bluuebunny/crossref_metadata_2025 huggingface dataset:
A first principles study on the full-Heusler compound Cr2MnAl
Authors: Li Jia , Li Yangxian , Zhou Guoxiang , Sun Yubao , Sun Chang Q.
Published: June 2009

The Hg2CuTi-type structure is found to be preferable energy wise than the Cu2MnAl-type structure for full-Heusler Cr2MnAl and exhibits half-metallic ferromagnetism based on first principles. The calculations for the mixed compounds with disorder between B and D sublattices reveal that the case of exchanging one atom maintains the half-metallicity while the case of exchanging two atoms loses it. The electronic structures of the atoms at sites A or C are affected mainly by the nearest-neighboring coordination while that of the atoms at site B are determined by the next-nearest-neighboring coordination.
Development and testing of a sustainable environmental restoration policy on eradicating the poverty trap in China's Changting County
Authors: Cao Shixiong , Zhong Binglin , Yue Hui , Zeng Heshui , Zeng Jinhua
Published: June 2009

It is widely accepted that environmental degradation and poverty are linked and that conservation and poverty reduction should be tackled together. However, success with integrated strategies has been elusive. Here, we present the results of a study that illustrates how development that combines environmental and economic perspectives and that provides appropriate compensation to affected populations can improve both nature and society, thereby eradicating the “poverty trap.” The results show that if we cannot improve the livelihood of local residents, we will be unable to restore degraded environments when state-owned property is transferred to private ownership to encourage better management by residents. In contrast, measures to eliminate poverty, combined with the development of green enterprises that improve the livelihoods of private land owners in the long term, is the precondition for successful ecological restoration.
Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal
Authors: Cartwright Julyan H. E. , Checa Antonio G. , Escribano Bruno , Sainz-Díaz C. Ignacio
Published: June 2009

Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre.
Nature
211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth.
Discuss Faraday Soc
5:48–54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton–Cabrera–Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces.
Philos Trans R Soc London Ser A
243:299–358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications.
Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates
Authors: Lukeš Julius , Leander Brian S. , Keeling Patrick J.
Published: June 2009

The majority of eukaryotic diversity is hidden in protists, yet our current knowledge of processes and structures in the eukaryotic cell is almost exclusively derived from multicellular organisms. The increasing sensitivity of molecular methods and growing interest in microeukaryotes has only recently demonstrated that many features so far considered to be universal for eukaryotes actually exist in strikingly different versions. In other words, during their long evolutionary histories, protists have solved general biological problems in many more ways than previously appreciated. Interestingly, some groups have broken more rules than others, and the Euglenozoa and the Alveolata stand out in this respect. A review of the numerous odd features in these 2 groups allows us to draw attention to the high level of convergent evolution in protists, which perhaps reflects the limits that certain features can be altered. Moreover, the appearance of one deviation in an ancestor can constrain the set of possible downstream deviations in its descendents, so features that might be independent functionally, can still be evolutionarily linked. What functional advantage may be conferred by the excessive complexity of euglenozoan and alveolate gene expression, organellar genome structure, and RNA editing and processing has been thoroughly debated, but we suggest these are more likely the products of constructive neutral evolution, and as such do not necessarily confer any selective advantage at all.
Darwin's place in the history of thought: A reevaluation
Authors: Richards Robert J.
Published: June 2009

Scholars have usually given Darwin's theory a neo-Darwinian interpretation. A more careful examination of the language of Darwin's notebooks and the language of the
Origin of Species
indicates that he reconstructed nature with a definite purpose: the final goal of man as a moral creature. In the aftermath of the
Origin
, Darwin, however, became more circumspect.
Mate choice and sexual selection: What have we learned since Darwin?
Authors: Jones Adam G. , Ratterman Nicholas L.
Published: June 2009

Charles Darwin laid the foundation for all modern work on sexual selection in his seminal book
The Descent of Man, and Selection in Relation to Sex
. In this work, Darwin fleshed out the mechanism of sexual selection, a hypothesis that he had proposed in
The Origin of Species
. He went well beyond a simple description of the phenomenon by providing extensive evidence and considering the far-reaching implications of the idea. Here we consider the contributions of Darwin to sexual selection with a particular eye on how far we have progressed in the last 150 years. We focus on 2 key questions in sexual selection. First, why does mate choice evolve at all? And second, what factors determine the strength of mate choice (or intensity of sexual selection) in each sex? Darwin provided partial answers to these questions, and the progress that has been made on both of these topics since his time should be seen as one of the great triumphs of modern evolutionary biology. However, a review of the literature shows that key aspects of sexual selection are still plagued by confusion and disagreement. Many of these areas are complex and will require new theory and empirical data for complete resolution. Overall, Darwin's contributions are still surprisingly relevant to the modern study of sexual selection, so students of evolutionary biology would be well advised to revisit his works. Although we have made significant progress in some areas of sexual selection research, we still have much to accomplish.
Postcopulatory sexual selection: Darwin's omission and its consequences
Authors: Eberhard William G.
Published: June 2009

In one of his few major oversights, Darwin failed to appreciate that male–male competition and sexual selection can continue even after copulation has begun. The postcopulatory equivalents of both direct male–male battles (sperm competition) and female choice (cryptic female choice) occur within the female's body. Recognition of this hidden, but intense, sexual competition provides new insights into a variety of fields. These include the hyperdiverse and paradoxically elaborate morphology of both sperm and male genitalia, the equally puzzling and elaborate morphology of nongenitalic male structures that are specialized to grasp and stimulate females, powerful manipulative effects of substances in male semen on female reproductive physiology, paradoxical male courtship behavior that occurs after copulation has already begun, variability in parental investments, and the puzzlingly complex and diverse interactions between sperm and female products that surround animal eggs and between male gametophytes and female tissues in flowering plants. Many bizarre traits are involved, including male genitalia that are designed to explode or fall apart during copulation leaving behind parts within the female, male genitalia that “sing” during copulation, potent seminal products that invade the female's body cavity and her nervous system to influence her behavior, and a virtual Kama Sutra of courtship behavior performed after rather than before genital coupling, including male–female dialogues during copulation.
Algorithmic design of self-assembling structures
Authors: Cohn Henry , Kumar Abhinav
Published: June 2009

We study inverse statistical mechanics: how can one design a potential function so as to produce a specified ground state? In this article, we show that unexpectedly simple potential functions suffice for certain symmetrical configurations, and we apply techniques from coding and information theory to provide mathematical proof that the ground state has been achieved. These potential functions are required to be decreasing and convex, which rules out the use of potential wells. Furthermore, we give an algorithm for constructing a potential function with a desired ground state.
Multiple ecological pathways to extinction in mammals
Authors: Davidson Ana D. , Hamilton Marcus J. , Boyer Alison G. , Brown James H. , Ceballos Gerardo
Published: June 2009

As human population and resource demands continue to grow, biodiversity conservation has never been more critical. About one-quarter of all mammals are in danger of extinction, and more than half of all mammal populations are in decline. A major priority for conservation science is to understand the ecological traits that predict extinction risk and the interactions among those predictors that make certain species more vulnerable than others. Here, using a new database of nearly 4,500 mammal species, we use decision-tree models to quantify the multiple interacting factors associated with extinction risk. We show that the correlates of extinction risk vary widely across mammals and that there are unique pathways to extinction for species with different lifestyles and combinations of traits. We find that risk is relative and that all kinds of mammals, across all body sizes, can be at risk depending on their specific ecologies. Our results increase the understanding of extinction processes, generate simple rules of thumb that identify species at greatest risk, and highlight the potential of decision-tree analyses to inform conservation efforts.
Graded synaptic transmission at the
Caenorhabditis elegans
neuromuscular junction
Authors: Liu Qiang , Hollopeter Gunther , Jorgensen Erik M.
Published: June 2009

Most neurotransmission is mediated by action potentials, whereas sensory neurons propagate electrical signals passively and release neurotransmitter in a graded manner. Here, we demonstrate that
Caenorhabditis elegans
neuromuscular junctions release neurotransmitter in a graded fashion. When motor neurons were depolarized by light-activation of channelrhodopsin-2, the evoked postsynaptic current scaled with the strength of the stimulation. When motor neurons were hyperpolarized by light-activation of halorhodopsin, tonic release of synaptic vesicles was decreased. These data suggest that both evoked and tonic neurotransmitter release is graded in response to membrane potential. Acetylcholine synapses are depressed by high-frequency stimulation, in part due to desensitization of the nicotine-sensitve ACR-16 receptor. By contrast, GABA synapses facilitate before becoming depressed. Graded transmission and plasticity confer a broad dynamic range to these synapses. Graded release precisely transmits stimulation intensity, even hyperpolarizing inputs. Synaptic plasticity alters the balance of excitatory and inhibitory inputs into the muscle in a use-dependent manner.
Darwin's “strange inversion of reasoning”
Authors: Dennett Daniel
Published: June 2009

Darwin's theory of evolution by natural selection unifies the world of physics with the world of meaning and purpose by proposing a deeply counterintuitive “inversion of reasoning” (according to a 19th century critic): “to make a perfect and beautiful machine, it is not requisite to know how to make it” [MacKenzie RB (1868) (Nisbet & Co., London)]. Turing proposed a similar inversion: to be a perfect and beautiful computing machine, it is not requisite to know what arithmetic is. Together, these ideas help to explain how we human intelligences came to be able to discern the reasons for all of the adaptations of life, including our own.
Dynamic responsiveness of the vascular bed as a regulatory mechanism in vasomotor control
Authors: Zamir Mair , Norton Katelyn , Fleischhauer Arlene , Frances Maria F. , Goswami Ruma , Usselman Charlotte W. , Nolan Robert P. , Shoemaker J. Kevin
Published: June 2009

The dynamics of blood supply to a vascular bed depend on lumped mechanical properties of that bed, namely the compliance (C), resistance (R), viscoelasticity (K), and inertance (L). While the study of regulatory mechanisms has so far placed the emphasis largely on R, it is not known how the remaining properties contribute collectively to the play of dynamics in vasomotor control. To examine this question and to establish some benchmark values of these properties, simultaneous measurements of pressure and flow waveforms in the vascular bed of the forearm were obtained from three groups: young healthy individuals, older hypertensives with controlled blood pressure, and older hypertensives with uncontrolled blood pressure. The values of R and C were found to vary within a wide range in each of the three groups to the extent that neither R nor C could be used independently as an indicator of health or age of the subjects tested. However, higher level dynamic properties of the bed, such as the time constants and damping index, which depend on combinations of C,K, and L, and which may reflect measures of the dynamic responsiveness or “sluggishness” of the system, were found to be maintained over a wide range of pulse pressures. These findings support a hypothesis that the pulsatile dynamics of blood supply to a vascular bed are adapted to the individual baseline values of R and C in different subjects with the effect of optimizing the level of dynamic responsiveness to changes in pressure or flow, and that this dynamic property of the vascular bed may be a protected and/or regulated property.
Multiple intermediate states precede pore block during N-type inactivation of a voltage-gated potassium channel
Authors: Prince-Carter Alison , Pfaffinger Paul J.
Published: June 2009

N-type inactivation of voltage-gated potassium channels is an autoinhibitory process that occurs when the N terminus binds within the channel pore and blocks conduction. N-type inactivation and recovery occur with single-exponential kinetics, consistent with a single-step reaction where binding and block occur simultaneously. However, recent structure–function studies have suggested the presence of a preinactivated state whose formation and loss regulate inactivation and recovery kinetics. Our studies on N-type inactivation of the Shaker-type AKv1 channel support a multiple-step inactivation process involving a series of conformational changes in distinct regions of the N terminus that we have named the polar, flex, and latch regions. The highly charged polar region forms interactions with the surface of the channel leading up to the side window openings between the T1 domain and the channel transmembrane domains, before the rate-limiting step occurs. This binding culminates with a specific electrostatic interaction between R18 and EDE161-163 located at the entrance to the side windows. The latch region appears to work together with the flex region to block the pore after polar region binding occurs. Analysis of tail currents for a latch region mutant shows that both blocked and unblocked states exist after the rate-limiting transition is passed. Our results suggest that at least two intermediate states exist for N-type inactivation: a polar region–bound state that is formed before the rate-limiting step, and a pre-block state that is formed by the flex and latch regions during the rate-limiting step.
A Multicenter Study on Optimizing Piperacillin-Tazobactam Use: Lessons on Why Interventions Fail
Authors: Gaynes Robert P. , Gould Carolyn V. , Edwards Jonathan , Antoine Theresa L. , Blumberg Henry M. , DeSilva Kathryn , King Mark , Kraman Alice , Pack Jan , Ribner Bruce , Seybold Ulrich , Steinberg James , Jernigan John A.
Published: June 2009

We examined interventions to optimize piperacillin-tazobactam use at 4 hospitals. Interventions for rotating house staff did not affect use. We could target empiric therapy in only 35% of cases. Because prescribing practices seemed to be institution specific, interventions should address attitudes of local prescribers. Interventions should target empiric therapy and ordering of appropriate cultures.
InterMap3D: predicting and visualizing co-evolving protein residues
Authors: Gouveia-Oliveira Rodrigo , Roque Francisco S. , Wernersson Rasmus , Sicheritz-Ponten Thomas , Sackett Peter W. , Mølgaard Anne , Pedersen Anders G.
Published: June 2009

Summary: InterMap3D predicts co-evolving protein residues and plots them on the 3D protein structure. Starting with a single protein sequence, InterMap3D automatically finds a set of homologous sequences, generates an alignment and fetches the most similar 3D structure from the Protein Data Bank (PDB). It can also accept a user-generated alignment. Based on the alignment, co-evolving residues are then predicted using three different methods: Row and Column Weighing of Mutual Information, Mutual Information/Entropy and Dependency. Finally, InterMap3D generates high-quality images of the protein with the predicted co-evolving residues highlighted.

Availability:  http://www.cbs.dtu.dk/services/InterMap3D/

Contact:  gorm@cbs.dtu.dk
Comments on the analysis of unbalanced microarray data
Authors: Kerr Kathleen F.
Published: June 2009

Motivation: Permutation testing is very popular for analyzing microarray data to identify differentially expressed (DE) genes; estimating false discovery rates (FDRs) is a very popular way to address the inherent multiple testing problem. However, combining these approaches may be problematic when sample sizes are unequal.

Results: With unbalanced data, permutation tests may not be suitable because they do not test the hypothesis of interest. In addition, permutation tests can be biased. Using biased P-values to estimate the FDR can produce unacceptable bias in those estimates. Results also show that the approach of pooling permutation null distributions across genes can produce invalid P-values, since even non-DE genes can have different permutation null distributions. We encourage researchers to use statistics that have been shown to reliably discriminate DE genes, but caution that associated P-values may be either invalid, or a less-effective metric for discriminating DE genes.

Contact:  katiek@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Co-Creation of a Retail Innovation: Shoppers and the Early Supermarket in Britain
Authors: Alexander Andrew , Nell Dawn , Bailey Adrian R. , Shaw Gareth
Published: June 2009

In this paper we examine shoppers' reactions to the development of early supermarket retailing in post-war Britain. Positioning our discussion in relation to multi-disciplinary contributions on the role of consumers in innovation, we argue that more attention needs to be given to the shopper's input in the debate on retail innovation, including the supermarket. New oral history data drawn from a nationwide survey is presented in support of our arguments. Shoppers' contributions to the supermarket innovation are shown to be multi-faceted in nature, incorporating processes of co-production and value creation; processes that were altered in the transition from counter-service to self-service retail environments. Shoppers' discussions of such alterations were frequently structured around four aspects of interaction; with the physical environment of the store, with the goods for sale, with other shoppers and with shop staff. Whilst increasingly part of ‘ordinary consumption’ routines, the data highlights that in the switch to the supermarket, shopping became a more reflective activity and one that resulted in a variety of experiences and emotions.
Viability of Oomycete Propagules Following Ingestion and Excretion by Fungus Gnats, Shore Flies, and Snails
Authors: Hyder Naveen , Coffey Michael D. , Stanghellini Michael E.
Published: June 2009

Sporangia of Phytophthora capsici and P. nicotianae, as well as hyphal swellings of Pythium splendens, P. sylvaticum, and P. ultimum, were ingested by adult shore flies but none were viable after passing through the digestive tract. Oospores of Pythium aphanidermatum retained their viability following ingestion by adult shore flies. Larval stages of fungus gnats and shore flies ingested sporangia of Phytophthora capsici, P. nicotianae, and P. ramorum, but they were not viable upon excretion. In contrast, hyphal swellings of Pythium splendens, P. sylvaticum, and P. ultimum, chlamydospores of Phytophthora ramorum, and oospores of Pythium aphanidermatum, retained their viability after passage through the digestive tract of these larvae. Snails were capable of ingesting and excreting viable sporangia and chlamydospores of P. ramorum, which upon excretion infected detached leaves. Although the impact of larvae and snails in the rapid dissemination of pathogen propagules is unknown, this work does highlight the possibility that some often-ignored animal–fungus interactions should be considered in long-range dispersal of pathogen propagules via food webs.
First Report of Septoria Leaf Spot of Pistachio in New Mexico
Authors: French J. M. , Heerema R. J. , Gordon E. A. , Goldberg N. P.
Published: June 2009

In September of 2008, a Septoria sp., the causal agent of Septoria leaf spot of pistachio (Pistacia vera L.) was isolated from leaf lesions in an orchard in southern New Mexico. Tree fruit and nut crops including pistachios are becoming an increasingly important part of New Mexico's agricultural industry with total cash receipts of $103 million in 2007 (3). This preliminary positive for Septoria prompted a survey of pistachio-growing counties in the state. The surveyed orchards accounted for approximately 30% of the pistachio acreage in New Mexico. Results indicated that all five pistachio-growing counties had orchards infected with a Septoria sp. Isolates of Septoria from leaf lesions were identified as Septoria pistaciarum Caracc. based on the following symptoms and morphological characteristics of the fungus: leaf lesions were usually circular, 0.5 to 3 mm in diameter, and contained many pycnidia per lesion; pycnidia were dark, ostiolate, and measured 101 to 255 × 69 to 133 μm; and conidia were hyaline, filiform, contained 3 to 9 septa, and measured 3 to 4 × 60 to 149 μm. Most orchards were only mildly affected. In severe cases, hundreds of leaf lesions were present on diseased leaves; large sections of the leaves turned tan and some trees defoliated prematurely. This widespread occurrence of Septoria leaf spot in New Mexico in 2008 suggests that the disease had already been present in the state for several years. A higher average rainfall in the summer of 2008 provided excellent conditions for disease development. Because of the high amounts of inoculum currently present in New Mexico orchards, Septoria leaf spot may emerge as a recurring disease problem for pistachio producers. This disease was first reported in the United States in Texas in 1971 and was also reported in Arizona in 1989 (1,2,4). To our knowledge, this is the first report of Septoria leaf spot of pistachio in New Mexico.

References: (1) A. Chitzandis. Ann. Inst. Phytopathol. Benaki 10:29, 1956. (2) J. L. Maas et al. Plant Dis. Rep. 55:72, 1971. (3) New Mexico Agricultural Statistics, Department of Agriculture, 2007. (4) D. J. Young and T. Michailides. Plant Dis. 73:775, 1989.
Hybrid LES–RANS: back scatter from a scale-similarity model used as forcing
Authors: Davidson Lars
Published: June 2009

A dissipative scale-similarity subgrid model was recently proposed in which only the dissipative part of the subgrid stresses was added to the momentum equations. This was achieved by adding the gradient of a subgrid stress only when its sign agreed with that of the corresponding viscous term. In the present work, this idea is used the other way around as forcing in hybrid large eddy simulation–Reynolds-averaged Navier–Stokes: only the part of a subgrid stress term that corresponds to back scatter is added to the momentum equations. The forcing triggers resolved turbulence in the transition region between the unsteady Reynolds-averaged Navier–Stokes and large eddy simulation regions. The new approach is evaluated for fully developed channel flow at
Re

τ

=4000. It is found that the forcing indeed does increase the resolved turbulence in the transition region. The magnitude of the production (i.e. back scatter) due to forcing in the equation for resolved kinetic energy is of the order of that due to the usual strain-rate production term. The present approach of using back scatter from a scale-similarity model can also probably be useful for triggering transition.
Application of monotone integrated large eddy simulation to Rayleigh–Taylor mixing
Authors: Youngs David L.
Published: June 2009

Rayleigh–Taylor (RT) instability occurs when a dense fluid rests on top of a light fluid in a gravitational field. It also occurs in an equivalent situation (in the absence of gravity) when an interface between fluids of different density is accelerated by a pressure gradient, e.g. in inertial confinement fusion implosions. Engineering models (Reynolds-averaged Navier–Stokes models) are needed to represent the effect of mixing in complex applications. However, large eddy simulation (LES) currently makes an essential contribution to understanding the mixing process and calibration or validation of the engineering models. In this paper, three cases are used to illustrate the current role of LES: (i) mixing at a plane boundary, (ii) break-up of a layer of dense fluid due to RT instability, and (iii) mixing in a simple spherical implosion. A monotone integrated LES approach is preferred because of the need to treat discontinuities in the flow, i.e. the initial density discontinuities or shock waves. Of particular interest is the influence of initial conditions and how this needs to be allowed for in engineering modelling. It is argued that loss of memory of the initial conditions is unlikely to occur in practical applications.
Large eddy simulation applications in gas turbines
Authors: Menzies Kevin
Published: June 2009

The gas turbine presents significant challenges to any computational fluid dynamics techniques. The combination of a wide range of flow phenomena with complex geometry is difficult to model in the context of Reynolds-averaged Navier–Stokes (RANS) solvers. We review the potential for large eddy simulation (LES) in modelling the flow in the different components of the gas turbine during a practical engineering design cycle. We show that while LES has demonstrated considerable promise for reliable prediction of many flows in the engine that are difficult for RANS it is not a panacea and considerable application challenges remain. However, for many flows, especially those dominated by shear layer mixing such as in combustion chambers and exhausts, LES has demonstrated a clear superiority over RANS for moderately complex geometries although at significantly higher cost which will remain an issue in making the calculations relevant within the design cycle.
The effects of turbidity and an invasive species on foraging success of rosyside dace (Clinostomus funduloides)
Authors: HAZELTON PETER D. , GROSSMAN GARY D.
Published: June 2009

1. Habitat degradation and biological invasions are important threats to fish diversity worldwide. We experimentally examined the effects of turbidity, velocity and intra‐ and interspecific competition on prey capture location, reactive distance and prey capture success of native rosyside dace (Clinostomus funduloides) and invasive yellowfin shiners (Notropis lutipinnis) in Coweeta Creek, North Carolina, U.S.A.

2. Increased turbidity and velocity produced significant decreases in the number of prey captured forward of the fish’s location. It is possible that this represents an increase in the amount of energy expended per prey captured.

3. We used Akaike’s Information Criterion (AIC) to evaluate competing explanatory models for reactive distance (10 generalised linear models, GLM) and prey capture success (9 generalised linear mixed models, GLMM).

4. Reactive distance decreased by 12% with an increase from 2 to 4 conspecifics, whereas a 10 NTU increase in turbidity reduced reactive distance by 9%. Capture success was affected by velocity, dominance and competition, and varied among species. A 6 cm s−1 increase in velocity produced a 28% decline in capture probability; however, dominant fish were 3.2 times more likely to capture a prey item than non‐dominant fish. Yellowfin shiners only were 0.62 times as likely to capture a prey item as rosyside dace. Both intra‐ and interspecific competition reduced capture probability, and fish in high density intraspecific or interspecific trials were 0.46 times and 0.44 times as likely to capture prey, respectively, as fish in two fish intraspecific trials.

5. These results suggest behavioural variables are as important as physical factors in determining reactive distance and capture probability by these minnows.
The sperm penetration assay predicts the litter size in pigs
Authors: Oh Shin‐Ae , You Young‐Ah , Park Yoo‐Jin , Pang Myung‐Geol
Published: June 2009

The prediction of sperm fertility is of paramount importance for breeding animals. Multiple laboratory approaches have been developed for this purpose, but they have yielded equivocal results. The objective of this study was to develop and standardize to a method for predicting fertility in vivo in boars using the in vitro penetration assay. To increase the sensitivity and reduce false‐negative results of the assay, each step in the procedure was standardized and quality control was applied. Maximum penetration of hamster zona‐free oocytes and immature porcine oocytes was obtained using heparin‐treated sperm cells. Hamster zona‐free oocytes showed a significantly higher penetration than immature porcine oocytes. To eliminate interassay variability, two frozen bull semen samples were applied. All possible variables related to the female were excluded. The SPA (sperm penetration assay using zona‐free oocytes) result showed significant correlation with historic average litter size but had no significant correlation with farrowing rates. To determine the normal range for the SPA, lower limits of the sperm fertility index were established as 1.2 for the small litter sizes (<8 piglets) and 2.5 for the large litter sizes. The overall accuracy was 92 and 96% respectively, for the small and large litter sizes. Our laboratory has standardized the procedure for the SPA, resulting in greatly increased sensitivities for small and large litter sizes. The protocol increases the ability to discriminate between good and poor fertility groups and it was highly effective at ranking 24 boars by litter size into large and small litter groups.
Husbandry stress exacerbates mycobacterial infections in adult zebrafish, Danio rerio (Hamilton)
Authors: Ramsay J M , Watral V , Schreck C B , Kent M L
Published: June 2009

Mycobacteria are significant pathogens of laboratory zebrafish, Danio rerio (Hamilton). Stress is often implicated in clinical disease and morbidity associated with mycobacterial infections but has yet to be examined with zebrafish. The aim of this study was to examine the effects of husbandry stressors on zebrafish infected with mycobacteria. Adult zebrafish were exposed to Mycobacterium marinum or Mycobacterium chelonae, two species that have been associated with disease in zebrafish. Infected fish and controls were then subjected to chronic crowding and handling stressors and examined over an 8‐week period. Whole‐body cortisol was significantly elevated in stressed fish compared to non‐stressed fish. Fish infected with M. marinum ATCC 927 and subjected to husbandry stressors had 14% cumulative mortality while no mortality occurred among infected fish not subjected to husbandry stressors. Stressed fish, infected with M. chelonae H1E2 from zebrafish, were 15‐fold more likely to be infected than non‐stressed fish at week 8 post‐injection. Sub‐acute, diffuse infections were more common among stressed fish infected with M. marinum or M. chelonae than non‐stressed fish. This is the first study to demonstrate an effect of stress and elevated cortisol on the morbidity, prevalence, clinical disease and histological presentation associated with mycobacterial infections in zebrafish. Minimizing husbandry stress may be effective at reducing the severity of outbreaks of clinical mycobacteriosis in zebrafish facilities.
Molecular characteristics of phytoplasmas associated with Flavescence dorée in clematis and grapevine and preliminary results on the role of Dictyophara europaea as a vector
Authors: Filippin L. , Jović J. , Cvrković T. , Forte V. , Clair D. , Toševski I. , Boudon‐Padieu E. , Borgo M. , Angelini E.
Published: June 2009

A survey was conducted over several years in Italy and the Balkans in order to gain an understanding of the relationship between the Flavescence dorée (FD) phytoplasma isolates found in clematis and grapevine. A total of 399 clematis and 107 grapevine samples were analyzed. The results showed that 36% of the Clematis vitalba plant samples were infected by phytoplasmas which, in grapevine, are associated with FD, a quarantine disease in Europe. Infected clematis plants were also found in areas where FD phytoplasma had never previously been reported to infect grapevine, such as Macedonia, Croatia and some areas of Italy and Serbia. Molecular data from three phytoplasma genomic fragments showed the presence of different FD phytoplasma isolates, all belonging to the 16SrV‐C subgroup, including the Italian FD‐C isolate, the isolate found in Serbia, an isolate similar to the French FD2000 and a new isolate typical of central Italy. A few clematis plants were infected with single nucleotide polymorphism, insertion or deletion mutants of the FD‐C isolate. Of all the potential Hemipteran vector species surveyed in Italy and Serbia, only 18 of 527 Dictyophara europaea individuals tested proved to be infected with the FD phytoplasma. Preliminary transmission experiments showed that this species is able to transmit the FD phytoplasma from clematis to grapevine. The presence of FD‐infected clematis and of D. europaea could, therefore, constitute a risk for FD epidemics in the European viticultural regions.
Variant Creutzfeldt‐Jakob disease and exposure to fractionated plasma products
Authors: Ward H. J. T. , MacKenzie J. M. , Llewelyn C. A. , Knight R. S. G. , Hewitt P. E. , Connor N. , Molesworth A. , Will R. G.
Published: June 2009

Background  The risk to public health of onward transmission of variant Creutzfeldt–Jakob disease (vCJD) via blood transfusion and plasma product administration is of on‐going concern, particularly with the recent reported detection of abnormal prion protein in a person with haemophilia.

Objectives  To describe the history of fractionated plasma product exposure in clinical cases of vCJD in the UK.

Methods  Through examination of records held at the National CJD Surveillance Unit (from relatives, general practices and hospitals).

Results  Nine out of 168 UK vCJD cases had a history of receipt of fractionated plasma products on 12 different occasions (1 pre‐vCJD risk in 1970, the remaining between 1989–1998). According to the UK CJD Incident Panel risk assessment criteria, 11 were low‐risk products and one was low or medium risk.

Conclusion  It is unlikely that any of the UK vCJD clinical cases to date were infected through exposure to fractionated plasma products. However, the possibility that such transmission may result in vCJD cases in the future cannot be excluded.
Novel blue light‐sensitive proteins from a metagenomic approach
Authors: Pathak G. P. , Ehrenreich A. , Losi A. , Streit W. R. , Gärtner W.
Published: June 2009

A microarray‐based approach was used to screen a soil metagenome for the presence of blue light (BL) photoreceptor‐encoding genes. The microarray carried 149 different 54‐mer oligonucleotides, derived from consensus sequences of light, oxygen and voltage (LOV) domain BL photoreceptor genes. Calibration of the microarrays allowed the detection of minimally 50 ng of genomic DNA against a background of 2–5 μg of genomic DNA. Identification of a positive cosmid clone was still possible for an amount of 0.25 ng against a background of 10 μg of labelled DNA clones. The array could readily identify targets carrying 4% sequence mismatch. Using the LOV microarray, up to 1200 library clones in concentrations of c. 20 ng each with a c. 40 kb insert size could be screened in a single batch. After calibration and reliability controls, the microarray was probed with cosmid‐cloned DNA from the thermophilic fraction of a soil sample. From this approach, a novel gene was isolated that encodes a protein consisting of several Per‐Arnt‐Sim domains, a LOV domain associated to a histidine kinase and a response regulator domain. The novel gene showed highest similarity to a known sequence from Kineococcus radiotolerans SRS30216 (58% identity for the LOV domain only) and to a gene from Methylibium petroleiphilum PM1 (57% identity). The gene, designated as ht‐met1 (Hamburg Thermophile Metagenome 1), was isolated and fully sequenced (3615 bp). ht‐met1 is followed by a second open reading frame encoding a Fe‐chelatase, an arrangement quite frequent for BL photoreceptors. The LOV domain region of ht‐met1 was subcloned and expressed yielding a fully functional, flavin‐containing LOV domain. Irradiation generated the typical LOV photochemistry, with the transient formation of a flavin‐protein photoadduct. The dark recovery lifetime was found as τREC = 120 s (20°C) and is among the fastest ones determined so far for bacterial LOV domains.
Maximal lipid oxidation in patients with type 2 diabetes is normal and shows an adequate increase in response to aerobic training
Authors: Mogensen M. , Vind B. F. , Højlund K. , Beck‐Nielsen H. , Sahlin K.
Published: June 2009

Aim: Insulin resistance in subjects with type 2 diabetes (T2D) and obesity is associated with an imbalance between the availability and the oxidation of lipids. We hypothesized that maximal whole‐body lipid oxidation during exercise (FATmax) is reduced and that training‐induced metabolic adaptation is attenuated in T2D.

Methods: Obese T2D (n = 12) and control (n = 11) subjects matched for age, sex, physical activity and body mass index completed 10 weeks of aerobic training. Subjects were investigated before and after training with maximal and submaximal exercise tests and euglycaemic–hyperinsulinaemic clamps combined with muscle biopsies.

Results: Training increased maximal oxygen consumption (VO2max) and muscle citrate synthase activity and decreased blood lactate concentrations during submaximal exercise in both groups (all p < 0.01). FATmax increased markedly (40–50%) in both T2D and control subjects after training (all p < 0.001). There were no significant differences in these variables and lactate threshold (%VO2max) between groups before or after training. Insulin‐stimulated glucose disappearance rate (Rd) was lower in T2D vs. control subjects both before and after training. Rd increased in response to training in both groups (all p < 0.01). There was no correlation between Rd and measures of oxidative capacity or lipid oxidation during exercise or the training‐induced changes in these parameters.

Conclusions: FATmax was not reduced in T2D, and muscle oxidative capacity increased adequately in response to aerobic training in obese subjects with and without T2D. These metabolic adaptations to training seem to be unrelated to changes in insulin sensitivity and indicate that an impaired capacity for lipid oxidation is not a major cause of insulin resistance in T2D.
Twice‐daily and three‐times‐daily dosing of a repaglinide/metformin fixed‐dose combination tablet provide similar glycaemic control
Authors: Raskin P. , Lewin A. , Reinhardt R. , Lyness W. ,   for the Repaglinide/Metformin Fixed‐Dose Combination Study Group
Published: June 2009

Aim: To assess the efficacy and safety of a new repaglinide/metformin fixed‐dose combination (FDC) tablet administered either twice a day (BID) or three times a day (TID) for the management of type 2 diabetes.

Methods: This was a 26‐week, multicentre, open‐label parallel trial in which subjects poorly controlled with mono‐ or dual‐oral antidiabetic therapy were randomized 1 : 1 : 1 to instead receive repaglinide/metformin FDC either BID or TID or a rosiglitazone/metformin FDC BID. Two primary hypotheses were tested in a hierarchical manner: (i) treatment with the repaglinide/metformin FDC BID is non‐inferior to that of the rosiglitazone/metformin FDC BID as measured by changes in haemoglobin A1c (HbA1c) (results presented in companion paper) and (ii) repaglinide/metformin BID is non‐inferior to repaglinide/metformin TID (as measured by changes in HbA1c). Additional efficacy and safety end‐points were also assessed.

Results: A total of 561 subjects were randomized; 383 completed the study. Repaglinide/metformin FDC BID was non‐inferior to repaglinide/metformin FDC TID with respect to HbA1c. Additionally, changes in mean fasting plasma glucose values from baseline to end of study were not significantly different between the BID and the TID dose groups. There were no major hypoglycaemic episodes reported in either group during the trial, and overall adverse event profiles were similar.

Conclusion: The efficacy of twice‐daily dosing of a repaglinide/metformin FDC tablet was non‐inferior to that of three‐times‐daily dosing.
Poly‐GLP‐1, a novel long‐lasting glucagon‐like peptide‐1 polymer, ameliorates hyperglycaemia by improving insulin sensitivity and increasing pancreatic beta‐cell proliferation
Authors: Ma X. , Hui H. , Liu Z. , He G. , Hu J. , Meng J. , Guan L. , Luo X.
Published: June 2009

Aim: The clinical value of glucagon‐like peptide‐1 (GLP‐1) is restricted because of its short half‐life. To overcome this limitation, a new polymer of GLP‐1 was developed by prodrug strategy, termed Poly‐GLP‐1, and its pharmacological properties were investigated.

Methods: The in vitro release kinetics of GLP‐1 from Poly‐GLP‐1 was analysed by Western blot. Plasma GLP‐1 levels following a single administration of Poly‐GLP‐1 were determined by enzyme‐linked immunosorbent assay. The in vitro effects of Poly‐GLP‐1 were evaluated using isolated pancreatic islets. The acute effects on glycaemic control and food intake were investigated in C57BL/6J mice s.c. administered with Poly‐GLP‐1. The chronic effects of Poly‐GLP‐1 on glycaemic control were further assessed in C57BL/6J and db/db mice treated twice daily for 6 weeks.

Results: Pro‐GLP‐1 dose dependently increased insulin secretion and decreased glucose, but did not exhibit the insulinotropic action in isolated pancreatic islets without plasma. The glucose‐lowering actions of Poly‐GLP‐1 (3 nmol/kg) remained no less than 12 h after a single injection. Poly‐GLP‐1 caused a durable restoration of glycaemic control, food intake and body weight gain in db/db mice following 6‐week administration. The chronic treatment with Poly‐GLP‐1 improved glucose tolerance and insulin sensitivity and increased β‐cell mass and proliferation in db/db mice. There was little effect on normal mice treated in the same manner.

Conclusions: Our results indicated that Poly‐GLP‐1, a novel GLP‐1 polymer, has long‐lasting and potent effects on glycaemic control in vivo, and these beneficial effects may be because of improvement of insulin sensitivity and promotion of islet growth and function.
The weight of US residence among immigrants: a systematic review
Authors: Oza‐Frank R. , Cunningham S. A.
Published: June 2009

As the number of immigrants in the USA continues to rise, it becomes increasingly important to understand how their health differs from native‐born individuals. Obesity is a public health concern and a component of health that may differ and change in important ways in immigrants. This research synthesizes the current literature on the relationship between immigrant duration of residence in the USA and body weight. Five databases from the health and social sciences were searched for all pertinent publications. Fifteen articles met inclusion criteria, 14 of which reported a significant, positive relationship between body mass index and duration of residence in the USA (all P‐values <0.10). Two studies reported a threshold effect of weight gain after 10 years of US residence, and another study reported that body mass index peaks after 21 years of duration for men and after 15 years for women. The results of this review suggest that weight gain prevention programmes would be beneficial for many immigrants within the first decade of residence in the USA. Prevention efforts may be more successful if nativity and acculturation are considered in addition to race/ethnicity. Future research is needed to identify the specific mechanisms through which living in the USA may adversely affect health outcomes.
Factors that may impede the weight loss response to exercise‐based interventions
Authors: Boutcher S. H. , Dunn S. L.
Published: June 2009

The results of exercise programmes designed to reduce body fat are disappointing. However, the reporting of weight loss as mean values disguises those individuals who do lose significant amounts of fat. Why some participants produce significant exercise‐induced fat loss whereas others lose little or increase fat stores is likely to be an outcome of a range of behavioural (e.g. sleep deprivation, caloric intake), inherited (e.g. muscle fibre type, gender) and physiological (e.g. hyperinsulinaemia, hypothyroidism) factors. The following review highlights possible factors involved in weight loss and discusses how individual differences may determine the extent of weight loss after an exercise intervention. Finally, implications for the treatment and prevention of obesity are discussed.