bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry
Authors: Bandeira Nuno , Olsen Jesper V. , Mann Matthias , Pevzner Pavel A.
Published: July 2008

Despite a recent surge of interest in database-independent peptide identifications, accurate de novo peptide sequencing remains an elusive goal. While the recently introduced spectral network approach resulted in accurate peptide sequencing in low-complexity samples, its success depends on the chance of presence of spectra from overlapping peptides. On the other hand, while multistage mass spectrometry (collecting multiple MS 3 spectra from each MS 2 spectrum) can be applied to all spectra in a complex sample, there are currently no software tools for de novo peptide sequencing by multistage mass spectrometry. We describe a rigorous probabilistic framework for analyzing spectra of overlapping peptides and show how to apply it for multistage mass spectrometry. Our software results in both accurate de novo peptide sequencing from multistage mass spectra (despite the inferior quality of MS 3 spectra) and improved interpretation of spectral networks. We further study the problem of de novo peptide sequencing with accurate parent mass (but inaccurate fragment masses), the protocol that may soon become the dominant mode of spectral acquisition. Most existing peptide sequencing algorithms (based on the spectrum graph approach) do not track the accurate parent mass and are thus not equipped for solving this problem. We describe a de novo peptide sequencing algorithm aimed at this experimental protocol and show that it improves the sequencing accuracy on both tandem and multistage mass spectrometry.

Availability: The open-source implementation of our software is available at http://proteomics.bioprojects.org.

Contact:  bandeira@ucsd.edu

Supplementary information:: Supplementary data are available at Bioinformatics online.
HELIQUEST: a web server to screen sequences with specific α-helical properties
Authors: Gautier Romain , Douguet Dominique , Antonny Bruno , Drin Guillaume
Published: July 2008

Summary: HELIQUEST calculates the physicochemical properties and amino acid composition of an α-helix and screens databank to identify protein segments possessing similar features. This server is also dedicated to mutating helices manually or automatically by genetic algorithm to design analogues of defined features.

Availability:  http://heliquest.ipmc.cnrs.fr

Contact:  gautier@ipmc.cnrs.fr
Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative
Authors: Fernandes Andrew D. , Atchley William R.
Published: July 2008

Motivation: In a nucleotide or amino acid sequence, not all sites evolve at the same rate, due to differing selective constraints at each site. Currently in computational molecular evolution, models incorporating rate heterogeneity always share two assumptions. First, the rate of evolution at each site is assumed to be independent of every other site. Second, the values of these rates are assumed to be drawn from a known prior distribution. Although often assumed to be small, the actual effect of these assumptions has not been previously quantified in the literature.

Results: Herein we describe an algorithm to simultaneously infer the set of n−1 relative rates that parameterize the likelihood of an n-site alignment. Unlike previous work (a) these relative rates are completely identifiable and distinct from the branch-length parameters, and (b) a far more general class of rate priors can be used, and their effects quantified. Although described in a Bayesian framework, we discuss a future maximum likelihood extension.

Conclusions: Using both synthetic data and alignments from the Myc, Max and p53 protein families, we find that inferring relative rather than absolute rates has several advantages. First, both empirical likelihoods and Bayes factors show strong preference for the relative-rate model, with a mean Δ ln P=−0.458 per alignment site. Second, the computed likelihoods and Bayes factors were essentially independent of the relative-rate prior, indicating that good estimates of the posterior rate distribution are not required a priori. Third, a novel finding is that rates can be accurately inferred even when up to ≈4 substitutions per site have occurred. Thus biologically relevant putative hypervariable sites can be identified as easily as conserved sites. Lastly, our model treats rates and tree branch-lengths as completely identifiable, allowing for the first time coherent simultaneous inference of branch-lengths and site-specific evolutionary rates.

Availability: Source code for the utility described is available under a BSD-style license at http://www.fernandes.org/txp/article/9/site-specific-relative-evolutionary-rates.

Contact:  andrew@fernandes.org

Supplementary information:  Supplementary data is available at Bioinformatics online.
Walk–run classification of symmetrical gaits in the horse: a multidimensional approach
Authors: Starke Sandra D , Robilliard Justine J , Weller Renate , Wilson Alan M , Pfau Thilo
Published: July 2008

Walking and running are two mechanisms for minimizing energy expenditure during terrestrial locomotion. Duty factor, dimensionless speed, existence of an aerial phase, percentage recovery (PR) or phase shift of mechanical energy and shape of the vertical ground reaction force profile have been used to discriminate between walking and running. Although these criteria work well for the classification of most quadrupedal gaits, they result in conflicting evidence for some gaits, such as the tölt (a symmetrical, four-beat gait used by Icelandic horses).

We use established pattern recognition methods to test the hypothesis that the tölt is a running gait based on anautomated and optimized decision drawn from four features(dimensionless speed, duty factor, length of aerial phase and PR for over 6000 strides from four symmetrical gaits in seven Icelandic horses) simultaneously. We compare this decision with the use of each of these features in isolation.

Sensitivity and specificity values were used to determine optimal thresholds for classifying tölt strides based on each feature separately. Duty factor and dimensionless speed indicate that tölt is more similar to running, while aerial phase and PR indicate that it is more similar to walking.

Then, two multidimensional pattern recognition approaches, multivariate Gaussian densities and linear discriminant analysis, were used and it was shown that, in terms of stochastic multidimensional discrimination, tölt is more similar to ‘running’. The approaches presented here have potential to be extended to studies on similar ‘ambling’ gaits in other quadrupeds.
Plasma-sprayed CaTiSiO
5
ceramic coating on Ti-6Al-4V with excellent bonding strength, stability and cellular bioactivity
Authors: Wu Chengtie , Ramaswamy Yogambha , Liu Xuanyong , Wang Guocheng , Zreiqat Hala
Published: July 2008

Novel Ca-Si-Ti-based sphene (CaTiSiO
5
) ceramics possess excellent chemical stability and cytocompatibility. The aim of this study was to prepare sphene coating on titanium alloy (Ti-6Al-4V) for orthopaedic applications using the plasma spray method. The phase composition, surface and interface microstructure, coating thickness, surface roughness and bonding strength of the plasma-sprayed sphene coating were analysed using X-ray diffraction, scanning electron microscopy, atomic force microscopy and the standard mechanical testing of the American Society for Testing and Materials, respectively. The results indicated that sphene coating was obtained with a uniform and dense microstructure at the interface of the Ti-6Al-4V surface and the thickness and surface roughness of the coating were approximately 150 and 10 μm, respectively. Plasma-sprayed sphene coating on Ti-6Al-4V possessed a significantly improved bonding strength and chemical stability compared with plasma-sprayed hydroxyapatite (HAp) coating. Plasma-sprayed sphene coating supported human osteoblast-like cell (HOB) attachment and significantly enhanced HOB proliferation and differentiation compared with plasma-sprayed HAp coating and uncoated Ti-6Al-4V. Taken together, plasma-sprayed sphene coating on Ti-6Al-4V possessed excellent bonding strength, chemical stability and cellular bioactivity, indicating its potential application for orthopaedic implants.
New frontiers in single-cell analysis
Authors: Templer Richard H , Ces Oscar
Published: July 2008

For this special issue of
J. R. Soc. Interface
we present an overview of the driving forces behind technological advances in the field of single-cell analysis. These range from increasing our understanding of cellular heterogeneity through to the study of rare cells, areas of research that cannot be tackled effectively using current high-throughput population-based averaging techniques.
Humphry Davy and the Royal Institution of Great Britain
Authors: Unwin Patrick R , Unwin Robert W
Published: July 2008

The abortive attempts of Sir Humphry Davy to introduce modest reforms at the Royal Society of London during his Presidency (1820–27) contrast with his (largely unstudied) earlier experience of administration at the Royal Institution of Great Britain (RI). Davy's attempts to combat the systemic weaknesses in governance and funding, and his role in effecting changes at the RI, in association with a core group of reformers, merit consideration. This paper analyses important aspects of the early management and social structure of the RI and examines the inner workings of the institution. It shows how and why the Library, its most valuable financial asset, and its celebrated Laboratory, developed along distinctive lines, each with its own support structures and intra-institutional interests. While acknowledging the roles traditionally ascribed to Count Rumford and Sir Joseph Banks, the paper highlights the contributions of other early patrons such as Thomas Bernard, son of a colonial governor of Massachusetts, and Earl Spencer, a leading European bibliophile and RI President from 1813 to 1825. The promotion of a Bill in Parliament in 1810, designed to transform the RI from a proprietary body politic into a corporation of members, and the subsequent framing of the bye-laws, provided opportunities to establish a more democratic structure of elected committees for the conduct of science.
Nonlinear feedback auxiliary signals for system interrogation and damage detection
Authors: D'Souza Kiran , Epureanu Bogdan I
Published: July 2008

Recently, a sensitivity-enhancement technique for system interrogation using linear controllers and eigenstructure assignment has been extended from linear to nonlinear systems. Nonlinearities have been accounted for by forming (higher dimensional) augmented systems that are designed for each trajectory of the nonlinear system, and are characterized by a specific forcing which ensures that the augmented systems follow that trajectory (when projected onto the original lower dimensional space). The use of system augmentation has several benefits beyond its ability to handle nonlinearities. For example, sensitivity can be increased compared with existing linear techniques through nonlinear feedback auxiliary signals (NFASs) because the constraint that the system is stable during its interrogation has to be applied only to the linearized closed-loop system, while the augmented linear system does not have that constraint. In this work, NFASs are designed for interrogating
linear
systems. System augmentation is used in a linear system because a nonlinear controller is employed to enhance sensitivity. In addition to the increased sensitivity, fewer controller actuator points and sensors are required compared with existing linear techniques due to the efficient use of added (augmented) equations. To demonstrate the approach, damage detection is considered as an application. Numerical simulations for linear mass–spring and mass–spring–damper systems are used to validate the approach and discuss the effects of noise.
Assortative sociality, limited dispersal, infectious disease and the genesis of the global pattern of religion diversity
Authors: Fincher Corey L , Thornhill Randy
Published: July 2008

Why are religions far more numerous in the tropics compared with the temperate areas? We propose, as an answer, that more religions have emerged and are maintained in the tropics because, through localized coevolutionary races with hosts, infectious diseases select for three anticontagion behaviours: in-group assortative sociality; out-group avoidance; and limited dispersal. These behaviours, in turn, create intergroup boundaries that effectively fractionate, isolate and diversify an original culture leading to the genesis of two or more groups from one. Religion is one aspect of a group's culture that undergoes this process. If this argument is correct then, across the globe, religion diversity should correlate positively with infectious disease diversity, reflecting an evolutionary history of antagonistic coevolution between parasites and hosts and subsequent religion genesis. We present evidence that supports this model: for a global sample of traditional societies, societal range size is reduced in areas with more pathogens compared with areas with few pathogens, and in contemporary countries religion diversity is positively related to two measures of parasite stress.
Pre-power stroke cross bridges contribute to force during stretch of skeletal muscle myofibrils
Authors: Rassier Dilson E
Published: July 2008

When activated skeletal muscle is stretched, force increases in two phases. This study tested the hypothesis that the increase in stretch force during the first phase is produced by pre-power stroke cross bridges. Myofibrils were activated in sarcomere lengths (SLs) between 2.2 and 2.5 μm, and stretched by approximately 5–15 per cent SL. When stretch was performed at 1 μm s
−1
 SL
−1
, the transition between the two phases occurred at a critical stretch (SL
c
) of 8.4±0.85 nm half-sarcomere (hs)
−1
and the force (critical force;
F
c
) was 1.62±0.24 times the isometric force (
n
=23). At stretches performed at a similar velocity (1 μm s
−1
 SL
−1
), 2,3-butanedione monoxime (BDM; 1 mM) that biases cross bridges into pre-power stroke states decreased the isometric force to 21.45±9.22 per cent, but increased the relative
F
c
to 2.35±0.34 times the isometric force and increased the SL
c
to 14.6±0.6 nm hs
−1
(
n
=23), suggesting that pre-power stroke cross bridges are largely responsible for stretch forces.
Modelling genetic regulation of growth and form in a branching sponge
Authors: Kaandorp Jaap A , Blom Joke G , Verhoef Jozef , Filatov Max , Postma M , Müller Werner E.G
Published: July 2008

We present a mathematical model of the genetic regulation controlling skeletogenesis and the influence of the physical environment on a branching sponge with accretive growth (e.g.Haliclona oculataorLubomirskia baikalensis). From previous work, it is known that high concentrations of silicate induce spicule formation and upregulate thesilicateingene. The upregulation of this gene activates locally the production of spicules in the sponge and the deposition of the skeleton. Furthermore, it is known that the expression of the geneIroquoisinduces the formation of an aquiferous system, consisting of exhalant and inhalant pores. We propose a model of the regulatory network controlling the separation in time and space of the skeletogenesis and the formation of the aquiferous system. The regulatory network is closely linked with environmental influences. In building a skeleton, silicate is absorbed from the environment. In our model, silicate is transported by diffusion through the environment and absorbed at the surface of a geometric model of the sponge, resulting in silicate gradients emerging in the neighbourhood of the sponge. Our model simulations predict sponge morphology and the positioning of the exhalant pores over the surface of the sponge.
Multiple gossip statements and their effect on reputation and trustworthiness
Authors: Sommerfeld Ralf D , Krambeck Hans-Jürgen , Milinski Manfred
Published: July 2008

Empirical and theoretical evidence from various disciplines indicates that reputation, reputation building and trust are important for human cooperation, social behaviour and economic progress. Recently, it has been shown that reputation gained in games of indirect reciprocity can be transmitted by gossip. But it has also been shown that gossiping has a strong manipulative potential. We propose that this manipulative potential is alleviated by the abundance of gossip. Multiple gossip statements give a better picture of the actual behaviour of a person, and thus inaccurate or fake gossip has little power as long as it is in the minority. In addition, we investigate the supposedly strong connection between reciprocity, reputation and trust. The results of this experimental study (with 11 groups of 12 students each) document that gossip quantity helps to direct cooperation towards cooperators. Moreover, reciprocity, trust and reputations transferred via gossip are positively correlated. This interrelation might have helped to reach the high levels of cooperation that can be observed in humans.
Where and when does a ring start and end? Testing the ring-species hypothesis in a species complex of Australian parrots
Authors: Joseph Leo , Dolman Gaynor , Donnellan Stephen , Saint Kathleen M , Berg Mathew L , Bennett Andrew T.D
Published: July 2008

Speciation, despite ongoing gene flow can be studied directly in nature in ring species that comprise two reproductively isolated populations connected by a chain or ring of intergrading populations. We applied three tiers of spatio-temporal analysis (phylogeny/historical biogeography, phylogeography and landscape/population genetics) to the data from mitochondrial and nuclear genomes of eastern Australian parrots of the Crimson RosellaPlatycercus eleganscomplex to understand the history and present genetic structure of the ring they have long been considered to form. A ring speciation hypothesis does not explain the patterns we have observed in our data (e.g. multiple genetic discontinuities, discordance in genotypic and phenotypic assignments where terminal differentiates meet). However, we cannot reject that a continuous circular distribution has been involved in the group's history or indeed that one was formed through secondary contact at the ‘ring's’ east and west; however, we reject a simple ring-species hypothesis as traditionally applied, with secondary contact only at its east. We discuss alternative models involving historical allopatry of populations. We suggest that population expansion shown by population genetics parameters in one of these isolates was accompanied by geographical range expansion, secondary contact and hybridization on the eastern and western sides of the ring. Pleistocene landscape and sea-level and habitat changes then established the birds' current distributions and range disjunctions. Populations now show idiosyncratic patterns of selection and drift. We suggest that selection and drift now drive evolution in different populations within what has been considered the ring.
Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles
Authors: Plevka Pavel , Tars Kaspars , Liljas Lars
Published: July 2008

A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild‐type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild‐type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild‐type virions is 7 times bigger than that of the octahedral particles.
Retracted: Gene duplication and functional evolution of Hox genes in fishes
Authors: Zou S. M. , Jiang X. Y.
Published: July 2008

RETRACTION

The following article from the Journal of Fish Biology has been retracted by agreement between the authors, the Journal Editor‐in‐Chief, Dr John Craig and Blackwell Publishing Ltd: ‘Gene duplication and functional evolution of Hox genes in fishes' by S. M. Zou & X. Y. Jiang, published online on 29 July 2008 in Wiley InterScience (www.interscience.wiley.com) and published in Volume 73, Issue 2, Pages 329–354 (August 2008).

The retraction has been agreed due to overlap between this article and several previously published articles.

With their power to shape animal morphology, few genes have captured the imagination of biologists as much as the evolutionarily conserved members of the Hox clusters. Hox genes encode transcription factors that play a key role in specifying the body plan in metazoans and are therefore essential in explaining patterns of evolutionary diversity. While each Hox cluster contains the same genes among the different mammalian species, this does not happen in ray‐finned fish, in which both the number and organization of Hox genes and even Hox clusters are variable. Teleost fishes provide the first unambiguous support for ancient whole‐genome duplication (third round) in an animal lineage. The number of genes differs in each cluster as a result of increased freedom to mutate after duplication. This has also allowed them to diverge and to adopt novel developmental roles. In this review, the authors have firstly focused on broadly outlining the duplication of Hox genes in fishes and discussing how comparative genomics is elucidating the molecular changes associated with the evolution of Hox genes expression and developmental function in the teleost fishes. Additional related research aspects, such as imaging of roles of microRNAs, chromatin regulation and evolutionary findings are also discussed.
The protective influence of ascorbic acid against the genotoxicity of waterborne lead exposure in Nile tilapia Oreochromis niloticus (L.)
Authors: Jiraungkoorskul W. , Sahaphong S. , Kangwanrangsan N. , Zakaria S.
Published: July 2008

The present study investigated the effects of lead (Pb) and ascorbic acid (AA) on Nile tilapia Oreochromis niloticus using the micronucleus (MN) and nuclear abnormality (NA) tests for periods of 7, 14 and 21 days. The MN frequencies in the erythrocytes, gill, liver and fin cells were analysed comparatively to evaluate the sensitivity and suitability of these different cell types. The NA shapes in erythrocytes were scored into blebbed nuclei (BL), lobed nuclei (LB), notched nuclei (NT) and binuclei (BN). It was observed that fish showed significant sensitivity to the different treatments. In general, the highest value of both MN and NA cells were significantly increased in the Pb‐treated group followed by the combination of the Pb and AA‐treated group. On the other hand, the MN and NA frequencies in erythrocytes were the most sensitive to the treatment and could provide more valuable information than those in gill, liver and fin cells. The frequencies of each NA shape in erythrocytes of all treatments were observed in the following ranked order NT > LB > BN > BL. The results demonstrated the efficacy of AA in reducing genotoxicity in fish induced by Pb. They showed the sensitivity and suitability of MN and NA frequencies in erythrocytes as pollution biomarkers.
Characterization of a major histocompatibility class II A gene (Clha‐DAA) with an embedded microsatellite marker in Atlantic herring (Clupea harengus L.)
Authors: Stet R. J. M. , Mudde K. , Wynne J. W. , Nooijen A. , Dahlgren T. G. , Ruzzante D. E. , AndrÉ C.
Published: July 2008

An Atlantic herring major histocompatibility class II A (Clha‐DAA) cDNA sequence has been characterized and was shown to encode a leader peptide, alpha‐1 domain, alpha‐2 domain, connecting peptide, transmembrane and cytoplasmic region. The Clha‐DAA protein sequence has all the characteristics of a teleost class II A protein with conserved cysteines in both the alpha‐1 and the alpha‐2 domains and two potential N‐linked glycosylation sites. Exon 2 sequences encoding the polymorphic alpha‐1 domain from different individuals were analysed and revealed the presence of at least two loci. The Clha‐DAA gene consists of four exons and three short introns. Four unique intron 3 sequences from multiple individuals were obtained and were shown to contain a (TG)n microsatellite sequence. Primers were optimized such that only a single microsatellite locus designated Clha‐DAA‐INTR3 was amplified. Four herring populations from the North Sea and the Baltic Sea were genotyped for Clha‐DAA‐INTR3. In total, 16 Clha‐DAA‐INTR3 alleles were detected; the distribution of the alleles showed no deviation from Hardy–Weinberg expectation. Levels of genetic differentiation among samples were of similar magnitude as have been reported earlier for neutral microsatellite loci between northern North Sea and Baltic Sea herring populations.
Speciation and demographic history of the Cortez bonefish, Albula sp. A (Albuliformes: Albulidae), in the Gulf of California inferred from mitochondrial DNA
Authors: Pfeiler E. , Watts T. , Pugh J. , Van DerHeiden A. M.
Published: July 2008

Nucleotide sequence data from a segment of the mitochondrial cytochrome b (Cyt b) gene were used to infer demographic history and examine conditions that may have led to speciation in the Cortez bonefish (Albula sp. A) in the Gulf of California, Mexico, a currently undescribed species of bonefish in the Albula vulpes complex. Analysis of molecular variance in 39 individuals collected from three localities along the eastern gulf coast, over c. 850 km, revealed a lack of population structure among localities (overall ΦST=−0·015), with 100% of the genetic variation distributed within populations. Analysis of combined sequences from these individuals using neutrality tests and the mismatch distribution provided evidence of a population expansion dating to the Pleistocene. The population expansion was supported by maximum likelihood estimates of changes in long‐term female effective population size (Nef). A molecular clock estimate of divergence, provisionally calibrated for the Cyt b gene in Albula, indicates that Albula sp. A and its sister species in the eastern Pacific, Albula esuncula, diverged from a common ancestor c. 5·0–8·8 million years ago. This date is about the time the Baja California peninsula separated from mainland Mexico during the formation of the Gulf of California. Oceanographic and ecological changes associated with the opening of the gulf likely provided conditions favourable for adaptive radiation and reproductive isolation, ultimately resulting in the allopatric formation of two separate lineages. The co‐occurrence of Albula sp. A and A. esuncula found today in the coastal Pacific waters of northern Mexico is most probably the result of secondary contact after speciation.
Somatolactin mRNA expression during the parr–smolt transformation in hatchery‐reared Atlantic salmon Salmo salar smolts
Authors: O’Keeffe A. M. , Hubert S. , Voisin M. , Houeix B. , Cotter D. , Cairns M. T.
Published: July 2008

Expression of somatolactin (SL) mRNA was quantified during smoltification at 2 week intervals during January and February and weekly during March, April and May 2004 in a line‐bred ranching stock of Atlantic salmon Salmo salar. Gene expression of SL (and a splice variant termed SL180) was lower in fish sampled in the later weeks of smoltification than in those at the beginning, a pattern opposite to that of gill Na+ K+‐ATPase activity.
Unusual mitochondrial genome structure of the freshwater gobyOdontobutis platycephala: rearrangement of tRNAs and an additional non‐coding region
Authors: Ki J.‐S. , Jung S.‐O. , Hwang D.‐S. , Lee Y.‐M. , Lee J.‐S.
Published: July 2008

Mitochondrial DNA was isolated from the Korean freshwater gobioid fishOdontobutis platycephalaby long‐polymerase chain reaction with conserved primers and this mtDNA was sequenced by primer walking using flanking sequences as sequencing primers. The resultantO. platycephalamtDNA sequence was found to be 17 588 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. Rearrangements of tRNAs (tRNA‐Ser, tRNA‐Leu, tRNA‐His) and an additional non‐coding region (533 bp) were present between the ND4 and ND5 genes. In the present paper, the basic characteristics of theO. platycephalamitochondrial genome is reported, including its structural organization, base composition of rRNAs, tRNAs and protein‐encoding genes, characteristics of mitochondrial tRNAs and the peculiar rearrangement features of some parts of the mtDNA. Phylogenetic analysis performed using the cytochromebgene sequences of 16 Korean freshwater fishes (15 gobioids) with the Bayesian algorithm showed thatO. platycephalaforms a clade (1·00 of posterior probability) with other species ofOdontobutis. This suggests that the observed rearrangement between the ND4 and ND5 genes in theO. platycephalamitogenome reflects independent events.
Phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals
Authors: GRÜNWALD NIKLAUS J. , GOSS ERICA M. , PRESS CAROLINE M.
Published: July 2008

Phytophthora ramorum is an oomycete plant pathogen classified in the kingdom Stramenopila. P. ramorum is the causal agent of sudden oak death on coast live oak and tanoak as well as ramorum blight on woody ornamental and forest understorey plants. It causes stem cankers on trees, and leaf blight or stem dieback on ornamentals and understorey forest species. This pathogen is managed in the USA and Europe by eradication where feasible, by containment elsewhere and by quarantine in many parts of the world. Genomic resources provide information on genes of interest to disease management and have improved tremendously since sequencing the genome in 2004. This review provides a current overview of the pathogenicity, population genetics, evolution and genomics of P. ramorum.

Taxonomy:  Phytophthora ramorum (Werres, De Cock & Man in't Veld): kingdom Stramenopila; phylum Oomycota; class Peronosporomycetidae; order Pythiales; family Pythiaceae; genus Phytophthora.

Host range:  The host range is very large and the list of known hosts continues to expand at the time of writing. Coast live oak and tanoak are ecologically, economically and culturally important forest hosts in the USA. Rhododendron, Viburnum, Pieris, Syringa and Camellia are key ornamental hosts on which P. ramorum has been found repeatedly, some of which have been involved in moving the pathogen via nursery shipments.

Disease symptoms:  P. ramorum causes two different diseases with differing symptoms: sudden oak death (bleeding lesions, stem cankers) on oaks and ramorum blight (twig dieback and/or foliar lesions) on tree and woody ornamental hosts.

Useful websites:  http://nature.berkeley.edu/comtf/, http://rapra.csl.gov.uk/, http://www.aphis.usda.gov/plant_health/plant_pest_info/pram/index.shtml, http://genome.jgi‐psf.org/Phyra1_1/Phyra1_1.home.html, http://pamgo.vbi.vt.edu/, http://pmgn.vbi.vt.edu/, http://vmd.vbi.vt.edu./, http://web.science.oregonstate.edu/bpp/labs/grunwald/resources.htm, http://www.defra.gov.uk/planth/pramorum.htm, http://www.invasive.org/browse/subject.cfm?sub=4603, http://www.forestry.gov.uk/forestry/WCAS‐4Z5JLL
The development of a nurse‐led liaison mental health service for older people in Chesterfield, Derbyshire, UK
Authors: HUGHES C. P.
Published: July 2008

Mental health problems are very common among older people in general hospitals. They are independent predictors of poor outcomes. Research indicates that appropriate interventions can improve outcomes. It is increasingly recognized that liaison mental health services have a key role in meeting the needs of older people in the general hospitals and educating and supporting staff. This paper describes aspects of the developmental and clinical work of a consultant nurse in developing a nurse‐led liaison mental health service for older people in Chesterfield, Derbyshire, UK. It describes the impact of this service on referral rates. It also details the results of an audit of 206 referrals assessed by the consultant nurse in the second year of the service. The analysis of data collected provides a profile of aspects of the role of a liaison nurse including reasons for referral, psychiatric diagnosis and interventions recommended. This paper also, uniquely, documents mental health liaison into a community hospital. Implications for the development of services are discussed.
Kalevala or Keats: poetic traditions as a model for multidisciplinary miscommunication and team splitting
Authors: DODWELL D.
Published: July 2008

Attention is drawn to the oral tradition in poetry and some ways in which it differs from written, literary poetry. Some of these differences mirror differences between the oral communication typical of a psychiatric ward nursing handover and the writing‐based communication styles of psychiatrists. In particular, the oral tradition tends to involve an interactive and participatory style, stewardship (rather than authorship) of the message, a less linear approach to time and valuing the use of familiar formulae. Neither style is intrinsically superior or inferior. The two styles have significant differences in context, intent and rules (i.e. in linguistic ‘pragmatics’). In mental health practice, the apparently shared vocabulary and setting conceals these differences. The fact that these variations are hidden increases the risks of miscommunication and of team splitting. The use of an analogy from poetry is intended to make the differences more explicit, and thus generate awareness, discussion and problem solving.
People with learning disabilities admitted to an assessment and treatment unit: impact on challenging behaviours and mental health problems
Authors: SLEVIN E. , MCCONKEY R. , TRUESDALE‐KENNEDY M. , TAGGART L.
Published: July 2008

This study describes the evaluation of an assessment and treatment unit for people with learning disabilities. Results showed the main reasons for admission for the 48 people admitted to the unit were because of challenging behaviours and mental health problems. Valid and reliable scales were used to measure the behaviours and mental health problems of those admitted across three‐time periods: pre‐admission, during admission and post‐admission. The analysis found significant reductions in challenging behaviours and mental health problems following admission to the unit. The unit was staffed by a multidisciplinary team with nurses making up the largest group of staff. A number of issues of concern are discussed including access to mental health services for people with learning disabilities, the need for robust community services and areas that require further research. In conclusion, the study found evidence supporting the value of the unit and how it may lessen distress in learning disabled people who are behaviourally disturbed. It is suggested that nurses played a key role in the unit but they need to make the support and caring they provide more visible. Nurses need to harness and make explicit the caring they provide for people with learning disabilities.
Mental health policy and integrated care: global perspectives
Authors: ZOLNIEREK C. D.
Published: July 2008

Although omitted from the World Health Organization's eight Millennium Development Goals, mental illness ranks fourth of the 10 leading causes of disability in the world and is expected to approach second place by 2020. Scarce resources challenge responses to mental health needs. Effective approaches must consider existing healthcare delivery networks, nurses as care providers, as well as social, cultural, political and historical contexts. This paper reviews policy development and care approaches to address mental health needs around the world. Challenges, successes and further needs are discussed. Selected articles were reviewed to represent varied approaches to address mental health needs in countries with diverse resources and infrastructures. Integrated systems offer one model for addressing mental health needs along with physical health needs within a population. While potentially an efficient strategy, caution is advised to ensure services are integrated and not merely added on top of an already overburdened system. As the largest group of healthcare professionals worldwide, nurses play a key role in the delivery of mental health services. Nurses have an opportunity, if not a responsibility, to collaborate across borders sharing education and innovative approaches to care delivery.
Attitudes to animal‐assisted therapy with farm animals among health staff and farmers
Authors: BERGET B. , EKEBERG Ø. , BRAASTAD B. O.
Published: July 2008

Green care is a concept that involves the use of farm animals, plants, gardens or the landscape in cooperation with health institutions for different target groups of clients. The present study aimed at examining psychiatric therapists' (n = 60) and farmers' (n = 15) knowledge, experience and attitudes to Green care and animal‐assisted therapy (AAT) with farm animals for people with psychiatric disorders. Most respondents had some or large knowledge about Green care, but experience with Green care was generally low in both groups. Both farmers and therapists believed that AAT with farm animals could contribute positively to therapy to a large or very large extent, with farmers being significantly more positive. Most of the therapists thought that AAT with farm animals contributes to increased skills in interactions with other humans, with female therapists being more positive than males. Two‐thirds of the therapists believed that AAT with farm animals to a large extent could contribute better to mental health than other types of occupational therapy. There were no differences in attitudes to AAT between psychiatrists/psychologists and psychiatric nurses. This study confirms the marked potential of offering AAT services with farm animals for psychiatric patients by documenting positive attitudes to it among psychiatric therapists.
Exploring the role and perspectives of mental health nurse practitioners following psychosocial interventions training
Authors: O'NEILL M. , MOORE K. , RYAN A.
Published: July 2008

Psychosocial interventions (PSI) offer a range of problem‐centred activities designed to improve the health and quality of life of clients and their carers. The paper reports the findings of a study on the roles and perspectives of mental health nurse practitioners towards clients with enduring mental illness and their carers following completion of PSI training. Focus groups interviews were conducted with PSI mental health nurse practitioners (n = 8) and data were analysed for thematic content. The results of the study indicated that PSI practitioners developed positive attitudes towards their client following PSI training and this attitudinal change enabled clients to develop more confidence and autonomy in managing the symptoms of their illness in a more empowered way. Focus group participants observed reduced levels of anxiety among clients and their carers. This was attributed to the ‘sense of hope’ within the caring milieu which was established as a result of collaborative working with the client and family. The findings suggest that there is a need for further exploration of the PSI practitioner role with a particular focus on the centrality of positive attitudes on the development of the therapeutic milieu for clients with severe and enduring mental ill health.
Health professionals' attitudes towards suicide prevention initiatives
Authors: BRUNERO S. , SMITH J. , BATES E. , FAIRBROTHER G.
Published: July 2008

Preventing suicide can depend upon the ability of a range of different health professionals to make accurate suicide risk assessments and treatment plans. The attitudes that clinicians hold towards suicide prevention initiatives may influence their suicide risk assessment and management skills. This study measures a group of non‐mental health professionals' attitude towards suicide prevention initiatives. Health professionals that had attended suicide prevention education showed significantly more positive attitudes towards suicide prevention initiatives. The findings in this study further support the effectiveness of educating non‐mental health professionals in suicide risk awareness and management.
Characterization of the innate immune signalling pathways in hepatocyte cell lines
Authors: Preiss S. , Thompson A. , Chen X. , Rodgers S. , Markovska V. , Desmond P. , Visvanathan K. , Li K. , Locarnini S. , Revill P.
Published: July 2008

Summary.  Hepatitis B virus (HBV) infection is a major cause of liver‐related morbidity and mortality. Toll‐like receptors (TLRs) have recently been recognized to play an important role in the pathogenesis of chronic hepatitis B (CH‐B). Furthermore, manipulation of TLR signalling pathways shows potential as an antiviral therapeutic strategy. Whether hepatocytes themselves possess intact TLR signalling pathways remains controversial. It is critical that cell culture models be developed to allow investigation of the interaction between HBV and the TLR signalling pathways. We have screened three hepatocyte cell lines for the integrity of pro‐inflammatory responses and antiviral cytokines following stimulation with interleukin‐1 (IL‐1) and different TLR ligands. We observed that Huh‐7, HepG2 and PH5CH8 cells selectively responded to IL‐1 and TLR2 ligands, leading to the activation of NF‐κB. In addition, the PH5CH8 cell lines were able to induce type 1 interferon (IFN) via both TLR3 and RIG‐I following stimulation with poly I:C, HepG2 cells mounted an IFN response via RIG‐I only, whereas Huh‐7 cells were unresponsive. We conclude that the hepatocyte cell lines investigated display a repertoire of TLR signalling, albeit limited, suggesting that hepatocytes may themselves play an active role in innate immune responses to viruses such as HBV. Furthermore, particular hepatoma cell lines are suitable for investigating the interaction between HBV and hepatocyte‐expressed pattern recognition receptors.
Pegylated‐interferon and ribavirin in liver transplant candidates and recipients with HCV cirrhosis: systematic review and meta‐analysis of prospective controlled studies
Authors: Xirouchakis E. , Triantos C. , Manousou P. , Sigalas A. , Calvaruso V. , Corbani A. , Leandro G. , Patch D. , Burroughs A.
Published: July 2008

Summary.  Pegylated interferon with ribavirin (Peg/R) is the most effective therapy for chronic hepatitis C virus (HCV) but its utility and effectiveness after liver transplantation has been difficult to assess. We evaluated efficacy, tolerability, and safety of Peg/R in liver transplant candidates and recipients with HCV cirrhosis. We searched medical databases and conference proceedings between January 1999 and January 2008 selecting randomized and nonrandomized studies. Primary end points meta‐analytically were: (1) sustained viral response (SVR) and (2) histological response. Secondary end points were: (1) treatment discontinuation, (2) mortality, and (3) rejection episodes. Pegylated interferons using either 1–1.5 mcg/kg of pegylated interferon alpha‐2b or 180 μg (pegylated interferon alpha‐2a combined with ribavirin 800–1200 mg/day were the most effective compared to any other regimen or no therapy. In three pretransplant studies the median SVR was 19.6% (19.6–50%). In six postransplant studies where a meta‐analysis was done the cumulative risk difference in SVR was 0.31% (95% CI, 0.18–0.44, p < 0.001). However histological response was not significantly better compared to no therapy or other antiviral regimens. There were no significant differences in discontinuation of therapy, acute or chronic rejection or mortality between optimal Peg/R vs no treatment or other regimens. Hence pegylated interferon plus ribavirin in full doses is effective pre and post transplant but has a low SVR rate. To date no significant histological improvement has been reported.
Alterations in natural killer cells and natural killer T cells during acute viral hepatitis E
Authors: Srivastava R. , Aggarwal R. , Bhagat M. R. , Chowdhury A. , Naik S.
Published: July 2008

Summary.  The mechanism of liver damage in acute hepatitis E is poorly understood. In this study, we assessed the frequency and activation status of natural killer (NK) and natural killer T (NKT) cells and cytotoxic activity of NK cells in the peripheral blood mononuclear cells (PBMCs) obtained from patients with hepatitis E (n = 41) and healthy controls (n = 61). Flow cytometry was used to assess NK (CD3−/CD56+) and NKT cell (CD3+/CD56+) fractions (% of PBMCs) and activation status (CD69+; % of NK, NKT cells). NK cell cytotoxicity was assessed using major histocompatibilities complex‐deficient K562 cells as target cells. In 14 patients, the studies were repeated during the convalescence period. Patients had fewer median (range) NK cells [8.9% (2.4–47.0) vs 11.2% (2.6–35.4)] and NKT cells [8.7% (2.8–34.1) vs 13.6% (2.3–36.9)] than controls (P < 0.05 each). Activation markers were present on large proportion of NK cells [43.5% (11.2–58.6) vs 15.5% (3.0–55.8)] and NKT cells [41.5% (17.4–71.1) vs 12.8% (3.3–63.2); P < 0.05 each] from patients. NK cell cytotoxicity was similar in patients and controls. During convalescence, all the parameters normalized. In conclusion, reversible alterations in NK and NKT cell number and activation status during acute hepatitis E suggest a role of these cells in the pathogenesis of this disease.
Prospective study of bone mineral density and metabolism in patients with chronic hepatitis C during pegylated interferon α and ribavirin therapy
Authors: Hofmann W. P. , Kronenberger B. , Bojunga J. , Stamm B. , Herrmann E. , Bücker A. , Mihm U. , Von Wagner M. , Zeuzem S. , Sarrazin C.
Published: July 2008

Summary.  The importance of osteoporosis as a complication of end‐stage liver disease is well known. However, significant osteopenia may occur in earlier stages of chronic hepatitis C (CHC). Furthermore, antiviral therapy may influence bone metabolism. Thirty patients with CHC genotype 1 infection and without established cirrhosis were treated with peginterferon‐alfa and ribavirin. Dual‐energy x‐ray absorptiometry was performed at baseline, after 48 weeks of therapy, and by the end of a 24‐week follow‐up period. Bone mineral density (BMD), T‐scores, and Z‐scores were assessed. Serum C‐terminal propeptide of type I collagen (CICP) and osteocalcin levels were measured. Thirteen patients had osteopenia (43%) and osteoporosis was present in four patients (13%). Antiviral therapy led to significant on‐treatment increases of lumbar spine and hip BMD (P ≤ 0.05) as well as T‐scores (P ≤ 0.05) and Z‐scores (P ≤ 0.01) irrespective of subsequent treatment response. Further analyses showed that in patients with sustained virological response (n = 19) most parameters remained highly above baseline values by the end of the 24‐week follow‐up period, while patients with virological relapse (n = 11) had decreases of BMD, T‐scores and Z‐scores thereafter that did not differ from baseline. Serum CICP and osteocalcin levels decreased during therapy. Osteocalcin levels remained below baseline in sustained responder, but showed an increase in relapsers by the end of the 24‐week follow‐up (P ≤ 0.05). Osteopenia is detectable in a substantial proportion of CHC patients without established cirrhosis. Antiviral therapy leads to an on‐treatment increase of BMD, which may last in those patients who achieve a sustained virological response.