bluuebunny/crossref_metadata_2025 huggingface dataset:
Axisymmetric flows from fluid injection into a confined porous medium
Authors: Guo Bo , Zheng Zhong , Celia Michael A. , Stone Howard A.
Published: February 2016

We study the axisymmetric flows generated from fluid injection into a horizontal confined porous medium that is originally saturated with another fluid of different density and viscosity. Neglecting the effects of surface tension and fluid mixing, we use the lubrication approximation to obtain a nonlinear advection-diffusion equation that describes the time evolution of the sharp fluid-fluid interface. The flow behaviors are controlled by two dimensionless groups: M, the viscosity ratio of displaced fluid relative to injected fluid, and Γ, which measures the relative importance of buoyancy and fluid injection. For this axisymmetric geometry, the similarity solution involving R2/T (where R is the dimensionless radial coordinate and T is the dimensionless time) is an exact solution to the nonlinear governing equation for all times. Four analytical expressions are identified as asymptotic approximations (two of which are new solutions): (i) injection-driven flow with the injected fluid being more viscous than the displaced fluid (Γ ≪ 1 and M < 1) where we identify a self-similar solution that indicates a parabolic interface shape; (ii) injection-driven flow with injected and displaced fluids of equal viscosity (Γ ≪ 1 and M = 1), where we find a self-similar solution that predicts a distinct parabolic interface shape; (iii) injection-driven flow with a less viscous injected fluid (Γ ≪ 1 and M > 1) for which there is a rarefaction wave solution, assuming that the Saffman-Taylor instability does not occur at the reservoir scale; and (iv) buoyancy-driven flow (Γ ≫ 1) for which there is a well-known self-similar solution corresponding to gravity currents in an unconfined porous medium [S. Lyle et al. “Axisymmetric gravity currents in a porous medium,” J. Fluid Mech. 543, 293–302 (2005)]. The various axisymmetric flows are summarized in a Γ-M regime diagram with five distinct dynamic behaviors including the four asymptotic regimes and an intermediate regime. The implications of the regime diagram are discussed using practical engineering projects of geological CO2 sequestration, enhanced oil recovery, and underground waste disposal.
Thermal evaporated hyperbranched Ag nanostructure as an effective secondary-electron trapping surface coating
Authors: He Y. N. , Peng W. B. , Cui W. Z. , Ye M. , Zhao X. L. , Wang D. , Hu T. C. , Wang R. , Li Y.
Published: February 2016

We study secondary electron yield (SEY) suppression of silver using a hyperbranched nanostructure obtained by thermal evaporation. First, we perform thermal evaporation at different residual gas pressures for studying the influence of pressure on surface morphologies. A self-assembled hyperbranched Ag nanostructure has been achieved at 100 Pa. Then, we further investigate the detailed formation process of the self-assembled hyperbranched Ag nanostructure qualitatively and find it to be dominated by “screening effect”. Finally, we study the obvious SEY suppression effect of this special structure. We show that 100 Pa is the best process condition within our experimental scope from the SEY suppression point of view. It exhibits maximum SEY (δmax) of ∼0.9. We also show that the combining of this nanostructure with the micro-porous surface we developed before can further improve its SEY suppression effect which leading to a δmax of ∼0.8. We propose a novel 2D rectangular-hemisphere hybrid trap model to perform numerical simulation of secondary electron dynamics for interpretation of the experimental results. In total, this work provides guidance to controllable preparation of low SEY metallic surfaces for potential applications in particle accelerators, RF microwave components and satellite systems.
Large-scale micromagnetic simulation of Nd-Fe-B sintered magnets with Dy-rich shell structures
Authors: Oikawa T. , Yokota H. , Ohkubo T. , Hono K.
Published: February 2016

Large-scale micromagnetic simulations have been performed using the energy minimization method on a model with structural features similar to those of Dy grain boundary diffusion (GBD)-processed sintered magnets. Coercivity increases as a linear function of the anisotropy field of the Dy-rich shell, which is independent of Dy composition in the core as long as the shell thickness is greater than about 15 nm. This result shows that the Dy contained in the initial sintered magnets prior to the GBD process is not essential for enhancing coercivity. Magnetization reversal patterns indicate that coercivity is strongly influenced by domain wall pinning at the grain boundary. This observation is found to be consistent with the one-dimensional pinning theory.
Size effects on the Néel temperature of antiferromagnetic NiO nanoparticles
Authors: Rinaldi-Montes Natalia , Gorria Pedro , Martínez-Blanco David , Fuertes Antonio B. , Puente-Orench Inés , Olivi Luca , Blanco Jesús A.
Published: February 2016

Among all antiferromagnetic transition metal monoxides, NiO presents the highest Néel temperature (TN ∼ 525 K). In this work, the size-dependent reduction of TN in NiO nanoparticles with average diameters (D) ranging from 4 to 9 nm is investigated by neutron diffraction. The scaling law followed by TN(D) is in agreement with the Binder theory of critical phenomena in low-dimensional systems. X-ray absorption fine structure measurements link the decrease of TN to the occurrence of size effects (average undercoordination, bond relaxation and static disorder) in the nearest and next-nearest Ni coordination shells that hold the key for the maintenance of the antiferromagnetic order.
Sexual health-related information delivery – are patient information leaflets still relevant?
Authors: Varma Rick , Chung Charles , Townsend Amanda , Power Melissa
Published: February 2016

Background
Patient information leaflets (PILs) are widely utilised within publically funded sexual health clinics to deliver sexual health-related information (SHRI); however, their continued value to clients in the era of social media is unclear. This study aimed to evaluate clients’ opinions on three newly developed PILs and examine client views on other forms of SHRI delivery. Methods: An anonymous self-administered questionnaire was completed by clients attending the Western Sydney Sexual Health Centre (WSSHC) in 2012. High-risk population (HRP) vs non-high-risk population (non-HRP) views on PILs vs alternative methods of SHRI delivery were analysed by using Mann–Whitney U, Wilcoxon, McNemar and χ2 tests. Results: Over half (210/315; (67%)) of the consecutive clients from a culturally diverse population completed the survey. Sex workers (SW) and young people (YP) were significantly likely to have a high school education than non-HRP (P < 0.039 and P < 0.032). Overall, PILs, a clinic website and the Sexual Health Information Link (SHIL), a state-wide website and telephone line, were ranked significantly higher as a means of SHRI delivery on a Likert scale than newer technologies including Facebook (P < 0.001), email (P < 0.001), mobile phone applications (P < 0.001), TVs in waiting rooms (P < 0.001) and business cards (P < 0.001). There was no significant difference in opinion between HRP and non-HRP. Conclusions: This study provides evidence for the ongoing use of PILs to deliver SHRI to clinic attendees, in conjunction with other forms of SHRI delivery such as websites and SHIL. Novel methods may require additional consumer engagement and a greater understanding of specific population’s needs.
Immunological Profile of the Yellow Clam Mesodesma mactroides (Mesodesmatidae) from the Southern Coast of Rio Grande do Sul, Brazil
Authors: Silva Santos Juan Jethro , Carvalho Yuri Bovi , Alcantara Lopes Diogo Luiz , Romano Luis Alberto
Published: February 2016

The yellow clam Mesodesma mactroides (Mesodesmatidae) is a sandy beach bivalve that is distributed from Rio de Janeiro, Brazil, to the south of Buenos Aires province, Argentina. The yellow clam population has been declining in recent decades. To increase our understanding of this species, we evaluated the immunological status of yellow clams collected during different seasons from various areas in the state of Rio Grande do Sul, Brazil. We characterized the hemocytes, determined the differential hemocyte counts (DHCs), calculated the apoptotic index, and evaluated the incidence of parasites in yellow clams through histological analysis. We identified two types of hemocyte (hyaline and granular) that showed significant variation in DHCs among sampling areas during the summer and winter. The apoptotic index only exhibited significant variation during the summer. Histopathological analysis results did not significantly differ among sampling areas. This work demonstrated that environmental variation (e.g., temperature and salinity) associated with anthropogenic actions may be affecting the immune system of yellow clams. However, more studies are needed to determine the full influence of these factors on the yellow clam's immune system and thus contribute to future management and aquaculture of the species.

Received May 10, 2015; accepted October 28, 2015.
The Utility of Multiple Synthesized Views in the Recognition of Unfamiliar Faces
Authors: Jones Scott P. , Dwyer Dominic M. , Lewis Michael B.
Published: February 2016

The ability to recognize an unfamiliar individual on the basis of prior exposure to a photograph is notoriously poor and prone to errors, but recognition accuracy is improved when multiple photographs are available. In applied situations, when only limited real images are available (e.g., from a mugshot or CCTV image), the generation of new images might provide a technological prosthesis for otherwise fallible human recognition. We report two experiments examining the effects of providing computer-generated additional views of a target face. In Experiment 1, provision of computer-generated views supported better target face recognition than exposure to the target image alone and equivalent performance to that for exposure of multiple photograph views. Experiment 2 replicated the advantage of providing generated views, but also indicated an advantage for multiple viewings of the single target photograph. These results strengthen the claim that identifying a target face can be improved by providing multiple synthesized views based on a single target image. In addition, our results suggest that the degree of advantage provided by synthesized views may be affected by the quality of synthesized material.
Seed-hoarding of Edward’s long-tailed rats Leopoldamys edwardsi in response to weevil infestation in cork oak Quercus variabilis
Authors: Cheng Jinrui , Zhang Hongmao
Published: February 2016

Seed hoarders show different hoarding and eating responses towards insect-infested seeds that can affect the fitness of both the seeds and insects. It remains unclear how seed hoarders adopt different strategies in eating and hoarding infested seeds with and without larvae concealed inside. Here we investigated hoarding and eating responses of Edward’s long-tailed rats Leopoldamys edwardsi (scatter hoarders) to weevil infestation of cork oak Quercus variabilis seeds within outdoor enclosures. We provided sound seeds, larvae-emerged seeds, (infested seeds where larvae have emerged) and larvae-concealed seeds (infested seeds with larvae concealed inside) to subjects independently (each seed type presented separately) and in pairwise combinations (sound and larvae-emerged seeds; sound and larvae-concealed seeds). We found that L. edwardsi removed, scatter hoarded and ate fewer larvae-emerged seeds than sound seeds. No difference was found between sound seeds and larvae-concealed seeds. These results suggest that sound and larvae-concealed seeds are more favored by L. edwardsi than larvae-emerged seeds. We posit that not only plants but also insects may benefit from the behavioral responses of hoarders to seed infestation under natural conditions.
Population genetic structure in the paddyfield warbler (Acrocephalus agricola Jerd.)
Authors: Zehtindjiev Pavel , Ilieva Mihaela , Hansson Bengt , Oparina Olga , Oparin Mihail , Bensch Staffan
Published: February 2016

Population genetic structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA) showed that there was no divergence between Bulgarian and Russian populations (FST = 0.007), whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: FST = 0.058; Bulgaria: FST = 0.114). The degree of differentiation between populations at nuclear markers (five microsatellite loci; FST ≈ 0) was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu’s FS tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler, is valuable for the long-term conservation of expanding migratory bird species.
Frog community responses to recent American bullfrog invasions
Authors: Li Yiming , Ke Zhunwei , Wang Yihua , Blackburn Tim M.
Published: February 2016

Native species may decline quickly when confronted with an exotic species to which they are not adapted. The extent of decline may depend on the abundance of an invader and the length of time since it first arrived in the community (residence time), and the interaction between these two variables. We tested these effects using data on the effects of American bullfrog Lithobates catesbeianus invasion on native frog communities in 65 permanent lentic waters on islands in the Zhoushan Archipelago, China. We examined variation in native frog abundance and species richness in relation to features of the American bullfrog invasion, habitat disturbance, characteristics of the water body and fish communities and the presence of red swamp crayfish. Bullfrog invaded sites had lower native frog density and species richness, higher submerged vegetation cover and greater frequency of repairs to the water body than did non-invaded sites. The minimum adequate general linear mixed models showed that both native frog density and species richness were negatively related to post-metamorphosis bullfrog density, and that native frog species richness was also positively related to the vegetation cover. There was no effect on either native frog density or species richness of residence time or its interaction with bullfrog density, or of the abundance of bullfrog tadpoles. The results suggested that post-metamorphosis bullfrogs had impacts on native frog communities in the islands, and that the extents of these impacts are proportional to post-metamorphosis bullfrog density.
Can native species crucian carp Carassius auratus recognizes the introduced red swamp crayfish Procambarus clarkii?
Authors: Cai Fengjin , Wu Zhengjun , He Nan , Wang Zhenxing , Huang Chengming
Published: February 2016

Procambarus clarkii is native to the south-central United States (Louisiana) and northeastern Mexico, and is a highly efficient predator that poses a damager to native species after its introduction or invasion. In its natural habitat, P. clarkii consumes Carassius auratus, however, whether C. auratus recognizes P. clarkii as a predator is not yet clear. In laboratory experiments, we investigated whether experienced and inexperienced C. auratus recognize P. clarkii as a predatory threat and the specific sensory modality used by C. auratus to respond to chemical and visual stimuli from P. clarkii. In the chemical stimuli experiment, two kinds of chemical stimuli were used, water from a tub containing P. clarkii previously fed with C. auratus (C. auratus diet cues) and water from a tub containing unfed P. clarkii (P. clarkii cues). In the visual experiment, experienced C. auratus decreased activity, but inexperienced C.auratus avoided the predator compartment. When C. auratus diet cues were presented, both experienced and inexperienced C. auratus increased the use of shelter, decreased activity in the initial response phase. Compared with the blank treatment, experienced C. auratus responded to P. clarkii cues by decreasing activity; however, inexperienced C. auratus showed no reduction in activity. C. auratus appears to recognize P. clarkii as a predator both through visual and chemical cues. Further analysis revealed that C. auratus may recognize P. clarkii visually through the disturbances caused by P. clarkii movement and chemically by detecting conspecific alarm cues in the diet of P. clarkii. The results also indicate that experienced C. auratus can recognize P. clarkii by innate chemical cues from P. clarkii, whereas inexperienced C. auratus cannot.
Warmer springs, laying date and clutch size of tree sparrows Passer montanus in Croatia
Authors: Dolenec Z. , Dolenec P. , Møller A.P.
Published: February 2016

Global surface air temperatures increased during the past 100 years. Many long-term studies of birds have reported a climatic influence on breeding performance. We analysed long-term changes in first laying date and clutch size for first clutches of sedentary, hole-nesting and socially monogamous tree sparrows Passer montanus during 1980–2009 in northwestern Croatia. Laying date advanced and spring temperature increased significantly during the study. Date of laying was significantly correlated with mean air spring temperature and advanced by 8.6 days during the 30 years period. Laying date was delayed in extremely cold, but not in extremely warm springs compared to years with normal temperatures. These results suggest that current climate change including extreme change does not have negative effects on timing of laying or clutch size. In contrast to laying date, clutch size did not vary systematically during the study period or with mean spring air temperature changes.
Invasion of the raccoon dog Nyctereutes procyonoides in Europe: History of colonization, features behind its success, and threats to native fauna
Authors: Kauhala Kaarina , Kowalczyk Rafal
Published: February 2016

We aimed to review the history of the introduction and colonization of the raccoon dog Nyctereutes procyonoides in Europe, the features behind its successful expansion and its impact on native fauna. The raccoon dog quickly colonized new areas after being introduced to the European part of the former Soviet Union. Today it is widespread in Northern and Eastern Europe and is still spreading in Central Europe. Features behind its success include its adaptability, high reproductive potential, omnivory, hibernation in northern areas, multiple introductions with > 9000 individuals from different localities, and tendency to wander enabling gene flow between populations. Firm evidence of the raccoon dog’s negative impact on native fauna, such as a reduction in bird populations, is still scarce. Raccoon dogs may destroy waterfowl nests, although a nest predation study in Latvia did not confirm this. Predator removal studies in Finland suggested that the raccoon dog’s impact on game birds is smaller than expected. However, raccoon dogs may have caused local extinction of frog populations, especially on islands. Raccoon dogs may compete with other carnivores for food, for example for carrion in winter, or for the best habitat patches. In northern Europe potential competitors include the red fox Vulpes vulpes and the badger Meles meles, but studies of their diets or habitat preferences do not indicate severe competition. The raccoon dog is an important vector of diseases and parasites, such as rabies, Echinococcus multilocularis and Trichinella spp. and this is no doubt the most severe consequence arising from the spread of this alien species in Europe.
Genetic variation and population dispersal of Yangtze voles Microtus fortis calamorum in the Dongting Lake region
Authors: Guo Zongming , Song Pengfei , GUO Cong , Song Zhaobin , Wang Yong , Li Bo , Zhang Meiwen , Ran Jianghong
Published: February 2016

To understand genetic variation and population dispersal in the Yangtze vole Microtus fortis calamorum distributed in the Dongting Lake region, 144 individuals were collected from six habitat patches. The mitochondrial DNA control region was sequenced and 17 haplotypes were observed. Of the six investigated populations, haplotype and nucleotide diversities of those from larger patches were higher than those from smaller patches. Nonparametric correlation analysis showed that patch size had a positive correlation with haplotype diversity (r = 0.943, P < 0.01). A neighbour-joining tree of the 17 haplotypes showed no geographic genetic structure among the six populations. Analysis of isolation by distance showed that genetic differentiation among the six populations was not positively related to geographic distance. Analysis of mismatch distribution indicated that the voles had passed through a population expansion. The pattern of haplotype distribution in the Changsha population suggests that the population was established by a founder effect [Current Zoology 58 (2): 211–220, 2012].
Social cliques in male northern muriquis Brachyteles hypoxanthus
Authors: Tokuda Marcos , Boubli Jean P. , Izar Patrícia , Strier Karen B.
Published: February 2016

Analyses of spatial relationships and social interactions provide insights into the social structure of animal societies and the ways in which social preferences among and between dyads affect higher order social relationships. In this paper we describe the patterns of spatial associations and social interactions among adult male northern muriquis in order to evaluate the dynamics of their social networks above the dyadic levels. Systematic observations were made on the 17 adult males present in a multi-male/multi-female group from April 2004 through February 2005, and in July 2005. Analyses of their spatial relationships identified two distinct male cliques; some adult males (called “N” males) were more connected to the females and immatures than other adult males (“MU” males), which were more connected to one another. Affiliative interactions were significantly higher among dyads belonging to the same clique than to different cliques. Although frequencies of dyadic agonistic interactions were similarly low among individuals within and between cliques, MU males appeared to be subordinate to N males. Nonetheless, there were no significant differences in the copulation rates estimated for MU males and N males. Mutual benefits of cooperation between MU and N cliques in intergroup encounters might explain their ongoing associations in the same mixed-sex group [Current Zoology 58 (2): 342–352, 2012].
Conflictive management of small mammals considered as pests: A long way to evidence-based policy making
Authors: Ferreira Catarina , Delibes-Mateos Miguel
Published: February 2016

This paper discusses the controversial management decisions made by policy-makers worldwide regarding poisoning campaigns aimed to control small mammal populations, often considered harmful economic pests. Aside from considerations regarding the biological consequences of these campaigns, we argue that when society rejects all values of science and expertise then only badly supported and negligent decisions will be made about conservation and management issues. The extermination of small mammal species, some of which play crucial ecological roles in several regions of the world, is just an example of such discredit and misinformation. Without a strong commitment towards evidence-based policy-making, economic investments in research and development could be entirely compromised [Current Zoology 58 (2): 353–357, 2012].
Genomes and evolutionary genomics of animals
Authors: Song Luting , Wangs Wen
Published: February 2016

Alongside recent advances and booming applications of DNA sequencing technologies, a great number of complete genome sequences for animal species are available to researchers. Hundreds of animals have been involved in whole genome sequencing, and at least 87 non-human animal species’ complete or draft genome sequences have been published since 1998. Based on these technological advances and the subsequent accumulation of large quantity of genomic data, evolutionary genomics has become one of the most rapidly advancing disciplines in biology. Scientists now can perform a number of comparative and evolutionary genomic studies for animals, to identify conserved genes or other functional elements among species, genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation. This review deals with the current ge-nomic and evolutionary research on non-human animals, and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals. It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom.
Construction of a microsatellite-based genetic linkage map for half-smooth tongue sole Cynoglossus semilaevis
Authors: Song Wentao , Miao Guidong , Zhao Yongwei , Niu Yuze , Pang Renyi , Liao Xiaolin , Shao Changwei , Chen Songlin
Published: February 2016

The half-smooth tongue sole Cynoglossus semilaevis is an important cultured marine fish and a promising model fish for the study of sex determination. Sex-specific genetic linkage maps of half-smooth tongue sole were developed with 567 markers (565 microsatellite markers and two SCAR markers). The parents and F1 progeny (92 individuals) were used as segregating populations. The female map was composed of 480 markers in 21 linkage groups, covering a total of 1388.1 cM, with an average interval 3.06 cM between markers. The male map consisted of 417 markers in 21 linkage groups, spanning 1480.9 cM, with an average interval of 3.75 cM. The female and male maps had 474 and 416 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1522.9 cM for females and 1649.1cM for males. Based on estimations of map length, the female and male maps covered 91.1% and 89.8% of the genome, respectively. Furthermore, two female-specific SCAR markers, f-382 and f-783, were mapped on LG15f (linkage group 15 in female maps). The present study presents a mid-density genetic linkage map for half-smooth tongue sole. These improved genetic linkage maps may facilitate systematic genome searches to identify quantitative trait loci (QTL), such as disease resistance, growth and sex-related traits, and are very useful for marker-assisted selection breeding programs for economically important traits in half-smooth tongue sole.
Mating behavior and sexual selection in a polygamous beetle
Authors: Lu Wen , Wang Qiao , Tian Mingyi , Xu Jin , Lv Jian , Qin Aizhi
Published: February 2016

Mating behavior and sexual selection in relation to morphometric traits in a polygamous beetle, Glenea cantor (F.) (Coleoptera: Cerambycidae), were investigated. Upon encounter, a male approached a female, mounted her, grasped her terminal abdomen with his hind tarsi, and attempted to mate. Successful mating lasted about 3.5 h. Although all traits measured in females and half of traits in males were significantly correlated with mating success, the primary selection on virgin females was the genital trait, the bursa copulatrix length, and that on males was the body length and hind tarsal length. Longer bursa copulatrix accommodated a larger ejaculate, suggesting that this female trait benefits the male that first mates with the female in terms of increasing ejaculate size to beat subsequent males in sperm competition. Under a female-biased sex ratio, more than 20% of matings failed within 20s after the male genitalia had been inserted into hers, suggesting that males assess genital features of the female before insemination and undertake cryptic male mate choice. Larger males were more capable of grasping females and achieving mating. During the premating struggle the male almost always used his hind tarsi to lift the female terminal abdomen to the position for his genitalia to insert, and as a result, males with longer hind tarsi achieved higher mating success.
Predicting wild boar damages to croplands in a mosaic of agricultural and natural areas
Authors: Ficetola Gentile Francesco , Bonardi Anna , Mairota Paola , Leronni Vincenzo , Padoa-Schioppa Emilio
Published: February 2016

Crop damages by wildlife is a frequent form of human-wildlife conflict. Identifying areas where the risk of crop damages is highest is pivotal to set up preventive measures and reduce conflict. Species distribution models are routinely used to predict species distribution in response of environmental changes. The aim of this paper was assessing whether species distribution models can allow to identify the areas most at risk of crop damages, helping to set up management strategies aimed at the mitigation of human-wildlife conflicts. We obtained data on wild boar Sus scrofa damages to crops in the Alta Murgia National Park, Southern Italy, and related them to landscape features, to identify areas where the risk of wild boar damages is highest. We used MaxEnt to build species distribution models. We identified the spatial scale at which landscape mostly affects the distribution damages, and optimized the regularization parameter of models, through an information-theoretic approach based on AIC. Wild boar damages quickly increased in the period 2007-2011; cereals and legumes were the crops more affected. Large areas of the park have a high risk of wild boar damages. The risk of damages was related to low cover of urban areas or olive grows, intermediate values of forest cover, and high values of shrubland cover within a 2-km radius. Temporally independent validation data demonstrated that models can successfully predict damages in the future. Species distribution models can accurately identify the areas most at risk of wildlife damages, as models calibrated on data collected during only a subset of years correctly predicted damages in the subsequent year.
Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples
Authors: Tende Talatuxs , Hansson Bengt , Ottosson Ulf , Bensch Staffan
Published: February 2016

Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media (ethanol, ASL buffer and Two-step storage). The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsatellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored highest in the majority of these tests.
Stable isotope evidence for trophic niche partitioning in a South African savanna rodent community
Authors: Codron Jacqueline , Duffy Kevin J , Avenant Nico L , Sponheimer Matt , Leichliter Jennifer , Paine Oliver , Sandberg Paul , Codron Daryl
Published: February 2016

Species’ partitioning of resources remains one of the most integral components for understanding community assembly. Analysis of stable carbon and nitrogen isotopes in animal tissues has the potential to help resolve patterns of partitioning because these proxies represent the individual’s diet and trophic niche, respectively. Using free-ranging rodents in a southern African savanna as a model community, we find that syntopic species within habitats occupy distinct isotope niches. Moreover, species with strongly overlapping isotope niches did not overlap in their spatial distribution patterns, suggesting an underlying effect of competitive exclusion. Niche conservatism appears to characterize the behaviour of most species in our sample - with little or no observed changes across habitats - with the exception of one species, Mastomys coucha. This species displayed a generalist distribution, being found in similar abundances across a variety of habitats. This spatial pattern was coupled with a generalist isotope niche that shifted across habitats, likely in response to changes in species composition over the same spatial gradient. The case for M. coucha supports contentions that past competition effects played a significant evolutionary role in shaping community structures of today, including the absence of strong interspecific niche overlaps within particular habitats. Our study highlights the value of stable isotope approaches to help resolve key questions in community ecology, and moreover introduces novel analytical approaches to quantifying isotope niche breadths and niche overlaps that are easily comparable with traditional metrices.
Rethinking phylogeographic structure and historical refugia in the rufous-capped babbler Cyanoderma ruficeps in light of range-wide genetic sampling and paleodistributional reconstructions
Authors: Hosner Peter A. , Liu Huatao , Peterson A. Townsend , Moyle Robert G.
Published: February 2016

Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderma ruficeps, and compare results to previous studies that examined this species across mainland China and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations (Nepal, Tibet, Myanmar, Yunnan), rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood.
Using the BirdTree.org website to obtain robust phylogenies for avian comparative studies: A primer
Authors: Rubolini Diego , Liker András , Garamszegi László Z. , Møller Anders P. , Saino Nicola
Published: February 2016

Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by including phylogenetic hypotheses into statistical analyses of species’ traits, for which birds often serve as excellent models. The online publication of the most complete molecular phylogeny of extant bird species (www.birdtree.org, BirdTree hereafter) now allows evolutionary biologists to rapidly obtain sets of equally plausible phylogenetic trees for any set of species to be incorporated as a phylogenetic hypothesis in comparative analyses. We discuss methods to use BirdTree tree sets for comparative studies, either by building a consensus tree that can be incorporated into standard comparative analyses, or by using tree sets to account for the effect of phylogenetic uncertainty. Methods accounting for phylogenetic uncertainty should be preferred whenever possible because they should provide more reliable parameter estimates and realistic confidence intervals around them. Based on a real comparative dataset, we ran simulations to investigate the effect of variation in the size of the random tree sets downloaded from BirdTree on the variability of parameter estimates from a bivariate relationship between mass-specific productivity and body mass. Irrespective of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small (< 0.15%) coefficients of variation. We argue that BirdTree, due to the ease of use and the major advantages over previous ‘traditional’ methods to obtain phylogenetic hypotheses of bird species (e.g. supertrees or manual coding of published phylogenies), will become the standard reference in avian comparative studies for years to come.
Economic Activity and the Spread of Viral Diseases: Evidence from High Frequency Data *
Authors: Adda Jérôme
Published: February 2016

Viruses are a major threat to human health, and—given that they spread through social interactions—represent a costly externality. This article addresses three main questions: (i) what are the unintended consequences of economic activity on the spread of infections; (ii) how efficient are measures that limit interpersonal contacts; (iii) how do we allocate our scarce resources to limit the spread of infections? To answer these questions, we use novel high frequency data from France on the incidence of a number of viral diseases across space, for different age groups, over a quarter of a century. We use quasi-experimental variation to evaluate the importance of policies reducing interpersonal contacts such as school closures or the closure of public transportation networks. While these policies significantly reduce disease prevalence, we find that they are not cost-effective. We find that expansions of transportation networks have significant health costs in increasing the spread of viruses, and that propagation rates are pro-cyclically sensitive to economic conditions and increase with inter-regional trade.
Reduction of Coronary Motion Artifacts in Prospectively Electrocardiography-Gated Coronary Computed Tomography Angiography Using Monochromatic Imaging at Various Energy Levels in Combination With a Motion Correction Algorithm on Single-Source Fast Tube Voltage Switching Dual-Energy Computed Tomography
Authors: Machida Haruhiko , Fukui Rika , Gao Jianbo , Tanaka Isao , Shen Yun , Suzuki Shigeru , Ishikawa Takuya , Ueno Eiko
Published: February 2016

Objectives

The aim of this study was to assess the effect of monochromatic imaging at various energy levels in combination with a motion correction algorithm (MCA) in single-source dual-energy coronary computed tomography angiography (CCTA) with fast switching of tube voltage on the reduction of coronary motion artifacts (CMA) in a phantom setting.

Materials and Methods

Using this dual-energy computed tomography technique with a phantom comprising models of coronary vessels filled with contrast medium and pulsating at constant heart rates of 60 to 100 beats per minute, we reconstructed monochromatic images of CCTA obtained at 50 to 90 keV with and without use of MCA. Cardiac motion was modeled by simulating the in vivo time-volume curve of the left ventricle. Two independent readers graded CMA in 9 coronary segments using a 5-point scale (1, poor; 3 to 5, interpretable; 5, excellent). At each heart rate, we compared the average score of CMA between images obtained at 50 to 90 keV with and without use of MCA using Wilcoxon signed rank test, and we compared the score among images obtained at 50 to 90 keV with use of MCA using Kruskal-Wallis and post hoc tests. We also compared the percentages of image interpretability and improvement in image interpretability among images obtained at 50 to 90 keV with use of MCA.

Results

With the use of MCA, the average score of CMA was significantly higher for images obtained at each energy level from 50 to 70 keV (P < 0.05) and was comparable at 80 and 90 keV, and it was comparable among those obtained at 50 to 70 keV. With its use, the percentages of image interpretability were similarly high at 50 to 70 keV at 60 to 80 beats per minute (78%–100%), and they were higher at 50 to 60 keV (72%–83%) than at 70 keV at 90 to 100 beats per minute (50%–56%). The percentages of improved image interpretability with MCA were similarly high at 50 to 70 keV at 60 to 80 beats per minute (56%–100%), and they were higher at 50 to 60 keV (62%–77%) than at 70 keV at 90 to 100 beats per minute (36%–43%). The percentages of image interpretability and improved image interpretability with MCA were insufficient at 80 and 90 keV.

Conclusions

Coronary motion artifacts were significantly reduced in images of monochromatic CCTA obtained at 50 to 70 keV in combination with MCA compared with those obtained without MCA, and the percentages of image interpretability and improved image interpretability with use of MCA were relatively high at 50 to 70 keV, and particularly at 50 to 60 keV, even at 90 to 100 beats per minute.
The importance of key supplier relationship management in supply chains
Authors: Teller Christoph , Kotzab Herbert , Grant David B. , Holweg Christina
Published: February 2016

Purpose

– The purpose of this paper is to investigate the impact of key supplier relationship management (KSRM) – understood as an aggregated supply chain management (SCM) process in the upstream direction – on the overall level of the execution of SCM within organizations.

Design/methodology/approach

– A conceptual model is developed from a theoretical framework and proposes the capability to do KSRM as a mediator between internal and external SCM resources and SCM execution. A survey of 174 managers representing different supply chain stages is used to test the model through variance-based structural equation modelling.

Findings

– The findings reveal that external SCM resources directly affect the capability to do KSRM. Nevertheless, internal resources show a considerable indirect impact through external resources and can thus be considered an indirect determinant. The capability to do KSRM in turn impacts upon the level of SCM execution, measured in terms of the integration of business processes, directly and substantially, as well as mediating the effect between SCM resources and the level of SCM execution.

Originality/value

– The main contribution of this paper is to empirically demonstrate the potential of KSRM for enhancing the level of SCM execution within organizations and consequently the level of integration in supply chains, leading to higher customer and shareholder value.
A phase I pharmacokinetics trial comparing PF‐05280586 (a potential biosimilar) and rituximab in patients with active rheumatoid arthritis
Authors: Cohen Stanley , Emery Paul , Greenwald Maria , Yin Donghua , Becker Jean‐Claude , Melia Lisa Ann , Li Ruifeng , Gumbiner Barry , Thomas Dolca , Spencer‐Green George , Meng Xu
Published: February 2016

Aims

Pharmacokinetic (PK) similarity was assessed among PF‐05280586 (a proposed biosimilar) vs. rituximab sourced from the European Union (rituximab‐EU) and the United States (rituximab‐US). Pharmacodynamics (PD), overall safety and immunogenicity were also evaluated.

Methods

Patients with active rheumatoid arthritis on a background of methotrexate and inadequate response to one or more tumour necrosis factor antagonist therapies were randomized to intravenous PF‐05280586, rituximab‐EU or rituximab‐US 1000 mg doses on study days 1 and 15.

Results

A total of 220 patients were randomized to receive study treatment as assigned. Of these, 198 met per‐protocol population criteria for inclusion in the PK data analysis. PF‐05280586, rituximab‐EU and rituximab‐US exhibited similar PK profiles following administration of assigned study drug on days 1 and 15. The 90% confidence intervals of test‐to‐reference ratios for Cmax, AUCT, AUC0–∞ and AUC2‐week were within the bioequivalence margin of 80.00–125.00% for comparisons of PF‐05280586 with rituximab‐EU, PF‐05280586 with rituximab‐US, and rituximab‐EU with rituximab‐US. All treatments resulted in a rapid and profound reduction in CD19+ B cells and sustained profound B cell suppression up to week 25. The incidence of antidrug antibody (ADA) response (n = 7, 10 and 9 for PF‐05280586, rituximab‐EU and rituximab‐US, respectively), time to ADA emergence and ADA titres were similar across treatments. None of the ADA‐positive samples was positive for neutralizing activity. No clinically meaningful differences in adverse events were identified.

Conclusions

The study demonstrated PK similarity among PF‐05280586, rituximab‐EU and rituximab‐US. In addition, all treatments showed comparable CD19+ B cell depletion PD responses, as well as safety and immunogenicity profiles.
Fused Lasso with the Adaptation of Parameter Ordering in Combining Multiple Studies with Repeated Measurements
Authors: Wang Fei , Wang Lu , Song Peter X.-K.
Published: February 2016

Combining multiple studies is frequently undertaken in biomedical research to increase sample sizes for statistical power improvement. We consider the marginal model for the regression analysis of repeated measurements collected in several similar studies with potentially different variances and correlation structures. It is of great importance to examine whether there exist common parameters across study-specific marginal models so that simpler models, sensible interpretations, and meaningful efficiency gain can be obtained. Combining multiple studies via the classical means of hypothesis testing involves a large number of simultaneous tests for all possible subsets of common regression parameters, in which it results in unduly large degrees of freedom and low statistical power. We develop a new method of fused lasso with the adaptation of parameter ordering (FLAPO) to scrutinize only adjacent-pair parameter differences, leading to a substantial reduction for the number of involved constraints. Our method enjoys the oracle properties as does the full fused lasso based on all pairwise parameter differences. We show that FLAPO gives estimators with smaller error bounds and better finite sample performance than the full fused lasso. We also establish a regularized inference procedure based on bias-corrected FLAPO. We illustrate our method through both simulation studies and an analysis of HIV surveillance data collected over five geographic regions in China, in which the presence or absence of common covariate effects is reflective to relative effectiveness of regional policies on HIV control and prevention.
Kinematic gait deficits at the trunk and pelvis: characteristic features in children with hereditary spastic paraplegia
Authors: Adair Brooke , Rodda Jillian , McGinley Jennifer L , Graham H Kerr , Morris Meg E
Published: February 2016

Aim

To examine the kinematic gait deviations at the trunk and pelvis of children with hereditary spastic paraplegia (HSP).

Method

This exploratory observational study quantified gait kinematics for the trunk and pelvis from 11 children with HSP (7 males, 4 females) using the Gait Profile Score and Gait Variable Scores (GVS), and compared the kinematics to data from children with typical development using a Mann–Whitney U test.

Results

Children with HSP (median age 11y 4mo, interquartile range 4y) demonstrated large deviations in the GVS for the trunk and pelvis in the sagittal and coronal planes when compared to the gait patterns of children with typical development (p=0.010–0.020). Specific deviations included increased range of movement for the trunk in the coronal plane and increased excursion of the trunk and pelvis in the sagittal plane. In the transverse plane, children with HSP demonstrated later peaks in posterior pelvic rotation.

Interpretation

The kinematic gait deviations identified in this study raise questions about the contribution of muscle weakness in HSP. Further research is warranted to determine contributing factors for gait dysfunction in HSP, especially the relative influence of spasticity and weakness.