bluuebunny/crossref_metadata_2025 huggingface dataset:
Current crowding-induced electromigration in SnAg3.0Cu0.5 microbumps
Authors: Chiang Kuo Ning , Lee Chien Chen , Lee Chang Chun , Chen Kuo Ming
Published: February 2006

To determine the relevance of current crowding to electromigration in the SnAg3.0Cu0.5 solder bump, a three-dimensional dual bumps simulation model was designed to demonstrate how current crowding can enhance the local atomic flux along the electron flow path. The finding of void formation occurred at the entrance points to the cathode sides and the enhancement of the growth and clustering of the intermetallic compound at the outgoing points of the anode sides along the electron flow path were verified experimentally. The tilting effect is obvious at the anode/chip side. The experimental mean-time-to-failure was observed, and Black’s equation with Joule heating effect were investigated as well.
Organic nanoparticle (hyperbranched polymer)-dispersed photopolymers for volume holographic storage
Authors: Tomita Yasuo , Furushima Kouji , Ochi Koichiro , Ishizu Koji , Tanaka Akihiro , Ozawa Masaaki , Hidaka Motohiko , Chikama Katsumi
Published: February 2006

We report on the use of hyperbranched polymers (HBPs) acting as mobile organic nanoparticles doped in methacrylate photopolymers for highly efficient volume holographic recording. Two types of reduced HBPs having the average size of 10nm are synthesized. The diffraction efficiency near 100% in the green (532nm) and substantive polymerization-shrinkage suppression in this photopolymer system are demonstrated. Periodic assembly of HBPs under holographic exposure is also observed.
Evolution of wetting layer of InAs∕GaAs quantum dots studied by reflectance difference spectroscopy
Authors: Chen Y. H. , Sun J. , Jin P. , Wang Z. G. , Yang Z.
Published: February 2006

For the InAs∕GaAs quantum-dot system, the evolution of the wetting layer (WL) with the InAs deposition thickness has been studied by reflectance difference spectroscopy (RDS) in combination with atomic force microscopy and photoluminescence. One transition related to the light hole in the WL has been observed clearly in RDS, from which its transition energy and in-plane optical anisotropy (OA) are determined. The evolution of WL with the InAs dot formation and ripening has been discussed. In addition, the remarkable changes in OA at the onsets of the dot formation and ripening have been observed, implying the mode transitions of atom transport between the WL and the dots.
Structure and thermal stability of gold nanoplates
Authors: Kan Caixia , Wang Guanghou , Zhu Xiaoguang , Li Cuncheng , Cao Bingqiang
Published: February 2006

Gold (Au) nanoplates with an average thickness of ∼70nm and several 10μm in edge size have been mass synthesized through a solution-phase method. Structural studies demonstrate that the Au nanoplates are single crystals with (111) planes as two basal surfaces. Fragmentation of Au nanoplates is found when temperature is higher than 450°C. Investigations on the thermal stability of Au nanoplates suggest that the melting and breaking start mainly at the (110) bounded edges, while the (111) surfaces of Au nanoplates show high stability. This work is valuable for Au nanostructures applied at elevated temperatures.
Principles of self-assembly of helical pores from dendritic dipeptides
Authors: Percec Virgil , Dulcey Andrés E. , Peterca Mihai , Ilies Monica , Nummelin Sami , Sienkowska Monika J. , Heiney Paul A.
Published: February 2006

The self-assembly of the dendritic dipeptides (4-3,4-3,5)nG2-CH
2
-Boc-
l
-Tyr-
l
-Ala-OMe and their achiral dendritic alcohol (4-3,4-3,5)nG2-CH
2
OH precursors, both with
n
= 1–16, where
n
represents the number of methylenic units in the alkyl groups of the dendron, are reported. All chiral dendritic dipeptides and achiral dendritic alcohols self-assemble into helical porous columns that are stable in both solution and solid state. The pore diameter (D
pore
) of the columns self-assembled from dendritic dipeptides is ≈10 Å larger than that of structures assembled from dendritic alcohols. The increase of the D
pore
at the transition from dendritic alcohol to dendritic dipeptide is accompanied by a decreased solid angle of the building block. This trend is in agreement with previous pore size-solid angle dependences observed with different protective groups of the dipeptide and primary structures of the dendron. However, within the series of dendritic alcohols and dendritic dipeptides with various
n
, the D
pore
increases when the solid angle increases. The results of these investigations together with those of previous studies on the role of dipeptide stereochemistry and protective groups on this self-assembly process provide the molecular principles required to program the construction of supramolecular helical pores with diameter controlled at the Å level from a single dendritic dipeptide architecture. These principles are expected to be valid for libraries of dendritic dipeptides based on dendrons and dipeptides with various primary structures.
Mitochondrial carriers in the cytoplasmic state have a common substrate binding site
Authors: Robinson Alan J. , Kunji Edmund R. S.
Published: February 2006

Mitochondrial carriers link biochemical pathways in the cytosol and mitochondrial matrix by transporting substrates across the inner mitochondrial membrane. Substrate recognition is specific for each carrier, but sequence similarities suggest the carriers have similar structures and mechanisms of substrate translocation. By considering conservation of amino acids, distance and chemical constraints, and by modeling family members on the known structure of the ADP/ATP translocase, we have identified a common substrate binding site. It explains substrate selectivity and proton coupling and provides a mechanistic link to carrier opening by substrate-induced perturbation of the salt bridges that seal the pathway to and from the mitochondrial matrix. It enables the substrate specificity of uncharacterized mitochondrial carriers to be predicted.
Homotypic fusion of early endosomes: SNAREs do not determine fusion specificity
Authors: Brandhorst Dorothea , Zwilling Daniel , Rizzoli Silvio O. , Lippert Undine , Lang Thorsten , Jahn Reinhard
Published: February 2006

Membrane fusion in the secretory pathway is mediated by soluble
N
-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins. Different fusion steps are thought to be effected by independent sets of SNAREs, but it is unclear whether specificity is determined by an intrinsic specificity of SNARE pairing or by upstream factors. Using a newly developed microscopy-based assay, we have investigated the SNARE specificity of homotypic early endosomal fusion. We show that early endosomes contain multiple sets of SNAREs, including, in addition to the putative early endosomal SNAREs, those involved in exocytosis and in fusion of late endosomes. We demonstrate that fusion is largely mediated by a complex formed by syntaxin 13, syntaxin 6, vti1a, and VAMP4, whereas the exocytic and late endosomal SNAREs play little or no role in the reaction. In contrast, proteoliposomes reconstituted with early endosomal SNAREs promiscuously fuse with liposomes containing exocytotic or late endosomal SNAREs. We conclude that the specificity of SNARE pairing does not suffice to determine the specificity of organelle fusion.
Creep and recrystallization of large polycrystalline masses. I. General continuum theory
Authors: Faria Sérgio H
Published: February 2006

This is the first of a series of works on the continuum mechanics and thermodynamics of creep and recrystallization of large polycrystalline masses. The general continuum theory presented here is suited to mono- and multi-mineral rocks. It encompasses several symmetry groups (e.g. orthotropic and transversely isotropic) and diverse crystal classes of triclinic, monoclinic and rhombic systems, among others. The cornerstone of the current approach is the theory of mixtures with continuous diversity, which allows one to regard the polycrystal as a ‘mixture of lattice orientations’. Following this picture, balance equations of mass, linear momentum, lattice spin, energy, dislocations, and entropy are set forth to describe the response of the polycrystal (i.e. the ‘mixture’), as well as of a group of crystallites sharing the same lattice orientation (
viz
. a ‘species’). The connection between the balance equations for a species and those for the mixture is established by homogenization rules, formulated for every field of the theory.
Global crack detection using bispectral analysis
Authors: Hillis Andrew J , Neild Simon A , Drinkwater Bruce W , Wilcox Paul D
Published: February 2006

This paper describes a global non-destructive testing technique for detecting fatigue cracking in engineering components. The technique measures the mixing of two ultrasonic sinusoidal waves which are excited by a small piezoceramic disc bonded to the test structure. This input signal excites very high-order modes of vibration of the test structure within the ultrasonic frequency range. The response of the structure is measured by a second piezoceramic disc and the received waveform is analysed using the bispectrum signal processing technique. Frequency mixing occurs as a result of nonlinearities within the test structure and fatigue cracking is shown to produce a strong mixing effect. The bispectrum is shown to be particularly suitable for this application due to its known insensitivity to noise. Experimental results on steel beams are used to show that fatigue cracks, corresponding to a reduction in the beam section of 8%, can be detected. It is also shown that the bispectrum can be used to quantify the extent of the cracking. A simple nonlinear spring model is used to interpret the results and demonstrate the robustness of the bispectrum for this application.
Canonical multi-symplectic structure on the total exterior algebra bundle
Authors: Bridges Thomas J
Published: February 2006

The aim of this paper is to construct multi-symplectic structures starting with the geometry of an oriented Riemannian manifold, independent of a Lagrangian or a particular partial differential equation (PDE). The principal observation is that on an
n
-dimensional orientable manifold
M
there is a canonical quadratic form
Θ
associated with the total exterior algebra bundle on
M
. On the fibre, which has dimension 2

n

, the form
Θ
can be locally decomposed into
n
classical symplectic structures. When concatenated, these
n
-symplectic structures define a partial differential operator,

J

∂

, which turns out to be a Dirac operator with multi-symplectic structure. The operator

J

∂

generalizes the product operator

J

(d/d
t
) in classical symplectic geometry, and
M
is a generalization of the base manifold (i.e. time) in classical Hamiltonian dynamics. The structure generated by
Θ
provides a natural setting for analysing a class of covariant nonlinear gradient elliptic operators. The operator

J

∂

is elliptic, and the generalization of Hamiltonian systems,

J

∂

Z
=∇
S
(
Z
), for a section
Z
of the total exterior algebra bundle, is also an elliptic PDE. The inverse problem—find
S
(
Z
) for a given elliptic PDE—is shown to be related to a variant of the Legendre transform on
k
-forms. The theory is developed for flat base manifolds, but the constructions are coordinate free and generalize to Riemannian manifolds with non-trivial curvature. Some applications and implications of the theory are also discussed.
Good reindeer mothers live longer and become better in raising offspring
Authors: Weladji Robert B , Gaillard Jean-Michel , Yoccoz Nigel G , Holand Øystein , Mysterud Atle , Loison Anne , Nieminen Mauri , Stenseth Nils Chr
Published: February 2006

Longevity is the main factor influencing individual fitness of long-lived, iteroparous species. Theories of life history evolution suggest this is because increased longevity allows individuals to (i) have more breeding attempts (time component), (ii) accumulate experience so as to become better able to rear offspring (experience component) or (iii) because individuals reaching old age have above-average quality (quality component). We assess empirically the relative influences of time, experience and quality on the relationship between longevity and individual fitness among female reindeer. Fitness increased with longevity due to all three processes. All females increased in success with age up to their penultimate year of life (experience component), the success of the terminal-breeding occasion was strongly dependent on longevity. Long-lived females had more successful breeding attempts during their life (time component), and had higher reproductive success at all ages, especially during the last year of life (individual quality component) than short-lived females. Our study reveals a more complex relationship between longevity and fitness in large mammals than the simple increase of the number of reproductive attempts when living longer.
Small object detection neurons in female hoverflies
Authors: Nordström Karin , O'Carroll David C
Published: February 2006

While predators such as dragonflies are dependent on visual detection of moving prey, social interactions make conspecific detection equally important for many non-predatory insects. Specialized ‘acute zones’ associated with target detection have evolved in several insect groups and are a prominent male-specific feature in many dipteran flies. The physiology of target selective neurons associated with these specialized eye regions has previously been described only from male flies. We show here that female hoverflies (Eristalis tenax)have several classes of neurons within the third optic ganglion (lobula) capable of detecting moving objects smaller than 1°. These neurons have frontal receptive fields covering a large part of the ipsilateral world and are tuned to a broad range of target speeds and sizes. This could make them suitable for detecting targets under a range of natural conditions such as required during predator avoidance or conspecific interactions.
Are capuchin monkeys (Cebus apella) inequity averse?
Authors: Dubreuil Diane , Gentile Maria Silvia , Visalberghi Elisabetta
Published: February 2006

It has been reported that capuchin monkeys reject a less preferred food (LPF) when they see a partner capuchin receive a more preferred food (PF) for performing the same task. This behaviour was taken as evidence of ‘inequity aversion’, but an alternative hypothesis is that capuchins reject the LPF because of the mere presence of the PF. We tested this hypothesis in a paradigm, which consisted of presenting two different foods (one PF and one LPF) on a tray and allowing the capuchin to take only the LPF. Refusals to initiate the trial and refusals to take and eat the LPF were higher when the PF was hidden (hiding condition) and when the PF was accumulated in sight but out of reach of the subject (accumulation condition) compared to when two pieces of LPF were placed on the tray (control condition). Interestingly, the subject behaved as in the control condition when its partner was given and ate the PF (partner condition). We argue that capuchins' refusals were due to the frustration of seeing and not obtaining the PF, and that seeing the partner eating increases the LPF acceptance.
The cost of catching up: increased winter mortality following structural growth compensation in the wild
Authors: Johnsson Jörgen I , Bohlin Torgny
Published: February 2006

Although laboratory and observational studies suggest that many animals are capable of compensatory growth after periods of food shortage, few field experiments have demonstrated structural growth compensation in the wild. Here, we addressed the hypotheses that (i) food restriction can induce structural compensatory growth in free-living animals, (ii) that compensation is proportional to the level of body size retardation and (iii) that compensation induces mortality costs. To test these, wild brown trout (
Salmo trutta
) yearlings were brought to the lab, tagged individually, subjected to four levels of food deprivation (including a control), released back into the native stream and recaptured after one, five and ten months. Brown trout fully restored condition and partially restored mass within a month, whereas compensation in structure (i.e. body length) was not evident until after five months, supporting hypothesis 1. As the level of growth compensation was similar among the three deprived groups, hypothesis 2 was not supported. A final recapture after winter revealed delayed mortality, apparently induced by the compensatory response in the deprived groups, which is consistent with hypothesis 3. To our knowledge, this is the first field experiment demonstrating structural compensatory growth and associated costs in a wild animal population.
Fungal plant endosymbionts alter life history and reproductive success of aphid predators
Authors: de Sassi Claudio , Müller Christine B , Krauss Jochen
Published: February 2006

Endosymbionts occur in most plant species and may affect interactions among herbivores and their predators through the production of toxic alkaloids. Here, we ask whether effects of mycotoxins produced by the symbiosis of the fungal endophyteNeotyphodium loliiand the grassLolium perenneare transmitted to the aphidophagous ladybirdCoccinella septempunctatawhen feeding on cereal aphidsRhopalosiphum padion infected plants. The larval development of coccinellids was extended, while their survival was reduced when feeding exclusively on aphids from infected plants. Ladybirds developing on aphids from infected plants showed reduced fecundity and impaired reproductive performance. Body size and symmetries of ladybird adults were not affected by the endophytes. Consistently strong, negative effects of endophytes on the lifetime performance of ladybirds indicates that mycotoxins are transmitted along food chains, causing significant damage for top predators. Such cascading effects will influence the population dynamics of aphid predators in the long term and could feedback to the primary plant producers.
Parasites alter host phenotype and may create a new ecological niche for snail hosts
Authors: Miura Osamu , Kuris Armand M , Torchin Mark E , Hechinger Ryan F , Chiba Satoshi
Published: February 2006

By modifying the behaviour and morphology of hosts, parasites may strongly impact host individuals, populations and communities. We examined the effects of a common trematode parasite on its snail host,Batillaria cumingi(Batillariidae). This widespread snail is usually the most abundant invertebrate in salt marshes and mudflats of the northeastern coast of Asia. More than half (52.6%,n=1360) of the snails in our study were infected. We found that snails living in the lower intertidal zone were markedly larger and exhibited different shell morphology than those in the upper intertidal zone. The large morphotypes in the lower tidal zone were all infected by the trematode,Cercaria batillariae(Heterophyidae). We used a transplant experiment, a mark-and-recapture experiment and stable carbon isotope ratios to reveal that snails infected by the trematode move to the lower intertidal zone, resume growth after maturation and consume different resources. By simultaneously changing the morphology and behaviour of individual hosts, this parasite alters the demographics and potentially modifies resource use of the snail population. Since trematodes are common and often abundant in marine and freshwater habitats throughout the world, their effects potentially alter food webs in many systems.
Streptomyces
inside-out: a new perspective on the bacteria that provide us with antibiotics
Authors: Chater Keith F
Published: February 2006

Many of the antibiotics used today are made by a group of bacteria called
Streptomyces
. Streptomycetes evolved about 450 million years ago as branched filamentous organisms adapted to the utilization of plant remains. They reproduce by sending up specialized aerial branches, which form spores. Aerial growth is parasitic on the primary colony, which is digested and reused for aerial growth. The reproductive phase is coordinated with the secretion of antibiotics, which may protect the colony against invading bacteria during aerial growth. A clue to the integration of antibiotic production and aerial growth is provided by
bldA
mutants, which are defective in both processes. These mutants lack the ability to translate a particularly rare codon, UUA, in the genetic code. The UUA codon (TTA in DNA) is present in several regulatory genes that control sets of antibiotic production genes, and in one,
bldH
that controls aerial mycelium formation. The regulatory genes for antibiotic production are all involved in self-reinforcing regulatory systems that potentially amplify the regulatory significance of small changes in the efficiency of translation of UUA codons. One of the regulatory targets of
bldH
is an extracellular protease inhibitor protein that is likely to delay the digestion of the primary biomass until the colony is ready for aerial growth. The use of the UUA codon to orchestrate different aspects of extracellular biology appeared very early in
Streptomyces
evolution.
Adventures in vascular biology: a tale of two mediators
Authors: Moncada S
Published: February 2006

I would like to thank the Royal Society for inviting me to deliver the Croonian Lecture. In so doing, the Society is adding my name to a list of very distinguished scientists who, since 1738, have preceded me in this task. This is, indeed, a great honour.

For most of my research career my main interest has been the understanding of the normal functioning of the blood vessel wall and the way this is affected in pathology. During this time, our knowledge of these subjects has grown to such an extent that many people now believe that the conquering of vascular disease is a real possibility in the foreseeable future.

My lecture concerns the discovery of two substances, prostacyclin and nitric oxide. I would like to describe the moments of insight and some of the critical experiments that contributed significantly to the uncovering of their roles in vascular biology. The process was often adventurous, hence the title of this lecture. It is the excitement of the adventure that I would like to convey in the text that follows.
New ways of preventing HIV infection: thinking simply, simply thinking
Authors: Short R.V
Published: February 2006

HIV infection is the greatest health crisis in human history. It continues to spread unchecked among the poor in the developing world because we have failed to design simple preventative methods that are available and affordable to those living on under $2 a day. Five new methods are discussed. (i)
A natural microbicide
. Intravaginal lime or lemon juice has been used for centuries as a traditional contraceptive. The juice can also kill HIV in the laboratory, but clinical trials are needed to see if vaginal application is acceptable, safe and effective. (ii)
Intravaginal oestrogen
. Monkeys can be protected from Simian immunodeficiency virus (SIV) infection by keratinizing the vagina with topical oestrogen. If women take the oral contraceptive pill vaginally it retains its contraceptive efficacy, and the oestrogen it contains should thicken the vagina and protect against HIV infection. Clinical trials are needed. (iii)
Male circumcision
. Removal of the inner foreskin removes the main site of HIV entry into the penis, resulting in a sevenfold reduction in susceptibility to infection. The practice needs to be promoted. (iv)
Post-coital penile hygiene
. Wiping the penis immediately after intercourse with lime or lemon juice or vinegar should kill the virus before it has had a chance to infect. A clinical trial of efficacy is needed. (v)
PhotoVoice
. Asking schoolchildren in developing countries to photograph their impressions of HIV/AIDS is a powerful way of getting them to discuss the subject openly, and develop their own preventative strategies.
Bioinformatic challenges for the next decade(s)
Authors: Eisenberg David , Marcotte Edward , McLachlan Andrew D , Pellegrini Matteo
Published: February 2006

The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules—DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer.
Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery
Authors: Blundell Tom L , Sibanda Bancinyane L , Montalvão Rinaldo Wander , Brewerton Suzanne , Chelliah Vijayalakshmi , Worth Catherine L , Harmer Nicholas J , Davies Owen , Burke David
Published: February 2006

Impressive progress in genome sequencing, protein expression and high-throughput crystallography and NMR has radically transformed the opportunities to use protein three-dimensional structures to accelerate drug discovery, but the quantity and complexity of the data have ensured a central place for informatics. Structural biology and bioinformatics have assisted in lead optimization and target identification where they have well established roles; they can now contribute to lead discovery, exploiting high-throughput methods of structure determination that provide powerful approaches to screening of fragment binding.
The origins and evolution of functional modules: lessons from protein complexes
Authors: Pereira-Leal Jose B , Levy Emmanuel D , Teichmann Sarah A
Published: February 2006

Modularity is an attribute of a system that can be decomposed into a set of cohesive entities that are loosely coupled. Many cellular networks can be decomposed into functional modules—each functionally separable from the other modules. The protein complexes in physical protein interaction networks are a good example of this, and here we focus on their origins and evolution. We investigate the emergence of protein complexes and physical interactions between proteins by duplication, and review other mechanisms. We dissect the dataset of protein complexes of known three-dimensional structure, and show that roughly 90% of these complexes contain contacts between identical proteins within the same complex. Proteins that are shared across different complexes occur frequently, and they tend to be essential genes more often than members of a single protein complex. We also provide a perspective on the evolutionary mechanisms driving the growth of other modular cellular networks such as transcriptional regulatory and metabolic networks.
Pathways of Change: Organizations in Transition
Authors: Erakovic Ljiljana , Powell Michael
Published: February 2006

This article discusses and illustrates organizational changes as initiated by ownership transition. It develops and elaborates three different pathways that organizations might follow through the process of transformation from government departments to state‐owned enterprises, and then to privately‐owned companies: the incremental, radical and reductive pathways. The research reported here is based on 11 case studies of New Zealand privatized companies. The pathway approach develops and extends existing models of transitional organizational trajectories, emphasizing the importance of antecedent conditions of organizational development, current environmental patterns and the strategic choices of the government and new owners.
Developing New Forms of Partnership With the ‘Market’ in the Procurement of Public Services
Authors: Bovaird Tony
Published: February 2006

This article provides a conceptual framework for understanding the key differences between newly emerging ‘market’ relationships and more traditional forms of procurement by public sector organizations. It highlights how multiple relationships between service clients in the public sector and other stakeholders mean that service clients may often co‐produce welfare changes in their communities in ways which professional and commercial providers cannot easily control and may not fully understand. It highlights the very different nature of collaborations which affect single commissioners and contractors (relational contracting), multiple commissioning bodies with a unified procurement policy (partnership procurement) and multiple commissioning bodies with diverse procurement policies empowered by a single purchasing body (distributed commissioning). The article suggests that traditional conceptions of the ‘market’ and of ‘market management’ are now outdated and need to be revised to take into account the potential of collaborative relationships between multiple stakeholders in the public domain.
Crossing the Great Divide – Using Multi‐method Analysis to Understand Opposition to Windfarms
Authors: Haggett Claire , Toke David
Published: February 2006

This paper demonstrates the possibilities for the complementary use of regression analysis and discourse analysis to further understand issues in public administration. To do so, an empirical study of opposition to wind energy planning applications is used. The application of logistical regression to analyse the factors which may influence windfarm planning applications is discussed, factors including the attitudes of local people. Discourse analytical techniques are then used to consider how anti‐windfarm campaigners manage accusations of ‘Not In My Back Yard’ (NIMBYism). This is done partly by linking their cause with wider environmental objectives. Although discourses and logistical regression models have very different ontologies, the paper demonstrates that there is no inevitable conflict between the epistemologies used in these two different methods, despite differences in the type of data being analysed.
The influence of anti‐endothelial/antiphospholipid antibodies on fibrin formation and lysis on endothelial cells
Authors: Patterson Angela M. , Ford Isobel , Graham Audrey , Booth Nuala A. , Greaves Mike
Published: February 2006

The prothrombotic mechanisms associated with antiphospholipid antibodies remain incompletely defined. Antibody binding to endothelial cells in vitro is a feature of antiphospholipid antibody‐positive sera. We hypothesised that impairment of endothelium‐dependent fibrinolysis by antiphospholipid/anti‐endothelial antibodies is a contributory factor in the pathogenesis of thrombosis. We also aimed to confirm the displacement of annexin‐V from endothelial cells and enhanced fibrin formation. Binding of immunoglobulin (Ig) from antiphospholipid antibody‐positive sera to endothelial cells was examined using a cell‐based enzyme‐linked immunosorbent assay. Effects on fibrin formation and lysis were examined on cultured endothelial cell monolayers. Plasminogen activator inhibitor‐1 (PAI‐1) was assayed in supernatants. We confirmed antibody binding to endothelial cells. With four of 14 antiphospholipid antibody‐positive sera there was some prolongation of fibrin clot lysis time, consistent with impairment of endothelial fibrinolytic activity. Secretion of PAI‐1 was significantly correlated with clot lysis time on endothelial cell monolayers incubated with antiphospholipid/anti‐endothelial antibody‐positive sera, but not with control sera. IgG from antiphospholipid antibody‐positive sera had little effect on endothelial cell surface annexin‐V expression. We conclude that impaired endothelial fibrinolysis is a potential prothrombotic mechanism in subjects with antiphospholipid antibodies. We were unable to confirm enhanced displacement of annexin‐V from endothelium by antiphospholipid antibodies.
Flow‐substrate interactions create and mediate leaf litter resource patches in streams
Authors: HOOVER TRENT M. , RICHARDSON JOHN S. , YONEMITSU NOBORU
Published: February 2006

1. The roles that streambed geometry, channel morphology, and water velocity play in the retention and subsequent breakdown of leaf litter in small streams were examined by conducting a series of field and laboratory experiments.

2. In the first experiment, conditioned red alder (Alnus rubra Bongard) leaves were released individually in three riffles and three pools in a second‐order stream. The transport distance of each leaf was measured. Several channel and streambed variables were measured at each leaf settlement location and compared with a similar number of measurements taken at regular intervals along streambed transects (‘reference locations’). Channel features (such as water depth) and substrate variables (including stone height, stone height‐to‐width ratio, and relative protrusion) were the most important factors in leaf retention.

3. In the second experiment, the role of settlement location and reach type in determining the rate of leaf litter breakdown was examined by placing individual conditioned red alder leaves in exposed and sheltered locations (on the upper and lower edges of the upstream face of streambed stones, respectively) in riffle and pool habitats. After 10 days, percent mass remaining of each leaf was measured. Generally, leaves broke down faster in pools than in riffles. However, the role of exposure in breakdown rate differed between reach types (exposed pool > sheltered pool > sheltered riffle > exposed riffle).

4. In the third experiment, the importance of substrate geometry on leaf litter retention was examined by individually releasing artificial leaves upstream of a series of substrate models of varying shape. Substrates with high‐angle upstream faces (were vertical or close to vertical), and that had high aspect ratios (were tall relative to their width), retained leaves more effectively.

5. These results show that streambed morphology is an important factor in leaf litter retention and breakdown. Interactions between substrate and flow characteristics lead to the creation of detrital resource patchiness, and may partition leaf litter inputs between riffles and pools in streams at baseflow conditions.
The functional role of native freshwater mussels in the fluvial benthic environment
Authors: HOWARD JEANETTE K. , CUFFEY KURT M.
Published: February 2006

1. Freshwater mussels are the dominant consumer biomass in many fluvial systems. As filter feeding grazers, mussels can remove large amounts of particulate matter from the water column and transfer these resources to the substrate as biodeposits (agglutinated mussel faeces and pseudofaeces). Mussel biodeposits are a nutrient rich and easily assimilated food source and therefore may have significant relevance to benthic community structure. This study examines the functional role of Margaritifera falcata in the South Fork Eel River, California.

2. We addressed two main questions: (i) Do mussels increase benthic resources in this system? (ii) If so, does this alter macroinvertebrate community structure?

3. Measurements and enclosure experiments in the South Fork Eel River show that mussels can play a significant role in local food webs by increasing available fine particulate matter (both organic and inorganic) on the substrate. We document increased benthic macroinvertebrate biomass for predators and collectors (Leptophlebidae) in the presence of mussels, but only in late summer.
How wide to cast the net? Cross‐taxon congruence of species richness, community similarity and indicator taxa in ponds
Authors: BILTON DAVID T. , MCABENDROTH LOUISE , BEDFORD ALAN , RAMSAY PAUL M.
Published: February 2006

1. Broad‐scale assessments of biodiversity often rely on the use of surrogate taxa, whose reliability has rarely been tested, particularly in freshwater systems. Here we use data from 46 ponds in two regions of the U.K. to explore the performance of macroinvertebrate taxa as surrogates for the rapid assessment of pond biodiversity. For the four dominant taxonomic groups in these ponds (Chironomidae, Coleoptera, Gastropoda and Trichoptera) we explore cross‐taxon species richness relationships in each of the two regions, and also determine the degree of concordance between the different taxa in accurately representing the similarity relationships between pond assemblages.

2. Patterns of cross‐taxon congruence in species richness were highly variable among taxa and study sites, making the use of a single taxon as a predictor of overall macroinvertebrate species richness problematic. In contrast, all four taxa show >70% congruence with the pattern of community similarity between sites resulting from the entire macroinvertebrate dataset, this result being consistent within and between regions. Canonical correspondence analysis demonstrated that all taxa were related in a similar manner to measured environmental parameters, meaning that limited additional ecological information is gained by including a wider range of pond taxa in rapid site assessment.

3. Single taxonomic groups can, therefore, perform consistently as indicators of community similarity between ponds, and no one taxon dramatically outperforms any other in this respect. The relative merits of the four focal taxa as surrogates for pond invertebrate assemblage composition are discussed with reference to ease of survey, ease of identification and ecological range occupied.

4. It is suggested that Coleoptera have a number of advantages as a surrogate taxon, being diverse, easily sampled, readily identified, taxonomically stable, ecologically well understood and occurring across a wide spectrum of pond types. They are therefore recommended for use as a focal group in rapid pond biodiversity assessments, employing an approach such as ours, which examines patterns of assemblage similarity, rather than species richness alone.
Nutrient uptake in streams draining agricultural catchments of the midwestern United States
Authors: BERNOT MELODY J. , TANK JENNIFER L. , ROYER TODD V. , DAVID MARK B.
Published: February 2006

1. Agriculture is a major contributor of non‐point source pollution to surface waters in the midwestern United States, resulting in eutrophication of freshwater aquatic ecosystems and development of hypoxia in the Gulf of Mexico. Agriculturally influenced streams are diverse in morphology and have variable nutrient concentrations. Understanding how nutrients are transformed and retained within agricultural streams may aid in mitigating increased nutrient export to downstream ecosystems.

2. We studied six agriculturally influenced streams in Indiana and Michigan to develop a more comprehensive understanding of the factors controlling nutrient retention and export in agricultural streams using nutrient addition and isotopic tracer studies.

3. Metrics of nutrient uptake indicated that nitrate uptake was saturated in these streams whereas ammonium and phosphorus uptake increased with higher concentrations. Phosphorus uptake was likely approaching saturation as evidenced by decreasing uptake velocities with concentration; ammonium uptake velocity also declined with concentration, though not significantly.

4. Higher whole‐stream uptake rates of phosphorus and ammonium were associated with the observed presence of stream autotrophs (e.g. algae and macrophytes). However, there was no significant relationship between measures of nutrient uptake and stream metabolism. Water‐column nutrient concentrations were positively correlated with gross primary production but not community respiration.

5. Overall, nutrient uptake and metabolism were affected by nutrient concentrations in these agriculturally influenced streams. Biological uptake of ammonium and phosphorus was not saturated, although nitrate uptake did appear to be saturated in these ecosystems. Biological activity in agriculturally influenced streams is higher relative to more pristine streams and this increased biological activity likely influences nutrient retention and transport to downstream ecosystems.
Litter quality, stream characteristics and litter diversity influence decomposition rates and macroinvertebrates
Authors: LEROY CARRI J. , MARKS JANE C.
Published: February 2006

1. We examined the relative importance of litter quality and stream characteristics in determining decomposition rate and the macroinvertebrate assemblage living on autumn‐shed leaves.

2. We compared the decomposition rates of five native riparian tree species (Populus fremontii, Alnus oblongifolia, Platanus wrightii, Fraxinus velutina and Quercus gambelii) across three south‐western streams in the Verde River catchment (Arizona, U.S.A.). We also compared the decomposition of three‐ and five‐species mixtures to that of single species to test whether plant species diversity affects rate.

3. Decomposition rate was affected by both litter quality and stream. However, litter quality accounted for most of the variation in decomposition rates. The relative importance of litter quality decreased through time, explaining 97% of the variation in the first week but only 45% by week 8. We also found that leaf mixtures decomposed more quickly than expected, when all the species included were highly labile or when the stream environment led to relatively fast decomposition.

4. In contrast to decomposition rate, differences in the invertebrate assemblage were more pronounced across streams than across leaf litter species within a stream. We also found significant differences between the invertebrate assemblage colonising leaf mixtures compared with that colonising pure species litter, indicating non‐additive properties of litter diversity on stream invertebrates.

5. This study shows that leaf litter diversity has the capacity to affect in‐stream decomposition rates and stream invertebrates, but that these effects depend on both litter quality and stream characteristics.
Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta)
Authors: Covacin C. , Shao R. , Cameron S. , Barker S. C.
Published: February 2006

The arrangement of genes in the mitochondrial (mt) genomes of most insects is the same, or near‐identical, to that inferred to be ancestral for insects. We sequenced the entire mt genome of the small pigeon louse, Campanulotes bidentatus compar, and part of the mt genomes of nine other species of lice. These species were from six families and the three main suborders of the order Phthiraptera. There was no variation in gene arrangement among species within a family but there was much variation in gene arrangement among the three suborders of lice. There has been an extraordinary number of gene rearrangements in the mitochondrial genomes of lice!
Sequence variation in trypsin‐ and chymotrypsin‐like cDNAs from the midgut of Ostrinia nubilalis: methods for allelic differentiation of candidate Bacillus thuringiensis resistance genes
Authors: Coates B. S. , Hellmich R. L. , Lewis L. C.
Published: February 2006

Midgut expressed alkaline serine proteases of Lepidoptera function in conversion of Bacillus thuringiensis (Bt) protoxin to active toxin, and reduced level of transcript T23 is associated with Ostrinia nubilalis resistance to Dipel® Bt formulations. Three groups of trypsin‐ (OnT25, OnT23, and OnT3) and two chymotrypsin‐like (OnC1 and OnC2) cDNAs were isolated from O. nubilalis midgut tissue. Intraspecific groupings are based on cDNA similarity and peptide phylogeny. Derived serine proteases showed a catalytic triad (His, Asp, and Ser; except transcript OnT23a), three substrate specificity‐determining residues, and three paired disulphide bonds. RT‐PCR indicated all transcripts are expressed in the midgut. Mendelian‐inherited genomic markers for loci OnT23, OnT3 and OnC1 will be useful for association of alleles with bioassayed Bt toxin resistance phenotypes.
Germ line transformation of the olive fly Bactrocera oleae using a versatile transgenesis marker
Authors: Koukidou M. , Klinakis A. , Reboulakis C. , Zagoraiou L. , Tavernarakis N. , Livadaras I. , Economopoulos A. , Savakis C.
Published: February 2006

The olive fruit fly (olive fly) Bactrocera oleae (Dacus), recently introduced in North America, is the most destructive pest of olives worldwide. The lack of an efficient gene transfer technology for olive fly has hampered molecular analysis, as well as development of genetic techniques for its control. We have developed a Minos‐based transposon vector carrying a self‐activating cassette which overexpresses the enhanced green fluorescent protein (EGFP). Efficient transposase‐mediated integration of one to multiple copies of this vector was achieved in the germ line of B. oleae by coinjecting the vector along with in vitro synthesized Minos transposase mRNA into preblastoderm embryos. The self‐activating gene construct combined with transposase mRNA present a system with potential for transgenesis of very diverse species.
Airway inflammation in subjects with gastro‐oesophageal reflux and gastro‐oesophageal reflux‐related asthma
Authors: CARPAGNANO G. E. , RESTA O. , VENTURA M. T. , AMORUSO A. C. , DI GIOIA G. , GILIBERTI T. , REFOLO L. , FOSCHINO‐BARBARO M. P.
Published: February 2006

Study objectives.  Asthma and gastro‐oesophageal reflux (GER) are both characterized by airway inflammation.

Design.  The purposes of this work were (i) to study airway inflammation in patients troubled by gastro‐oesophageal reflux (GER) and GER associated with asthma, (ii) to ascertain whether GER can aggravate asthma by exacerbating the pre‐existing airway inflammation and oxidative stress and (iii) to establish the validity of analysing breath condensate and induced sputum when studying the airways of subjects affected by GER.

Patient s and methods.  We enrolled 14 patients affected by mild asthma associated with GER (40 ±12 years), nine with mild but persistent asthma (39 ± 13 years), eight with GER (35 ± 11 years) and 17 healthy subjects (37 ± 9 years). Sputum cell counts and concentrations of interleukin‐4 (IL‐4), IL‐6 and 8‐isoprostane were measured in breath condensate and supernatant.

Measurements and results.  GER‐related asthma is characterized by an eosinophilic inflammation, as determined by elevated concentrations of IL‐4 in breath condensate and sputum supernatant, and by sputum cell analysis. GER alone presents a neutrophilic pattern of inflammation when determined by elevated concentrations of IL‐6 in sputum cell analysis. A concomitant increase has been found in 8‐isoprostane in GER associated (or not associated) with asthma.

Conclusions.  We conclude that GER is characterized by a neutrophilic airway inflammation and by increased oxidative stress. GER does not however aggravate pre‐existing airway inflammation in asthma patients. Determinations of inflammatory and oxidant markers in the breath condensate of subjects with GER reflect these measured in the induced sputum.