bluuebunny/crossref_metadata_2025 huggingface dataset:
A biogenic origin for anomalous fine‐grained magnetic material at the Paleocene‐Eocene boundary at Wilson Lake, New Jersey
Authors: Lippert Peter C. , Zachos James C.
Published: December 2007

The Paleocene‐Eocene Thermal Maximum, which occurred ∼55.5 Ma, was caused by a massive release of carbon, as indicated by an ∼3‰ negative carbon isotope excursion recorded in the marine, atmospheric, and terrestrial reservoirs. One suggested source for the carbon, a cometary impactor, is based on the sudden appearance and high concentration of single‐domain (SD) magnetite in Paleocene‐Eocene (P‐E) boundary cores from the North Atlantic continental margin. We evaluate the potential sources of SD magnetite at the P‐E boundary by presenting new magnetic hysteresis, low‐temperature magnetic remanence, and transmission electron microscopy data from the North Atlantic coastal ocean. Our results show a similar increase in SD material but demonstrate that the magnetic material has a biogenic origin. These findings indicate that the high concentrations of SD magnetite immediately above the P‐E boundary are the result of unusual accumulations and/or preservation of magnetotactic bacteria. Such bacteria typically occupy the oxic‐anoxic transition zone near the sediment‐water interface or in the water column. The high abundances of SD magnetite in sediments from across the shelf may be an artifact of nonsteady state redox conditions and exceptional preservation of SD magnetite. It may also indicate that the oxic‐anoxic redox boundary shifted into the water column. The latter explanation implies transient eutrophy of the coastal ocean in this region, most likely due to seasonally enhanced runoff, and increased stratification and nutrient loading.
“Virtual water”: An unfolding concept in integrated water resources management
Authors: Yang Hong , Zehnder Alexander
Published: December 2007

In its broadest sense, virtual water refers to the water required for the production of food commodities. Issues relating to virtual water have drawn much attention in scientific communities and the political sphere since the mid 1990s. This paper provides a critical review of major research issues and results in the virtual water literature and pinpoints the remaining questions and the direction of research in future virtual water studies. We conclude that virtual water studies have helped to raise the awareness of water scarcity and its impact on food security and to improve the understanding of the role of food trade in compensating for water deficit. However, the studies so far have been overwhelmingly concerned with the international food trade, and many solely quantified virtual water flows associated with food trade. There is a general lack of direct policy relevance to the solutions to water scarcity and food insecurity, which are often local, regional, and river basin issues. The obscurity in the conceptual basis of virtual water also entails some confusion. The methodologies and databases of the studies are often crude, affecting the robustness and reliability of the results. Looking ahead, future virtual water studies need to enhance the policy relevance by strengthening their linkages with national and regional water resources management. Meanwhile, integrated approaches taking into consideration the spatial and temporal variations of blue and green water resources availability and the complexity of natural, socioeconomic, and political conditions are necessary in assessing the trade‐offs of the virtual water strategy in dealing with water scarcity. To this end, interdisciplinary efforts and quantitative methods supported by improved data availability are greatly important.
Changes in Autophagy after Traumatic Brain Injury
Authors: Liu Cindy L , Chen Shaoyi , Dietrich Dalton , Hu Bingren R
Published: December 2007

Autophagy is the chief machinery for bulk degradation of superfluous or aberrant cytoplasmic components. This study used the rat moderate fluid percussion injury model to investigate whether the autophagy pathway plays a key role after traumatic brain injury (TBI). Induction of autophagy is manifested by accumulation of autophagosomes (APs), observable under transmission electron microscopy (EM). Two hallmarks of autophagy, i.e., the microtubule-associated protein light chain 3 (LC3)-II and the autophagy-related gene (ATG)12-ATG5 conjugates, were explored by biochemical and confocal microscopic analyses of brain tissues. Under EM, both APs and autolysosomes were markedly accumulated in neurons from 4 h onward after TBI. Western blot analysis showed that ATG12-ATG5 conjugate was markedly redistributed during 5 to 15 days in brain tissues after TBI. LC3-II conjugate was initially unchanged but was drastically upregulated from 24 h onward in the pre-AP-containing fraction after TBI. LC-3 immunostaining was mainly located in living neurons under confocal microscopy. These results clearly show that the autophagy pathway is persistently activated after TBI. Because the autophagy pathway is the chief machinery for bulk elimination of aberrant cell components, we propose that activation of this pathway serves as a protective mechanism for maintaining cellular homeostasis after TBI.
The X1 method for accurate and efficient prediction of heats of formation
Authors: Wu Jianming , Xu Xin
Published: December 2007

We propose the X1 method which combines the density functional theory method with a neural network (NN) correction for an accurate yet efficient prediction of heats of formation. It calculates the final energy by using B3LYP∕6-311+G(3df,2p) at the B3LYP∕6-311+G(d,p) optimized geometry to obtain the B3LYP standard heats of formation at 298K with the unscaled zero-point energy and thermal corrections at the latter basis set. The NN parameters cover 15 elements of H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, and Cl. The performance of X1 is close to the Gn theories, giving a mean absolute deviation of 1.43kcal∕mol for the G3∕99 set of 223molecules up to 10 nonhydrogen atoms and 1.48kcal∕mol for the X1∕07 set of 393molecules up to 32 nonhydrogen atoms.
Robust nonadiabatic molecular dynamics for metals and insulators
Authors: Stella L. , Meister M. , Fisher A. J. , Horsfield A. P.
Published: December 2007

We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrödinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.
Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride
Authors: Jayaraman Saivenkataraman , Maginn Edward J.
Published: December 2007

The melting point, enthalpy of fusion, and thermodynamic stability of two crystal polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride are calculated using a thermodynamic integration-based atomistic simulation method. The computed melting point of the orthorhombic phase ranges from 365 to 369 K, depending on the classical force field used. This compares reasonably well with the experimental values, which range from 337 to 339 K. The computed enthalpy of fusion ranges from 19 to 29 kJ∕mol, compared to the experimental values of 18.5−21.5 kJ∕mol. Only one of the two force fields evaluated in this work yielded a stable monoclinic phase, despite the fact that both give accurate liquid state densities. The computed melting point of the monoclinic polymorph was found to be 373 K, which is somewhat higher than the experimental range of 318–340 K. The computed enthalpy of fusion was 23 kJ∕mol, which is also higher than the experimental value of 9.3−14.5 kJ∕mol. The simulations predict that the monoclinic form is more stable than the orthorhombic form at low temperature, in agreement with one set of experiments but in conflict with another. The difference in free energy between the two polymorphs is very small, due to the fact that a single trans-gauche conformational difference in an alkyl sidechain distinguishes the two structures. As a result, it is very difficult to construct simple classical force fields that are accurate enough to definitively predict which polymorph is most stable. A liquid phase analysis of the probability distribution of the dihedral angles in the alkyl chain indicates that less than half of the dihedral angles are in the gauche-trans configuration that is adopted in the orthorhombic crystal. The low melting point and glass forming tendency of this ionic liquid is likely due to the energy barrier for conversion of the remaining dihedral angles into the gauche-trans state. The simulation procedure used to perform the melting point calculations is an extension of the so-called pseudosupercritical path sampling procedure. This study demonstrates that the method can be effectively applied to quite complex systems such as ionic liquids and that the appropriate choice of tethering potentials for a key step in the thermodynamic path can enable first order phase transitions to be avoided.
Interaction of water with LiCl, LiBr, and LiI in the deeply supercooled region
Authors: Souda Ryutaro
Published: December 2007

The hydration mechanism of lithium halides was studied using time-of-flight secondary ion mass spectrometry as a function of temperature. The lithium halides embedded in thin films of amorphous solid water segregate to the surface at temperatures higher than 135–140K, with efficiency increasing in the order of LiCl, LiBr, and LiI. A monolayer of LiCl and LiI adsorbed on the surface of amorphous solid water tends to diffuse into the bulk at 160K. The infrared absorption band revealed that the aqueous lithium-halide solutions and crystals are formed simultaneously at 160K; these phenomena are explicable as a consequence of the evolution of supercooled liquid water. The strong surfactant effect is inferred to arise from hydration of a contact ion pair having hydrophilic (lithium) and hydrophobic (halide) moieties. Furthermore, bulk diffusion of lithium halides might result from the formation of a solvent-separated ion pair in supercooled liquid water. The presence of two liquid phases of water with different local structures is probably responsible for the formation of these two hydrates, consistent with the calculated result reported by Jungwirth and Tobias[J. Phys. Chem. B 106, 6361 (2002)].
Tungsten nanocrystal memory devices improved by supercritical fluid treatment
Authors: Chen C. H. , Chang T. C. , Liao I. H. , Xi P. B. , Tsai C. T. , Yang P. Y. , Hsieh Joe , Chen Jason , Chen U. S. , Chen J. R.
Published: December 2007

A supercritical CO2 (SCCO2) fluid technique is proposed to improve electrical characteristics for W nanocrystal nonvolatile memory devices, since the thickness and quality of tunnel oxide are critical issues for the fabrication of nonvolatile memory devices. After SCCO2 treatments, C-V curves are restored to normal, as well as the leakage current of W nanocrystal memory devices are reduced significantly. It reveals that W nanocrystal memory devices could be formed with shorter oxidation time, moreover, dangling bonds and trapping states initially created within an incomplete oxidized film will be efficiently repaired after SCCO2 treatment.
Large attractive depletion interactions in soft repulsive–sphere binary mixtures
Authors: Cinacchi Giorgio , Martínez-Ratón Yuri , Mederos Luis , Navascués Guillermo , Tani Alessandro , Velasco Enrique
Published: December 2007

We consider binary mixtures of soft repulsive spherical particles and calculate the depletion interaction between two big spheres mediated by the fluid of small spheres, using different theoretical and simulation methods. The validity of the theoretical approach, a virial expansion in terms of the density of the small spheres, is checked against simulation results. Attention is given to the approach toward the hard-sphere limit and to the effect of density and temperature on the strength of the depletion potential. Our results indicate, surprisingly, that even a modest degree of softness in the pair potential governing the direct interactions between the particles may lead to a significantly more attractive total effective potential for the big spheres than in the hard-sphere case. This might lead to significant differences in phase behavior, structure, and dynamics of a binary mixture of soft repulsive spheres. In particular, a perturbative scheme is applied to predict the phase diagram of an effective system of big spheres interacting via depletion forces for a size ratio of small and big spheres of 0.2; this diagram includes the usual fluid-solid transition but, in the soft-sphere case, the metastable fluid-fluid transition, which is probably absent in hard-sphere mixtures, is close to being stable with respect to direct fluid-solid coexistence. From these results, the interesting possibility arises that, for sufficiently soft repulsive particles, this phase transition could become stable. Possible implications for the phase behavior of real colloidal dispersions are discussed.
Coupling constant behavior of eigenvalues of Zakharov-Shabat systems
Authors: Klaus Martin , Mityagin Boris
Published: December 2007

We consider the eigenvalues of the non-self-adjoint Zakharov-Shabat systems as the coupling constant of the potential is varied. In particular, we are interested in eigenvalue collisions and eigenvalue trajectories in the complex plane. We identify shape features in the potential that are responsible for the occurrence of collisions and we prove asymptotic formulas for large coupling constants that tell us where eigenvalues collide or where they emerge from the continuous spectrum. Some examples are provided which show that the asymptotic methods yield results that compare well with exact numerical computations.
Fingerprints of spatial charge transfer in quantum cascade lasers
Authors: Nelander R. , Wacker A. , Pereira M. F. , Revin D. G. , Soulby M. R. , Wilson L. R. , Cockburn J. W. , Krysa A. B. , Roberts J. S. , Airey R. J.
Published: December 2007

We show that mid-infrared transmission spectroscopy of a quantum cascade laser provides clear-cut information on changes in charge location at different bias. Theoretical simulations of the evolution of the gain/absorption spectrum for a λ∼7.4 μm InGaAs/AlInAs/InP quantum cascade laser have been compared with the experimental findings. Transfer of electrons between the ground states in the active region and the states in the injector goes hand in hand with a decrease of discrete intersubband absorption peaks and an increase of broad, high-energy absorption toward the continuum delocalized states above the barriers.
Phase field approach for strain-induced magnetoelectric effect in multiferroic composites
Authors: Ni Y. , Khachaturyan A. G.
Published: December 2007

The strain-mediated magnetoelectric coupling in piezoelectric-piezomagnetic composites with arbitrary spatial arrangement of particles of constituent phases is investigated. The free energy of such a composite is formulated as a functional of a phase field that is a shape function describing a spatial distribution of the phases. The free energy is obtained by a minimizing of the extended Landau free energy complemented by the electrostatic and strain-induced interactions caused by piezoelectric and piezomagnetic strains. The magnetoelectric coupling tensor derived from this functional also depends on a composite microstructure. A minimization of this functional with respect to configurational variables gives the optimal composite architecture. It is shown that a platelike configuration of constituent phases provides the largest strength of magnetoelectric coupling. The phase field computer modeling confirms this conclusion.
Enhanced electronic conductivity in Si-substituted calcium aluminate
Authors: Bertoni Mariana I. , Mason Thomas O. , Medvedeva Julia E. , Wang Yongqiang , Freeman Arthur J. , Poeppelmeier Kenneth R.
Published: December 2007

Improved conductivity has been achieved by controllable substitution of an ultraviolet electronic conductor. The transparent conducting oxide system, H-doped Ca12Al(14−x)SixO(33+x/2) with x=0−4, exhibits a conductivity strongly dependent on the substitution level. Four-point direct current conductivity increases with x from 0.15 to 0.61 S/cm at room temperature. The observed conductivity behavior is consistent with the predictions of our first principles density functional calculations for the Si-substituted system with x=0, 2, and 4. Furthermore, the Seebeck coefficient is composition dependent suggesting the existence of an activated mobility associated with small polaron conduction.
Temperature dependence of the dielectric, piezoelectric, and elastic constants for Pb(Mg1∕3Nb2∕3)O3–PbZrO3–PbTiO3 piezocrystals
Authors: Zhang Shujun , Lee Sung-Min , Kim Dong-Ho , Lee Ho-Yong , Shrout Thomas R.
Published: December 2007

Pb ( Mg 1 ∕ 3 Nb 2 ∕ 3 ) O 3 – Pb Zr O 3 – Pb Ti O 3 (PMN-PZT) ferroelectric single crystals were grown successfully using the solid state crystal growth method. The crystals were found to exhibit higher Curie temperatures TCs and ferroelectric phase transition temperatures TR-Ts when compared to the binary Pb(Mg1∕3Nb2∕3)O3–PbTiO3 system. Specifically the composition 0.4Pb(Mg1∕3Nb2∕3)O3–0.25PbZrO3–0.35PbTiO3 which lies close to the rhombohedral-tetragonal morphotropic phase boundary, was investigated. The full set of materials constants, including elastic (c and s), piezoelectric (d, g, e, and h), and dielectric permittivity (ε∕ε0), were determined using the IEEE standards as a function of temperature ranging between 25 and 100°C. The electromechanical coupling factors k33 and k32 were found to be 93.3% and 93.5%, respectively, with corresponding piezoelectric coefficients d33 and d32 on the order of 1530 and −1440pC∕N. Together with high phase transition temperatures (TC of 216°C and TR-T on the order of 144°C) and high coercive field EC ∼4.6kV∕cm, make PMN-PZT single crystals promising candidates for high temperature actuator and transducer applications.
Localization-induced inhomogeneous screening of internal electric fields in AlGaN-based quantum wells
Authors: Murotani Hideaki , Saito Takuya , Kato Nobuo , Yamada Yoichi , Taguchi Tsunemasa , Ishibashi Akihiko , Kawaguchi Yasutoshi , Yokogawa Toshiya
Published: December 2007

The influence of both localization and internal electric field on the microscopic photoluminescence (PL) properties of AlGaN-based quantum wells (QWs) has been studied by means of scanning near-field optical microscopy (SNOM). SNOM-PL images of three QWs with different well-layer thicknesses were measured under an illumination-collection mode. A correlation was observed between the PL intensity and the PL peak wavelength: a shorter-PL wavelength indicates a stronger intensity for a wider QW. The correlation is caused by an inhomogeneous screening of the internal electric field.
Optical constants of CuGa5Se8 crystals
Authors: León M. , Serna R. , Levcenko S. , Nateprov A. , Nicorici A. , Merino J. M. , Friedrich E. J. , Arushanov E.
Published: December 2007

Spectral dependence of the real ε1(ω) and imaginary ε2(ω) parts of the complex dielectric function, complex refractive index, absorption coefficient, and normal-incidence reflectivity of CuGa5Se8 crystals with slightly different Cu contents are modeled using Adachi’s model for interband transitions. The results are in good agreement with the experimental data over the entire range of photon energies. The model parameters are determined using the simulated annealing algorithm.
Effect of the Schottky barrier height on the detection of midgap levels in 4H-SiC by deep level transient spectroscopy
Authors: Reshanov S. A. , Pensl G. , Danno K. , Kimoto T. , Hishiki S. , Ohshima T. , Itoh H. , Yan Fei , Devaty R. P. , Choyke W. J.
Published: December 2007

The effect of the Schottky barrier height on the detection of the concentration of midgap defects using deep level transient spectroscopy (DLTS) is experimentally and theoretically studied for EH6 and EH7 defects in 4H-SiC. In this special case, the DLTS signal height for EH6 and EH7 increases with increasing barrier height and saturates at values above 1.5 and 1.7eV, respectively. Below 1.1eV, the DLTS peak completely disappears for both defects. The experimental data are explained by a theoretical model. The course of the quasi-Fermi level in the space charge region is calculated as a function of the reverse current through it, which is determined by the barrier height, and the reverse bias applied.
An electrospray-based, ozone-free air purification technology
Authors: Tepper Gary , Kessick Royal , Pestov Dmitry
Published: December 2007

A zero-pressure-drop, ozone-free air purification technology is reported. Contaminated air was directed into a chamber containing an array of electrospray wick sources. The electrospray sources produce an aerosol of tiny, electrically charged aqueous droplets. Charge was transferred from the droplets onto polar and polarizable species in the contaminated air stream and the charged contaminants were extracted using an electric field and deposited onto a metal surface. Purified air emerged from the other end of the chamber. The very small aqueous electrospray droplets completely evaporate so that the process is essentially dry and no liquid solvent is collected or recirculated. The air purification efficiency was measured as a function of particle size, air flow rate, and specific system design parameters. The results indicate that the electrospray-based air purification system provides high air purification efficiency over a wide range of particle size and, due to the very low power and liquid consumption rate, can be scaled up for the purification of arbitrarily large quantities of air.
A hyperspectral fluorescence lifetime probe for skin cancer diagnosis
Authors: De Beule P. A. A. , Dunsby C. , Galletly N. P. , Stamp G. W. , Chu A. C. , Anand U. , Anand P. , Benham C. D. , Naylor A. , French P. M. W.
Published: December 2007

The autofluorescence of biological tissue can be exploited for the detection and diagnosis of disease but, to date, its complex nature and relatively weak signal levels have impeded its widespread application in biology and medicine. We present here a portable instrument designed for the in situ simultaneous measurement of autofluorescence emission spectra and temporal decay profiles, permitting the analysis of complex fluorescence signals. This hyperspectral fluorescence lifetime probe utilizes two ultrafast lasers operating at 355 and 440nm that can excite autofluorescence from many different biomolecules present in skin tissue including keratin, collagen, nicotinamide adenine dinucleotide (phosphate), and flavins. The instrument incorporates an optical fiber probe to provide sample illumination and fluorescence collection over a millimeter-sized area. We present a description of the system, including spectral and temporal characterizations, and report the preliminary application of this instrument to a study of recently resected (<2h) ex vivo skin lesions, illustrating its potential for skin cancer detection and diagnosis.
Surface plasmon enhanced ultraviolet emission from ZnO films deposited on Ag∕Si(001) by magnetron sputtering
Authors: You J. B. , Zhang X. W. , Fan Y. M. , Qu S. , Chen N. F.
Published: December 2007

The ZnO films were grown on Ag∕Si(001) substrates by sputtering Ag and ZnO targets successively in a pure Ar ambient. A significant enhancement of ZnO ultraviolet emission and a reduction of its full width of half maximum have been observed while introducing a 100nm Ag interlayer between ZnO film and Si substrate. Furthermore, a complete suppression of the defect related visible emission was also found for the ZnO∕Ag∕Si sample. This improved optical performance of ZnO is attributed to the resonant coupling between Ag surface plasmon and ultraviolet emission of ZnO.
Tuning of the in-plane strain in cuprate thin films using a solid-solution compound as a buffer layer
Authors: Hanawa M. , Tsukada I.
Published: December 2007

In order to tune the epitaxial strain between a superconducting cuprate thin film and a substrate, we introduce a buffer layer of LaSrAl1−zGazO4 which forms solid solutions for the entire range from z=0–1. Thin films of La1.875Ba0.125CuO4∕LaSrAl1−zGazO4 grown by pulsed laser deposition have been characterized by x-ray diffraction and resistivity measurements. The c-axis length of La1.875Ba0.125CuO4 on the buffer layer reveals a systematic change with z indicating that the epitaxial strain is reasonably controlled. The films within the composition range of z=0.2–0.6 show superconductivity with systematic change of the critical temperature, while the sample with z=0.8 is insulating below 100K.
Colloidal matter in water extracts from forest soils
Authors: Dreves Alexander , Andersen Nils , Grootes Pieter M. , Nadeau Marie-Josée , Garbe-Schönberg Carl-Dieter
Published: December 2007

Environmental context. Little is known about the proportion of tiny dispersed particles and true solutions in soil water although the distinction has a major influence on transport processes of organic matter, fertiliser and pollutants in soils and thus, e.g., on carbon storage, and its role in global warming. Our study has found a noticeable amount of tiny particles (range 17 nm to 1.0 μm) in filtered soil water, that have a different chemical composition and a lower bioavailability of their organic components in comparison to the soluble part. This significant occurrence and the ecological relevance of colloids for the transport and storage of soil constituents highlights the need to partition soil water content into ‘particulate’ and ‘dissolved’ since the access to soil pores determines particle transport.
Abstract. Water-extracted organic matter (WEOM) is widely used as a surrogate for natural organic matter in soil water in the investigation of soil carbon dynamics. Information about the dissolved or colloidal nature of the organic matter is scarce since dissolved organic matter (DOM) is simply operationally defined by filtration: ‘DOM is what passes through the filter’. Water extracts of two topsoil horizons from both a deciduous (Steinkreuz) and a coniferous (Rotthalmünster) forest, located in Bavaria (Germany), were filtered through a 1-μm quartz filter and analysed regarding the amount of colloids in the range ~17 nm to 1.0 μm, the chemical composition and the radiocarbon concentration of both the colloidal and the dissolved fraction separated by high-speed centrifugation. Up to 13.9 wt-% of the total charge of the water extracts belongs to the colloidal fraction. The colloidal fraction has a higher relative proportion of metals and older organic C than the dissolved fraction. This demonstrates the dual nature of WEOM and the need for a more careful definition of DOM.
A herpesvirus ubiquitin-specific protease is critical for efficient T cell lymphoma formation
Authors: Jarosinski Keith , Kattenhorn Lisa , Kaufer Benedikt , Ploegh Hidde , Osterrieder Nikolaus
Published: December 2007

The herpesvirus ubiquitin-specific protease (USP) family, whose founding member was discovered as a protease domain embedded in the large tegument protein of herpes simplex virus 1 (HSV-1), is conserved across all members of the
Herpesviridae
. Whether this conservation is indicative of an essential function of the enzyme
in vivo
has not yet been established. As reported here, USP activity is conserved in Marek's disease virus (MDV), a tumorigenic alphaherpesvirus. A single amino acid substitution that abolishes the USP activity of the MDV large tegument protein diminishes MDV replication
in vivo
, and severely limits the oncogenic potential of the virus. Expression of the USP transcripts in MDV-transformed cell lines further substantiates this hypothesis. The herpesvirus USP thus appears to be required not only to maintain a foothold in the immunocompetent host, but also to contribute to malignant outgrowths.
The modularity of pollination networks
Authors: Olesen Jens M. , Bascompte Jordi , Dupont Yoko L. , Jordano Pedro
Published: December 2007

In natural communities, species and their interactions are often organized as nonrandom networks, showing distinct and repeated complex patterns. A prevalent, but poorly explored pattern is ecological modularity, with weakly interlinked subsets of species (modules), which, however, internally consist of strongly connected species. The importance of modularity has been discussed for a long time, but no consensus on its prevalence in ecological networks has yet been reached. Progress is hampered by inadequate methods and a lack of large datasets. We analyzed 51 pollination networks including almost 10,000 species and 20,000 links and tested for modularity by using a recently developed simulated annealing algorithm. All networks with >150 plant and pollinator species were modular, whereas networks with <50 species were never modular. Both module number and size increased with species number. Each module includes one or a few species groups with convergent trait sets that may be considered as coevolutionary units. Species played different roles with respect to modularity. However, only 15% of all species were structurally important to their network. They were either hubs (i.e., highly linked species within their own module), connectors linking different modules, or both. If these key species go extinct, modules and networks may break apart and initiate cascades of extinction. Thus, species serving as hubs and connectors should receive high conservation priorities.
Randomized algorithms for the low-rank approximation of matrices
Authors: Liberty Edo , Woolfe Franco , Martinsson Per-Gunnar , Rokhlin Vladimir , Tygert Mark
Published: December 2007

We describe two recently proposed randomized algorithms for the construction of low-rank approximations to matrices, and demonstrate their application (inter alia) to the evaluation of the singular value decompositions of numerically low-rank matrices. Being probabilistic, the schemes described here have a finite probability of failure; in most cases, this probability is rather negligible (10−17is a typical value). In many situations, the new procedures are considerably more efficient and reliable than the classical (deterministic) ones; they also parallelize naturally. We present several numerical examples to illustrate the performance of the schemes.
Double-Blind, Randomized, Crossover Trial of 3 Hand Rub Formulations: Fast-Track Evaluation of Tolerability and Acceptability
Authors: Pittet Didier , Allegranzi Benedetta , Sax Hugo , Chraiti Marie-Noelle , Griffiths William , Richet Hervé ,   World Health Organization Global Patient Safety Challenge Alcohol-Based Handrub Task Force
Published: December 2007

Objective.

To compare healthcare workers' skin tolerance for and acceptance of 3 alcohol-based hand rub formulations.

Design.

Double-blind, randomized, crossover clinical trial.

Setting.

Intensive care unit in a university hospital.

Participants.

Thirty-eight healthcare workers (HCWs).

Intervention.

A total of 3 alcohol-based hand rub formulations (hereafter, formulations A, B, and C) were used in random order for 3-5 consecutive working days during regular nursing shifts. Formulations A and B contained the same emollient, and formulations B and C contained the same alcohol at the same concentration. Use of each test formulation was separated by a “washout” period of at least 2 days. A visual assessment of skin integrity by a blinded observer using a standard 6-item scale was conducted before and after the use of each formulation. Univariate and multivariate analyses were used for the assessment of risk factors for skin alteration, and product acceptability was assessed by use of a customized questionnaire after the use of each formulation.

Results.

Thirty-eight HCWs used each of 3 formulations for a median of 3 days (range, 3-5 days). The mean amount of product used daily (±SD) was 54.9 ± 23.5 mL (median, 50.9 mL). Both subjective and objective evaluation of skin conditions after use showed lower HCW tolerance for product C. Male sex (odds ratio [OR], 3.17 [95% confidence interval {CI}, 1.1-8.8]), fair or very fair skin (OR, 3.01 [95% CI, 1.1-7.9]), skin alteration before hand rub use (OR, 3.73 [95% CI, 1.7-8.1]), and use of formulation C (OR, 8.79 [95% CI, 2.7-28.4]) were independently associated with skin alteration.

Conclusions.

This protocol permits a fast-track comparison of HCWs' skin tolerance for different alcohol-based hand rub formulations that are used in healthcare settings. The emollient in formulation C may account for its inferior performance.
Physicians' Perceptions, Beliefs, Attitudes, and Knowledge Concerning Antimicrobial Resistance in a Brazilian Teaching Hospital
Authors: Guerra Carla Morales , Pereira Carlos Alberto Pires , Neto Armando R. Neves , Cardo Denise Mary , Correa Luci
Published: December 2007

This cross-sectional survey assessed physicians' perceptions, knowledge and practices concerning antimicrobial resistance. Ninety-nine percent of participants reported that they perceived antimicrobial resistance as an important problem, and 86.7% agreed that antimicrobials are overprescribed, but only 2.9% rated “practicing antimicrobial control” as the most important strategy for preventing resistance. The results of this study warrant educational programs on antimicrobial resistance and the distribution of information regarding local antimicrobial susceptibility testing.
Relationship Between Rates of Antimicrobial Consumption and the Incidence of Antimicrobial Resistance inStaphylococcus aureusandPseudomonas aeruginosaIsolates From 47 French Hospitals
Authors: Rogues A. M. , Dumartin C. , Amadéo B. , Venier A. G. , Marty N. , Parneix P. , Gachie J. P.
Published: December 2007

Objective.

To investigate relationships between rates of antimicrobial consumption and the incidence of antimicrobial resistance inStaphylococcus aureusandPseudomonas aeruginosaisolates from hospitals.

Methods.

We conducted an observational study that used retrospective data from 2002 and linear regression to model relationships. Hospitals were asked to collect data on consecutiveS. aureusandP. aeruginosaisolates, consumption rates for antibiotics (ie, anti-infectives for systemic use as defined by Anatomical Therapeutic Chemical class J01), and hospital characteristics, including infection control policies. Rates of methicillin resistance inS. aureusand rates of ceftazidime and ciprofloxacin resistance inP. aeruginosawere expressed as the percentage of isolates that were nonsusceptible (ie, either resistant or intermediately susceptible) and as the incidence of nonsuceptible isolates (ie, the number of nonsuceptible isolates recovered per 1,000 patient-days). The rate of antimicrobial consumption was expressed as the number of defined daily doses per 1,000 patient-days.

Setting.

Data were obtained from 47 French hospitals, and a total of 12,188S. aureusisolates and 6,370P. aeruginosaisolates were tested.

Results.

In the multivariate analysis, fewer antimicrobials showed a significant association between the consumption rate and the percentage of isolates that were resistant than an association between the consumption rate and the incidence of resistance. The overall rate of antibiotic consumption, not including the antibiotics used to treat methicillin-resistantS. aureusinfection, explained 13% of the variance between hospitals in the incidence of methicillin resistance amongS. aureusisolates. The incidence of methicillin resistance inS. aureusisolates increased with the use of ciprofloxacin and levofloxacin and with the percentage of the hospital's beds located in intensive care units (adjusted multivariate coefficient of determination [aR2], 0.30). ForP. aeruginosa, the incidence of ceftazidime resistance was greater in hospitals with higher consumption rates for ceftazidime, levofloxacin, and gentamicin (aR2, 0.37). The incidence of ciprofloxacin resistance increased with the use of fluoroquinolones and with the percentage of a hospital's beds located in intensive care (aR2, 0.28).

Conclusions.

A statistically significant relationship existed between the rate of fluoroquinolone use and the rate of antimicrobial resistance amongS. aureusandP. aeruginosaisolates. The incidence of resistant isolates showed a stronger association with the rate of antimicrobial use than did the percentage of isolates with resistance.
Case-Control Study of Pediatric Cardiothoracic Surgical Site Infections
Authors: Holzmann-Pazgal Galit , Hopkins-Broyles Diane , Recktenwald Angela , Hohrein Melinda , Kieffer Patricia , Huddleston Charles , Anshuman Sharma , Fraser Victoria
Published: December 2007

A retrospective case-control study was performed to determine the risks and outcomes associated with pediatric cardiothoracic surgical site infection. Undergoing more than 1 cardiothoracic operative procedure, having preoperative infection, and undergoing surgery on a Monday were significant risk factors. Cardiothoracic surgical site infection increased hospital and pediatric intensive care unit length of stay. Deep surgical site infection significantly increased mortality.
Development of an Algorithm for Surveillance of Ventilator-Associated Pneumonia With Electronic Data and Comparison of Algorithm Results With Clinician Diagnoses
Authors: Klompas Michael , Kleinman Ken , Platt Richard
Published: December 2007

Objective.

Surveillance for ventilator-associated pneumonia (VAP) using standard Centers for Disease Control and Prevention (CDC) criteria is labor intensive and involves many subjective assessments. We sought to improve the efficiency and objectivity of VAP surveillance by adapting the CDC criteria to make them amenable to evaluation with electronic data.

Design.

Prospective comparison of the accuracy of VAP surveillance by use of an algorithm with responses to prospective queries made to intensive care physicians. CDC criteria for VAP were used as a reference standard to evaluate the algorithm and clinicians' reports.

Setting.

Three surgical intensive care units and 2 medical intensive care units at an academic hospital.

Methods.

A total of 459 consecutive patients who received mechanical ventilation for a total of 2,540 days underwent surveillance by both methods during consecutive 3-month periods. Electronic surveillance criteria were chosen to mirror the CDC definition. Quantitative thresholds were substituted for qualitative criteria. Purely subjective criteria were eliminated. Increases in ventilator-control settings were taken to indicate worsening oxygenation. Semiquantitative Gram stain of pulmonary secretion samples was used to assess whether there was sputum purulence.

Results.

The algorithm applied to electronic data detected 20 patients with possible VAP. All cases of VAP were confirmed in accordance with standard CDC criteria (100% positive predictive value). Prospective survey of clinicians detected 33 patients with possible VAP. Seventeen of the 33 possible cases were confirmed (52% positive predictive value). Overall, 21 cases of confirmed VAP were identified by either method. The algorithm identified 20 (95%) of 21 known cases, whereas the survey of clinicians identified 17 (81%) of 21 cases.

Conclusions.

Surveillance for VAP using electronic data is feasible and has high positive predictive value for cases that meet CDC criteria. Further validation of this method is warranted.
Contamination of Examination Gloves in patient Rooms and Implications for Transmission of Antimicrobial-Resistant Microorganisms
Authors: Diaz Maureen H. , Silkaitis Christina , Malczynski Michael , Noskin Gary A. , Warren John R. , Zembower Teresa
Published: December 2007

An assessment of bacterial contamination on examination gloves indicated that contaminated gloves may be a mechanism of indirect bacterial transmission from the hands of healthcare workers to patients. This mechanism is indicated by the recovery of identical Acinetobacter baumannii isolates from gloves and from the clinical cultures of a patient with invasive infection.
Defects in Rhizobial Cyclic Glucan and Lipopolysaccharide Synthesis Alter Legume Gene Expression During Nodule Development
Authors: D'Antuono Alejandra L. , Ott Thomas , Krusell Lene , Voroshilova Vera , Ugalde Rodolfo A. , Udvardi Michael , Lepek Viviana C.
Published: December 2007

cDNA array technology was used to compare transcriptome profiles of Lotus japonicus roots inoculated with a Mesorhizobium loti wild-type and two mutant strains affected in cyclic β(1-2) glucan synthesis (cgs) and in lipopolysaccharide synthesis (lpsβ2). Expression of genes associated with the development of a fully functional nodule was significantly affected in plants inoculated with the cgs mutant. Array results also revealed that induction of marker genes for nodule development was delayed when plants were inoculated with the lpsβ2 mutant. Quantitative real-time reverse-transcriptase polymerase chain reaction was used to quantify gene expression of a subset of genes involved in plant defense response, redox metabolism, or genes that encode for nodulins. The majority of the genes analyzed in this study were more highly expressed in roots inoculated with the wild type compared with those inoculated with the cgs mutant strain. Some of the genes exhibited a transient increase in transcript levels during intermediate steps of normal nodule development while others displayed induced expression during the final steps of nodule development. Ineffective nodules induced by the glucan mutant showed higher expression of phenylalanine ammonia lyase than wild-type nodules. Differences in expression pattern of genes involved in early recognition and signaling were observed in plants inoculated with the M. loti mutant strain affected in the synthesis of cyclic glucan.
Hessian Fly (Mayetiola destructor) Attack Causes a Dramatic Shift in Carbon and Nitrogen Metabolism in Wheat
Authors: Zhu Lieceng , Liu Xuming , Liu Xiang , Jeannotte Richard , Reese John C. , Harris Marion , Stuart Jeffrey J. , Chen Ming-Shun
Published: December 2007

Carbon and nitrogen (C/N) metabolism and allocation within the plant have important implications for plant-parasite interactions. Many plant parasites manipulate the host by inducing C/N changes that benefit their own survival and growth. Plant resistance can prevent this parasite manipulation. We used the wheat–Hessian fly (Mayetiola destructor) system to analyze C/N changes in plants during compatible and incompatible interactions. The Hessian fly is an insect but shares many features with plant pathogens, being sessile during feeding stages and having avirulence (Avr) genes that match plant resistance genes in gene-for-gene relationships. Many wheat genes involved in C/N metabolism were differentially regulated in plants during compatible and incompatible interactions. In plants during compatible interactions, the content of free carbon-containing compounds decreased 36%, whereas the content of free nitrogen-containing compounds increased 46%. This C/N shift was likely achieved through a coordinated regulation of genes in a number of central metabolic pathways, including glycolysis, the tricarboxylic acid cycle, and amino-acid synthesis. Our data on plants during compatible interactions support recent findings that Hessian fly larvae create nutritive cells at feeding (attack) sites and manipulate host plants to enhance their own survival and growth. In plants during incompatible interactions, most of the metabolic genes examined were not affected or down-regulated.
Responses of Two Contrasting Genotypes of Rice to Brown Planthopper
Authors: Wang Yuanyuan , Wang Xiaolan , Yuan Hongyu , Chen Rongzhi , Zhu Lili , He Ruifeng , He Guangcun
Published: December 2007

Rice (Oryza sativa L.) and brown planthoppers (BPH) (Nilaparvata lugens Stål) provide an ideal system for studying molecular mechanisms involved in the interactions between plants and phloem-feeding insects. The phenotypic responses and changes in transcript profiles of seedlings representing two rice cultivars differing in resistance to the BPH were analyzed. In the BPH-compatible (susceptible) cv. MH63, BPH feeding reduced three examined plant growth parameters (leaf area expansion, height increases, and dry weight increases) and photosynthetic rates of the leaves. In the BPH-incompatible (resistant) cv. B5, BPH feeding caused slight reductions in protein and sucrose contents, but the plants maintained their photosynthetic activity and grew normally. A cDNA microarray containing 1,920 suppression subtractive hybridization clones was used to explore the transcript profiles differences in the two cultivars under control and BPH-feeding conditions. In total, 160 unique genes were detected as being significantly affected by BPH feeding in rice plants, covering a wide range of functional categories, and there were 38 genes that showed the similar transcript pattern in both genotypes. The physiological responses and transcript profiles of plants represented in both genotypes suggested that multiple pathways might be involved in reprogramming of BPH-infested rice plants. The differences in transcript levels between the compatible and incompatible interactions revealed in this study were not only the reaction of resistance and susceptibility but also reflections of different damage rates and genotypic backgrounds of the rice cultivars.
Early Palaeozoic dentine and patterned scales in the embryonic catshark tail
Authors: Johanson Zerina , Tanaka Mikiko , Chaplin Natalie , Smith Moya
Published: December 2007

Regular scale patterning, restricted to the caudalmost tail and organized into two opposing rows on each side of the tail, is observed in few chondrichthyans. These evenly spaced scales, in dorsal and ventral rows, develop in an iterative sequence from the caudal tip, either side of the notochord. They are subsequently lost as a scattered pattern of placoid scales develops on the body and fins. An identical organized pattern is observed in tail scales of
Scyliorhinus canicula
(catshark), where the expression of sonic hedgehog signal is restricted to the epithelium of developing scales and remains localized to the scale pocket. Regulation of iterative scale position by sonic hedgehog is deeply conserved in vertebrate phylogeny.

These scales also reveal an archaic histological structure of a dentine type found in the oldest known shark scales from the Ordovician and Silurian. This combination of regulated pattern and ancient dentine occurs only in the tail, representing the primary scalation. Scattered body scales in elasmobranchs such as
S. canicula
originate secondarily from differently regulated development, one with typical orthodentine around a central pulp cavity. These observations emphasize the modular nature of chondrichthyan scale development and illustrate previously undetected variation as an atavism in extant chondrichthyan dentine.