bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluid mixtures: Contrasts of theoretical and simulation approaches, and comparison with experimental alkane properties
Authors: White Ronald P. , Lipson Jane E. G.
Published: August 2009

In this work we compare lattice and continuum versions of the same theory, as derived in the previous paper (Paper I), to predict the behavior of simple alkane mixtures. In the course of doing this we use characteristic parameters obtained for the pure alkane fluids; no fits of mixture properties are involved. Our two sets of predictions are tested against experimental data and against new Monte Carlo simulation results. The experimental properties of interest include mixed pressure-volume-temperature surfaces, as well as a variety of coexistence diagrams characterizing mixed system liquid-vapor equilibria. We contrast the performance of the lattice and continuum approaches and discuss the results in the context of underlying model approximations as derived in Paper I.
Matrix method calculation of the Kerr effect transient and ac stationary responses of arbitrary shaped macromolecules
Authors: Kalmykov Yuri P.
Published: August 2009

A new and simple matrix method of evaluating the Kerr effect transient and ac stationary responses of rigid polar and polarizable particles (macromolecules) of arbitrary shape undergoing the noninertial anisotropic rotational diffusion in the presence of an external electric field is presented. The matrix calculations are accomplished by solving the corresponding coupled differential-recurrence equations for the statistical moments (ensemble averages of the Wigner D functions). The results so obtained are in agreement with previously available solutions for various particular cases and are amenable to comparison with experiment.
Analysis of size effects in Pb(Zr0.54Ti0.46)O3 thin film capacitors with platinum and LaNiO3 conducting oxide electrodes
Authors: Bouregba R. , Sama N. , Soyer C. , Remiens D.
Published: August 2009

The problem of thickness dependence of dielectric and ferroelectric properties of Pb(Zr0.54Ti0.46)O3 (PZT) thin film capacitors is addressed. Experimental data collected on PZT capacitors with different thicknesses and different electrode configurations, using platinum and LaNiO3 conducting oxide, are examined within the prism of existing models. Available literature data, abounding but contradictory, led us to conclude that in the range of thickness investigated, size effect under all its aspects, i.e., increase in coercive field (Ec) as well as decrease in both dielectric permittivity and remnant polarization (Pr), result basically from existence of a depolarization field. It is shown however that the latter arises from interface chemistry, mostly related to the upper surface of the films, instead of finite screening length in the electrodes unlike commonly accepted. Moreover it is established that increase in Ec and decrease in Pr are not concomitant, and significant degradation of one or the other of these values strongly depends on whether a static potential, due to charged defects, is present or not at this interface.
High-temperature lasing characteristics of randomly assembled ZnO nanowires with a ridge waveguide
Authors: Yang H. Y. , Yu S. F. , Liang H. K. , Pang C. , Yan B. , Yu T.
Published: August 2009

High-temperature lasing characteristics of randomly assembled ZnO nanowires at ultraviolet wavelength are investigated. Lasing emission was observed from the randomly assembled ZnO nanowires for temperature up to 500 K. The corresponding lasing mechanism is attributed to the coherent random lasing action via the formation of closed-loop cavity modes. Furthermore, ridge waveguide lasers using the randomly assembled ZnO nanowires as the active medium were fabricated. It is found that the width of the ridge waveguides restricted the size of the closed-loop cavity modes such that the corresponding characteristic temperature can be increased by 10 K.
High-resolution laser lithography system based on two-dimensional acousto-optic deflection
Authors: Koechlin Manuel , Poberaj Gorazd , Günter Peter
Published: August 2009

We present an advanced high-resolution, compact laser lithography system for fast prototyping of complex integrated optics devices comprising microring resonators and photonic crystal structures. Precise and flexible structuring of photoresist patterns is achieved by combing three linear stages (xyz) for sample positioning and a two-dimensional acousto-optical deflector for laser beam steering and intensity control. A continuous wave diode laser operating at a wavelength of 375 nm is used to illuminate all types of photoresists including SU-8. Using a microscope objective with a numerical aperture of 1.40, structure widths of ∼200 nm can be obtained. The write-field covered by acousto-optic deflection can be as large as 200×200 μm2 when using an objective with a focal length of 4.5 mm. With a two-step lithography process, gaps as small as 150 nm between adjacent structures have been achieved, yielding superior photoresist masks for microring resonators with coupling ports.
Microwave propagation in graphene
Authors: Deligeorgis G. , Dragoman M. , Neculoiu D. , Dragoman D. , Konstantinidis G. , Cismaru A. , Plana R.
Published: August 2009

We report on measurements and modeling of microwave propagation in graphene. In deep contrast with carbon nanotubes, which display very high impedances in the microwave range, planar waveguides patterned directly on graphene display a 50 Ω impedance, which is tuned slightly by an applied dc. The high values of kinetic impedance in carbon nanotubes were not observed in graphene.
Influence of the ZnO buffer on the guided mode structure in Si/ZnO/Ag multilayers
Authors: Haug F.-J. , Söderström T. , Cubero O. , Terrazzoni-Daudrix V. , Ballif C.
Published: August 2009

We present a study of the optical mode structure in metal-dielectric multilayer structures that represent amorphous silicon thin film solar cells with metallic back contact. Knowledge of the modal structure represents a first step toward describing absorption enhancement by the interface texture in solar cells. We present a method for determining experimentally the dispersion relations of multilayer films by coupling polarized light in a spectral reflection measurement to eigenmodes, using a one-dimensional sinusoidal grating. Because the used grating represents only a minor perturbation that establishes the coupling, the experimental data is well explained by the modal structure of a geometry with flat interfaces. On the basis of the measured mode structure, we propose an explanation for the beneficial effect of a low index buffer layer between the silicon absorber and the metallic back reflector.
Nonlinear dynamics of kink-unstable spheromak equilibria
Authors: García-Martínez Pablo Luis , Farengo Ricardo
Published: August 2009

The nonlinear evolution of several kink-unstable, force-free equilibria inside a cylindrical flux conserver is studied by solving the nonlinear, three-dimensional, time-dependent equations of resistive magnetohydrodynamics (MHD). The stability properties of the equilibria are controlled by the slope, α, of the linear λ(ψ) profile (where λ=μ0J⋅B/B2 and ψ is the poloidal flux). Very unstable configurations (with α well beyond the stability threshold) are observed to fully relax toward the Taylor state, as predicted by relaxation theory. In contrast, marginally unstable cases undergo only partial relaxation. Since we consider decaying plasmas without open flux (no driving), the partial relaxation process is a result of the dynamics of marginally unstable configurations. The effect of the Lundquist number, S, on a fixed initial condition (a fixed α) is studied. Increasing S leads to a higher level of fluctuations and poloidal flux amplification. However, it is found that, despite the stronger activity, the final level of relaxation is determined only by the initial slope α (for the high S regime considered here). The nonaxisymmetric activity produced by the instability is studied. The relaxation event begins with a dominant n=1 kink mode responsible for poloidal flux amplification and ends with a low activity period (of several tens of Alfvén times) which produces a current redistribution process that flattens the λ profile. Finally, the MHD dynamo field is investigated.
Magnetically tuned mechanical resonances in magnetoelectric multilayer capacitors
Authors: Israel C. , Petrov V. M. , Srinivasan G. , Mathur N. D.
Published: August 2009

Poled multilayer capacitors based on barium titanate represent model magnetoelectric systems because the interdigitated planar electrodes are nowadays based on a magnetostrictive material, namely nickel. Here we demonstrate electrically excited mechanical resonances that can be magnetically tuned. Nonmonotonic variations in resonant frequency with applied magnetic field are interpreted in terms of the influence of magnetostriction on the Young’s modulus of the electrodes, i.e., the ΔEY effect.
Nonaxisymmetric shaping of tokamaks preserving quasiaxisymmetry
Authors: Ku Long-Poe , Boozer Allen H.
Published: August 2009

If quasiaxisymmetry is preserved, nonaxisymmetric shaping can be used to design tokamaks that do not require current drive, are resilient to disruptions, and have robust plasma stability without feedback. Suggestions for addressing the critical issues of tokamaks can only be validated when presented with sufficient specificity that validating experiments can be designed. The purpose of this paper is to provide that specificity for nonaxisymmetric shaping. Whether nonaxisymmetric shaping is essential, or just an alternative strategy, to the success of tokamak fusion systems can only be assessed after axisymmetric alternatives are suggested and subjected to a similar study. Sequences of three-field-period quasiaxisymmetric plasmas are studied. These sequences address the questions: (1) What can be achieved at various levels of nonaxisymmetric shaping? (2) What simplifications to the coils can be achieved by going to a larger aspect ratio? (3) What range of shaping can be achieved in a single experimental facility? The sequences of plasmas found in this study provide a set of interesting and potentially important configurations.
Reduction of the loads on a cylinder undergoing harmonic in-line motion
Authors: Marzouk Osama A. , Nayfeh Ali H.
Published: August 2009

We use the finite-difference computational fluid dynamics method to study in detail the flow field around a circular cylinder in a uniform stream while undergoing in-line harmonic motion. For a given motion amplitude, there exists a critical forcing frequency below which the lift and drag can be period-n, quasiperiodic, or chaotic. Similarly, for a given frequency, there exists a critical amplitude below which the lift and drag can be period-n, quasiperiodic, or chaotic. Above these critical conditions, the lift and drag are synchronous with the forcing. The lift nearly vanishes and the mean drag drops and saturates at a value that is independent of the driving frequency, whereas the oscillatory drag quadratically depends on it. We relate these features to changes in the wake and the surface-pressure distribution. We examine the influence of the Reynolds number on these critical frequency and amplitude. Second- and higher-order spectral analyses show remarkable changes in the linear and quadratic coupling between the lift and drag when synchronization takes place; it destroys the two-to-one coupling between them in the cases of no motion and synchronization due to cross-flow motion.
Universal scaling of semiconductor nanowires bandgap
Authors: Li S. , Yang G. W.
Published: August 2009

We have established an analytical model to investigate the bandgap energy of III-V and II-V semiconductor nanowires (NWs) by taking size and surface effect into account and found that there is a universal scaling of bandgap between bandgap energy Eg and structural factor K of NWs, Eg∼K−1, which meaning that the bandgap energy of semiconductor NWs usually increases with the structural factor decreasing. This scaling rule has a general insight into the basic physics involved in size effect of semiconductor NWs bandgap.
Ekman destabilization of inertially stable baroclinic abyssal flow on a sloping bottom
Authors: Swaters Gordon E.
Published: August 2009

Baroclinic abyssal currents on a sloping bottom, which are nonlinearly stable in the sense of Liapunov in the absence of dissipation, are shown to be destabilized by the presence of a bottom Ekman boundary layer for any positive value of the Ekman number. When the abyssal flow is baroclinically unstable, the dissipation acts to reduce the inviscid growth rates except near the marginal stability boundary where it acts to increase the inviscid growth rates. It is shown that when the abyssal flow is baroclinically stable, the Ekman destabilization corresponds to the kinematic wave phase velocity lying outside the range of the inertial topographic Rossby phase velocities. The transition mechanism described here might provide a dynamical bridge between the nonrotational roll-wave instability that can occur in supercritical abyssal overflows and frictionally induced destabilization in subinertial geostrophically balanced baroclinic abyssal currents. In addition, the theory presented here suggests a dissipation-induced destabilization mechanism for coastal downwelling fronts whose cross-slope potential vorticity gradient does not satisfy the necessary condition for baroclinic instability.
Small amplitude ion-acoustic double layers in a plasma with superthermal electrons and thermal positrons
Authors: Tribeche Mouloud , Boubakour Nadia
Published: August 2009

Small-amplitude ion-acoustic double layers (IA-DLs) in a plasma with superthermal electrons and thermal positrons are investigated. Due to the electron superthermality and the relative fraction of positrons, our plasma model can admit compressive as well as rarefactive IA-DLs. As the electrons evolve toward their thermodynamic equilibrium, the negative IA-DL shrinks and, beyond a certain critical value of the electron spectral index κc, develops into a positive structure allowing therefore the existence of compressive IA-DLs. This critical value is lowered as the number of positrons becomes important. As the superthermal character of the plasma increases, the threshold pc above which only compressive IA-DLs are admitted is shifted toward higher values. Our investigation may help to understand the DL structures observed in the ionosphere and the auroral acceleration regions.
Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps
Authors: Singer Amit , Erban Radek , Kevrekidis Ioannis G. , Coifman Ronald R.
Published: August 2009

Nonlinear independent component analysis is combined with diffusion-map data analysis techniques to detect good observables in high-dimensional dynamic data. These detections are achieved by integrating local principal component analysis of simulation bursts by using eigenvectors of a Markov matrix describing anisotropic diffusion. The widely applicable procedure, a crucial step in model reduction approaches, is illustrated on stochastic chemical reaction network simulations.
T cell receptor sharing by cytotoxic T lymphocytes facilitates efficient virus control
Authors: Chaudhri Geeta , Quah Ben J. , Wang Yang , Tan Abel H. Y. , Zhou Jie , Karupiah Gunasegaran , Parish Christopher R.
Published: August 2009

A remarkable feature of the adaptive immune system is the speed at which small numbers of antigen-specific lymphocytes can mediate a successful immune response. Rapid expansion of T and B lymphocyte clones that have receptors specific for a particular antigen is one of the primary means by which a swift response is generated. Although much of this clonal expansion is caused by the division of antigen-specific cells, here we demonstrate an additional mechanism by which the pool of effector T cells against a viral infection can quickly enlarge. Our data show that virus-specific CD8+cytotoxic T lymphocytes (CTL) can transfer their T cell receptors (TCR) to recipient CTL of an unrelated specificity that, as a consequence, gain the antigen specificity of the donor T cell. This process occurs within minutes via membrane exchange and results in the recipient CTL acquiring the ability to recognize and eliminate cells targeted by the donor TCR, while still retaining the antigen specificity of its own TCR. Such receptor sharing allows rapid, proliferation-independent expansion of virus-specific T cell clones of low frequency and plays a highly significant antiviral role that can protect the host from an otherwise lethal infection.
Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets
Authors: Hong Xin , Hammell Molly , Ambros Victor , Cohen Stephen M.
Published: August 2009

microRNAs comprise a few percent of animal genes and have been recognized as important regulators of a diverse range of biological processes. Understanding the biological functions of miRNAs requires effective means to identify their targets. Combined efforts from computational prediction, miRNA over-expression or depletion, and biochemical purification have identified thousands of potential miRNA-target pairs in cells and organisms. Complementarity to the miRNA seed sequence appears to be a common principle in target recognition. Other features, including miRNA-target duplex stability, binding site accessibility, and local UTR structure might affect target recognition. Yet computational approaches using such contextual features have yielded largely nonoverlapping results and experimental assessment of their impact has been limited. Here, we compare two large sets of miRNA targets: targets identified using an improved Ago1 immunopurification method and targets identified among transcripts up-regulated after Ago1 depletion. We found surprisingly limited overlap between these sets. The two sets showed enrichment for target sites with different molecular, structural and functional properties. Intriguingly, we found a strong correlation between UTR length and other contextual features that distinguish the two groups. This finding was extended to all predicted microRNA targets. Distinct repression mechanisms could have evolved to regulate targets with different contextual features. This study reveals a complex relationship among different features in miRNA-target recognition and poses a new challenge for computational prediction.
Template synthesis, characterization, in vitro antimicrobial, and DNA cleavage studies of Co(II), Ni(II), Cu(II), and Zn(II) complexes with 15-membered N2O2 diazadioxa macrocycles
Authors: Patil Sangamesh A. , Kamble Udaykumar V. , Badami Prema S.
Published: August 2009

A novel series of 15-membered diazadioxa macrocyclic complexes [MLCl2] (M = Co(II), Ni(II), Cu(II), and Zn(II) ) have been synthesized via the condensation reaction of salicylaldehyde and 1,2-dibromoethane with a 3-subtituted-4-amino-5-hydrazino-1,2,4-triazole in the presence of transition metal ions as templates in ethanol. The mode of bonding and overall geometry of the complexes have been inferred through IR, 1H NMR, 13C NMR, EPR, electronic spectral studies, conductivity, magnetic, thermal, and electrochemical studies. All the complexes are soluble in DMF and DMSO and are non-electrolytes. All these complexes have been screened for their antibacterial (Escherichia coli, Staphylococus aureus, Salmonella typhi, Pseudomonas aeruginosa) and antifungal activities (Aspergillus niger, Aspergillus flavus, and Cladosporium) by the minimum inhibitory concentration method. The DNA cleavage is studied by agarose gel electrophoresis. An octahedral geometry is proposed for all the complexes.
Direct synthesis of trifluoromethyl decorated diphenylphosphites. Unusual non-bonded structural features in bis-[(2-trifluoromethyl)phenylphosphite: [2-(CF3)C6H4]2P(O)H]
Authors: Pailloux Sylvie , Duesler Eileen N. , Smith Karen Ann , Paine Robert T. , Klaehn John R. , McIlwain Michael E.
Published: August 2009

A direct, Grignard reagent-based route for the syntheses of [2-(CF3)C6H4]2P(O)H (1) and [3,5-(CF3)2C6H3]2P(O)H (2) has been developed and the isolation and characterization of these crystalline reagents is described. The crystal structures for 1 and 2 were determined and the structure of 1 reveals unexpected close non-bonded interaction between F-atoms of one CF3 group and the back-side of the central phosphorus atom.
Residue levels of organochlorines and organophosphates in water, fish and sediments from Lake Victoria-Kenyan portion
Authors: Werimo K. , Bergwerff A. A. , Seinen W.
Published: August 2009

Water, fish and sediments were sampled from May 2000 to December 2006 at 19 different locations in Lake Victoria-Kenyan part. They were analyzed for organochlorines (HCB, Lindane, DDT and Endosulfan) and organophosphate (diazinon). All organochlorines in water, fish and sediments were below detection limit of 0.5 μg l−1, 1.0 μg kg−1 body weight and 1.0 μg kg−1 dry weight, respectively. Comparison of the results of these samples in Lake Victoria with those analyzed during 1993 suggests that the concentrations of these compounds have not increased in the lake.

Therefore it was concluded that there were neither environmental nor human health hazards posed by these compounds to the water or sediments.
Water pollution studies in the rivers of the Edirne Region–Turkey
Authors: Sakcali M. Serdal , Yilmaz Ruya , Gucel Salih , Yarci Celal , Ozturk Munir
Published: August 2009

Physico-chemical parameters of Tunca, Merich, Arda and Ergene rivers, in the Edirne region of Turkey, were investigated. Studies were carried out during 1998–2004 and the data obtained were compared with EU threshold levels. The results showed that the total concentrations of P, Pb, Cu, Ni, Mn and Co were higher than these threshold levels. There is an urgent need for Turkey to limit water pollution from a wide range of dangerous substances, particularly at a time when it is being considered as an EU candidate. Turkey will be required to achieve a satisfactory status in its waters by 2015, in particular in the waters of the rivers investigated in this paper that border Bulgaria and Greece. Levels of pollutants which pose a significant risk to the aquatic environment need to be monitored and strictly controlled.
Comparison of shipboard and satellite measurements of surface water temperature and chlorophyll a in Lake Ontario
Authors: Watkins James M.
Published: August 2009

The binational Lake Ontario Lower Aquatic Foodweb Assessment program (LOLA) intensively sampled Lake Ontario in the Spring (April 28-May 3), Summer (August 10–11 and August 19–21) and Fall (September 21–25) of 2003. However, the timing of shipboard surveys often misses critical periods in biological productivity. We directly compared surface water temperature and chlorophyll a (chl a) measurements made during these cruises to Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images for May 3, August 18, and September 21, 2003. Satellite measurements were strongly correlated to shipboard measurements for surface water temperature (r2 = 0.98) and chl a (r2 = 0.62, offshore sites only). The OC4 algorithm for chl a greatly overestimated nearshore sites because of the probable presence of color producing agents other than chl a. However, its relative reliability for offshore sites adds confidence in using the imagery to fill the gaps between sampling cruises.
Macroinvertebrate community structure in created wetlands of different successional stage
Authors: Spieles Douglas J. , Horn Jonathan D.
Published: August 2009

We analyzed biogeochemical characteristics of two temperate constructed wetlands in early and late spring to evaluate the utility of the macroinvertebrate community as an indicator of ecosystem development. The wetlands were similar in area, hydrologic regime, and influent water quality, but one was younger (15 y) and supported an early successional plant community while the older system (45 y) was forested. To characterize structural habitat in the two wetlands we analyzed water and soil quality, plant community characteristics, coarse woody debris, topographic variance and hydrologic regime. The correlation of macroinvertebrate community characteristics with structural variables was compared among wetlands, and macroinvertebrates were compared temporally within wetlands. Despite differences in nutrient concentration, substrate conditions, plant cover, and microtopography, the overall macroinvertebrate guild structure in the two systems was similar in terms of taxa richness, Simpson diversity, tolerance, and trophic distribution. Total abundance of macroinvertebrates was significantly correlated with a number of structural wetland characteristics, but trophic distribution was correlated only with nutrient availability. Temporal changes were apparent in both wetlands. The two wetlands supported proportionally different guild biomass in early spring, with the forested wetland dominated by grazing herbivores and shredders and the non-forested system by detritivores and predators. In late spring, however, there was no statistical difference in trophic distribution among the two wetlands, as both were dominated by grazing herbivores. These results suggest that macroinvertebrate community characteristics have limited utility as an indicator of successional development in created wetlands, as community characteristics are readily influenced by nutrient availability and temporal changes.
Nha Trang Bay marine protected area, Vietnam: Initial trends in coral structure and some preliminary linkages between these trends and human activities (2002–2005)
Authors: Dung Le Doan
Published: August 2009

Nha Trang Bay marine protected area was establishted in 2002 as a pilot initiative to enable adequate management of the reef communities, while providing opportunities for alternative income to the local community. A re-assessment of the data obtained during the baseline survey performed in 2002 and of an inventory performed in 2005 indicates a reasonable decline in hard coral structure in the marine protected area. The reef of Hon Mun, a core zone at the hearth of the marine protected area and an attraction for underwater tourists, showed some recovery of the coral cover. Reefs in the buffer area of Hon Mieu and Hon Mot showed, on the contrary, great declines in the coral cover and abundance. These reefs are those most affected by human derived impacts, including urban run-off, mariculture, fishing, tourism, etc. The most distant reef, at Hon Tre, although formally a core zone, is allegedly under strong fishing pressure owing to lack of surveillance enforcement. The major impact, so far, seems to be a marked change in coral cover and species, especially in the deeper area. Despite the lack of data replication in the present work, it is becoming evident that coastal development and particularly, fisheries and mariculture which depend on great amounts of wild seed and feed collected in the area, may become antagonistic activities to the recovery of the reef to earlier states. Managers devising future management plans now have a base for re-consideration regime of adjacent industrial activities.
Coastal aquaculture and shrimp farming in North Vietnam and environmental cost estimation
Authors: Lan Tran Dinh
Published: August 2009

This study aims to present an overview of coastal aquaculture, particularly of shrimp farming in North Vietnam, and to estimate environmental costs for coastal shrimp farming in Hai Phong City, as a case study. To achieve the study objectives, the main method employed was the economy model for environmental cost estimation. The study results show the continuous increase in area (10.5% to 31.8%) and yield (43,221.7 to 65,258.0 tons) of coastal aquaculture in all six provinces of North Vietnam. For seven years (1995–2001), the area of shrimp farming in Hai Phong City increased by 85%, while the yield increased by 348%. Estimation of environmental costs using an experimental model was developed for Hai Phong due to shrimp farming development with input contribution from over 60 farms in 2001–2003. Parameters input into the model are costs for each shrimp farm, including: Square Area (ha), Yield (kg), Shrimp price (Vietnamese dong (VND) kg−1), Total replacement cost due to conversion of natural resources to shrimp farms (VND), Juvenile cost (VND), Food cost (VND), Culturing technical cost (VND), Fuel cost (VND), Chemical cost (VND), Medical cost (VND), Energy cost (VND), Disease prevention cost (VND), Water control cost (VND), Labour cost (VND). The developed model shows that the environmental cost will increase by 0.39% for every one unit of shrimp yield increased. Applying economic models (experimental models) to estimation of environmental costs of coastal shrimp farming and aquaculture generally allows promotion of some quantitative inputs to planning for sustainable aquaculture in North Vietnam.
The Place2Be: Measuring the effectiveness of a primary school‐based therapeutic intervention in England and Scotland
Authors: Lee Rachael C. , Tiley Clare E. , White Jemma E.
Published: August 2009

Aim: There is increasing awareness of the prevalence of mental health disorders in children in the UK, but research on the efficacy of interventions meeting this need is limited. This study assessed whether The Place2Be model of individual and group intervention has a positive influence on children's social and emotional wellbeing. Providing emotional and therapeutic support to school age children in England and Scotland, The Place2Be delivers school‐based therapeutic interventions to around 47,000 children in 143 primary schools, two secondary schools and one independent school. Method: Strengths and Difficulties Questionnaire data was collected from a national sample of primary school children aged 4–11 (N=1,864) both before and after accessing an individual (n =1,645) or group (n =215) intervention. Results: Repeated measures t‐tests revealed that children had significantly lower Total Difficulties scores post‐intervention than pre‐intervention as rated by their class teachers and parents (Teacher‐rated: p<0.001, d = 0.39; Parent‐rated: p<0.001, d = 0.47). Children also had significantly higher Prosocial scores post‐intervention (Teacher‐rated: p<0.001, d = 0.25; Parent‐rated: p<0.001, d = 0.15). Conclusions: Children's social and emotional behaviour, as perceived by their teachers and parents, was improved following therapeutic intervention with The Place2Be. These findings have important implications for service providers looking to commission projects for the benefit of their local community.
Counselling in UK secondary schools: A comprehensive review of audit and evaluation data
Authors: Cooper Mick
Published: August 2009

Aims: The purpose of this study was to develop a comprehensive picture of the nature and outcomes of counselling in secondary schools in the UK. Method: Audit and evaluation studies of schools counselling were identified using a systematic literature search. Thirty studies were found and analysed using a variety of methods. Typically, counselling services provided purely person‐centred, or person‐centred‐based, forms of therapy. Results: Averaged across all studies, clients had a mean age of 13.86 and attended for 6.35 sessions of counselling. The average percentage of female clients per study was 56.31%. Most frequently, clients presented with family issues, with anger issues particularly prevalent in males. Around 60% of clients began counselling with ‘abnormal’ or borderline levels of psychological distress. Counselling was associated with large improvements in mental health (mean weighted effect size = 0.81), with around 50% of clinically distressed clients demonstrating clinical improvement. On average, just over 80% of respondents rated counselling as moderately or very helpful, with teachers giving it a mean rating of 8.22 on a 10‐point scale of helpfulness. For clients, the most helpful aspect of counselling was the opportunity to talk and be listened to, while pastoral care staff emphasised the counsellor's independence, expertise and confidentiality. There were some indications that counselling may indirectly benefit students’ capacities to study and learn. Discussion: School‐based counselling appears to be of considerable benefit to young people in the UK, but there is a need for this finding to be verified through controlled trials.
How do secondary school counsellors work with other professionals?
Authors: Cromarty Karen , Richards Kaye
Published: August 2009

Aim: This study explores how secondary school counsellors work with other professionals within and outside schools in the delivery of services. Method: Sixteen school counsellors from across the UK were interviewed, in four different focus groups – two in England (n=8) and two in Scotland (n=8). Results: The findings indicate that the professional relationships counsellors have with other colleagues have a direct influence upon the quality of the service they feel able to offer. Time spent with colleagues when setting up services was viewed as highly beneficial, as was time spent building relationships and connections with colleagues within the school and from external agencies and organisations, as well as having a senior member of staff to liaise with. It is apparent that attending to relationships outside of the counselling room may influence the positive outcomes for the counselling service and its clients generally. Conclusions: Implications of these findings may influence the ways in which counsellors are employed by commissioners, and how counsellors use their time allocation in schools to ensure that effective services are both achieved and maintained.
Transcriptional Suppression by Transient Recruitment of ARIP4 to Sumoylated Nuclear Receptor Ad4BP/SF-1
Authors: Ogawa Hidesato , Komatsu Tomoko , Hiraoka Yasushi , Morohashi Ken-ichirou
Published: August 2009

The small ubiquitin-like modifier SUMO conjugates transcription factors and suppresses their respective activation of target genes. Although various SUMO-modified transcription factors have been isolated, mechanisms whereby sumoylated-substrates modulate transcription remain unknown. Here, we purified ARIP4 (AR interacting protein 4, a Rad54 family member and a SNF2 chromatin remodeling factor), which interacts with sumoylated Ad4BP/SF-1 through two SUMO-interacting motifs and one Ad4BP/SF-1–binding region. Remarkably, ARIP4 also interacts selectively with other sumoylated nuclear receptors including LRH-1, AR, and GR. Interestingly, the ATPase activity of ARIP4 was stimulated in the presence of sumoylated Ad4BP/SF-1 and the Ad4BP/SF-1–binding site containing double-stranded DNA. ChIP assays and siRNA studies strongly suggested that ARIP4 temporally suppresses Ad4BP/SF-1–mediated transcription through its transient recruitment to target genes. These findings suggest that ARIP4 may be a cofactor that modulates SUMO-mediated fine-tuning of transcriptional suppression.
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
Authors: Defrance Matthieu , van Helden Jacques
Published: August 2009

Motivation: Discovering cis-regulatory elements in genome sequence remains a challenging issue. Several methods rely on the optimization of some target scoring function. The information content (IC) or relative entropy of the motif has proven to be a good estimator of transcription factor DNA binding affinity. However, these information-based metrics are usually used as a posteriori statistics rather than during the motif search process itself.

Results: We introduce here info-gibbs, a Gibbs sampling algorithm that efficiently optimizes the IC or the log-likelihood ratio (LLR) of the motif while keeping computation time low. The method compares well with existing methods like MEME, BioProspector, Gibbs or GAME on both synthetic and biological datasets. Our study shows that motif discovery techniques can be enhanced by directly focusing the search on the motif IC or the motif LLR.

Availability:  http://rsat.ulb.ac.be/rsat/info-gibbs

Contact:  defrance@bigre.ulb.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
The effects of probe binding affinity differences on gene expression measurements and how to deal with them
Authors: Dannemann Michael , Lorenc Anna , Hellmann Ines , Khaitovich Philipp , Lachmann Michael
Published: August 2009

Motivation: When comparing gene expression levels between species or strains using microarrays, sequence differences between the groups can cause false identification of expression differences. Our simulated dataset shows that a sequence divergence of only 1% between species can lead to falsely reported expression differences for >50% of the transcripts—similar levels of effect have been reported previously in comparisons of human and chimpanzee expression. We propose a method for identifying probes that cause such false readings, using only the microarray data, so that problematic probes can be excluded from analysis. We then test the power of the method to detect sequence differences and to correct for falsely reported expression differences. Our method can detect 70% of the probes with sequence differences using human and chimpanzee data, while removing only 18% of probes with no sequence differences. Although only 70% of the probes with sequence differences are detected, the effect of removing probes on falsely reported expression differences is more dramatic: the method can remove 98% of the falsely reported expression differences from a simulated dataset. We argue that the method should be used even when sequence data are available.

Contact:  lachmann@eva.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
Authors: Maenhout Steven , De Baets Bernard , Haesaert Geert
Published: August 2009

Motivation: Phenotypic data collected in breeding programs and marker-trait association studies are often analyzed by means of linear mixed models. In these models, the covariance between the genetic background effects of all genotypes under study is modeled by means of pairwise coefficients of coancestry. Several marker-based coancestry estimation procedures allow to estimate this covariance matrix, but generally introduce a certain amount of bias when the examined genotypes are part of a breeding program. CoCoa implements the most commonly used marker-based coancestry estimation procedures and as such, allows to select the best fitting covariance structure for the phenotypic data at hand. This better model fit translates into an increased power and improved type I error control in association studies and an improved accuracy in phenotypic prediction studies. The presented software package also provides an implementation of the new Weighted Alikeness in State (WAIS) estimator for use in hybrid breeding programs. Besides several matrix manipulation tools, CoCoa implements two different bending heuristics, in case the inverse of an ill-conditioned coancestry matrix estimate is needed.

Availability and Implementation: The software package CoCoa is freely available at http://webs.hogent.be/cocoa. Source code, manual, binaries for 32 and 64-bit Linux systems and an installer for Microsoft Windows are provided. The core components of CoCoa are written in C++, while the graphical user interface is written in Java.

Contact:  steven.maenhout@hogent.be
Statistical methods for gene set co-expression analysis
Authors: Choi YounJeong , Kendziorski Christina
Published: August 2009

Motivation: The power of a microarray experiment derives from the identification of genes differentially regulated across biological conditions. To date, differential regulation is most often taken to mean differential expression, and a number of useful methods for identifying differentially expressed (DE) genes or gene sets are available. However, such methods are not able to identify many relevant classes of differentially regulated genes. One important example concerns differentially co-expressed (DC) genes.

Results: We propose an approach, gene set co-expression analysis (GSCA), to identify DC gene sets. The GSCA approach provides a false discovery rate controlled list of interesting gene sets, does not require that genes be highly correlated in at least one biological condition and is readily applied to data from individual or multiple experiments, as we demonstrate using data from studies of lung cancer and diabetes.

Availability: The GSCA approach is implemented in R and available at www.biostat.wisc.edu/∼kendzior/GSCA/.

Contact:  kendzior@biostat.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Aqueous Extract of Brazilian Green Propolis: Primary Components, Evaluation of Inflammation and Wound Healing by Using Subcutaneous Implanted Sponges
Authors: Moura Sandra Aparecida Lima de , Negri Giuseppina , Salatino Antônio , Lima Luiza Dias da Cunha , Dourado Luana Pereira Antunes , Mendes Juliana Barros , Andrade Silvia Passos , Ferreira Mônica Alves Neves Diniz , Cara Denise Carmona
Published: August 2009

Propolis is a chemically complex resinous bee product which has gained worldwide popularity as a means to improve health condition and prevent diseases. The main constituents of an aqueous extract of a sample of green propolis from Southeast Brazil were shown by high performance liquid chromatography/mass spectroscopy/mass spectroscopy to be mono‐ and di‐O‐caffeoylquinic acids; phenylpropanoids known as important constituents of alcohol extracts of green propolis, such as artepillin C and drupanin were also detected in low amounts in the aqueous extract. The anti‐inflammatory activity of this extract was evaluated by determination of wound healing parameters. Female Swiss mice were implanted subcutaneously with polyesther‐polyurethane sponge discs to induce wound healing responses, and administered orally with green propolis (500 mg kg−1). At 4, 7 and 14 days post‐implantation, the fibrovascular stroma and deposition of extracellular matrix were evaluated by histopathologic and morphometric analyses. In the propolis‐treated group at Days 4 and 7 the inflammatory process in the sponge was reduced in comparison with control. A progressive increase in cell influx and collagen deposition was observed in control and propolis‐treated groups during the whole period. However, these effects were attenuated in the propolis‐treated group at Days 4 and 7, indicating that key factors of the wound healing process are modulated by propolis constituents.
Driving Saints to Sin: How Increasing the Difficulty of Voting Dissuades Even the Most Motivated Voters
Authors: McNulty John E. , Dowling Conor M. , Ariotti Margaret H.
Published: August 2009

The consolidation of polling places in the Vestal Central School District in New York State during the district's 2006 budget referendum provides a naturalistic setting to study the effects of polling consolidation on voter turnout on an electorate quite distinct from previous work by Brady and McNulty (2004, The costs of voting: Evidence from a natural experiment. Presented at the Annual Meeting of the Society for Political Methodology, Palo Alto, CA). In particular, voters in local elections are highly motivated and therefore might be thought to be less affected by poll consolidation. Nevertheless, through a matching analysis we find that polling consolidation decreases voter turnout substantially, by about seven percentage points, even among this electorate, suggesting that even habitual voters can be dissuaded from going to the polls. This finding has implications for how election administrators ought to handle cost-cutting measures like consolidation.
Baroreflex Sensitivity Is Impaired in Patients with Obstructive Jaundice
Authors: Song Jian-gang , Cao Yun-fei , Sun Yu-ming , Ge Yan-hu , Xu Xue-wu , Yang Li-qun , Liu Zhi-qiang , Song Shao-li , Yu Wei-feng
Published: August 2009

Background

Obstructive jaundice is associated with enhanced susceptibility to hypotensive shock, renal failure, and toxic effects of endotoxin, which results in high perioperative morbidity and mortality. Since the normal arterial baroreflex function is necessary for hemodynamic homeostasis and improving survival in sepsis, this study aimed to determine whether baroreflex sensitivity was impaired in jaundiced patients.

Methods

Thirty-five patients with obstructive jaundice scheduled for surgery were included, and 30 nonjaundiced patients served as controls. A modified Oxford pharmacologic technique was used for evaluating baroreflex sensitivity immediately before the surgery. Potential factors that may affect baroreflex sensitivity in jaundice, such as liver biochemistry, plasma concentrations of methionine-enkephalin, atrial natriuretic peptide and nitrate, were also measured.

Results

Patients with obstructive jaundice had decreased sensitivity in both the sympathetic and vagal components of the baroreflex, as compared with the controls (P < 0.01). There was a significant inverse correlation between plasma atrial natriuretic peptide concentration and decreased sympathetic baroreflex sensitivity in the jaundiced group (r = -0.44, P = 0.008).

Conclusions

Baroreflex sensitivity is impaired in patients with obstructive jaundice, which may contribute to their enhanced susceptibility to the well-known perioperative complications. The underlying mechanisms for such a change may be associated with an increased level of plasma atrial natriuretic peptide.
Delayed Treatment with Isoflurane Attenuates Lipopolysaccharide and Interferon γ–induced Activation and Injury of Mouse Microglial Cells
Authors: Kim Jie-Ae , Li Liaoliao , Zuo Zhiyi
Published: August 2009

Background

Isoflurane pretreatment can induce protection against lipopolysaccharide and interferon gamma (IFNgamma)-induced injury and activation of mouse microglial cells. This study's goal was to determine whether delayed isoflurane treatment is protective.

Methods

Mouse microglial cells were exposed to various concentrations of isoflurane for 1 h immediately after the initiation of lipopolysaccharide (10 or 1000 ng/ml) and IFNgamma (10 U/ml) stimulation or to 2% isoflurane for 1 h at various times after initiation of the stimulation. Nitrite production, lactate dehydrogenase release, and cell viability measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay were assessed after stimulation with lipopolysaccharide and IFNgamma for 24 h. Inducible nitric oxide synthase (iNOS) protein expression was quantified by Western blotting. The iNOS expression in mouse brain was also studied.

Results

Isoflurane applied 0 and 2 h after the initiation of lipopolysaccharide and IFNgamma stimulation improved cell viability. Isoflurane at 2%, but not at 1 or 3%, reduced the lipopolysaccharide and IFNgamma-induced nitrite production and decreased cell viability. Aminoguanidine, an iNOS inhibitor, also attenuated this decreased cell viability. Chelerythrine and bisindolylmalemide IX, protein kinase C inhibitors, abolished isoflurane effects on cell viability and iNOS expression after lipopolysaccharide and IFNgamma application. Isoflurane also decreased lipopolysaccharide-induced iNOS expression in mouse brain. Late isoflurane application to microglial cells reduced lipopolysaccharide and IFNgamma-induced lactate dehydrogenase release that was not inhibited by aminoguanidine.

Conclusions

These results suggest that delayed isoflurane treatment can reduce lipopolysaccharide and IFNgamma-induced activation and injury of microglial cells. These effects may be mediated by protein kinase C.