bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of swift heavy ion irradiation and thermal annealing on nearly immiscible W/Ni multilayer structure
Authors: Bagchi Sharmistha , Potdar Satish , Singh F. , Lalla N. P.
Published: October 2007

The effect of 120 MeV Au9+ ion irradiation and thermal annealing on [W(25 Å)∕Ni(25 Å)]×10 multilayers, grown on float-glass and silicon substrates, has been studied. Wide-angle x-ray diffraction studies of pristine, as well as irradiated W/Ni multilayers, show deterioration of the superlattice structure, but x-ray reflectivity (XRR) studies reveal a nearly unaffected multilayer structure. Analysis of the XRR data using “Parratt’s formalism” does show a significant increase of W/Ni interface roughness. The observed differences in wide-angle and low-angle scattering results of the irradiated W/Ni multilayers suggest significant difference in the interlayer and intralayer mixing induced by swift heavy ion irradiation. XRR results also reveal the fluence dependence of layer densification. Plane, as well as cross-sectional transmission electron microscopy, carried out in imaging and diffraction modes very clearly shows that at higher fluence the intralayer microstructure becomes nanocrystalline (1–2 nm) and at some places amorphous too. But, the definition of the W and Ni layers still remains intact. This has been understood in terms of competition between low miscibility at the W/Ni interface and ion-beam mixing kinetics.
Resistive wall mode feedback control in EXTRAP T2R with improved steady-state error and transient response
Authors: Brunsell P. R. , Olofsson K. E. J. , Frassinetti L. , Drake J. R.
Published: October 2007

Experiments in the EXTRAP T2R reversed field pinch [P. R. Brunsell, H. Bergsåker, M. Cecconello et al., Plasma Phys. Control. Fusion 43, 1457 (2001)] on feedback control of m=1 resistive wall modes (RWMs) are compared with simulations using the cylindrical linear magnetohydrodynamic model, including the dynamics of the active coils and power amplifiers. Stabilization of the main RWMs (n=−11,−10,−9,−8,+5,+6) is shown using modest loop gains of the order G∼1. However, other marginally unstable RWMs (n=−2,−1,+1,+2) driven by external field errors are only partially canceled at these gains. The experimental system stability limit is confirmed by simulations showing that the latency of the digital controller ∼50μs is degrading the system gain margin. The transient response is improved with a proportional-plus-derivative controller, and steady-state error is improved with a proportional-plus-integral controller. Suppression of all modes is obtained at high gain G∼10 using a proportional-plus-integral-plus-derivative controller.
Microscopic structure and dynamics of molten Se50Te50 alloys
Authors: Katcho N. A. , Zetterström P. , Lomba E. , Otero-Díaz L. C. , Wang Y. D. , Ren Y. , Gruner S.
Published: October 2007

In this work we investigate the microscopic structure and dynamics of the molten equimolar alloy, Se50Te50 using a combination of neutron and x-ray diffraction experiments, reverse Monte Carlo analysis, and first principles molecular dynamics. The range of temperatures studied covers the semiconductor/metal transition. From our results it can be seen that the latter is associated with an increase in coordination numbers and a reduced tendency to heterocoordination. In agreement with previous inelastic neutron scattering experiments, our molecular dynamics calculation predict a certain widening of the stretching vibrational modes band in connection with the increase of coordination and the presence of longer bonds in the metallic phase.
A configurational temperature for molecules with hard-core or discontinuous interactions
Authors: Rickayzen G. , Heyes D. M.
Published: October 2007

We extend the usual formula for a configurational temperature so that it applies to condensates in which the molecules interact through hard-core or discontinuous potentials. The new formula involves extra terms which may be calculated during the course of a simulation. The formula is tested by its application to a number of systems with discontinuous or hard-core potentials in thermodynamic equilibrium. Metropolis Monte Carlo simulations were performed on these systems in a canonical ensemble and the configurational temperature is compared with the input temperature. The two are in agreement to within less than 0.1%.
Effect of kerf filler on the electromechanical coupling coefficient of an ultrasonic transducer array element
Authors: Kim Jungsoon , Kim Moojoon , Cao Wenwu
Published: October 2007

Electromechanical coupling coefficient directly reflects the electromechanical energy conversion capability of a piezoelectric device. We show theoretically that the kerf filler in the ultrasonic array transducer can degrade this coupling coefficient. A closed form expression has been derived that can quantitatively describe the electromechanical coupling coefficient of an ultrasonic transducer array element with arbitrary aspect ratio and having polymer kerf filler in between transducer elements.
Cobaltocene as a spin filter
Authors: Liu Rui , Ke San-Huang , Yang Weitao , Baranger Harold U.
Published: October 2007

In the context of investigating organic molecules for molecular electronics, doping molecular wires with transition metal atoms provides additional means of controlling their transport behavior. The incorporation of transition metal atoms may generate spin dependence because the conduction channels of only one spin component align with the chemical potential of the leads, resulting in a spin polarized electric current. The possibility to create such a spin polarized current is investigated here with the organometallic moiety cobaltocene. According to our calculations, cobaltocene contacted with gold electrodes acts as a robust spin filter: Applying a voltage less than 0.2V causes the current of one spin component crossing the molecular bridge to be two orders of magnitude larger than the other. We address the key issue of sensitivity to molecule-lead geometry by showing that a weak barrier generated by CH2 groups between the cobaltocene and the leads is crucial in reducing the sensitivity to the contact geometry while only reducing the current modestly. These results suggest cobaltocene as a robust basic building block for molecular spintronics.
Effect of surface roughness on rate-dependent slip in simple fluids
Authors: Priezjev Nikolai V.
Published: October 2007

Molecular dynamics simulations are used to investigate the influence of molecular-scale surface roughness on the slip behavior in thin liquid films. The slip length increases almost linearly with the shear rate for atomically smooth rigid walls and incommensurate structures of the liquid/solid interface. The thermal fluctuations of the wall atoms lead to an effective surface roughness, which makes the slip length weakly dependent on the shear rate. With increasing the elastic stiffness of the wall, the surface roughness smoothes out and the strong rate dependence is restored again. Both periodically and randomly corrugated rigid surfaces reduce the slip length and its shear rate dependence.
Self-assembly of CdSe∕ZnSe(001) quantum dot structures mediated by a tellurium cap layer
Authors: Mahapatra S. , Brunner K. , Bougerol C.
Published: October 2007

Ensembles of CdSe∕ZnSe quantum dots (QDs), with different self-assembled patterns, have been realized by depositing amorphous Te (a-Te) onto an epitaxial CdSe layer and subsequently desorbing it. During temperature ramp up for desorption, Te forms an epitaxially oriented polycrystalline layer along the grain boundaries of which, desorption initiates. Consequently, the underlying CdSe layer is first exposed in narrow trenches, within which QDs nucleate preferentially. The morphology of the polycrystalline Te layer, which strongly depends on the a-Te cap layer thickness, governs the spatial pattern of the QDs. By a variant technique, wherein a noncrystallizing amorphous layer is intentionally patterned before desorption, QDs might be positioned on predefined sites.
Thermal annealing effect on the interface structure of high-κ LaScO3 on silicon
Authors: Liu F. , Duscher G.
Published: October 2007

The thermal stability of LaScO3 on Si was examined by various transmission electron microscopy techniques. The film remained amorphous up to 700°C and became polycrystalline at 800°C. All samples showed an interfacial layer about 3.5nm thick, except for the 1000°C-annealed sample, which had a thicker interfacial layer containing a thin silicate layer close to the interface with the substrate. Although the chemical composition of the bulk film was stoichiometric, the interfacial layer was oxygen-rich after postannealing. The interfacial layer remained amorphous up to 1000°C, indicating that this interfacial layer itself may be used as a gate dielectric.
Longitudinally propagating traveling waves of the mammalian tectorial membrane
Authors: Ghaffari Roozbeh , Aranyosi Alexander J. , Freeman Dennis M.
Published: October 2007

Sound-evoked vibrations transmitted into the mammalian cochlea produce traveling waves that provide the mechanical tuning necessary for spectral decomposition of sound. These traveling waves of motion that have been observed to propagate longitudinally along the basilar membrane (BM) ultimately stimulate the mechano-sensory receptors. The tectorial membrane (TM) plays a key role in this process, but its mechanical function remains unclear. Here we show that the TM supports traveling waves that are an intrinsic feature of its visco-elastic structure. Radial forces applied at audio frequencies (2–20 kHz) to isolated TM segments generate longitudinally propagating waves on the TM with velocities similar to those of the BM traveling wave near its best frequency place. We compute the dynamic shear storage modulus and shear viscosity of the TM from the propagation velocity of the waves and show that segments of the TM from the basal turn are stiffer than apical segments are. Analysis of loading effects of hair bundle stiffness, the limbal attachment of the TM, and viscous damping in the subtectorial space suggests that TM traveling waves can occur
in vivo
. Our results show the presence of a traveling wave mechanism through the TM that can functionally couple a significant longitudinal extent of the cochlea and may interact with the BM wave to greatly enhance cochlear sensitivity and tuning.
Ecological consequences of early Late Pleistocene megadroughts in tropical Africa
Authors: Cohen Andrew S. , Stone Jeffery R. , Beuning Kristina R. M. , Park Lisa E. , Reinthal Peter N. , Dettman David , Scholz Christopher A. , Johnson Thomas C. , King John W. , Talbot Michael R. , Brown Erik T. , Ivory Sarah J.
Published: October 2007

Extremely arid conditions in tropical Africa occurred in several discrete episodes between 135 and 90 ka, as demonstrated by lake core and seismic records from multiple basins [Scholz CA, Johnson TC, Cohen AS, King JW, Peck J, Overpeck JT, Talbot MR, Brown ET, Kalindekafe L, Amoako PYO,
et al.
(2007)
Proc Natl Acad Sci USA
104:16416–16421]. This resulted in extraordinarily low lake levels, even in Africa's deepest lakes. On the basis of well dated paleoecological records from Lake Malawi, which reflect both local and regional conditions, we show that this aridity had severe consequences for terrestrial and aquatic ecosystems. During the most arid phase, there was extremely low pollen production and limited charred-particle deposition, indicating insufficient vegetation to maintain substantial fires, and the Lake Malawi watershed experienced cool, semidesert conditions (<400 mm/yr precipitation). Fossil and sedimentological data show that Lake Malawi itself, currently 706 m deep, was reduced to an ≈125 m deep saline, alkaline, well mixed lake. This episode of aridity was far more extreme than any experienced in the Afrotropics during the Last Glacial Maximum (≈35–15 ka). Aridity diminished after 95 ka, lake levels rose erratically, and salinity/alkalinity declined, reaching near-modern conditions after 60 ka. This record of lake levels and changing limnological conditions provides a framework for interpreting the evolution of the Lake Malawi fish and invertebrate species flocks. Moreover, this record, coupled with other regional records of early Late Pleistocene aridity, places new constraints on models of Afrotropical biogeographic refugia and early modern human population expansion into and out of tropical Africa.
TLR4polymorphisms, infectious diseases, and evolutionary pressure during migration of modern humans
Authors: Ferwerda Bart , McCall Matthew B. B. , Alonso Santos , Giamarellos-Bourboulis Evangelos J. , Mouktaroudi Maria , Izagirre Neskuts , Syafruddin Din , Kibiki Gibson , Cristea Tudor , Hijmans Anneke , Hamann Lutz , Israel Shoshana , ElGhazali Gehad , Troye-Blomberg Marita , Kumpf Oliver , Maiga Boubacar , Dolo Amagana , Doumbo Ogobara , Hermsen Cornelus C. , Stalenhoef Anton F. H. , van Crevel Reinout , Brunner Han G. , Oh Djin-Ye , Schumann Ralf R. , de la Rúa Concepcion , Sauerwein Robert , Kullberg Bart-Jan , van der Ven André J. A. M. , van der Meer Jos W. M. , Netea Mihai G.
Published: October 2007

Infectious diseases exert a constant evolutionary pressure on the genetic makeup of our innate immune system. Polymorphisms in Toll-like receptor 4 (TLR4) have been related to susceptibility to Gram-negative infections and septic shock. Here we show that two polymorphisms ofTLR4, Asp299Gly and Thr399Ile, have unique distributions in populations from Africa, Asia, and Europe. Genetic and functional studies are compatible with a model in which the nonsynonymous polymorphism Asp299Gly has evolved as a protective allele against malaria, explaining its high prevalence in subSaharan Africa. However, the same allele could have been disadvantageous after migration of modern humans into Eurasia, putatively because of increased susceptibility to severe bacterial infections. In contrast, the Asp299Gly allele, when present in cosegregation with Thr399Ile to form the Asp299Gly/Thr399Ile haplotype, shows selective neutrality. Polymorphisms inTLR4exemplify how the interaction between our innate immune system and the infectious pressures in particular environments may have shaped the genetic variations and function of our immune system during the out-of-Africa migration of modern humans.
Phylogenomic analysis of the emergence of GC-rich transcription elements
Authors: Khuu Patricia , Sandor Maurice , DeYoung Jennifer , Ho P. Shing
Published: October 2007

We have applied a comparative phylogenomic analysis to study the evolutionary relationships between GC content, CpG-dinucleotide content (CpGs), potential nuclear factor I (NFI) binding sites, and potential Z-DNA forming regions (ZDRs) as representative structural and functional GC-rich genomic elements. Our analysis indicates that CpG and NFI sites emerged with a general accretion of GC-rich sequences downstream of the eukaryotic transcription start site (TSS). Two distinct classes of ZDRs are observed at different locations proximal to the eukaryotic TSS. A robust CA/TG class of ZDRs was seen to emerge upstream of the TSS and independently of GC content, CpGs, and NFIs, whereas a second, weaker CG type appears to have evolved along with these downstream GC-rich elements. Taken together, the results provide a model for how GC-rich structural and functional eukaryotic markers emerge relative to each other, and indicate two distinct transition points for their occurrence: the first at the pro/eukaryotic boundary, and the second at or near the amniotic boundary.
Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer
Authors: Kendall Jude , Liu Qing , Bakleh Amy , Krasnitz Alex , Nguyen Ken C. Q. , Lakshmi B. , Gerald William L. , Powers Scott , Mu David
Published: October 2007

We used high-resolution array analysis to discover a recurrent lung cancer amplicon located at 14q13.3. Low-level gain of this region was detected in 15% of lung cancer samples, and high-level amplification was detected in an additional 4% of samples. High-level focal amplification appears to be specific to lung cancers, because it was not detected in >500 samples of other tumor types. Mapping of the commonly amplified region revealed there are three genes in the core region, all of which encode transcription factors with either established lung developmental function (TTF1/NKX2-1,NKX2-8) or potential lung developmental function (PAX9). All three genes were overexpressed to varying degrees in amplified samples, althoughTTF1/NKX2-1was not expressed in the squamous cancer subtype, consistent with previous reports. Remarkably, overexpression of any pairwise combination of these genes showed pronounced synergy in promoting the proliferation of immortalized human lung epithelial cells. Analysis of human lung cancer cell lines by both RNAi and ectopic overexpression further substantiates an oncogenic role for these transcription factors. These results, taken together with previous reports of oncogenic alterations of transcription factors involved in lung development (p63, CEBPA), suggest genetic alterations that directly interfere with transcriptional networks normally regulating lung development may be a more common feature of lung cancer than previously realized.
Yeast culture (
Saccharomyces cerevisiae
) supplementation in growing animals in the dairy industry.
Authors: Lascano G. J. , Heinrichs A. J.
Published: October 2007

Increasing the digestibility of ruminant diets and thereby improving nutrient efficiency is an important aspect of ruminant nutrition. This improvement in nutrient utilization must initially come from an improved rumen digestion and utilization. Yeast products have been added to the diets of monogastric as well as ruminant animals for many years to improve their productivity with a variety of results. In the dairy industry, yeast has been used since the early 1900s as an enhancer in milk production and in growing animals to improve their gains and efficiency. The mode of action of yeast products (live and dead) has not been able to be completely described, but many hypotheses are related to a change in rumen fermentation pattern with increases in volatile fatty acids (VFAs), neutral detergent fibre (NDF) digestibility and disappearance, organic matter digestibility, bacteria and protozoa population and decreases in lactic acid concentrations, lag time of dry matter (DM) degradation and stabilization of rumen pH, with an overall benefit in the rumen environment leading to improvement in the metabolic performance of the animal. The aim of this review is to survey the effects of yeast supplementation in growing ruminant animals and the effects that have been noted in the literature especially in the dairy industry.
Abandonment of agricultural land: an overview of drivers and consequences.
Authors: Rey Benayas J. M. , Martins A. , Nicolau J. M. , Schulz J. J.
Published: October 2007

Agricultural activities and their complex effects on nature conservation, and the services that ecosystems deliver to humans are controversial. We present an overview of land abandonment, its driving forces and its consequences for landscape, biodiversity and humans. A descriptive metaanalysis of independently published studies highlighted the fact that the abandonment of agricultural land is a phenomenon mostly driven by socio-economic factors such as immigration into areas where new economic opportunities are offered to rural people. Ecological drivers such as elevation and land mismanagement leading to soil erosion are of secondary importance. We identified the major problems related to abandonment of agricultural land and quantified their relative importance. In order of decreasing importance, they were biodiversity loss, increase of fire frequency and intensity, soil erosion and desertification, loss of cultural and/or aesthetic values, reduction of landscape diversity and reduction of water provision. The impacts of these problems were not equally relevant in all regions of the world. The abandonment of agricultural land may also benefit humans. The benefits include passive revegetation and active reforestation, water regulation, soil recovery, nutrient cycling and increased biodiversity and wilderness. In a world that is becoming less natural and more intensively exploited by humans, we suggest that (1) farmland must be viewed in a context of multi-functionality to take advantage of ecosystem goods and services, (2) at the global scale, the abandonment of agricultural land is mostly positive for humans and (3) there is a need for the implementation of policies based on the payments for environmental services that encourage human societies to reconcile agricultural use, nature conservation and ecological restoration.
Agritourism and its potential contribution to the agricultural economy.
Authors: Che D.
Published: October 2007

Agritourism, a growing segment of the tourism industry, has been driven by agricultural restructuring, the movement towards multifunctional agriculture, increased discretionary incomes and demand for rural experiences. In this essay, the differential agritourism responses to agricultural restructuring are reviewed. In the European Union (EU), rural development policies and structural adjustment funding have enabled farmers, many in peripheral areas, to capitalize on historic structures that can be converted into tourist accommodations. In settler nations where agritourism has been supported to a lesser degree with marketing grants, hunting on ranches and day activities on peri-urban farms respectively capitalize on wildlife and accessibility to large urban populations. Producer motivations in agritourism are social as well as economic. Agritourism can provide the economic justification for keeping the land in agriculture, but lifestyle justifications including the desire to live in rural areas, spending time with family and independence are also important. Economic benefits from agritourism can vary widely depending on the level of investment and activities emphasized. Economic activities that extend the season for direct retailing of value-added secondary products produced on the farm and/or sold in on-farm retail shops are critical for success. The amount of infrastructural investment and wages paid may have lesser returns. Additionally, agritourism may differentially benefit farmers by favouring larger farms with extensive livestock/arable enterprises and subsidy payments. Rather than increased infrastructural investments, agritourism development may be better enhanced through government support of strategic alliances and cooperative marketing, quality initiatives and e-commerce.
New developments in understanding the role of salicylic acid in plant defence.
Authors: Molinari S.
Published: October 2007

Salicylic acid (SA) is currently considered as a key molecule in activating plant defence against various insects and pathogenic invaders. Its role in determining the so-called systemic acquired resistance (SAR), that confers long-lasting protection against a broad spectrum of pathogens, has definitely been established. The activation of an SA-dependent signalling pathway is also associated with more specific plant defences, such as those determined by gene-for-gene recognition of the pathogen by plants carrying resistance genes (
R
-genes). A recent further impulse in the investigation of the role of SA, both in local defences and SAR, has come either from genetic screens of
Arabidopsis
or from SA-degrading transgenic plants that express the bacterial salicylate hydroxylase gene (
NahG
). Genetic screens of
Arabidopsis
and the recently developed microarray technology allowed us to identify several genes involved in SA synthesis and signalling. However, the biochemical mechanisms by which SA can exert its many functions are not clear yet and the scope of this review is to report on such mechanisms. SA signalling is indicated here as a complex network operating through gene expressions and biochemical pathways which are finely regulated by SA concentration. According to its level in plants, SA may operate as a beneficial anti-inflammatory compound or as a cell killer. New developments in understanding the role of SA in plant defence are reported from studies on root response to soil pests, such as root-knot nematodes. The role of SA in diseases of roots has been reviewed here for the first time, as most of our knowledge on this matter is based on studies carried out on leaves.
Ozone impacts on forests.
Authors: Paoletti E.
Published: October 2007

Ozone is the air pollutant of major concern for forests, and is also recognized as a significant greenhouse gas. Current background O
3
levels in the Northern Hemisphere have increased around 2-4.5 times since pre-industrial times. Although many questions remain, we now know a great deal about how O
3
affects forests at the cell/leaf level (by inducing a cascade of biochemical, physiological and morphological responses) and at the tree/canopy level (by affecting allocation and carbon strength, reproduction, hydrology and the response to co-occurring stressors). The most significant O
3
impact is on the regulatory capacity of resource allocation rather than on productivity. However, forest ecosystems are much complex. Gas exchange measurements carried out at steady state suggest that O
3
reduces stomatal conductance and thus increases protection from drought and additional O
3
. Ozone, however, may impair stomatal control and predispose trees to drought stress under dynamic conditions, as those in forests. Ozone-induced increases in sap-flow have been shown to result in stem growth losses, depletion of soil moisture in the rooting zone and reduced streamflow, with implications for all the forest hydrological processes. In addition, species-specific and individual-specific responses to O
3
affect forest competition and biodiversity. There is a need to scale from the cell and leaf level up to the ecosystem and regional level, and to develop a biologically significant and usable standard to protect forests from O
3
. Further work is needed for understanding the cause/effect-based relationships between O
3
and other stresses at the stand and ecosystem level. Modelling may provide new insights into O
3
impacts on forests, even though scalar and conceptual uncertainties still limit the current understanding of basic physiological mechanisms.
Mach configuration in pseudo-stationary compressible flow
Authors: Chen Shuxing
Published: October 2007

This paper is devoted to studying the local structure of Mach reflection, which occurs in the problem of the shock front hitting a ramp. The compressible flow is described by the full unsteady Euler system of gas dynamics. Because of the special geometry, the motion of the fluid can be described by self-similar coordinates, so that the unsteady flow becomes a pseudo-stationary flow in this coordinate system. When the slope of the ramp is less than a critical value, the Mach reflection occurs. The wave configuration in Mach reflection is composed of three shock fronts and a slip line bearing contact discontinuity. The local existence of a flow field with such a configuration under some assumptions is proved in this paper. Our result confirms the reasonableness of the corresponding physical observations and numerical computations in Mach reflection. In order to prove the result, we formulate the problem to a free boundary value problem of a pseudo-stationary Euler system. In this problem two unknown shock fronts are the free boundary, and the slip line is also an unknown curve inside the flow field. The proof contains some crucial ingredients. The slip line will be transformed to a fixed straight line by a generalized Lagrange transformation. The whole free boundary value problem will be decomposed to a fixed boundary value problem of the Euler system and a problem to updating the location of the shock front. The Euler system in the subsonic region is an elliptic-hyperbolic composite system, which will be decoupled to the elliptic part and the hyperbolic part at the level of principal parts. Then some sophisticated estimates and a suitable iterative scheme are established. The proof leads to the existence and stability of the local structure of Mach reflection.
Feature construction from synergic pairs to improve microarray-based classification
Authors: Hanczar Blaise , Zucker Jean-Daniel , Henegar Corneliu , Saitta Lorenza
Published: October 2007

Motivation: Microarray experiments that allow simultaneous expression profiling of thousands of genes in various conditions (tissues, cells or time) generate data whose analysis raises difficult problems. In particular, there is a vast disproportion between the number of attributes (tens of thousands) and the number of examples (several tens). Dimension reduction is therefore a key step before applying classification approaches. Many methods have been proposed to this purpose, but only a few of them considered a direct quantification of transcriptional interactions. We describe and experimentally validate a new dimension reduction and feature construction method, which assesses interactions between expression profiles to improve microarray-based classification accuracy.

Results: Our approach relies on a mutual information measure that exposes some elementary constituents of the information contained in a pair of gene expression profiles. We show that their analysis implies a term that represents the information of the interaction between the two genes. The principle of our method, called FeatKNN, is to exploit the information provided by highly synergic gene pairs to improve classification accuracy. First, a heuristic search selects the most informative gene pairs. Then, for each selected pair, a new feature, representing the classification margin of a KNN classifier in the gene pairs space, is constructed. We show experimentally that the interactional information has a degree of significance comparable to that of the gene expression profiles considered separately. Our method has been tested with different classifiers and yielded significant improvements in accuracy on several public microarray databases. Moreover, a synthetic assessment of the biological significance of the concept of synergic gene pairs suggested its ability to uncover relevant mechanisms underlying interactions among various cellular processes.

Contact:  hanczar_blaise@yahoo.fr

Supplementary information: Complementary results can be found on the companion website at http://featknn.nutriomique.org
Naïve Bayes for microRNA target predictions—machine learning for microRNA targets
Authors: Yousef Malik , Jung Segun , Kossenkov Andrew V. , Showe Louise C. , Showe Michael K.
Published: October 2007

Motivation: Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this region of the mRNA target. Methods that do not rely on conservation generate numbers of predictions, which are too large to validate. We describe a target prediction method (NBmiRTar) that does not require sequence conservation, using instead, machine learning by a naïve Bayes classifier. It generates a model from sequence and miRNA:mRNA duplex information from validated targets and artificially generated negative examples. Both the ‘seed’ and ‘out-seed’ segments of the miRNA:mRNA duplex are used for target identification.

Results: The application of machine-learning techniques to the features we have used is a useful and general approach for microRNA target gene prediction. Our technique produces fewer false positive predictions and fewer target candidates to be tested. It exhibits higher sensitivity and specificity than algorithms that rely on conserved genomic regions to decrease false positive predictions.

Availability: The NBmiRTar program is available at http://wotan.wistar.upenn.edu/NBmiRTar/

Contact:  yousef@wistar.org

Supplementary information:  http://wotan.wistar.upenn.edu/NBmiRTar/
Landscape context not patch size determines bumble-bee density on flower mixtures sown for agri-environment schemes
Authors: Heard M.S , Carvell C , Carreck N.L , Rothery P , Osborne J.L , Bourke A.F.G
Published: October 2007

Bumble-bee declines across Europe have been linked to loss of habitat and forage availability due to agricultural intensification. These declines may have severe ecological and commercial consequences since bumble-bees pollinate a range of wildflowers and crops. In England, attempts are being made to reintroduce forage resources through agri-environment schemes, yet there are few data on how the area of forage, or the landscape context in which it is provided, affects their success. We investigated the effects of sown forage patches on bumble-bees across sites varying in landscape characteristics. Bumble-bee densities were higher on sown patches compared with control habitats but did not vary with patch size, i.e. total forager numbers were proportional to patch area. Importantly, the relative response to sown forage patches varied widely across a landscape gradient such that their impact in terms of attracting foraging bumble-bees was greatest where the proportion of arable land was highest.
A multiple-site similarity measure independent of richness
Authors: Baselga Andrés , Jiménez-Valverde Alberto , Niccolini Gilles
Published: October 2007

The Diserud–Ødegaard multiple-site similarity index makes use of data on species shared by two or more sites, but produces equal similarity values in two different circumstances: species loss and true species turnover. We developed a new multiple-site similarity measure, which is independent of richness and performs better than the Diserud–Ødegaard index under conditions of equal richness between sites, because it discriminates between situations in which shared species are distributed evenly among sites or concentrated in few pairs of sites. We conducted several simulations to assess the relative performance of both the indices. The use of the new measure is recommended, enabling the simultaneous analysis of turnover and richness gradients based on two independent measures.
A multiscale model of thrombus development
Authors: Xu Zhiliang , Chen Nan , Kamocka Malgorzata M , Rosen Elliot D , Alber Mark
Published: October 2007

A two-dimensional multiscale model is introduced for studying formation of a thrombus (clot) in a blood vessel. It involves components for modelling viscous, incompressible blood plasma; non-activated and activated platelets; blood cells; activating chemicals; fibrinogen; and vessel walls and their interactions. The macroscale dynamics of the blood flow is described by the continuum Navier–Stokes equations. The microscale interactions between the activated platelets, the platelets and fibrinogen and the platelets and vessel wall are described through an extended stochastic discrete cellular Potts model. The model is tested for robustness with respect to fluctuations of basic parameters. Simulation results demonstrate the development of an inhomogeneous internal structure of the thrombus, which is confirmed by the preliminary experimental data. We also make predictions about different stages in thrombus development, which can be tested experimentally and suggest specific experiments. Lastly, we demonstrate that the dependence of the thrombus size on the blood flow rate in simulations is close to the one observed experimentally.
Ensemble estimation of polarization ellipse parameters
Authors: Walden A.T , Medkour T
Published: October 2007

An ellipse describes the polarized part of a partially polarized quasi-monochromatic plane wave field. Its azimuth angle and aspect ratio are functions of the elements of the covariance matrix associated with the polarized part at a particular time instant. Given an ensemble ofKindependent samples at that time, the distributions of the estimators of these parameters are derived. The estimation is thus based on a sample ensemble at any time, and does not assume temporal stationarity. Additionally, the azimuth angle estimator has an angular distribution so that non-standard statistical methods are needed when deriving its mean and standard deviation.
Preferences for symmetry in human faces in two cultures: data from the UK and the Hadza, an isolated group of hunter-gatherers
Authors: Little Anthony C , Apicella Coren L , Marlowe Frank W
Published: October 2007

Many studies show agreement within and between cultures for general judgements of facial attractiveness. Few studies, however, have examined the attractiveness of specific traits and few have examined preferences in hunter-gatherers. The current study examined preferences for symmetry in both the UK and the Hadza, a hunter-gatherer society of Tanzania. We found that symmetry was more attractive than asymmetry across both the cultures and was more strongly preferred by the Hadza than in the UK. The different ecological conditions may play a role in generating this difference. Such variation in preference may be adaptive if it reflects adaptation to local conditions. Symmetry is thought to indicate genetic quality, which may be more important among the Hadza with much higher mortality rates from birth onwards. Hadza men who were more often named as good hunters placed a greater value on symmetry in female faces. These results suggest that high quality Hadza men are more discriminating in their choice of faces. Hadza women had increased preferences for symmetry in men's faces when they were pregnant or nursing, perhaps due to their increased discrimination and sensitivity to foods and disease harmful to a foetus or nursing infant. These results imply that symmetry is an evolutionarily relevant trait and that variation in symmetry preference appears strategic both between cultures and within individuals of a single culture.
Ant semiochemicals limit apterous aphid dispersal
Authors: Oliver Thomas H , Mashanova Alla , Leather Simon R , Cook James M , Jansen Vincent A.A
Published: October 2007

Some organisms can manipulate the nervous systems of others or alter their physiology in order to obtain benefit. Ants are known to limit alate aphid dispersal by physically removing wings and also through chemical manipulation of the alate developmental pathway. This results in reduced dispersal and higher local densities of aphids, which benefit ants in terms of increased honeydew and prey availability. Here, we show that the walking movement of mutualistic apterous aphids is also reduced by ant semiochemicals. Aphids walk slower and their dispersal from an unsuitable patch is hampered by ants. If aphid walking dispersal has evolved as a means of natural enemy escape, then ant chemicals may act as a signal indicating protection; hence, reduced dispersal could be adaptive for aphids. If, however, dispersal is primarily a means to reduce competition or to maintain persistent metapopulations, then manipulation by ants could be detrimental. Such manipulation strategies, common in host–parasite and predator–prey interactions, may be more common in mutualism than expected.
Captive breeding and embryonic development of Chiloscyllium punctatum Muller & Henle, 1838 (Elasmobranchii: Hemiscyllidae)
Authors: Harahush B. K. , Fischer A. B. P. , Collin S. P.
Published: October 2007

The fecundity, embryonic development, growth and viability of captive Chiloscyllium punctatum were investigated over two breeding and laying seasons. Chiloscyllium punctatum is an oviparous species, which lays rectangular eggs from late July to February. The six adult female C. punctatum in the open ocean display tank at UnderWater World, Mooloolaba, Australia laid a total of 692 eggs between July 2004 and February 2006, with 228 of those being viable. This equates to each female laying 115·3 eggs over the two seasons, with 38 viable. The embryos are first visible to the naked eye at c. 18 days post deposition (dpd), while pre‐hatching is first seen c. 35 dpd, and the embryos hatch at an average of 153 dpd (temperature 21–25° C). Embryonic growth is most rapid from 99 dpd until hatching. An average of 21·4% of the eggs hatched over the two seasons.
Small‐scale variability in growth and condition of dab Limanda limanda (L.) larvae in relation to an Irish Sea tidal‐mixing front off the west coast of the Isle of Man
Authors: Lee O. , Danilowicz B. S. , Nash R. D. M.
Published: October 2007

The small‐scale variability in condition and growth of dab Limanda limanda larvae was investigated in relation to a tidal‐mixing front (Manx West Coast front) off the west coast of the Isle of Man, Irish Sea. RNA:DNA ratios and otolith microincrement analysis were used to estimate nutritional status and recent growth rates of larvae captured on 5 May 1999 in mixed, frontal and stratified waters associated with this front. RNA:DNA ratios were significantly higher at the Manx West Coast front compared to mixed waters, although recent growth rates did not vary significantly with water column stability. More favourable feeding conditions associated with frontal waters from previously reported large‐scale investigations in the Irish Sea were reflected on a smaller spatial scale. Although frontal accumulation of dab larvae was not observed in the current study, dab larvae found in the stratified and frontal waters were significantly larger than those captured in the mixed waters. This pattern could suggest an offshore movement of dab larvae into more favourable waters as they develop.
Summer stream habitat partitioning by sympatric Arctic charr, Atlantic salmon and brown trout in two sub‐arctic rivers
Authors: Heggenes J. , Saltveit S. J.
Published: October 2007

Summer habitat use by sympatric Arctic charr Salvelinus alpinus, young Atlantic salmon Salmo salar and brown trout Salmo trutta was studied by two methods, direct underwater observation and electrofishing, across a range of habitats in two sub‐arctic rivers. More Arctic charr and fewer Atlantic salmon parr were observed by electrofishing in comparison to direct underwater observation, perhaps suggesting a more cryptic behaviour by Arctic charr. The three species segregated in habitat use. Arctic charr, as found by direct underwater observation, most frequently used slow (mean ±s.d. water velocity 7·2 ± 16·6 cm s−1) or often stillwater and deep habitats (mean ±s.d. depth 170·1 ± 72·1 cm). The most frequently used mesohabitat type was a pool. Young Atlantic salmon favoured the faster flowing areas (mean ±s.d. water velocity 44·0 ± 16·8 cm s−1 and depth 57·1 ± 19·0 cm), while brown trout occupied intermediate habitats (mean ±s.d. water velocity 33·1 ± 18·6 cm s−1 and depth 50·2 ± 18·0 cm). Niche overlap was considerable. The Arctic charr observed were on average larger (total length) than Atlantic salmon and brown trout (mean ±s.d. 21·9 ± 8·0, 10·2 ± 3·1 and 13·4 ± 4·5 cm). Similar habitat segregation between Atlantic salmon and brown trout was found by electrofishing, but more fishes were observed in shallower habitats. Electrofishing suggested that Arctic charr occupied habitats similar to brown trout. These results, however, are biased because electrofishing was inefficient in the slow‐deep habitat favoured by Arctic charr. Habitat use changed between day and night in a similar way for all three species. At night, fishes held positions closer to the bottom than in the day and were more often observed in shallower stream areas mostly with lower water velocities and finer substrata. The observed habitat segregation is probably the result of interference competition, but the influence of innate selective differences needs more study.
Presence of the Guinean puffer Sphoeroides marmoratus (Lowe, 1838) in the Mediterranean Sea
Authors: Vacchi M. , Bussotti S. , Miglietta A. M. , Guidetti P.
Published: October 2007

The collection of a single specimen of the Guinean puffer Sphoeroides marmoratus from the Ionian Sea in September 1977, misidentified at that time as Lagocephalus lagocephalus, shows that this subtropical species of fish has occurred in the Mediterranean Sea from 30 years ago.
Photophilic behaviour in surface‐ and cave‐dwelling Atlantic mollies Poecilia mexicana (Poeciliidae)
Authors: Parzefall J. , Kraus C. , Tobler M. , Plath M.
Published: October 2007

The phototactic behaviour of surface‐ and cave‐dwelling Atlantic mollies Poecilia mexicana was examined. Surface‐dwelling Atlantic mollies, as well as light‐ and dark‐reared cave fish showed photophilic behaviour under all light intensities used (620, 50 and 3 lx).
Environment‐related life‐history trait variations of the red‐bellied piranha Pygocentrus nattereri in two river basins of the Bolivian Amazon
Authors: Duponchelle F. , Lino F. , Hubert N. , Panfili J. , Renno J.‐F. , Baras E. , Torrico J. P. , Dugue R. , Nuñez J.
Published: October 2007

Life‐history traits of Pygocentrus nattereri were compared in two populations inhabiting connected tributaries of the upper Madera River: the white water Mamoré River and the clear water Iténez River. As white waters provide better trophic conditions than clear waters, the size at maturity, fecundity, reproductive effort, condition and growth of P. nattereri should be greater in the more productive white water river (Mamoré) than in the less‐productive clear water river (Iténez). Breeding periods were highly seasonal and similar in both rivers and under strong influence of photoperiod. Oocyte size‐frequency distributions, together with the frequent occurrence of recovering females indicated that an individual female spawns at least twice during the breeding season. As predicted, fish of the Mamoré were significantly larger at maturity and had higher fecundity and condition factor values than those of the Iténez. Fish from both rivers matured as yearlings. The higher growth potential of females was better expressed in the Mamoré than in the Iténez, where growth differences between sexes were weak. Females had a significantly better growth in the Mamoré than in the Iténez. The observed life‐history traits associations were consistent with the hypothesis of better trophic conditions in the Mamoré. In addition, previous genetic analyses evidenced that the colonization of the two basins is recent and that extant populations have very similar genetic backgrounds. This suggests that the observed variations in life‐history traits of P. nattereri are not related to historical factors (genetic drift) between two phylogeographically distinct lineages, but rather due to the contrasting environmental conditions in the white and clear waters.
Juvenile sockeye salmon distribution, size, condition and diet during years with warm and cool spring sea temperatures along the eastern Bering Sea shelf
Authors: Farley E. V. , Murphy J. M. , Adkison M. , Eisner L.
Published: October 2007

Interannual variations in distribution, size, indices of feeding and condition of juvenile Bristol Bay sockeye salmon Oncorhynchus nerka collected in August to September (2000–2003) during Bering–Aleutian Salmon International Surveys were examined to test possible mechanisms influencing their early marine growth and survival. Juvenile sockeye salmon were mainly distributed within the southern region of the eastern Bering Sea, south of 57°0′ N during 2000 and 2001 and farther offshore, south of 58°0′ N during 2002 and 2003. In general, juvenile sockeye salmon were significantly larger (P < 0·05) and had significantly higher indices of condition (P < 0·05) during 2002 and 2003 than during 2000 and 2001. The feeding index was generally higher for age 1.0 year sockeye salmon than age 2.0 year during all years. Among‐year comparisons suggested that Pacific sand lance Ammodytes hexapterus were important components of the juvenile sockeye salmon diet during 2000 and 2001 (20 to 50% of the mean wet mass) and age 0 year walleye pollock Theragra chalcogramma were important components during 2002 and 2003 (50 to 60% of the mean wet mass). Warmer sea temperatures during spring and summer of 2002 and 2003 probably increased productivity on the eastern Bering Sea shelf, enhancing juvenile sockeye salmon growth.