bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weighted compromise trees: a method to summarize competing phylogenetic hypotheses
Authors: Sharkey Michael J. , Stoelb Stephanie , Miranda‐Esquivel Daniel R. , Sharanowski Barabara J. 
Published: October 2012

AbstractA new consensus method for summarizing competing phylogenetic hypotheses, weighted compromise, is described. The method corrects for a bias inherent in majority‐rule consensus/compromise trees when the source trees exhibit non‐independence due to ambiguity in terminal clades. Suggestions are given for its employment in parsimony analyses and tree resampling strategies such as bootstrapping and jackknifing. An R function is described that can be used with the programming language R to produce the consensus.
Influence of constraint‐induced movement therapy upon evoked potentials in rats with cerebral infarction
Authors: Joo Hyung W. , Hyun Jung K. , Kim Tae U. , Chae Sang H. , Lee Young I. , Lee Seong J. 
Published: October 2012

AbstractConstraint‐induced movement therapy (CIMT) is an effective treatment promoting motor recovery of upper extremity function in stroke patients. The objective of the present study was to determine the effect of CIMT on the evoked potentials in rats with focal cerebral cortical ischemia induced by endothelin‐1 (ET‐1). Thirty rats were randomly assigned to the sham, infarct or CIMT groups. ET‐1 was injected stereotaxically into the forelimb area of the cerebral cortex in the dominant hemisphere. Custom‐made constraint jackets were applied to limit movement of the unaffected forelimb in the CIMT group. Motor and sensory function of the forelimb was evaluated by a pellet retrieval task and forearm asymmetry test. Electrophysiologic changes were evaluated by motor‐evoked potentials (MEPs) and somatosensory‐evoked potentials (SEPs). The location and extent of cerebral ischemia were confirmed and compared histologically. The CIMT group showed better recovery in the pellet retrieval task. Forelimb use was more symmetrical in the CIMT group. The waveform of the SEP was reversed and delayed in the infarct group, but it was preserved in the CIMT group with amplitude decrease only. The estimated volume of infarction was smaller in the CIMT group, although statistically not significant. The results demonstrate that CIMT can promote recovery of motor function in focal cerebral cortical infarcts, and that recovery may be related to reorganization of the cerebral neuronal network in the somatosensory pathway.
The real war on cancer: the evolutionary dynamics of cancer suppression
Authors: Nunney Leonard 
Published: October 2012

AbstractCancer is a disease of multicellular animals caused by unregulated cell division. The prevailing model of cancer (multistage carcinogenesis) is based on the view that cancer results after a series of (generally somatic) mutations that knock out the genetic mechanisms suppressing unregulated cell growth. The chance of these mutations occurring increases with size and longevity, leading to Peto's paradox: why don't large animals have a higher lifetime incidence of cancer than small animals? The solution to this paradox is evolution. From an evolutionary perspective, an increasing frequency of prereproductive cancer deaths results in natural selection for enhanced cancer suppression. The expected result is a prereproductive risk of cancer across species that is independent of life history. However, within species, we still expect cancer risk to increase with size and longevity. Here, I review the evolutionary model of cancer suppression and some recent empirical evidence supporting it. Data from humans and domestic dogs confirm the expected intraspecific association between size and cancer risk, while results from interspecific comparisons between rodents provide the best evidence to date of the predicted recruitment of additional cancer suppression mechanisms as species become larger or longer lived.
How should we grow cities to minimize their biodiversity impacts?
Authors: Sushinsky Jessica R. , Rhodes Jonathan R. , Possingham Hugh P. , Gill Tony K. , Fuller Richard A. 
Published: October 2012

AbstractUrbanization causes severe environmental degradation and continues to increase in scale and intensity around the world, but little is known about how we should design cities to minimize their ecological impact. With a sprawling style of urban development, low intensity impact is spread across a wide area, and with a compact form of development intense impact is concentrated over a small area; it remains unclear which of these development styles has a lower overall ecological impact. Here, we compare the consequences of compact and sprawling urban growth patterns on bird distributions across the city of Brisbane, Australia. We predicted the impact on bird populations of adding 84 642 houses to the city in either a compact or sprawling design using statistical models of bird distributions. We show that urban growth of any type reduces bird distributions overall, but compact development substantially slows these reductions at the city scale. Urban‐sensitive species particularly benefited from compact development at the city scale because large green spaces were left intact, whereas the distributions of nonnative species expanded as a result of sprawling development. As well as minimizing ecological disruption, compact urban development maintains human access to public green spaces. However, backyards are smaller, which impacts opportunities for people to experience nature close to home. Our results suggest that cities built to minimize per capita ecological impact are characterized by high residential density, with large interstitial green spaces and small backyards, and that there are important trade‐offs between maintaining city‐wide species diversity and people's access to biodiversity in their own backyard.
Toward a loss of functional diversity in stream fish assemblages under climate change
Authors: Buisson Laëtitia , Grenouillet Gaël , Villéger Sébastien , Canal Julie , Laffaille Pascal 
Published: October 2012

AbstractThe assessment of climate change impacts on biodiversity has so far been biased toward the taxonomic identification of the species likely either to benefit from climate modifications or to experience overall declines. There have still been few studies intended to correlate the characteristics of species to their sensitivity to climate change, even though it is now recognized that functional trait‐based approaches are promising tools for addressing challenges related to global changes. In this study, two functional indices (originality and uniqueness) were first measured for 35 fish species occurring in French streams. They were then combined to projections of range shifts in response to climate change derived from species distribution models. We set out to investigate: (1) the relationship between the degrees of originality and uniqueness of fish species, and their projected response to future climate change; and (2) the consequences of individual responses of species for the functional diversity of fish assemblages. After accounting for phylogenetic relatedness among species, we have demonstrated that the two indices used measure two complementary facets of the position of fish species in a functional space. We have also rejected the hypothesis that the most original and/or less redundant species would necessarily experience the greatest declines in habitat suitability as a result of climate change. However, individual species range shifts could lead simultaneously both to a severe decline in the functional diversity of fish assemblages, and to an increase in the functional similarity among assemblages, supporting the hypothesis that disturbance favors communities with combination of common traits and biotic homogenization as well. Our findings therefore emphasize the importance of going beyond the simple taxonomic description of diversity to provide a better assessment of the likely future effects of environmental changes on biodiversity, thus helping to design more effective conservation and management measures.
Long‐term Follow‐up Helicobacter Pylori Reinfection Rate and Its Associated Factors in Korea
Authors: Kim Min Soo , Kim Nayoung , Kim Sung Eun , Jo Hyun Jin , Shin Cheol Min , Lee Sang Hyub , Park Young Soo , Hwang Jin‐Hyeok , Kim Jin‐Wook , Jeong Sook‐Hyang , Lee Dong Ho , Kim Jung Mogg , Jung Hyun Chae 
Published: October 2012

AbstractBackgroundThe reinfection rate of Helicobacter pylori has been reported to be low in developed countries but high in developing countries. The aim of this study is to evaluate the long‐term reinfection rate of H. pylori and to investigate its associated risk factors in South Korea.MethodsDuring 2003–2010, H. pylori‐positive 970 patients received standard proton pump inhibitor (PPI)‐based triple eradication therapy, and follow‐up H. pylori tests were performed with 13C urea breath test or invasive tests (Giemsa histology, CLO test, and culture) 4 weeks after completion of treatment. A total of 331 patients who were maintained an H. pylori‐eradicated state at 1 year after eradication were divided into two groups according to reinfection. For the evaluation of risk factors of reinfection, gender, age, smoking, alcohol, income, education, gastrointestinal symptoms, clinical diagnosis, histologic atrophic gastritis or intestinal metaplasia, and clarithromycin resistance were analyzed.ResultsThe follow‐up period was 18–95 months (mean: 37.1 months), and H. pylori reappeared in 36 of 331 patients (10.9%), resulting in the annual reinfection rate of 3.51% per year. Multivariate analysis showed that male gender (HR 2.28; 95% CI, 1.05–5.00, p = .037) and low monthly family income (≤5000$ vs >5000$) (HR 3.54; 95% CI, 1.08–11.67, p = .038) were associated with H. pylori reinfection.ConclusionThis long‐term reinfection rate of H. pylori stayed rather low (3.51% per year), and male and low income determined the reinfection, factors already known to be important for H. pylori infection.
T cells and their eons‐old obsession with MHC
Authors: Yin Lei , Scott‐Browne James , Kappler John W. , Gapin Laurent , Marrack Philippa 
Published: October 2012

SummaryT cells bearing receptors made up of α and β chains (TCRs) usually react with peptides bound to major histocompatibility complex proteins (MHC). This bias could be imposed by positive selection, the phenomenon that selects thymocytes to mature into T cells only if the TCRs they bear react with low but appreciable affinity with MHC + peptide combinations in the thymus cortex. However, it is also possible that the polypeptides of TCRs themselves do not have random specificities but rather are biased toward reaction with MHC. Evolution would therefore have selected for a collection of TCR variable elements that are prone to react with MHC. If this were to be so, positive selection would act on thymocytes bearing a pre biased collection of TCRs to pick out those that react to some extent, but not too well, with self MHC + self‐peptides. A problem with studies of this evolutionary idea is the fact that there are many TCR variable elements and that these differ considerably in the amino acids with which they contact MHC. However, recent experiments by our group and others suggest that one group of TCR variable elements, those related to the mouse Vβ8 family, has amino acids in their CDR2 regions that consistently bind a particular site on an MHC α‐helix. Other groups of variable elements may use different patterns of amino acids to achieve the same goal. Mutation of these amino acids reduces the ability of T cells and thymocytes to react with MHC. These amino acids are present in the variable regions of distantly related species such as sharks and human. Overall the data indicate that TCR elements have indeed been selected by evolution to react with MHC proteins. Many mysteries about TCRs remain to be solved, including the nature of auto‐recognition, the basis of MHC allele specificity, and the very nature and complexity of TCRs on mature T cells.
A 5‐year survey (2007–2011) of enteric viruses in Korean aquatic environments and the use of coliforms as viral indicators
Authors: Lee Gyu‐Cheol , Jheong Weon‐Hwa , Kim Min‐jeong , Choi Don Hyeok , Baik Kyoung‐Hee 
Published: October 2012

AbstractThree hundred and thirty‐nine water samples obtained from 90 locations in Korea from 2007 to 2011 were tested for the presence of enteric viruses (EV), total coliforms (TC), and fecal coliforms (FC). A total culturable virus assay revealed that 89 samples (26.3%) were positive for EVs, the average concentration being 5.8 most probable number (MPN)/100 L. The Han river basin exhibited the highest contamination by EVs (occurrence, 41.3%; average concentration, 24.0 MPN/100 L). EV contamination was found more frequently in river water (occurrence, 33.6%; concentration, 8.4 MPN/100 L) than in lake water or groundwater. The concentration of EVs was highest in spring (7.7 MPN/100 L), whereas it was found most frequently in winter (36.1%). The number of TCs ranged from 0 – 1.2 × 105 colony forming units (CFU)/100 mL and that of FCs from 0–6.2 × 103 CFU/100 mL per sample. Statistical analyses showed that the presence of EVs, TCs and FCs did not correlate significantly with temperature or turbidity. In addition, presence of TCs and FCs was not significantly correlated with presence of EVs. In conclusion, TCs and FCs may not be accurate microbial indicators of waterborne EVs in Korean aquatic environments.
Macrostress: do large‐scale ecological patterns exist in the glucocorticoid stress response of vertebrates?
Authors: Jessop Tim S. , Woodford Romy , Symonds Matthew R. E. 
Published: October 2012

SummaryDisturbances, or stressors, are pervasive in nature and profoundly influence fitness of individuals and, ultimately, species extinction risk. Glucocorticoid (GC) hormones affect multiple physiological and behavioural traits regulating the responses of vertebrates to stressors. Current understanding of what influencesGCstress response variation among species is poor. However, identifying environmental causes of species‐level variation in theGCstress response is important to understanding macroevolutionary patterns in this key physiological system and potentially offers a metric for evaluating species risk to global change.We tested whetherGCstress response of 22 reptile and 66 bird species exposed to a uniform capture stress protocol could be predicted from aGCstressor space model. This model predicts that species‐level variation inGCs results from multivariate selection from environmental gradients and species‐specific metabolic sensitivities. Thus, these multivariate selection interactions delimit the cumulative selection intensity causingGCstress response variation among vertebrates.Using phylogenetic generalized least square regression analysis, we ranked models incorporating putative variables pertaining to the corticosterone stress response (CSR) for reptiles and birds separately. The top‐ranked models explained between 14% and 33% of species variation in theCSR. Models indicated that combinations of variables including increasing body mass, net primary productivity and latitude influenced GC stress responsiveness in reptiles and birds.We conclude thatGCstress response variation among species represents, in part, evolution to species‐specific traits and large‐scale environmental variation. Further improvement to predicting species variation inGCstress response could be achieved by expanding our stressor space model to integrate microevolutionary and ecological processes.There is a pressing need to identify physiological traits that predict species responses to environmental change. Conceptually, the use of plasmaGClevels as a species‐specific marker for environmental tolerance could be plausible. However, we identify three major knowledge gaps and ensuing research areas to aid understanding of the utility of variation inGCstress response as a metric for inferring how species might respond to global change.
Niche dimensionality links biodiversity and invasibility of microbial communities
Authors: Eisenhauer Nico , Schulz Wiebke , Scheu Stefan , Jousset Alexandre 
Published: October 2012

SummaryBiodiversity is a central factor driving community invasibility. Diverse communities exploit resources more efficiently, leaving less free niche space available to invaders. Niche partitioning, however, is only possible in complex resource environments, and we hypothesized that resource richness drives the biodiversity–invasibility relationship.We tested the effect of two biodiversity indices, taxonomic richness and functional dissimilarity, on the invasibility ofPseudomonas fluorescenscommunities in microcosms of varying resource richness, herein used as a proxy for niche dimensionality, because differentP. fluorescensgenotypes differed in their ability to use those resources.Invader success was negatively correlated with the diversity of the resident community, with functional dissimilarity being of greater significance than taxonomic richness. Varied niche dimensionality revealed different mechanisms determining community invasibility: at low niche dimensionality, invasibility was driven by the presence of particular genotypes (identity effect) rather than by the biodiversity of the resident community. At high niche dimensionality, functional dissimilarity increased community productivity and reduced invasion, most likely through complementarity effects.The results show that functionally dissimilar bacterial strains efficiently exploit their environment, reducing the resources available for invasive species. These findings call for the preservation of functionally dissimilar taxa to warrant resistance of communities against invasive species, in particular, in environments of high niche dimensionality.
The joint contribution of insomnia and obstructive sleep apnoea on sickness absence
Authors: Sivertsen Børge , Björnsdóttir Erla , Øverland Simon , Bjorvatn Bjørn , Salo Paula 
Published: October 2012

SummarySeveral studies have indicated a high degree of overlap between insomnia and obstructive sleep apnoea, but little is known regarding how the overlap may affect adverse outcomes associated with each of the disorders. The aim of the current study was to examine the separate and combined effects of symptoms of insomnia and obstructive sleep apnoea on long‐term sick leave. We used an historical cohort design with 4 years follow‐up. Information on sick leave was obtained from Norwegian official registry data, and merged with health information from the Hordaland Health Study in western Norway, 1997–99. A total of 6892 participants aged 40–45 years were assessed for self‐reported symptoms of insomnia and obstructive sleep apnoea (snoring and breathing cessations), as well as confounding factors. The level of overlap between insomnia and obstructive sleep apnoea was low (7–12%). Both insomnia and obstructive sleep apnoea alone were significant risk factors for subsequent sick leave after adjusting for confounding factors (odds ratios ranging from 1.4 to 2.3). Having comorbid insomnia and obstructive sleep apnoea increased the risk significantly. There was an additive interaction effect between the two conditions in the unadjusted analyses, but this was reduced to a non‐significant level when adjusting for confounders. This study is the first to report the separate and combined effects of insomnia and obstructive sleep apnoea on any adverse outcome. Having both insomnia and obstructive sleep apnoea increased the risk of later sick leave, but there was no evidence of an independent synergy effect of the two conditions.
Coincidence of maximum severity of powdery mildew on grape leaves and the carbohydrate sink‐to‐source transition
Authors: Merry A. M. , Evans K. J. , Corkrey R. , Wilson S. J. 
Published: October 2012

Grapevine leaves infected with powdery mildew are a source of inoculum for fruit infection. Leaves emerging on a single primary shoot of Vitis vinifera cv. Cabernet Sauvignon were exposed to average glasshouse temperatures of 18°C (0·23 leaves emerging/day) or 25°C (0·54 leaves emerging/day). All leaves on 8–10 shoots with approximately 20 leaves each were inoculated with Erysiphe necator conidia to assess disease severity after 14 days in the 25°C glasshouse. Two photosynthetic ‘source’ leaves per shoot on the remaining 8–10 shoots were treated with 14CO2 to identify, by autoradiography, the leaf position completing the carbohydrate sink‐to‐source transition. There was a clear association between the mean modal leaf position for maximum severity of powdery mildew (position 3·7 for 18°C; position 4·4 for 25°C) and the mean position of the leaf completing the sink‐to‐source transition (position 3·8 for 18°C; position 4·7 for 25°C). The mean modal leaf position for the maximum percentage of conidia germinating to form secondary hyphae was 4·2 for additional plants grown in the 25°C glasshouse. A higher rate of leaf emergence resulted in a greater proportion of diseased leaves per shoot. A Bayesian model, consisting of component models for disease severity and leaf ontogenic resistance, had parameters representing the rate and magnitude of pathogen colonization that differed for shoots developing in different preinoculation environments. The results support the hypothesis that the population of leaves in a vineyard capable of supporting substantial pathogen colonization will vary according to conditions for shoot development.
Tracing the origins of White Tip disease of Cirsium arvense and its causal agent, Phoma macrostoma
Authors: EVANS H C , SEIER M K , DERBY J‐A , FALK S , BAILEY K L 
Published: October 2012

SummaryCirsium arvense (Asteraceae) is known as creeping thistle in its native range in the UK and Canada thistle in its invasive North American range. Recently, the fungus Phoma macrostoma was registered in Canada as a bioherbicide in turfgrass, where it causes severe chlorosis (White Tip disease) and death of C. arvense and other broadleaved weeds. It was hypothesised that the disease originated in the UK on its thistle host and, therefore, that fungal isolates from both countries should be biologically and genetically similar. Twenty‐six strains in the genus Phoma– isolated during surveys in the UK – were compared morphologically with the type culture of P. macrostoma, tested for bioherbicidal activity using the inoculum mat bioassay and genetically screened with bioherbicide‐specific primers. White tip disease was found to be restricted to the eastern and southern counties of England. Phoma macrostoma was isolated consistently from diseased bleached tissues. Bioherbicidal isolates of P. macrostoma occupy a unique clade, which is phylogenetically distinct but morphologically indistinguishable from the type culture. Most isolates from the UK had the same bioherbicidal activity and similar genetic make‐up as strain SRC 94‐44B, the active ingredient in the registered Canadian product. The origin of all bioherbicidal strains found to date has a clear presence in both Canada and the UK, with strong genetic similarities, supporting the view of a common ancestry. Thus, on the evidence presented, the ‘white tip’ clade of P. macrostoma evolved in southern England. Therefore, the bioherbicide based on strain SRC 94‐44B should also be eligible for registration in the UK, based on the pest risk assessment data already available.