bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery, validation and characterization of 1039 cattle single nucleotide polymorphisms
Authors: Donthu R. , Larkin D. M. , Heaton M. P. , Lewin H. A. 
Published: November 2009

SummaryWe identified ∼13 000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat‐masked BAC‐end sequences from the cattle RPCI‐42 BAC library with whole‐genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency ≥0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every ∼3 Mbp on average. Twenty‐four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi‐breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome‐wide association studies and applications in animal breeding.
Interspecific relationships among growth, mortality and xylem traits of woody species from New Zealand
Authors: Russo Sabrina E. , Jenkins Kerry L. , Wiser Susan K. , Uriarte Maria , Duncan Richard P. , Coomes David A. 
Published: November 2009

Summary 1. Wood density is considered a key functional trait influencing the growth and survival of woody plants and has been shown to be related to a slow–fast rate‐of‐living continuum. Wood density is, however, an emergent trait arising from several vascular properties of wood, including the diameter and frequency of xylem conduits. 2. We aimed to test the hypotheses that there is a set of inter‐related trade‐offs linked to the different functions of wood, that these trade‐offs have direct consequences for tree growth and survival and that these trade‐offs underlie the observed correlations between wood density and demographic rates. We evaluated the covariation between xylem anatomical traits among woody species of New Zealand and whether that covariation had the potential to constrain variation in wood density and demographic rates. 3. Several xylem traits were strongly correlated with each other, but wood density was not correlated with any of them. We also found no significant relationships between wood density and growth or mortality rate. Instead, growth was strongly related to xylem traits associated with hydraulic capacity (conduit diameter and a conductivity index) and to maximum height, whereas mortality rate was strongly correlated only with maximum height. The diameter and frequency of conduits exhibited a significant negative relationship, suggesting a trade‐off, which restricted variation in wood density and growth rate, but not mortality rate. 4. Our results suggest, for woody species in New Zealand, that growth rate is more closely linked to xylem traits determining hydraulic conductance, rather than wood density. We also found no evidence that denser woods conferred higher survival, or that risk of cavitation caused by wide conduits increased mortality. 5. In summary, we found little support for the idea that wood density is a good proxy for position along a fast–slow rate‐of‐living continuum. Instead, the strong, negative relationship between vessel diameter and frequency may constrain the realized diversity of demographic niches of tree species in New Zealand. Trade‐offs in function therefore have the potential to shape functional diversity and ecology of forest communities by linking selection on structure and function to population‐level dynamics.
Validation of potential therapeutic targets in alveolar soft part sarcoma: an immunohistochemical study utilizing tissue microarray
Authors: Lazar Alexander J , Lahat Guy , Myers Sarah E , Smith Kerrington D , Zou Changye , Wang Wei‐Lien , Lopez‐Terrada Dolores , Lev Dina 
Published: November 2009

Aims:  The molecular signature of alveolar soft part sarcoma (ASPS) is a specific der(17)t(X;17)(p11.2;q25) translocation, resulting in a chimeric transcription factor (ASPSCR1–TFE3). When this disease is no longer amenable to surgical curative intervention, uniformly efficacious therapies are lacking. The aim of this study was to evaluate the expression of potential molecular therapeutic targets in a cohort of ASPS tumour samples.Methods and results:  Immunohistochemical analysis for hepatocyte growth factor, c‐Met, phosphorylated c‐Met, phosphorylated AKT, phosphorylated MEK, epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), p53 and vimentin was performed on an ASPS tissue microarray, yielding complete data from 26 tumours. Activation of c‐Met and its downstream effectors was noted, whereas only limited EGFR expression was seen. VEGF was expressed to varying degrees. Only one sample exhibited strong nuclear p53 expression, while 10 expressed low levels. Vimentin expression was negative in the vast majority of samples (96%).Conclusions:  There is a crucial need for better anti‐ASPS therapies. Activated c‐Met and the phosphorylation of its downstream effectors validate an intact signalling cascade probably induced by the ASPSCR1–TFE3 chimeric transcription factor. The angiogenic phenotype of these tumours is supported by increased angiogenic factor expression. Combination therapies targeting both tumour cells and angiogenesis merit further investigation.
Oncocytic versus mitochondrion‐rich follicular thyroid tumours: should we make a difference?
Authors: Tsybrovskyy Oleksiy , Rößmann‐Tsybrovskyy Martina 
Published: November 2009

Aims:  To separate true oncocytic neoplasms from mitochondrion‐rich non‐oncocytic lesions based on the intracellular relationship between major cell organelles, and to establish the diagnostic and clinical relevance of this distinction.Methods and results:  Tissue samples from 276 follicular adenomas, 194 follicular carcinomas, 162 normal thyroids and 296 non‐neoplastic lesions were classified as conventional, mitochondrion‐rich or oncocytic based on the immunohistochemically assessed quantity and intracellular distribution of mitochondria and endoplasmic reticulum (ER) and nuclear position. Pathological and clinical features were compared among the groups. In oncocytes, densely packed mitochondria resulted in homogeneous immunolabelling of basal cytoplasmic regions, whereas ER and the nuclei were typically displaced to the apical position. This aberrant organelle distribution was not observed in non‐oncocytes, which allowed reliable distinction between oncocytic and mitochondrion‐rich lesions. Clinically, mitochondrial increase in non‐oncocytic lesions was associated with neoplasia, malignancy and higher cancer recurrence rates. Similar correlation, albeit less pronounced, was observed within the oncocytic tumour group. By contrast, oncocytic change per se was not associated with neoplasia, malignancy or cancer aggressiveness.Conclusions:  True oncocytic neoplasms can be distinguished from mitochondrion‐rich non‐oncocytic tumours based on aberrant distribution of all major cell organelles. This distinction has immediate clinical relevance and should be implemented in practice.
Overexpression of RAD51 occurs in aggressive prostatic cancer
Authors: Mitra Anita , Jameson Charles , Barbachano Yolanda , Sanchez Lydia , Kote‐Jarai Zsofia , Peock Susan , Sodha Nayanta , Bancroft Elizabeth , Fletcher Anne , Cooper Colin , Easton Douglas ,   on behalf of The IMPACT Steering committee and IMPACT and EMBRACE Collaborators, Eeles Rosalind , Foster Christopher S 
Published: November 2009

Aims:  To test the hypothesis that, in a matched series of prostatic cancers, either with or without BRCA1 or BRCA2 mutations, RAD51 protein expression is enhanced in association with BRCA mutation genotypes.Methods and results:  RAD51 expression identified immunohistochemically was compared between prostatic cancers occurring in BRCA1 or BRCA2 mutation carriers and controls. RAD51 protein expression in the cytoplasm and nuclei of the benign tissues was significantly less than in the malignant tissues (P < 0.001). In all cancers, cytoplasmic expression of RAD51 was more prevalent and associated with higher Gleason score (P < 0.05) irrespective of BRCA mutational status, than its expression in benign tissues (P < 0.001). Although nuclear immunoreactivity was not observed in BRCA‐associated cancers with Gleason score ≤7, it was significantly increased in all other groups of prostatic cancers when compared with benign tissues (P < 0.001).Conclusions:  RAD51 protein is strongly expressed in high‐grade prostatic cancers, whether sporadic or associated with BRCA germ‐line mutations. Distinct localization of RAD51 between cytoplasm and nucleus, particularly in cancers of Gleason score ≤7, reflects distinct levels of RAD51 regulatory activity, from transcription to DNA repair. This biomarker may be of value in identifying patients requiring urgent treatment at diagnosis as well as in analysing biological mechanisms underlying aggressive phenotype of human prostatic cancer.
Allergic rhinitis and the common cold – high cost to society
Authors: Hellgren J. , Cervin A. , Nordling S. , Bergman A. , Cardell L. O. 
Published: November 2009

To cite this article: Hellgren J, Cervin A, Nordling S, Bergman A, Cardell LO. Allergic rhinitis and the common cold – high cost to society. Allergy 2010; 65: 776–783.AbstractBackground:  The common cold and allergic rhinitis constitute a global health problem that affects social life, sleep, school and work performance and is likely to impose a substantial economic burden on society because of absence from work and reduced working capacity. This study assesses the loss of productivity as a result of both allergic rhinitis and the common cold in the Swedish working population.Methods:  Four thousand questionnaires were sent to a randomized adult population, aged 18–65 years, in Sweden, stratified by gender and area of residence (metropolitan area vs rest of the country). The human capital approach was used to assign monetary value to lost productivity in terms of absenteeism (absence from work), presenteeism (reduced working capacity while at work) and caregiver absenteeism (absence from work to take care of a sick child).Results:  Thousand two hundred and thirteen individuals responded, response rate 32%. The mean productivity loss was estimated at 5.1 days or € 653 per worker and year, yielding a total productivity loss in Sweden of € 2.7 billion a year. Of the total costs, absenteeism (44%) was the dominant factor, followed by presenteeism (37%) and caregiver absenteeism (19%). Poisson regression analyses revealed that women, people in the 18–29 year age group, and respondents with ‘doctor‐diagnosed asthma’ reported more lost days than the rest of the group.Conclusion:  In Sweden, the cost of rhinitis is € 2.7 billion a year in terms of lost productivity. A reduction in lost productivity of 1 day per individual and year would potentially save € 528 million.
Murine and human Langerhans cells express a functional histamine H4 receptor: modulation of cell migration and function
Authors: Gschwandtner M. , Rossbach K. , Dijkstra D. , Bäumer W. , Kietzmann M. , Stark H. , Werfel T. , Gutzmer R. 
Published: November 2009

To cite this article: Gschwandtner M, Rossbach K, Dijkstra D, Bäumer W, Kietzmann M, Stark H, Werfel T, Gutzmer R. Murine and human Langerhans cells express a functional histamine H4 receptor: modulation of cell migration and function. Allergy 2010; 65: 840–849.AbstractBackground:  Histamine is an important mediator of allergic reactions, and recent studies indicated that the function of different types of antigen presenting cells (APC) can be modulated by histamine, in particular via the newly described histamine H4 receptor (H4R). Therefore, we investigated possible interactions of histamine via the H4R on Langerhans cells (LC), which represent the professional APC in the skin and therefore have an important role in the initiation and maintenance of allergic skin diseases.Methods:  The expression of the H4R was evaluated by real‐time PCR, flow cytometry and immunofluorescence staining. The function of the H4R was determined by intracellular flow cytometric measurement of chemokine production and LC migration assays.Results:  Here, we show H4R expression on in vitro generated monocyte‐derived LC (mRNA and protein) and on primary LC from murine and human skin samples (protein). The immunofluorescence staining in murine and human skin samples clearly proved that LC express the H4R in situ. Stimulation with histamine or a H4R agonist downregulated the chemokine (C‐C motif) ligand 2 (CCL2) in human monocyte‐derived LC and primary LC. Prestimulation with a selective H4R antagonist abolished this effect. Moreover, migration of LC from the epidermis was increased after H4R agonist stimulation in ex vivo migration assays using human epidermis and murine in vivo assays.Conclusion:  Our findings show that LC express a functional H4R and point towards a possible pathogenic relevance of the H4R in inflammatory and allergic diseases.
Isolation by distance in a continuous population under stochastic demographic fluctuations
Authors: ROBLEDO‐ARNUNCIO J. J. , ROUSSET F. 
Published: November 2009

AbstractThe local density of individuals is seldom uniform in space and time within natural populations. Yet, formal approaches to the process of isolation by distance in continuous populations have encountered analytical difficulties in describing genetic structuring with demographic heterogeneities, usually disregarding local correlations in the movement and reproduction of genes. We formulate exact recursions for probabilities of identity in continuous populations, from which we deduce definitions of effective dispersal () and effective density (De) that generalize results relating spatial genetic structure, dispersal and density in lattice models. The latter claim is checked in simulations where estimates of effective parameters obtained from demographic information are compared with estimates derived from spatial genetic patterns in a plant population evolving in a heterogeneous and dynamic habitat. The simulations further suggest that increasing spatio‐temporal correlations in local density reduce and generally decrease the product , with dispersal kurtosis influencing their sensitivity to density fluctuations. As in the lattice model, the expected relationship between the product and the genetic structure statistic ar holds under fluctuating density, irrespective of dispersal kurtosis. The product D σ2 between observed census density and the observed dispersal rate over one generation will generally be an upwardly biased (up to 400% in simulations) estimator of in populations distributed in spatially aggregated habitats.
Antagonistic coevolution across productivity gradients: an experimental test of the effects of dispersal
Authors: LOPEZ‐PASCUA L. D. C. , BROCKHURST M. A. , BUCKLING A. 
Published: November 2009

AbstractCoevolution commonly occurs in spatially heterogeneous environments, resulting in variable selection pressures acting on coevolving species. Dispersal across such environments is predicted to have a major impact on local coevolutionary dynamics. Here, we address how co‐dispersal of coevolving populations of host and parasite across an environmental productivity gradient affected coevolution in experimental populations of bacteria and their parasitic viruses (phages). The rate of coevolution between bacteria and phages was greater in high‐productivity environments. High‐productivity immigrants (∼2% of the recipient population) caused coevolutionary dynamics (rates of coevolution and degree of generalist evolution) in low‐productivity environments to be largely indistinguishable from high‐productivity environments, whereas immigration from low‐productivity environments (∼0.5% of the population) had no discernable impact. These results could not be explained by demography alone, but rather high‐productivity immigrants had a selective advantage in low‐productivity environments, but not vice versa. Coevolutionary interactions in high‐productivity environments are therefore likely to have a disproportionate impact on coevolution across the landscape as a whole.
Fitness measures in selection analyses: sensitivity to the overall number of offspring produced in a lifetime
Authors: DUGDALE H. L. , NOUVELLET P. , POPE L. C. , BURKE T. , MACDONALD D. W. 
Published: November 2009

AbstractAge at first (α) and last (ω) breeding are important life‐history traits; however, the direction and strength of selection detected on traits may vary depending on the fitness measure used. We provide the first estimates of lifetime breeding success (LBS) and λind (the population growth rate of an individual) of European badgers Meles meles, by genotyping 915 individuals, sampled over 18 years, for 22 microsatellites. Males are slightly larger than females, and the opportunity for selection was slightly greater for males, as predicted. λind and LBS both performed well in predicting the number of grand‐offspring, and both detected selection for a late ω, until the age of eight. Differential selection (S′α) for an early α, however, was only detected using LBS, not with λind. In declining populations (λind < 1) selection favours reproduction later in life, whereas early reproduction is selected in increasing populations (λind > 1). As 41% of badgers were assigned only one offspring (λind < 1), whereas 40% were assigned more than two (λind > 1), this cancelled out S′α measured by λind.
Ecological niche modelling as an exploratory tool for identifying species limits: an example based on Mexican muroid rodents
Authors: MARTÍNEZ‐GORDILLO D. , ROJAS‐SOTO O. , ESPINOSA de los MONTEROS A. 
Published: November 2009

AbstractNiche conservatism theory suggests that recently diverged sister species share the same ecological niche. However, if the ecological niche evolves as part of the speciation process, the ecological pattern could be useful for recognizing cryptic species. In a broad sense systematists agree that the niche characters could be used for species differentiation. However, to date such characters have been ignored. We used the genetic algorithm for rule‐set production for modelling the ecological niche as a means of inferring ecological divergence in allopatric populations of muroid rodents for which taxonomic identity is uncertain. Our results show that niche differentiation is significant in most of the identified phylogroups. The differentiation is likely associated with natural evolutionary units, which can be identified by applying species concepts based on phylogenetic and ecological patterns (e.g. phylogenetic, cohesive, evolutionary). Even so, the role of the niche partition within phylogenetic reconstruction may be a limited one.
Avian colour perception predicts behavioural responses to experimental brood parasitism in chaffinches
Authors: AVILÉS J. M. , VIKAN J. R. , FOSSøY F. , ANTONOV A. , MOKSNES A. , RØSKAFT E. , STOKKE B. G. 
Published: November 2009

AbstractHosts of cuckoos have evolved defences allowing them to discriminate and reject parasite eggs. Mechanisms of discrimination are mostly visually mediated, and have been studied using approaches that do not account for what the receiver (i.e. host) actually can discriminate. Here, for the first time we apply a perceptual model of colour discrimination to study behavioural responses to natural variation in parasite egg appearance in chaffinches Fringilla coelebs. Discrimination of parasite eggs gradually increased with increasing differences in chromatic contrasts as perceived by birds between parasite and host eggs. These results confirm that colour differences of the eggs as perceived by birds are important integral parts of a matching signal used by chaffinch hosts.
Degeneration patterns of the olfactory receptor genes in sea snakes
Authors: KISHIDA T. , HIKIDA T. 
Published: November 2009

AbstractThe sense of smell relies on the diversity of olfactory receptor (OR) repertoires in vertebrates. It has been hypothesized that different types of ORs are required in terrestrial and marine environments. Here we show that viviparous sea snakes, which do not rely on a terrestrial environment, have significantly lost ORs compared with their terrestrial relatives, supporting the hypothesis. On the other hand, oviparous sea snakes, which rely on a terrestrial environment for laying eggs, still maintain their ORs, reflecting the importance of the terrestrial environment for them. Furthermore, we found one Colubroidea snake (including sea snakes and their terrestrial relatives)‐specific OR subfamily which had diverged widely during snake evolution after the blind snake–Colubroidea snake split. Interestingly, no pseudogenes are included in this subfamily in sea snakes, and this subfamily seems to have been expanding rapidly even in an underwater environment. These findings suggest that the Colubroidea‐specific ORs detect nonvolatile odorants.
Did the introduction of maize into Europe provide enemy‐free space to Ostrinia nubilalis? Parasitism differences between two sibling species of the genus Ostrinia
Authors: PÉLISSIÉ B. , PONSARD S. , TOKAREV Y. S. , AUDIOT P. , PÉLISSIER C. , SABATIER R. , MEUSNIER S. , CHAUFAUX J. , DELOS M. , CAMPAN E. , MALYSH J. M. , FROLOV A. N. , BOURGUET D. 
Published: November 2009

AbstractWe examined whether maize offers enemy‐free space (EFS) to its pest Ostrinia nubilalis, and may thereby have contributed to its divergence from the sibling species, Ostrinia scapulalis, feeding mainly on mugwort, when introduced into Europe five centuries ago. We collected Ostrinia larvae on maize (70 populations, 8425 individuals) and mugwort (10 populations, 1184 individuals) and recorded parasitism using both traditional (counting emerging parasitoids) and molecular methods (detection by specific polymerase chain reaction). The main parasitoid was Macrocentrus cingulum (Braconidae). On mugwort, parasitism was twice that on maize, and parasitoid‐related mortality was 8 times higher. This suggests that maize affords substantial EFS to Ostrinia feeding on it. The lower Mortality:Infestation ratio in maize suggests that O. nubilalis’ immune response might be stronger than that of O. scapulalis. If so, adapting to maize and diverging from O. scapulalis would decrease the impact of parasitism on O. nubilalis at both ecological and evolutionary levels.
Spatial regression techniques for inter‐population data: studying the relationships between morphological and environmental variation
Authors: PEREZ S. I. , DINIZ‐FILHO J. A. F. , BERNAL V. , GONZALEZ P. N. 
Published: November 2009

AbstractUnderstanding the importance of environmental dimensions behind the morphological variation among populations has long been a central goal of evolutionary biology. The main objective of this study was to review the spatial regression techniques employed to test the association between morphological and environmental variables. In addition, we show empirically how spatial regression techniques can be used to test the association of cranial form variation among worldwide human populations with a set of ecological variables, taking into account the spatial autocorrelation in data. We suggest that spatial autocorrelation must be studied to explore the spatial structure underlying morphological variation and incorporated in regression models to provide more accurate statistical estimates of the relationships between morphological and ecological variables. Finally, we discuss the statistical properties of these techniques and the underlying reasons for using the spatial approach in population studies.