bluuebunny/crossref_metadata_2025 huggingface dataset:
Release of Mitochondrial Apoptogenic Factors and Cell Death are Mediated by CK2 and NADPH Oxidase
Authors: Kim Gab Seok , Jung Joo Eun , Narasimhan Purnima , Sakata Hiroyuki , Yoshioka Hideyuki , Song Yun Seon , Okami Nobuya , Chan Pak H
Published: December 2011

Activation of the NADPH oxidase subunit, NOX2, and increased oxidative stress are associated with neuronal death after cerebral ischemia and reperfusion. Inhibition of NOX2 by casein kinase 2 (CK2) leads to neuronal survival, but the mechanism is unknown. In this study, we show that in copper/zinc-superoxide dismutase transgenic (SOD1 Tg) mice, degradation of CK2α and CK2α′ and dephosphorylation of CK2β against oxidative stress were markedly reduced compared with wild-type (WT) mice that underwent middle cerebral artery occlusion. Inhibition of CK2 pharmacologically or by ischemic reperfusion facilitated accumulation of poly(ADP-ribose) polymers, the translocation of apoptosis-inducing factor (AIF), and cytochrome c release from mitochondria after ischemic injury. The eventual enhancement of CK2 inhibition under ischemic injury strongly increased 8-hydroxy-2′-deoxyguanosine and phosphorylation of H2A.X. Furthermore, CK2 inhibition by tetrabromocinnamic acid (TBCA) in SOD1 Tg and gp91 knockout (KO) mice after ischemia reperfusion induced less release of AIF and cytochrome c than in TBCA-treated WT mice. Inhibition of CK2 in gp91 KO mice subjected to ischemia reperfusion did not increase brain infarction compared with TBCA-treated WT mice. These results strongly suggest that NOX2 activation releases reactive oxygen species after CK2 inhibition, triggering release of apoptogenic factors from mitochondria and inducing DNA damage after ischemic brain injury.
The Promise of Service Learning in a Pediatric Audiology Course on Clinical Training With the Pediatric Population
Authors: Kaf Wafaa A. , Strong Elizabeth C.
Published: December 2011

Purpose

This study investigated the effectiveness of service learning (SL) and its impact on students’ clinical competency, interest in pediatric audiology as a career, and levels of community engagement, as well as its impact on the community.

Method

Forty-eight students enrolled in an SL pediatric audiology course providing hearing and middle ear testing to 292 children, ages 6 months to 5 years. Another 10 non-SL students served as a control group. SL surveys were administered to students before and after the SL experience and post hoc to the non-SL group to assess their perceived readiness for evaluating children and their interest in pediatric audiology. Parents and community partner staff members completed another survey to provide feedback about their experience with the SL activity.

Results

The students’ ratings were higher post-SL than pre-SL, and their learning gain was positively ranked post-SL compared with the non-SL group. Also, 71% of the SL students expressed positive interest in pediatric audiology post-SL compared with 37% of the non-SL group. Responses from community partners were also positive.

Conclusions

Embedding SL into a pediatric audiology course increased student interest in pediatric audiology as a career and enhanced readiness to evaluate young children.
Ear Asymmetries and Asymmetric Directional Microphone Hearing Aid Fittings
Authors: Cord Mary T. , Surr Rauna K. , Walden Brian E. , Dittberner Andrew B.
Published: December 2011

Purpose

To determine whether an asymmetry between ears for speech understanding in noise was related to performance with, or preference for, 1 of 2 asymmetric microphone fittings in which omnidirectional processing was provided to 1 ear and directional processing to the other.

Method

Twenty-eight adults with symmetric sensorineural hearing impairment were recruited from the clinic population. Sixteen individuals had symmetric hearing-in-noise ability between their right and left ears, and 12 participants had an asymmetry for speech understanding in noise between ears. A repeated measures design was used. Interactions between various microphone fittings and speech signal locations in noise were assessed in the laboratory. In addition, the listeners with asymmetry between ears for hearing in noise completed a field trial comparing the 2 fittings in everyday listening situations.

Results

Laboratory testing resulted in different patterns of performance for the 2 groups. Field trial results revealed that participants generally noticed little difference between the 2 fittings in everyday life and did not express a strong preference for 1 fitting over the other.

Conclusion

An asymmetry between ears for speech understanding in noise did not result in preference for 1 asymmetric fitting over the other in everyday listening situations.
Cortical High-Gamma Responses in Auditory Processing
Authors: Cervenka Mackenzie C. , Nagle Stephanie , Boatman-Reich Dana
Published: December 2011

Purpose

This tutorial provides an introduction to cortical auditory spectral responses, focusing on event-related activity in the high-gamma frequencies (60–150 Hz), their recent emergence in neuroscience research, and potential clinical applications.

Method

Auditory high-gamma responses are described and compared with traditional cortical evoked responses, including the auditory evoked N1 response. Methods for acquiring and analyzing spectral responses, including time-frequency analyses, are discussed and contrasted with more familiar time-domain averaging approaches. Four cases are presented illustrating high-gamma response patterns associated with normal and impaired auditory processing.

Conclusions

Cortical auditory high-gamma responses may provide a useful clinical measure of auditory processing.
Addressing Qualified Personnel Shortages for Children Who Are Deaf or Hard of Hearing With an Interdisciplinary Service Learning Program
Authors: Pakulski Lori A.
Published: December 2011

Purpose

To describe the student training benefits for speech-language pathology graduate students involved in an interdisciplinary, community-based intervention program at a Midwestern university for families of preschool children who were deaf or hard of hearing (DHH) and auditory-based spoken language users.

Method

The Auditory and Language Enriched Program was developed to provide graduate students with a clinically relevant service learning opportunity that also met some unique community needs of families in the community. Specifically, students learned to provide families with imaginative ways to expose their children who were DHH to language and literacy and nurture their natural curiosity and zest for learning.

Results

Statistically significant improvement was noted between pre- and postintervention questionnaires of knowledge and skill related to intervention for this population by a single group of students.

Conclusions

An interdisciplinary service learning approach to intervention might provide opportunities for university graduate programs to address the immediate and long-term needs of families who have chosen a spoken language outcome for their young children who are DHH while simultaneously providing invaluable experience with low-incidence populations for their preservice graduate students.
Carbon fiber reinforced polymer dimensional stability investigations for use on the laser interferometer space antenna mission telescope
Authors: Sanjuán J. , Preston A. , Korytov D. , Spector A. , Freise A. , Dixon G. , Livas J. , Mueller G.
Published: December 2011

The laser interferometer space antenna (LISA) is a mission designed to detect low frequency gravitational waves. In order for LISA to succeed in its goal of direct measurement of gravitational waves, many subsystems must work together to measure the distance between proof masses on adjacent spacecraft. One such subsystem, the telescope, plays a critical role as it is the laser transmission and reception link between spacecraft. Not only must the material that makes up the telescope support structure be strong, stiff, and light, but it must have a dimensional stability of better than 1 pm Hz−1/2 at 3 mHz and the distance between the primary and the secondary mirrors must change by less than 2.5 μm over the mission lifetime. Carbon fiber reinforced polymer is the current baseline material; however, it has not been tested to the pico meter level as required by the LISA mission. In this paper, we present dimensional stability results, outgassing effects occurring in the cavity and discuss its feasibility for use as the telescope spacer for the LISA spacecraft.
Extending cluster description to bimetallic nanowires: The ideal solid solution alloy case
Authors: Maras E. , Braems I. , Berthier F.
Published: December 2011

We present a comprehensive study of the equilibrium properties of two codeposited species for an alloy that forms an ideal solution, on a one-dimensional chain. By use of a cluster description we provide exact formulae of the coverages, the total density of clusters, the cluster size distribution, and the chemical composition of each cluster. These analytical results, that are proved to be in agreement with Monte Carlo simulations, strongly differ from the ones derived in the mean-field framework. Indeed, we show by depicting the codeposit at the macroscopic, mesoscopic, and atomic scales, that its features are to be related to the chemical heterogeneities at the edges of the clusters.
Fractal structures in two-metal electrodeposition systems I: Pb and Zn
Authors: Nakouzi Elias , Sultan Rabih
Published: December 2011

Pattern formation in two-metal electrochemical deposition has been scarcely explored in the chemical literature. In this paper, we report new experiments on zinc-lead fractal co-deposition. Electrodeposits are grown in special cells at a fixed large value of the zinc ion concentration, while that of the lead ion is increased gradually. A very wide diversity of morphologies are obtained and classified. Most of the deposited domains are almost exclusively Pb or Zn. But certain regions originating at the base cathode, ranging from a short grass alley to dense, grown-up bushes or shrubs, manifest a combined Pb-Zn composition. Composition is determined using scanning electron microscopy/energy dispersive x ray measurements as well atomic absorption spectroscopy. Pb domains are characterized by shiny leaf-like and dense deposits as well as flowers with round, balloon-like corollas. The Zn zones display a greater variety of morphologies such as thick trunks and thin and fine branching, in addition to minute “cigar flower” structures. The various morphologies are analyzed and classified from the viewpoint of fractal nature, characterized by the box-count fractal dimension. Finally, macroscopic spatial alternation between two different characteristic morphologies is observed under certain conditions.
High-Tc and high-Jc SmFeAs(O,F) films on fluoride substrates grown by molecular beam epitaxy
Authors: Ueda Shinya , Takeda Soichiro , Takano Shiro , Yamamoto Akiyasu , Naito Michio
Published: December 2011

Superconducting thin films of SmFeAs(O,F) were prepared by molecular beam epitaxy on fluoride substrates. In our process, F-free SmFeAsO films were grown first, and F was subsequently introduced to the films by diffusion from an overlayer of SmF3. By this simple process, record high Tc, namely, Tcon (Tcend) = 57.8 K (56.4 K) was obtained in a film on CaF2. Furthermore, the films on CaF2 showed high critical current density over 1 MA/cm2 in the self-field at 5 K. The correlation between superconductivity and epitaxial strain in SmFeAs(O,F) films is discussed.
Thermal exchange bias field drifts after 10 keV He ion bombardment: Storage temperature dependence and initial number of coupling sites
Authors: Schmidt Christoph , Weis Tanja , Engel Dieter , Ehresmann Arno
Published: December 2011

Sputter deposited Mn83Ir17(30 nm)/Co70Fe30(10 nm)/Ta thin films have been investigated for their thermal exchange bias field drift at different storage temperatures after 10 keV He+ ion bombardment in an externally applied in-plane magnetic field. It is experimentally shown that the drift coefficient in an intermediate time interval, as given in a recently developed model, is proportional to T and proportional to the initial number of coupling sites in the polycrystalline exchange bias layer system used.
Temperature dependent tuning of the flat band voltages of TiO2/Si interfaces
Authors: Nasim F. , Ali A. , Bhatti A. S. , Naseem S.
Published: December 2011

In this work, we present study of charge accumulation at the TiO2/Si interfaces and its variation in the TiO2 thin films sputter-deposited on n-Si, p-Si, and B-implanted Si substrates at various growth temperatures. TiO2 films, deposited in an oxygen deficient environment, showed significant growth of rutile phase and absence of anatase phase in the as-grown films. Annealing in air resulted in emergence of anatase phase, thus improving the ratio of anatase to rutile phase in TiO2 films. The flatband voltages determined from capacitance-voltage measurements were observed to be high in the rutile phase TiO2 and dropped considerably on annealing, due to formation of the anatase phase. The drop in the flatband voltages on annealing was also observed to depend strongly on the initial growth temperature. Films grown at high temperatures showed relatively low flatband voltages as compared to the films grown at room temperature. It is demonstrated that VFB strongly depends on the interface traps, and oxide-related defects were two orders of magnitude smaller than interface traps. The amount of depletion of the interface charge was found to depend on annealing. In the end, we also demonstrate that interface traps and oxide defects are not the only factors affecting the band bending, but the underlying substrate also plays an important role.
Hot carriers relaxation in highly excited polar semiconductors: Hot phonons versus phonon–plasmon coupling
Authors: Tea Eric , Hamzeh Hani , Aniel Frédéric
Published: December 2011

We present a study of the photo-excited charge carriers relaxation dynamics in polar semiconductors comparing calculations to pump probe experiments. Hot carrier densities in the 1018cm-3 range can easily be photo-generated using moderately intense optical excitations. This can lead to known phenomena, namely, hot phonon populations and the coupling of polar optical phonons with plasmon modes. However, these two phenomena can affect the hot carriers relaxation and have never been examined together. This is a problem for the theoretical study of future Hot Carrier Solar Cells, where the conditions allow both of these phenomena to occur. The charge carriers dynamics and the coupling of polar optical phonons with plasmon modes are treated by a Full Band Ensemble Monte Carlo simulation code featuring a self-consistent dielectric function. To take into consideration hot phonon populations and the subsequent phonon bottleneck for the carriers relaxation, the charge carriers simulation code is coupled to a phonon dedicated Ensemble Monte Carlo code. This enables for the first time an accurate study of both the charge carriers and phonon systems dynamics, the latter being most of the time overly simplified in previous studies. The present work explores to which extent the two aforementioned phenomena affect the photo-generated charge carriers relaxation in GaAs and can be easily adapted to other polar semiconductors.
Stable, biocompatible lipid vesicle generation by solvent extraction-based droplet microfluidics
Authors: Teh Shia-Yen , Khnouf Ruba , Fan Hugh , Lee Abraham P.
Published: December 2011

In this paper, we present a microfluidic platform for the continuous generation of stable, monodisperse lipid vesicles 20–110 μm in diameter. Our approach utilizes a microfluidic flow-focusing droplet generation design to control the vesicle size by altering the system’s fluid flow rates to generate vesicles with narrow size distribution. Double emulsions are first produced in consecutive flow-focusing channel geometries and lipid membranes are then formed through a controlled solvent extraction process. Since no strong solvents are used in the process, our method allows for the safe encapsulation and manipulation of an assortment of biological entities, including cells, proteins, and nucleic acids. The vesicles generated by this method are stable and have a shelf life of at least 3 months. Here, we demonstrate the cell-free in vitro synthesis of proteins within lipid vesicles as an initial step towards the development of an artificial cell.
Size dependent bandgap of molecular beam epitaxy grown InN quantum dots measured by scanning tunneling spectroscopy
Authors: Kumar Mahesh , Rajpalke Mohana K. , Bhat Thirumaleshwara N. , Roul Basanta , Kalghatgi A. T. , Krupanidhi S. B.
Published: December 2011

InN quantum dots (QDs) were grown on Si (111) by epitaxial Stranski-Krastanow growth mode using plasma-assisted molecular beam epitaxy. Single-crystalline wurtzite structure of InN QDs was verified by the x-ray diffraction and transmission electron microscopy. Scanning tunneling microscopy has been used to probe the structural aspects of QDs. A surface bandgap of InN QDs was estimated from scanning tunneling spectroscopy (STS) I-V curves and found that it is strongly dependent on the size of QDs. The observed size-dependent STS bandgap energy shifts with diameter and height were theoretical explained based on an effective mass approximation with finite-depth square-well potential model.
Modulating emission from acceptor in donor-acceptor diblock copolymers by plasmon resonance energy transfer
Authors: Kong Fan , Zhang Xueqin , Lang Xianzhong , Lin Baoping , Yang Yimin , Qiu Teng
Published: December 2011

We have investigated the optical properties of all-conjugated block copolymers, poly(2,5-dioctyloxy-p-phenylene)-b-poly[3-(2,5,8-trioxanonyl) thiophene] (PPP-b-P3TT), coupled silver nanocap array. The photoluminescence (PL) enhancement of the acceptor is increased with the mole fraction of the P3TT block in the coupled copolymer. The emission from the PPP blocks and the absorption of the P3TT blocks match the plasmon resonance frequency of the silver nanocap array. The emission from the PPP blocks is absorbed by the silver nanocap array to propagate surface plasmons or surface plasmon polaritons near the interfaces of the conjugated polymer/silver nanocap array, whose energies can be transferred to the P3TT blocks. As a result, more than 14-fold PL enhancement of the P3TT blocks has been observed in the coupled copolymer by photoexcitation at the absorption maximum of the PPP blocks.
Forming-free resistive switching behaviors in Cr-embedded Ga2O3 thin film memories
Authors: Lee Dai-Ying , Tseng Tseung-Yuen
Published: December 2011

Resistive switching behaviors are studied for the rapid thermal annealing (RTA) Ga2O3 thin film embedding a Cr metal layer. By modifying the thickness, area, and RTA temperature of the device, the thermal-induced resistive switching is similar to those induced by the electrical forming process. The conducting filaments composed of oxygen vacancies are created by the Cr diffusion and oxidization during RTA. The related carrier conduction mechanism obeys space charge limited conduction theory accompanied by the formation/rupture of the conducting filaments at the interface between Ti and Cr:Ga2O3 film. This study demonstrates a convenient process to fabricate forming-free resistive switching memory devices.
Gd plasma source modeling at 6.7 nm for future lithography
Authors: Li Bowen , Dunne Padraig , Higashiguchi Takeshi , Otsuka Takamitsu , Yugami Noboru , Jiang Weihua , Endo Akira , O’Sullivan Gerry
Published: December 2011

Plasmas containing gadolinium have been proposed as sources for next generation lithography at 6.x nm. To determine the optimum plasma conditions, atomic structure calculations have been performed for Gd11+ to Gd27+ ions which showed that n = 4 − n = 4 resonance transitions overlap in the 6.5–7.0 nm region. Plasma modeling calculations, assuming collisional-radiative equilibrium, predict that the optimum temperature for an optically thin plasma is close to 110 eV and that maximum intensity occurs at 6.76 nm under these conditions. The close agreement between simulated and experimental spectra from laser and discharge produced plasmas indicates the validity of our approach.
Multimode terahertz-wave generation using coherent Cherenkov radiation
Authors: Kan K. , Yang J. , Ogata A. , Kondoh T. , Norizawa K. , Yoshida Y.
Published: December 2011

Multimode terahertz(THz)-wave generation using coherent Cherenkov radiation (CCR) was investigated. The frequency spectra of CCR, which utilized a metal-wrapped hollow dielectric tube of 7 mm outer radius and a picosecond electron bunch of 27 MeV beam energy, were measured by a Michelson interferometer with a 4.2 K silicon bolometer. In this study, discrete spectral components at frequencies of 0.09, 0.14, and 0.36 THz were observed experimentally and explained as transverse magnetic (TM) modes of TM03, TM04, and TM09, respectively, according to a theoretical calculation for the tube.
Tunable singlet-triplet splitting in a few-electron Si/SiGe quantum dot
Authors: Shi Zhan , Simmons C. B. , Prance J. R. , King Gamble John , Friesen Mark , Savage D. E. , Lagally M. G. , Coppersmith S. N. , Eriksson M. A.
Published: December 2011

We measure the excited-state spectrum of a Si/SiGe quantum dot as a function of in-plane magnetic field and identify the spin of the lowest three eigenstates in an effective two-electron regime. We extract the singlet-triplet splitting, an essential parameter for spin qubits, from the data. We find it to be tunable by lateral displacement of the dot, which is realized by changing two gate voltages on opposite sides of the device. We present calculations showing the data are consistent with a spectrum in which the first excited state of the dot is a valley-orbit state.
The two dimensional electron system as a nanoantenna in the microwave and terahertz bands
Authors: Iñarrea Jesús
Published: December 2011

We study the magnetoresistance of two-dimensional electron systems under several radiation sources of different frequencies for moderate power. We use the model of radiation-driven electron orbits extended to this regime. First, we consider the case of two different radiations and we find a regime of superposition or interference of harmonic motions, i.e., a modulated magnetoresistance response with pulses and beats. Finally, we consider a multiple photoexcitation case where we propose the two-dimensional electron system as a potential nanoantenna device or ultrasensitive detector for the microwave and terahertz bands. Thus, these results could be of special interest in nanophotonics and nanoelectronics.
Transient capacitance of light-emitting electrochemical cells
Authors: Davis Y. A. , Crooker P. P. , Haegel N. M. , Yoshioka Y. , MacKenzie J. D.
Published: December 2011

We present time-dependent measurements of the capacitance, current, and optical emission of light-emitting electrochemical cells as a constant voltage bias is applied and removed. We find that the capacitance increases more rapidly than the light or current and can be oscillatory in time. The transient behavior suggests that the capacitance is determined by a combination of ion distribution, free carrier screening and junction width.
Note: Automated maskless micro-multidomain photoalignment
Authors: Culbreath Christopher , Glazar Nikolaus , Yokoyama Hiroshi
Published: December 2011

We present a fully automated maskless exposure system for the fabrication of microscopic orientational surface alignment patterns. The maskless system allows us to fabricate arbitrary surface patterns over a 2 mm × 2 mm area with a resolution of 2.2 μm. A confocal autofocus system insures accurate and repeatable focus. Microscopic orientational surface patterns have been demonstrated to exhibit a variety of novel functionalities, such as surface alignment multi-stability.
Charge transfer complex states in diketopyrrolopyrrole polymers and fullerene blends: Implications for organic solar cell efficiency
Authors: Moghe D. , Yu P. , Kanimozhi C. , Patil S. , Guha S.
Published: December 2011

The spectral photocurrent characteristics of two donor-acceptor diketopyrrolopyrrole (DPP)-based copolymers (PDPP-BBT and TDPP-BBT) blended with a fullerene derivative [6,6]-phenyl C61-butyric acid methyl ester (PCBM) were studied using Fourier-transform photocurrent spectroscopy (FTPS) and monochromatic photocurrent (PC) method. PDPP-BBT:PCBM shows the onset of the lowest charge transfer complex (CTC) state at 1.42 eV, whereas TDPP-BBT:PCBM shows no evidence of the formation of a midgap CTC state. The FTPS and PC spectra of P3HT:PCBM are also compared. The larger singlet state energy difference of TDPP-BBT and PCBM compared to PDPP-BBT/P3HT and PCBM obliterates the formation of a midgap CTC state resulting in an enhanced photovoltaic efficiency over PDPP-BBT:PCBM.
Strong visible and near infrared luminescence in undoped YAG single crystals
Authors: Varney C. R. , Reda S. M. , Mackay D. T. , Rowe M. C. , Selim F. A.
Published: December 2011

Strong luminescence peaks were observed at 700 and 800 nm in undoped yttrium aluminum garnet (YAG) single crystals. They were attributed to low level of iron impurities as confirmed by Glow Discharge Mass Spectrometry analysis. The 800 nm was only excited by high energy band at 270 nm; the reason behind that was discussed. Photoluminescence measurements revealed a large number of luminescence peaks in all YAG crystals regardless of the growth conditions due to native defects and low-level impurities. These luminescence centers have significant effects on the optical properties of rare-earth doped YAG crystals and their performance in laser and scintillation applications. Excitons released in the lattice may be easily captured by iron ions instead of Ce3+ ions and the scintillation output is substantially decreased. Nevertheless, Undoped YAG crystals may have the potential to be developed into efficient scintillators.
Place-Specific Economic Base Multipliers
Authors: Mulligan Gordon F , Vias Alex C
Published: December 2011

There is now wide realization that US nonmetropolitan areas are remarkably heterogeneous. Consequently the estimation of employment multipliers should address the diverse attributes and settings of these regions. In response, in this paper we outline a means for estimating cross-sectional economic base multipliers that vary from one place to another. Multipliers of this sort can be used to assess the impacts of new projects but should not be used to forecast growth. The discussion focuses on America's micropolitan counties, which are those significant urban clusters located outside of the nation's metropolitan areas. The multiplier estimates account for numerous contextual conditions of both the natural and human-created variety. All estimates are made from employment data pooled across the 1980, 1990, and 2000 censuses. Micropolitan counties with high human capital, low specialization, abundant natural amenities, and isolated locations have relatively more local employment and therefore larger multipliers.
Efficient Synthesis of Ellagic Acid Salts Using Distillable Ionic Liquids
Authors: Chowdhury Shahana A. , Dean Pamela M. , Vijayaraghavan R. , MacFarlane D. R.
Published: December 2011

A direct, one pot synthesis of an ellagic acid salt was achieved at room temperature by dimerization of ethyl gallate using N,N-dimethylammonium N′,N′-dimethylcarbamate, a distillable ionic liquid, as solvent.
An exploratory analysis of active and low energy behaviour in Australian adolescents
Authors: Roydhouse Jessica K. , Allman-Farinelli Margaret , McGeechan Kevin , Ferrar Katia , Olds Timothy
Published: December 2011

Adolescents engage in a complex range of low energy-consuming and active behaviours not easily captured by single behavioural measures. This study aims to describe the associations among adolescent active and low energy behaviours. Data were obtained from adolescents aged 12–16 years (n = 1532) participating in a nationally representative survey. Thirty-nine variables measuring activities were stratified by sex and age and then analysed using principal components analysis with Varimax rotation. Four components were derived for younger girls (21.7% of the variance) and younger boys (20.2%), six for older girls (29.7%) and five for older boys (25.6%). Academic-related behaviours positively correlated with each other and negatively with television use for all age–sex groups. Computer use correlated positively with academic-related behaviours for older boys but negatively with active behaviours for younger boys and girls. Active behaviours correlated positively with each other. For older girls, low energy expenditure, household-based behaviours were negatively correlated with active behaviours. Computer use appears to differ across age groups, and leisure and academic use should be differentiated. The positive associations among different active behaviours and their negative associations with home-based, low energy expenditure behaviours are of interest for intervention development.
Harbouring pests: rabbit warrens in agricultural landscapes
Authors: Barrio I. C. , Villafuerte R. , Tortosa F. S.
Published: December 2011

Context
Warrens are central to rabbit biology and available warren space can set a limit to the number of rabbits living in an area. Therefore, quantifying and analysing the distribution of rabbit warrens is a key step towards the management of the species in agricultural lands where it causes significant damage to crops.

Aims
The present study investigates the distribution and spatial pattern of wild rabbit (Oryctolagus cuniculus) warrens in an intensively managed agricultural landscape within the rabbit’s native range in semiarid southern Spain, where rabbits constitute an emerging pest problem.

Methods
All natural rabbit warrens within two sites were mapped, and information on their size, use and protection was recorded. The effects of environmental variables (e.g. habitat features and distances to key resources) in determining warren occurrence were evaluated using binomial generalised linear models (GLM).

Key results
The main variable explaining warren occurrence was the distance to the nearest neighbouring warren. Habitat variables and the distances to key resources played only a secondary role, and were mainly related to frequent ploughing linked to agricultural practices that prevent warren construction.

Conclusions
Habitat instability resulting from agricultural practices (i.e. frequent ploughing and intensive human disturbance) promotes warren construction on stable grounds only and partly explains the clumped spatial pattern found. However, warren occurrence in intensively managed agricultural areas seems to be more constrained by the proximity of neighbouring warrens that would facilitate rabbit recolonisation from patches nearby. Despite becoming increasingly scarce as a result of agricultural intensification, these unploughed remnants may act as safe islands for digging warrens.

Implications
The management of unploughed patches and the connectivity among them in semiarid agroecosystems of southern Spain is therefore of utmost importance to the management of rabbits as an agricultural pest.
Cullin 3 mediates SRC-3 ubiquitination and degradation to control the retinoic acid response
Authors: Ferry Christine , Gaouar Samia , Fischer Benoit , Boeglin Marcel , Paul Nicodeme , Samarut Eric , Piskunov Aleksandr , Pankotai-Bodo Gabriella , Brino Laurent , Rochette-Egly Cecile
Published: December 2011

SRC-3 is an important coactivator of nuclear receptors including the retinoic acid (RA) receptor α. Most of SRC-3 functions are facilitated by changes in the posttranslational code of the protein that involves mainly phosphorylation and ubiquitination. We recently reported that SRC-3 is degraded by the proteasome in response to RA. Here, by using an RNAi E3-ubiquitin ligase entry screen, we identified CUL-3 and RBX1 as components of the E3 ubiquitin ligase involved in the RA-induced ubiquitination and subsequent degradation of SRC-3. We also show that the RA-induced ubiquitination of SRC-3 depends on its prior phosphorylation at serine 860 that promotes binding of the CUL-3–based E3 ligase in the nucleus. Finally, phosphorylation, ubiquitination, and degradation of SRC-3 cooperate to control the dynamics of transcription. In all, this process participates to the antiproliferative effect of RA.
HORIZONTAL EUROPEANISATION IN CONTEXTUAL PERSPECTIVE
Authors: Mau Steffen , Mewes Jan
Published: December 2011

In the current discourse it is frequently stated that in the course of European integration and globalisation we witness more intensified and more frequent transactions spanning across national borders. These assumptions relate not only to transactions in the economic sphere or to forms of political co-operation, but to the individual lifeworlds as well. Yet concerning the latter dimension, research into the patterns and dynamics of interpersonal interaction, relationships, and forms of mobility across national borders is scarce. This paper is a contribution towards filling this research lacuna. It addresses the question of the extent to which horizontal Europeanisation, understood as different forms of individual cross-border activities within the European Union, depends on characteristics at the country level. From a comparative perspective we will analyse the transnational mobility and cross-border networks of European citizens within a European context. Empirically, we refer to data from the Eurobarometer 65.1 (2006), which allows us to answer the question how certain contextual variables, such as internationalisation, modernisation, and characteristics such as the respective country's geography, affect people's participation in cross-border activities. Based on a sample of 25 European countries, we will demonstrate that geographic characteristics drive social transnationalism less than internationalisation, Europeanisation, and modernisation, which contribute to a proliferation of individual transnational activities across the European Union.
Satellite observations make it possible to estimate Poyang Lake’s water budget
Authors: Feng Lian , Hu Chuanmin , Chen Xiaoling , Li Rongfang
Published: December 2011

Using moderate resolution imaging spectroradiometer (MODIS) satellite imagery with hydrologic and meteorological data, we developed a box model to estimate the water exchange between Poyang Lake (the largest freshwater lake of China) and the Changjiang (Yangtze) River from 2000 to 2009. Significant intra- and inter-annual variability of the water budget was found, with an annual mean outflow of Poyang Lake of 120.2 ± 31.2 billion m3 during 2000–2009 and a declining trend of 5.7 billion m3 yr−1 (p = 0.09). The impoundment of the Three Gorges Dam (TGD) on the Changjiang River in June 2003 led to a rapid lake–river outflow of 760.6 million m3 day−1, resulting in a loss of 7864.5 million m3 of water from the lake in a short period. Shortly thereafter, a statistically significant decrease in the drainage basin’s runoff coefficient was discovered. These findings provide large-scale evidence on how local precipitation and the TGD control the lake’s water budget, where continuous monitoring using the established approach and satellite data may provide critical information to help make water management decisions.
Patterns of change: whose fingerprint is seen in global warming?
Authors: Hegerl Gabriele , Zwiers Francis , Tebaldi Claudia
Published: December 2011

Attributing observed climate change to causes is challenging. This letter communicates the physical arguments used in attribution, and the statistical methods applied to explore to what extent different possible causes can be used to explain the recent climate records. The methods use fingerprints of climate change that are identified on the basis of the physics governing our climate system, and through the use of climate model experiments. These fingerprints characterize the geographical and vertical pattern of the expected changes caused by external influences, for example, greenhouse gas increases and changes in solar radiation, taking also into account how these forcings and their effects vary over time. These time–space fingerprints can be used to discriminate between observed climate changes caused by different external factors. Attribution assessments necessarily take the natural variability of the climate system into account as well, evaluating whether an observed change can be explained in terms of this internal variability alone, and estimating the contribution of this source of variability to the observed change. Hence the assessment that a large part of the observed recent warming is anthropogenic is based on a rigorous quantitative analysis of these joint drivers and their effects, and proceeds through a much more comprehensive and layered analysis than a comparison at face value of model simulations with observations.
Optimized application of penalized regression methods to diverse genomic data
Authors: Waldron Levi , Pintilie Melania , Tsao Ming-Sound , Shepherd Frances A. , Huttenhower Curtis , Jurisica Igor
Published: December 2011

Motivation: Penalized regression methods have been adopted widely for high-dimensional feature selection and prediction in many bioinformatic and biostatistical contexts. While their theoretical properties are well-understood, specific methodology for their optimal application to genomic data has not been determined.

Results: Through simulation of contrasting scenarios of correlated high-dimensional survival data, we compared the LASSO, Ridge and Elastic Net penalties for prediction and variable selection. We found that a 2D tuning of the Elastic Net penalties was necessary to avoid mimicking the performance of LASSO or Ridge regression. Furthermore, we found that in a simulated scenario favoring the LASSO penalty, a univariate pre-filter made the Elastic Net behave more like Ridge regression, which was detrimental to prediction performance. We demonstrate the real-life application of these methods to predicting the survival of cancer patients from microarray data, and to classification of obese and lean individuals from metagenomic data. Based on these results, we provide an optimized set of guidelines for the application of penalized regression for reproducible class comparison and prediction with genomic data.

Availability and Implementation: A parallelized implementation of the methods presented for regression and for simulation of synthetic data is provided as the pensim R package, available at http://cran.r-project.org/web/packages/pensim/index.html.

Contact:  chuttenh@hsph.harvard.edu; juris@ai.utoronto.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Short-term choice behaviour in a mixed fishery: investigating métier selection in the Danish gillnet fishery
Authors: Andersen Bo Sølgaard , Ulrich Clara , Eigaard Ole Ritzau , Christensen Anne-Sofie
Published: December 2011

Andersen, B. S., Ulrich, C., Eigaard, O. R., and Christensen, A-S. 2012. Short-term choice behaviour in a mixed fishery: investigating métier selection in the Danish gillnet fishery. – ICES Journal of Marine Science, 69: 131–143. The study presents a short-term effort allocation modelling approach based on a discrete choice random utility model combined with a survey questionnaire to examine the selection of métiers (a combination of fishing area and target species) in the Danish North Sea gillnet fishery. Key decision variables were identified from the survey questionnaire, and relevant proxies for the decision function were identified based on available landings and effort information. Additional variables from the survey questionnaire were further used to validate and verify the outcome of the choice model. Commercial fishers in a mixed fishery make use of a number of decision variables used previously in the literature, but also a number of decision parameters rarely explicitly accounted for, such as price, weather, and management regulation. The seasonal availability of individual target species and within-year changes in monthly catch ration were the main explanatory drivers, but gillnetters were also responsive to information on the whole fishery, fish prices, and distance travelled to fishing grounds. Heterogeneous responses were evident from geographic differences in home harbour, which underpins the need to understand alternative fishing strategies among individual gillnetters better.
Modelling non-stationary natural mortality in catch-at-age models
Authors: Jiao Yan , Smith Eric P. , O'Reilly Rob , Orth Donald J.
Published: December 2011

Jiao, Y., Smith, E. P., O'Reilly, R., and Orth, D. J. 2012. Modelling non-stationary natural mortality in catch-at-age models. – ICES Journal of Marine Science, 69: 105–118. Non-stationarity in the natural mortality of many species has been discussed among research scientists, but no generally applicable models/methods have been developed where a statistical catch-at-age (SCA) model framework is used. Using the Atlantic weakfish (Cynoscion regalis) fishery as an example, several SCA models are developed to assess the population dynamics, then compared. Models used included (i) an SCA with constant natural mortality, (ii) an SCA with unknown natural mortality, but with a hierarchical prior distribution from a mixture of distributions based on life-history information, (iii) an SCA with age-specific unknown natural mortality, (iv) an SCA with time-varying natural mortality, following a random-walk process, and (v) an SCA with age-specific time-varying natural mortality. The last two models imply that the population dynamics are not stationary. A Bayesian approach was used to estimate parameters, and performance of the models was compared through goodness-of-fit and the retrospective patterns of the models. A simulation study was then conducted to test the uncertainty resulting from model selection, the efficiency of using the best model selected based on deviance information criterion, and whether changes in natural mortality could be detected. An SCA with time-varying natural mortality, following a random-walk process, is proposed for the example fishery here. The estimated non-stationary temporal patterns in natural mortality were linked further to climate–ocean oscillation indices, to diagnose possible mechanisms/linkages to these temporal variations in natural mortality.
Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses
Authors: Rosenzweig Noah , Tiedje James M. , Quensen John F. , Meng Qingxiao , Hao Jianjun J.
Published: December 2011

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.
Efficacy and Stability of Integrating Fungicide and Cultivar Resistance to Manage Fusarium Head Blight and Deoxynivalenol in Wheat
Authors: Willyerd K. T. , Li C. , Madden L. V. , Bradley C. A. , Bergstrom G. C. , Sweets L. E. , McMullen M. , Ransom J. K. , Grybauskas A. , Osborne L. , Wegulo S. N. , Hershman D. E. , Wise K. , Bockus W. W. , Groth D. , Dill-Macky R. , Milus E. , Esker P. D. , Waxman K. D. , Adee E. A. , Ebelhar S. E. , Young B. G. , Paul P. A.
Published: December 2011

Integration of host resistance and prothioconazole + tebuconazole fungicide application at anthesis to manage Fusarium head blight (FHB) and deoxynivalenol (DON) in wheat was evaluated using data from over 40 trials in 12 U.S. states. Means of FHB index (index) and DON from up to six resistance class–fungicide management combinations per trial (susceptible treated [S_TR] and untreated [S_UT]; moderately susceptible treated [MS_TR] and untreated [MS_UT]; moderately resistant treated [MR_TR] and untreated [MR_UT]) were used in multivariate meta-analyses, and mean log response ratios across trials were estimated and transformed to estimate mean percent control ([Formula: see text]) due to the management combinations relative to S_UT. All combinations led to a significant reduction in index and DON (P < 0.001). MR_TR was the most effective combination, with a [Formula: see text] of 76% for index and 71% for DON, followed by MS_TR (71 and 58%, respectively), MR_UT (54 and 51%, respectively), S_TR (53 and 39%, respectively), and MS_UT (43 and 30%, respectively). Calculations based on the principle of treatment independence showed that the combination of fungicide application and resistance was additive in terms of percent control for index and DON. Management combinations were ranked based on percent control relative to S_UT within each trial, and nonparametric analyses were performed to determine management combination stability across environments (trials) using the Kendall coefficient of concordance (W). There was a significant concordance of management combinations for both index and DON (P < 0.001), indicating a nonrandom ranking across environments and relatively low variability in the within-environment ranking of management combinations. MR_TR had the highest mean rank (best control relative to S_UT) and was one of the most stable management combinations across environments, with low rank stability variance (0.99 for index and 0.67 for DON). MS_UT had the lowest mean rank (poorest control) but was also one of the most stable management combinations. Based on Piepho's nonparametric rank-based variance homogeneity U test, there was an interaction of management combination and environment for index (P = 0.011) but not for DON (P = 0.147), indicating that the rank ordering for index depended somewhat on environment. In conclusion, although the magnitude of percent control will likely vary among environments, integrating a single tebuconazole + prothioconazole application at anthesis with cultivar resistance will be a more effective and stable management practice for both index and DON than either approach used alone.