bluuebunny/crossref_metadata_2025 huggingface dataset:
All-optical signal gating using ytterbium-doped fiber and a pair of thermally expanded core fibers
Authors: Nguyen Linh Viet , Chung Youngjoo
Published: October 2009

We report all-optical signal gating using ytterbium-doped fiber (YDF) and a pair of thermally expanded core fibers (TECFs). Splicing the YDF with two TECFs at their expanded-core ends, we obtained an interference pattern in the transmission spectrum of the device. When pumped by a laser diode at 980 nm, the interference fringes shift to longer wavelength due mainly to the resonantly enhanced nonlinearity of the YDF. Consequently, signals within the interference pattern can be gated or blocked all optically. Full gating of cw signals at 1564.21 and 1564.54 nm were obtained using a pump power of about 38.44 mW.
Determination of elementary first integrals of a generalized Raychaudhuri equation by the Darboux integrability method
Authors: Choudhury A. Ghose , Guha Partha , Khanra Barun
Published: October 2009

The Darboux integrability method is particularly useful to determine first integrals of nonplanar autonomous systems of ordinary differential equations, whose associated vector fields are polynomials. In particular, we obtain first integrals for a variant of the generalized Raychaudhuri equation, which has appeared in string inspired modern cosmology.
Ion flux mapping in an inertial-electrostatic confinement device using a chordwire diagnostic
Authors: Murali S. Krupakar , Santarius J. F. , Kulcinski G. L.
Published: October 2009

Theoretical study of ion microchannels that form in an inertial-electrostatic confinement (IEC) device has helped understand the behavior of ions of various energies within a microchannel and has also predicted that smaller grids produce a more converged core. However, such theoretical work has many limitations that make experimental work indispensable. In the present paper the experimental measurements of ion flow patterns into the cathode grid and their consequences (using a “chordwire” diagnostic that intercepts ions streaming into the IEC core) are reported. Experimental measurements also have quantified the interruption of the ion flow due to the adverse influence of the high voltage stalk. In addition, the chordwire arrangement can be used to study the radiation damage of materials.
Theoretical studies of UO2(OH)(H2O)n+, UO2(OH)2(H2O)n, NpO2(OH)(H2O)n, and PuO2(OH)(H2O)n+ (n≤21) complexes in aqueous solution
Authors: Cao Zhiji , Balasubramanian K.
Published: October 2009

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO2(OH)+, UO2(OH)2, NpO2(OH), and PuO2(OH)+ complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO2(H2O)52+ is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.
A Lagrangian approach to droplet condensation in atmospheric clouds
Authors: Sidin Ryan S. R. , IJzermans Rutger H. A. , Reeks Michael W.
Published: October 2009

The condensation of microdroplets in model systems, reminiscent of atmospheric clouds, is investigated numerically and analytically. Droplets have been followed through a synthetic turbulent flow field composed of 200 random Fourier modes, with wave numbers ranging from the integral scales [O(102 m)] to the Kolmogorov scales [O(10−3 m)]. As the influence of all turbulence scales is investigated, direct numerical simulation is not practicable, making kinematic simulation the only viable alternative. Two fully Lagrangian droplet growth models are proposed: a one-way coupled model in which only adiabatic cooling of a rising air parcel is considered, and a two-way coupled model which also accounts for the effects of local vapor depletion and latent heat release. The simulations with the simplified model show that the droplet size distribution becomes broader in the course of time and resembles a Gaussian distribution. This result is supported by a theoretical analysis which relates the droplet surface-area distribution to the dispersion of droplets in the turbulent flow. Although the droplet growth is stabilized by vapor depletion and latent heat release in the two-way coupled model, the calculated droplet size distributions are still very broad. The present results may provide an explanation for the rapid growth of droplets in the coalescence stage of rain formation, as broad size distributions are likely to lead to enhanced collision rates between droplets.
Thermal contact resistance between graphene and silicon dioxide
Authors: Chen Z. , Jang W. , Bao W. , Lau C. N. , Dames C.
Published: October 2009

The thermal contact resistance between graphene and silicon dioxide was measured using a differential 3ω method. The sample thicknesses were 1.2 (single-layer graphene), 1.5, 2.8, and 3.0 nm, as determined by atomic force microscopy. All samples exhibited approximately the same temperature trend from 42 to 310 K, with no clear thickness dependence. The contact resistance at room temperature ranges from 5.6×10−9 to 1.2×10−8 m2 K/W, which is significantly lower than previous measurements involving related carbon materials. These results underscore graphene’s potential for applications in microelectronics and thermal management structures.
Quantum cluster theory for the polarizable continuum model. I. The CCSD level with analytical first and second derivatives
Authors: Cammi R.
Published: October 2009

We present a general formulation of the coupled-cluster (CC) theory for a molecular solute described within the framework of the polarizable continuum model (PCM). The PCM-CC theory is derived in its complete form, called PTDE scheme, in which the correlated electronic density is used to have a self-consistent reaction field, and in an approximate form, called PTE scheme, in which the PCM-CC equations are solved assuming the fixed Hartree–Fock solvent reaction field. Explicit forms for the PCM-CC-PTDE equations are derived at the single and double (CCSD) excitation level of the cluster operator. At the same level, explicit equations for the analytical first derivatives of the PCM basic energy functional are presented, and analytical second derivatives are also discussed. The corresponding PCM-CCSD-PTE equations are given as a special case of the full theory.
Transport properties in nontwist area-preserving maps
Authors: Szezech J. D. , Caldas I. L. , Lopes S. R. , Viana R. L. , Morrison P. J.
Published: October 2009

Nontwist systems, common in the dynamical descriptions of fluids and plasmas, possess a shearless curve with a concomitant transport barrier that eliminates or reduces chaotic transport, even after its breakdown. In order to investigate the transport properties of nontwist systems, we analyze the barrier escape time and barrier transmissivity for the standard nontwist map, a paradigm of such systems. We interpret the sensitive dependence of these quantities upon map parameters by investigating chaotic orbit stickiness and the associated role played by the dominant crossing of stable and unstable manifolds.
10

μ
m
minority-carrier diffusion lengths in Si wires synthesized by Cu-catalyzed vapor-liquid-solid growth
Authors: Putnam Morgan C. , Turner-Evans Daniel B. , Kelzenberg Michael D. , Boettcher Shannon W. , Lewis Nathan S. , Atwater Harry A.
Published: October 2009

The effective electron minority-carrier diffusion length, Ln,eff, for 2.0 μm diameter Si wires that were synthesized by Cu-catalyzed vapor-liquid-solid growth was measured by scanning photocurrent microscopy. In dark, ambient conditions, Ln,eff was limited by surface recombination to a value of ≤0.7 μm. However, a value of Ln,eff=10.5±1 μm was measured under broad-area illumination in low-level injection. The relatively long minority-carrier diffusion length observed under illumination is consistent with an increased surface passivation resulting from filling of the surface states of the Si wires by photogenerated carriers. These relatively large Ln,eff values have important implications for the design of high-efficiency, radial-junction photovoltaic cells from arrays of Si wires synthesized by metal-catalyzed growth processes.
Magnetization-controlled conductance in (Ga,Mn)As-based resonant tunneling devices
Authors: Tran M. , Peiro J. , Jaffrès H. , George J.-M. , Mauguin O. , Largeau L. , Lemaître A.
Published: October 2009

We report on experimental evidence of a magnetization-controlled conductance in AlAs/GaAs/AlAs resonant tunneling diodes contacted by a (Ga,Mn)As ferromagnetic electrode. Large shifts of the resonance voltages occur as the magnetization is rotated from in-plane to out-of-plane directions resulting in a singular tunneling anisotropic magnetoresistance signal. This opens the way to control the tunneling current upon the magnetization orientation of the magnetic layer, playing the role of a magnetic gate.
Recoil by Auger electrons: Theory and application
Authors: Demekhin Ph. V. , Scheit S. , Cederbaum L. S.
Published: October 2009

General equations accounting for the molecular dynamics induced by the recoil of a fast Auger electron are presented. The implications of the degree of localization of the molecular orbitals of diatomic molecules involved in the Auger decay are analyzed. It is shown that the direct and exchange terms of the Auger transition matrix element may give rise to opposite signs and hence to opposite directions of the recoil momenta transferred to the nuclear vibrational motion. Consequently, these terms have a different impact on the recoil-induced nuclear dynamics in the final Auger decay state. The developed theory is applied to study the influence of the recoil on the interatomic Coulombic decay (ICD) following the K-LL Auger decay of the Ne dimer. Our calculations illustrate a significant effect of the recoil of nuclei on the computed wave packets propagating on the potential energy curve populated by the Auger decay. The corresponding final states of the Auger process decay further by ICD. We show that the recoil momentum imparted onto the nuclei modifies the computed ICD spectra considerably.
Molecular acidity: A quantitative conceptual density functional theory description
Authors: Liu Shubin , Schauer Cynthia K. , Pedersen Lee G.
Published: October 2009

Accurate predictions of molecular acidity using ab initio and density functional approaches are still a daunting task. Using electronic and reactivity properties, one can quantitatively estimate pKa values of acids. In a recent paper [S. B. Liu and L. G. Pedersen, J. Phys. Chem. A 113, 3648 (2009)], we employed the molecular electrostatic potential (MEP) on the nucleus and the sum of valence natural atomic orbital (NAO) energies for the purpose. In this work, we reformulate these relationships on the basis of conceptual density functional theory and compare the results with those from the thermodynamic cycle method. We show that MEP and NAO properties of the dissociating proton of an acid should satisfy the same relationships with experimental pKa data. We employ 27 main groups and first to third row transition metal-water complexes as illustrative examples to numerically verify the validity of these strong linear correlations. Results also show that the accuracy of our approach and that of the conventional method through the thermodynamic cycle are statistically similar.
Transparent and flexible polymerized graphite oxide thin film with frequency-dependent dielectric constant
Authors: Lee D. W. , Seo J. W. , Jelbert G. R. , de Los Santos L. , Cole J. M. , Panagopoulos C. , Barnes C. H. W.
Published: October 2009

Here we report on the preparation of transparent and flexible polymerized graphite oxide, which is composed of carbons with sp3-hybridized orbitals and a nonplanar ring structure, and which demonstrates dispersion in its dielectric constant at room temperature. This frequency dependence renders the material suitable for creating miniaturized, flexible, and transparent variable capacitors, allowing for smaller and simpler integrated electronic devices. We discuss this polarizability in terms of space charge effects.
Strongly birefringent metamaterials as negative index terahertz wave plates
Authors: Weis P. , Paul O. , Imhof C. , Beigang R. , Rahm M.
Published: October 2009

We report an alternative approach for the design and fabrication of thin wave plates with high transmission in the terahertz regime. The wave plates are based on strongly birefringent cut-wire-pair metamaterials that exhibit refractive indices of opposite signs for orthogonal polarization components of an incident wave. As examples, we fabricated and investigated a quarter- and a half-wave plate with high intensity transmittance. The wave plates displayed a maximum figure of merit (FOM) of 23 at a frequency around 1.3 THz where the refractive index was n′=−1.7. This corresponds to one of the highest FOMs reported at terahertz frequencies.
Effect of substrate piezoelectricity on surface acoustic wave propagation in humidity-sensitive structures with porphyrin layers
Authors: Čiplys D. , Rimeika R. , Sereika A. , Poderys V. , Rotomskis R. , Shur M. S.
Published: October 2009

The impact of air humidity on surface acoustic wave (SAW) propagation in different piezoelectric substrates (lithium niobate, lithium tantalate, and gallium nitride on sapphire) with nanostructured meso-tetra(4 sulfonatophenyl) porphyrin (TPPS4) overlays has been investigated. The humidity-induced increase in SAW attenuation is proportional to the electromechanical coupling constant of the substrate and is attributed to the viscoelastic loss due to interaction of water adsorbing TPPS4 material with electric field of the SAW. The humidity-induced decrease in SAW velocity does not depend on the substrate piezoelectric properties and is explained by the changes in TPPS4 layer mechanical properties due to adsorbed moisture.
Interface and bulk magnetism of Co2Cr0.6Fe0.4Al and Co2CrAl thin films
Authors: Jourdan Martin , Jorge Elena Arbelo , Herbort Christian , Kallmayer Michael , Klaer Peter , Elmers Hans-Joachim
Published: October 2009

The interface and bulk magnetic properties of epitaxial thin films of the Heusler compounds Co2Cr0.6Fe0.4Al/Mg/AlOx and CoCr2Al/Mg/AlOx are investigated. We compare the magnetization measured by x-ray magnetic circular dichroism experiments in surface sensitive total electron yield mode (information depth of 2–3 nm) and in bulk sensitive transmission mode. The pronounced temperature dependence of the magnetoresistance of tunneling junctions with Heusler electrodes, which is often related to weakened interface magnetism, is discussed. Evidence is given that this explanation does not apply to the compounds investigated here.
Laboratory observation of the valence anion of cyanoacetylene, a possible precursor for negative ions in space
Authors: Goebbert Daniel J. , Khuseynov Dmitry , Sanov Andrei
Published: October 2009

Valence anions of cyanoacetylene, HCCCN−, are synthesized by the 1,2-H2+ abstraction reaction of O− with acrylonitrile, H2C=CHCN, while the competing 1,1-H2+ channel of the same reaction yields the cyanovinylidene anions, CCHCN−. The key to the formation of the elusive, adiabatically weakly bound HCCCN− is the bent −Ċ=Ċ–C≡skeleton of the reactant. The photoelectron spectrum of HCCCN−, measured by means of photoelectron imaging at 532 nm, consists of a broad structureless band with a vertical detachment energy of 1.04±0.05 eV. The observed anions are stable counterparts of the low-lying anionic resonances of cyanoacetylene, which may contribute (by way of dissociative attachment) to the formation of carbon-rich and CN-containing negative ions in extraterrestrial environments.
Number of sensors versus time to detection in wildfires
Authors: Fierens Pablo I.
Published: October 2009

The lack of extensive research in the application of inexpensive wireless sensor nodes for the early detection of wildfires motivated us to investigate the cost of such a network. As a first step, in this paper we present several results that relate the time to detection and the burned area to the number of sensor nodes in the region that is protected. We prove that the probability distribution of the size of the burned area at the moment of detection is approximately exponential, given that some hypotheses hold: the positions of the sensor nodes are independent random variables uniformly distributed and the number of sensor nodes is large. This conclusion depends neither on the number of ignition points nor on the propagation model of the fire.
Platypus venom: source of novel compounds
Authors: Koh Jennifer M. S. , Bansal Paramjit S. , Torres Allan M. , Kuchel Philip W.
Published: October 2009

An anatomical feature of the platypus (Ornithorhynchus anatinus) that is seen in only one other mammal, the echidna, is that the male has a crural glandular system that produces venom that is used for defence and territorial–breeding functions; whether the echidna is similarly venomous is not yet established. Platypus venom contains many novel proteins and peptides that are different from those in reptilian venom. It also causes pain and symptoms that are not experienced by any other kind of envenomation. Five types of proteins and peptides have been isolated and identified from platypus venom, namely: defensin-like peptides (DLPs); Ornithorhynchus venom C-type natriuretic peptides (OvCNPs); Ornithorhynchus nerve growth factor; hyaluronidase; and l-to-d-peptide isomerase. The structures of DLPs and OvCNPs have already been studied and they are very similar to β-defensin-12 and mammalian C-type natriuretic peptides, respectively. A special mammalian l-to-d-peptide isomerase that is responsible for interconverting the l- and d-peptide isomers is also found in platypus venom. Isomerase activity has recently been discovered in platypus tissues other than the venom gland. It is possible that similar kinds of enzymes might exist in other mammals and play important, as yet unknown, biological roles. Considering the fact that some animal venoms have already been widely used in pharmaceutical applications, research into platypus venom may lead to the discovery of new molecules and potent drugs that are useful biomedical tools.
A review of mucormycosis in the platypus (Ornithorhynchus anatinus)
Authors: Connolly Joanne H.
Published: October 2009

Many infectious agents and parasites have been reported from the platypus (Ornithorhynchus anatinus), but most do not cause serious disease. The fungus, Mucor amphibiorum, is the only disease agent known to cause significant morbidity and mortality in the free-living platypus in Tasmania. Infection has also been reported in free-ranging cane toads and green tree frogs from mainland Australia, but not confirmed in platypuses from the mainland. This paper reviews mucormycosis in the platypus and includes the epidemiology, clinical features, mycology, pathology as well as possible surveillance, treatment and/or control modalities. The emergence and geographical spread of mucormycosis as a disease entity in Tasmanian platypuses from 1982 till 2005 are discussed. The host, agent and environment factors of the traditional epidemiological paradigm are discussed as they contribute to the conditions that lead to the selection or emergence of Mucor amphibiorum as a pathogen in a population of platypuses.
Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?
Authors: Huttley Gavin
Published: October 2009

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.
Affinity for phosphatidylinositol 4,5-bisphosphate determines muscarinic agonist sensitivity of Kv7 K+ channels
Authors: Hernandez Ciria C. , Falkenburger Björn , Shapiro Mark S.
Published: October 2009

Kv7 K+-channel subunits differ in their apparent affinity for PIP2 and are differentially expressed in nerve, muscle, and epithelia in accord with their physiological roles in those tissues. To investigate how PIP2 affinity affects the response to physiological stimuli such as receptor stimulation, we exposed homomeric and heteromeric Kv7.2, 7.3, and 7.4 channels to a range of concentrations of the muscarinic receptor agonist oxotremorine-M (oxo-M) in a heterologous expression system. Activation of M1 receptors by oxo-M leads to PIP2 depletion through Gq and phospholipase C (PLC). Chinese hamster ovary cells were transiently transfected with Kv7 subunits and M1 receptors and studied under perforated-patch voltage clamp. For Kv7.2/7.3 heteromers, the EC50 for current suppression was 0.44 ± 0.08 µM, and the maximal inhibition (Inhibmax) was 74 ± 3% (n = 5–7). When tonic PIP2 abundance was increased by overexpression of PIP 5-kinase, the EC50 was shifted threefold to the right (1.2 ± 0.1 µM), but without a significant change in Inhibmax (73 ± 4%, n = 5). To investigate the muscarinic sensitivity of Kv7.3 homomers, we used the A315T pore mutant (Kv7.3T) that increases whole-cell currents by 30-fold without any change in apparent PIP2 affinity. Kv7.3T currents had a slightly right-shifted EC50 as compared with Kv7.2/7.3 heteromers (1.0 ± 0.8 µM) and a strongly reduced Inhibmax (39 ± 3%). In contrast, the dose–response curve of homomeric Kv7.4 channels was shifted considerably to the left (66 ± 8 nM), and Inhibmax was slightly increased (81 ± 6%, n = 3–4). We then studied several Kv7.2 mutants with altered apparent affinities for PIP2 by coexpressing them with Kv7.3T subunits to boost current amplitudes. For the lower affinity (Kv7.2 (R463Q)/Kv7.3T) or higher affinity (Kv7.2 (R463E)/Kv7.3T) channels, the EC50 and Inhibmax were similar to Kv7.4 or Kv7.3T homomers (0.12 ± 0.08 µM and 79 ± 6% [n = 3–4] and 0.58 ± 0.07 µM and 27 ± 3% [n = 3–4], respectively). The very low-affinity Kv7.2 (R452E, R459E, and R461E) triple mutant was also coexpressed with Kv7.3T. The resulting heteromer displayed a very low EC50 for inhibition (32 ± 8 nM) and a slightly increased Inhibmax (83 ± 3%, n = 3–4). We then constructed a cellular model that incorporates PLC activation by oxo-M, PIP2 hydrolysis, PIP2 binding to Kv7-channel subunits, and K+ current through Kv7 tetramers. We were able to fully reproduce our data and extract a consistent set of PIP2 affinities.
Healthcare Worker Knowledge of Measurement and Documentation of Tuberculin Skin Test Reaction
Authors: James Scott H. , Dumois Juan A. , Messina Allison F. , Gould Jay L. , Berman David M.
Published: October 2009

A cross-sectional survey of 210 healthcare workers at a pediatric teaching hospital was performed to assess knowledge of published guidelines for proper measurement and documentation of tuberculin skin test Results. We conclude that many healthcare workers have inadequate knowledge for optimal measurement and documentation of tuberculin skin test results.
Self-consistent simulations of the interaction between fusion-born alpha particles and lower hybrid waves in ITER
Authors: Schneider M. , Eriksson L.-G. , Imbeaux F. , Artaud J-F.
Published: October 2009

In order to control the plasma current profile, it might be necessary to apply lower hybrid waves in ITER and future fusion reactors, since they are capable of generating off-axis current. However, the efficiency of the lower hybrid current drive may be affected by parasitic absorption by fusion-born alpha particles. In order to quantify this absorption, a consistent coupling has been established between (i) the DELPHINE code which calculates the LH wave propagation and absorption on electrons and alpha particles and (ii) the SPOT orbit following Monte Carlo code augmented with an operator accounting for the interaction between fast ions and radio-frequency waves. The LH wave absorption in the ITER steady-state reference scenario 4 (ITER Technical Basis 2002 ITER EDA Documentation Series No 24, Report G A0 FDR 1 01-07-13 R1.0) has been analysed for the LH source frequencies of 5 and 3.7 GHz. Results indicate that the alpha parasitic absorption is weak for both cases: 0.08% and less than 3% for 5 GHz and 3.7 GHz, respectively.
Providing Continuity of Care for Chronic Diseases in the Aftermath of Katrina: From Field Experience to Policy Recommendations
Authors: Arrieta Martha I. , Foreman Rachel D. , Crook Errol D. , Icenogle Marjorie L.
Published: October 2009

This study sought to elicit challenges and solutions in the provision of health care to those with chronic diseases after Hurricane Katrina in coastal Alabama and Mississippi. In-depth interviews with 30 health and social service providers (key informants) and 4 focus groups with patients with chronic diseases were conducted. Subsequently an advisory panel of key informants was convened. Findings were summarized and key informants submitted additional feedback. The chronic diseases identified as medical management priorities by key informants were mental health, diabetes mellitus, hypertension, respiratory illness, end-stage renal disease, cardiovascular disease, and cancer. The most frequently mentioned barrier to providing care was maintaining continuity of medications. Contributing factors were inadequate information (inaccessible medical records, poor patient knowledge) and financial constraints. Implemented or suggested solutions included relaxation of insurance limitations preventing advance prescription refills; better predisaster patient education to improve medical knowledge; promotion of personal health records; support for information technology systems at community health centers, in particular electronic medical records; improved allocation of donated medications/medical supplies (centralized coordination, decentralized distribution); and networking between local responders and external aid. (Disaster Med Public Health Preparedness. 2009;3:174–182)
Correction for Verling
et al.
, Supply-side invasion ecology: characterizing propagule pressure in coastal ecosystems
Authors: Verling Emma , Ruiz Gregory M. , Smith L. David , Galil Bella , Whitman Miller A. , Murphy Kathleen R.
Published: October 2009

Correction for ‘Supply-side invasion ecology: characterizing propagule pressure in coastal ecosystems’ by Emma Verling, Gregory M. Ruiz, L. David Smith, Bella Galil, A. Whitman Miller and Kathleen R. Murphy (Proc. R. Soc. B
272
, 1249–1256.
(doi:
10.1098/rspb.2005.3090
)).

A reference was omitted from the print version of this paper; the missing reference is as follows: Simberloff, D. 1989 Which insect introductions succeed and which fail? In
Biological Invasions: a global perspective
(ed. J. A. Drake, F. Di Castri, R. H. Groves, F. J. Kruger, H. A. Mooney, M. Rejmanek & M. H. Williamson), pp. 61–75. Chichester, UK: Wiley & Sons Ltd.
A novel strategy of transcription regulation by intragenic nucleosome ordering
Authors: Vaillant Cédric , Palmeira Leonor , Chevereau Guillaume , Audit Benjamin , d'Aubenton-Carafa Yves , Thermes Claude , Arneodo Alain
Published: October 2009

Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5′ gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5′ and 3′ gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a “crystal-like” array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly compacted nucleosomes. This adaptability confers “bi-stable” properties to chromatin and is a key to its dynamics. Compared to crystal-like genes, bi-stable genes present higher transcriptional plasticity, higher sensitivity to chromatin regulators, higher H3 turnover rate, and lower H2A.Z enrichment. The results strongly suggest that transcription elongation is facilitated by higher chromatin compaction. The data allow us to propose a new paradigm of transcriptional control mediated by the stability and the level of compaction of the intragenic chromatin architecture and open new ways for investigating eukaryotic gene expression regulation.
On the valences of bonds in the oxycomplexes of Sn2+
Authors: Brown I. David
Published: October 2009

The differences between Wang and Liebau's [Wang & Liebau (2007). Acta Cryst. B63, 216–228] stoichiometric valence (atomic valence) and structural valence (bond-valence sum) observed in Sn2+ and other lone-pair cation oxycomplexes arises from their use of the Brese & O'Keeffe bond-valence parameters which are based on the assumption that the bond-valence parameter b = 0.37 Å applies to all bond types. According to the theory of the bond-valence model, the bond-valence sum is necessarily equal to the ionic charge, implying that in the Wang and Liebau model the ionic charges are equal to the structural valence. If charges are chosen equal to the stoichiometric valence, the bond-valence parameters for Sn2+—O bonds are R
0 = 1.859 Å, b = 0.55 Å. While both models are theoretically valid, only the standard model relates bond valences to the concept of atomic valence. Wang and Liebau's suggestion that cation–lone-pair bonds make a significant contribution to the valence sums is confirmed, but such bonds cannot account for the full difference between the stoichiometric and structural valences because they are present in only a few compounds.
Clinical trial: the effects of a fermented milk containing three probiotic bacteria in patients with irritable bowel syndrome – a randomized, double‐blind, controlled study
Authors: SIMRÉN M. , ÖHMAN L. , OLSSON J. , SVENSSON U. , OHLSON K. , POSSERUD I. , STRID H.
Published: October 2009

Background  The effects of probiotic bacteria in IBS remain controversial.

Aim  To study the effects of a probiotic product on IBS symptoms.

Methods  We randomized 74 IBS patients to receive 8 weeks of daily treatment with 400 mL milk fermented with the yoghurt bacteria and containing Lactobacillus paracasei, ssp. paracasei F19, Lactobacillus acidophilus La5 and Bifidobacterium lactis Bb12 (Cultura; active) or acidified milk without these bacteria (control). The primary endpoint was the proportion of subjects reporting adequate relief of their IBS symptoms at least 50% of the weeks. IBS symptom severity, psychological symptoms and quality of life were assessed.

Results  The proportion of responders was 38% (14/37 patients) in the active group and 27% (10/37 patients) in the control group (P = 0.3). IBS symptom severity improved significantly in both groups during the treatment period. This change was greater in the active group during the first 2 weeks, but thereafter, no significant group differences were seen.

Conclusions  We could not detect a clearly positive effect of fermented milk containing three probiotic bacteria on GI symptoms in IBS patients compared with the control treatment. However, a trend towards a more favourable effect during the first weeks was seen in the active group.

Aliment Pharmacol Ther 31, 218–227
Thermotectonic evolution of the Ukrainian Donbas Foldbelt revisited: new constraints from zircon and apatite fission track data
Authors: Danišík M. , Sachsenhofer R. F. , Frisch W. , Privalov V. A. , Panova E. A. , Spiegel C.
Published: October 2009

The Donbas Foldbelt (DF) is the compressionally deformed segment of a large Late Palaeozoic rift cross‐cutting the southern part of the East European Craton and is traditionally described as a classic example of an inverted intracratonic rift basin. Proposed formational models are often controversial and numerous issues are still a matter of speculation, primarily due to the lack of absolute time constraints and insufficient knowledge of the thermal evolution. We investigate the low‐temperature thermal history of the DF by means of zircon fission track and apatite fission track (AFT) thermochronology applied to Upper Carboniferous sediments. In all samples, the AFT chronometer was reset shortly after deposition in the Early Permian (∼275 Ma). Samples contained kinetically variable apatites that are sensitive to different temperatures and using statistic‐based component analysis incorporating annealing characteristics of individual grains assessed by Dpar , we identified several distinct age populations, ranging from the Late Permian (∼265 Ma) to the Late Cretaceous (∼70 Ma). We could thus constrain the thermal history of the DF during a ∼200 Myr long period following the thermal maximum. We found that earliest cooling of Permian and Permo‐Triassic age is recorded on the basin margins whereas the central parts were residing in or slowly cooling through the apatite partial annealing zone during Jurassic and most of Cretaceous times, and then finally cooled to near‐surface conditions latest around the Cretaceous/Palaeogene boundary. Our data show that Permian erosion was less significant and Mesozoic erosion more significant than generally assumed. Inversion and pop‐up of the DF occurred in the Cretaceous and not in the Permian as previously thought. This is indicated by overall Cretaceous AFT ages in the central parts of the basin.
Feedbacks of sedimentation on crustal heat flow: New insights from the Vøring Basin, Norwegian Sea
Authors: Theissen S. , Rüpke L. H.
Published: October 2009

Basement heat flow is one of the key unknowns in sedimentary basin analysis. Its quantification is challenging not in the least due to the various feedback mechanisms between the basin and lithosphere processes. This study explores two main feedbacks, sediment blanketing and thinning of sediments during lithospheric stretching, in a series of synthetic models and a reconstruction case study from the Norwegian Sea. Three types of basin models are used: (1) a newly developed one‐dimensional (1D) forward model, (2) a decompaction/backstripping approach and (3) the commercial basin modelling software TECMOD2D for automated forward basin reconstructions. The blanketing effect of sedimentation is reviewed and systematically studied in a suite of 1D model runs. We find that even for moderate sedimentation rates (0.5 mm year−1), basement heat flow is depressed by ∼25% with respect to the case without sedimentation; for high sedimentation rates (1.5 mm year−1), basement heat flow is depressed by ∼50%. We have further compared different methods for computing sedimentation rates from the presently observed stratigraphy. Here, we find that decompaction/backstripping‐based methods may systematically underestimate sedimentation rates and total subsidence. The reason for this is that sediments are thinned during lithosphere extension in forward basin models while there are not in backstripping/decompaction approaches. The importance of sediment blanketing and differences in modelling approaches is illustrated in a reconstruction case study from the Norwegian Sea. The thermal and structural evolution of a transect across the Vøring Basin has been reconstructed using the backstripping/decompaction approach and TECMOD2D. Computed total subsidence curves differ by up to ∼3 km and differences in computed basement heat flows reach up to 50%. These findings show that strong feedbacks exist between basin and lithosphere processes and that resolving them require integrated lithosphere‐scale basin models.
Predicting pasture root density from soil spectral reflectance: field measurement
Authors: KUSUMO B. H. , HEDLEY M. J. , HEDLEY C. B. , ARNOLD G. C. , TUOHY M. P.
Published: October 2009

This paper reports the development and evaluation of a field technique for in situ measurement of root density using a portable spectroradiometer. The technique was evaluated at two sites in permanent pasture on contrasting soils (an Allophanic and a Fluvial Recent soil) in the Manawatu region, New Zealand. Using a modified soil probe, reflectance spectra (350–2500 nm) were acquired from horizontal surfaces at three depths (15, 30 and 60 mm) of an 80‐mm diameter soil core, totalling 108 samples for both soils. After scanning, 3‐mm soil slices were taken at each depth for root density measurement and soil carbon (C) and nitrogen (N) analysis. The two soils exhibited a wide range of root densities from 1.53 to 37.03 mg dry root g−1 soil. The average root density in the Fluvial soil (13.21 mg g−1) was twice that in the Allophanic soil (6.88 mg g−1). Calibration models, developed using partial least squares regression (PLSR) of the first derivative spectra and reference data, were able to predict root density on unknown samples using a leave‐one‐out cross‐validation procedure. The root density predictions were more accurate when the samples from the two soil types were separated (rather than grouped) to give sub‐populations (n = 54) of spectral data with more similar attributes. A better prediction of root density was achieved in the Allophanic soil (r2 = 0.83, ratio prediction to deviation (RPD ) = 2.44, root mean square error of cross‐validation (RMSECV ) = 1.96 mg g −1) than in the Fluvial soil (r2 = 0.75, RPD = 1.98, RMSECV = 5.11 mg g −1). It is concluded that pasture root density can be predicted from soil reflectance spectra acquired from field soil cores. Improved PLSR models for predicting field root density can be produced by selecting calibration data from field data sources with similar spectral attributes to the validation set. Root density and soil C content can be predicted independently, which could be particularly useful in studies examining potential rates of soil organic matter change.
Strengthening conflict‐of‐interest policies in medicine
Authors: Cosgrove Lisa , Bursztajn Harold J.
Published: October 2009

Rationale, aims and objectives  Conflict‐of‐interest (COI) policies have played a vital role in protecting the integrity of science as well as protecting patients' welfare. However, the usefulness of these policies could be enhanced by addressing gaps in disclosure requirements, especially insofar as these gaps may impede the intended neutrality of COI policies. For example, current COI policies have not addressed potential conflicts created by indirect industry funding, such as when pharmaceutical companies provide general funding to researchers' academic departments or to medical educational programmes. Nor do they address the consequent creation of climates of opinion, which may marginalize important criticisms and undermine progress on this important policy issue.

Methods  The authors used a critical thinking approach to analyze the gaps in existing COI policies.

Conclusion  Taking the position that a more adequate system of checks and balances is needed, the authors offer specific recommendations for improving current policies and for addressing the issue of indirect support.
Social cognition in children with Down's syndrome: challenges to research and theory building
Authors: Cebula K. R. , Moore D. G. , Wishart J. G.
Published: October 2009

Characterising how socio‐cognitive abilities develop has been crucial to understanding the wider development of typically developing children. It is equally central to understanding developmental pathways in children with intellectual disabilities such as Down's syndrome. While the process of acquisition of socio‐cognitive abilities in typical development and in autism has received considerable attention, socio‐cognitive development in Down's syndrome has received far less scrutiny. Initial work in the 1970s and 1980s provided important insights into the emergence of socio‐cognitive abilities in the children's early years, and recently there has been a marked revival of interest in this area, with research focusing both on a broader range of abilities and on a wider age range. This annotation reviews some of these more recent findings, identifies outstanding gaps in current understanding, and stresses the importance of the development of theory in advancing research and knowledge in this field. Barriers to theory building are discussed and the potential utility of adopting a transactional approach to theory building illustrated with reference to a model of early socio‐cognitive development in Down's syndrome. The need for a more extensive model of social cognition is emphasised, as is the need for larger‐scale, finer‐grained, longitudinal work which recognises the within‐individual and within‐group variability which characterises this population. The value of drawing on new technologies and of adapting innovative research paradigms from other areas of typical and atypical child psychology is also highlighted.
Prospective comparison of Fibroscan, King’s score and liver biopsy for the assessment of cirrhosis in chronic hepatitis C infection
Authors: Cross T. J. S. , Calvaruso V. , Maimone S. , Carey I. , Chang T. P. , Pleguezuelo M. , Manousou P. , Quaglia A. , Grillo F. , Dhillon A. P. , Dusheiko G. M. , Burroughs A. K. , Harrison P. M.
Published: October 2009

Summary.  Historically, liver biopsy (LB) was the sole method to evaluate the severity of hepatic fibrosis in patients with chronic hepatitis C infection. However, LB is expensive and associated with a risk of severe complications. Therefore, noninvasive tests have been developed to assess the severity of liver fibrosis. The accuracy of Fibroscan (FS) and King’s score (KS) was evaluated individually and in combination using liver histology as the reference standard. One hundred and eighty‐seven patients were identified who had undergone a biopsy with a diagnosis of chronic hepatitis C virus (HCV) mono‐infection (HCV RNA‐positive by RT‐PCR), attending King’s College Hospital (n = 88) or the Royal Free Hospital (n = 99) (London) between May 2006 and December 2007. Liver fibrosis was scored using the Ishak method; significant fibrosis was defined as Ishak fibrosis stage F3–F6, and cirrhosis defined as Ishak fibrosis F5–F6. The diagnostic accuracy of each test was assessed by area under receiver operator characteristic curves (AUROC). Median age was 49 years (43–54) and 115 (61%) were male. The AUROC for FS, KS and FS + KS for the diagnosis of Ishak F3–F6 were 0.83, 0.82 and 0.85, respectively and for the diagnosis of cirrhosis (≥F5) were 0.96, 0.89 and 0.93, respectively. The negative predictive values for the diagnosis of cirrhosis using the optimal cut‐off results for fibrsocan (10.05 kPa), KS (24.3) and the two combined (26.1) were 98%, 91% and 94%, respectively. The noninvasive markers and, particularly, FS were effective tests for the prediction of cirrhosis in chronic hepatitis C. Both KS and FS also had clinical utility for the prediction of Ishak fibrosis stages F3–F6.
Genetic diversity and phylogeography in two diploid ferns, Asplenium fontanum subsp. fontanum and A. petrarchae subsp. bivalens, in the western Mediterranean
Authors: HUNT H. V. , ANSELL S. W. , RUSSELL S. J. , SCHNEIDER H. , VOGEL J. C.
Published: October 2009

Asplenium fontanum subsp. fontanum and A. petrarchae subsp. bivalens are diploid rock ferns of limestone outcrops of the western Mediterranean region. Asplenium fontanum subsp. fontanum occurs from Valencia through northeastern Spain to the Alpes‐Maritimes and Swiss Jura. Asplenium petrarchae subsp. bivalens occurs only on Majorca, in Valencia and possibly in southern Spain. We analysed allozyme and chloroplast genetic marker diversity in 75 populations of A. fontanum subsp. fontanum and 12 populations of A. petrarchae subsp. bivalens sampled from across their respective ranges. The two species show similar levels of species and population genetic diversity to one another and to other diploid European Asplenium taxa. Both are predominantly outbreeding, as indicated by FIS = 0.108 and 0.167 respectively. Substantial between‐population differentiation results largely from differentiation between regions. Isolation by distance operates over limited geographic ranges, up to 50 km. In A. fontanum subsp. fontanum, the major geographical differentiation between Valencia and the rest of the taxon range probably represents an ancient range fragmentation. A less pronounced differentiation divides populations in the SW from those in the NE of the range, with evidence for a biogeographic link between the eastern Pyrenees and southeastern France. High diversity in the Pyrenees may either represent ancient population differentiation, or a suture zone. In A. petrarchae subsp. bivalens, populations on Majorca exhibit a subset of the genetic diversity present in Valencia, although the two regions are strongly differentiated by differing allele frequencies. Dispersal from the mainland may have founded Majorcan populations, although a role for in situ island survival cannot be excluded.
Hybridization involving independent gametophytes in the Vandenboschia radicans complex (Hymenophyllaceae): a new perspective on the distribution of fern hybrids
Authors: EBIHARA ATSUSHI , MATSUMOTO SADAMU , ITO MOTOMI
Published: October 2009

To test our hypothesis of hybrid formation involving the ‘independent gametophyte’ phenomenon in ferns, we identified the genomic formulae and ploidy level of gametophytes of the Vandenboschia radicans complex at the periphery of a sporophyte population. We identified haploid gametophytes of V. kalamocarpa (one of the two putative parents of V.×stenosiphon) in a hybrid sporophyte population in Japan that lacks fertile non‐hybrid individuals. Furthermore, diploid sporophytes of the species were not found within a 50‐km radius. This finding supports a hypothesis of hybridization involving the ‘independent gametophyte’ phenomenon and provides a new perspective on the geographical distribution of fern hybrids.