bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature independent shear piezoelectric response in relaxor-PbTiO3 based crystals
Authors: Li Fei , Zhang Shujun , Xu Zhuo , Wei Xiaoyong , Luo Jun , Shrout Thomas R.
Published: December 2010

The temperature dependence of the shear piezoelectric responses in relaxor-PbTiO3 based perovskite crystals with rhombohedral, orthorhombic, and tetragonal phases were investigated. Based on thermodynamic analysis, high shear piezoelectric coefficients (d24) and good thermal stability were predicted in orthorhombic crystals, owing to the “vertical” orthorhombic-rhombohedral phase boundary. By resonance measurements, shear piezoelectric coefficient d24 was found to be on the order of ∼2100 pC/N at room temperature, maintaining same value over the temperature range of −50–100 °C. In contrast, the shear piezoelectric coefficients d15, with values of 3300, 3600, and 2000 pC/N at room temperature for rhombohedral, orthorhombic, and tetragonal crystals, respectively, exhibited strong temperature dependent behavior due to their respective ferroelectric-ferroelectric phase transitions.
Top-emitting organic light-emitting diodes: Influence of cavity design
Authors: Hofmann Simone , Thomschke Michael , Freitag Patricia , Furno Mauro , Lüssem Björn , Leo Karl
Published: December 2010

We report on red top-emitting organic light-emitting diode structures with higher order cavities. The emission zone is placed in the first, second, and third antinodes of the electric field in the cavity by increasing the hole transport layer thickness. Furthermore, the thicknesses of the cathode and the capping layer are varied to achieve high efficiencies. Using doped charge transport layers and a phosphorescent emitter, we reach up to 29%, 17%, and 12% external quantum efficiencies for first, second, and third order devices, respectively. An optical model is further used to analyze the angular dependent emission.
The vertically stacked organic sensor-transistor on a flexible substrate
Authors: Jeong Shin Woo , Jeong Jin Wook , Chang Seongpil , Kang Seung Youl , Cho Kyoung Ik , Ju Byeong Kwon
Published: December 2010

The authors report on the photo-response characteristics of flexible sensor-transistor circuits (ST-circuits) made with (poly(3-hexylethiophene)/phenyl-C61-butryic acid methyl ester) (P3HT/PCBM) bulk heterojunction polymer and pentacene-based organic field-effect transistors, which are stacked via poly(dimethylsiloxane) (PDMS) on the plastic substrate. The results indicate that the anode-source current is variable because of both the charge separation of the photogenerated excitons and the accumulated charges at the OFET channel layer. The light dependent photo response (ΔI/I0) is modulated from 0.47 to 1.9 by the gate-source voltage at the fixed anode-source voltage of the ST-circuits.
Resonant manifestation of intrinsic nonlinearity within electroelastic micropower generators
Authors: Stanton Samuel C. , Erturk Alper , Mann Brian P. , Inman Daniel J.
Published: December 2010

This letter investigates the nonlinear response of a bimorph energy harvester comprised of lead zirconate titanate (PZT-5A) laminates. For near resonant excitations, we demonstrate significant intrinsic nonlinear behavior despite geometrically linear motion. Fourth order elastic and electroelastic tensor values for PZT-5A are identified following methods recently published concerning a PZT-5H bimorph. A response trend indicative of a nonlinear dissipative mechanism is discussed as well as the inadequacy of linear modeling. The PZT-5A bimorph exhibits an increased softening frequency response in comparison to PZT-5H. The results contained herein are also applicable to electroelastic sensor and actuator technologies.
Surface photoemission in a high-brightness electron beam radio frequency gun
Authors: Qian H. J. , Murphy J. B. , Shen Y. , Tang C. X. , Wang X. J.
Published: December 2010

We report the experimental characterization of high-brightness electron beam generation from a magnesium (Mg) photocathode. Both the quantum efficiency (QE) and the thermal emittance of an Mg cathode are experimentally investigated. The measured QE∼0.2% is the highest reported for a metal cathode. We observed no change in the Mg cathode thermal emittance as the QE varies from 0.015% to 0.15%. The upper-limit of the thermal emittance, 0.5 mm mrad, is about 50% lower than the theoretical prediction. Our results demonstrated the feasibility of having a high QE and a low thermal emittance simultaneously for a robust metal photocathode.
Nickel-affected silicon crystallization and silicidation on polyimide by multipulse excimer laser annealing
Authors: Alberti A. , La Magna A. , Cuscunà M. , Fortunato G. , Spinella C. , Privitera V.
Published: December 2010

Nickel enhanced amorphous Si crystallization and silicidation on polyimide were studied during multipulse excimer laser annealing (ELA) from submelting to melting conditions. A ∼8 nm thick Ni film was deposited on a 100 nm thick α-Si layer at ∼70 °C in order to promote partial nickel diffusion into silicon. In the submelting regime, Ni atoms distributed during deposition in α-Si and the thermal gradient due to the presence of the plastic substrate were crucial to induce low fluence (≥0.08 J/cm2) Si crystallization to a depth which is strictly related to the starting Ni profile. Αmorphous-Si crystallization is not expected on pure Si at those low fluences. Additional pulses at higher fluences do not modify the double poly-Si/α-Si structure until melting conditions are reached. At a threshold of ∼0.2 J/cm2, melting was induced simultaneously in the polycrystalline layer as well as in the residual α-Si due to a thermal gradient of ∼200 °C. Further increasing the laser fluence causes the poly-Si layer to be progressively melted to a depth which is proportional to the energy density used. As a consequence of the complete Si melting, columnar poly-Si grains are formed above 0.3 J/cm2. For all fluences, a continuous NiSi2 layer is formed at the surface which fills the large Si grain boundaries, with the beneficial effect of flattening the poly-Si surface. The results would open the perspective of integrating Ni-silicide layers as metallic contacts on Si during α-Si-crystallization by ELA on plastic substrate.
Large converse magnetoelectric coupling effect at room temperature in CoPd/PMN-PT (001) heterostructure
Authors: Kim Ju-Hyun , Ryu Kwang-Su , Jeong Jae-Woo , Shin Sung-Chul
Published: December 2010

We report a large converse magnetoelectric (CME) effect at room temperature in a multiferroic heterostructure formed from thin layers of perpendicularly magnetized CoxPd1-x alloys deposited on a piezoelectric single-crystal of lead magnesium niobate-lead titanate PMN-PT(001). The CME results from a strain-induced reorientation of the CoPd magnetization. By varying the composition and thickness of the CoxPd1-x film, a large converse magnetoelectric coupling constant, α=8×10−7 s/m, at room temperature was found for 10 nm Co0.25Pd0.75. This large CME effect results from combining a highly magnetostrictive CoPd alloy with highly piezoelectric PMN-PT.
Thermoelectric properties and electronic structure of substituted Heusler compounds: NiTi0.3−xScxZr0.35Hf0.35Sn
Authors: Ouardi Siham , Fecher Gerhard H. , Balke Benjamin , Schwall Michael , Kozina Xeniya , Stryganyuk Gregory , Felser Claudia , Ikenaga Eiji , Yamashita Yoshiyuki , Ueda Shigenori , Kobayashi Keisuke
Published: December 2010

The effect of Ti substitution by Sc on the thermoelectric properties of the Heusler compounds NiTi0.3−xScxZr0.35Hf0.35Sn (where 0<x≤0.05) was studied. The thermoelectric properties were investigated by measuring the electrical conductivity, Seebeck coefficient, and thermal conductivity. A reduction of the thermal conductivity by a factor of 2 was obtained by substitution of Ti by Sc. The pure compound NiTi0.3Zr0.35Hf0.35Sn showed n-type conductivity with a Seebeck coefficient of −288 μV/K at 350 K, while under Sc substitution the system switched to p-type behavior. A maximum Seebeck coefficient of +230 μV/K (350 K) was obtained by 4% Sc substitution, which is the highest value for p-type thermoelectric compounds based on Heusler alloys. The electronic structure was studied by photoelectron spectroscopy excited by hard x-ray synchrotron radiation. Massive in gap states are observed for the parent compound. This proves that the electronic states close to the Fermi energy play a key role on the behavior of the transport properties. Especially, they are responsible for the high, negative Seebeck coefficient of the parent compound.
Tuning the period of elastic MnAs/GaAs(001) α−β pattern by Fe deposition
Authors: Vidal F. , Spezzani C. , Breitwieser R. , Marangolo M. , Eddrief M. , Sacchi M. , Etgens V. H.
Published: December 2010

The α−β elastic striped pattern of MnAs/GaAs(001) is shown to be perturbed by Fe overlayer growth. After nanometric Fe thin film deposition, the elastic pattern is still present in the 10–45 °C temperature range, but the period of the pattern increases by up to 40% for MnAs epilayers 70 to 400 nm thick. This observation can be interpreted within a simple model calculation of the pattern elastic energy, providing quantitative agreement with the experimental results.
Improving the plasticity of a high strength Fe–Si–Ti ultrafine composite by introduction of an immiscible element
Authors: Park J. M. , Kim D. H. , Kim K. B. , Eckert J.
Published: December 2010

A heterostructured Fe71Si15Ti10Cu4 ultrafine composite has been developed. The addition of Cu with large positive enthalpy of mixing with the main constituent element (Fe) leads to evolution of a unique microstructure with different length-scale heterogeneities, i.e., formation of spherical colonies containing length-scale heterogeneity of lamellar spacing and precipitation of nanoscale multitwinned Cu within α-Fe layers. These macroscopic and microscopic structural heterogeneities are able to simultaneously achieve high strength and plasticity, together with pronounced work hardening by avoiding the deformation instability.
Approaches to investigate delamination and interfacial toughness in coated systems: an overview
Authors: Chen Jinju , Bull S J
Published: December 2010

The fundamental property which often dictates the performance of a coating is its adhesion to the substrate and thus there are many techniques to measure adhesion. The choice of methods is dependent on many factors such as the mechanical properties of the coating and substrate, the interface properties, the microstructure of the coating/substrate system, residual stress, coating thickness and the intended application. Most tests aim to introduce a stable interfacial crack and make it propagate under controlled conditions and model this process to determine adhesion. The corresponding models are either stress analysis-based or energy-based. With the advent of miniature systems and very thin functional coatings, there is a need for characterization of adhesion at small length scales and some specific tests have been developed which are not appropriate for thicker coatings. Among these, indentation and scratch methods have the widest range of applicability but it is necessary to analyse the failure mechanisms before choosing an appropriate model to extract adhesion parameters. This paper reviews the main quantitative adhesion tests for coatings and highlights the tests which can be used to assess submicrometre coatings and thin films. The paper also highlights the modelling and analysis methods necessary to extract reliable adhesion properties illustrating this with examples for submicrometre coatings on silicon and architectural glass.
Comparison of dynamic and quasi-static measurements of thin film adhesion
Authors: Tran Phuong , Kandula Soma S , Geubelle Philippe H , Sottos Nancy R
Published: December 2010

Adhesive failure and the attendant delamination of a thin film on a substrate is controlled by the fracture energy required to propagate a crack along the interface. Numerous testing protocols have been introduced to characterize this critical property, but are limited by difficulties associated with applying precise loads, introducing well-defined pre-cracks, tedious sample preparation and complex analysis of plastic deformation in the films. The quasi-static four-point bend test is widely accepted in the microelectronics industry as the standard for measuring adhesion properties for a range of multilayer thin film systems. Dynamic delamination methods, which use laser-induced stress waves to rapidly load the thin film interface, have recently been offered as an alternative method for extracting interfacial fracture energy. In this work, the interfacial fracture energy of an aluminium (Al) thin film on a silicon (Si) substrate is determined for a range of dynamic loading conditions and compared with values measured under quasi-static conditions in a four-point bend test. Controlled dynamic delamination of the Al/Si interface is achieved by efficient conversion of the kinetic energy associated with a laser-induced stress wave into fracture energy. By varying the laser fluence, the fracture energy is investigated over a range of stress pulse amplitudes and velocities. For lower amplitudes of the stress wave, the fracture energy is nearly constant and compares favourably with the critical fracture energy obtained using the four-point bend technique, about 2.5 J m−2. As the pulse amplitude increases, however, a rate dependence of the dynamic fracture energy is observed. The fracture energy increases almost linearly with pulse amplitude until reaching a plateau value of about 6.0 J m−2.
In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies
Authors: Novotný Ivan , Blažíková Michaela , Staneˇk David , Herman Petr , Malinsky Jan
Published: December 2010

The U4/U6·U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) is an essential pre-mRNA splicing factor, which is assembled in a stepwise manner before each round of splicing. It was previously shown that the tri-snRNP is formed in Cajal bodies (CBs), but little is known about the dynamics of this process. Here we created a mathematical model of tri-snRNP assembly in CBs and used it to fit kinetics of individual snRNPs monitored by fluorescence recovery after photobleaching. A global fitting of all kinetic data determined key reaction constants of tri-snRNP assembly. Our model predicts that the rates of di-snRNP and tri-snRNP assemblies are similar and that ∼230 tri-snRNPs are assembled in one CB per minute. Our analysis further indicates that tri-snRNP assembly is approximately 10-fold faster in CBs than in the surrounding nucleoplasm, which is fully consistent with the importance of CBs for snRNP formation in rapidly developing biological systems. Finally, the model predicted binding between SART3 and a CB component. We tested this prediction by Förster resonance energy transfer and revealed an interaction between SART3 and coilin in CBs.
Bid‐Ask Spreads, Volume, and Volatility: Evidence from Livestock Markets
Authors: Frank Julieta , Garcia Philip
Published: December 2010

Using literature‐based measures and a modified Bayesian method specified here, we estimate liquidity costs and their determinants for the live cattle and hog futures markets. Volume and volatility are simultaneously determined and significantly related to the bid‐ask spread. Daily volume is negatively related to the spread while volatility and average volume per transaction display positive relationships. Electronic trading has a significant competitive effect on liquidity costs, particularly in the live cattle market. Results are sensitive to the bid‐ask spread measure, with our modified Bayesian method providing estimates most consistent with expectations and the competitive structure in these markets.
Childhood Skin Rashes
Authors: Seo Ha-Neul , Evans Benedict
Published: December 2010

While the most prevalent skin conditions in the paediatric age group include acne, dermatitis/eczema, bacterial and fungal infections, recent articles published in InnovAiT cover these topics in detail. This article aims to provide an overview of some of the conditions frequently encountered in the paediatric dermatology clinic, considering in particular birthmarks, vascular malformations, neonatal skin conditions, paediatric skin tumours, mucocutaneous syndromes and infections, including viral exanthems.
Impact of Preoperative Statin Therapy on Adverse Postoperative Outcomes in Patients Undergoing Vascular Surgery
Authors: Le Manach Yannick , Ibanez Esteves Cristina , Bertrand Michelle , Goarin Jean Pierre , Fléron Marie-Hélène , Coriat Pierre , Koskas Fabien , Riou Bruno , Landais Paul
Published: December 2010

Background

Chronic statin therapy is associated with reduced postoperative mortality. Renal and cardiovascular benefits have been described, but the effect of chronic statin therapy on postoperative adverse events has not yet been explored.

Methods

In this observational study involving 1,674 patients undergoing aortic reconstruction, we prospectively assessed chronic statin therapy compared with no statin therapy, with regard to serious outcomes, by propensity score and multivariable methods.

Results

In propensity-adjusted multivariable logistic regression (c-index: 0.83), statins were associated with an almost threefold reduction in the risk of death in patients undergoing major vascular surgery (odds ratio: 0.40; 95% CI: 0.28-0.59) and an almost twofold reduction in the risk of postoperative myocardial infarction (odds ratio: 0.52; 95% CI: 0.38-0.71). Likewise, the use of chronic statin therapy was associated with a reduced risk of postoperative stroke and renal failure. Statins did not significantly reduce the risk of pneumonia, multiple organ dysfunction syndrome, and surgical complications; however, in the case of postoperative multiple organ dysfunction syndrome (odds ratio: 0.34; 95% CI: 0.12-0.94) and surgical complications (odds ratio: 0.39; 95% CI: 0.17-0.86), reduced mortality was observed.

Conclusions

Chronic statin therapy was associated with a reduction in all cardiac and vascular outcomes after major vascular surgery. Furthermore, in major adverse events, such as multiple organ dysfunction syndrome and surgical complications, statins were also associated with decreased mortality.
Penguin heat-retention structures evolved in a greenhouse Earth
Authors: Thomas Daniel B. , Ksepka Daniel T. , Fordyce R. Ewan
Published: December 2010

Penguins (Sphenisciformes) inhabit some of the most extreme environments on Earth. The 60+ Myr fossil record of penguins spans an interval that witnessed dramatic shifts in Cenozoic ocean temperatures and currents, indicating a long interplay between penguin evolution and environmental change. Perhaps the most celebrated example is the successful Late Cenozoic invasion of glacial environments by crown clade penguins. A major adaptation that allows penguins to forage in cold water is the humeral arterial plexus, a vascular counter-current heat exchanger (CCHE) that limits heat loss through the flipper. Fossil evidence reveals that the humeral plexus arose at least 49 Ma during a ‘Greenhouse Earth’ interval. The evolution of the CCHE is therefore unrelated to global cooling or development of polar ice sheets, but probably represents an adaptation to foraging in subsurface waters at temperate latitudes. As global climate cooled, the CCHE was key to invasion of thermally more demanding environments associated with Antarctic ice sheets.
Aquatic manoeuvering with counter-propagating waves: a novel locomotive strategy
Authors: Curet Oscar M. , Patankar Neelesh A. , Lauder George V. , MacIver Malcolm A.
Published: December 2010

Many aquatic organisms swim by means of an undulating fin. These undulations often form a single wave travelling from one end of the fin to the other. However, when these aquatic animals are holding station or hovering, there is often a travelling wave from the head to the tail, and another moving from the tail to the head, meeting in the middle of the fin. Our study uses a biomimetic fish robot and computational fluid dynamics on a model of a real fish to uncover the mechanics of these inward counter-propagating waves. In addition, we compare the flow structure and upward force generated by inward counter-propagating waves to standing waves, unidirectional waves, and outward counter-propagating waves (i.e. one wave travelling from the middle of the fin to the head, and another wave travelling from the middle of the fin to the tail). Using digital particle image velocimetry to capture the flow structure around the fish robot, and computational fluid dynamics, we show that inward counter-propagating waves generate a clear mushroom-cloud-like flow structure with an inverted jet. The two streams of fluid set up by the two travelling waves ‘collide’ together (forming the mushroom cap) and collect into a narrow jet away from the cap (the mushroom stem). The reaction force from this jet acts to push the body in the opposite direction to the jet, perpendicular to the direction of movement provided by a single travelling wave. This downward jet provides a substantial increase in the perpendicular force when compared with the other types of fin actuation. Animals can thereby move upward if the fin is along the bottom midline of the body (or downward if on top); or left–right if the fins are along the lateral margins. In addition to illuminating how a large number of undulatory swimmers can use elongated fins to move in unexpected directions, the phenomenon of counter-propagating waves provides novel motion capabilities for systems using robotic undulators, an emerging technology for propelling underwater vehicles.
Human tools of the European tertiary? Artefacts, brains and minds in evolutionist reasoning, 1870–1920
Authors: Sommer Marianne
Published: December 2010

This essay explores evolutionary reasoning and notions of progress at the turn of the twentieth century by focusing on the various interpretations used to understand eoliths. These ‘dawn’ (Greek
eos
) ‘stones’ (Greek
lithos
) were contested objects and I focus on three geographic episodes in which they were used to support scientific, and sometimes socially inspired, accounts of human origins. Particular attention is paid to the work of Gabriel de Mortillet (1821–98), James Reid Moir (1879–1944) and Henry Fairfield Osborn (1857–1935).
Electrokinetic self-propulsion by inhomogeneous surface kinetics
Authors: Yariv Ehud
Published: December 2010

Electrokinetic self-propulsion was conceptually proven in recent experiments wherein bimetallic nano-rods were observed to migrate when placed in aqueous solutions. We present here a systematic theoretical model of the self-propulsion mechanism, analysing the steady-state transport occurring about an autonomously moving inhomogeneous particle. The non-uniform catalysis on the particle surface is modelled via position-dependent cation redox coefficients. The particle shape is axisymmetric but otherwise arbitrary, as are the distributions of the (possibly discontinuous) kinetic coefficients along its boundary. We formulate the mathematical problem governing this electrokinetic transport. In the thin-Debye-layer limit, the microscale description is transformed into a macroscale one, applying in the electro-neutral bulk. Effective boundary conditions represent asymptotic matching with the Debye-layer fields. A linearized model is derived for weak variation of the kinetic coefficients and is solved for a spherical-particle geometry. With a view towards understanding existing experiments, the macroscale model is used for analysing slender particles. Matched asymptotic expansions provide the particle velocity as a functional of its shape and kinetic-coefficient distributions. The predicted self-propulsion is in the direction observed in nanorod experiments.
The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus
Authors: Adams Ben , McHardy Alice Carolyn
Published: December 2010

Punctuated antigenic change is believed to be a key element in the evolution of influenza A; clusters of antigenically similar strains predominate worldwide for several years until an antigenically distant mutant emerges and instigates a selective sweep. It is thought that a region of East–Southeast Asia with year-round transmission acts as a source of antigenic diversity for influenza A and seasonal epidemics in temperate regions make little contribution to antigenic evolution. We use a mathematical model to examine how different transmission regimes affect the evolutionary dynamics of influenza over the lifespan of an antigenic cluster. Our model indicates that, in non-seasonal regions, mutants that cause significant outbreaks appear before the peak of the wild-type epidemic. A relatively large proportion of these mutants spread globally. In seasonal regions, mutants that cause significant local outbreaks appear each year before the seasonal peak of the wild-type epidemic, but only a small proportion spread globally. The potential for global spread is strongly influenced by the intensity of non-seasonal circulation and coupling between non-seasonal and seasonal regions. Results are similar if mutations are neutral, or confer a weak to moderate antigenic advantage. However, there is a threshold antigenic advantage, depending on the non-seasonal transmission intensity, beyond which mutants can escape herd immunity in the non-seasonal region and there is a global explosion in diversity. We conclude that non-seasonal transmission regions are fundamental to the generation and maintenance of influenza diversity owing to their epidemiology. More extensive sampling of viral diversity in such regions could facilitate earlier identification of antigenically novel strains and extend the critical window for vaccine development.
The origin and dynamic evolution of chemical information transfer
Authors: Steiger Sandra , Schmitt Thomas , Schaefer H. Martin
Published: December 2010

Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general.
The impact of environmental change on host–parasite coevolutionary dynamics
Authors: Mostowy Rafal , Engelstädter Jan
Published: December 2010

Environmental factors are known to affect the strength and the specificity of interactions between hosts and parasites. However, how this shapes patterns of coevolutionary dynamics is not clear. Here, we construct a simple mathematical model to study the effect of environmental change on host–parasite coevolutionary outcome when interactions are of the matching-alleles or the gene-for-gene type. Environmental changes may effectively alter the selective pressure and the level of specialism in the population. Our results suggest that environmental change altering the specificity of selection in antagonistic interactions can produce alternating time windows of cyclical allele-frequency dynamics and cessation thereof. This type of environmental impact can also explain the maintenance of polymorphism in gene-for-gene interactions without costs. Overall, our study points to the potential consequences of environmental variation in coevolution, and thus the importance of characterizing genotype-by-genotype-by-environment interactions in natural host–parasite systems, especially those that change the direction of selection acting between the two species.
Seed-dispersal distributions by trumpeter hornbills in fragmented landscapes
Authors: Lenz Johanna , Fiedler Wolfgang , Caprano Tanja , Friedrichs Wolfgang , Gaese Bernhard H. , Wikelski Martin , Böhning-Gaese Katrin
Published: December 2010

Frugivorous birds provide important ecosystem services by transporting seeds of fleshy fruited plants. It has been assumed that seed-dispersal kernels generated by these animals are generally leptokurtic, resulting in little dispersal among habitat fragments. However, little is known about the seed-dispersal distribution generated by large frugivorous birds in fragmented landscapes. We investigated movement and seed-dispersal patterns of trumpeter hornbills (
Bycanistes bucinator
) in a fragmented landscape in South Africa. Novel GPS loggers provide high-quality location data without bias against recording long-distance movements. We found a very weakly bimodal seed-dispersal distribution with potential dispersal distances up to 14.5 km. Within forest, the seed-dispersal distribution was unimodal with an expected dispersal distance of 86 m. In the fragmented agricultural landscape, the distribution was strongly bimodal with peaks at 18 and 512 m. Our results demonstrate that seed-dispersal distributions differed when birds moved in different habitat types. Seed-dispersal distances in fragmented landscapes show that transport among habitat patches is more frequent than previously assumed, allowing plants to disperse among habitat patches and to track the changing climatic conditions.
Unshelled abalone and corrupted urchins: development of marine calcifiers in a changing ocean
Authors: Byrne Maria , Ho Melanie , Wong Eunice , Soars Natalie A. , Selvakumaraswamy Paulina , Shepard-Brennand Hannah , Dworjanyn Symon A. , Davis Andrew R.
Published: December 2010

The most fragile skeletons produced by benthic marine calcifiers are those that larvae and juveniles make to support their bodies. Ocean warming, acidification, decreased carbonate saturation and their interactive effects are likely to impair skeletogenesis. Failure to produce skeleton in a changing ocean has negative implications for a diversity of marine species. We examined the interactive effects of warming and acidification on an abalone (Haliotis coccoradiata) and a sea urchin (Heliocidaris erythrogramma) reared from fertilization in temperature and pH/pCO2treatments in a climatically and regionally relevant setting. Exposure of ectodermal (abalone) and mesodermal (echinoid) calcifying systems to warming (+2°C to 4°C) and acidification (pH 7.6–7.8) resulted in unshelled larvae and abnormal juveniles.Haliotisdevelopment was most sensitive with no interaction between stressors. ForHeliocidaris, the percentage of normal juveniles decreased in response to both stressors, although a +2°C warming diminished the negative effect of low pH. The number of spines produced decreased with increasing acidification/pCO2, and the interactive effect between stressors indicated that a +2°C warming reduced the negative effects of low pH. At +4°C, the developmental thermal tolerance was breached. Our results show that projected near-future climate change will have deleterious effects on development with differences in vulnerability in the two species.
Genomic signatures of diet-related shifts during human origins
Authors: Babbitt Courtney C. , Warner Lisa R. , Fedrigo Olivier , Wall Christine E. , Wray Gregory A.
Published: December 2010

There are numerous anthropological analyses concerning the importance of diet during human evolution. Diet is thought to have had a profound influence on the human phenotype, and dietary differences have been hypothesized to contribute to the dramatic morphological changes seen in modern humans as compared with non-human primates. Here, we attempt to integrate the results of new genomic studies within this well-developed anthropological context. We then review the current evidence for adaptation related to diet, both at the level of sequence changes and gene expression. Finally, we propose some ways in which new technologies can help identify specific genomic adaptations that have resulted in metabolic and morphological differences between humans and non-human primates.
Costs of memory: lessons from ‘mini’ brains
Authors: Burns James G. , Foucaud Julien , Mery Frederic
Published: December 2010

Variation in learning and memory abilities among closely related species, or even among populations of the same species, has opened research into the relationship between cognition, ecological context and the fitness costs, and benefits of learning and memory. Such research programmes have long been dominated by vertebrate studies and by the assumption of a relationship between cognitive abilities, brain size and metabolic costs. Research on these ‘large brained’ organisms has provided important insights into the understanding of cognitive functions and their adaptive value. In the present review, we discuss some aspects of the fitness costs of learning and memory by focusing on ‘mini-brain’ studies. Research on learning and memory in insects has challenged some traditional positions and is pushing the boundaries of our understanding of the evolution of learning and memory.
The soxRS response of Escherichia coli can be induced in the absence of oxidative stress and oxygen by modulation of NADPH content
Authors: Krapp Adriana R. , Humbert María Victoria , Carrillo Néstor
Published: December 2010

ThesoxRSregulon protectsEscherichia colicells against superoxide and nitric oxide. Oxidation of the SoxR sensor, a [2Fe–2S]-containing transcriptional regulator, triggers the response, but the nature of the cellular signal sensed by SoxR is still a matter of debate.In vivo, the sensor is maintained in a reduced, inactive state by the activities of SoxR reductases, which employ NADPH as an electron donor. The hypothesis that NADPH levels affect deployment of thesoxRSresponse was tested by transformingE. colicells with genes encoding enzymes and proteins that lead to either build-up or depletion of the cellular NADPH pool. Introduction of NADP+-reducing enzymes, such as wheat non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase orE. colimalic enzyme, led to NADPH accumulation, inhibition of thesoxRSregulon and enhanced sensitivity to the superoxide propagator methyl viologen (MV). Conversely, expression of pea ferredoxin (Fd), a redox shuttle that can oxidize NADPH via ferredoxin-NADP(H) reductase, resulted in execution of thesoxRSresponse in the absence of oxidative stress, and in higher tolerance to MV. Processes that caused NADPH decline, including oxidative stress and Fd activity, correlated with an increase in total (NADP++NADPH) stocks. SoxS expression can be induced by Fd expression or by MV in anaerobiosis, under conditions in which NADPH is oxidized but no superoxide can be formed. The results indicate that activation of thesoxRSregulon inE. colicells exposed to superoxide-propagating compounds can be triggered by depletion of the NADPH stock rather than accumulation of superoxide itself. They also suggest that bacteria need to finely regulate homeostasis of the NADP(H) pool to enable proper deployment of this defensive response.
Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii
Authors: Tanigawa Kana , Watanabe Koichi
Published: December 2010

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080T, was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.
Recombinant lactobacilli expressing linoleic acid isomerase can modulate the fatty acid composition of host adipose tissue in mice
Authors: Rosberg-Cody Eva , Stanton Catherine , O'Mahony Liam , Wall Rebecca , Shanahan Fergus , Quigley Eamonn M. , Fitzgerald Gerald F. , Ross R. Paul
Published: December 2010

We have previously demonstrated that oral administration of a metabolically activeBifidobacterium brevestrain, with ability to formcis-9,trans-11 conjugated linoleic acid (CLA), resulted in modulation of the fatty acid composition of the host, including significantly elevated concentrations ofc9,t11 CLA and omega-3 (n-3) fatty acids in liver and adipose tissue. In this study, we investigated whether a recombinant lactobacillus expressing linoleic acid isomerase (responsible for production oft10,c12 CLA) fromPropionibacterium acnes(PAI) could influence the fatty acid composition of different tissues in a mouse model. Linoleic-acid-supplemented diets (2 %, w/w) were fed in combination with either a recombinantt10,c12 CLA-producingLactobacillus paracaseiNFBC 338 (Lb338), or an isogenic (vector-containing) control strain, to BALB/c mice for 8 weeks. A third group of mice received linoleic acid alone (2 %, w/w). Tissue fatty acid composition was assessed by GLC at the end of the trial. Ingestion of the strain expressing linoleic acid isomerase was associated with a 4-fold increase (P<0.001) int10,c12 CLA in adipose tissues of the mice when compared with mice that received the isogenic non-CLA-producing strain. The livers of the mice that received the recombinant CLA-producing Lb338 also contained a 2.5-fold (albeit not significantly) higher concentration oft10,c12 CLA, compared to the control group. These data demonstrate that a single gene (encoding linoleic acid isomerase) expressed in an intestinal microbe can influence the fatty acid composition of host fat.
Cytochrome c 4 is required for siderophore expression by Legionella pneumophila, whereas cytochromes c 1 and c 5 promote intracellular infection
Authors: Yip Emily S. , Burnside Denise M. , Cianciotto Nicholas P.
Published: December 2010

A panel of cytochromecmaturation (ccm) mutants ofLegionella pneumophiladisplayed a loss of siderophore (legiobactin) expression, as measured by both the chrome azurol S assay and aLegionella-specific bioassay. These data, coupled with the finding thatccmtranscripts are expressed by wild-type bacteria grown in deferrated medium, indicate that the Ccm system promotes siderophore expression byL. pneumophila. To determine the basis of this newfound role for Ccm, we constructed and tested a set of mutants specifically lacking individualc-type cytochromes. Whereas ubiquinol-cytochromecreductase (petC) mutants specifically lacking cytochromec1andcycBmutants lacking cytochromec5had normal siderophore expression,cyc4mutants defective for cytochromec4completely lacked legiobactin. These data, along with the expression pattern ofcyc4mRNA, indicate that cytochromec4in particular promotes siderophore expression. In intracellular infection assays,petCmutants andcycBmutants, but notcyc4mutants, had a reduced ability to infect both amoebae and macrophage hosts. Likeccmmutants, thecycBmutants were completely unable to grow in amoebae, highlighting a major role for cytochromec5in intracellular infection. To our knowledge, these data represent both the first direct documentation of the importance of ac-type cytochrome in expression of a biologically active siderophore and the first insight into the relative importance ofc-type cytochromes in intracellular infection events.
The Drosophila melanogaster transcriptome by paired-end RNA sequencing
Authors: Daines Bryce , Wang Hui , Wang Liguo , Li Yumei , Han Yi , Emmert David , Gelbart William , Wang Xia , Li Wei , Gibbs Richard , Chen Rui
Published: December 2010

RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64–100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
Authors: Lamm Ayelet T. , Stadler Michael R. , Zhang Huibin , Gent Jonathan I. , Fire Andrew Z.
Published: December 2010

We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5′ ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
Authors: Riddle Nicole C. , Minoda Aki , Kharchenko Peter V. , Alekseyenko Artyom A. , Schwartz Yuri B. , Tolstorukov Michael Y. , Gorchakov Andrey A. , Jaffe Jacob D. , Kennedy Cameron , Linder-Basso Daniela , Peach Sally E. , Shanower Gregory , Zheng Haiyan , Kuroda Mitzi I. , Pirrotta Vincenzo , Park Peter J. , Elgin Sarah C.R. , Karpen Gary H.
Published: December 2010

Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the “silencing” marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin–heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both “activation” marks (e.g., H3K4me3 and H3K36me3) and “silencing” marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
Authors: Lu Zhi John , Yip Kevin Y. , Wang Guilin , Shou Chong , Hillier LaDeana W. , Khurana Ekta , Agarwal Ashish , Auerbach Raymond , Rozowsky Joel , Cheng Chao , Kato Masaomi , Miller David M. , Slack Frank , Snyder Michael , Waterston Robert H. , Reinke Valerie , Gerstein Mark B.
Published: December 2010

We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and data from the modENCODE consortium, we are able to separate known C. elegans ncRNAs from coding sequences and other genomic elements with a high level of accuracy (97% AUC on an independent validation set), and find more than 7000 novel ncRNA candidates, among which more than 1000 are located in the intergenic regions of C. elegans genome. Based on the validation set, we estimate that 91% of the approximately 7000 novel ncRNA candidates are true positives. We then analyze 15 novel ncRNA candidates by RT-PCR, detecting the expression for 14. In addition, we characterize the properties of all the novel ncRNA candidates and find that they have distinct expression patterns across developmental stages and tend to use novel RNA structural families. We also find that they are often targeted by specific transcription factors (∼59% of intergenic novel ncRNA candidates). Overall, our study identifies many new potential ncRNAs in C. elegans and provides a method that can be adapted to other organisms.