bluuebunny/crossref_metadata_2025 huggingface dataset:
A multiscale subgrid model for both free vortex flows and wall-bounded flows
Authors: Bricteux L. , Duponcheel M. , Winckelmans G.
Published: October 2009

A new subgrid-scale (SGS) model which has an adequate behavior in both vortical flows and wall-bounded flows is proposed. In wall-bounded flows with “wall-resolved” large eddy simulation (LES), the theory predicts that the SGS dissipation should vanish as y+3 near the wall. In free vortex flows, one needs to have models which do not dissipate energy in the strongly vortical and essentially laminar part of the flow, e.g., in the vortex core regions. The wall adapting local eddy (WALE) viscosity model of Nicoud and Ducros [Flow, Turbul. Combust. 62, 183 (1999)] has the correct near-wall behavior. It is, however, demonstrated here that it produces values of effective eddy viscosity which are too high in vortical flows: this constitutes a major drawback for LES of vortex flows. On the other hand, the regularized variational multiscale models are suitable to simulate vortical flows as demonstrated by Cocle et al. [Complex Effects in LES (Springer, New York, 2007), p. 56], but they do not have a correct behavior in wall-bounded flows as shown by Jeanmart and Winckelmans [Phys. Fluids 19, 055110 (2007)]. The model presented here aims at combining the strengths of the two models: it is a multiscale model, thus acting on the high pass filtered LES field, and for which the SGS viscosity is evaluated using the WALE model, itself also computed using the high pass filtered field. Hence, this model is only active when there is locally a significant high wavenumber content in the flow and it has a natural near-wall damping behavior. The ability of this model to simulate vortex and wall-bounded flows is demonstrated on three test cases. The first case is the turbulent channel flow at Reτ=395 and Reτ=590. The second test concerns a counter-rotating four-vortex system at ReΓ=20 000. The third case concerns a two-vortex system in ground effect at ReΓ=20 000. It is shown that the model allows to perform successfully the LES of these flows with the proper dissipative behavior in both the near-wall and the vortical regions.
Excited-state reversible geminate recombination in two dimensions
Authors: Park Kihyun , Shin Kook Joe , Kim Hyojoon
Published: October 2009

Excited-state reversible geminate recombination with two different lifetimes and quenching is investigated in two dimensions. From the exact Green function in the Laplace domain, analytic expressions of two-dimensional survival and binding probabilities are obtained at short and long times. We find that a new pattern of kinetic transition occurs in two dimensions. The long-time effective survival probabilities show a pattern of (ln t)−1→constant→et depending on the rate constants while the effective binding probabilities show t−1(ln t)−2→t−1→et.
Tailoring simultaneous photonic and phononic band gaps
Authors: Sadat-Saleh Said , Benchabane Sarah , Baida Fadi Issam , Bernal Maria-Pilar , Laude Vincent
Published: October 2009

The simultaneous existence of photonic and phononic band gaps opens up many possibilities for enhancing acousto-optical interactions at a common wavelength scale. We term such structures phoxonic crystals. By computing the existence and dependence of phoxonic band gaps on the choice of lattice and unit cell, we obtain a hierarchy of two-dimensional phoxonic crystal structures. The single-atom hexagonal and square lattices, and some multiple-atom hexagonal lattices, including honeycomb and heterometric lattices, are investigated. For definiteness, arrays of air holes in lithium niobate are considered in the computations. It is observed that decreasing the symmetry of the lattice by adding atoms of different sizes inside the unit cell leads to larger phoxonic band gaps. Examples of designs for operation at an optical wavelength of 1550 nm are given. The corresponding phononic frequencies are in the gigahertz range.
Streamer-induced transport in electron temperature gradient turbulence
Authors: Hauff T. , Jenko F.
Published: October 2009

The question if and how streamers (i.e., radially elongated vortices) can lead to an enhancement of the electron heat transport in electron temperature gradient turbulence is addressed. To this aim, the electrons are treated as passive tracers, and their decorrelation mechanisms with respect to the advecting electrostatic potential are studied. A substantial transport enhancement is found in a wide region of parameter space.
An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions
Authors: Lin Yuchun , Baumketner Andrij , Deng Shaozhong , Xu Zhenli , Jacobs Donald , Cai Wei
Published: October 2009

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.
Nanoscale dislocation patterning by scratching in an atomic force microscope
Authors: Ponce F. A. , Wei Q. Y. , Wu Z. H. , Fonseca-Filho H. D. , Almeida C. M. , Prioli R. , Cherns D.
Published: October 2009

The nature of nanoscratching as a lithographic technique for site-selective generation of dislocations is investigated for use in the growth of nanostructures. Linear arrays of dislocations have been selectively introduced into (001) indium phosphide crystals by dragging a diamond tip in an atomic force microscope. The nature of plastic deformation is found to depend on the scratch direction. For ⟨110⟩ directions, anisotropic butterflylike structures with mostly screw dislocations indicate rotational motion in the vicinity of the advancing tip. For ⟨100⟩ directions, the dislocations do not propagate far from the surface, possibly due to interlocking between dislocations on different slip planes, with a surface morphology suggesting melting of the near surface region by frictional heat. These results indicate that growth of nanostructures should be highly dependent on the direction of the nanoscratch.
Study of fast-electron transport in laser-illuminated spherical targets
Authors: Yaakobi B. , Gotchev O. V. , Betti R. , Stoeckl C.
Published: October 2009

The transport and scattering of fast electrons created by the two-plasmon-decay instability are studied by comparing the hard x-ray signal from two identically irradiated targets: a 1-mm-diam solid Cu sphere and a 1-mm-diam solid CH sphere, both coated with a 15 μm layer of CH. Comparing the results with Monte Carlo code simulations shows the role of scattering in the higher-Z Cu target. We find evidence that the fast electrons are created with a wide angular divergence and that higher-energy electrons transmitted through the target are reflected back into the target. Because of scattering, the fast-electron energy deposition (preheat) in Cu is about half that in CH, namely, ∼0.15% of the laser energy for Cu as compared with ∼0.30% for CH. Embedded high-Z layers in imploding fusion targets, because of the scattering, could provide protection against preheat.
Neutron yield saturation in plasma focus: A fundamental cause
Authors: Lee S.
Published: October 2009

Plasma focus research in the direction of fusion energy faces the limitation of observed neutron saturation; the neutron yield Yn falls away from Yn∼E02, the scaling deteriorating as storage energy E0 increases toward 1 MJ. Numerical experiments confirm that Yn∼E02 applies at low energies and drops to Yn∼E00.8 toward 25 MJ; deteriorating already at several hundred kilojoules. We point out that the cause is the dynamic resistance of the axial phase that is constant for all plasma foci. This dynamic resistance dominates the circuit as capacitor bank surge impedance becomes insignificant at large E0, causing current, hence neutron “saturation.”
High power thermoelectrically cooled and uncooled quantum cascade lasers with optimized reflectivity facet coatings
Authors: Maulini Richard , Lyakh Arkadiy , Tsekoun Alexei , Go Rowel , Pflügl Christian , Diehl Laurent , Capasso Federico , Patel C. Kumar N.
Published: October 2009

We present a method of preserving the device wall-plug efficiency by adjusting mirror losses with facet coatings for longer cavity quantum cascade lasers. An experimental study of output power and wall-plug efficiency as functions of mirror losses was performed by varying the front facet coating reflectivity with a high-reflectivity-coated rear facet. The use of optimized reflectivity coatings on 7-mm-long chips resulted in continuous-wave output power of 2.9W at 293K for thermoelectrically cooled devices mounted on AlN submounts and average and continuous-wave output power in excess of 1W for uncooled devices emitting at 4.6μm.
Particle-in-cell and hypernetted chain models of two-component, two-temperature coupled classical plasmas
Authors: Rose D. V. , Genoni T. C. , Welch D. R. , Clark R. E. , Campbell R. B. , Mehlhorn T. A. , Flicker D. G.
Published: October 2009

Three-dimensional simulations of moderately to strongly coupled electron-ion and multicomponent classical plasmas using the particle-in-cell method are presented. The simulations resolve sub-Debye-length interparticle spacing to accurately model the dynamics of these systems. We consider realistic mass ratios and quasiequilibrium conditions with different component temperatures which are relevant on short time scales. The simulation results are in very good agreement with classical hypernetted chain calculations for dense electron-ion and ion-ion plasmas. Our results demonstrate the feasibility and utility of large-scale particle-in-cell simulations for the modeling and analysis of multicomponent moderately and strongly coupled plasmas.
Real-time band structure changes of GaAs during continuous dynamic compression to 5 GPa
Authors: Grivickas P. , McCluskey M. D. , Gupta Y. M.
Published: October 2009

Real time changes of the GaAs band structure were determined using time-resolved photoluminescence (PL) spectroscopy, with nanosecond resolution, in single-event continuous compression experiments. Continuous compression to 5 GPa over 150 ns was achieved by impacting fused silica buffers preceding the GaAs crystals. PL spectra and compression wave profiles were measured simultaneously for uniaxial strain compression along the [100] orientation. Below 3 GPa, PL peaks from Te donors and Zn acceptors showed a blueshift upon compression, consistent with a widening of the band gap. At 3 GPa, the PL intensity decreased abruptly, due to a direct-to-indirect transition.
Influence of heat treatments on electrical properties of ZnO films grown by molecular-beam epitaxy
Authors: Oh D. C. , Park S. H. , Goto H. , Im I. H. , Jung M. N. , Chang J. H. , Yao T. , Song J. S. , Bae C. H. , Han C. S. , Koo K. W.
Published: October 2009

We report on the influence of heat treatments on the electrical properties of ZnO films grown by molecular-beam epitaxy. We note that the electrical resistance of the ZnO films is significantly changed by the heat treatments: the electrical resistance increases with the increase of ambient temperature, but above a critical temperature the resistance decreases with the increase of temperature, irrespective of ambient gases. On the other hand, it is found that the large amount of photocurrent is generated in the ZnO films, exposed to white sources: the photocurrent decreases with the increase of the obtained resistance, and the current increases with the decrease of the resistance. Also, it is shown that the x-ray diffraction linewidth of the ZnO films is significantly decreased by the heat treatments. These indicate that the increase/decrease of the electrical resistance is ascribed to the annihilation/formation of the residual donor-type defects in the ZnO films by the heat treatments. It is suggested that the increase of the electrical resistance is due to the annihilation of Zni-complex defects, while the decrease of the electrical resistance is due to the formation of VO-complex defects.
Growth responses of sugarcane to mycorrhizal spore density and phosphorus rate
Authors: Kelly R. M. , Edwards D. G. , Thompson J. P. , Magarey R. C.
Published: October 2009

Arbuscular mycorrhizal (AM) fungi, commonly found in long-term cane-growing fields in northern Queensland, are linked with both negative and positive growth responses by sugarcane (Saccharum spp.), depending on P supply. A glasshouse trial was established to examine whether AM density might also have an important influence on these growth responses. Mycorrhizal spores (Glomus clarum), isolated from a long-term cane block in northern Queensland, were introduced into a pasteurised low-P cane soil at 5 densities (0, 0.06, 0.25, 1, 4 spores/g soil) and with 4 P treatments (0, 8.2, 25, and 47 mg/kg). At 83 days after planting, sugarcane tops responded positively to P fertilizer, although responses attributable to spore density were rarely observed. In one case, addition of 4 spores/g led to a 53% yield response over those without AM at 8 mg P/kg, or a relative benefit of 17 mg P/kg. Root colonisation was reduced for plants with nil or 74 mg P/kg. For those without AM, P concentration in the topmost visible dewlap (TVD) leaf increased significantly with fertiliser P (0.07 v. 0.15%). However, P concentration increased further with the presence of AM spores. Irrespective of AM, the critical P concentration in the TVD leaf was 0.18%. This study confirms earlier reports that sugarcane is poorly responsive to AM. Spore density, up to 4 spores/g soil, appears unable to influence this responsiveness, either positively or negatively. Attempts to gain P benefits by increasing AM density through rotation seem unlikely to lead to yield increases by sugarcane. Conversely, sugarcane grown in fields with high spore densities and high plant-available P, such as long-term cane-growing soils, is unlikely to suffer a yield reduction from mycorrhizal fungi.
The effects of condensed tannins from Dorycnium rectum on skatole and indole ruminal biogenesis for grazing sheep
Authors: Tavendale Michael H. , Lane Geoffrey A. , Schreurs Nicola M. , Fraser Karl , Meagher Lucy P.
Published: October 2009

Skatole and indole are flavour compounds formed in the rumen, which are key factors in the pastoral flavour of meat and milk products. A selection of indolic compounds has been screened for their potential to form skatole and indole on in vitro fermentation, with rumen inocula collected from New Zealand pasture-fed sheep. Typically, 8% (P < 0.005) of added tryptophan was converted to indole and 54% (P < 0.001) was converted to skatole via indole acetic acid (IAA). The addition to rumen inocula of a condensed tannin (CT) fraction isolated from the forage legume, Dorycnium rectum, reduced the conversion of plant protein to skatole and indole by 75% and specifically inhibited the transformation of IAA to skatole by 85% (P < 0.001). The conversion of tryptophan to indole or IAA was not affected by CTs. The inhibitory effect of CTs on the conversion of tryptophan to skatole was prevented by the addition of polyethylene glycol (PEG) to the rumen inocula prior to the addition of CTs, but not by the addition of PEG subsequent to CTs, demonstrating that interactions between CTs and microbes involved in skatole biosynthesis are not reversible by PEG. This study is the first to demonstrate that isolated CTs have an inhibitory effect on the conversion of protein to skatole and indole by rumen microbes, and that CTs specifically inhibit the transformation of IAA to skatole by rumen microbes.
Comparative levels of dimethyltryptamine- and tyramine-related alkaloid toxins in Australian cultivars and some wild populations of Phalaris aquatica
Authors: Culvenor R. A. , Reed K. F. M. , McDonald S. E.
Published: October 2009

Phalaris (Phalaris aquatica L.) is a temperate perennial grass which occasionally causes toxicity in livestock. Immunoassays (ELISAs) were used to measure the level of the dimethyltryptamine and related alkaloid group (TRYP) and the tyramine-related group of alkaloids (TYR) in cultivars, breeding populations and wild accessions of phalaris. Herbage was sampled from grazed swards or spaced plants at several sites and times. Component alkaloids in 4 cultivars were also determined by thin-layer chromatography (TLC).
Levels of TYR were higher than TRYP at all times of sampling. Alkaloid levels varied widely with site and sampling time, green herbage sampled in autumn being much higher than herbage sampled from July onwards. Plants sampled in autumn usually appeared moisture stressed and this may have been 1 factor causing high alkaloid levels in autumn. Comparative levels of TRYP in older cultivars agreed with published information. Two semi-winter dormant cultivars, Australian and the new and closely-related Australian II, were both higher than other cultivars in TRYP (maximum levels 18–20 mg/100 g fresh weight) but similar to most in TYR. Among winter-active cultivars, Holdfast and Sirolan were very low in TRYP (maximum levels <0.5 mg/100 g fresh weight) but Holdfast was the highest of all cultivars in TYR. While we argue on the basis of the TLC analyses and from previous work that the bulk of TYR in phalaris cultivars is N-methyltyramine, Holdfast was an exception in having one-third of its TYR as the less toxic hordenine in TLC analyses. Other new cultivars, Landmaster and Atlas PG, and breeding populations being developed as potential cultivars for acid soils or with improved grazing tolerance were generally higher than Holdfast and Sirolan, and similar to Sirosa, in TRYP (maximum levels 1–5 mg/100 g fresh weight). All were less than Holdfast in TYR. Two sets of wild accessions, 1 of which is being used in the development of a cultivar for the North-West Slopes of NSW, were relatively high in TYR alkaloids.
Associative effects between feeds when concentrate supplements are fed to grazing dairy cows: a review of likely impacts on metabolisable energy supply
Authors: Doyle P. T. , Francis S. A. , Stockdale C. R.
Published: October 2009

Efficient conversion of grazed pasture and supplementary feeds into milk is essential to the profitability of dairy farming in southern Australia as costs of production continue to rise. The application of diet formulation approaches to the nutritional management of grazing dairy cows provides unique challenges in predicting the interactions that occur between grazed herbage and supplementary feeds. How feed intake and associative effects between feeds in lactating dairy cows grazing pasture might affect estimated metabolisable energy supplied by the diet are examined. The effects of increasing feed intake in high-producing dairy cows on decreasing the digestibility of energy, and the compensatory effects of reduced methane production, are reviewed. The factors affecting intake of grazing cows and possible effects on digestibility are considered, and include characteristics of the pasture/forage and amounts and forms of concentrates. Estimates of the potential magnitude of negative associative effects in dairy cows have been made using 2 datasets from recent experiments. Finally, the potential importance of understanding and predicting the magnitude of associative effects for efficient pasture-based dairy production is discussed. It is concluded that although associative effects between feeds in grazing dairy cows cannot be predicted with certainty, and although they involve complex interactions among a number of variables, ignoring their occurrence can lead to significant errors in both feed evaluation and ration formulation.
Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly
Ceratitis capitata
Authors: Schetelig Marc F. , Scolari Francesca , Handler Alfred M. , Kittelmann Sebastian , Gasperi Giuliano , Wimmer Ernst A.
Published: October 2009

Insect transgenesis is mainly based on the random genomic integration of DNA fragments embedded into non-autonomous transposable elements. Once a random insertion into a specific location of the genome has been identified as particularly useful with respect to transgene expression, the ability to make the insertion homozygous, and lack of fitness costs, it may be advantageous to use that location for further modification. Here we describe an efficient method for the modification of previously inserted transgenes by the use of the site-specific integration system from phage
phiC31
in a tephritid pest species, the Mediterranean fruit fly
Ceratitis capitata
. First, suitable transgenic strains with randomly integrated
attP
landing sites within transposon-based vectors were identified by molecular and functional characterization. Second, donor plasmids containing an
attB
site, with additional markers, and transposon ends were integrated into
attP
sites by
phiC31
integrase-mediated recombination. Third, transposase-encoding ‘jumpstarter’ strains were created and mated to transgenic strains resulting in the postintegrational excision of transposon ends, which left stably integrated transgene insertions that could not be remobilized. This three-step integration and stabilization system will allow the combination of several transgene-encoded advantageous traits at evaluated genomic positions to generate optimized strains for pest control that minimize environmental concerns.
Stepwise formation of P-cluster in nitrogenase MoFe protein
Authors: Lee Chi Chung , Blank Michael A. , Fay Aaron W. , Yoshizawa Janice M. , Hu Yilin , Hodgson Keith O. , Hedman Britt , Ribbe Markus W.
Published: October 2009

The P-cluster of nitrogenase is one of the most complex biological metallocenters known to date. Despite the recent advances in the chemical synthesis of P-cluster topologs, the biosynthetic mechanism of P-cluster has not been well defined. Here, we present a combined biochemical, electron paramagnetic resonance, and X-ray absorption spectroscopy/extended X-ray absorption fine-structure investigation of the maturation process of P-clusters in Δ
nifH
molybdenum-iron (MoFe) protein. Our data indicate that the previously identified, [Fe
4
S
4
]-like cluster pairs in Δ
nifH
MoFe protein are indeed the precursors to P-clusters, which can be reductively coupled into the mature [Fe
8
S
7
] structures in the presence of Fe protein, MgATP, and dithionite. Moreover, our observation of a biphasic maturation pattern of P-clusters in Δ
nifH
MoFe protein provides dynamic proof for the previously hypothesized, stepwise assembly mechanism of the two P-clusters in the α
2
β
2
-tetrameric MoFe protein, i.e., one P-cluster is formed in one αβ dimer before the other in the second αβ dimer.
Adjudication Deferred: Command Responsibility for War Crimes and US Military Justice from My Lai to Haditha and Beyond
Authors: Peters William C.
Published: October 2009

The public international law doctrine of command responsibility, like many firmly accepted rules in law, is more clearly stated than consistently applied. Intended to establish a base level of order and responsibility for sustained violence endemic to the inherently ugly nature of war, even state militaries of fully mature Western democracies demonstrate difficulty appreciating its importance and applying its law.
Using Single-Case Design and Personalized Behavior Change Projects to Teach Research Methods
Authors: Morgan David L.
Published: October 2009

Students in research methods courses, especially those taught in an intense format, might be hard pressed to actually conduct research studies due to logistics and time constraints. I describe the use of single-case research design and a personalized behavior project as an alternative research project for students in an undergraduate psychology methods course. Students were able to complete the project, including the collection, analysis, and interpretation of data, within the confines of an intensive, 6-week course.
“This is a Public Service Announcement”: Evaluating and Redesigning Campaigns to Teach Attitudes and Persuasion
Authors: Koch Erika J. , Lomore Christine D.
Published: October 2009

We present an assignment that requires students to apply their knowledge of the social psychology of attitudes and persuasion to critique and redesign a public service announcement. Students in a 200-level social psychology course evaluated the assignment by indicating their overall attitudes toward the assignment. Students rated the assignment positively, reporting that it would help them to evaluate advertisements in the future, that it helped them to gain a better understanding of the course material, that it helped them to learn to apply social psychological concepts and theories, and that it was enjoyable.
On 50 Years of Giving Psychology Away: An Interview with Philip Zimbardo
Authors: Slavich George M.
Published: October 2009

Philip G. Zimbardo, emeritus professor of psychology at Stanford University, is internationally recognized as the voice and face of contemporary American psychology. He earned his PhD in social psychology from Yale University in 1959 and has since received seven honorary doctorates for his contributions to psychology and society. The author of more than 300 publications and 50 books, Zimbardo's research spans 20 topics, including shyness, evil, teaching, persuasion, hypnosis, dissonance, time perspective, and heroism. He is best known for his landmark study, the Stanford Prison Experiment; his widely seen TV series, Discovering Psychology; and his best-selling textbook, Psychology and Life. He is past president of the Western Psychological Association (WPA) and the American Psychological Association (APA), and has received distinguished teaching awards from WPA, APA, Stanford University, Phi Beta Kappa, and the Society for the Teaching of Psychology. His aim to “give psychology away” is evident in all he does.

George M. Slavich is a Beck Institute Scholar, Society in Science: Branco Weiss Fellow, and National Institute of Mental Health Postdoctoral Fellow in Psychology and Medicine at the University of California, San Francisco. He completed undergraduate and graduate coursework at Stanford University, received his PhD in clinical psychology from the University of Oregon, and completed clinical training at McLean Hospital/Harvard Medical School. His research investigates the characteristics, causes, and consequences of life stress in major depression. He is also deeply devoted to teaching and mentoring. He founded the Stanford Undergraduate Psychology Conference and WPA Student Council; he also cofounded the Society of Clinical Psychology's Section on Graduate Student and Early Career Psychologists. For these contributions and others, he received the 2004 Albert Bandura Graduate Research Award, the 2005 Edwin B. Newman Graduate Research Award, and the 2005 Wilbert J. McKeachie Teaching Excellence Award.
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Authors: Beckstette Michael , Homann Robert , Giegerich Robert , Kurtz Stefan
Published: October 2009

Motivation: Profile hidden Markov models (pHMMs) are currently the most popular modeling concept for protein families. They provide sensitive family descriptors, and sequence database searching with pHMMs has become a standard task in today's genome annotation pipelines. On the downside, searching with pHMMs is computationally expensive.

Results: We propose a new method for efficient protein family classification and for speeding up database searches with pHMMs as is necessary for large-scale analysis scenarios. We employ simpler models of protein families called position-specific scoring matrices family models (PSSM-FMs). For fast database search, we combine full-text indexing, efficient exact p-value computation of PSSM match scores and fast fragment chaining. The resulting method is well suited to prefilter the set of sequences to be searched for subsequent database searches with pHMMs. We achieved a classification performance only marginally inferior to hmmsearch, yet, results could be obtained in a fraction of runtime with a speedup of >64-fold. In experiments addressing the method's ability to prefilter the sequence space for subsequent database searches with pHMMs, our method reduces the number of sequences to be searched with hmmsearch to only 0.80% of all sequences. The filter is very fast and leads to a total speedup of factor 43 over the unfiltered search, while retaining >99.5% of the original results. In a lossless filter setup for hmmsearch on UniProtKB/Swiss-Prot, we observed a speedup of factor 92.

Availability: The presented algorithms are implemented in the program PoSSuMsearch2, available for download at http://bibiserv.techfak.uni-bielefeld.de/possumsearch2/.

Contact:  beckstette@zbh.uni-hamburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bethesda Hospitals' Emergency Preparedness Partnership: A Model for Transinstitutional Collaboration of Emergency Responses
Authors: Henderson David K. , Malanoski Michael P. , Corapi Gene , Passamani Eugene , Notobartolo Cynthia , Gillette Chris , Hawes Patricia , Lee Laura M.
Published: October 2009

The events of September 11, 2001 identified a need for health care institutions to develop flexible, creative, and adaptive response mechanisms in the event of a local, regional, or national disaster. The 3 major health care institutions in Bethesda, MD—the National Naval Medical Center (NNMC), the Suburban Hospital Healthcare System (SHHS), and the National Institutes of Health Clinical Center (NIHCC)—have created a preparedness partnership that outstrips what any of the institutions could provide independently by pooling complementary resources. The creation of the partnership initially was driven by geographic proximity and by remarkably complementary resources. This article describes the creation of the partnership, the drivers and obstacles to creation, and the functioning and initial accomplishments of the partnership. The article argues that similar proximity and resource relationships exist among institutions at academic centers throughout the United States and suggests that this partnership may serve as a template for other similarly situated institutions. (Disaster Med Public Health Preparedness. 2009;3:168–173)
Evolution of climate niches in European mammals?
Authors: Dormann Carsten F. , Gruber Bernd , Winter Marten , Herrmann Dirk
Published: October 2009

Our ability to predict consequences of climate change is severely impaired by the lack of knowledge on the ability of species to adapt to changing environmental conditions. We used distribution data for 140 mammal species in Europe, together with data on climate, land cover and topography, to derive a statistical description of their realized climate niche. We then compared climate niche overlap of pairs of species, selected on the basis of phylogenetic information. In contrast to expectations, related species were not similar in their climate niche. Rather, even species pairs that had a common ancestor less than 1 Ma already display very high climate niche distances. We interpret our finding as a strong interspecific competitive constraint on the realized niche, rather than a rapid evolution of the fundamental niche. If correct, our results imply a very limited usefulness of climate niche models for the prediction of future mammal distributions.
Decreasing stochasticity through enhanced seasonality in measles epidemics
Authors: Mantilla-Beniers N. B. , Bjørnstad O. N. , Grenfell B. T. , Rohani P.
Published: October 2009

Seasonal changes in the environment are known to be important drivers of population dynamics, giving rise to sustained population cycles. However, it is often difficult to measure the strength and shape of seasonal forces affecting populations. In recent years, statistical time-series methods have been applied to the incidence records of childhood infectious diseases in an attempt to estimate seasonal variation in transmission rates, as driven by the pattern of school terms. In turn, school-term forcing was used to show how susceptible influx rates affect the interepidemic period. In this paper, we document the response of measles dynamics to distinct shifts in the parameter regime using previously unexplored records of measles mortality from the early decades of the twentieth century. We describe temporal patterns of measles epidemics using spectral analysis techniques, and point out a marked decrease in birth rates over time. Changes in host demography alone do not, however, suffice to explain epidemiological transitions. By fitting the time-series susceptible–infected–recovered model to measles mortality data, we obtain estimates of seasonal transmission in different eras, and find that seasonality increased over time. This analysis supports theoretical work linking complex population dynamics and the balance between stochastic and deterministic forces as determined by the strength of seasonality.
One-step electrohydrodynamic production of drug-loaded micro- and nanoparticles
Authors: Enayati Marjan , Ahmad Zeeshan , Stride Eleanor , Edirisinghe Mohan
Published: October 2009

The objective of this work was to produce drug-loaded nanometre- and micrometre-scale particles using a single-step process that provides control over particle size and size distribution. Co-axial electrohydrodynamic processing was used, at ambient temperature and pressure, with poly(lactic-co-glycolic acid) as the polymeric coating material and oestradiol as the encapsulated drug. The particle diameter was varied from less than 120 nm to a few micrometres, by simple methodical adjustments in the processing parameters (polymer concentration and applied voltage).
In vitro
studies were performed to determine the drug release profile from the particles during unassisted and ultrasound-stimulated degradation in simulated body fluid. An encapsulation efficiency of approximately 70% was achieved and release of the drug was sustained for a period of over 20 days. Exposing the particles to ultrasound (22.5 kHz) increased the rate of release by approximately 8 per cent. This processing method offers several advantages over conventional emulsification techniques for the preparation of drug-loaded particles. Most significantly, process efficiency and the drug's functionality are preserved, as complex multistep processing involving harsh solvents, other additives and elevated temperatures or pressures are avoided. Production rates of 10
12
particles min
−1
can be achieved with a single pair of co-axial needles and the process is amenable to being scaled up by using multiple sets.
Modelling the layer-specific three-dimensional residual stresses in arteries, with an application to the human aorta
Authors: Holzapfel Gerhard A. , Ogden Ray W.
Published: October 2009

This paper provides the first analysis of the three-dimensional state of residual stress and stretch in an artery wall consisting of three layers (intima, media and adventitia), modelled as a circular cylindrical tube. The analysis is based on experimental results on human aortas with non-atherosclerotic intimal thickening documented in a recent paper by Holzapfel
et al.
(

Holzapfel
et al.
2007

Ann. Biomed. Eng.
35
, 530–545 (
doi:10.1007/s10439-006-9252-z
)). The intima is included in the analysis because it has significant thickness and load-bearing capacity, unlike in a young, healthy human aorta. The mathematical model takes account of bending and stretching in both the circumferential and axial directions in each layer of the wall. Previous analysis of residual stress was essentially based on a simple application of the opening-angle method, which cannot accommodate the three-dimensional residual stretch and stress states observed in experiments. The geometry and nonlinear kinematics of the intima, media and adventitia are derived and the associated stress components determined explicitly using the nonlinear theory of elasticity. The theoretical results are then combined with the mean numerical values of the geometrical parameters and material constants from the experiments to illustrate the three-dimensional distributions of the stretches and stresses throughout the wall. The results highlight the compressive nature of the circumferential stress in the intima, which may be associated with buckling of the intima and its delamination from the media, and show that the qualitative features of the stretch and stress distributions in the media and adventitia are unaffected by the presence or absence of the intima. The circumferential residual stress in the intima increases significantly as the associated residual deformation in the intima increases while the corresponding stress in the media (which is compressive at its inner boundary and tensile at its outer boundary) is only slightly affected. The theoretical framework developed herein enables the state of residual stress to be calculated directly, serves to improve insight into the mechanical response of an unloaded artery wall and can be extended to accommodate more general geometries, kinematics and states of residual stress as well as more general constitutive models.
Estimating Young's modulus of zona pellucida by micropipette aspiration in combination with theoretical models of ovum
Authors: Khalilian Morteza , Navidbakhsh Mahdi , Valojerdi Mojtaba Rezazadeh , Chizari Mahmoud , Yazdi Poopak Eftekhari
Published: October 2009

The zona pellucida (ZP) is the spherical layer that surrounds the mammalian oocyte. The physical hardness of this layer plays a crucial role in fertilization and is largely unknown because of the lack of appropriate measuring and modelling methods. The aim of this study is to measure the biomechanical properties of the ZP of human/mouse ovum and to test the hypothesis that Young's modulus of the ZP varies with fertilization. Young's moduli of ZP are determined before and after fertilization by using the micropipette aspiration technique, coupled with theoretical models of the oocyte as an elastic incompressible half-space (half-space model), an elastic compressible bilayer (layered model) or an elastic compressible shell (shell model). Comparison of the models shows that incorporation of the layered geometry of the ovum and the compressibility of the ZP in the layered and shell models may provide a means of more accurately characterizing ZP elasticity. Evaluation of results shows that although the results of the models are different, all confirm that the hardening of ZP will increase following fertilization. As can be seen, different choices of models and experimental parameters can affect the interpretation of experimental data and lead to differing mechanical properties.
Hydrodynamic constraints on prey-capture performance in forward-striking snakes
Authors: Van Wassenbergh Sam , Brecko Jonathan , Aerts Peter , Stouten Ilona , Vanheusden Gwen , Camps Andy , Van Damme Raoul , Herrel Anthony
Published: October 2009

Some specialized aquatic snakes such asNatrix tessellatastrike at fish by rapidly accelerating their head towards the prey with their mouth opened widely. This strategy is believed to be suboptimal as relatively high drag forces act on the open jaws and, therefore, probably limit strike speed. Moreover, the bow wave in front of the snake's jaws could push prey away from the mouth, thus potentially explaining the relatively low capture success observed in these animals (<20%). Here, we used laser-scan based computational fluid dynamics to test these potential constraints on prey-capture performance forN. tessellata. Our simulations showed that drag force indeed increases drastically for striking at a high gape angle. However, we estimated the overall cost in slowing down strike speed to be less pronounced due to the instationary dynamics of the system. In contrast to the expectations, forward displacement of prey was relatively limited (<13% of head length), and forceful collisions between prey and the leading edge of the jaw regularly occurred. However, our models showed that precise aiming by the snake was needed to reduce the chance of deviating the prey to a path bypassing the mouth. Our study also indicated several hydrodynamic advantages for snakes to strike at relatively large prey.
Distribution of vaccine/antivirals and the ‘least spread line’ in a stratified population
Authors: Goldstein E. , Apolloni A. , Lewis B. , Miller J. C. , Macauley M. , Eubank S. , Lipsitch M. , Wallinga J.
Published: October 2009

We describe a prioritization scheme for an allocation of a sizeable quantity of vaccine or antivirals in a stratified population. The scheme builds on an optimal strategy for reducing the epidemic's initial growth rate in a stratified mass-action model. The strategy is tested on the EpiSims network describing interactions and influenza dynamics in the population of Utah, where the stratification we have chosen is by age (0–6, 7–13, 14–18, adults). No prior immunity information is available, thus everyone is assumed to be susceptible—this may be relevant, possibly with the exception of persons over 50, to the 2009 H1N1 influenza outbreak. We have found that the top priority in an allocation of a sizeable quantity of seasonal influenza vaccinations goes to young children (0–6), followed by teens (14–18), then children (7–13), with the adult share being quite low. These results, which rely on the structure of the EpiSims network, are compared with the current influenza vaccination coverage levels in the US population.
Organic preservation of fossil musculature with ultracellular detail
Authors: McNamara Maria , Orr Patrick J. , Kearns Stuart L. , Alcalá Luis , Anadón Pere , Peñalver-Mollá Enrique
Published: October 2009

The very labile (decay-prone), non-biomineralized, tissues of organisms are rarely fossilized. Occurrences thereof are invaluable supplements to a body fossil record dominated by biomineralized tissues, which alone are extremely unrepresentative of diversity in modern and ancient ecosystems. Fossil examples of extremely labile tissues (e.g. muscle) that exhibit a high degree of morphological fidelity are almost invariably replicated by inorganic compounds such as calcium phosphate. There is no consensus as to whether such tissues can be preserved with similar morphological fidelity as organic remains, except when enclosed inside amber. Here, we report fossilized musculature from an approximately 18 Myr old salamander from lacustrine sediments of Ribesalbes, Spain. The muscle is preserved organically, in three dimensions, and with the highest fidelity of morphological preservation yet documented from the fossil record. Preserved ultrastructural details include myofilaments, endomysium, layering within the sarcolemma, and endomysial circulatory vessels infilled with blood. Slight differences between the fossil tissues and their counterparts in extant amphibians reflect limited degradation during fossilization. Our results provide unequivocal evidence that high-fidelity organic preservation of extremely labile tissues is not only feasible, but likely to be common. This is supported by the discovery of similarly preserved tissues in the Eocene Grube Messel biota.
Ecological constraints and benefits of philopatry promote group-living in a social but non-cooperatively breeding fish
Authors: Wong Marian Y. L.
Published: October 2009

Why non-breeding subordinates of many animal societies tolerate group-living remains a pertinent question in evolutionary biology. The ecological constraints and benefits of philopatry hypotheses have the potential to explain the maintenance of group-living by specifying the ecological conditions favouring delayed dispersal over independent breeding by subordinates. In this study, I used field and laboratory experiments to investigate the role of ecological and social factors on the dispersal decisions of non-breeding subordinates in the coral-dwelling fish,Paragobiodon xanthosomus(Gobiidae). Subordinate dispersal was strongly influenced by ecological constraints (habitat saturation and risks of movement) and benefits of philopatry (relative coral size). Social factors, namely social rank and forcible eviction, did not affect the occurrence of subordinate dispersal. These results suggest that selection has favoured subordinateP. xanthosomus, which employ a mixed strategy—switching tactics in response to three ecological factors—despite having low mobility and extreme habitat-specific requirements. Furthermore, this study demonstrates the generality of the ecological constraints and benefits of philopatry hypotheses as explanations for group-living in species where subordinates are unrelated to breeders, provide no help and do not strictly delay dispersal.
Sex-specific chemical cues from immatures facilitate the evolution of mate guarding inHeliconiusbutterflies
Authors: Estrada Catalina , Yildizhan Selma , Schulz Stefan , Gilbert Lawrence E.
Published: October 2009

Competition for mates has substantial effects on sensory systems and often leads to the evolution of extraordinary mating behaviours in nature. The ability of males to find sexually immature females and associate with them until mating is a remarkable example. Although several aspects of such pre-copulatory mate guarding have been investigated, little is known about the mechanisms used by males to locate immature females and assess their maturity. These are not only key components of the origin and maintenance of this mating strategy, but are also necessary for inferring the level to which females cooperate and thus the incidence of sexual conflict. We investigated the cues involved in recognition of immature females inHeliconius charithonia, a butterfly that exhibits mate guarding by perching on pupae. We found that males recognized female pupae using sex-specific volatile monoterpenes produced by them towards the end of pupal development. Considering the presumed biosynthetic pathways of such compounds and the reproductive biology ofHeliconius, we propose that these monoterpenes are coevolved signals and not just sex-specific cues exploited by males. Their maintenance, despite lack of female mate choice, may be explained by variation in cost that females pay with this male behaviour under heterogeneous ecological conditions.