bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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.
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.
Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles
Authors: Plevka Pavel , Tars Kaspars , Liljas Lars 
Published: July 2008

AbstractA 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.
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

SUMMARY 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
Delayed intravascular haemolysis following multiple asymptomatic ABO‐incompatible red blood cell transfusions in a patient with hepatic failure
Authors: Tormey C. A. , Stack G. 
Published: July 2008

ABO‐incompatible red blood cell (RBC) transfusions have rarely been associated with delayed haemolysis. However, we report the case of a 75‐year‐old man (blood type O) with hepatic disease, who received 5 units of incompatible type B RBCs over 8 days. The patient did not develop symptomatic or biochemical evidence of haemolysis until 7–8 days after the first incompatible RBC unit. The patient had a low anti‐B antibody titre (1 : 64) prior to the first transfusion. The onset of haemolysis was temporally associated with an increase in anti‐B and the infusion of fresh‐frozen plasma. In conclusion, a patient with hepatic failure experienced a delayed haemolytic transfusion reaction after receiving multiple ABO‐incompatible RBC transfusions that were initially well‐tolerated. We speculate that the delayed haemolysis may have resulted from an anamnestic antibody response to the initial incompatible transfusion, or possibly as a result of the transfusion of fresh‐frozen plasma, which might have repleted low complement levels.
Transferable Ageing Provisions in Individual Health Insurance Contracts
Authors: Baumann Florian , Meier Volker , Werding Martin 
Published: July 2008

Abstract
We consider lifetime health insurance contracts in which ageing provisions are used to smooth the premium profile. The capital stock accumulated for each individual can be decomposed into two parts: a premium insurance and an annuitized life insurance, only the latter being transferable between insurers without triggering premium changes through risk segmentation. In a simulation based on German data, the transferable share declines in age and falls with an increasing age of entry into the contract. In spite of different benefit profiles, it is almost identical for women and men.
How Do Banks Determine Capital? Evidence from Germany
Authors: Kleff Volker , Weber Martin 
Published: July 2008

AbstractWe analyse whether the determinants of capital found in the previous literature hold for the special German banking sector comprising three characteristic banking groups including savings banks, cooperative banks and other banks, which differ regarding their ownership and their access to the capital market. Through the use of accounting data from German banks between 1992 and 2001 we find evidence in accordance with the buffer theory of capital for all German banking groups. Furthermore, we also detect some remarkable differences between the three banking groups regarding their determination of capital due to institutional characteristics.
A Model Incorporating Potential Skewed X‐Inactivation in MZ Girls Suggests that X‐Linked QTLs Exist for Several Social Behaviours Including Autism Spectrum Disorder
Authors: Loat C. S. , Haworth C. M. A. , Plomin R. , Craig I. W. 
Published: July 2008

SummarySex differences in the frequency and patterns of behaviours are frequently observed and largely unexplained. We have investigated the possible role of X‐linked genes in the aetiology of social behaviour problems, including those involved in autistic spectrum disorders. A novel approach has been implemented. This is based on predictions following from stochastic patterns of X‐inactivation of lower concordance of monozygous female (MZF) twins than MZM twins for behaviours underpinned by X‐linked QTLs and the converse that DZF twins are expected to correlate more strongly for X‐linked traits than DZM twins because unlike males, females always have at least one X chromosome in common. These expectations were tested in an ongoing longitudinal cohort study in which all twins born in England and Wales between 1994 and 1996 were invited to take part. 1000 each of MZF, MZM, DZF and DZM pairs from TEDS were tested at 7 and 8 years of age. The results suggest the persistent influence of X‐linked genes on cognition and social behaviour problems, including those involved in autistic spectrum disorders, from early to middle childhood. This emphasises the potential importance of X‐linked genes in the developmental trajectories of behaviour and mental health and the need to stratify genetic analysis of behaviours by gender.
Localization of the Wilson disease protein in murine intestine
Authors: Weiss Karl Heinz , Wurz Judith , Gotthardt Daniel , Merle Uta , Stremmel Wolfgang , Füllekrug Joachim 
Published: July 2008

AbstractWilson disease is an inherited disorder of human copper metabolism, characterized by gradual accumulation of copper in tissues, predominantly liver and brain. The gene defect lies in the Wilson disease protein ATP7B, a copper transporting ATPase highly active in hepatocytes. In the liver, ATP7B is essential for excretion of excess copper into the bile and for copper loading of ceruloplasmin in the Golgi apparatus. The extrahepatic role of ATP7B is not yet completely understood. We analysed the intestinal expression of ATP7B in mice using RT‐PCR, Western blot and indirect immunofluorescence. We found abundant expression of ATP7B in stomach and small intestine, but not in colon. Using confocal microscopy we demonstrate a Golgi localization of ATP7B in enterocytes. In response to elevated copper, the Wilson disease protein shows an intracellular trafficking pattern in the intestinal polarized cell line CaCo‐2, moving away from the Golgi apparatus to dispersed vesicles. This suggests a role for intestinal ATP7B in sequestration of copper in intracellular vesicles for maintenance of copper homeostasis in the enterocyte. In conclusion, the expression of ATP7B in the small intestine might represent an additional regulatory mechanism to fine‐tune intestinal copper absorption.
The effectiveness of volunteer nest protection on the nest success of Northern Lapwings Vanellus vanellus on Dutch arable farms
Authors: KRAGTEN STEVEN , NAGEL JAN C. , DE SNOO GEERT R. 
Published: July 2008

Clutches of ground‐nesting farmland birds are often destroyed by farming operations, resulting in insufficient reproductive success and subsequently declining populations. The aim of this study was to investigate whether volunteer nest protection can enhance nest success of ground‐nesting birds. The study compared nest success of protected and unprotected Northern Lapwing Vanellus vanellus nests over 2 years on arable farms in the Netherlands. Because of different crop management, nest success of ground‐breeding birds might differ between organic and conventional arable farms. The effectiveness of volunteer nest protection was therefore investigated on both farm types. Although nest protection significantly reduced nest loss due to farming operations, there were no significant differences in total clutch survival of protected and unprotected nests. However, sample sizes of unprotected nests, and protected nests on organic farms, were relatively small, which may have reduced statistical power. There were indications that protected nests were predated or deserted more often. We recommend exploring different ways to improve the effectiveness of volunteer nest protection through a further reduction of nest loss due to farming operations and predation.
Influence of within‐patch habitat quality on high‐AndeanPolylepisbird abundance
Authors: LLOYD HUW 
Published: July 2008

Habitat restoration strategies for fragmented high Andean forest landscapes must consider the influence of within‐patch habitat quality on bird abundance. I examined vegetation and bird abundance at three locations within a highly fragmentedPolylepisforest landscape in the Cordillera Vilcanota, southern Peru. Across the landscape, there was significant variation in the vegetation structure ofPolylepisforest patches of different size categories, especially in terms of tree girth, tree height, tree density, and canopy vegetation structure. Principal Component Analysis extracted five factors of habitat quality, which together accounted for 74.2% of the variability within 15 habitat variables.Polylepisbird species differed in their responses to habitat quality but, overall, variation inPolylepisbird abundance was not fully captured by the range of habitat quality variables. Tall, dense vegetation cover was clearly important for 11 conservation‐important species, a high density of large trees was important for 10 species and primary forest ground cover was important for eight species. Habitat quality exhibited no significant influence on the abundance of only one species –Asthenes urubambensis. The abundance of seven species was associated with lower elevation forest, but only one species was associated with higher elevation forest. Management of habitat quality in large and medium remnant forest patches throughout the Cordillera Vilcanota, particularly in the 3800–4200 m elevation range, will be a cornerstone in ensuring the persistence of the majority of conservation‐important bird species populations.
Land‐use changes may explain the recent range expansion of the Black‐shouldered Kite Elanus caeruleus in southern Europe
Authors: BALBONTÍN JAVIER , NEGRO JUAN JOSÉ , SARASOLA JOSÉ HERNÁN , FERRERO JUAN JOSÉ , RIVERA DOMINGO 
Published: July 2008

Occasional observations of Black‐shouldered Kites Elanus caeruleus in Europe date back to the mid‐19th century, but it was only recorded as a breeding species in the early 1960s in Portugal and a few years later in neighbouring Spain. This recent colonization, possibly from Africa where the species is abundant, may be due to climate change, land‐use changes in southern Europe, or both. As a first step to understanding this range expansion process we have developed a habitat selection model using data from the current strongholds of its European distribution. Comparing the proportion of different habitat types around 46 breeding sites and 45 randomly chosen plots, we have found that the area of cultivated parklands known as dehesas in Spain is a strong predictor of the current distribution range of breeding pairs of Black‐shouldered Kites. Specifically, the percentage of dehesas with planted cereal and a low density of trees (i.e. < 7 trees/ha and thus a savannah‐like habitat) within the study plots explained 44.6% of the residual deviance in our model. The minimal adequate model classified 81.3% of breeding sites and random plots correctly. Our results suggest that Black‐shouldered Kites may have taken advantage of the gradual increase of cultivated dehesas in the second half of the 20th century to expand its range in Europe. This particular type of dehesa is structurally similar to the African savannahs where the species thrives and may offer a higher density of rodents than traditional dehesas, which primarily contain pastureland for livestock ranching.
Dental hygiene work in a clinical trial
Authors: Luís HS , Morgado I , Assunção V , Bernardo MF , Leroux B , Martin MD , DeRouen TA , Leitão J 
Published: July 2008

Abstract:  Dental hygiene activities were developed as part of a randomized clinical trial designed to assess the safety of low‐level mercury exposure from dental amalgam restorations. Along with dental‐hygiene clinical work, a community programme was implemented after investigators noticed the poor oral hygiene habits of participants, and the need for urgent action to minimize oral health problems in the study population.Objectives:  Clinical and community activity goal was to promote oral health and prevent new disease. Community activities involved participants and their fellow students and were aimed at providing education on oral health in a school environment.Methods:  Dental hygienists developed clinical work with prophylaxis, sealants application and topical fluoride and implemented the community programme with in‐class sessions on oral health themes. Twice a month fluoride mouthrinses and bi‐annual tooth brushing instructional activity took place. Participation at dental‐hygiene activities, sealed teeth with no need of restoration and dental‐plaque‐index were measures used to evaluate success of the programme for the participants.Results:  Improvement in dental hygiene is shown by the decrease in dental plaque index scores (P < 0.0001); also sealants integrity is achieved in 86.3% of teeth. 888 (13.7%) teeth with sealants had to be restored or were lost. Children participated actively on dental hygiene activities. Teachers became aware of the problem and included oral‐health in school curricula.Conclusion:  Dental hygiene activities have shown to be helpful to promote dental hygiene, promote oral health and to provide school‐age children with education on habits that will be important for their future good health.