bluuebunny/crossref_metadata_2025 huggingface dataset:
Calibration and object correspondence in camera networks with widely separated overlapping views
Authors: Yin Fei , Makris Dimitrios , Velastin Sergio A. , Ellis Tim
Published: October 2014

This study contributes in two ways to the research of multi‐camera object tracking in the context of visual surveillance. Firstly, a semi‐automatic scene calibration method is proposed to deal with mapping a network of cameras with overlapped fields of view onto a single ground plane view, even when the overlap is not substantial. The proposed method uses a semi‐supervised approach that combines tracked blobs with user‐selected line scene features to recover the homographies between camera views that are both simple and accurate. Then, based on the scene calibration information, the intersection points of the projected vertical axis of single camera blobs are used to make object correspondences across multiple views. The method works in mixed environments of both pedestrians and vehicles, and is shown to be accurate and robust against segmentation noise and occlusions. Finally, the advantage of the proposed method is demonstrated by quantitative tracking performance evaluation and comparison against previous methods.
Evaluation of gas permeation through barrier layers for organic electronic devices by helium detector method
Authors: Jeong Eun‐Wook , Kim Dong‐Yong , Choi In‐Kyun , Park Hong‐Seok , Hui Kwun Nam , Cho Young‐Rae
Published: October 2014

Evaluation of gas permeation properties through barrier layers is important for the development of flexible organic light‐emitting devices (FOLEDs). In this reported work, an helium (He) leak detector was used in a novel permeation test for metallic barrier layers. Aluminium (Al) or chromium (Cr) film was deposited as a barrier layer onto a polyethylene terephthalate (PET) substrate using a magnetron sputtering system. For the samples of PET substrates with Al and Cr films at thicknesses of 200 nm, the He pressures were 3.1 × 10−6 and 1.3 × 10−5 Torr, respectively, as measured via He detector testing. The poor permeation blocking by the Cr film was because of microcracks. The He pressure for samples with 1 000 nm thick Al coating and for Al foil (30 μm) showed different values of 3.2 × 10−8 and 1.1 × 10−10 Torr, respectively, which indicated high sensitivity in a low permeation range. The high sensitivity in permeation properties measured by He detector testing reflected the qualities of He that include one of the lightest weights known to science and a very small size. This He detector test will be useful in the development of long‐life FOLEDs, as it will aid the measuring of the gas permeation properties of barrier layers that are highly effective in blocking water vapour.
Bilinear covariants and spinor fields duality in quantum Clifford algebras
Authors: Abłamowicz Rafał , Gonçalves Icaro , da Rocha Roldão
Published: October 2014

Classification of quantum spinor fields according to quantum bilinear covariants is introduced in a context of quantum Clifford algebras on Minkowski spacetime. Once the bilinear covariants are expressed in terms of algebraic spinor fields, the duality between spinor and quantum spinor fields can be discussed. Thus, by endowing the underlying spacetime with an arbitrary bilinear form with an antisymmetric part in addition to a symmetric spacetime metric, quantum algebraic spinor fields and deformed bilinear covariants can be constructed. They are thus compared to the classical (non quantum) ones. Classes of quantum spinor fields classes are introduced and compared with Lounesto's spinor field classification. A physical interpretation of the deformed parts and the underlying \documentclass[12pt]{minimal}\begin{document}$\mathbb {Z}$\end{document}Z-grading is proposed. The existence of an arbitrary bilinear form endowing the spacetime already has been explored in the literature in the context of quantum gravity [S. W. Hawking, “The unpredictability of quantum gravity,” Commun. Math. Phys. 87, 395 (1982)]. Here, it is shown further to play a prominent role in the structure of Dirac, Weyl, and Majorana spinor fields, besides the most general flagpoles and flag-dipoles. We introduce a new duality between the standard and the quantum spinor fields, by showing that when Clifford algebras over vector spaces endowed with an arbitrary bilinear form are taken into account, a mixture among the classes does occur. Consequently, novel features regarding the spinor fields can be derived.
Signal evaluations using singular value decomposition for Thomson scattering diagnostics
Authors: Tojo H. , Yamada I. , Yasuhara R. , Yatsuka E. , Funaba H. , Hatae T. , Hayashi H. , Itami K.
Published: October 2014

This paper provides a novel method for evaluating signal intensities in incoherent Thomson scattering diagnostics. A double-pass Thomson scattering system, where a laser passes through the plasma twice, generates two scattering pulses from the plasma. Evaluations of the signal intensities in the spectrometer are sometimes difficult due to noise and stray light. We apply the singular value decomposition method to Thomson scattering data with strong noise components. Results show that the average accuracy of the measured electron temperature (Te) is superior to that of temperature obtained using a low-pass filter (<20 MHz) or without any filters.
Atom probe tomography studies of Al2O3 gate dielectrics on GaN
Authors: Mazumder Baishakhi , Liu Xiang , Yeluri Ramya , Wu Feng , Mishra Umesh K. , Speck James S.
Published: October 2014

Atom probe tomography was used to achieve three-dimensional characterization of in situ Al2O3/GaN structures grown by metal organic chemical vapor deposition (MOCVD). Al2O3 dielectrics grown at three different temperatures of 700, 900, and 1000 °C were analyzed and compared. A low temperature GaN cap layer grown atop Al2O3 enabled a high success rate in the atom probe experiments. The Al2O3/GaN interfaces were found to be intermixed with Ga, N, and O over the distance of a few nm. Impurity measurements data showed that the 1000 °C sample contains higher amounts of C (4 × 1019/cm3) and lower amounts of H (7 × 1019/cm3), whereas the 700 °C sample exhibits lower C impurities (<1017/cm3) and higher H incorporation (2.2 × 1020/cm3). On comparing with Al2O3 grown by atomic layer deposition (ALD), it was found that the MOCVD Al2O3/GaN interface is comparatively abrupt. Scanning transmission electron microscopy data showed that the 900 °C and 1000 °C MOCVD films exhibit polycrystalline nature, while the ALD films were found to be amorphous.
Folding mechanism of a polymer chain with short-range attractions
Authors: Leitold Christian , Dellago Christoph
Published: October 2014

We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling. The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are coupled via harmonic springs, the non-neighboring monomers interact via a hard core and a short-ranged attractive potential. For a sufficiently small interaction range λ, the system undergoes a first-order freezing transition from an expanded, disordered phase to a compact crystalline state. Using a new shooting move tailored to polymers combined with a committor analysis, we study the transition state ensemble of an N = 128 chain and search for possible reaction coordinates based on likelihood maximization. We find that typical transition states consist of a crystalline nucleus with one or more chain fragments attached to it. Furthermore, we show that the number of particles in the crystalline core is not well suited as a reaction coordinate. We then present an improved reaction coordinate, which includes information from the potential energy and the overall crystallinity of the polymer.
High-efficiency passive full wave rectification for electromagnetic harvesters
Authors: Yilmaz Mehmet , Tunkar Bassam A. , Park Sangtak , Elrayes Karim , Mahmoud Mohamed A. E. , Abdel-Rahman Eihab , Yavuz Mustafa
Published: October 2014

We compare the performance of four types of full-wave bridge rectifiers designed for electromagnetic energy harvesters based on silicon diodes, Schottky diodes, passive MOSFETs, and active MOSFETs. Simulation and experimental results show that MOSFET-type rectifiers are more efficient than diode-type rectifiers, reaching voltage and power efficiency of 99% for ideal voltage source with input amplitudes larger than 800 mV. Since active MOSFETs require extra components and an external DC power supply, we conclude that passive MOSFETs are superior for micro-power energy harvesting systems. We demonstrate passive MOSFET rectifiers implemented using discrete, off-shelf components and show that they outperform all electromagnetic harvester rectifiers hitherto reported obtaining a power efficiency of 95%. Furthermore, we show that passive MOSFET rectifiers do not affect the center frequency, harvesting bandwidth, or optimal resistance of electromagnetic harvesters. We demonstrate a complete power management module by adding a capacitor to the rectifier output terminal. We found that this configuration changed the optimal resistive load from 40 Ω to 55 Ω and decreased output power efficiency to 86%.
Elastodynamic behavior of the three dimensional layer-by-layer metamaterial structure
Authors: Aravantinos-Zafiris N. , Sigalas M. M. , Economou E. N.
Published: October 2014

In this work, we numerically investigate for the first time the elastodynamic behavior of a three dimensional layer-by-layer rod structure, which is easy to fabricate and has already proved to be very efficient as a photonic crystal. The Finite Difference Time Domain method was used for the numerical calculations. For the rods, several materials were examined and the effects of all the geometric parameters of the structure were also numerically investigated. Additionally, two modifications of the structure were included in our calculations. The results obtained here (for certain geometric parameters), exhibiting a high ratio of longitudinal over transverse sound velocity and therefore a close approach to ideal pentamode behavior over a frequency range, clearly show that the layer-by-layer rod structure, besides being an efficient photonic crystal, is a very serious contender as an elastodynamic metamaterial.
Annealing temperature and barrier thickness effect on the structural and optical properties of silicon nanocrystals/SiO2 superlattices
Authors: López-Vidrier J. , Hernández S. , Hiller D. , Gutsch S. , López-Conesa L. , Estradé S. , Peiró F. , Zacharias M. , Garrido B.
Published: October 2014

The effect of the annealing temperature and the SiO2 barrier thickness of silicon nanocrystal (NC)/SiO2 superlattices (SLs) on their structural and optical properties is investigated. Energy-filtered transmission electron microscopy (TEM) revealed that the SL structure is maintained for annealing temperatures up to 1150 °C, with no variation on the nanostructure morphology for different SiO2 barrier thicknesses. Nevertheless, annealing temperatures as high as 1250 °C promote diffusion of Si atoms into the SiO2 barrier layers, which produces larger Si NCs and the loss of the NC size control expected from the SL approach. Complementary Raman scattering measurements corroborated these results for all the SiO2 and Si-rich oxynitride layer thicknesses. In addition, we observed an increasing crystalline fraction up to 1250 °C, which is related to a decreasing contribution of the suboxide transition layer between Si NCs and the SiO2 matrix due to the formation of larger NCs. Finally, photoluminescence measurements revealed that the emission of the superlattices exhibits a Gaussian-like lineshape with a maximum intensity after annealing at 1150 °C, indicating a high crystalline degree in good agreement with Raman results. Samples submitted to higher annealing temperatures display a progressive emission broadening, together with an increase in the central emission wavelength. Both effects are related to a progressive broadening of the size distribution with a larger mean size, in agreement with TEM observations. On the other hand, whereas the morphology of the Si NCs is unaffected by the SiO2 barrier thickness, the emission properties are slightly modified. These observed modifications in the emission lineshape allow monitoring the precipitation process of Si NCs in a direct non-destructive way. All these experimental results evidence that an annealing temperature of 1150 °C and 1-nm SiO2 barrier can be reached whilst preserving the SL structure, being thus the optimal structural SL parameters for their use in optoelectronics.
A dynamic and ultrafast group delay tuning mechanism in two microcavities side-coupled with a waveguide system
Authors: Wang Boyun , Wang Tao , Tang Jian , Li Xiaoming , Zhu Youjiang
Published: October 2014

We theoretically propose a dynamic and ultrafast group delay tuning mechanism in two microcavities side-coupled to a waveguide system through external optical pump beams. The optical Kerr effect modulation method is applied to improve tuning rate with response time of subpicoseconds or even femtoseconds. The group delay of an all-optical analog to electromagnetically induced transparency effect can be controlled by tuning either the frequency of photonic crystal microcavities or the propagation phase of line waveguide. Group delay is controlled between 5.88 and 70.98 ps by dynamically tuning resonant frequencies of the microcavities. Alternatively, the group delay is controlled between 1.86 and 12.08 ps by dynamically tuning the propagation phase of line waveguide. All observed schemes are analyzed rigorously through finite-difference time-domain simulations and coupled-mode formalism. Results show a new direction toward microstructure integration optical pulse trapping and all-optical dynamical storage of light devices in optical communication and quantum information processing.
Hard x-ray nanofocusing by refractive lenses of constant thickness
Authors: Seiboth F. , Scholz M. , Patommel J. , Hoppe R. , Wittwer F. , Reinhardt J. , Seidel J. , Knaut M. , Jahn A. , Richter K. , Bartha J. W. , Falkenberg G. , Schroer C. G.
Published: October 2014

In order to focus light or x rays, the thickness of a refractive lens is typically varied over its aperture. Here, we present a refractive x-ray lens made of lamellae of constant thickness, the refractive lamellar lens. Refractive power is created by a specific bending of the lamellae rather than by a concave lens profile. This very special design has the technological advantage that materials like sapphire or diamond can be used to make lenses by coating techniques. A first lens prototype focused x rays with a photon energy E = 15.25 keV to a lateral beam size of 164 nm × 296 nm full width at half maximum.
A Nth-order linear algorithm for extracting diffuse correlation spectroscopy blood flow indices in heterogeneous tissues
Authors: Shang Yu , Yu Guoqiang
Published: October 2014

Conventional semi-infinite analytical solutions of correlation diffusion equation may lead to errors when calculating blood flow index (BFI) from diffuse correlation spectroscopy (DCS) measurements in tissues with irregular geometries. Very recently, we created an algorithm integrating a Nth-order linear model of autocorrelation function with the Monte Carlo simulation of photon migrations in homogenous tissues with arbitrary geometries for extraction of BFI (i.e., αDB). The purpose of this study is to extend the capability of the Nth-order linear algorithm for extracting BFI in heterogeneous tissues with arbitrary geometries. The previous linear algorithm was modified to extract BFIs in different types of tissues simultaneously through utilizing DCS data at multiple source-detector separations. We compared the proposed linear algorithm with the semi-infinite homogenous solution in a computer model of adult head with heterogeneous tissue layers of scalp, skull, cerebrospinal fluid, and brain. To test the capability of the linear algorithm for extracting relative changes of cerebral blood flow (rCBF) in deep brain, we assigned ten levels of αDB in the brain layer with a step decrement of 10% while maintaining αDB values constant in other layers. Simulation results demonstrate the accuracy (errors < 3%) of high-order (N ≥ 5) linear algorithm in extracting BFIs in different tissue layers and rCBF in deep brain. By contrast, the semi-infinite homogenous solution resulted in substantial errors in rCBF (34.5% ≤ errors ≤ 60.2%) and BFIs in different layers. The Nth-order linear model simplifies data analysis, thus allowing for online data processing and displaying. Future study will test this linear algorithm in heterogeneous tissues with different levels of blood flow variations and noises.
Ni doping on Cu surfaces: Reduced copper resistivity
Authors: Zheng P. Y. , Deng R. P. , Gall D.
Published: October 2014

The resistivity of 9.3-nm-thick epitaxial and polycrystalline Cu is reduced by 11%–13% when coated with 0.75 nm Ni. Sequential in situ and ex situ transport measurements show that this is due to electron surface scattering which exhibits a specularity p = 0.7 for the Cu-vacuum interface that transitions to completely diffuse (p = 0) when exposed to air. In contrast, Ni-coated surfaces exhibit partial specularity with p = 0.3 in vacuum and p = 0.15 in air, as Cu2O formation is suppressed, leading to a smaller surface potential perturbation and a lower density of localized surface states, yielding less diffuse electron scattering.
Effect of microstrain on the magnetic properties of BiFeO3 nanoparticles
Authors: Mocherla Pavana S. V. , Karthik C. , Ubic R. , Ramachandra Rao M. S. , Sudakar C.
Published: October 2014

We report on size induced microstrain-dependent magnetic properties of BiFeO3 nanoparticles. The microstrain is found to be high (ε > 0.3%) for smaller crystallite sizes (d < 30 nm), and shows a sharp decrease as the particle size increases. The presence of pseudo-cubic symmetry is evidenced for these nanoparticles. Raman spectral studies suggest straightening of the Fe-O-Fe bond angle accompanied by a decrease in FeO6 octahedral rotation for d < 65 nm. The magnetization shows a dip around 30 nm, half the size of spin cycloid length for BiFeO3, due to a decrease in rhombohedral distortion with crystallite size. We also observe a similar trend in the TN with respect to size indicating that the microstrain plays a significant role in controlling the magnetic property of BiFeO3.
Soil amendments of fly ash: effects on function and biochemical activity of Carthamus tinctorius L. plants
Authors:   Qurratul, Jan Sumira , Khan Riyazzuddin ,   Mahmooduzzafar, Siddiqi T.O.
Published: October 2014

Proper disposal and recycling of different industrial waste materials have long been recognized as a prime environmental concern. The present study evaluated the effects of soil amendment of fly ash, a major industrial waste material, on soil properties, plant growth, productivity and metabolites production of safflower (Carthamus tinctorius L.). The soil was amended with varied concentrations of fly ash (0%, 5%, 10%, 25%, 50%, 75% per pot) prior to sowing under field conditions in the herbal garden of Jamia Hamdard. Sampling was conducted at different growth stages, i.e. pre-flowering, flowering and post-flowering. Our results demonstrate that fly ash concentrations up to 25% improved the physicochemical properties of the soil as compared to non-treated control resulting in increased availability to the plant of macro and micronutrients and thereby stimulating plant growth and productivity. Contents of photosynthetic pigments, sugars, protein, and nitrate reductase (NR) activity increased under 25% fly ash amendment. The highest beneficial effect was found during the flowering stage > pre-flowering > post-flowering stages. Further increase in fly ash concentration reduced the stimulated effects on the plants, exhibiting a minimum under 75% fly ash application. Thus, it was concluded that incorporation of 25% fly ash to the cultivation soil not only improves the physicochemical properties of the soil, but also contributes to better growth, yield and metabolism of safflower.
Caffeine supplementation and peak anaerobic power output
Authors: Glaister Mark , Muniz‐Pumares Daniel , Patterson Stephen D. , Foley Paul , McInnes Gillian
Published: October 2014

The aim of this study was to investigate the effects of caffeine supplementation on peak anaerobic power output (Wmax). Using a counterbalanced, randomised, double‐blind, placebo‐controlled design, 14 well‐trained men completed three trials of a protocol consisting of a series of 6‐s cycle ergometer sprints, separated by 5‐min passive recovery periods. Sprints were performed at progressively increasing torque factors to determine the peak power/torque relationship and Wmax. Apart from Trial 1 (familiarisation), participants ingested a capsule containing 5 mg·kg−1 of caffeine or placebo, one hour before each trial. The effects of caffeine on blood lactate were investigated using capillary samples taken after each sprint. The torque factor which produced Wmax was not significantly different (p ≥ 0.05) between the caffeine (1.15 ± 0.08 N·m·kg−1) and placebo (1.13 ± 0.10 N·m·kg−1) trials. There was, however, a significant effect (p < 0.05) of supplementation on Wmax, with caffeine producing a higher value (1885 ± 303 W) than placebo (1835 ± 290 W). Analysis of the blood lactate data revealed a significant (p < 0.05) torque factor × supplement interaction with values being significantly higher from the sixth sprint (torque factor 1.0 N·m·kg−1) onwards following caffeine supplementation. The results of this study confirm previous reports that caffeine supplementation significantly increases blood lactate and Wmax. These findings may explain why the majority of previous studies, which have used fixed‐torque factors of around 0.75 N·m·kg−1 and thereby failing to elicit Wmax, have failed to find an effect of caffeine on sprinting performance.
Influence of players' vocalisations on soccer referees' decisions
Authors: Lex Heiko , Pizzera Alexandra , Kurtes Marija , Schack Thomas
Published: October 2014

The influence of a potentially fouled player's vocalisations on the referee's decisions was investigated. Experienced soccer referees watched video clips of real‐match situations that were presented either without sound or with sound where a player's vocalisations were clearly audible and made judgements regarding fouls, direction of play and personal penalties. The results revealed that players’ vocalisations had no impact on the foul decisions of the referees. However, once a referee made a foul decision, the player's vocalisations led to an increased number of personal penalties (increase in yellow cards) for the foul‐causing player. In addition to crowd noise, a player's vocalisations during a foul are used as a proximal cue in the referee's decision‐making process.
Central Line–Associated Bloodstream Infections in Neonates with Gastrointestinal Conditions: Developing a Candidate Definition for Mucosal Barrier Injury Bloodstream Infections
Authors: Coffin Susan E. , Klieger Sarah B. , Duggan Christopher , Huskins W. Charles , Milstone Aaron M. , Potter-Bynoe Gail , Raphael Bram , Sandora Thomas J. , Song Xiaoyan , Zerr Danielle M. ,   Pediatric Prevention EpiCenter Consortium
Published: October 2014

Objective.

To develop a candidate definition for central line–associated bloodstream infection (CLABSI) in neonates with presumed mucosal barrier injury due to gastrointestinal (MBI-GI) conditions and to evaluate epidemiology and microbiology of MBI-GI CLABSI in infants

Design.

Multicenter retrospective cohort study.

Setting.

Neonatal intensive care units from 14 US children’s hospitals and pediatric facilities.

Methods.

A multidisciplinary focus group developed a candidate MBI-GI CLABSI definition based on presence of an MBI-GI condition, parenteral nutrition (PN) exposure, and an eligible enteric organism. CLABSI surveillance data from participating hospitals were supplemented by chart review to identify MBI-GI conditions and PN exposure.

Results.

During 2009–2012, 410 CLABSIs occurred in 376 infants. MBI-GI conditions and PN exposure occurred in 149 (40%) and 324 (86%) of these 376 neonates, respectively. The distribution of pathogens was similar among neonates with versus without MBI-GI conditions and PN exposure. Fifty-nine (16%) of the 376 initial CLABSI episodes met the candidate MBI-GI CLABSI definition. Subsequent versus initial CLABSIs were more likely to be caused by an enteric organism (22 of 34 [65%] vs 151 of 376 [40%]; P = .009) and to meet the candidate MBI-GI CLABSI definition (19 of 34 [56%] vs 59 of 376 [16%]; P < .01).

Conclusions.

While MBI-GI conditions and PN exposure were common, only 16% of initial CLABSIs met the candidate definition of MBI-GI CLABSI. The high proportion of MBI-GI CLABSIs among subsequent infections suggests that infants with MBI-GI CLABSI should be a population targeted for further surveillance and interventional research.

Infect Control Hosp Epidemiol 2014;35(11):1391–1399
Lanthionine synthetase C–like protein 2 (LanCL2) is a novel regulator of Akt
Authors: Zeng Min , van der Donk Wilfred A. , Chen Jie
Published: October 2014

The serine/threonine protein kinase Akt controls a wide range of biochemical and cellular processes under the modulation of a variety of regulators. In this study, we identify the lanthionine synthetase C–like 2 (LanCL2) protein as a positive regulator of Akt activation in human liver cells. LanCL2 knockdown dampens serum- and insulin-stimulated Akt phosphorylation, whereas LanCL2 overexpression enhances these processes. Neither insulin receptor phosphorylation nor the interaction between insulin receptor substrate and phosphatidylinositide 3-kinase (PI3K) is affected by LanCL2 knockdown. LanCL2 also does not function through PP2A, a phosphatase of Akt. Instead, LanCL2 directly interacts with Akt, with a preference for inactive Akt. Moreover, we show that LanCL2 also binds to the Akt kinase mTORC2, but not phosphoinositide-dependent kinase 1. Whereas LanCL2 is not required for the Akt-mTORC2 interaction, recombinant LanCL2 enhances Akt phosphorylation by target of rapamycin complex 2 (mTORC2) in vitro. Finally, consistent with a function of Akt in regulating cell survival, LanCL2 knockdown increases the rate of apoptosis, which is reversed by the expression of a constitutively active Akt. Taken together, our findings reveal LanCL2 as a novel regulator of Akt and suggest that LanCL2 facilitates optimal phosphorylation of Akt by mTORC2 via direct physical interactions with both the kinase and the substrate.
Acute increase of α-synuclein inhibits synaptic vesicle recycling evoked during intense stimulation
Authors: Busch David J. , Oliphint Paul A. , Walsh Rylie B. , Banks Susan M. L. , Woods Wendy S. , George Julia M. , Morgan Jennifer R.
Published: October 2014

Parkinson's disease is associated with multiplication of the α-synuclein gene and abnormal accumulation of the protein. In animal models, α-synuclein overexpression broadly impairs synaptic vesicle trafficking. However, the exact steps of the vesicle trafficking pathway affected by excess α-synuclein and the underlying molecular mechanisms remain unknown. Therefore we acutely increased synuclein levels at a vertebrate synapse and performed a detailed ultrastructural analysis of the effects on presynaptic membranes. At stimulated synapses (20 Hz), excess synuclein caused a loss of synaptic vesicles and an expansion of the plasma membrane, indicating an impairment of vesicle recycling. The N-terminal domain (NTD) of synuclein, which folds into an α-helix, was sufficient to reproduce these effects. In contrast, α-synuclein mutants with a disrupted N-terminal α-helix (T6K and A30P) had little effect under identical conditions. Further supporting this model, another α-synuclein mutant (A53T) with a properly folded NTD phenocopied the synaptic vesicle recycling defects observed with wild type. Interestingly, the vesicle recycling defects were not observed when the stimulation frequency was reduced (5 Hz). Thus excess α-synuclein impairs synaptic vesicle recycling evoked during intense stimulation via a mechanism that requires a properly folded N-terminal α-helix.
Knowledge: A Very Short Introduction
Authors: Nagel Jennifer
Published: October 2014

What is knowledge? How does it differ from mere belief? Do you need to be able to justify a claim in order to count as knowing it? Knowledge: A Very Short Introduction considers these epistemological questions alongside new puzzles arising from recent discoveries about humanity, language, and the mind. It explains the formation of major historical theories of knowledge, and shows how contemporary philosophers have developed new ways of understanding knowledge, using ideas from logic, linguistics, and psychology. Covering topics ranging from relativism and the problem of scepticism to the trustworthiness of internet sources, this VSI uses everyday examples to explain the key issues and debates.
Agricultural Economics and Economics: Influence and Counter‐Influence, 1910–1960
Authors: Nerlove Marc
Published: October 2014

This paper examines the effects which agricultural economists had on developments in economics and on economic policies during the years 1910‐1960. These developments are viewed against the backdrop of what was happening in the economy at large and particularly with respect to farmers, and of major books and articles in economics published in the period. Some ideas of agricultural economists and the influence they had are discussed. Agricultural issues and agricultural economists, in the broad sense, had a profound influence on the development of general economics and on economic policies during this period.
ExportAid: database of RNA elements regulating nuclear RNA export in mammals
Authors: Giulietti Matteo , Milantoni Sara Armida , Armeni Tatiana , Principato Giovanni , Piva Francesco
Published: October 2014

Motivation: Regulation of nuclear mRNA export or retention is carried out by RNA elements but the mechanism is not yet well understood. To understand the mRNA export process, it is important to collect all the involved RNA elements and their trans-acting factors.

Results: By hand-curated literature screening we collected, in ExportAid database, experimentally assessed data about RNA elements regulating nuclear export or retention of endogenous, heterologous or artificial RNAs in mammalian cells. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to mutations or polymorphisms. Currently, ExportAid stores 235 and 96 RNA elements, respectively, increasing and decreasing export efficiency, and 98 neutral assessed sequences.

Availability and implementation: Freely accessible without registration at http://www.introni.it/ExportAid/ExportAid.html . Database and web interface are implemented in Perl, MySQL, Apache and JavaScript with all major browsers supported.

Contact:  f.piva@univpm.it
Curation, integration and visualization of bacterial virulence factors in PATRIC
Authors: Mao Chunhong , Abraham David , Wattam Alice R. , Wilson Meredith J.C. , Shukla Maulik , Yoo Hyun Seung , Sobral Bruno W.
Published: October 2014

Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org ) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity.

Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A–C bacterial pathogen genera, Mycobacterium , Salmonella , Escherichia , Shigella , Listeria and Bartonella , using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein–protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC.

Availability and implementation: All tools and data are freely available at PATRIC ( http://patricbrc.org ).

Contact:  cmao@vbi.vt.edu .

Supplementary information:  Supplementary data are available at Bioinformatics online.
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring
Authors: Tian Ye , Zhang Bai , Hoffman Eric P. , Clarke Robert , Zhang Zhen , Shih Ie-Ming , Xuan Jianhua , Herrington David M. , Wang Yue
Published: October 2014

Summary: We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN’s ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data.

Availability: Source code and compiled package are freely available for download at http://apps.cytoscape.org/apps/kddn

Contact:  yuewang@vt.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
WhopGenome: high-speed access to whole-genome variation and sequence data in R
Authors: Wittelsbürger Ulrich , Pfeifer Bastian , Lercher Martin J.
Published: October 2014

Summary: The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R’s built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.

Availability and implementation: The WhopGenome R package is available on CRAN at http://cran.r-project.org/web/packages/WhopGenome/ . A Bioconductor package has been submitted.

Contact:  lercher@cs.uni-duesseldorf.de
The RNA shapes studio
Authors: Janssen Stefan , Giegerich Robert
Published: October 2014

Motivation : Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.

Results : We have rebuilt the original RNA shapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNA shapes , RNA alishapes and pknots RG, including its recent extension p K iss . As a spin-off, we obtain heretofore unavailable functionality: e. g. with p K iss , we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool p A li K iss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.

Availability and implementation : As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio .

Contact : bibi-help@cebitec.uni-bielefeld.de
William Cecil Slingsby, Norway, and British Mountaineering, 1872–1914
Authors: Readman Paul
Published: October 2014

Using the example of William Cecil Slingsby (1849–1929), one of the leading British alpinists active before 1914, this article reassesses late-Victorian and Edwardian mountaineering. It is particularly concerned with the motivations of mountaineers: what drew individuals such as Slingsby to the heights of Norway and elsewhere? Engaging with recent trends in scholarship, the article argues that interpretations which assign priority to aggressively masculine and imperialistic factors can be problematic. As Slingsby’s example shows, climbing was closely associated with a particular form of manliness throughout the period between the 1870s and the Great War, but the performance of this manliness involved embracing a cheerful domesticity as well as valorising robustly male derring-do and toughness in adversity. As for imperialist motivations, by the late nineteenth century these mattered less than might be thought, even to mountaineers who—like Slingsby—were ardent imperialists. A second and important aim of this article is to shed light on British cultural interactions with Norway. In his day, Slingsby was perhaps the best-known Englishman in Norway, and he was certainly one of the leading promoters of Anglo-Norwegian exchange in Britain. His mountaineering was importantly connected to the ethnic and philological ties he and other contemporaries (such as W.G. Collingwood) discerned between the two countries. Finally, the article also seeks to draw attention to Slingsby himself, a figure about whom almost nothing has been written by professional historians, despite his significance as a mountaineer and the existence of a considerable body of archival evidence relating to his life.
Starch Characteristics Influencing Resistant Starch Content of Cooked Buckwheat Groats
Authors: Lu Lu , Baik Byung‐Kee
Published: October 2014

Cooked buckwheat groats are suggested to contain a greater amount of resistant starch (RS) than cereal grains. High RS content, in addition to dietary fibers present in groats, contributes to the low‐calorie, high‐fiber food status of buckwheat. Six buckwheat genotypes exhibiting high, medium, and low RS content of cooked groats were selected, and starches were isolated to determine their functional properties to explore the possible cause of high RS content of cooked buckwheat groats. Apparent and actual amylose contents were 27.4 and 31.6–34.5% in high, 27.4–28.6 and 32.5–33.7% in medium, and 21.4–25.6 and 24.5–32.0% in low RS genotypes, respectively. Genotypes of high RS content exhibited greater amylose leaching based on total starch content during cooking than genotypes of low RS content, mainly because of higher amylose content in the former than latter. Genotypes of low RS content exhibited a relatively high content of amylose‐lipid complexes, as determined with a differential scanning calorimeter (DSC). Gelatinization enthalpy and degree of amylopectin retrogradation determined with a DSC were not related to RS content. An evident relationship was observed between RS content of cooked groats and amylose retrogradation determined by gel hardness (r = 0.91, P < 0.05), cohesiveness (r = 0.89, P < 0.05), and syneresis (r = 0.88, P < 0.05). Increases in starch amylose content, amylose leaching capacity, and amylose retrogradation, as well as a decrease in the amount of amylose‐lipid complexes all appear to be related to high RS content of cooked buckwheat groats.
Role reversal in a predator–prey interaction
Authors: Sánchez-Garduño Faustino , Miramontes Pedro , Marquez-Lago Tatiana T
Published: October 2014

Predator–prey relationships are one of the most studied interactions in population ecology. However, little attention has been paid to the possibility of role exchange between species, despite firm field evidence of such phenomena in nature. In this paper, we build a mathematical model capable of reproducing the main phenomenological features of role reversal in a classical system and present results for both the temporal and spatio-temporal cases. We show that, depending on the choice of parameters, our role-reversal dynamical system exhibits excitable-like behaviour, generating waves of species' concentrations that propagate through space. Our findings fill a long-standing gap in modelling ecological interactions and can be applicable to better understanding ecological niche shifts and planning of sustainable ecosystems.
The mechanics of hyperactivation in adhered human sperm
Authors: Ooi E. H , Smith D. J , Gadêlha H , Gaffney E. A , Kirkman-Brown J
Published: October 2014

Hyperactivation is an important phenomenon exhibited by mammalian sperm during the process of acquiring fertilization capacity. The majority of studies have focused on incubation-induced hyperactivation in non-human species, which typically differ in size, shape, and are more homogeneous than human sperm. We develop an alternative approach via drug-induction, using high-speed imaging and analysis of same-cell changes in the flagellar movement of adhered cells. Following stimulation with 4-aminopyridine, approximately two-thirds (21 of 34) of the cells analysed exhibited a waveform with a single characteristic frequency; in all cases, the frequency was lower than before stimulation. The remaining cells (13 of 34) exhibited a more complex motility with multiple-frequency modes. The lowest mode in all cases was lower than the frequency prior to stimulation. Flagellar bending increased in all cells following stimulation and was significantly greater in the multiple-frequency responders. Despite the increased bending, time-averaged hydrodynamic power dissipation decreased significantly when assessed across all cells, the effect being significantly greater in the multiple-frequency responders than single frequency. These results reveal the heterogeneity of responses of human sperm to a hyperactivating stimulus, the methodology being potentially useful for assessing dynamic responses to stimuli in human sperm, and physiological selection of cells for assisted reproduction.
Acidiphilium iwatense sp. nov., isolated from an acid mine drainage treatment plant, and emendation of the genus Acidiphilium
Authors: Okamura Keiko , Kawai Akiko , Wakao Norio , Yamada Takeshi , Hiraishi Akira
Published: October 2014

Several strains of aerobic, acidophilic, chemo-organotrophic bacteria belonging to the genus

Acidiphilium

were isolated from an acid mine drainage (AMD) (pH 2.2) treatment plant. 16S rRNA gene sequence comparisons showed that most of the novel isolates formed a phylogenetically coherent group (designated Group Ia) distinguishable from any of the previously established species of the genus

Acidiphilium

at <98 % similarity. This was supported by genomic DNA–DNA hybridization assays. The Group Ia isolates were characterized phenotypically by an oval cell morphology, non-motility, growth in the range pH 2.0–5.5 (optimum pH 3.5), lack of photosynthetic pigment and the presence of C19 : 0 cyclo ω8c as the main component of the cellular fatty acids and ubiquinone-10 as the major quinone. On the basis of these data, the name Acidiphilium
iwatense sp. nov. is proposed to accommodate the Group Ia isolates, and the description of the genus

Acidiphilium

is emended. The type strain of Acidiphilium
iwatense sp. nov. is MS8T ( = NBRC 107608T = KCTC 23505T).
Diversifying mechanisms in the on-farm evolution of crop mixtures
Authors: Thomas Mathieu , Thépot Stéphanie , Jouanne-Pin Sophie , Galic Nathalie , Remoué Carine , Goldringer Isabelle
Published: October 2014

While modern agriculture relies on genetic homogeneity in the field, some farmers grow genetically heterogeneous crops and exchange seeds. Such diversifying practices associated with seed recycling may allow adaptation of crops to their environment. This socio-genetical model constitutes an original experimental evolution design called On-Farm Dynamic Management (OFDM). Studying OFDM can help understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environmental conditions. We studied a farmer-led initiative where a mixture of four French wheat landraces called "Mélange de Touselles" (MDT) was created and distributed within a farmers' network. Fifteen populations derived by farmers from the initial mixture were sampled after 2 to 7 generations of cultivation on their farm. Twenty-one space-time samples of 80 individuals were genotyped using 17 microsatellites markers and characterized for their heading date in a "common-garden" experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. A rapid differentiation of the mixture was detected, larger at the phenotypic and gene levels compared to the neutral genetic level, indicating a potential divergent selection. We identified two interacting selection processes: variation of the mixture component frequencies and evolution of the within-variety diversity, that shaped the standing variability available within the mixture. These results confirm that farmers' practices increase genetic diversity and allow crop evolution, which is critical in the context of global change. OFDM appears as a promising model of crop experimental evolution.
Shroom3 contributes to the maintenance of the glomerular filtration barrier integrity
Authors: Yeo Nan Cher , O’Meara Caitlin C. , Bonomo Jason A. , Veth Kerry N. , Tomar Ritu , Flister Michael J. , Drummond Iain A. , Bowden Donald W. , Freedman Barry I. , Lazar Jozef , Link Brian A. , Jacob Howard J.
Published: October 2014

Genome-wide association studies (GWAS) identify regions of the genome correlated with disease risk but are restricted in their ability to identify the underlying causative mechanism(s). Thus, GWAS are useful “roadmaps” that require functional analysis to establish the genetic and mechanistic structure of a particular locus. Unfortunately, direct functional testing in humans is limited, demonstrating the need for complementary approaches. Here we used an integrated approach combining zebrafish, rat, and human data to interrogate the function of an established GWAS locus (SHROOM3) lacking prior functional support for chronic kidney disease (CKD). Congenic mapping and sequence analysis in rats suggested Shroom3 was a strong positional candidate gene. Transferring a 6.1-Mb region containing the wild-type Shroom3 gene significantly improved the kidney glomerular function in FHH (fawn-hooded hypertensive) rat. The wild-type Shroom3 allele, but not the FHH Shroom3 allele, rescued glomerular defects induced by knockdown of endogenous shroom3 in zebrafish, suggesting that the FHH Shroom3 allele is defective and likely contributes to renal injury in the FHH rat. We also show for the first time that variants disrupting the actin-binding domain of SHROOM3 may cause podocyte effacement and impairment of the glomerular filtration barrier.