bluuebunny/crossref_metadata_2025 huggingface dataset:
Knee morphometric risk factors for acute anterior cruciate ligament injury in skeletally immature patients
Authors: Shaw K. Aaron , Dunoski Brian , Mardis Neil , Pacicca Donna
Published: March 2015

Study design

Retrospective, case–control.

Purpose

Knee morphometric risk factors for noncontact anterior cruciate ligament (ACL) injury have been a popular topic with skeletally mature patients. Little research has focused on the skeletally immature, with conflicting conclusions. This study performs a comprehensive analysis of identified parameters thought to predispose to ACL injury in a skeletally immature cohort.

Methods

A retrospective review of pediatric patients undergoing knee magnetic resonance imaging (MRI) was performed over a 4-year period. Inclusionary criteria included mid-substance ACL disruption, skeletal immaturity, noncontact injury, without associated ligamentous disruption, and no medical condition associated with ligamentous laxity. MRI studies were analyzed by a pediatric musculoskeletal radiologist, measuring identified bony parameters, and compared with an age-matched control group without ligamentous injury. Data were analyzed using unpaired t-tests and logistic regression.

Results

One hundred and twenty-eight patients sustained an ACL disruption, 39 met all inclusionary criteria (66 excluded for associated ligamentous disruption, 23 skeletally mature, three traumatic mechanisms, one with Marfan syndrome). When compared to an age-matched control cohort, the notch width index (NWI) was found to be significantly smaller in the ACL-injured group ( p = 0.046). Subgroups analysis demonstrated significant differences in morphometric parameters between subjects with isolated ACL injuries and concomitant medial collateral ligament (MCL) strain.

Conclusions

The NWI was significantly smaller in the ACL injury group. Significant differences were noted between isolated ACL injuries and ACL injuries with an MCL strain. This study further highlights the need for incorporating associated injury patterns when investigating the influence of morphometric factors for ACL injury in the skeletally immature.

Level of evidence

Level III.
Predicting adolescent's cyberbullying behavior: A longitudinal risk analysis
Authors: Barlett Christopher P.
Published: March 2015

The current study used the risk factor approach to test the unique and combined influence of several possible risk factors for cyberbullying attitudes and behavior using a four‐wave longitudinal design with an adolescent US sample. Participants (N = 96; average age = 15.50 years) completed measures of cyberbullying attitudes, perceptions of anonymity, cyberbullying behavior, and demographics four times throughout the academic school year. Several logistic regression equations were used to test the contribution of these possible risk factors. Results showed that (a) cyberbullying attitudes and previous cyberbullying behavior were important unique risk factors for later cyberbullying behavior, (b) anonymity and previous cyberbullying behavior were valid risk factors for later cyberbullying attitudes, and (c) the likelihood of engaging in later cyberbullying behavior increased with the addition of risk factors. Overall, results show the unique and combined influence of such risk factors for predicting later cyberbullying behavior. Results are discussed in terms of theory.
Understanding affluent adolescent adjustment: The interplay of parental perfectionism, perceived parental pressure, and organized activity involvement
Authors: Randall Edin T. , Bohnert Amy M. , Travers Lea V.
Published: March 2015

This cross‐sectional study examined relations between affluent adolescent adjustment and culturally salient factors within parent–child relationship and extracurricular domain. Bootstrapping techniques evaluated mediated effects among parental perfectionism, perceived parental pressure, intensity of organized activity (OA) involvement, and adolescent adjustment (i.e., depressive and anxiety symptoms, life satisfaction) within a sample of 10th graders and their parents (n = 88 parent–child pairs) from four high schools in affluent communities. Findings indicated that adolescents with more perfectionistic parents perceived more parental pressure and experienced poorer adjustment. Results also demonstrated that affluent adolescents who perceived more parental pressure were more intensely involved in OAs, but that higher OA intensity was linked to better adjustment. Findings highlight the importance of considering parental perfectionism when understanding adolescent behaviors and psychological outcomes, confirm the negative direct effects of parental pressure on adjustment, and corroborate prior research dispelling that highly intense OA involvement is linked to adolescent maladjustment.
Safety Culture and Care: A Program to Prevent Surgical Errors
Authors: Hemingway Maureen White , O'Malley Catherine , Silvestri Sandra
Published: March 2015

Surgical errors are under scrutiny in health care as part of ensuring a culture of safety in which patients receive quality care. Hospitals use safety measures to compare their performance against industry benchmarks. To understand patient safety issues, health care providers must have processes in place to analyze and evaluate the quality of the care they provide. At one facility, efforts made to improve its quality and safety led to the development of a robust safety program with resources devoted to enhancing the culture of safety in the Perioperative Services department. Improvement initiatives included changing processes for safety reporting and performance improvement plans, adding resources and nurse roles, and creating communication strategies around adverse safety events and how to improve care. One key outcome included a 54% increase in the percentage of personnel who indicated in a survey that they would speak up if they saw something negatively affecting patient care.
Diffusive boundary layers over varying topography
Authors: Dell R. W. , Pratt L. J.
Published: March 2015

Diffusive bottom boundary layers can produce upslope flows in a stratified fluid. Accumulating observations suggest that these boundary layers may drive upwelling and mixing in mid-ocean ridge flank canyons. However, most studies of diffusive bottom boundary layers to date have concentrated on constant bottom slopes. We present a study of how diffusive boundary layers interact with various idealized topography, such as changes in bottom slope, slopes with corrugations and isolated sills. We use linear theory and numerical simulations in the regional ocean modeling system (ROMS) model to show changes in bottom slope can cause convergences and divergences within the boundary layer, in turn causing fluid exchanges that reach far into the overlying fluid and alter stratification far from the bottom. We also identify several different regimes of boundary-layer behaviour for topography with oceanographically relevant size and shape, including reversing flows and overflows, and we develop a simple theory that predicts the regime boundaries, including what topographies will generate overflows. As observations also suggest there may be overflows in deep canyons where the flow passes over isolated bumps and sills, this parameter range may be particularly significant for understanding the role of boundary layers in the deep ocean.
The Effect of Exercise and Distraction on Blood Pressure Recovery Following an Anger-Provoking Stressor in Normotensive Young Adults
Authors: Routledge Faye S. , McFetridge-Durdle Judith A. , Macdonald Marilyn , Breau Lynn , Campbell Tavis
Published: March 2015

Ruminating about a prior anger provoking event is found to elevate blood pressure (BP) and delay BP recovery. Delayed BP recovery may be associated with increased risk of hypertension. Interventions that improve BP recovery may be beneficial for cardiovascular health. The purposes of this study were to evaluate the influence of rumination and anger on BP reactivity and recovery, to compare the effect of an exercise intervention or distraction intervention on BP recovery and to explore if exercise improved BP recovery by distracting participants from stressor-related rumination and anger. Healthy, normotensive participants (n = 79, mean age 22.2 ± 4.0 years) underwent an anger-recall interview stressor task, 3 min of exercise (walking), distraction (reading) or no-intervention (quiet sitting) and a 15 min recovery period. State anger reactivity was associated with Δ diastolic (D) BP reactivity and approached significance with Δ systolic (S) BP reactivity. Trait rumination was associated with greater SBP during recovery. Δ SBP recovery did not differ between the exercise, distraction and no-intervention groups. Although there were no differences in Δ DBP recovery between the exercise and no-intervention groups, distraction improved Δ DBP recovery compared to the exercise intervention but not the no-intervention. The proportion of anger-related thoughts (state rumination) in the exercise group did not differ from the distraction or no-intervention groups. However, a smaller proportion of participants in the distraction intervention reported an anger-related thought during recovery compared to the no-intervention group with 76% of their thoughts relating to the provided distraction. Overall, post-stressor exercise was not found to improve BP recovery while reading was effective at distracting individuals from angry thoughts (state rumination) but had no effect on BP compared to no-intervention.
Body Position Influences Cardiovascular Disgust Reactivity
Authors: Schienle Anne , Übel Sonja , Rössler Andreas , Schwerdtfeger Andreas , Karl Lackner Helmut
Published: March 2015

It has been suggested that elevated trait disgust constitutes a vulnerability factor for fainting episodes. We tested the hypothesis that disgust-prone individuals are susceptible to vasovagal syncope by means of a tilt table experiment, during which 30 women were presented with disgusting pictures in a supine and a 70° upright position. The results showed that relative to disgust elicitation in the supine position, tilting reduced diastolic blood pressure during disgust elicitation, which could indicate increased risk for presyncope. Moreover, self-reported disgust proneness was positively correlated with heart rate during disgust induction in the tilted position. This association may point to a compensatory mechanism that aims at stabilizing mean arterial pressure. Disgust-prone individuals possibly utilized this mechanism more extensively to prevent fainting. Future investigations with a longer duration should follow up on this finding and compare the onset of presyncope between high and low disgust-prone individuals.
A Study of Teacher–Learner Interactions: A Continuum Between Monologic and Dialogic Interactions
Authors: Kathard Harsha , Pillay Daisy , Pillay Mershen
Published: March 2015

Purpose

Teachers and learners must be able to shift flexibly along the continuum of monologic and dialogic interactional repertoires to advance learning. This article describes how teachers and learners interacted during whole-class instruction along the continuum between monologic and dialogic interaction in primary school classrooms in Western Cape, South Africa.

Method

A video-observation method was used to analyze teacher–learner interactions (TLIs) across 15 lessons in intermediate-phase classrooms. TLIs were analyzed in relation to indicators such as authority, questions, feedback, explanation, metalevel connection, and collaboration. The transcriptions of TLIs were described using quantitative and qualitative techniques.

Results

The study found that teachers sustained dominant monologic interactions by asserting their authority, asking mainly closed-ended questions, and providing confirming/correcting feedback that constrained the interaction. Learners had limited opportunities for explanations or collaboration. Across most lessons, there were episodic shifts from monologic TLIs to transitional TLIs. These transitions were achieved by using mainly open-ended questions and feedback to expand the interaction. Dialogic TLIs were not evident.

Conclusions

Monologic TLIs were dominant, closing down opportunities for communication. Although transitional TLIs were evident, they were episodic and showed the potential for opening interaction opportunities. The absence of dialogic TLIs suggested that collaborative engagement opportunities were unavailable. The opportunity for intervention to increase dialogic TLIs is discussed.
Call for Studies in Implementation Science: Improving Reading Comprehension in School-Age Children
Authors: Nippold Marilyn A.
Published: March 2015

Purpose

In this article, the Editor of
Language, Speech, and Hearing Services in Schools
makes the case for more studies in implementation science in order to improve the reading comprehension of school-age children, particularly those with specific language impairment and nonspecific language impairment.
Electrolyte pore/solution partitioning by expanded grand canonical ensemble Monte Carlo simulation
Authors: Moucka Filip , Bratko Dusan , Luzar Alenka
Published: March 2015

Using a newly developed grand canonical Monte Carlo approach based on fractional exchanges of dissolved ions and water molecules, we studied equilibrium partitioning of both components between laterally extended apolar confinements and surrounding electrolyte solution. Accurate calculations of the Hamiltonian and tensorial pressure components at anisotropic conditions in the pore required the development of a novel algorithm for a self-consistent correction of nonelectrostatic cut-off effects. At pore widths above the kinetic threshold to capillary evaporation, the molality of the salt inside the confinement grows in parallel with that of the bulk phase, but presents a nonuniform width-dependence, being depleted at some and elevated at other separations. The presence of the salt enhances the layered structure in the slit and lengthens the range of inter-wall pressure exerted by the metastable liquid. Solvation pressure becomes increasingly repulsive with growing salt molality in the surrounding bath. Depending on the sign of the excess molality in the pore, the wetting free energy of pore walls is either increased or decreased by the presence of the salt. Because of simultaneous rise in the solution surface tension, which increases the free-energy cost of vapor nucleation, the rise in the apparent hydrophobicity of the walls has not been shown to enhance the volatility of the metastable liquid in the pores.
Femtosecond transient infrared and stimulated Raman spectroscopy shed light on the relaxation mechanisms of photo-excited peridinin
Authors: Di Donato Mariangela , Ragnoni Elena , Lapini Andrea , Foggi Paolo , Hiller Roger G. , Righini Roberto
Published: March 2015

By means of one- and two-dimensional transient infrared spectroscopy and femtosecond stimulated Raman spectroscopy, we investigated the excited state dynamics of peridinin, a carbonyl carotenoid occurring in natural light harvesting complexes. The presence of singly and doubly excited states, as well as of an intramolecular charge transfer (ICT) state, makes the behavior of carbonyl carotenoids in the excited state very complex. In this work, we investigated by time resolved spectroscopy the relaxation of photo-excited peridinin in solvents of different polarities and as a function of the excitation wavelength. Our experimental results show that a characteristic pattern of one- and two-dimensional infrared bands in the C=C stretching region allows monitoring the relaxation pathway. In polar solvents, moderate distortions of the molecular geometry cause a variation of the single/double carbon bond character, so that the partially ionic ICT state is largely stabilized by the solvent reorganization. After vertical photoexcitation at 400 nm of the S2 state, the off-equilibrium population moves to the S1 state with ca. 175 fs time constant; from there, in less than 5 ps, the non-Franck Condon ICT state is reached, and finally, the ground state is recovered in 70 ps. That the relevant excited state dynamics takes place far from the Franck Condon region is demonstrated by its noticeable dependence on the excitation wavelength.
A prototype hand-held tri-modal instrument for in vivo ultrasound, photoacoustic, and fluorescence imaging
Authors: Kang Jeeun , Chang Jin Ho , Wilson Brian C. , Veilleux Israel , Bai Yanhui , DaCosta Ralph , Kim Kang , Ha Seunghan , Lee Jong Gun , Kim Jeong Seok , Lee Sang-Goo , Kim Sun Mi , Lee Hak Jong , Ahn Young Bok , Han Seunghee , Yoo Yangmo , Song Tai-Kyong
Published: March 2015

Multi-modality imaging is beneficial for both preclinical and clinical applications as it enables complementary information from each modality to be obtained in a single procedure. In this paper, we report the design, fabrication, and testing of a novel tri-modal in vivo imaging system to exploit molecular/functional information from fluorescence (FL) and photoacoustic (PA) imaging as well as anatomical information from ultrasound (US) imaging. The same ultrasound transducer was used for both US and PA imaging, bringing the pulsed laser light into a compact probe by fiberoptic bundles. The FL subsystem is independent of the acoustic components but the front end that delivers and collects the light is physically integrated into the same probe. The tri-modal imaging system was implemented to provide each modality image in real time as well as co-registration of the images. The performance of the system was evaluated through phantom and in vivo animal experiments. The results demonstrate that combining the modalities does not significantly compromise the performance of each of the separate US, PA, and FL imaging techniques, while enabling multi-modality registration. The potential applications of this novel approach to multi-modality imaging range from preclinical research to clinical diagnosis, especially in detection/localization and surgical guidance of accessible solid tumors.
Experimental apparatus with full optical access for combustion experiments with laminar flames from a single circular nozzle at elevated pressures
Authors: Joo Peter H. , Gao Jinlong , Li Zhongshan , Aldén Marcus
Published: March 2015

The design and features of a high pressure chamber and burner that is suitable for combustion experiments at elevated pressures are presented. The high pressure combustion apparatus utilizes a high pressure burner that is comprised of a chamber burner module and an easily accessible interchangeable burner module to add to its flexibility. The burner is well suited to study both premixed and non-premixed flames. The optical access to the chamber is provided through four viewports for direct visual observations and optical-based diagnostic techniques. Auxiliary features include numerous access ports and electrical connections and as a result, the combustion apparatus is also suitable to work with plasmas and liquid fuels. Images of methane flames at elevated pressures up to 25 atm and preliminary results of optical-based measurements demonstrate the suitability of the high pressure experimental apparatus for combustion experiments.
Structure and dynamics of POPC bilayers in water solutions of room temperature ionic liquids
Authors: Benedetto Antonio , Bingham Richard J. , Ballone Pietro
Published: March 2015

Molecular dynamics simulations in the NPT ensemble have been carried out to investigate the effect of two room temperature ionic liquids (RTILs), on stacks of phospholipid bilayers in water. We consider RTIL compounds consisting of chloride ([bmim][Cl]) and hexafluorophosphate ([bmim][PF6]) salts of the 1-buthyl-3-methylimidazolium ([bmim]+) cation, while the phospholipid bilayer is made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our investigations focus on structural and dynamical properties of phospholipid and water molecules that could be probed by inelastic and quasi-elastic neutron scattering measurements. The results confirm the fast incorporation of [bmim]+ into the lipid phase already observed in previous simulations, driven by the Coulomb attraction of the cation for the most electronegative oxygens in the POPC head group and by sizeable dispersion forces binding the neutral hydrocarbon tails of [bmim]+ and of POPC. The [bmim]+ absorption into the bilayer favours the penetration of water into POPC, causes a slight but systematic thinning of the bilayer, and further stabilises hydrogen bonds at the lipid/water interface that already in pure samples (no RTIL) display a lifetime much longer than in bulk water. On the other hand, the effect of RTILs on the diffusion constant of POPC (DPOPC) does not reveal a clearly identifiable trend, since DPOPC increases upon addition of [bmim][Cl] and decreases in the [bmim][PF6] case. Moreover, because of screening, the electrostatic signature of each bilayer is only moderately affected by the addition of RTIL ions in solution. The analysis of long wavelength fluctuations of the bilayers shows that RTIL sorption causes a general decrease of the lipid/water interfacial tension and bending rigidity, pointing to the destabilizing effect of RTILs on lipid bilayers.
Variational cross-validation of slow dynamical modes in molecular kinetics
Authors: McGibbon Robert T. , Pande Vijay S.
Published: March 2015

Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics and slow dynamical modes of biomolecular systems. However, the lack of a unified theoretical framework for choosing between alternative models has hampered progress, especially for non-experts applying these methods to novel biological systems. Here, we consider cross-validation with a new objective function for estimators of these slow dynamical modes, a generalized matrix Rayleigh quotient (GMRQ), which measures the ability of a rank-m projection operator to capture the slow subspace of the system. It is shown that a variational theorem bounds the GMRQ from above by the sum of the first m eigenvalues of the system’s propagator, but that this bound can be violated when the requisite matrix elements are estimated subject to statistical uncertainty. This overfitting can be detected and avoided through cross-validation. These result make it possible to construct Markov state models for protein dynamics in a way that appropriately captures the tradeoff between systematic and statistical errors.
The role of Ag buffer layer in Fe islands growth on Ge (111) surfaces
Authors: Fu Tsu-Yi , Wu Jia-Yuan , Jhou Ming-Kuan , Hsu Hung-Chan
Published: March 2015

Sub-monolayer iron atoms were deposited at room temperature on Ge (111)-c(2 × 8) substrates with and without Ag buffer layers. The behavior of Fe islands growth was investigated by using scanning tunneling microscope (STM) after different annealing temperatures. STM images show that iron atoms will cause defects and holes on substrates at room temperature. As the annealing temperature rises, iron atoms pull out germanium to form various kinds of alloyed islands. However, the silver layer can protect the Ag/Ge(111)-(√3×√3) reconstruction from forming defects. The phase diagram shows that ring, dot, and triangular defects were only found on Ge (111)-c(2 × 8) substrates. The kinds of islands found in Fe/Ge system are similar to Fe/Ag/Ge system. It indicates that Ge atoms were pulled out to form islands at high annealing temperatures whether there was a Ag layer or not. But a few differences in big pyramidal or strip islands show that the silver layer affects the development of islands by changing the surface symmetry and diffusion coefficient. The structure characters of various islands are also discussed.
Existence domains of slow and fast ion-acoustic solitons in two-ion space plasmas
Authors: Maharaj S. K. , Bharuthram R. , Singh S. V. , Lakhina G. S.
Published: March 2015

A study of large amplitude ion-acoustic solitons is conducted for a model composed of cool and hot ions and cool and hot electrons. Using the Sagdeev pseudo-potential formalism, the scope of earlier studies is extended to consider why upper Mach number limitations arise for slow and fast ion-acoustic solitons. Treating all plasma constituents as adiabatic fluids, slow ion-acoustic solitons are limited in the order of increasing cool ion concentrations by the number densities of the cool, and then the hot ions becoming complex valued, followed by positive and then negative potential double layer regions. Only positive potentials are found for fast ion-acoustic solitons which are limited only by the hot ion number density having to remain real valued. The effect of neglecting as opposed to including inertial effects of the hot electrons is found to induce only minor quantitative changes in the existence regions of slow and fast ion-acoustic solitons.
Far-field measurements of short-wavelength surface plasmons
Authors: Blau Yochai , Gjonaj Bergin , David Asaf , Dolev Shimon , Shterman Doron , Bartal Guy
Published: March 2015

We present direct far-field measurements of short-wavelength surface plasmon polaritons (SPP) by conventional optics means. Plasmonic wavelength as short as 231 nm was observed for 532 nm illumination on a Ag−Si3N4 platform, demonstrating the capability to characterize SPPs well below the optical diffraction limit. This is done by scaling a sub-wavelength interferometric pattern to a far-field resolvable periodicity. These subwavelength patterns are obtained by coupling light into counter-propagating SPP waves to create a standing-wave pattern of half the SPP wavelength periodicity. Such patterns are mapped by a scattering slit, tilted at an angle so as to increase the periodicity of the intensity pattern along it to more than the free-space wavelength, making it resolvable by diffraction limited optics. The simplicity of the method as well as its large dynamic range of measurable wavelengths make it an optimal technique to characterize the properties of plasmonic devices and high-index dielectric waveguides, to improve their design accuracy and enhance their functionality.
On calculating the potential vorticity flux
Authors: Hsu Pei-Chun , Diamond P. H.
Published: March 2015

We discuss and compare different approaches to calculating the dynamics of anisotropic flow structure formation in quasi two-dimensional turbulence based on potential vorticity (PV) transport in real space. The general structure of the PV flux in the relaxation processes is deduced non-perturbatively. The transport coefficients of the PV flux are then systematically calculated using perturbation theory. We develop two non-perturbative relaxation models: the first is a mean field theory for the dynamics of minimum enstrophy relaxation based on the requirement that the mean flux of PV dissipates total potential enstrophy but conserves total fluid kinetic energy. The results show that the structure of PV flux has the form of a sum of a positive definite hyper-viscous and a negative or positive viscous flux of PV. Turbulence spreading is shown to be related to PV mixing via the link of turbulence energy flux to PV flux. In the relaxed state, the ratio of the PV gradient to zonal flow velocity is homogenized. This homogenized quantity sets a constraint on the amplitudes of PV and zonal flow in the relaxed state. The second relaxation model is derived from symmetry principles alone. The form of PV flux contains a nonlinear convective term in addition to viscous and hyper-viscous terms. For both cases, the transport coefficients are calculated using perturbation theory. For a broad turbulence spectrum, a modulational calculation of the PV flux gives both a negative viscosity and a positive hyper-viscosity. For a narrow turbulence spectrum, the result of a parametric instability analysis shows that PV transport is also convective. In both relaxation and perturbative analyses, it is shown that turbulent PV transport is sensitive to flow structure, and the transport coefficients are nonlinear functions of flow shear.
Thermally activated coercivity in core-shell permanent magnets
Authors: Bance S. , Fischbacher J. , Schrefl T.
Published: March 2015

Finite element micromagnetic simulations are used to compute the temperature-dependent hysteresis properties of Nd2Fe14B permanent magnets in order to assess the influence of a hard (Dy,Nd)2Fe14B shell. The simulations show that the 4 nm thick shell cancels out the reduction in coercivity from an outer defect layer, which is known to exist at the grain boundaries in NdFeB permanent magnets. Activation volumes are computed and shown to depend on the structure's configuration as well as the temperature.
Magnetization processes in core/shell exchange-spring structures
Authors: Jiang J. S.
Published: March 2015

The magnetization reversal processes in cylindrical and spherical soft core/hard shell exchange-spring structures are investigated via the analytical nucleation theory and are verified with numerical micromagnetic simulations. At small core sizes, the nucleation of magnetic reversal proceeds via the modified bulging mode, where the transverse component of the magnetization is only semi-coherent in direction and the nucleation field contains a contribution from self-demagnetization. For large core sizes, the modified curling mode, where the magnetization configuration is vortex-like, is favored at nucleation. The preference for the modified curling mode is beneficial in that the flux-closure allows cylindrical and spherical core/shell exchange-spring elements to be densely packed into bulk permanent magnets without affecting the nucleation field, thereby offering the potential for high energy product.
Influence of controlled surface oxidation on the magnetic anisotropy of Co ultrathin films
Authors: Di N. , Kubal J. , Zeng Z. , Greeley J. , Maroun F. , Allongue P.
Published: March 2015

We studied the influence of controlled surface-limited oxidation of electrodeposited epitaxial Co(0001)/Au(111) films on their magnetic anisotropy energy using real time in situ magneto optical Kerr effect and density functional theory (DFT) calculations. We investigated the Co first electrochemical oxidation step which we demonstrate to be completely reversible and determined the structure of this oxide layer. We show that the interface magnetic anisotropy of the Co film increases by 0.36 erg/cm2 upon Co surface oxidation. We performed DFT calculations to determine the different surface structures in a wide potential range as well as the charge transfer at the Co surface. Our results suggest that the magnetic anisotropy change is correlated with a positive charge increase of 0.54 e− for the Co surface atom upon oxidation.
Generation of a magnetic island by edge turbulence in tokamak plasmas
Authors: Poyé A. , Agullo O. , Muraglia M. , Garbet X. , Benkadda S. , Sen A. , Dubuit N.
Published: March 2015

We investigate, through extensive 3D magneto-hydro-dynamics numerical simulations, the nonlinear excitation of a large scale magnetic island and its dynamical properties due to the presence of small-scale turbulence. Turbulence is induced by a steep pressure gradient in the edge region [B. D. Scott, Plasma Phys. Controlled Fusion 49, S25 (2007)], close to the separatrix in tokamaks where there is an X-point magnetic configuration. We find that quasi-resonant localized interchange modes at the plasma edge can beat together and produce extended modes that transfer energy to the lowest order resonant surface in an inner stable zone and induce a seed magnetic island. The island width displays high frequency fluctuations that are associated with the fluctuating nature of the energy transfer process from the turbulence, while its mean size is controlled by the magnetic energy content of the turbulence.
A General Method Towards Efficient Synthesis and Fluorescence Tuning of Carbon Black-Derived Carbon Dots via Controlled Liquid Oxidization
Authors: Yuan Haoran , Li Denian , Liu Yan , Xiong Chuanxi
Published: March 2015

Efficient synthesis and controlled modification of carbon dots (CDs) with tuneable properties on the basis of facile technical routes are of great significance for user-defined applications as well as more insightful understanding of the unique fluorescence from carbon nanomaterials. In this work, we report an improved nitric acid oxidization method towards low-cost and rapid preparation of fluorescent CDs. This is achieved by using industrial carbon black specimens as the precursor and implementing a reduced pressure distillation for the purpose of eliminating excessive acids. Unexpectedly, the product exhibits an interesting dual luminescence behaviour with tuneable characteristics that differs from all previously reported CDs. The strongest emissions at fixed or varied excitations can be simultaneously tuned from blue to green or yellow by simply prolonging the time of acid oxidization. These emissions show distinct stabilities in acid and alkaline environments, thereby making the resultant CDs very promising candidates for pH probes. It is further revealed that this simple synthesis and fluorescence tuning strategy is also applicable to CDs from other carbon blacks.
Assessing allele-specific expression across multiple tissues from RNA-seq read data
Authors: Pirinen Matti , Lappalainen Tuuli , Zaitlen Noah A. ,   GTEx Consortium, Dermitzakis Emmanouil T. , Donnelly Peter , McCarthy Mark I. , Rivas Manuel A.
Published: March 2015

Motivation: RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.

Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally.

Availability and implementation: http://www.well.ox.ac.uk/~rivas/mamba/. R-sources and data examples http://www.iki.fi/mpirinen/

Contact: matti.pirinen@helsinki.fi or rivas@well.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer’s disease
Authors: Agarwal Swapna , Ghanty Pradip , Pal Nikhil R.
Published: March 2015

Motivation: Alzheimer’s disease (AD) is a dementia that gets worse with time resulting in loss of memory and cognitive functions. The life expectancy of AD patients following diagnosis is ∼7 years. In 2006, researchers estimated that 0.40% of the world population (range 0.17–0.89%) was afflicted by AD, and that the prevalence rate would be tripled by 2050. Usually, examination of brain tissues is required for definite diagnosis of AD. So, it is crucial to diagnose AD at an early stage via some alternative methods. As the brain controls many functions via releasing signalling proteins through blood, we analyse blood plasma proteins for diagnosis of AD.

Results: Here, we use a radial basis function (RBF) network for feature selection called feature selection RBF network for selection of plasma proteins that can help diagnosis of AD. We have identified a set of plasma proteins, smaller in size than previous study, with comparable prediction accuracy. We have also analysed mild cognitive impairment (MCI) samples with our selected proteins. We have used neural networks and support vector machines as classifiers. The principle component analysis, Sammmon projection and heat-map of the selected proteins have been used to demonstrate the proteins’ discriminating power for diagnosis of AD. We have also found a set of plasma signalling proteins that can distinguish incipient AD from MCI at an early stage. Literature survey strongly supports the AD diagnosis capability of the selected plasma proteins.

Availability and implementation: The FSRBF code is available at https://sites.google.com/site/agarwalswapna/publications.

Contact: agarwal.swapna@gmail.com or swapna_r@isical.ac.in

Supplementary information: Supplementary data are available at Bioinformatics online.
The impact of dust in host galaxies on quasar luminosity functions
Authors: Shirakata Hikari , Okamoto Takashi , Enoki Motohiro , Nagashima Masahiro , Kobayashi Masakazu A. R. , Ishiyama Tomoaki , Makiya Ryu
Published: March 2015

We have investigated effects of dust attenuation on quasar luminosity functions at z ∼ 2 using a semi-analytic galaxy formation model combined with a large cosmological N-body simulation. We estimate the dust attenuation of quasars self-consistently with that of galaxies by considering the dust in their host bulges. We find that the luminosity of the bright quasars is strongly dimmed by the dust attenuation, ∼2 mag in the B-band. Assuming the empirical bolometric corrections for active galactic nuclei (AGNs) by Marconi et al., we find that this dust attenuation is too strong to explain the B-band and X-ray quasar luminosity functions simultaneously. We consider two possible mechanisms that weaken the dust attenuation. As such a mechanism, we introduce a time delay for AGN activity, that is, gas fuelling to a central black hole starts sometime after the beginning of the starburst induced by a major merger. The other is the anisotropy in the dust distribution. We find that in order to make the dust attenuation of the quasars negligible, either the gas accretion into the black holes has to be delayed at least three times the dynamical time-scale of their host bulges or the dust covering factor is as small as ∼0.1.
Computational Analysis of Kilohertz Frequency Spinal Cord Stimulation for Chronic Pain Management
Authors: Lempka Scott F. , McIntyre Cameron C. , Kilgore Kevin L. , Machado Andre G.
Published: March 2015

AbstractAbstract

Using a computational model, it was shown that kilohertz frequency spinal cord stimulation (KFSCS) used at clinical intensities probably does not cause the direct activation or conduction block of dorsal column or dorsal root fibers. Possible sites of action for KFSCS to be explored include synaptic terminals, cell bodies, and dendrites. Computational analyses suggest that KFSCS for pain management may not function through direct activation or conduction block of spinal cord fibers, and alternative concepts should be explored and evaluated.

Background:

Kilohertz frequency spinal cord stimulation (KHFSCS) is an emerging therapy for treating refractory neuropathic pain. Although KHFSCS has the potential to improve the lives of patients experiencing debilitating pain, its mechanisms of action are unknown and thus it is difficult to optimize its development. Therefore, the goal of this study was to use a computer model to investigate the direct effects of KHFSCS on specific neural elements of the spinal cord.

Methods:

This computer model consisted of two main components: (1) finite element models of the electric field generated by KHFSCS and (2) multicompartment cable models of axons in the spinal cord. Model analysis permitted systematic investigation into a number of variables (e.g., dorsal cerebrospinal fluid thickness, lead location, fiber collateralization, and fiber size) and their corresponding effects on excitation and conduction block thresholds during KHFSCS.

Results:

The results of this study suggest that direct excitation of large-diameter dorsal column or dorsal root fibers require high stimulation amplitudes that are at the upper end or outside of the range used in clinical KHFSCS (i.e., 0.5 to 5 mA). Conduction block was only possible within the clinical range for a thin dorsal cerebrospinal fluid layer.

Conclusions:

These results suggest that clinical KHFSCS may not function through direct activation or conduction block of dorsal column or dorsal root fibers. Although these results should be validated with further studies, the authors propose that additional concepts and/or alternative hypotheses should be considered when examining the pain relief mechanisms of KHFSCS.
Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended descriptions of the genus Octadecabacter and its species and reclassification of Octadecabacter jejudonensis

Park and Yoon 2014

as Pseudooctadecabacter jejudonensis gen. nov., comb. nov.
Authors: Billerbeck Sara , Orchard Julia , Tindall Brian J. , Giebel Helge-Ansgar , Brinkhoff Thorsten , Simon Meinhard
Published: March 2015

A heterotrophic, Gram-negative, aerobic bacterium, designated strain SB1T, was isolated from surface water of the southern North Sea. Comparison of 16S rRNA gene sequences revealed that strain SB1T is affiliated to the genus Octadecabacter within the marine Roseobacter clade (family Rhodobacteraceae), with Octadecabacter antarcticus as the closest described species (98.2 % sequence similarity to the type strain). DNA–DNA hybridization indicated that SB1T represents a distinct species within this genus. On marine agar, strain SB1T formed beige, circular and convex colonies. Cells were irregular, motile rods. Growth occurred between 4 and 25 °C and was optimal at 20 °C, and at pH 7–9 (optimum pH 7.5–8.5) and NaCl concentrations between 1 and 6 % (optimum 2–4 %). The DNA G+C content of SB1T was 54.7 mol%. The fatty acids (>1 %) comprised 10 : 0 3-OH, 12 : 1 3-OH, 16 : 1ω7c, 16 : 0, 18 : 2ω7,12, 18 : 1ω7c, 18 : 0 and 11-methyl 18 : 1ω7c. The sole respiratory lipoquinone was ubiquinone Q-10 and the polar lipid pattern indicated the presence of the phospholipids phosphatidylglycerol and phosphatidylcholine, as well as unidentified aminolipid AL1, phospholipids PL1 and PL3 and lipids L1, L2 and L4. On the basis of phylogenetic and phenotypic differences, strain SB1T represents a novel species in the genus Octadecabacter, for which we propose the name Octadecabacter temperatus sp. nov. The type strain is SB1T ( = DSM 26878T = LMG 27946T). Furthermore, our results suggest the reclassification of Octadecabacter jejudonensis as the type species of a new genus, Pseudooctadecabacter gen. nov., as Pseudooctadecabacter jejudonensis comb. nov. (type strain SSK2-1T = KCTC 32535T = CECT 8397T). Finally, emended descriptions of the genus Octadecabacter and its species Octadecabacter antarcticus and Octadecabacter arcticus are also provided.
Index-based map-to-sequence alignment in large eukaryotic genomes
Authors: Verzotto Davide , Teo Audrey S.M. , Hillmer Axel M. , Nagarajan Niranjan
Published: March 2015

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kbp–2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging due to the lack of efficient and freely available software for robustly aligning maps to sequences. Here we introduce two new map-to-sequence alignment algorithms that efficiently and accurately align high-throughput mapping datasets to large, eukaryotic genomes while accounting for high error rates. In order to do so, these methods (OPTIMA for glocal and OPTIMA-Overlap for overlap alignment) exploit the ability to create efficient data structures that index continuous-valued mapping data while accounting for errors. We also introduce an approach for evaluating the significance of alignments that avoids expensive permutation-based tests while being agnostic to technology-dependent error rates. Our benchmarking results suggest that OPTIMA and OPTIMA-Overlap outperform state-of-the-art approaches in sensitivity (1.6–2× improvement) while simultaneously being more efficient (170–200%) and precise in their alignments (99% precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust and provide improved sensitivity while guaranteeing high precision.
Visual cues determine hippocampal directional selectivity
Authors: Acharya Lavanya , M. Aghajan Zahra , Vuong Cliff , Moore Jason J. , Mehta Mayank R.
Published: March 2015

Both spatial and directional information are necessary for navigation. Rodent hippocampal neurons show spatial selectivity in all environments1, but directional tuning only on linear paths2–8.The sensory mechanisms underlying directionality are unknown, though vestibular and visual cues are thought to be crucial. However, hippocampal neurons are thought to show no angular modulation during two-dimensional random foraging despite the presence of vestibular and visual cues6,7. Additionally, specific aspects of visual cues have not been directly linked to hippocampal responses in rodents. To resolve these issues we manipulated vestibular and visual cues in a series of experiments. We first measured hippocampal activity during random foraging in real world (RW) where we found that neurons’ firing exhibited significant modulation by head-direction. In fact, the fraction of modulated neurons was comparable to that in the head-direction system9. These findings are contrary to commonly held beliefs about hippocampal directionality6,7. To isolate the contribution of visual cues we measured neural responses in a visually similar virtual reality (VR) where the range of vestibular inputs is minimized5,10,11. Significant directional modulation was not only found in VR, but it was comparable to that in RW. Several additional experiments revealed that changes in the angular information contained in the visual cues induced corresponding changes in hippocampal head-directional modulation. Remarkably, for head-directionally modulated neurons, the ensemble activity was biased towards the sole visual cue. These results demonstrate that robust vestibular cues are not required for hippocampal directional selectivity, while visual cues are not only sufficient but also play a causal role in driving hippocampal responses.
Medicago truncatula Natural Resistance-Associated Macrophage Protein1 Is Required for Iron Uptake by Rhizobia-Infected Nodule Cells
Authors: Tejada-Jiménez Manuel , Castro-Rodríguez Rosario , Kryvoruchko Igor , Lucas M. Mercedes , Udvardi Michael , Imperial Juan , González-Guerrero Manuel
Published: March 2015

Iron is critical for symbiotic nitrogen fixation (SNF) as a key component of multiple ferroproteins involved in this biological process. In the model legume Medicago truncatula, iron is delivered by the vasculature to the infection/maturation zone (zone II) of the nodule, where it is released to the apoplast. From there, plasma membrane iron transporters move it into rhizobia-containing cells, where iron is used as the cofactor of multiple plant and rhizobial proteins (e.g. plant leghemoglobin and bacterial nitrogenase). MtNramp1 (Medtr3g088460) is the M. truncatula Natural Resistance-Associated Macrophage Protein family member, with the highest expression levels in roots and nodules. Immunolocalization studies indicate that MtNramp1 is mainly targeted to the plasma membrane. A loss-of-function nramp1 mutant exhibited reduced growth compared with the wild type under symbiotic conditions, but not when fertilized with mineral nitrogen. Nitrogenase activity was low in the mutant, whereas exogenous iron and expression of wild-type MtNramp1 in mutant nodules increased nitrogen fixation to normal levels. These data are consistent with a model in which MtNramp1 is the main transporter responsible for apoplastic iron uptake by rhizobia-infected cells in zone II.