bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetization of ternary alloys based on Fe0.65Ni0.35 invar with 3d transition metal additions: An ab initio study
Authors: Onoue Masatoshi , Trimarchi Giancarlo , Freeman Arthur J. , Popescu Voicu , Matsen Marc R.
Published: January 2015

Smart susceptors are being developed for use as tooling surfaces in molding machines that use apply electro-magnetic induction heating to mold and form plastics or metal powders into structural parts, e.g., on aerospace and automotive manufacturing lines. The optimal magnetic materials for the induction heating process should have large magnetization, high magnetic permeability, but also small thermal expansion coefficient. The Fe0.65Ni0.35 invar alloy with its negligible thermal expansion coefficient is thus a natural choice for this application. Here, we use density functional theory as implemented through the Korringa-Kohn-Rostoker method within the coherent-potential approximation, to design new alloys with the large magnetization desired for smart susceptor applications. We consider the Fe0.65–xNi0.35–yMx+y alloys derived from Fe0.65Ni0.35 invar adding a third element M = Sc, Ti, V, Cr, Mn, or Co with concentration (x + y) reaching up to 5 at. %. We find that the total magnetization depends linearly on the concentration of M. Specifically, the early 3d transition metals from Sc to Cr decrease the magnetization with respect to that of the invar alloy whereas Mn and Co increase it.
Differential capacitance of the electric double layer: The interplay between ion finite size and dielectric decrement
Authors: Nakayama Yasuya , Andelman David
Published: January 2015

We study the electric double layer by combining the effects of ion finite size and dielectric decrement. At high surface potential, both mechanisms can cause saturation of the counter-ion concentration near a charged surface. The modified Grahame equation and differential capacitance are derived analytically for a general expression of a permittivity ε(n) that depends on the local ion concentration, n, and under the assumption that the co-ions are fully depleted from the surface. The concentration at counter-ion saturation is found for any ε(n), and a criterion predicting which of the two mechanisms (steric vs. dielectric decrement) is the dominant one is obtained. At low salinity, the differential capacitance as function of surface potential has two peaks (so-called camel-shape). Each of these two peaks is connected to a saturation of counter-ion concentration caused either by dielectric decrement or by their finite size. Because these effects depend mainly on the counter-ion concentration at the surface proximity, for opposite surface-potential polarity either the cations or anions play the role of counter-ions, resulting in an asymmetric camel-shape. At high salinity, we obtain and analyze the crossover in the differential capacitance from a double-peak shape to a uni-modal one. Finally, several nonlinear models of the permittivity decrement are considered, and we predict that the concentration at dielectrophoretic saturation shifts to higher concentration than those obtained by the linear decrement model.
Method and apparatus for characterization of electric field-induced aggregation in pre-crystalline protein solutions
Authors: Wakamatsu Takashi
Published: January 2015

The article presents a method and an apparatus for the characterization of protein aggregation under an applied internal electric field. The method is based on a forward light scattering technique that is highly sensitive to aggregates in pre-crystalline protein solutions. Transparent conductive films are used as electrodes for a planar thin sample cell, which enables precise measurement of the forward light scattering at small angles through the electrodes. Evaluation of the protein aggregation under applied electric fields was demonstrated for a model lysozyme protein. In situ measurements of crystallizing lysozyme solutions under a low applied voltage revealed that the forward static light scattering profiles changed with time into power law profiles. This indicates the formation of lysozyme fractal clusters under applied electric fields in the pre-crystalline state. The method and the apparatus presented here can sensitively evaluate the promotion process in protein crystallization under an applied electric field.
Sub-terahertz amplification in a semiconductor superlattice with moving charge domains
Authors: Makarov V. V. , Hramov A. E. , Koronovskii A. A. , Alekseev K. N. , Maximenko V. A. , Greenaway M. T. , Fromhold T. M. , Moskalenko O. I. , Balanov A. G.
Published: January 2015

We theoretically study the high-frequency response of charge domains traveling through a strongly coupled semiconductor superlattice with an applied harmonic electromagnetic signal. Our calculations show that the superlattice alone can amplify signals with a frequency close to the domain transient frequency. Moreover, we show that if the superlattice is connected to a resonator, amplification becomes possible for much higher frequencies of the external signal (several hundred GHz). These promising results open the way to using semiconductor superlattices as efficient sub-THz amplifiers.
Note: The design of thin gap chamber simulation signal source based on field programmable gate array
Authors: Hu Kun , Lu Houbing , Wang Xu , Li Feng , Liang Futian , Jin Ge
Published: January 2015

The Thin Gap Chamber (TGC) is an important part of ATLAS detector and LHC accelerator. Targeting the feature of the output signal of TGC detector, we have designed a simulation signal source. The core of the design is based on field programmable gate array, randomly outputting 256-channel simulation signals. The signal is generated by true random number generator. The source of randomness originates from the timing jitter in ring oscillators. The experimental results show that the random number is uniform in histogram, and the whole system has high reliability.
Note: An improved driver section for a diaphragmless shock tube
Authors: Randazzo J. B. , Tranter R. S.
Published: January 2015

Improvements to equipment lifetime and measurement reproducibility have been made by modifying the actuating mechanism of a diaphragmless shock tube that is used for high temperature gas kinetic studies. The modifications have two major benefits while retaining the simplicity of the original apparatus. First, the reproducibility of shock wave generation has been greatly improved and is demonstrated with 50 nearly identical experiments on the dissociation of cyclohexene at T2 = 1765 ± 13 K and P2 = 120 ± 1 Torr, demonstrating the capability for signal averaging over many experiments. Second, the lifetime of the bellows which forms the heart of the actuator is considerably improved, significantly increasing the time between replacements.
Magnetic-tunnel-junction based low-energy nonvolatile flip-flop using an area-efficient self-terminated write driver
Authors: Suzuki Daisuke , Hanyu Takahiro
Published: January 2015

A nonvolatile flip-flop (NV-FF) that makes it possible to minimize the backup energy before power-off is proposed. The use of a self-terminated write driver with continuous voltage monitoring enables automatic write-current termination to be performed immediately after the desired data are written, resulting in great energy saving. Moreover, by utilizing single-ended circuitry together with a symmetrical write current path structure, both a nonvolatile storage function and self-termination are compactly embedded in the NV-FF without performance degradation. As a result, the backup energy is reduced by 83% compared to that of the average of conventional magnetic tunnel junction (MTJ)-based NV-FFs with no self-termination. It is also demonstrated that total transistor counts are reduced by 43% compared to a conventional MTJ-based NV-FF with self-termination.
Strain-induced structural, band-structure and piezoelectric evolutions in Al0.5Ga0.5N alloy
Authors: Duan Yifeng , Lv Dong , Liu Kun , Wu Hongbo , Qin Lixia , Shi Liwei , Tang Gang
Published: January 2015

Structural phase transition, band structure, and piezoelectric response of Al0.5Ga0.5N alloy under uniaxial and biaxial strains are systematically investigated using first-principle calculations. The main findings are summarized as follows: (I) Although the wurtzite structure transforms to an intermediate graphite-like structure for both uniaxial and biaxial strains, the second-order phase transition is found for uniaxial strain and the first-order transition for biaxial strain. The transition is driven by the mechanical and dynamical instabilities for uniaxial strain, and by the mechanical instability for biaxial strain. (II) The wurtzite phase always remains the direct band structure, whereas the band gap of graphite-like phase is always indirect. The band gaps of wurtzite and graphite-like phases are greatly reduced by internal strains. (III) The drastic enhancements in piezoelectric response are observed near phase transition, which is attributed to the flat and shallow local energy minima associated with two different phases. Our calculated results are compared with the available experimental and other theoretical data, and good agreements are obtained.
Irreversible magnetization and self-interaction investigated by thermal activation in Pr2Fe14B magnets
Authors: Li Z. B. , Shen B. G. , Zhang M. , Zhang Y. , Hu F. X. , Sun J. R.
Published: January 2015

The irreversible magnetization is investigated by thermal activation, which results from the nucleation of reversed domain from defect region at grain surface to perfect region within grain owing to the self-interaction. In the irreversible magnetization, the self-interaction unit involves two parts, i.e., the domain wall in perfect region and a small part in defect region. A larger volume of defect region involved in the self-interaction unit leads to the significant reduction of energy barrier, resulting in a lower coercivity. These investigations demonstrate that magnetization behavior could be manipulated by the self-interaction at grain outer layer.
Dual optical marker Raman characterization of strained GaN-channels on AlN using AlN/GaN/AlN quantum wells and 15N isotopes
Authors: Qi Meng , Li Guowang , Protasenko Vladimir , Zhao Pei , Verma Jai , Song Bo , Ganguly Satyaki , Zhu Mingda , Hu Zongyang , Yan Xiaodong , Mintairov Alexander , Xing Huili Grace , Jena Debdeep
Published: January 2015

This work shows that the combination of ultrathin highly strained GaN quantum wells embedded in an AlN matrix, with controlled isotopic concentrations of Nitrogen enables a dual marker method for Raman spectroscopy. By combining these techniques, we demonstrate the effectiveness in studying strain in the vertical direction. This technique will enable the precise probing of properties of buried active layers in heterostructures, and can be extended in the future to vertical devices such as those used for optical emitters and for power electronics.
Longer battery lifetime provided by a priority load control algorithm on stand-alone photovoltaic system
Authors: Faxas-Guzmán J. , Fernández Romero Antonio J. , Roa-Escalante G. , Tafur Juan P. , Urbina A.
Published: January 2015

Access to electricity has a positive impact on the socio-economic activity in rural livelihoods. Stand-alone photovoltaic (SAPV) systems are the most popular PV application for rural electrification in areas nonconnected to the grid, but it is still relatively expensive. Batteries are considered as a weak component of the system, comprising an important part of the total cost and are usually replaced multiple times during PV system lifetime. A priority load control algorithm has been developed in order to gain a better energy management over system loads and the battery storage, and therefore guarantee the energy supply for critical loads and extends the battery service lifetime. This will increase the reliability of the system and the end-user satisfaction. This article describes a stand-alone PV system model used for the development of a priority load control algorithm and explains and implements the algorithm. The results of several test scenario simulations are shown and discussed.
Controlling spin–orbit interaction in a ferromagnetic Fe/Au double layer
Authors: Samarin Sergey N. , Artamonov Oleg M. , Baraban Alexander P. , Kostylev Mikhail , Guagliardo Paul , Williams James F.
Published: January 2015

Using spin-polarized single- and two-electron spectroscopy, we probe exchange and spin–orbit interaction in a double layer of Fe and Au on W(110) and measure the spin asymmetry of the Bloch spectral density function of the sample. In a 5 ML iron film, the spin-orbit contribution to the measured asymmetry of the (e,2e) spectra was not detectable, whereas a deposition of about 1 ML of gold introduced a substantial spin-orbit component in the measured asymmetry. At the same time, this double layer still exhibits ferromagnetic properties: (i) the spectral density function asymmetry demonstrate imbalance of spin-up and spin-down electron densities in the valence band and (ii) the Stoner excitation asymmetry has almost the same value as in a pure Fe film.
Gravity induced crease-to-wrinkle transition in soft materials
Authors: Liang Xudong , Cai Shengqiang
Published: January 2015

Creasing and wrinkling instability are two distinct surface instability modes characterized by localized singular folds and continuous smooth undulations, respectively. In this article, we show that the surface of a soft elastomer may develop wrinkles or creases under compression and the action of gravitational force, depending on the magnitude of gravitational force. Using linear perturbation analysis and numerical calculations, we establish a phase map with respective creasing domain, wrinkling domain and the domain of homogenous deformation. When the gravitational force is small, the surface of the elastomer forms creases when the compressive strain is beyond a critical value, while the surface of the elastomer forms wrinkles under compression when the gravitation force is large.
Persisting structures in almost saturated magnetic states and their implication for coercivity in a grain system revealed by a large-scale two-dimensional Ginzburg-Landau type simulation
Authors: Iwano Kaoru , Mitsumata Chiharu , Ono Kanta
Published: January 2015

We investigate magnetization processes expected for thin films by using a two-dimensional Ginzburg-Landau type model augmented by a long-range dipole-dipole interaction. For homogeneous systems without any extrinsic effects, we find several persisting structures with opposite magnetization in almost saturated magnetic states. They take relatively stable forms, typically, a line, a honeycomb, and so on, which originate from the global connectivity of the initial maze in the sense of percolation. For systems with square-like grain structures, on the other hand, we find maze-like structures that are patterned beyond grain boundaries for zero field. For saturated fields, we again recognize the line-type structure in some grains but do not recognize it in the other grains, strongly depending on the initial pattern in each grain. When we decrease the field, such distinctions are maintained and the latter grains keep their magnetization down to some critical field. The result indicates the duality of the so-called magnetic separability as well as a mechanism of finite coercive fields in the presence of the grain boundaries.
An intelligent control strategy of fractional short circuit current maximum power point tracking technique for photovoltaic applications
Authors: Sher Hadeed Ahmed , Murtaza Ali F. , Noman Abdullah , Addoweesh Khaled E. , Chiaberge Marcello
Published: January 2015

This paper presents an improved Fractional Short Circuit Current (FSCC) Maximum Power Point Tracking (MPPT) technique in which an additional control loop is used to find the proper moment to measure the SCC. The target is to reduce the power losses in MPPT process that occur as a result of intermittent time based short circuit current measurements. The proposed modification enables the conventional FSCC MPPT to decide intelligently about the measurement of SCC thus reduces the number of times the photovoltaic (PV) module is isolated from the load. Although number of algorithms for tracking MPPT has been reported, the proposed method suits well for low cost PV applications. A Matlab/Simulink based model is employed to test the functional abilities of the proposed method. The comparison of the proposed method and conventional time based FSCC method is also presented in the simulation analysis. Finally, a 130 W prototype based on the dSPACE DS1104 controller and experimental results are presented to verify the effectiveness of the proposed method. The technique is verified under uniform shading conditions. The results show satisfactory performance against test conditions.
SnO2 buffer layer deposition for thin film solar cells with superstrate configuration
Authors: Vigil-Galán O. , Jiménez-Olarte D. , Contreras-Puente G. , Courel Maykel
Published: January 2015

The most commonly used commercial conducting glass is the coated SnO2:F glass substrate. However, it usually presents poor morphological properties and therefore is not adequate for solar cell applications. In this work, we report results about the morphological properties improvement of commercial conductive glass by the deposition of a SnO2 buffer layer by spray pyrolysis technique. The use of a high resistivity transparent layer (buffer) onto low resistivity transparent oxide has been found to improve the solar cell performance. The methodology for improving film morphology through the deposition of SnO2 buffer layers by spray pyrolysis technique, with appropriate electro-optical properties, is presented. The solar cell results related to the use of an automatized spray pyrolysis system are presented.
Patterning of self-assembled monolayers by phase-shifting mask and its applications in large-scale assembly of nanowires
Authors: Gao Fan , Zhang Dakuan , Wang Jianyu , Sheng Yun , Yan Shancheng , Wang Xinran , Chen Kunji , Shen Jiancang , Pan Lijia , Zhou Minmin , Shi Yi
Published: January 2015

A nonselective micropatterning method of self-assembled monolayers (SAMs) based on laser and phase-shifting mask (PSM) is demonstrated. Laser beam is spatially modulated by a PSM, and periodic SAM patterns are generated sequentially through thermal desorption. Patterned wettability is achieved with alternating hydrophilic/hydrophobic stripes on octadecyltrichlorosilane monolayers. The substrate is then used to assemble CdS semiconductor nanowires (NWs) from a solution, obtaining well-aligned NWs in one step. Our results show valuably the application potential of this technique in engineering SAMs for integration of functional devices.
Feeding niche preference of the mudsnail Peringia ulvae
Authors: Araújo Cristiano V. M. , Moreira-Santos Matilde , Patrício Joana , Martins Irene , Moreno-Garrido Ignacio , Blasco Julián , Marques João C. , Ribeiro Rui
Published: January 2015

The feeding behaviour of Peringia ulvae was studied with the aim of assessing its preferential feeding niche (habit) as well as its potential role in controlling or preventing the occurrence of macroalgal blooms. Both these aspects were studied in the Mondego estuary because of the clear long-lasting eutrophication process that favours the growth of two opportunistic macroalgae, Gracilaria spp. and Ulva spp., over the local beds of the macrophyte Zostera nolteii, which is another potential food source. All three species, both with and without periphyton, were used as a single food source in feeding experiments to assess different feeding parameters of the gastropod. Sediment with microphytobenthos was used together with the latter three species in feeding niche preference experiments. None of the food types provided were resistant to grazing. Higher levels of grazing occurred on Ulva spp. (apical parts) and Z. nolteii, both with periphyton. The presence of periphyton did not change grazing rates. When a choice between each food type was offered, the sediment was clearly the feeding niche preferred by the snails. As P. ulvae spent more time on the sediment (preferred feeding niche), the hypothesis that it has a role in preventing macroalgal blooms was not supported.
Movement patterns and habitat use of juvenile mangrove whiprays (Himantura granulata)
Authors: Davy Lauren E. , Simpfendorfer Colin A. , Heupel Michelle R.
Published: January 2015

Understanding the extent of movements and space use of animals is necessary to identify vital habitats and better conserve and manage vulnerable species. We used acoustic telemetry to examine movement patterns and habitat use of juvenile mangrove whiprays (Himantura granulata) in an intertidal bay at Orpheus Island, Australia. Thirteen juveniles were acoustically monitored between March and December 2012, and in July 2012, four active tracks were completed. The majority of the acoustically monitored rays remained within the intertidal bay for the entire monitoring period. Tidal changes caused rays to move from the inner-bay mangrove (high tide) habitat to coral reef in the outer bay (low tide). Actively tracked rays moved in a directed way during running tides, remaining in shallow water. During periods of high and low tide, when rays refuged in mangrove or reef habitats, movement was limited and sinuosity was high. In mangrove areas, rays were most commonly observed refuging under or close to mangrove roots, and rarely in open sand areas. Refuging behaviour in mangrove and reef habitats suggested that predation risk may be the predominant factor influencing the movement of small rays. The continuous use of intertidal habitats demonstrates their importance to Himantura granulata.
Community participation in health service reform: the development of an innovative remote Aboriginal primary health-care service
Authors: Reeve Carole , Humphreys John , Wakerman John , Carroll Vicki , Carter Maureen , O'Brien Tim , Erlank Carol , Mansour Rafik , Smith Bec
Published: January 2015

The aim of this study was to describe the reorientation of a remote primary health-care service, in the Kimberley region of Australia, its impact on access to services and the factors instrumental in bringing about change. A unique community-initiated health service partnership was developed between a community-controlled Aboriginal health organisation, a government hospital and a population health unit, in order to overcome the challenges of delivering primary health care to a dispersed, highly disadvantaged Aboriginal population in a very remote area. The shared goals and clear delineation of responsibilities achieved through the partnership reoriented an essentially acute hospital-based service to a prevention-focussed comprehensive primary health-care service, with a focus on systematic screening for chronic disease, interdisciplinary follow up, health promotion, community advocacy and primary prevention. This formal partnership enabled the primary health-care service to meet the major challenges of providing a sustainable, prevention-focussed service in a very remote and socially disadvantaged area.
Time-limited effects of emotional arousal on item and source memory
Authors: Wang Bo , Sun Bukuan
Published: January 2015

Two experiments investigated the time-limited effects of emotional arousal on consolidation of item and source memory. In Experiment 1, participants memorized words (items) and the corresponding speakers (sources) and then took an immediate free recall test. Then they watched a neutral, positive, or negative video 5, 35, or 50 min after learning, and 24 hours later they took surprise memory tests. Experiment 2 was similar to Experiment 1 except that (a) a reality monitoring task was used; (b) elicitation delays of 5, 30, and 45 min were used; and (c) delayed memory tests were given 60 min after learning. Both experiments showed that, regardless of elicitation delay, emotional arousal did not enhance item recall memory. Second, both experiments showed that negative arousal enhanced delayed item recognition memory only at the medium elicitation delay, but not in the shorter or longer delays. Positive arousal enhanced performance only in Experiment 1. Third, regardless of elicitation delay, emotional arousal had little effect on source memory. These findings have implications for theories of emotion and memory, suggesting that emotion effects are contingent upon the nature of the memory task and elicitation delay.
Harmonic degree 1 maps are diffeomorphisms: Lewy’s theorem for curved metrics
Authors: Martin Gaven
Published: January 2015

In 1936, H. Lewy showed that the Jacobian determinant of a harmonic homeomorphism between planar domains does not vanish and thus the map is a diffeomorphism. This built on the earlier existence results of Rado and Kneser. Schoen and Yau generalised this result to degree

1
1

harmonic mappings between closed Riemann surfaces. Here we give a new approach that establishes all these results in complete generality.
Arithmetic of abelian varieties in Artin-Schreier extensions
Authors: Pries Rachel , Ulmer Douglas
Published: January 2015

We study abelian varieties defined over function fields of curves in positive characteristic

p
p

, focusing on their arithmetic in the system of Artin-Schreier extensions. First, we prove that the

L
L

-function of such an abelian variety vanishes to high order at the center point of its functional equation under a parity condition on the conductor. Second, we develop an Artin-Schreier variant of a construction of Berger. This yields a new class of Jacobians over function fields for which the Birch and Swinnerton-Dyer conjecture holds. Third, we give a formula for the rank of the Mordell-Weil groups of these Jacobians in terms of the geometry of their fibers of bad reduction and homomorphisms between Jacobians of auxiliary Artin-Schreier curves. We illustrate these theorems by computing the rank for explicit examples of Jacobians of arbitrary dimension

g
g

, exhibiting Jacobians with bounded rank and others with unbounded rank in the tower of Artin-Schreier extensions. Finally, we compute the Mordell-Weil lattices of an isotrivial elliptic curve and a family of non-isotrivial elliptic curves. The latter exhibits an exotic phenomenon whereby the angles between lattice vectors are related to point counts on elliptic curves over finite fields. Our methods also yield new results about supersingular factors of Jacobians of Artin-Schreier curves.
The Institute for the Study of Non–Model Organisms and other fantasies
Authors: Sullivan William
Published: January 2015

In his classic novel Invisible Cities, Italo Calvino describes a series of fantastic imagined cities that fulfill core human needs that remain unmet in ordinary cities. In light of the recent founding of a number of high-profile biomedical institutes, Calvino's descriptions encourage us to consider the unmet needs of the biomedical community and imagine unorthodox institutes designed to fulfill these needs.
Ploidy variation in multinucleate cells changes under stress
Authors: Anderson Cori A. , Roberts Samantha , Zhang Huaiying , Kelly Courtney M. , Kendall Alexxy , Lee ChangHwan , Gerstenberger John , Koenig Aaron B. , Kabeche Ruth , Gladfelter Amy S.
Published: January 2015

Ploidy variation is found in contexts as diverse as solid tumors, drug resistance in fungal infection, and normal development. Altering chromosome or genome copy number supports adaptation to fluctuating environments but is also associated with fitness defects attributed to protein imbalances. Both aneuploidy and polyploidy can arise from multinucleate states after failed cytokinesis or cell fusion. The consequences of ploidy variation in syncytia are difficult to predict because protein imbalances are theoretically buffered by a common cytoplasm. We examined ploidy in a naturally multinucleate fungus, Ashbya gossypii. Using integrated lac operator arrays, we found that chromosome number varies substantially among nuclei sharing a common cytoplasm. Populations of nuclei range from 1N to >4N, with different polyploidies in the same cell and low levels of aneuploidy. The degree of ploidy variation increases as cells age. In response to cellular stress, polyploid nuclei diminish and haploid nuclei predominate. These data suggest that mixed ploidy is tolerated in these syncytia; however, there may be costs associated with variation as stress homogenizes the genome content of nuclei. Furthermore, the results suggest that sharing of gene products is limited, and thus there is incomplete buffering of ploidy variation despite a common cytosol.
Heterochromatin formation via recruitment of DNA repair proteins
Authors: Kirkland Jacob G. , Peterson Misty R. , Still Christopher D. , Brueggeman Leo , Dhillon Namrita , Kamakaka Rohinton T.
Published: January 2015

Heterochromatin formation and nuclear organization are important in gene regulation and genome fidelity. Proteins involved in gene silencing localize to sites of damage and some DNA repair proteins localize to heterochromatin, but the biological importance of these correlations remains unclear. In this study, we examined the role of double-strand-break repair proteins in gene silencing and nuclear organization. We find that the ATM kinase Tel1 and the proteins Mre11 and Esc2 can silence a reporter gene dependent on the Sir, as well as on other repair proteins. Furthermore, these proteins aid in the localization of silenced domains to specific compartments in the nucleus. We identify two distinct mechanisms for repair protein–mediated silencing—via direct and indirect interactions with Sir proteins, as well as by tethering loci to the nuclear periphery. This study reveals previously unknown interactions between repair proteins and silencing proteins and suggests insights into the mechanism underlying genome integrity.
Conditional regulation of Puf1p, Puf4p, and Puf5p activity altersYHB1mRNA stability for a rapid response to toxic nitric oxide stress in yeast
Authors: Russo Joseph , Olivas Wendy M.
Published: January 2015

Puf proteins regulate mRNA degradation and translation through interactions with 3′ untranslated regions (UTRs). Such regulation provides an efficient method to rapidly alter protein production during cellular stress. YHB1 encodes the only protein to detoxify nitric oxide in yeast. Here we show that YHB1 mRNA is destabilized by Puf1p, Puf4p, and Puf5p through two overlapping Puf recognition elements (PREs) in the YHB1 3′ UTR. Overexpression of any of the three Pufs is sufficient to fully rescue wild-type decay in the absence of other Pufs, and overexpression of Puf4p or Puf5p can enhance the rate of wild-type decay. YHB1 mRNA decay stimulation by Puf proteins is also responsive to cellular stress. YHB1 mRNA is stabilized in galactose and high culture density, indicating inactivation of the Puf proteins. This condition-specific inactivation of Pufs is overcome by Puf overexpression, and Puf4p/Puf5p overexpression during nitric oxide exposure reduces the steady-state level of endogenous YHB1 mRNA, resulting in slow growth. Puf inactivation is not a result of altered expression or localization. Puf1p and Puf4p can bind target mRNA in inactivating conditions; however, Puf5p binding is reduced. This work demonstrates how multiple Puf proteins coordinately regulate YHB1 mRNA to protect cells from nitric oxide stress.
Pan1 regulates transitions between stages of clathrin-mediated endocytosis
Authors: Bradford Mary Katherine , Whitworth Karen , Wendland Beverly
Published: January 2015

Endocytosis is a well-conserved process by which cells invaginate small portions of the plasma membrane to create vesicles containing extracellular and transmembrane cargo proteins. Dozens of proteins and hundreds of specific binding interactions are needed to coordinate and regulate these events. Saccharomyces cerevisiae is a powerful model system with which to study clathrin-mediated endocytosis (CME). Pan1 is believed to be a scaffolding protein due to its interactions with numerous proteins that act throughout the endocytic process. Previous research characterized many Pan1 binding interactions, but due to Pan1's essential nature, the exact mechanisms of Pan1's function in endocytosis have been difficult to define. We created a novel Pan1-degron allele, Pan1-AID, in which Pan1 can be specifically and efficiently degraded in <1 h upon addition of the plant hormone auxin. The loss of Pan1 caused a delay in endocytic progression and weakened connections between the coat/actin machinery and the membrane, leading to arrest in CME. In addition, we determined a critical role for the central region of Pan1 in endocytosis and viability. The regions important for endocytosis and viability can be separated, suggesting that Pan1 may have a distinct role in the cell that is essential for viability.
Latin American Agriculture in a World of Trade Agreements
Authors: Josling Tim , Paggi Mechel , Wainio John , Yamazaki Fumiko
Published: January 2015

Latin American and Caribbean (LAC) countries are members of 29 distinct free trade agreements with other Latin American partners, and 44 such agreements exist between an LAC country and other countries. Among the LAC countries linked by an Free Trade Agreement (FTA), a large percentage of trade is already duty free though many trade barriers in agriculture persist. There is a significant difference in the trade patterns among the LAC countries. The Southern Cone countries, for example, have extensive agricultural exports to Asia and to the European Union (EU), and have few FTAs with regional countries. By contrast, countries in Central America and the Andean region have extensive trade agreements with each other, and have fewer exports outside the region. Meanwhile, other regions are negotiating ambitious mega‐agreements, particularly the Trans Pacific Partnership (TPP) and the Trans‐Atlantic Trade and Investment Partnership (T‐TIP). These could have significant impacts on the region, including trade diversion and preference erosion in major import markets. Several possible avenues exist for Latin American countries to accomplish the following: counter the impact of a TPP and T‐TIP on agricultural exports; strengthen existing bilateral trade agreements within the region; link existing multi‐country agreements such as Mercado Común del Sur (MERCOSUR) and the Pacific Alliance to North American Free Trade Agreement (NAFTA); consolidate the current trade agreements with the EU; or “sign on” to the TPP. This last option would be more attractive if China were to become a TPP participant. If China is not interested in joining the TPP, then for some countries a direct FTA with China could be contemplated.
Disease Beyond the Arch: A Systematic Review of Middle Aortic Syndrome in Childhood
Authors: Rumman Rawan K. , Nickel Cheri , Matsuda-Abedini Mina , Lorenzo Armando J. , Langlois Valerie , Radhakrishnan Seetha , Amaral Joao , Mertens Luc , Parekh Rulan S.
Published: January 2015

BACKGROUND

Middle aortic syndrome (MAS) is a rare clinical entity in childhood, characterized by a severe narrowing of the distal thoracic and/or abdominal aorta, and associated with significant morbidity and mortality. MAS remains a relatively poorly defined disease. This paper systematically reviews the current knowledge on MAS with respect to etiology, clinical impact, and therapeutic options.

METHODS

A systematic search of 3 databases (Embase, MEDLINE, and Cochrane Central Register of Controlled Trials) yielded 1,252 abstracts that were screened based on eligibility criteria resulting in 184 full-text articles with 630 reported cases of childhood MAS. Data extracted included patient characteristics, clinical presentation, vascular phenotype, management, and outcomes.

RESULTS

Most cases of MAS are idiopathic (64%), 15% are associated with Mendelian disorders, and 17% are related to inflammatory diseases. Extra-aortic involvement including renal (70%), superior mesenteric (30%), and celiac (22%) arteries is common, especially among those with associated Mendelian disorders. Inferior mesenteric artery involvement is almost never reported. The majority of cases (72%) undergo endovascular or surgical management with residual hypertension reported in 34% of cases, requiring medication or reintervention. Clinical manifestations and extent of extra-aortic involvement are lacking.

CONCLUSIONS

MAS presents with significant involvement of visceral arteries with over two thirds of cases having renal artery stenosis, and one third with superior mesenteric artery stenosis. The extent of disease is worse among those with genetic and inflammatory conditions. Further studies are needed to better understand etiology, long-term effectiveness of treatment, and to determine the optimal management of this potentially devastating condition.
Deterministic identification of specific individuals from GWAS results
Authors: Cai Ruichu , Hao Zhifeng , Winslett Marianne , Xiao Xiaokui , Yang Yin , Zhang Zhenjie , Zhou Shuigeng
Published: January 2015

Motivation : Genome-wide association studies (GWASs) are commonly applied on human genomic data to understand the causal gene combinations statistically connected to certain diseases. Patients involved in these GWASs could be re-identified when the studies release statistical information on a large number of single-nucleotide polymorphisms. Subsequent work, however, found that such privacy attacks are theoretically possible but unsuccessful and unconvincing in real settings.

Results : We derive the first practical privacy attack that can successfully identify specific individuals from limited published associations from the Wellcome Trust Case Control Consortium (WTCCC) dataset. For GWAS results computed over 25 randomly selected loci, our algorithm always pinpoints at least one patient from the WTCCC dataset. Moreover, the number of re-identified patients grows rapidly with the number of published genotypes. Finally, we discuss prevention methods to disable the attack, thus providing a solution for enhancing patient privacy.

Availability and implementation : Proofs of the theorems and additional experimental results are available in the support online documents. The attack algorithm codes are publicly available at https://sites.google.com/site/zhangzhenjie/GWAS_attack.zip . The genomic dataset used in the experiments is available at http://www.wtccc.org.uk/ on request.

Contact : winslett@illinois.edu or zhenjie@adsc.com.sg

Supplementary information:  Supplementary data are available from Bioinformatics online.
MetAmp: combining amplicon data from multiple markers for OTU analysis
Authors: Zhbannikov Ilya Y. , Foster James A.
Published: January 2015

Motivation: We present a novel method and corresponding application, MetAmp, to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using data from known microbial genomes. When amplicons for multiple markers such as the 16S rRNA gene hypervariable regions are available, MetAmp improves the accuracy of OTU-based methods for characterizing bacterial composition and community structure. MetAmp works best with at least three markers, and is applicable to non-bacterial analyses and to non 16S markers. Our application and testing have been limited to 16S analysis of microbial communities.

Results: We clustered standard test sequences derived from the Human Microbiome Mock Community test sets and compared MetAmp and other tools with respect to their ability to recover OTUs for these benchmark bacterial communities. MetAmp compared favorably to QIIME, UPARSE and Mothur using amplicons from one, two, and three markers.

Availability and implementation: MetAmp is available at http://izhbannikov.github.io/MetAmp/

Contact:  ilyaz@uidaho.edu , foster@uidaho.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection
Authors: Schmelcher Mathias , Shen Yang , Nelson Daniel C. , Eugster Marcel R. , Eichenseher Fritz , Hanke Daniela C. , Loessner Martin J. , Dong Shengli , Pritchard David G. , Lee Jean C. , Becker Stephen C. , Foster-Frey Juli , Donovan David M.
Published: January 2015

Objectives

In the light of increasing drug resistance in Staphylococcus aureus, bacteriophage endolysins [peptidoglycan hydrolases (PGHs)] have been suggested as promising antimicrobial agents. The aim of this study was to determine the antimicrobial activity of nine enzymes representing unique homology groups within a diverse class of staphylococcal PGHs.

Methods

PGHs were recombinantly expressed, purified and tested for staphylolytic activity in multiple in vitro assays (zymogram, turbidity reduction assay and plate lysis) and against a comprehensive set of strains (S. aureus and CoNS). PGH cut sites in the staphylococcal peptidoglycan were determined by biochemical assays (Park–Johnson and Ghuysen procedures) and MS analysis. The enzymes were tested for their ability to eradicate static S. aureus biofilms and compared for their efficacy against systemic MRSA infection in a mouse model.

Results

Despite similar modular architectures and unexpectedly conserved cleavage sites in the peptidoglycan (conferred by evolutionarily divergent catalytic domains), the enzymes displayed varying degrees of in vitro lytic activity against numerous staphylococcal strains, including cell surface mutants and drug-resistant strains, and proved effective against static biofilms. In a mouse model of systemic MRSA infection, six PGHs provided 100% protection from death, with animals being free of clinical signs at the end of the experiment.

Conclusions

Our results corroborate the high potential of PGHs for treatment of S. aureus infections and reveal unique antimicrobial and biochemical properties of the different enzymes, suggesting a high diversity of potential applications despite highly conserved peptidoglycan target sites.
OXY-2-15, a novel variant showing increased ceftazidime hydrolytic activity
Authors: Nijhuis R. H. T. , Oueslati S. , Zhou K. , Bosboom R. W. , Rossen J. W. A. , Naas T.
Published: January 2015

Objectives

Klebsiella oxytoca is a member of the family of Enterobacteriaceae and often contains the β-lactamase blaOXY gene. Although this β-lactamase does not naturally hydrolyse ceftazidime, this study describes possible in vivo selection of a clinical K. oxytoca isolate showing increased MICs of ceftazidime.

Methods

To reveal the molecular mechanism underlying this unusual resistance phenotype, WGS, cloning, overexpression, MIC and steady-state kinetic studies were performed.

Results

A patient was treated for a septic episode with ceftazidime (4 g/day). This therapy was based on earlier culture results in which, amongst others, a K. oxytoca (Velp-1) isolate was identified. After 11 days of treatment, K. oxytoca Velp-2 was isolated from a pus sample drained from the wound. The isolate showed increased resistance to ceftazidime (MIC ≥64 mg/L) compared with the original K. oxytoca isolate (Velp-1). WGS revealed the presence of a novel blaOXY-2 allele, designated blaOXY-2-15, with a two amino acid deletion at Ambler positions 168 and 169 compared with OXY-2-2. Cloning blaOXY-2-15 into Escherichia coli TOP10 resulted in increased MICs of ceftazidime, but reduced MICs of most other β-lactams compared with OXY-2-2. Steady-state kinetics confirmed the results of the MIC data, showing clearly significant ceftazidime hydrolysis.

Conclusions

This report shows the risk of in vivo selection of ceftazidime-resistant K. oxytoca isolates after prolonged ceftazidime treatment. Furthermore, it is the first known report of a K. oxytoca isolate conferring resistance to ceftazidime by a two amino acid deletion in the omega loop of OXY-2-2.
Treatment outcomes of surgery, antifungal therapy and immunotherapy in ocular and vascular human pythiosis: a retrospective study of 18 patients
Authors: Permpalung Nitipong , Worasilchai Navaporn , Plongla Rongpong , Upala Sikarin , Sanguankeo Anawin , Paitoonpong Leilani , Mendoza Leonel , Chindamporn Ariya
Published: January 2015

Objectives

Human pythiosis is a life-threatening disease for which no standard treatment protocols with proven efficacy exist. We present the results of our institutional pythiosis treatment protocol, composed of surgery, antifungal agents, iron chelator (only vascular cases) and immunotherapy.

Methods

We retrospectively analysed patients with proven vascular and ocular pythiosis in King Chulalongkorn Memorial Hospital from April 2003 to May 2013. Fisher's exact test and Wilcoxon's rank-sum test were used. The MICs of seven antifungal agents and combination drugs were investigated in eight clinical Pythium insidiosum strains.

Results

Eighteen patients were evaluated. Disease-free surgical margins were obtained in all surviving patients with vascular pythiosis (P = 0.08). Patients who underwent eye enucleation were significantly older than those who did not (P < 0.05). Patients with vascular or ocular pythiosis did not differ significantly in the median time from disease onset to first surgery or in the relationship between the type of P. insidiosum antigen and treatment outcomes. In vitro susceptibility profiles of all isolates demonstrated that no single agent or combination treatment was substantially more effective than the others. The highest MIC was detected for amphotericin B, followed in order by voriconazole, fluconazole, anidulafungin, caspofungin, itraconazole and terbinafine. No synergistic effects of the combination drug treatments were found.

Conclusions

Surgery with adequate surgical margins is a crucial determinant of survival in patients with vascular pythiosis. Itraconazole and terbinafine do not have synergistic effects on Thai P. insidiosum strains. The role of immunotherapy remains inconclusive for both vascular and ocular pythiosis.
Potency of irritation by benzylidenemalononitriles in humans correlates with TRPA1 ion channel activation
Authors: Lindsay Christopher D. , Green Christopher , Bird Mike , Jones James T. A. , Riches James R. , McKee Katherine K. , Sandford Mark S. , Wakefield Debra A. , Timperley Christopher M.
Published: January 2015

We show that the physiological activity of solid aerosolized benzylidenemalononitriles (BMNs) including ‘tear gas’ (CS) in historic human volunteer trials correlates with activation of the human transient receptor potential ankyrin 1 ion channel (hTRPA1). This suggests that the irritation caused by the most potent of these compounds results from activation of this channel. We prepared 50 BMNs and measured their hTRPA1 agonist potencies. A mechanism of action consistent with their physiological activity, involving their dissolution in water on contaminated body surfaces, cell membrane penetration and reversible thiolation by a cysteine residue of hTRPA1, supported by data from nuclear magnetic resonance experiments with a model thiol, explains the structure–activity relationships. The correlation provides evidence that hTRPA1 is a receptor for irritants on nociceptive neurons involved in pain perception; thus, its activation in the eye, nose, mouth and skin would explain the symptoms of lachrymation, sneezing, coughing and stinging, respectively. The structure–activity results and the use of the BMNs as pharmacological tools in future by other researchers may contribute to a better understanding of the TRPA1 channel in humans (and other animals) and help facilitate the discovery of treatments for human diseases involving this receptor.