes which punctuated Jewish history are equally suited to address the massive extinctions which characterize natural history. Theologies of divine hiddenness, restraint, and radical immanence, coming together in the sixteenth‐century mystical cosmogony of Isaac Luria, have been rehabilitated and reworked by modern Jewish thinkers in the post‐Darwin era.
INTERPRETING THE WORD AND THE WORLD
Authors: Brooke John Hedley
Published: May 2011

Abstract.  The purpose of this essay is to introduce a collection of five papers, originally presented at the 2009 summer conference of the International Society for Science and Religion, which explore the reception of Darwin's science in different religious traditions. Comparisons are drawn between Jewish, Christian, Islamic, and Indian responses to biological evolution, with particular reference to the problem of suffering and to the exegetical and hermeneutic issues involved.
DARWIN AND THE OTHER CHRISTIAN TRADITION
Authors: McMullin Ernan
Published: May 2011

Abstract.  Augustine, and following him some major theologians of the early Christian church, noted the apparent discrepancies between the first two chapters of Genesis and suggested an interpretation for these chapters significantly different from the literal. After examining a selection of the relevant texts, we shall follow the later fortunes of this interpretation in brief outline, figuring in particular an unlikely trio: Suarez, St. George Mivart, and Thomas Henry Huxley. Moral: Darwinian theory might plausibly be construed as implementing, unawares, a suggestion from that other Christian tradition.
FAITH‐BASED SOCIAL SERVICES: FROM COMMUNITARIAN TO INDIVIDUALISTIC VALUES
Authors: McMillin Stephen Edward
Published: May 2011

Abstract.  This article argues that a primary, contemporary product of four moments in the history of faith‐based social services has been a highly selective and inconsistent use of the notion of human rights by churches and church leaders. Churches still occasionally reference a communitarian sense of human rights and public good but now more commonly use the rhetoric of individual rights to contest specific political positions and social policies in the arena of the social service agencies these churches sponsor. Changing church views of human nature are not sweeping changes, but small changes of degree that still have the power to powerfully reorient social relations. In this sense, churches that sponsor social services increasingly espouse a privatized, economic, and individualistic “Civil Society” in sharp contrast to communitarian notions of social citizenship that formerly better reflected churches’ operating ontology.
Combining the Intensity and Sequencing of the Poverty Experience: A Class of Longitudinal Poverty Indices
Authors: Mendola Daria , Busetta Annalisa , Milito Anna Maria
Published: May 2011

Traditional measures of the persistence of poverty do not devote enough attention to the sequence of spells of poverty. We propose a new class of indices which measures the severity of chronic poverty, taking into account the way in which spells of poverty and non-poverty follow one another along individual life courses. All the years spent in poverty concur with the measurement of the persistency of poverty, albeit with a decreasing contribution provided that the distance between two consecutive spells of poverty becomes longer. Moreover, the distance from the poverty line and the poverty persistence probabilities are explicitly taken into account. A macrolevel index, which allows comparisons across nations and accounts for the mobility in the national income distributions, is also provided and it is used to explain the differentials of persistence of poverty among young European adults.