bluuebunny/crossref_metadata_2025 huggingface dataset:
On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water
Authors: Bieler Noah S. , Hünenberger Philippe H.
Published: April 2015

Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical problem of how to properly sample these states, along with achieving a sufficient number of interconversion transitions. In this study, the two issues are addressed in the context of a decaalanine peptide in water, by considering the 310-, α-, and π-helical states. The simulations rely on the ball-and-stick local-elevation umbrella-sampling (B&S-LEUS) method. In this scheme, the states are defined as hyperspheres (balls) in a (possibly high dimensional) collective-coordinate space and connected by hypercylinders (sticks) to ensure transitions. A new object, the pipe, is also introduced here to handle curvilinear pathways. Optimal sampling within the so-defined space is ensured by confinement and (one-dimensional) memory-based biasing potentials associated with the three different kinds of objects. The simulation results are then analysed in terms of free energies using reweighting, possibly relying on two distinct sets of collective coordinates for the state definition and analysis. The four possible choices considered for these sets are Cartesian coordinates, hydrogen-bond distances, backbone dihedral angles, or pairwise sums of successive backbone dihedral angles. The results concerning decaalanine underline that the concept of conformational state may be extremely ambiguous, and that its tentative absolute definition as a free-energy basin remains subordinated to the choice of a specific analysis space. For example, within the force-field employed and depending on the analysis coordinates selected, the 310-helical state may refer to weakly overlapping collections of conformations, differing by as much as 25 kJ mol−1 in terms of free energy. As another example, the π-helical state appears to correspond to a free-energy basin for three choices of analysis coordinates, but to be unstable with the fourth one. The problem of conformational-state definition may become even more intricate when comparison with experiment is involved, where the state definition relies on spectroscopic or functional observables.
Fabrication and characterization of spin injector using a high-quality B2-ordered-Co2FeSi0.5Al0.5/MgO/Si(100) tunnel contact
Authors: Kawame Yu , Akushichi Taiju , Takamura Yota , Shuto Yusuke , Sugahara Satoshi
Published: April 2015

We successfully fabricate a (100)-orientated B2-type-Co2FeSi0.5Al0.5 (CFSA)/MgO/Si(100) tunnel contact that is promising for an efficient spin injector for Si channels. The MgO barrier is formed by radical oxidation of an Mg thin film deposited on a Si(100) surface at room temperature and successive radical oxygen annealing at 400 °C. The CFSA electrode is grown on the MgO barrier at 400 °C by ultrahigh-vacuum molecular beam deposition, and it exhibits a (100)-orientated columnar polycrystalline structure with a high degree (63%) of B2-order. The MgO barrier near the interface of the CFSA/MgO junction is crystallized with the (100) orientation, i.e., the spin filter effect due to the MgO barrier could be expected for this junction. A three-terminal Si-channel spin-accumulation device with a CFSA/MgO/Si(100) spin injector is fabricated, and the Hanle effect of accumulated spin polarized electrons injected from this contact to the Si channel is observed.
Detection of current-driven magnetic domains in [Co/Pd] nanowire by tunneling magnetoresistive sensor
Authors: Okuda Mitsunobu , Miyamoto Yasuyoshi , Miyashita Eiichi , Saito Nobuo , Hayashi Naoto , Nakagawa Shigeki
Published: April 2015

Current-driven magnetic domain walls in magnetic nanowires have attracted a great deal of interest in terms of both physical studies and engineering applications. The anomalous Hall effect measurement is widely used for detecting the magnetization direction of current-driven magnetic domains in a magnetic nanowire. However, the problem with this measurement is that the detection point for current-driven domain wall motion is fixed at only the installed sensing wire across the specimen nanowire. A potential solution is the magnetic domain scope method, whereby the distribution of the magnetic flux leaking from the specimen can be analyzed directly by contact-scanning a tunneling magnetoresistive field sensor on a sample. In this study, we fabricated specimen nanowires consisting of [Co (0.3)/Pd (1.2)]21/Ta(3) films (units in nm) with perpendicular magnetic anisotropy on Si substrates. A tunneling magnetoresistive sensor was placed on the nanowire surface and a predetermined current pulse was applied. Real-time detection of the current-driven magnetic domain motion was successful in that the resistance of the tunneling magnetoresistive sensor was changed with the magnetization direction beneath the sensor. This demonstrates that magnetic domain detection using a tunneling magnetoresistive sensor is effective for the direct analysis of micro magnetic domain motion.
Dynamical screening of van der Waals interactions in nanostructured solids: Sublimation of fullerenes
Authors: Tao Jianmin , Yang Jing , Rappe Andrew M.
Published: April 2015

Sublimation energy is one of the most important properties of molecular crystals, but it is difficult to study, because the attractive long-range van der Waals (vdW) interaction plays an important role. Here, we apply efficient semilocal density functional theory (DFT), corrected with the dynamically screened vdW interaction (DFT + vdW), the Rutgers-Chalmers nonlocal vdW-DF, and the pairwise-based dispersion-corrected DFT-D2 developed by Grimme and co-workers, to study the sublimation of fullerenes. We find that the short-range part, which accounts for the interaction due to the orbital overlap between fullerenes, is negligibly small. Our calculation shows that there exists a strong screening effect on the vdW interaction arising from the valence electrons of fullerenes. On the other hand, higher-order contributions can be as important as the leading-order term. The reasons are that (i) the surface of fullerene molecules is metallic and thus highly polarizable, (ii) the band gap of fullerene solids is small (less than 2 eV), and (iii) fullerene molecules in the solid phase are so densely packed, yielding the high valence electron density and small equilibrium intermolecular distances (the first nearest neighbor distance is only about 10 Å for C60). However, these two effects make opposite contributions, leading to significant error cancellation between these two contributions. We demonstrate that, by considering higher-order contributions and the dynamical screening, the DFT + vdW method can yield sublimation energies of fullerenes in good agreement with reference values, followed by vdW-DF and DFT-D2. The insights from this study are important for a better understanding of the long-range nature of vdW interactions in nanostructured solids.
Measurement at microwave frequencies of the magnetic properties of small quantities of powdered or diluted samples
Authors: Pura Jose Luis , Muñoz José María , Alejos Óscar , Hernández-Gómez Pablo , Torres Carlos
Published: April 2015

Transmission line techniques are a convenient way to determine the electromagnetic properties of a variety of materials in the ranges of radio and microwave frequencies. Traditional methods based on the measurement of the four scattering parameters can be successfully replaced for the method presented here, in which no change in the geometry is needed, since two independent measurements are carried out, with and without an applied magnetic field. In addition, given the small size of the sample holder, the required amount of material can be drastically reduced, and allow the use of a lumped circuit model, then reducing the inherent difficulties associated with the use of distributed parameters. Even though this kind of model requires the involved wavelengths to be much larger than the size of the system, this requirement can be overcome as long as the tested materials have relative ϵ or μ lower than 100. Furthermore, the use of short-circuited transmission lines simplifies sample holding and systematizes the measurement process, which is an important target when dealing with measurements within the radio and microwave frequency ranges.
Pd/Ag coated fiber Bragg grating sensor for hydrogen monitoring in power transformers
Authors: Ma G. M. , Jiang J. , Li C. R. , Song H. T. , Luo Y. T. , Wang H. B.
Published: April 2015

Compared with conventional DGA (dissolved gas analysis) method for on-line monitoring of power transformers, FBG (fiber Bragg grating) hydrogen sensor represents marked advantages over immunity to electromagnetic field, time-saving, and convenience to defect location. Thus, a novel FBG hydrogen sensor based on Pd/Ag (Palladium/Silver) along with polyimide composite film to measure dissolved hydrogen concentration in large power transformers is proposed in this article. With the help of Pd/Ag composite coating, the enhanced performance on mechanical strength and sensitivity is demonstrated, moreover, the response time and sensitivity influenced by oil temperature are solved by correction lines. Sensitivity measurement and temperature calibration of the specific hydrogen sensor have been done respectively in the lab. And experiment results show a high sensitivity of 0.055 pm/(μl/l) with instant response time about 0.4 h under the typical operating temperature of power transformers, which proves a potential utilization inside power transformers to monitor the health status by detecting the dissolved hydrogen concentration.
Theoretical analysis of the background intensity distribution in X-ray Birefringence Imaging using synchrotron bending-magnet radiation
Authors: Sutter John P. , Dolbnya Igor P. , Collins Stephen P. , Harris Kenneth D. M. , Edwards-Gau Gregory R. , Palmer Benjamin A.
Published: April 2015

In the recently developed technique of X-ray Birefringence Imaging, molecular orientational order in anisotropic materials is studied by exploiting the birefringence of linearly polarized X-rays with energy close to an absorption edge of an element in the material. In the experimental setup, a vertically deflecting high-resolution double-crystal monochromator is used upstream from the sample to select the appropriate photon energy, and a horizontally deflecting X-ray polarization analyzer, consisting of a perfect single crystal with a Bragg reflection at Bragg angle of approximately 45°, is placed downstream from the sample to measure the resulting rotation of the X-ray polarization. However, if the experiment is performed on a synchrotron bending-magnet beamline, then the elliptical polarization of the X-rays out of the electron orbit plane affects the shape of the output beam. Also, because the monochromator introduces a correlation between vertical position and photon energy to the X-ray beam, the polarization analyzer does not select the entire beam, but instead selects a diagonal stripe, the slope of which depends on the Bragg angles of the monochromator and the polarization analyzer. In the present work, the final background intensity distribution is calculated analytically because the phase space sampling methods normally used in ray traces are too inefficient for this setup. X-ray Birefringence Imaging data measured at the Diamond Light Source beamline B16 agree well with the theory developed here.
Spontaneous phase separation during self-assembly in bi-dispersed spherical iron oxide nanoparticle monolayers
Authors: Stanley Jacob , Boucheron Leandra , Lin Binhua , Meron Mati , Shpyrko Oleg
Published: April 2015

Recent developments in the synthesis of iron oxide nanoparticles have resulted in the ability to fabricate roughly spherical particles with extremely high size uniformity (low polydispersity). These particles can form self-assembled monolayer films at an air-water interface. When the polydispersity of the particles is low, these monolayers can be well-ordered over a length scale dozens of times the particle size. The van der Waals force between the particles is what drives this self-assembly. Through the use of Grazing Incidence X-Ray Diffraction we demonstrate that, when these films are formed at the liquid surface from bi-dispersed solutions containing 10 and 20 nm spherical particles suspended in chloroform, the particles phase separate into well-ordered patches during the self-assembly process. Furthermore, the domain sizes of these phase separated regions are at most 2–3 times smaller than that of a film comprising only mono-dispersed particles and their degree of disorder is comparable. This is shown for multiple solutions with differing ratios of 10 and 20 nm particles.
Anisotropic magnetoresistance effect in sub-micron nickel disks
Authors: Wren T. , Kazakova O.
Published: April 2015

The hysteretic transport properties of vortex states in sub-micron nickel disks are measured using the anisotropic magnetoresistance (AMR) effect and correlated with the magnetization state of the disks using in-situ magnetic force microscopy and micromagnetic modelling. The magnetoresistance behavior is described by a simple AMR model; however, the nucleation and annihilation fields of the vortex state differ when the magnetic field is applied parallel (0°) or perpendicular (90°) to the applied current within the sample plane. In the 0° orientation, the vortex magnetoresistance behaves similar to that reported in the literature. However, in the 90° orientation, the vortex nucleates and annihilates at lower applied fields than in the 0° orientation. Moreover, in the latter orientation, the annihilation process occurs in a two-step transition. This difference is attributed to the effect of the inhomogeneous current distribution within the magnetic disk.
Oxygen-induced immediate onset of the antiferromagnetic stacking in thin Cr films on Fe(001)
Authors: Berti Giulia , Brambilla Alberto , Calloni Alberto , Bussetti Gianlorenzo , Finazzi Marco , Duò Lamberto , Ciccacci Franco
Published: April 2015

We investigated the magnetic coupling of ultra-thin Cr films grown at 600 K on a Fe(001)-p(1 × 1)O substrate by means of spin-polarized photoemission spectroscopy. Our findings show that the expected antiferromagnetic stacking of the magnetization in Cr(001) layers occurs right from the first atomic layer at the Cr/Fe interface. This is at variance with all previous observations in similar systems, prepared in oxygen-free conditions, which always reported on a delayed onset of the magnetic oscillations due to the occurrence of significant chemical alloying at the interface, which is substantially absent in our preparation.
P-ρ-T measurements of H2O up to 260 GPa under laser-driven shock loading
Authors: Kimura T. , Ozaki N. , Sano T. , Okuchi T. , Sano T. , Shimizu K. , Miyanishi K. , Terai T. , Kakeshita T. , Sakawa Y. , Kodama R.
Published: April 2015

Pressure, density, and temperature data for H2O were obtained up to 260 GPa by using laser-driven shock compression technique. The shock compression technique combined with the diamond anvil cell was used to assess the equation of state models for the P-ρ-T conditions for both the principal Hugoniot and the off-Hugoniot states. The contrast between the models allowed for a clear assessment of the equation of state models. Our P-ρ-T data totally agree with those of the model based on quantum molecular dynamics calculations. These facts indicate that this model is adopted as the standard for modeling interior structures of Neptune, Uranus, and exoplanets in the liquid phase in the multi-Mbar range.
Plasmonic circular polarization analyzer formed by unidirectionally controlling surface plasmon propagation
Authors: Li Jiaming , Tang Peng , Liu Wei , Huang Tao , Wang Jiajian , Wang Yanqi , Lin Feng , Fang Zheyu , Zhu Xing
Published: April 2015

Analyzing the polarization of a circularly polarized light is a critical issue. We have fabricated a spiral nano-structure on the Au film by using focused ion beam etching technique. The fabricated structure can be used as a plasmonic circular polarization analyzer. By designing the relative orientation of two nano-apertures in the spiral structural unit, the propagation direction of the surface plasmon polaritons excited by circularly polarized light of opposite handedness can be controlled. Therefore, the spiral structure could be used to accurately determine the helicity of the excited circularly polarized light. Based on the results of scanning near-field optical microscopy, the obtained circular polarization extinction ratio of this structure was above 500. This structure can be used for a flexible detecting size and a very wide spectrum.
Surface modification of multilayer graphene using Ga ion irradiation
Authors: Wang Quan , Shao Ying , Ge Daohan , Yang Qizhi , Ren Naifei
Published: April 2015

The effect of Ga ion irradiation intensity on the surface of multilayer graphene was examined. Using Raman spectroscopy, we determined that the irradiation caused defects in the crystal structure of graphene. The density of defects increased with the increase in dwell times. Furthermore, the strain induced by the irradiation changed the crystallite size and the distance between defects. These defects had the effect of doping the multilayer graphene and increasing its work function. The increase in work function was determined using contact potential difference measurements. The surface morphology of the multilayer graphene changed following irradiation as determined by atomic force microscopy. Additionally, the adhesion between the atomic force microscopy tip and sample increased further indicating that the irradiation had caused surface modification, important for devices that incorporate graphene.
Plasmonic broadband absorber by stacking multiple metallic nanoparticle layers
Authors: Ji Ting , Peng Lining , Zhu Yuntao , Yang Fan , Cui Yanxia , Wu Xueyan , Liu Liu , He Sailing , Zhu Furong , Hao Yuying
Published: April 2015

High efficiency, broadband plasmonic absorbers are constructed based on a stack of alternating metallic nanoparticle layers (MNLs) and SiO2 slabs on top of a reflective Ag substrate. Experimental results show that the stacks with thick MNLs absorb light better than those with thin MNLs when the number of MNL/SiO2 cells (N) is small (e.g., 1 or 2), but the situation gets reversed when N is greater than 3. When the nominal thickness of MNL is as thin as 5 nm, the acquired Ag nanoparticles are so small that light penetration through all of the stacked MNLs in the proposed design is possible. Thus, an increase in N leads to a growing number of light trapping elements. Our simulation reveals that the Ag nanoparticles at different layers are hybridized to excite rich localized plasmonic resonances, resulting in multiple absorption peaks at optical frequencies and thus a broader absorption band. The broadband absorbers with an integrated absorption efficiency of 96% over the 300–1100 nm wavelength range were achieved by stacking 18 MNL/SiO2 cells. The proposed absorbers can be used for applications in solar energy harvesting and thermal emission tailoring, due to their easy fabrication procedure and excellent optical properties.
Current-induced spin-orbit torque switching of perpendicularly magnetized Hf|CoFeB|MgO and Hf|CoFeB|TaOx structures
Authors: Akyol Mustafa , Yu Guoqiang , Alzate Juan G. , Upadhyaya Pramey , Li Xiang , Wong Kin L. , Ekicibil Ahmet , Khalili Amiri Pedram , Wang Kang L.
Published: April 2015

We study the effect of the oxide layer on current-induced perpendicular magnetization switching properties in Hf|CoFeB|MgO and Hf|CoFeB|TaOx tri-layers. The studied structures exhibit broken in-plane inversion symmetry due to a wedged CoFeB layer, resulting in a field-like spin-orbit torque (SOT), which can be quantified by a perpendicular (out-of-plane) effective magnetic field. A clear difference in the magnitude of this effective magnetic field (HzFL) was observed between these two structures. In particular, while the current-driven deterministic perpendicular magnetic switching was observed at zero magnetic bias field in Hf|CoFeB|MgO, an external magnetic field is necessary to switch the CoFeB layer deterministically in Hf|CoFeB|TaOx. Based on the experimental results, the SOT magnitude (HzFL per current density) in Hf|CoFeB|MgO (−14.12 Oe/107 A cm−2) was found to be almost 13× larger than that in Hf|CoFeB|TaOx (−1.05 Oe/107 A cm−2). The CoFeB thickness dependence of the magnetic switching behavior, and the resulting  HzFL generated by in-plane currents are also investigated in this work.
Highly (002) textured large grain bcc Cr80Mn20 seed layer on Cr50Ti50 amorphous layer for FePt-C granular film
Authors: Jeon Seong-Jae , Hinata Shintaro , Saito Shin , Takahashi Migaku
Published: April 2015

Effect of bcc Cr80Mn20 seed layer and Cr50Ti50 amorphous texture inducing layer on the heteroepitaxy system in FePt-C granular film was studied by introducing a new concept of the layered structure. The concept suggested that the large grain seed layer in which the crystallographic texture was initially formed on an amorphous layer in the layered structure can reduce the angular distribution of (002) c-axis crystal orientation in the FePt-C granular film owing to heteroepitaxial growth. Structure analysis by X-ray diffraction revealed that (1) when the substrate heating temperature was elevated from 300 °C to 500 °C, grain size in the seed layer increased from 9.8 nm to 11.6 nm, and then decreased with further increasing the substrate temperature. The reduction of the grain size over 500 °C corresponds to the crystallization of the amorphous texture inducing layer, (2) when the grain size increased from 9.8 nm to 11.6 nm, the angular distribution of the (002) orientation in the seed layer dramatically decreased from 13.7° to 4.1°. It was shown that the large grain seed layer increased the perpendicular hysteresis in FePt-C granular film.
Smog and socioeconomics: an evaluation of equity in traffic-related air pollution generation and exposure
Authors: Sider Timothy , Hatzopoulou Marianne , Eluru Naveen , Goulet-Langlois Gabriel , Manaugh Kevin
Published: April 2015

How traffic-related air pollution generation and exposure is distributed among different population groups is an important environmental justice concern. From a social equity perspective, many questions arise at the metropolitan scale. Do socially disadvantaged communities have higher exposure levels to traffic-related air pollution? Do discrepancies exist wherein neighborhoods are not exposed to levels of pollution similar to those they themselves generate? And, is there a relationship between this discrepancy and social disadvantage? These questions are examined for the Montreal Metropolitan Region through the development of an integrated transport and emissions model. Two measures of traffic-related air pollution are estimated at the traffic analysis zone level: (1) generation (average emissions per household), and (2) exposure (average residential zone concentration). A social disadvantage index is also calculated that incorporates elements of social and material deprivation. Three levels of inequity exist regarding emissions, exposure, and socioeconomics. Social disadvantage was found to have a positive relationship with exposure, meaning that the most socially disadvantaged communities tend to experience the highest levels of traffic-related air pollution. Spatial discrepancies in emission generation versus emission exposure are also present for most of the metropolitan region. Furthermore, the communities that face a double burden of greater disadvantage and higher exposure also tend to create the lowest quantities of pollution.
Gradual rasterization: redefining spatial resolution in transport modelling
Authors: Moeckel Rolf , Donnelly Rick
Published: April 2015

It is a challenge to find the appropriate level of spatial resolution in transport modelling. While the zone system has substantial influence on model results, the resolution and design of zones is rarely analyzed systematically, and even less commonly adjusted to a specific modelling need. In this paper we present a new methodology to automatically create a new zone system based on the quadtree algorithm specific to transport modelling. Gradual raster cells are generated, where smaller raster cells tend to be used in urban areas and larger raster cells dominate in low-density, rural areas. As changing the zonal resolution affects the number of intrazonal and interzonal trips, an algorithm has been developed that adjusts intrazonal trips in line with the network resolution. Trip tables of a travel demand model for the state of Georgia, USA were disaggregated using this new zone system of gradual raster cells. The traffic assignment results validate significantly better than when using the original zone system.
Urban peripheries: reflecting on politics and projects in Amsterdam, Milan, and Paris
Authors: Savini Federico , Majoor Stan , Salet Willem
Published: April 2015

In this paper we question the political and financial drivers of urban development in the contemporary context of multiactor and multilevel governance. We focus on the processes that drive spatial planning and large-scale development projects in the inner periphery of three metropolitan areas: Amsterdam, Paris, and Milan. Peripheral development is conceptualized as the outcome of the realignment of three major sources of urban power: the national government, the core city, and large market investors. Early research has largely demonstrated how each of these elements influences metropolitan transformations, often separately, with special focus on economic logics of development. We propose to instead empirically investigate the political drivers of the changing relationship between these three powers. Focusing on three particular projects, we show how different spatial outcomes of peripheral development spring from a particular articulation of the relationship between the three sources of power. These relationships are pinned over electoral strategies of power consolidation, political confrontation between emerging parties, and their (dis)connections with business interests.
Effect of the type of dietary fat when added as an energy source on animal performance, carcass characteristics and meat quality of intensively reared Friesian steers
Authors: Guerrero A. , Muela E. , Valero M. V. , Prado I. N. , Campo M. M. , Olleta J. L. , Catalán O. , Sañudo C.
Published: April 2015

The effects of different fats in the diet were evaluated on the basis of animal performance, carcass and meat-quality traits. Four groups of eight Friesian steers were intensively finished with concentrate and cereal straw given ad libitum. Four different types of fats were included at a 4% level in the diet, namely, palm oil, sunflower oil, tallow and hydrogenated fat. The feeding trial lasted for 84 days. There were no differences on animal performance or carcass characteristics, except for animals from the hydrogenated-fat diet, which had the greatest percentage of muscle and moisture, and the lowest percentage of fat in a 6th rib dissection. Meat colour, texture, lipid oxidation and consumer acceptability did not differ among the diets. Nevertheless, the effects of ageing or display time were more important than those of the source of fat. Intramuscular fatty acid profile was hardly influenced by the fat source. In conclusion, the type of fat added at the final stage of the rearing process, at a 4% of inclusion level, did not produce noticeable variations on productive parameters or product quality. This would allow to formulate rations for cattle, using the most profitable source of fat (added at low levels), without having variability on the product quality.
Determining maturity and population structure in Macrozamia parcifolia (Zamiaceae), a threatened Australian cycad
Authors: Borsboom Adrian C. , Wang Jian , Forster Paul I.
Published: April 2015

There is difficulty assigning maturity to non-arborescent (trunkless) cycad species and as a consequence in determining the mature–immature structure of populations, which is important for their management, particularly for those under threat. The aim of this investigation was to find a reliable and simple method to determine maturity for the threatened, non-arborescent cycad Macrozamia parcifolia P.I. Forst. & D.L. Jones, and to incorporate this information into a population structure. Measurements were taken from tagged plants on four quadrats in eucalypt-dominated open forest in south-eastern Queensland, Australia. Using a single time-point dataset of three variables associated with the longest mature leaf, basal petiole width coupled with several years of coning evidence was found best at distinguishing mature plants. Choice of this variable and the threshold point to class non-coning plants as mature or immature was through a classification-tree model using a binary recursive partitioning process, the tree being pruned to identify the best variable and threshold point via a cross-validation process. This simple, reliable method to determine maturity was still effective when using a single time-point dataset for coning evidence. The method can be applied to other threatened, non-arborescent cycads, which could aid in their conservation management. The structure of M. parcifolia population was bimodal. The mode that encompassed immature plants was broadly reverse-J shaped, indicating younger immature plants had highest mortality. Reasons for the bimodality are possibly complex, but could simply highlight a non-lineal relationship of basal petiole width with plant age.
Low survival rather than breeding success explains little penguin population decline on Granite Island
Authors: Colombelli-Négrel Diane
Published: April 2015

Over the past decade, populations of little penguins (Eudyptula minor) have been seriously declining across South Australia for reasons still not fully understood. In the present study, I investigated breeding performance and return rates of little penguins on Granite Island for 17 years in relation to patterns of population decline. I focussed on the impacts of human disturbance, breeding site, abandonment and predation on breeding success. The average breeding success was 1.05±0.12 fledglings per pair; and breeding success increased since 1990, despite population decline. Breeding site was the main factor affecting breeding success. I found no effect of predation or abandonment on breeding success, but there was a negative effect of predation on the number of dead chicks found. In addition, I found a negative effect of human disturbance. Despite the observed increase in breeding success, return rates were extremely low for both adults (16.3%) and fledglings (2.3%). Population modelling confirmed the observed population decline on Granite Island, with subadult survival being the most critical variable affecting population growth. The present study thus highlighted the need for further studies into factors affecting survival of adults and subadults.
Centrosome and microtubule functions and dysfunctions in meiosis: implications for age-related infertility and developmental disorders
Authors: Schatten Heide , Sun Qing-Yuan
Published: April 2015

The effects of oocyte aging on meiotic spindle dynamics have been well recognised, but the mechanisms underlying the effects are not well understood. In this paper we review the role of centrosomes and the microtubule cytoskeleton in meiotic spindle formation and maintenance, and the impact of oocyte aging on spindle integrity resulting in centrosome and microtubule dysfunctions that are associated with aneuploidy. Loss of spindle integrity includes dispersion of proteins from the centrosome core structure and loss of attachment of microtubules to centrosomes and kinetochores, which will result in abnormal chromosome separation. The inability of centrosomal proteins to accurately associate with the centrosome structure may be the result of destabilisation of the core structure itself or of microtubule destabilisation at the centrosome-facing microtubule areas that are acetylated in fresh oocytes but may not be acetylated in aging oocytes. Microtubule destabilisation prevents accurate motor-driven transport of centrosomal proteins along microtubules to form and maintain a functional centrosome. Other factors to form and maintain the MII spindle include signal transductions that affect microtubule dynamics and stability. Understanding the mechanisms underlying centrosome and microtubule dysfunctions during oocyte aging will allow diagnosis and analysis of oocyte quality and abnormalities as important aspects for targeted treatment of aging oocytes to extend or restore viability and developmental capacity. New therapeutic approaches will allow improvements in reproductive success rates in IVF clinics, as well as improvements in reproductive success rates in farm animals. This review is focused on: (1) centrosome and microtubule dynamics in fresh and aging oocytes; (2) regulation of centrosome and/or microtubule dynamics and function; and (3) possible treatments to extend the oocyte’s reproductive capacity and viability span.
Injury alters intrinsic functional connectivity within the primate spinal cord
Authors: Chen Li Min , Mishra Arabinda , Yang Pai-Feng , Wang Feng , Gore John C.
Published: April 2015

Significance

This is the first study, to our knowledge, to demonstrate intrinsic functional connectivity within the spinal cords of monkeys, replicating and extending recent similar discoveries in humans. Our observations of spatially correlated patterns of MRI signals at rest indicate that neurons in different parts of the spinal horns show synchronized fluctuations in activity at rest just as found in the brain. Injury to the cord disrupts the integrity of this interhorn connectivity within and across spinal segments, showing these intrinsic correlations have functional relevance and mirror behavioral deficits in the injured monkeys. Quantification of the intrinsic functional connectivity within the spine after injury therefore has considerable potential as an imaging biomarker of spinal cord functional integrity, something long needed in clinical practice.
Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases
Authors: Byrne Robert T. , Jenkins Huw T. , Peters Daniel T. , Whelan Fiona , Stowell James , Aziz Naveed , Kasatsky Pavel , Rodnina Marina V. , Koonin Eugene V. , Konevega Andrey L. , Antson Alfred A.
Published: April 2015

Significance

RNA-binding proteins use diverse mechanisms for generating specificity toward distinct RNA molecules. Different subfamilies of bacterial dihydrouridine synthases (Dus) modify specific uridines in tRNA, but the mechanism for selection of the target nucleotide is unknown. We solved crystal structures of the U16-specific Dus from
Escherichia coli
complexed with two different tRNAs. These structures reveal that the tRNA is bound in a completely different orientation from that observed in a U20-specific enzyme. The major reorientation of the substrate tRNA, driven by unique amino acid “binding signatures” and plasticity in the position of the C-terminal recognition domain, appears to be an evolutionary innovation to the known strategies that define specificity of enzymes toward tRNA.
Evaluation of Dietary Soy Sensitivity in Snake River Cutthroat Trout
Authors: Ham Brian R , Barrows Frederic T , Huttinger Amberly , Duff Glenn C , Yeoman Carl J , Maskill Mark G , Sealey Wendy M
Published: April 2015

The shift in commercial diet formulations for Rainbow Trout Oncorhynchus mykiss toward formulations that include more plant ingredients, specifically an increased inclusion of soy products, may have negative implications for less-domesticated trout species fed these modern diets. Therefore, the objective of this study was to examine the effects of increasing dietary soybean meal and soy protein concentrate inclusion on growth efficiency and intestinal health of Cutthroat Trout O. clarkii. To achieve this objective, a feeding trial was conducted with juvenile Snake River Cutthroat Trout O. clarkii behnkei fed a practical type formulation that included 0, 5, 10, 15, or 30% dietary soybean meal or soy protein concentrate. Feed and consumption, weight gain, proximate composition, intestinal health, and survival were compared. Juvenile Snake River Cutthroat Trout (initial weight, 28.1 ± 1.0 g/fish [mean ± SD]) were stocked at 20 fish per tank in 200-L tanks with three replicate tanks per diet. Fish were fed their respective diets for 10 weeks. Final fish weight was affected by dietary soy inclusion level (P = 0.0001) but not type (P = 0.7790), and no interaction was observed (P = 0.6019). Snake River Cutthroat Trout fed the diets with the highest level of soy protein inclusion (30%) were significantly larger than fish fed all other diets and had a final average fish weight of greater than 130 g (P = 0.0001). Feed conversion ratios were higher in fish fed diets with 0% and 5% soy inclusion than in fish fed the 10% or 30% soy inclusion diets (P = 0.0044). No significant effect of soy inclusion level (P = 0.0825) on feed intake was observed. Increased inflammation and decreased vacuolization, however, was observed in histological samples of the intestine of Cutthroat Trout fed the 30% soybean meal and soy protein concentrate diets. Additional research is necessary to determine whether the intestinal pathology observed can predispose Cutthroat Trout to pathogenic disease and/or negatively affect growth with extended feeding.
Participant Expectations in Pulmonary Hypertension–Related Research Studies
Authors: Gray Michael P. , Aldrighetti Rino , Fagan Karen A.
Published: April 2015

The Pulmonary Hypertension Association (PHA) is a patient advocacy organization seeking to find ways to prevent, improve treatment for, and cure pulmonary hypertension (PH) and to provide hope for the PH community through support, education, research, advocacy, and awareness. Many patients involved with PHA are also involved in various PH‐specific research studies; however, the patient expectations and priorities for PH‐specific research are currently unknown or not well examined. Our objective was to identify the current modes of study entry, priorities within research, and expectations over the course of study involvement for patient constituents of PHA. A 29‐question online survey was designed by PHA and disseminated to the PHA patient constituency on its Facebook page through a post on November 29, 2012. Responses were collected on SurveyMonkey through December 10, 2012. Respondents were divided into parallel survey tracks, depending on whether the respondent indicated previous participation in research studies. These two cohorts of individuals were analyzed and, where appropriate, compared with tests of association. A total of 234 respondents were included in the final data analysis, with 95 (40.6%) reporting previous participation in research studies. These respondents reported an overall positive experience in their research studies (64.9% very good, 21.3% good, 12.8% neutral, 1.1% bad). Of the respondents with previous research study participation, 91.1% indicated that receipt of the study outcome after participation would positively influence their decision to participate in future research; despite this, only 41.17% reported receiving information of this sort after their participation. Research participation is a strong interest of PHA patient constituents; clear and consistent communication from the research team is an expectation of many participants. Despite this expectation, 58.83% of respondents indicated they did not receive communication from the research team after participation. This offers an opportunity not only to improve participants’ experiences but also to increase the likelihood of future study participation.
Arakelov motivic cohomology I
Authors: Holmstrom Andreas , Scholbach Jakob
Published: April 2015

This paper introduces a new cohomology theory for schemes of finite type over an arithmetic ring. The main motivation for this Arakelov-theoretic version of motivic cohomology is the conjecture on special values ofLL-functions and zeta functions formulated by the second author. Taking advantage of the six functors formalism in motivic stable homotopy theory, we establish a number of formal properties, including pullbacks for arbitrary morphisms, pushforwards for projective morphisms between regular schemes, localization sequences,hh-descent. We round off the picture with a purity result and a higher arithmetic Riemann-Roch theorem.

In a sequel to this paper, we relate Arakelov motivic cohomology to classical constructions such as arithmeticKKand Chow groups and the height pairing.
Eigenspace arrangements of reflection groups
Authors: Miller Alexander
Published: April 2015

The lattice of intersections of reflecting hyperplanes of a complex reflection group

W
W

may be considered as the poset of

1
1

-eigenspaces of the elements of

W
W

. In this paper we replace

1
1

with an arbitrary eigenvalue and study the topology and homology representation of the resulting poset. After posing the main question of whether this poset is shellable, we show that all its upper intervals are geometric lattices and then answer the question in the affirmative for the infinite family

G
(
m
,
p
,
n
)

G(m,p,n)

of complex reflection groups, and the first 31 of the 34 exceptional groups, by constructing CL-shellings. In addition, we completely determine when these eigenspaces of

W
W

form a

K
(
π
,
1
)

K(\pi ,1)

(resp. free) arrangement.

For the symmetric group, we also extend the combinatorial model available for its intersection lattice to all other eigenvalues by introducing balanced partition posets, presented as particular upper order ideals of Dowling lattices, study the representation afforded by the top (co)homology group, and give a simple map to the posets of pointed

d
d

-divisible partitions.
Quantitative visibility estimates for unrectifiable sets in the plane
Authors: Bond M. , Łaba I. , Zahl J.
Published: April 2015

The “visibility” of a planar set

S
S

from a point

a
a

is defined as the normalized size of the radial projection of

S
S

from

a
a

to the unit circle centered at

a
a

. Simon and Solomyak in 2006 proved that unrectifiable self-similar one-sets are invisible from every point in the plane. We quantify this by giving an upper bound on the visibility of

δ
\delta

-neighborhoods of such sets. We also prove lower bounds on the visibility of

δ
\delta

-neighborhoods of more general sets, based in part on Bourgain’s discretized sum-product estimates.
The yeast Hot1 transcription factor is critical for activating a single target gene,STL1
Authors: Bai Chen , Tesker Masha , Engelberg David
Published: April 2015

Transcription factors are commonly activated by signal transduction cascades and induce expression of many genes. They therefore play critical roles in determining the cell's fate. The yeast Hog1 MAP kinase pathway is believed to control the transcription of hundreds of genes via several transcription factors. To identify the bona fide target genes of Hog1, we inducibly expressed the spontaneously active variant Hog1D170A+F318Lin cells lacking the Hog1 activator Pbs2. This system allowed monitoring the effects of Hog1 by itself. Expression of Hog1D170A+F318Lin pbs2∆ cells imposed induction of just 105 and suppression of only 26 transcripts by at least twofold. We looked for the Hog1-responsive element within the promoter of the most highly induced gene, STL1 (88-fold). A novel Hog1 responsive element (HoRE) was identified and shown to be the direct target of the transcription factor Hot1. Unexpectedly, we could not find this HoRE in any other yeast promoter. In addition, the only gene whose expression was abolished in hot1∆ cells was STL1. Thus Hot1 is essential for transcription of just one gene, STL1. Hot1 may represent a class of transcription factors that are essential for transcription of a very few genes or even just one.
Synaptic neuropeptide release by dynamin-dependent partial release from circulating vesicles
Authors: Wong Man Yan , Cavolo Samantha L. , Levitan Edwin S.
Published: April 2015

Neurons release neuropeptides, enzymes, and neurotrophins by exocytosis of dense-core vesicles (DCVs). Peptide release from individual DCVs has been imaged in vitro with endocrine cells and at the neuron soma, growth cones, neurites, axons, and dendrites but not at nerve terminals, where peptidergic neurotransmission occurs. Single presynaptic DCVs have, however, been tracked in native terminals with simultaneous photobleaching and imaging (SPAIM) to show that DCVs undergo anterograde and retrograde capture as they circulate through en passant boutons. Here dynamin (encoded by the shibire gene) is shown to enhance activity-evoked peptide release at the Drosophila neuromuscular junction. SPAIM demonstrates that activity depletes only a portion of a single presynaptic DCV's content. Activity initiates exocytosis within seconds, but subsequent release occurs slowly. Synaptic neuropeptide release is further sustained by DCVs undergoing multiple rounds of exocytosis. Synaptic neuropeptide release is surprisingly similar regardless of anterograde or retrograde DCV transport into boutons, bouton location, and time of arrival in the terminal. Thus vesicle circulation and bidirectional capture supply synapses with functionally competent DCVs. These results show that activity-evoked synaptic neuropeptide release is independent of a DCV's past traffic and occurs by slow, dynamin-dependent partial emptying of DCVs, suggestive of kiss-and-run exocytosis.
Loránd Eötvös
Authors: Hargittai István , Hargittai Magdolna
Published: April 2015

The history of Eötvös Loránd University represents the history of Hungarian universitas. Loránd Eötvös was a physicist whose achievements in classical physics paved the way to Albert Einstein’s theory of general relativity. The beginnings of higher education in Hungary reach back to medieval times with emphasis on theology and gradually extending toward philosophy and the humanities, medicine, and natural sciences. Mathematics has occupied a special place of world-renowned excellence in Hungarian science. The memorabilia include, among many others, those for the political theorist István Bibó, the philosopher György (Georg) Lukács, the chemist George de Hevesy, and the mathematicians Pál (Paul) Erdős, Lipót (Leopold) Fejér, Kornél (Cornelius) Lánczos, Alfréd Rényi, Frigyes Riesz, and Pál Turán.
Theodore von Kármán
Authors: Hargittai István , Hargittai Magdolna
Published: April 2015

The aerodynamicist, engineer, and innovator Theodore von Kármán studied and started his research career in Budapest. Similarly, many other celebrated Hungarian engineers and inventors trained at the Budapest University of Technology and Economics and its predecessors. The Nobel laureate George A. Olah excelled in basic chemical research, others excelled in river regularization, the electrification of the railways, innovations of the internal combustion engine, and many more. Our coverage includes memorabilia of the Nobel laureate Georg von Békésy, Zoltán Bay, who produced and detected echoes of radar waves from the Moon, the British inventors James Watt and George Stephenson, the American pioneer of the personal computer Steve Jobs, Ernő Rubik’s Magic Cube, the inventor of the ball-point pen, and many others representative of Hungarian and international contributors to technology and engineering.