bluuebunny/crossref_metadata_2025_split huggingface dataset:
The palaeoxylological record of Metapodocarpoxylon libanoticum (Edwards) Dupéron‐Laudoueneix et Pons and the Gondwana Late Jurassic–Early Cretaceous continental biogeography
Authors: Philippe M. , Cuny G. , Bamford M. , Jaillard E. , Barale G. , Gomez B. , Ouaja M. , Thévenard F. , Thiébaut M. , Von Sengbusch P. 
Published: June 2010

AbstractAim  Vertebrates, palynomorphs and leaf floras each give a different picture of continental biogeography of Northern Gondwana during the Middle Jurassic–Early Cretaceous interval. A new biogeographical marker is required to get a clearer picture.Location  Northern part of the Gondwana during the Middle Jurassic–Early Cretaceous interval.Methods  Comparisons and correlations of wood data from the literature and new material.Results  We have selected Metapodocarpoxylon Dupéron‐Laudoueneix et Pons because it has a restricted distribution, temporally and geographically; it is a well‐defined Mesozoic fossil wood monospecific genus, and there are wide‐ranging data on its distribution.Conclusions  Metapodocarpoxylon distribution draws a clear latitudinal belt extending from Lebanon westward to Peru. Climate being the main factor of plant distribution at a global scale, the Metapodocarpoxylon area probably underlines a climatic belt. This has several implications, for example, choosing among different Global Circulation Models or discussing dinosaur distribution.
Regionalization of the avifauna of the Baja California Peninsula, Mexico: a parsimony analysis of endemicity and distributional modelling approach
Authors: Rojas‐Soto Octavio R. , Alcántara‐Ayala Othón , Navarro Adolfo G. 
Published: June 2010

AbstractAim To analyse the distributional patterns of the Baja California Peninsula's resident avifauna, and to generate a regionalization based on a method that uses a parsimony analysis (parsimony analysis of endemicity, PAE) of point data and modelled potential distributions.Location The Baja California Peninsula, Mexico.Methods A data base was constructed containing records of 113 species of resident terrestrial birds present in the Baja California Peninsula. Records and localities were obtained from the literature and from specimens housed in scientific collections world‐wide. Raw data points and potential distribution maps obtained using the software Genetic Algorithms for Rule‐set Prediction (GARP), were analysed with PAE.Results The data base consisted of 4164 unique records (only one combination of species/locality) belonging to 113 terrestrial resident bird species, in a total of 809 localities. From the point distribution matrix, the analysis generated 500 equally parsimonious trees, from which a strict consensus cladogram with 967 steps was obtained. The cladogram shows a basal polytomy and some geographical correspondence of a few resolved groups obtained in the analysis. These results do not allow the recognition of areas defined by avifaunistic associations. From the potential distribution matrix, the analysis generated 501 equally parsimonious trees, and a strict consensus cladogram of 516 steps was obtained. The cladogram shows a higher resolution because of the number of resolved groups with better geographical correspondence and therefore regions are well‐defined.Main conclusions The correspondence of some groupings of species suggest their validity as areas with biogeographical (historical and/or ecological) meaning. This regionalization in the Baja California avifauna seems to be consistent with previous regionalizations for other groups. Hence, PAE is a useful tool for area categorization if reliable point records and prediction tools are available. Our results suggest that the geographical definition is much better using potential data generated by GARP, particularly when they are contrasted with the results from point data. Thus, this is an excellent alternative for developing biogeographical studies, as well as for improving the use of data from scientific collections and other sources of biodiversity information.
Marine nematode deep‐sea biodiversity – hyperdiverse or hype?
Authors: Lambshead P. John D. , Boucher Guy 
Published: June 2010

AbstractNematodes have been identified as a potentially hyperdiverse group and the deep sea as a potentially hyperdiverse environment (i.e. > 1 million species). A large‐scale data set from the equatorial central Pacific is used to estimate regional diversity with results that challenge this view; regional diversity is higher in some coastal waters despite lower sample diversity in coastal waters than in the deep sea. The data suggests a paradigm where the deep sea has modest regional diversity, despite high local diversity through patch dynamics, because similar patches in a similar habitat are repeated for considerable distances. Disturbance in shallow water dominates over patch‐dynamic mechanisms reducing local diversity but regional diversity is high because of the close packing of multiple habitats within a single region. The Pacific data are also used to demonstrate the pitfalls of extrapolating from local to global diversity. There is no reason to conclude that nematodes are less diverse than other benthic groups, indeed where direct comparison is possible the Nematoda appear to be as diverse as the Polychaeta, the most diverse macrofaunal taxon. This analysis is not consistent with the hypothesis that either marine nematodes or the deep‐sea benthos are hyperdiverse raising the question whether any environment or metazoan taxon has more than a million species.
The Indochinese–Sundaic faunal transition at the Isthmus of Kra: an analysis of resident forest bird species distributions
Authors: Hughes Jennifer B. , Round Philip D. , Woodruff David S. 
Published: June 2010

AbstractAim  To establish the geographical position of the biogeographical transition between Indochinese and Sundaic faunas using distributional data for the best‐documented taxon, the birds.Methods  Distributional data of 544 resident forest and forest edge bird species of Thailand and the Thai–Malay peninsula were examined at 45 sites spanning 15° of latitude from northern‐most Thailand to the southern peninsular Malaysia. Sites were grouped into 23 degree or half‐degree latitudinal zones and avifaunal similarity coefficients were calculated between each zone.Results  A Mantel test revealed a significant transition between northern Indochinese and southern Sundaic (Indomalay) avifauna assemblages just north of the Isthmus of Kra (10°30′ N). Northern and southern range limits of 152 species (> 269 species and subspecies combined) lie between 11° and 13° N.Main conclusions  This transition between zoogeographical subregions is not coincident with the widely recognized transition between floristic provinces which is traditionally placed 400–500 km further south at the Kangar–Pattani line, but is associated with a change from wet seasonal evergreen dipterocarp rain forest to mixed moist deciduous forest north of the Isthmus of Kra in the northern Thai–Malay peninsula. Climatological and ecological factors associated with the distribution of forest types today are reviewed and it is hypothesized that the avian transition tracks the northern phytogeographical boundary. Palaeogeographical factors, including hypothetical Neogene seaways, which may account for the historical development of both phytogeographical and avifaunal transitions are also described.
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Authors: Webb-Robertson Bobbie-Jo M. , Cannon William R. , Oehmen Christopher S. , Shah Anuj R. , Gurumoorthi Vidhya , Lipton Mary S. , Waters Katrina M. 
Published: June 2010

AbstractMotivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (MS/MS) studies. It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic).Results: We present a support vector machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity and polarity for the quantitative prediction of proteotypic peptides. Using three independently derived AMT databases (Shewanella oneidensis, Salmonella typhimurium, Yersinia pestis) for training and validation within and across species, the SVM resulted in an average accuracy measure of ∼0.83 with an SD of &lt;0.038. Furthermore, we demonstrate that these results are achievable with a small set of 13 variables and can achieve high proteome coverage.Availability: http://omics.pnl.gov/software/STEPP.phpContact: bj@pnl.govSupplementary information: Supplementary data are available at Bioinformatics online.
A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals
Authors: Clark Taane G. , Campino Susana G. , Anastasi Elisa , Auburn Sarah , Teo Yik Y. , Small Kerrin , Rockett Kirk A. , Kwiatkowski Dominic P. , Holmes Christopher C. 
Published: June 2010

Abstract
Motivation: Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.
Results: We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.
Availability and implementation: The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloads
Contact: taane.clark@lshtm.ac.uk
Distribution of deep-water corals of the Flemish Cap, Flemish Pass, and the Grand Banks of Newfoundland (Northwest Atlantic Ocean): interaction with fishing activities
Authors: Murillo F. J. , Durán Muñoz P. , Altuna A. , Serrano A. 
Published: June 2010

Abstract
Murillo, F. J., Durán Muñoz, P., Altuna, A., and Serrano, A. 2011. Distribution of deep-water corals of the Flemish Cap, Flemish Pass, and the Grand Banks of Newfoundland (Northwest Atlantic Ocean): interaction with fishing activities. – ICES Journal of Marine Science, 68: 319–332. The distribution of deep-water corals of the Flemish Cap, Flemish Pass, and the Grand Banks of Newfoundland is described based on bycatch from Spanish/EU bottom trawl groundfish surveys between 40 and 1500 m depth. In all, 37 taxa of deep-water corals were identified in the study area: 21 alcyonaceans (including the gorgonians), 11 pennatulaceans, 2 solitary scleractinians, and 3 antipatharians. The greatest diversity of coral species was on the Flemish Cap. Corals were most abundant along the continental slope, between 600 and 1300 m depth. Soft corals (alcyonaceans), sea fans (gorgonians), and black corals (antipatharians) were most common on bedrock or gravel, whereas sea pens (pennatulaceans) and cup corals (solitary scleractinians) were found primarily on mud. The biomass of deep-water corals in the bycatches was highest in previously lightly trawled or untrawled areas, and generally low in the regularly fished grounds. The information derived from bottom-trawl bycatch records is not sufficient to map vulnerable marine ecosystems (VMEs) accurately, but pending more detailed habitat mapping, it provides a valuable indication of the presence/absence of VMEs that can be used to propose the candidate areas for bottom fishery closures or other conservation measures.
History and dynamics of the overexploitation of the blackspot sea bream (Pagellus bogaraveo) in the Bay of Biscay
Authors: Lorance Pascal 
Published: June 2010

Abstract
Lorance, P. 2011. History and dynamics of the overexploitation of the blackspot sea bream (Pagellus bogaraveo) in the Bay of Biscay. – ICES Journal of Marine Science, 68: 290–301. The blackspot sea bream (Pagellus bogaraveo) used to be a major species in the landings from the Bay of Biscay up to the early 1980s. Nowadays, it is only a minor bycatch. Up to the mid-1970s, more than 15 000 t of blackspot sea bream were landed annually in Spanish and French ports. Thereafter, catches declined sharply from 1975 to 1985 and have stayed at low levels ever since. Here, the full history of the fishery collapse is described, using time-series of landings dating back to the early 1900s. Fishing mortalities of the main demersal stocks (hake, anglerfish, sole) were in the range 0.2–0.5 during the last 30 years. It is likely that the blackspot sea bream stock was exploited at a similar level, which is shown here to be unsustainable. The blackspot sea bream is highly sensitive to overfishing because of its protandrous hermaphroditism, with late first maturity (8 years) as females and rather low productivity. According to a yield-per-recruit model, the biomass of fecund females (BFF) is reduced to <20% of virgin BFF for a fishing mortality around 0.2. A dynamic model assuming a simple stock–recruitment relationship fitted to the reconstructed landings explained the collapse, with estimated fishing mortalities never exceeding 0.5.
Maternal presence and environmental enrichment affect food neophobia of piglets
Authors: Oostindjer Marije , Muñoz Julia Mas , Van den Brand Henry , Kemp Bas , Bolhuis J. Elizabeth 
Published: June 2010

Young omnivores show food neophobia in order to avoid the potential harmful effects of ingesting unfamiliar food items. We investigated whether the presence of the mother and an enriched rearing environment would reduce food neophobia in piglets. A mother may provide information on suitable food types to include in the diet, whereas an enriched environment may stimulate behavioural development and reduce reactivity towards novel stimuli (including food). Five barren-reared or enriched-reared piglets per litter were exposed to two novel food items in the presence, and the other five per litter in the absence, of the mother in a 7 min test. Maternal presence reduced food neophobia profoundly as reflected in a reduced latency to touching the food, a higher proportion of piglets sampling the two different food items and a higher intake. Latency to touch the food, however, was affected by maternal presence more strongly for barren-reared piglets than for enriched-reared piglets, and in the absence of the sow, consumption of one novel food type and time spent in the feeding area were higher for enriched-reared piglets.Environmental enrichment does have the potential to reduce food neophobia, but the presence of the mother during the encounter with novel food seems more efficient in decreasing food neophobia of piglets.
Iron defecation by sperm whales stimulates carbon export in the Southern Ocean
Authors: Lavery Trish J. , Roudnew Ben , Gill Peter , Seymour Justin , Seuront Laurent , Johnson Genevieve , Mitchell James G. , Smetacek Victor 
Published: June 2010

The iron-limited Southern Ocean plays an important role in regulating atmospheric CO
2
levels. Marine mammal respiration has been proposed to decrease the efficiency of the Southern Ocean biological pump by returning photosynthetically fixed carbon to the atmosphere. Here, we show that by consuming prey at depth and defecating iron-rich liquid faeces into the photic zone, sperm whales (
Physeter macrocephalus
) instead stimulate new primary production and carbon export to the deep ocean. We estimate that Southern Ocean sperm whales defecate 50 tonnes of iron into the photic zone each year. Molar ratios of C
export
∶Fe
added
determined during natural ocean fertilization events are used to estimate the amount of carbon exported to the deep ocean in response to the iron defecated by sperm whales. We find that Southern Ocean sperm whales stimulate the export of 4 × 10
5
tonnes of carbon per year to the deep ocean and respire only 2 × 10
5
tonnes of carbon per year. By enhancing new primary production, the populations of 12 000 sperm whales in the Southern Ocean act as a carbon sink, removing 2 × 10
5
tonnes more carbon from the atmosphere than they add during respiration. The ability of the Southern Ocean to act as a carbon sink may have been diminished by large-scale removal of sperm whales during industrial whaling.
Neural control of behavioural choice in juvenile crayfish
Authors: Liden William H. , Phillips Mary L. , Herberholz Jens 
Published: June 2010

Natural selection leads to behavioural choices that increase the animal's fitness. The neuronal mechanisms underlying behavioural choice are still elusive and empirical evidence connecting neural circuit activation to adaptive behavioural output is sparse.We exposed foraging juvenile crayfish to approaching shadows of different velocities and found that slow-moving shadows predominantly activated a pair of giant interneurons, which mediate tail-flips that thrust the animals backwards and away from the approaching threat. Tail-flips also moved the animals farther away from an expected food source, and crayfish defaulted to freezing behaviour when faced with fast-approaching shadows. Under these conditions, tail-flipping, an ineffective and costly escape strategy was suppressed in favour of freezing, a more beneficial choice. The decision to freeze also dominated in the presence of a more desirable resource; however, the increased incentive was less effective in suppressing tail-flipping when paired with slow-moving visual stimuli that reliably evoked tail-flips in most animals. Together this suggests that crayfish make value-based decisions by weighing the costs and benefits of different behavioural options, and they select adaptive behavioural output based on the activation patterns of identifiable neural circuits.
Comparison of the Intersurgical SolusTM laryngeal mask airway and the i‐gel supralaryngeal device
Authors: Amini S. , Khoshfetrat M. 
Published: June 2010

SummaryWe compared the performance of the Intersurgical SolusTM laryngeal mask airway (LMA) with that of the i‐gel in 120 patients of ASA physical status during general anaesthesia with respect to oropharyngeal leak pressure, peak airway pressure, airway manipulation, insertion time, fibreoptic view, ventilatory parameters, and peri‐operative complications. After receiving a standardised induction of anaesthesia, either a Solus LMA (60 patients) or an i‐gel (60 patients) was inserted. One hundred and fifteen patients completed the study. The leak pressure was significantly higher in the LMA group than the i‐gel group (mean (SD) 22.7 (7.7) cmH2O vs 19.3 (7.1) cmH2O; p = 0.02). A better fibreoptic view of the larynx was obtained in patients in the LMA group (p = 0.02) compared to those in the i‐gel group and less airway manipulation was required in the LMA group (p < 0.01). Both devices have good performance with very low peri‐operative complications. However, the Solus LMA provides a better oropharyngeal seal, provides a better fibreoptic view, and requires less manipulation to secure the airway than the i‐gel.
The dispersal and deposition of hydrochorous plant seeds in drainage ditches
Authors: SOOMERS HESTER , WINKEL DEBORAH N. , DU YUN , WASSEN MARTIN J. 
Published: June 2010

Summary1. Surface water is an important dispersal vector for wetland plant species. However, most previous studies on hydrochory (i.e. water dispersal) have focused on ecosystems with relatively rapid water flow. Therefore, there is a need to study such dispersal in slow‐flowing or stagnant waterbodies, such as drainage ditches, which might act as dispersal corridors between habitat patches.2. To gain insight into the mechanisms by which seeds are transported in drainage ditches, the effect of the velocity of wind and water on the rate of transport of floating seeds of three wetland species (Carex pseudocyperus L., Iris pseudacorus L. and Sparganium erectum L.) was investigated. Furthermore, in release and retrace experiments with painted C. pseudocyperus seeds, a number of factors potentially determining the probability of seed deposition were investigated.3. Net wind speed was found to be the main factor determining the rate at which seeds are transported in drainage ditches. No relation between water flow at middepth in the ditches and seed transport was found. Wind speed and flow at the water surface were positively related. The effect of wind speed on the rate of transport of floating seeds was greater for S. erectum seeds, because a greater ratio of their volume protrudes from the water, than for C. pseudocyperus and I. pseudacorus seeds.4. The principal factors that determine seed deposition were aquatic plant cover, ditch slope and indentations in the ditch bank. Seeds changed direction if the wind direction changed, or if there was a bend in the ditch. The final pattern of deposition was related to mean net wind speed. Mean transport distance after 2 days varied between 34 and 451 m.5. Unlike in rivers, seed transport in ditches was determined by wind speed and direction, enabling multidirectional seed dispersal. We conclude that in slow‐flowing waters, wind is a more important driver for hydrochorous seed transport than the flow of water. This sheds a new light on hydrochory and has important consequences for the management of otherwise fragmented wetland remnants.
Functional explanations for variation in bark thickness in tropical rain forest trees
Authors: Paine Charles Eliot Timothy , Stahl Clément , Courtois Elodie A. , Patiño Sandra , Sarmiento Carolina , Baraloto Christopher 
Published: June 2010

Summary 1. The complex structure of tree bark reflects its many functions, which include structural support as well as defence against fire, pests and pathogens. Thick bark, however, might limit respiration by the living tissues of the trunk. Nevertheless, little research has addressed community‐level variation in bark thickness, and to the best of our knowledge, no one has tested multiple hypotheses to explain variation in bark thickness. 2. We conducted an extensive survey of bark thickness within and among species of trees in the tropical rain forests of French Guiana. Trunk bark thickness increased by 1·2 mm per 10 cm increase in stem diameter, and varied widely at all taxonomic levels. Mean trunk bark thickness was 4·5 mm (range: 0·5–29 mm), which was less that found in two Amazonian rain forests in previous studies. This survey of bark thickness should be of use for forest management since tree survival through fire is strongly predicted by bark thickness. 3. We combined the survey data with multiple datasets to test several functional hypotheses proposed to explain variation in bark thickness. We found bark to provide an average of 10% of the flexural rigidity of tree stems, which was substantially less than that found in the only other study of bark stiffness. Bark thickness was uncorrelated with species’ association with fire‐prone habitats, suggesting that the influence of fire on bark thickness does not extend into moist Forests. There was also little evidence that bark thickness is affected by its function as a defence against herbivory. Nor was there evidence that thick bark limits trunk respiration. 4. A re‐analysis of previously collected anatomical data indicated that variation in rhytidome (non‐conducting outer bark) thickness explains much of the variation in overall bark thickness. As rhytidome is primarily involved in protecting the living tissues of the trunk, we suggest that bark thickness is driven mostly by its defensive function. 5. Functional explanations for the variation in bark thickness were not clear‐cut. Nevertheless, this study provides a foundation for further investigation of the functional bases of bark in tropical trees.