bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory sample turnaround times: do they cause delays in the ED?
Authors: Gill Dipender , Galvin Sean , Ponsford Mark , Bruce David , Reicher John , Preston Laura , Bernard Stephani , Lafferty Jessica , Robertson Andrew , Rose‐Morris Anna , Stoneham Simon , Rieu Romelie , Pooley Sophie , Weetch Alison , McCann Lloyd 
Published: September 2010

AbstractObjectives  Blood tests are requested for approximately 50% of patients attending the emergency department (ED). The time taken to obtain the results is perceived as a common reason for delay. The objective of this study was therefore to investigate the turnaround time (TAT) for blood results and whether this affects patient length of stay (LOS) and to identify potential areas for improvement.Methods  A time‐in‐motion study was performed at the ED of the John Radcliffe Hospital (JRH), Oxford, UK. The duration of each of the stages leading up to receipt of 101 biochemistry and haematology results was recorded, along with the corresponding patient's LOS.Results  The findings reveal that the mean time for haematology results to become available was 1 hour 6 minutes (95% CI: 29 minutes to 2 hours 13 minutes), while biochemistry samples took 1 hour 42 minutes (95% CI: 1 hour 1 minute to 4 hours 21 minutes), with some positive correlation noted with the patient LOS, but no significant variation between different days or shifts.Conclusions  With the fastest 10% of samples being reported within 35 minutes (haematology) and 1 hour 5 minutes (biochemistry) of request, our study showed that delays can be attributable to laboratory TAT. Given the limited ability to further improve laboratory processes, the solutions to improving TAT need to come from a collaborative and integrated approach that includes strategies before samples reach the laboratory and downstream review of results.
Patterns of colonization, evolution and gene flow in species of the genusPatellain the Macaronesian Islands
Authors: SÁ‐PINTO ALEXANDRA , BRANCO MADALENA , SAYANDA DIOGO , ALEXANDRINO PAULO 
Published: September 2010

AbstractThe study of phylogeographical patterns may contribute to a better understanding of factors affecting the dispersal of organisms in ecological and historical times. For intertidal organisms, islands are particularly suitable models allowing the test of predictions related to the efficacy of pelagic larvae dispersal. Here, we study the phylogeographical patterns and gene flow within three groups of species of the genusPatellapresent in the Macaronesian Islands that have been previously shown to be monophyletic. The genetic variability of around 600 bp of the mitochondrial gene cytochromecoxidase subunit I was studied by single strand conformation polymorphism and/or sequencing for seven species of limpets. A total of 420 samples were analysed from the Macaronesian archipelagos, North Africa, and Atlantic and Mediterranean shores of the Iberian Peninsula. No clear geographical pattern or temporal congruence was found between the three groups of species, pointing to independent histories and colonization events. However, for the three groups, the split between the Macaronesian and the mainland forms most probably occurred before 3.9 million years ago, predating the establishment of the current circulation patterns. The presence of pelagic larvae in these species is shown to be insufficient to ensure gene flow between continental and Macaronesian populations and between the Macaronesian archipelagos. In the endangered Azorean populations ofPatella candei, there is restricted gene flow to Flores and Graciosa.
Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps
Authors: STONE GRAHAM N. , ATKINSON RACHEL J. , ROKAS ANTONIS , ALDREY JOSÉ‐LUIS NIEVES , MELIKA GEORGE , Ács ZOLTAN , CSÓKA GYÖRGY , HAYWARD ALEXANDER , BAILEY RICHARD , BUCKEE CAROLINE , McVEAN GILEAN A. T. 
Published: September 2010

AbstractOak gallwasps (Hymenoptera, Cynipidae, Cynipini) are one of seven major animal taxa that commonly reproduce by cyclical parthenogenesis (CP). A major question in research on CP taxa is the frequency with which lineages lose their sexual generations, and diversify as purely asexual radiations. Most oak gallwasp species are only known from an asexual generation, and secondary loss of sex has been conclusively demonstrated in several species, particularly members of the holarctic genus Andricus. This raises the possibility of widespread secondary loss of sex in the Cynipini, and of diversification within purely parthenogenetic lineages. We use two approaches based on analyses of allele frequency data to test for cryptic sexual generations in eight apparently asexual European species distributed through a major western palaearctic lineage of the gallwasp genus Andricus. All species showing adequate levels of polymorphism (7/8) showed signatures of sex compatible with cyclical parthenogenesis. We also use DNA sequence data to test the hypothesis that ignorance of these sexual generations (despite extensive study on this group) results from failure to discriminate among known but morphologically indistinguishable sexual generations. This hypothesis is supported: 35 sequences attributed by leading cynipid taxonomists to a single sexual adult morphospecies, Andricus burgundus, were found to represent the sexual generations of at least six Andricus species. We confirm cryptic sexual generations in a total of 11 Andricus species, suggesting that secondary loss of sex is rare in Andricus.
Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe
Authors: RAJABI‐MAHAM HASSAN , ORTH ANNIE , BONHOMME FRANÇOIS 
Published: September 2010

AbstractFew genetic data document the postglacial history of the western house mouse, Mus musculus domesticus. We address this by studying a sample from the southeastern tip of the Fertile Crescent in the Iranian province of Ahvaz. Including other published and unpublished data from France, Germany, Italy, Bulgaria, Turkey and other places in Iran, altogether 321 mitochondrial D‐loop sequences are simultaneously analysed. The patterns of coalescence obtained corroborate the classical proposal according to which the Fertile Crescent is where commensalism with humans has started in the Western Hemisphere, and from where the subspecies has expanded further west. Our data also clearly show that despite multiple colonisations and long‐range transportation, there is still a rather high ΦST of 0.39. The original expansion signal is still recognisable, with two well‐separated derived clades, allowing us to propose a hypothetical scenario in which expansion toward Europe and Asia Minor took at least two routes, tentatively termed the Mediterranean and the Bosphorus/Black Sea routes. This scenario resembles that of another domesticated species, the goat, and fits with the known progression of Neolithic culture. Given the concomitance of both phenomena around 12 000 years ago, we propose a recalibration of the D‐loop mutation rate to a much faster tick of ~40% per site per million years (Myr). This value should be used for intrasubspecific polymorphism, while the interspecific rate in Mus is presently estimated at 6–10%/site/Myr. This is in keeping with the now well recognised fact that only a subfraction of segregating mutations go to fixation.
Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples
Authors: NAPOLITANO CONSTANZA , BENNETT MAGDALENA , JOHNSON WARREN E. , O’BRIEN STEPHEN J. , MARQUET PABLO A. , BARRÍA IVÁN , POULIN ELIE , IRIARTE AGUSTÍN 
Published: September 2010

AbstractThe carnivore community of the altiplano ecosystem of the high Andes, including the Andean mountain cat (Leopardus jacobita) and pampas cat (Leopardus colocolo), is one of the least studied in the world. We determined the origin of 186 carnivore samples (184 faeces and two skulls) collected above 3000 m above sea level in northern Chile, including 33 from the Andean mountain cat and 75 from the pampas cat using diagnostic molecular genetic sequence variation. We determined for the first time food habits, habitat and physiographic associations, and general patterns of molecular genetic variation of the Andean mountain cat and the pampas cat in Chile. Both species had narrow dietary niches dominated by small rodents and there was a wide overlap in diet composition (0.82), suggesting low levels of prey partitioning between species. The mountain viscacha (Lagidium viscacia) made up a large proportion of the biomass of the diet of both species, especially for the Andean mountain cat (93.9% vs. 74.8% for the pampas cat), underscoring the importance of further research and conservation focus on this vanishing prey species. Although the probability of finding Andean mountain cat scats increased with altitude and slope, there was substantial geographical overlap in distribution between species, revealing that the pampas cat distribution includes high‐altitude grassland habitats. The Andean mountain cat had relatively low levels of mitochondrial DNA (mtDNA) genetic variation (two mtDNA haplotypes) compared with the pampas cat (17 mtDNA haplotypes), suggestive of a distinct evolutionary history and relatively smaller historic populations. These insights will facilitate and provide tools and hypotheses for much‐needed research and conservation efforts on these species and this ecosystem.
Postglacial range expansion from northern refugia by the wood frog,Rana sylvatica
Authors: LEE‐YAW JULIE A. , IRWIN JASON T. , GREEN DAVID M. 
Published: September 2010

AbstractAlthough the range dynamics of North American amphibians during the last glacial cycle are increasingly better understood, the recolonization history of the most northern regions and the impact of southern refugia on patterns of intraspecific genetic diversity and phenotypic variation in these regions are not well reconstructed. Here we present the phylogeographic history of a widespread and primarily northern frog,Rana sylvatica. We surveyed 551 individuals from 116 localities across the species’ range for a 650‐bp region of the NADH dehydrogenase subunit 2 and tRNATRPmitochondrial genes. Our phylogenetic analyses revealed two distinct clades corresponding to eastern and western populations, as well as a Maritime subclade within the eastern lineage. Patterns of genetic diversity support multiple refugia. However, high‐latitude refugia in the Appalachian highlands and modern‐day Wisconsin appear to have had the biggest impact on northern populations. Clustering analyses based on morphology further support a distinction between eastern and western wood frogs and suggest that postglacial migration has played an important role in generating broad‐scale patterns of phenotypic variation in this species.
Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin‐encoding bacteriophage
Authors: DEGNAN PATRICK H. , MORAN NANCY A. 
Published: September 2010

AbstractThe facultative endosymbiont of aphids, Hamiltonella defensa, kills parasitoid wasp larvae, allowing aphid hosts to survive and reproduce. This protection may depend on toxins that are encoded by the genomes of H. defensa and of its bacteriophage (APSE). Strains of H. defensa vary in degree of protection conferred upon Acyrthosiphon pisum (pea aphid). Although H. defensa is known to undergo some horizontal transmission among aphid maternal lineages, divergence, recombination, and population structure in H. defensa and APSE have not been characterized. We performed a multilocus sequence analysis of 10 bacterial and five phage loci for strains isolated from A. pisum and other aphid species. The H. defensa chromosome was found to be largely clonal, allowing us to generate a well‐resolved H. defensa strain phylogeny. In contrast, APSE chromosomes undergo recombination and numerous H. defensa strains have probably lost the phage. Within a set of H. defensa strains that are indistinguishable on the basis of chromosomal genes or restriction digests of chromosomal fragments, loss of APSE is associated with decreased protection, strongly suggesting that APSE‐encoded genes contribute to the defensive phenotype. Thus, homologous recombination of APSE genes and sexual transmission of symbionts and phage are likely factors influencing the exchange of ecologically important genes among symbionts. Although H. defensa has been lost, transferred and gained within A. pisum, one subclade of H. defensa appears to be universal within a subclade of the aphid genus Uroleucon, suggesting a transition from facultative, horizontal transmission to strictly vertical inheritance.
Colonization genetics of an animal‐dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington
Authors: YANG S. , BISHOP J. G. , WEBSTER M. S. 
Published: September 2010

AbstractPopulation founding and spatial spread may profoundly influence later population genetic structure, but their effects are difficult to quantify when population history is unknown. We examined the genetic effects of founder group formation in a recently founded population of the animal‐dispersed Vaccinium membranaceum (black huckleberry) on new volcanic deposits at Mount St Helens (Washington, USA) 24 years post‐eruption. Using amplified fragment length polymorphisms and assignment tests, we determined sources of the newly founded population and characterized genetic variation within new and source populations. Our analyses indicate that while founders were derived from many sources, about half originated from a small number of plants that survived the 1980 eruption in pockets of remnant soil embedded within primary successional areas. We found no evidence of a strong founder effect in the new population; indeed genetic diversity in the newly founded population tended to be higher than in some of the source regions. Similarly, formation of the new population did not increase among‐population genetic variance, and there was no evidence of kin‐structured dispersal in the new population. These results indicate that high gene flow among sources and long‐distance dispersal were important processes shaping the genetic diversity in this young V. membranaceum population. Other species with similar dispersal abilities may also be able to colonize new habitats without significant reduction in genetic diversity or increase in differentiation among populations.
Landscape characteristics influence morphological and genetic differentiation in a widespread raptor (Buteo jamaicensis)
Authors: HULL JOSHUA M. , HULL ANGUS C. , SACKS BENJAMIN N. , SMITH JEFF P. , ERNEST HOLLY B. 
Published: September 2010

AbstractLandscape‐scale population genetic structure in vagile vertebrates was commonly considered to be a contradiction in terms whereas recent studies have demonstrated behaviour and habitat associated structure in several such species. We investigate whether landscape features influence morphological and genetic differentiation in a widespread, mobile raptor. To accurately describe genetic differentiation associated with regional landscape factors, we first investigated subspecies relationships at a continental scale. We used 17 microsatellite loci and five morphological measurements to investigate differentiation between eastern and western subspecies of red‐tailed hawks (Buteo jamaicensis) and to identify patterns between differentiation and habitat within western North America. Bayesian and frequency‐based analyses of microsatellite data revealed clear distinctions betweenB. j. borealis(eastern) andB. j. calurus(western) samples. Furthermore, hawks sampled in Texas were stouter than those collected from the Rocky Mountains and farther west. Among western samples, birds from the Great Basin, Rocky Mountains, and Washington were significantly different in morphology than those from Oregon and California. We identified a pattern of isolation by distance among western breeding sites around the Sierra Nevada. Given the long‐range dispersal capabilities of raptors, this pattern suggests that population‐specific habitat preferences, corresponding with habitat breaks between eastern and western slopes of the Sierra Nevada, and/or regionally variable population densities limit migration between the Mediterranean habitat of central California and the xeric habitats of southern California and interior west. We suggest habitat preferences and regionally disparate population densities may play a role in shaping genetic structure in vagile avian taxa.
On the origin of non‐tidal flaser bedding in point bar deposits of the river Ajay, Bihar and West Bengal, NE India
Authors: BHATTACHARYA ASOKKUMAR 
Published: September 2010

ABSTRACTFlaser bedding of non‐tidal origin has been described from point bar deposits of the Ajay river, NE India. Mud drapes are deposited during waning flood phases. The preferential accumulation of curled, desiccated mud laminae in ripple troughs during periods of exposure produces mud streaks resembling classical flaser bedding. This process of non‐tidal flaser formation is unlike the common tidal origin related to flood and ebb cycles, and the less common mechanism of formation in fluvial systems by deposition of mud in ripple troughs after floods.
Response of reef coral communities to sea‐level rise: a Holocene model from Mauritius (Western Indian Ocean)
Authors: MONTAGGIONI LUCIEN F. , FAURE GÉRARD 
Published: September 2010

ABSTRACTThe fringing reef at Pointe‐au‐Sable (Mauritius, Indian Ocean) was used to examine the effects of Holocene sea‐level rise on coral growth. This reef is about 1000 m wide and comprises a forereef slope (30 m maximum depth), a narrow reef crest and a very shallow backreef (1·5 m maximum depth).Four major coral communities were recognized, which developed within relatively narrow depth ranges: a Pachyseris/Oulophyllia community (deeper than 20 m), an Acropora‘tabulate’Faviid community (20–6 m); a robust branching Acropora community (less than 6 m) and a Pavona community (less than 10m). Three high‐recovery cores show the Holocene reef sequence is a maximum of 19·3 m thick and comprises four coral biofacies which are similar to counterparts identified in modern communities: robust branching, tabular‐branching, robust branching‐domal and foliaceous coral facies.A minimum sea‐level curve for the past 7500 years was constructed. Using distribution patterns of coral biofacies and radiocarbon dates from corals, reconstruction of reef growth history indicates that both offshore and onshore reef zones were developing coevally, aggrading at rates of 4·3 mm year−1 from 6900 years B.P. The reef caught up with sea‐level only after sea‐level stabilized. Changes in coral community and reef growth rates were driven principally by increasing water agitation due to the decrease in accommodation space. Based on the composition of the successive coral assemblages, the reef appears to have grown through successive equilibrium stages.
Flow parameters of turbidity currents in a low‐sinuosity giant deep‐sea channel
Authors: KLAUCKE INGO , HESSE R. , RYAN W. B. F. 
Published: September 2010

ABSTRACTFlow parameters (velocity and density) for turbidity currents in the Northwest Atlantic Mid‐Ocean Channel (NAMOC) have been determined based on two different approaches, channel geometry and grain‐size distributions of turbidites. Channel geometry has been obtained by a quantitative morphological analysis of the NAMOC which shows three genetically different segments in the upper 2000 km: (1) an upper 350 km‐long ‘equilibrium channel’, (2) a middle 700 km‐long ‘modified equilibrium channel’and (3) a lower ‘basement‐controlled channel’which is more than 1000 km‐long. In contrast to other meandering submarine channels the NAMOC has very low sinuosities and gradients. A consistently higher right‐hand levee limits mean flow velocities to 3ms−1 and channel geometry indicates mean flow velocities of 0·86 m s−1 that decrease within the equilibrium channel to 0·05 m s−1. Grain‐size distributions on the levees and in the channel suggest strong vertical velocity and density gradients for bank‐full flows with velocities of up to 8 m s−1 and excess densities up to 87 kg m−3 at the base, and 0·45 m s−1 and 4 kg m−3 at the top. The internal shear produced by these strong vertical gradients results in a decoupling of the current head and body. Channel geometry appears to be mainly the result of the slowly moving dilute body of the current.
Facies analysis and correlation of high‐order sequences in middle–outer ramp successions: variations in exported carbonate on basin‐wide δ13Ccarb (Kimmeridgian, NE Spain)
Authors: BÁDENAS BEATRIZ , AURELL MARC , GRÖCKE DARREN R. 
Published: September 2010

AbstractCarbonate mud that accumulated in the deep parts of a late Kimmeridgian carbonate ramp (Iberian Basin, NE Spain) was partly derived by resedimentation from shallow water production areas. High‐frequency sea‐level changes, probably driven by climatic changes in tune with precession and short‐eccentricity cycles, affected carbonate production and the amount of exported sediment. Facies analysis and correlation of three outcrops located in middle and outer ramp settings allows a comparison of high‐order sequences (bundles of beds and sets of bundles) across a ramp transect and an assessment of the carbonate factory. Analysis of the storm deposits found in middle ramp settings identifies deepening to shallowing high‐frequency cycles based on the level of exported carbonate. In outer ramp areas, many of the bundles exhibit a thinning trend, indicating a progressive decrease of carbonate production and hence, carbonate export during periods of high‐frequency sea‐level rise. δ13Ccarb values show a gradual increase through the studied long‐term transgressive interval ranging from 1·5‰ to 2·8‰. Within this long‐term evolutionary trend, short‐term δ13Ccarb fluctuations occur that correspond with some of the high‐order cycles defined from sedimentary facies analysis. These short‐term δ13Ccarb shifts are interpreted as shifts in carbonate export from shallow reef regions to the outer ramp. A consequence of this study is that variation in δ13Ccarb can be used for correlation in outer ramp successions, at least on a basin‐wide scale.
Climatic control on Quaternary fluvial sedimentology of a Fenland Basin river, England
Authors: BRIANT REBECCA M. , BATEMAN MARK D. , RUSSELL COOPE G. , GIBBARD PHILIP L. 
Published: September 2010

AbstractUnderstanding and interpreting climate response from ancient fluvial deposits requires a combined approach of detailed sedimentological description and interpretation, local climate proxies, and the accurate comparison of these sequences with further independent climate records. Application of these multiple lines of evidence is particularly effective in the Quaternary Period, where higher resolution and more detailed palaeoenvironmental reconstruction are possible. This paper presents results from a Devensian (Weichselian) age sequence in northern Fenland, England, that integrates these approaches. Detailed sedimentological description has identified three fluvial facies associations overlain by a period of ice‐wedge cast formation. Fossil plant and coleopteran material within these sediments have been studied to provide palaeoenvironmental reconstructions for the local landscape, including quantitative temperature estimates using the mutual climatic range method on fossil Coleoptera. In addition, joint application of radiocarbon and optically stimulated luminescence (OSL) dating allows this sequence to be compared with the stacked marine isotope record, although dates do not agree well at the limit of the radiocarbon technique. Sedimentological interpretations, palaeoenvironments and global ice‐volume variations (a proxy for climatic severity) are all in agreement and show clearly how the River Nene responded to subtle changes in climate and vegetation cover during the Devensian (Weichselian) Stage. The level of detail possible in this reconstruction shows the importance of this approach in understanding fluvial response to past climate changes.