bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear permittivity spectra of supercooled ionic liquids: Observation of a “hump” in the third-order permittivity spectra and comparison to double-well potential models
Authors: Patro L. N. , Burghaus O. , Roling B.
Published: April 2017

We have measured the third-order permittivity spectra ε33 of a monocationic and of a dicationic liquid close to the glass transition temperature by applying ac electric fields with large amplitudes up to 180 kV/cm. A peak (“hump”) in the modulus of ε33 is observed for a mono-cationic liquid after subtraction of the dc contribution from the imaginary part of ε33. We show that the origin of this experimental “hump” is a peak in the imaginary part of ε33, with the peak height strongly increasing with decreasing temperature. Overall, the spectral shape of the third-order permittivity of both ionic liquids is similar to the predictions of a symmetric double well potential model, although this model does not predict a “hump” in the modulus. In contrast, an asymmetric double well potential model predicts a “hump,” but the spectral shape of both the real and imaginary part of ε33 deviates significantly from the experimental spectra. These results show that not only the modulus of ε33 but also its phase is an important quantity when comparing experimental results with theoretical predictions.
Transducer design for AlN Lamb wave resonators
Authors: Zou Jie , Lin Chih-Ming , Lam C. S. , Pisano Albert P.
Published: April 2017

AlN Lamb wave resonators enjoy advanced and attractive properties for enabling the next-generation single-chip radio frequency front-end, but their moderate effective electromechanical coupling coefficient (k2eff) poses a limit to their application in filters and multiplexers. Despite the fact that the reported k2eff enhancement techniques of doped AlN thin films which are expensive and trade off the quality factor (Q), the transducer topology itself extensively impacts the k2eff value. Although an AlN cross-sectional Lame mode resonator exhibiting a k2eff of 6.34% has been demonstrated without the need for changing the piezoelectric material, a detailed study of transducer design for AlN Lamb wave resonators has not been conducted. In this work, we investigate the impact of (i) transducer configurations, (ii) electrode materials, (iii) electrode thicknesses, and (iv) interdigital transducer duty factors on the k2eff dispersive characteristics of one-port AlN Lamb wave resonators by using the finite element analysis approach. By properly designing and optimizing the transducers, the k2eff of one-port AlN Lamb wave resonators can be boosted to as high as 7.7%, showing great potential for applications of cellular frequency selection.
A complex-valued first integral of Navier-Stokes equations: Unsteady Couette flow in a corrugated channel system
Authors: Marner F. , Gaskell P. H. , Scholle M.
Published: April 2017

For a two-dimensional incompressible viscous flow, a first integral of the governing equations of motion is constructed based on a reformulation of the unsteady Navier-Stokes equations in terms of complex variables and the subsequent introduction of a complex potential field; complementary solid and free surface boundary conditions are formulated. The methodology is used to solve the challenging problem of unsteady Couette flow between two sinusoidally varying corrugated rigid surfaces utilising two modelling approaches to highlight the versatility of the first integral. In the Stokes flow limit, the results obtained in the case of steady flow are found to be in excellent agreement with corresponding investigations in the open literature. Similarly, for unsteady flow, the results are in accord with related investigations, exploring material transfer between trapped eddies and the associated bulk flow, and vice versa. It is shown how the work relates to the classical complex variable method for solving the biharmonic problem and perspectives are provided as to how the first integral may be further utilised to investigate other fluid flow features.
Active MEMS metamaterials for THz bandwidth control
Authors: Shih Kailing , Pitchappa Prakash , Manjappa Manukumara , Ho Chong Pei , Singh Ranjan , Yang Bin , Singh Navab , Lee Chengkuo
Published: April 2017

We experimentally demonstrate a microelectromechanical system (MEMS) based metamaterial with actively tunable resonance bandwidth characteristics, operating in the terahertz (THz) spectral region. The broadband resonance characteristic feature of the MEMS metamaterial is achieved by integrating sixteen microcantilever resonators of identical lengths but with continuously varying release lengths, to form a supercell. The MEMS metamaterial showed broadband resonance characteristics with a full width half maximum (FWHM) value of 175 GHz for resonators with a metal thickness of 900 nm and was further improved to 225 GHz by reducing the metal thickness to 500 nm. The FWHM resonance bandwidth of the MEMS metamaterial was actively switched to 90 GHz by electrostatically controlling the out-of-plane release height of the constituent microcantilever resonators. Furthermore, the electrically controlled resonance bandwidth allows for the active phase engineering with relatively constant intensity at a given frequency based on the reconfiguration state of the MEMS metamaterial. This enables a pathway for the realization of actively controlled transmission or reflection based on dynamically programmable THz metamaterials.
Enhanced accuracy of x-ray spectra reconstruction from filtered diode array measurements by adding a time integrated spectrometer
Authors: Ehrlich Y. , Cohen S. , Frank Y. , Malka A. , Hurvitz G. , Levy I. , Davis J. , Keiter P. A. , Drake R. P. , Shvarts D. , Fraenkel M. , Shpilman Z.
Published: April 2017

A new approach for the spectral reconstruction of time-dependent emission of soft x-ray sources based on the measurement of filtered x-ray diode array systems is suggested. Two reconstruction methods, based on this approach, are demonstrated using both simulated and measured data. The methods use the filtered x-ray diode measurement together with a co-aligned, time-integrated, spectrally resolved measurement, such as transmission grating spectroscopy. The additional experimental information allows for high accuracy spectral reconstruction, even for plasmas far from local thermodynamic equilibrium where the traditional reconstruction methods may miss some important source spectral features. For the demonstrated cases, the accuracy of the new reconstruction methods is better than 10% for the energy dependent flux and 1% of the total flux, which is higher than the accuracy of previous methods and better than the accuracy of the measurement itself.
Understanding the impact of insulating and conducting endplate boundary conditions on turbulence in CSDX through nonlocal simulations
Authors: Vaezi P. , Holland C. , Thakur S. C. , Tynan G. R.
Published: April 2017

The Controlled Shear Decorrelation Experiment (CSDX) linear plasma device provides a unique platform for investigating the underlying physics of self-regulating drift-wave turbulence/zonal flow dynamics. A minimal model of 3D drift-reduced nonlocal cold ion fluid equations which evolves density, vorticity, and electron temperature fluctuations, with proper sheath boundary conditions, is used to simulate dynamics of the turbulence in CSDX and its response to changes in parallel boundary conditions. These simulations are carried out using the BOUndary Turbulence (BOUT++) framework and use equilibrium electron density and temperature profiles taken from experimental measurements. The results show that density gradient-driven drift-waves are the dominant instability in CSDX. However, the choice of insulating or conducting endplate boundary conditions affects the linear growth rates and energy balance of the system due to the absence or addition of Kelvin-Helmholtz modes generated by the sheath-driven equilibrium E × B shear and sheath-driven temperature gradient instability. Moreover, nonlinear simulation results show that the boundary conditions impact the turbulence structure and zonal flow formation, resulting in less broadband (more quasi-coherent) turbulence and weaker zonal flow in conducting boundary condition case. These results are qualitatively consistent with earlier experimental observations.
The influence of femtosecond laser wavelength on waveguide fabrication inside fused silica
Authors: Hernandez-Rueda Javier , Clarijs Jasper , van Oosten Dries , Krol Denise M.
Published: April 2017

We have investigated the effect of the laser wavelength on the fabrication of optical waveguides and tracks of modified material via direct laser writing inside fused silica. The size of the laser-inscribed tracks, the material modification thresholds, the structural changes, and the waveguide writing energy range show a strong dependence on laser wavelengths ranging from ultraviolet to near-infrared. We used numerical simulations that consider the laser-excited electron plasma dynamics (via multiple rate equations) along with Gaussian beams theory to calculate the size of the laser-affected volume that has been further compared with the experimental results. This study yields insight into how to predict and design the spatial features of laser-inscribed lines and also aids of understanding the underlying physical mechanisms linked to laser-glass interaction when using different laser wavelengths.
Ultraintense laser absorption and γ-ray synchrotron radiation in near critical density plasmas
Authors: Chang H. X. , Qiao B. , Zhang Y. X. , Xu Z. , Yao W. P. , Zhou C. T. , He X. T.
Published: April 2017

Ultraintense laser absorption and γ-ray synchrotron radiation in near-critical-density (NCD) plasmas are investigated. Besides the known skin-depth emission and reinjected electron synchrotron emission in NCD plasmas, we find a new γ-ray emission mechanism, where γ-rays are dominantly produced by the Transversely Oscillating Electron synchrotron Emission (TOEE). In this new TOEE mechanism, electrons mainly oscillate in the transverse direction under the balance between the longitudinal laser ponderomotive force and the restoring electrostatic force. A great amount of γ photons are emitted in the transverse direction, where the peak radiation power is enhanced by twice and the photon divergence angle is relatively decreased. The features of γ-rays produced from this new TOEE mechanism have been identified and compared with the other two mechanisms by two-dimensional particle-in-cell simulations.
Self-bending elastic waves and obstacle circumventing in wireless power transfer
Authors: Tol S. , Xia Y. , Ruzzene M. , Erturk A.
Published: April 2017

We demonstrate self-bending of elastic waves along convex trajectories by means of geometric and phased arrays. Potential applications include ultrasonic imaging and manipulation, wave focusing, and wireless power transfer around obstacles. The basic concept is illustrated through a geometric array, which is designed to implement a phase delay profile among the array elements that leads to self-bending along a specified circular trajectory. Experimental validation is conducted for the lowest asymmetric Lamb wave mode in a thin plate over a range of frequencies to investigate the bandwidth of the approach. Experiments also illustrate the functionality of the array as a transmitter to deliver elastic wave energy to a receiver/harvester located behind a large obstacle for electrical power extraction. It is shown that the trajectory is not distorted by the presence of the obstacle and circumventing is achieved. A linear phased array counterpart of the geometric array is then constructed to illustrate the concept by imposing proper time delays to the array elements, which allows the generation of different trajectories using the same line source. This capability is demonstrated by tailoring the path diameter in the phased array setting, which offers the flexibility and versatility to induce a variety of convex trajectories for self-bending elastic waves.
Photoinduced entropy of InGaN/GaN p-i-n double-heterostructure nanowires
Authors: Alfaraj Nasir , Mitra Somak , Wu Feng , Ajia Idris A. , Janjua Bilal , Prabaswara Aditya , Aljefri Renad A. , Sun Haiding , Khee Ng Tien , Ooi Boon S. , Roqan Iman S. , Li Xiaohang
Published: April 2017

The photoinduced entropy of InGaN/GaN p-i-n nanowires was investigated using temperature-dependent (6–290 K) photoluminescence. We also analyzed the photocarrier dynamics in the InGaN active regions using time-resolved photoluminescence. An increasing trend in the amount of generated photoinduced entropy of the system above 250 K was observed, while we observed an oscillatory trend in the generated entropy of the system below 250 K that stabilizes between 200 and 250 K. Strong exciton localization in indium-rich clusters, carrier trapping by surface defect states, and thermodynamic entropy effects were examined and related to the photocarrier dynamics. We conjecture that the amount of generated photoinduced entropy of the system increases as more non-radiative channels become activated and more shallowly localized carriers settle into deeply localized states; thereby, additional degrees of uncertainty related to the energy of states involved in thermionic transitions are attained.
Heavy nucleus-acoustic spherical solitons in self-gravitating super-dense plasmas
Authors: Mamun A. A. , Amina M. , Schlickeiser R.
Published: April 2017

Heavy nucleus-acoustic (HNA) spherical solitons (SSs) associated with HNA waves (in which the inertia is provided by the heavy and light nuclear species, and restoring force is provided by the degenerate pressure of electron species) in self-gravitating degenerate (super-dense) quantum plasmas have been theoretically investigated. The reductive perturbation method has been employed to derive a modified Korteweg-de Vries equation. The new basic features (e.g., polarity, amplitude, width, etc.) of the HNA SSs (associated with electrostatic and self-gravitational potentials) are identified, and are found to be significantly modified by the effects of ultra-relativistically degenerate electron pressure, dynamics of non-degenerate light and heavy nuclear species, self-gravitational field, and spherical geometry. It is found that depending on the plasma parameters, the HNA SSs with either positive (negative) or negative (positive) electrostatic (self-gravitational) potential exist in such realistic astrophysical plasma systems. The applications of our results in some astrophysical compact objects (containing heavy and light nuclear species, and degenerate electron species) are briefly discussed.
Determination of the mean inner potential of cadmium telluride via electron holography
Authors: Cassidy C. , Dhar A. , Shintake T.
Published: April 2017

Mean inner potential is a fundamental material parameter in solid state physics and electron microscopy and has been experimentally measured in CdTe, a technologically important semiconductor. As a first step, the inelastic mean free path for electron scattering in CdTe was determined, using electron energy loss spectroscopy, to enable precise thickness mapping of thin CdTe lamellae. The obtained value was λi(CdTe, 300 kV) = 192 ± 10 nm. This value is relatively large, given the high density of the material, and is discussed in the text. Next, electron diffraction and specimen tilting were employed to identify weakly diffracting lattice orientations, to enable the straightforward measurement of the electron phase shift. Finally, electron holography was utilized to quantitatively map the phase shift experienced by electron waves passing through a CdTe crystal, with several different propagation vectors. Utilization of both thickness and phase data allowed computation of mean inner potential as V0 (CdTe) = 14.0 ± 0.9 V, within the range of previous theoretical estimates.
Emergence of a weak topological insulator from the BixSey family
Authors: Majhi Kunjalata , Pal Koushik , Lohani Himanshu , Banerjee Abhishek , Mishra Pramita , Yadav Anil K. , Ganesan R. , Sekhar B. R. , Waghmare Umesh V. , Anil Kumar P. S.
Published: April 2017

We report the emergence of a weak topological insulator (WTI), BiSe, of the Bi-chalcogenide family with an indirect bandgap of 42 meV. Its structural unit consists of a bismuth bilayer (Bi2), a known quantum spin hall insulator sandwiched between two units of Bi2Se3 which are three dimensional strong topological insulators. Our density functional theory calculations confirm the WTI phase and angle resolved photo-emission spectroscopy measurements carried out on cleaved single crystal flakes show Rashba states that closely agree with our theoretical predictions. Finally, we present a comparison between electronic and magneto-transport properties measured on single crystal flakes and thin films of BiSe.
Characteristics of layered tin disulfide deposited by atomic layer deposition with H2S annealing
Authors: Lee Seungjin , Shin Seokyoon , Ham Giyul , Lee Juhyun , Choi Hyeongsu , Park Hyunwoo , Jeon Hyeongtag
Published: April 2017

Tin disulfide (SnS2) has attracted much attention as a two-dimensional (2D) material. A high-quality, low-temperature process for producing 2D materials is required for future electronic devices. Here, we investigate tin disulfide (SnS2) layers deposited via atomic layer deposition (ALD) using tetrakis(dimethylamino)tin (TDMASn) as a Sn precursor and H2S gas as a sulfur source at low temperature (150° C). The crystallinity of SnS2 was improved by H2S gas annealing. We carried out H2S gas annealing at various conditions (250° C, 300° C, 350° C, and using a three-step method). Angle-resolved X-ray photoelectron spectroscopy (ARXPS) results revealed the valence state corresponding to Sn4+ and S2- in the SnS2 annealed with H2S gas. The SnS2 annealed with H2S gas had a hexagonal structure, as measured via X-ray diffraction (XRD) and the clearly out-of-plane (A1g) mode in Raman spectroscopy. The crystallinity of SnS2 was improved after H2S annealing and was confirmed using the XRD full-width at half-maximum (FWHM). In addition, high-resolution transmission electron microscopy (HR-TEM) images indicated a clear layered structure.
Disclosure of newly diagnosed HIV infection and condom use at first sex after diagnosis: a study of young Black men who have sex with men
Authors: Crosby Richard A. , Mena Leandro , Arnold Trisha
Published: April 2017

Background
The first purpose of the present study was to determine whether young Black men who have sex with men (YBMSM) disclose their newly diagnosed HIV infection to a male or female partner, and to determine whether this disclosure is related to condom use; the second was to identify correlates of disclosing newly diagnosed HIV infection to male sex partners, including a measure of partner-related barriers to condom use. Methods: A sample of 125 HIV-infected YBMSM (age 15–29 years) provided cross-sectional data used for both study purposes. Recruitment occurred in a mid-size city in the southern US experiencing inordinately high prevalence and incidence rates of HIV among YBMSM. Significance was defined by an α level of <0.05. Results: Eighty-eight YBMSM (70.4%) indicated disclosing their newly diagnosed HIV status to the first male partner they had sex with after being diagnosed. Of these, nine (9.1%) reported that condoms were not used during ensuing sex with that partner. However, of the men not disclosing, 27.0% reported not using condoms for ensuing sex (P = 0.009). Similar findings were observed relative to sex with females (P = 0.057). Regarding the second study purpose, in addition to a protective effect of advancing age, men scoring at or above the median on a measure of partner-related barriers to condom use were 2.4-fold more likely to not disclose compared with men scoring below the median (P = 0.04). Conclusion: For YBMSM, a beneficial counselling objective relative to disclosing newly diagnosed HIV may be to help men resolve perceptions of partner-related barriers to condom use.
Reconstructing the spectrotemporal modulations of real-life sounds from fMRI response patterns
Authors: Santoro Roberta , Moerel Michelle , De Martino Federico , Valente Giancarlo , Ugurbil Kamil , Yacoub Essa , Formisano Elia
Published: April 2017

Significance

The sounds we encounter in everyday life (e.g. speech, voices, animal cries, wind, rain) are complex and various. How the human brain analyses their acoustics remains largely unknown. This research shows that mathematical modelling in combination with high spatial resolution functional magnetic resonance imaging enables reverse engineering of the human brain computations underlying real-life listening. Importantly, the research reveals that even general auditory processing mechanisms in the human brain are optimized for fine-grained analysis of the most behaviorally relevant sounds (i.e., speech, voices). Most likely, this observation reflects the evolutionary feat that, for humans, discriminating between speech sounds is more crucial than distinguishing, for example, between barking dogs.
The Shiʿa Afghan Community: Between Transnational Links and Internal Hurdles
Authors: Therme Clément
Published: April 2017

This article aims to present a political analysis of the relationship between the Shiʿa community in Afghanistan and the new political system that emerged after the US military intervention of 2001. In light of the sectarian conflicts in the greater Middle East and the connection between South West Asia and the Syrian war since 2011, this article illustrates the limits of the social empowerment of the Shiʿa communities in Afghanistan. The article outlines the internal religious scene and the connections between āyatollāhs (marājeʿ), mainly from Iran or Iraq, and Afghan Shiʿite believers. It also examines how the Afghan Shiʿite community differs from those of Iran and Iraq.
Deformation twin and martensite in the Fe–36%Ni alloy during cryorolling
Authors: Zheng Jianjun , Li Changsheng , He Shuai , Ma Biao , Song Yanlei
Published: April 2017

In this paper, the microstructural evolution and deformation mechanism of the cryorolled Fe–36%Ni alloy was investigated. Deformation twinning was confirmed to be activated at the early stage of cryorolling (CR) and subsequently suppressed due to microstructure refinement. The existence of [Formula: see text] and [Formula: see text] peaks revealed that the [Formula: see text] ( α′-M) phase transformation was induced during the CR process. The stress-assisted martensite and strain-induced martensite were detected to be transformed at the grain boundary and intersection of deformation twins, respectively. Owing to the co-effect of the temperature raise and mechanical stabilisation, the α′-M phase transformation was suppressed during the CR process. Therefore, the amount of the α′-M was limited in the tested alloy.
Welding of unique and advanced ductile intermetallic alloys for high-temperature applications
Authors: David S. A. , Deevi S. C.
Published: April 2017

Intermetallic alloys represent a unique class of materials with atomic arrangements that are different from those of conventional disordered alloys. Among them are alloys based on Ni3Al, Fe3Al, and TiAl. Intermetallic alloys have unique properties, such as high melting point, low density, high-temperature strength, and high-temperature corrosion and oxidation resistance. Their only disadvantage is the lack of ductility at room temperature and at elevated temperatures. However, they can be ductilised by micro- and macroalloying. Application of intermetallic alloys for structural use at elevated temperature depends on their ability to be welded using conventional welding procedures. This paper focuses on the development of these alloys, their behaviour when subjected to weld thermal cycles, and their weldability. Most intermetallic alloys are susceptible to cracking during or after welding, but some can be modified to have good weldability. The paper discusses welding and weldability of Ni3Al-, Fe3Al-, and TiAl-based intermetallic alloys. In addition, the weldability of other long-range ordered alloys, of the type (Fe, Ni)3V and (Fe, Co)3V, are briefly discussed.
GOP-1 promotes apoptotic cell degradation by activating the small GTPase Rab2 in C. elegans
Authors: Yin Jianhua , Huang Yaling , Guo Pengfei , Hu Siqi , Yoshina Sawako , Xuan Nan , Gan Qiwen , Mitani Shohei , Yang Chonglin , Wang Xiaochen
Published: April 2017

Apoptotic cells generated by programmed cell death are engulfed by phagocytes and enclosed within plasma membrane–derived phagosomes. Maturation of phagosomes involves a series of membrane-remodeling events that are governed by the sequential actions of Rab GTPases and lead to formation of phagolysosomes, where cell corpses are degraded. Here we identified gop-1 as a novel regulator of apoptotic cell clearance in Caenorhabditis elegans. Loss of gop-1 affects phagosome maturation through the RAB-5–positive stage, causing defects in phagosome acidification and phagolysosome formation, phenotypes identical to and unaffected by loss of unc-108, the C. elegans Rab2. GOP-1 transiently associates with cell corpse–containing phagosomes, and loss of its function abrogates phagosomal association of UNC-108. GOP-1 interacts with GDP-bound and nucleotide-free UNC-108/Rab2, disrupts GDI-UNC-108 complexes, and promotes activation and membrane recruitment of UNC-108/Rab2 in vitro. Loss of gop-1 also abolishes association of UNC-108 with endosomes, causing defects in endosome and dense core vesicle maturation. Thus, GOP-1 is an activator of UNC-108/Rab2 in multiple processes.
Splenic Ly6Ghigh mature and Ly6Gint immature neutrophils contribute to eradication of S. pneumoniae
Authors: Deniset Justin F. , Surewaard Bas G. , Lee Woo-Yong , Kubes Paul
Published: April 2017

The spleen plays an integral protective role against encapsulated bacterial infections. Our understanding of the associated mechanisms is limited to thymus-independent (TI) antibody production by the marginal zone (MZ) B cells, leaving the contribution of other splenic compartments such as the red pulp (RP) largely unexplored despite asplenic patients succumbing to the infection in the first 24 h, suggesting important antibody-independent mechanisms. In this study, using time-lapse intravital imaging of the spleen, we identify a tropism for Streptococcus pneumoniae in this organ mediated by tissue-resident MZ and RP macrophages and a protective role for two distinct splenic neutrophil populations (Ly6Ghi and Ly6Gintermediate) residing in the splenic RP. Splenic mature neutrophils mediated pneumococcal clearance in the spleen by plucking bacteria off the surface of RP macrophages that caught the majority of bacteria in a complement-dependent manner. This neutrophil phagocytic capacity was further enhanced after TI antibody production. Resident immature neutrophils (Ly6Gintermediate) in the spleen undergo emergency proliferation and mobilization from their splenic niche after pneumococcal stimulation to increase the effector mature neutrophil pool. We demonstrate that splenic neutrophils together with two macrophage populations and MZ B cells regulate systemic S. pneumoniae clearance through complementary mechanisms.
Location in the spleen dictates the function of murine neutrophils
Authors: Scapini Patrizia , Cassatella Marco A.
Published: April 2017

In this issue of JEM, Deniset et al. (https://doi.org/10.1084/jem.20161621) provide new data that extend our knowledge on the mechanisms whereby Streptococcus pneumoniae is cleared by the spleen. The authors identify novel populations of murine splenic neutrophils that localize in the red pulp and the marginal zone. During the acute phases of S. pneumoniae infection, these populations of splenic neutrophils act in concert with specialized macrophage and B cell populations to provide very rapid innate immune protection.
Tension-activated channels in the mechanism of osmotic fitness in Pseudomonas aeruginosa
Authors: Çetiner Uğur , Rowe Ian , Schams Anthony , Mayhew Christina , Rubin Deanna , Anishkin Andriy , Sukharev Sergei
Published: April 2017

Pseudomonas aeruginosa (PA) is an opportunistic pathogen with an exceptional ability to adapt to a range of environments. Part of its adaptive potential is the ability to survive drastic osmolarity changes. Upon a sudden dilution of external medium, such as during exposure to rain, bacteria evade mechanical rupture by engaging tension-activated channels that act as osmolyte release valves. In this study, we compare fast osmotic permeability responses in suspensions of wild-type PA and Escherichia coli (EC) strains in stopped-flow experiments and provide electrophysiological descriptions of osmotic-release channels in PA. Using osmotic dilution experiments, we first show that PA tolerates a broader range of shocks than EC. We record the kinetics of cell equilibration reported by light scattering responses to osmotic up- and down-shocks. PA exhibits a lower water permeability and faster osmolyte release rates during large osmotic dilutions than EC, which correlates with better survival. To directly characterize the PA tension-activated channels, we generate giant spheroplasts from this microorganism and record current responses in excised patches. Unlike EC, which relies primarily on two types of channels, EcMscS and EcMscL, to generate a distinctive two-wave pressure ramp response, PA exhibits a more gradual response that is dominated by MscL-type channels. Genome analysis, cloning, and expression reveal that PA possesses one MscL-type (PaMscL) and two MscS-type (PaMscS-1 and 2) proteins. In EC spheroplasts, both PaMscS channels exhibit a slightly earlier activation by pressure compared with EcMscS. Unitary currents reveal that PaMscS-2 has a smaller conductance, higher anionic preference, stronger inactivation, and slower recovery compared with PaMscS-1. We conclude that PA relies on MscL as the major valve defining a high rate of osmolyte release sufficient to curb osmotic swelling under extreme shocks, but it still requires MscS-type channels with a strong propensity to inactivation to properly terminate massive permeability response.
Gaussian elimination for sparse matrices: an introduction
Authors: Duff I. S. , Erisman A. M. , Reid J. K.
Published: April 2017

This chapter provides an introduction to the use of Gaussian elimination for solving sets of linear equations that are sparse. We examine the three principle phases of most computer programs for this task: ANALYSE, FACTORIZE, and SOLVE. We stress the importance of acceptable overheads and of numerical stability, but are not concerned with algorithmic or implementation details which are the subjects of later chapters.
Implementing Gaussian elimination without symbolic factorize
Authors: Duff I. S. , Erisman A. M. , Reid J. K.
Published: April 2017

We describe the implementation of the ordering and solution algorithms of Chapter 7, emphasizing the use of a dynamic data structure for the pivoting strategy of Markowitz (1957) for unsymmetric matrices. We also study the use of static data structures for numerical factorization and solution. We examine hybrid techniques that combine sparse and dense matrix manipulation, methods based on code generation, and the use of drop tolerances. We consider various ways in which these approaches have been adapted to exploit parallelism.
The solve phase
Authors: Duff I. S. , Erisman A. M. , Reid J. K.
Published: April 2017

We examine the SOLVE phase in the direct solution of sparse systems. Here we assume that the factors have been computed and we study the efficient use of these to determine the solution through forward and back-substitution. We use the trees described in the previous chapters to study the efficient solution of sparse right-hand sides including the computation of null-space bases. We consider the parallelization of the SOLVE phase.
Mapping genes for calcium signaling and their associated human genetic disorders
Authors: Hörtenhuber Matthias , Toledo Enrique M , Smedler Erik , Arenas Ernest , Malmersjö Seth , Louhivuori Lauri , Uhlén Per
Published: April 2017

Motivation

Signal transduction via calcium ions (Ca2+) represents a fundamental signaling pathway in all eukaryotic cells. A large portion of the human genome encodes proteins used to assemble signaling systems that can transduce signals with diverse spatial and temporal dynamics.

Results

Here, we provide a map of all of the genes involved in Ca2+ signaling and link these genes to human genetic disorders. Using Gene Ontology terms and genome databases, 1805 genes were identified as regulators or targets of intracellular Ca2+ signals. Associating these 1805 genes with human genetic disorders uncovered 1470 diseases with mutated ‘Ca2+ genes’. A network with scale-free properties appeared when the Ca2+ genes were mapped to their associated genetic disorders.

Availability and Implementation

The Ca2+ genome database is freely available at http://cagedb.uhlenlab.org and will foster studies of gene functions and genetic disorders associated with Ca2+ signaling.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evolving Failures in the Delivery of Human Immunodeficiency Virus Care: Lessons From a Ugandan Meningitis Cohort 2006–2016
Authors: Flynn Andrew G. , Meya David B. , Hullsiek Katherine Huppler , Rhein Joshua , Williams Darlisha A. , Musubire Abdu , Morawski Bozena M. , Taseera Kabanda , Sadiq Alisat , Ndyatunga Liberica , Roediger Mollie , Rajasingham Radha , Bohjanen Paul R. , Muzoora Conrad , Boulware David R.
Published: April 2017

Background

Because of investments in human immunodeficiency virus (HIV) care in sub-Saharan Africa, the number of people aware of their status and receiving antiretroviral therapy (ART) has increased; however, HIV/acquired immune deficiency syndrome (AIDS) mortality still remains high.

Methods

We performed retrospective analysis of 3 sequential prospective cohorts of HIV-infected Ugandan adults presenting with AIDS and meningitis from 2006 to 2009, 2010 to 2012, and 2013 to 2016. Participants were categorized as follows: (1) unknown HIV status; (2) known HIV+ without ART; (3) known HIV+ with previous ART. We further categorized 2006 and 2013 cohort participants by duration of HIV-status knowledge and of ART receipt.

Results

We screened 1353 persons with suspected meningitis. Cryptococcus was the most common pathogen (63%). Over the decade, we observed an absolute increase of 37% in HIV status knowledge and 59% in antecedent ART receipt at screening. The 2006 cohort participants were new/recent HIV diagnoses (65%) or known HIV+ but not receiving ART (35%). Many 2013 cohort participants were new/recent HIV diagnoses (34%) and known HIV+ with <1 month ART (20%), but a significant proportion were receiving ART 1–4 months (11%) and >4 months (30%). Four percent of participants discontinued ART. From 2010 to 2016, meningitis cases per month increased by 33%.

Conclusions

Although improved HIV screening and ART access remain much-needed interventions in resource-limited settings, greater investment in viral suppression and opportunistic infection care among the growing HIV-infected population receiving ART is essential to reducing ongoing AIDS mortality.
Type VI Secretion Systems of Erwinia amylovora Contribute to Bacterial Competition, Virulence, and Exopolysaccharide Production
Authors: Tian Yanli , Zhao Yuqiang , Shi Linye , Cui Zhongli , Hu Baishi , Zhao Youfu
Published: April 2017

The type VI secretion system (T6SS) plays a major role in mediating interbacterial competition and might contribute to virulence in plant pathogenic bacteria. However, the role of T6SS in Erwinia amylovora remains unknown. In this study, 33 deletion mutants within three T6SS clusters were generated in E. amylovora strain NCPPB1665. Our results showed that all 33 mutants displayed reduced antibacterial activities against Escherichia coli as compared with that of the wild-type (WT) strain, indicating that Erwinia amylovora T6SS are functional. Of the 33 mutants, 19 exhibited reduced virulence on immature pear fruit as compared with that of the WT strain. Among them, 6, 1, and 12 genes belonged to T6SS-1, T6SS-2, and T6SS-3 clusters, respectively. Interestingly, these 19 mutants also produced less amylovoran or levan or both. These findings suggest that E. amylovora T6SS play a role in bacterial competition and virulence possibly by influencing exopolysaccharide production.
GNAQ TT(-695/-694)GC Polymorphism Is Associated with Increased Gq Expression, Vascular Reactivity, and Myocardial Injury after Coronary Artery Bypass Surgery
Authors: Frey Ulrich H. , Klenke Stefanie , Mitchell Anna , Knüfermann Tim , Jakob Heinz , Thielmann Matthias , Siffert Winfried , Peters Jürgen
Published: April 2017

Background

Angiotensin II receptor type 1–mediated activation of the α-subunit of the heterotrimeric Gq protein evokes increased vasoconstriction and may promote hypertrophy-induced myocardial damage. The authors recently identified a TT(-695/-694)GC polymorphism in the human Gq promoter, the GC allele being associated with an increased prevalence of cardiac hypertrophy. In this article, the authors tested whether the TT(-695/-694)GC polymorphism is associated with differences in (1) myocardial Gq protein expression, (2) vascular reactivity, and (3) myocardial damage after coronary artery bypass grafting.

Methods

Gq protein expression was measured in right atrial muscle from 55 patients undergoing coronary artery bypass grafting as were skin perfusion changes (n = 18; laser Doppler imaging), saphenous vein ring vascular reactivity (n = 50, organ bath) in response to angiotensin II, and myocardial damage (227 patients undergoing coronary artery bypass grafting), as assessed by postoperative cardiac troponin I concentration.

Results

Myocardial Gq expression was greater in GC/GC genotypes (GC/GC vs. TT/TT: 1.27-fold change; P = 0.006). Skin perfusion after intradermal angiotensin II injection decreased only in GC/GC genotypes (P = 0.0002). Saphenous vein rings exposed to increasing angiotensin II concentrations showed an almost doubled maximum contraction in GC/GC compared with individuals with the TT/TT genotype (P = 0.022). In patients undergoing coronary artery bypass grafting, baseline cardiac ejection fraction was different (GC/GC: 55 ± 13%; GC/TT: 54 ± 14%; TT/TT: 48 ± 15%; P = 0.037) and postoperative peak cardiac troponin I was greater in patients with the GC/GC (11.5 ± 13.8 ng/ml) than in patients with the GC/TT (9.2 ± 9.2 ng/ml) or patients with the TT/TT genotype (6.6 ± 4.8 ng/ml, P = 0.015).

Conclusions

The GC/GC genotype of the TT(-695/-694)GC polymorphism is associated with increased Gq protein expression, augmented angiotensin II receptor type 1–related vasoconstriction, and increased myocardial injury after coronary artery bypass grafting, highlighting the impact of Gq genotype variation.
Inhibition of Metabotropic Glutamate Receptor Subtype 1 Alters the Excitability of the Commissural Pyramidal Neuron in the Rat Anterior Cingulate Cortex after Chronic Constriction Injury to the Sciatic Nerve
Authors: Gao Shi-Hao , Shen Lin-Lin , Wen Hui-Zhong , Zhao Yan-Dong , Ruan Huai-Zhen
Published: April 2017

Background

Inhibition of the metabotropic glutamate receptor subtype 1 in the anterior cingulate cortex has an analgesic effect during sustained nociceptive hypersensitivity. However, the specific changes in different subtypes of anterior cingulate cortex layer 5 pyramidal neurons, as well as the distinct effect of metabotropic glutamate receptor subtype 1 inhibition on different neuronal subtypes, have not been well studied.

Methods

Retrograde labeling combined with immunofluorescence, whole cell clamp recording, and behavioral tests combined with RNA interference were performed in a rat model of chronic constriction injury to the sciatic nerve.

Results

Commissural layer 5 pyramidal neurons (projecting to the contralateral cortex) existed in the anterior cingulate cortex. The voltage-gated potassium channel subunit 2–mediated current in these neurons were substantially reduced after chronic constriction injury (current densities at +30 mV for the sham, and chronic constriction injury neurons were [mean ± SD] 10.22 ± 3.42 pA/pF vs. 5.58 ± 2.71 pA/pF, respectively; n = 11; P < 0.01), which increased the spike width and fast afterhyperpolarization potential, resulting in hyperexcitability. Inhibition of metabotropic glutamate receptor subtype 1 alleviated the down-regulation of voltage-gated potassium channel subunit 2 currents (current density increased by 8.11 ± 3.22 pA/pF; n = 7; P < 0.01). Furthermore, knockdown of voltage-gated potassium channel subunit 2 current in the commissural neurons attenuated the analgesic effect of metabotropic glutamate receptor subtype 1 inhibition (n = 6 rats; P < 0.05).

Conclusions

The effect of metabotropic glutamate receptor subtype 1 inhibition on commissural anterior cingulate cortex layer 5 pyramidal neurons is likely different with the modification of previously studied hyperpolarization-activated/cyclic nucleotide-gated channel-dependent neurons but relies on the alteration of voltage-gated potassium channel subunit 2 currents. These results will contribute to a better understanding of the therapeutic role of metabotropic glutamate receptor subtype 1 in chronic pain.
Peripartum Anesthetic Management of the Opioid-tolerant or Buprenorphine/Suboxone-dependent Patient
Authors: PAN AILEEN , ZAKOWSKI MARK
Published: April 2017

Opioid abuse and dependence continues to rise in both the general population and pregnancy, with opioid overdose deaths having quadrupled in the last 15 years. Illicit drug use in last 30 days of pregnancy was over 4% with almost 0.6% documented maternal opiate use at time of birth. The management of the opioid-tolerant, buprenorphine-dependent or methadone-dependent patient in the peripartum period is reviewed. Options for treatment of opioid dependence, acute pain management, and perioperative multimodal analgesia are discussed. The effects of maternal management on neonatal abstinence syndrome are also reviewed.
Beyond cascade screening: detection of familial hypercholesterolaemia at childhood immunization and other strategies
Authors: Martin Andrew C. , Bell Damon A. , Brett Tom , Watts Gerald F.
Published: April 2017

Purpose of review

Familial hypercholesterolaemia is a common genetic disorder that accelerates premature coronary heart disease. Although effective treatments are available, the majority of individuals remain undiagnosed. We review new evidence for improving the detection of familial hypercholesterolaemia.

Recent findings

Recent studies have demonstrated that universal screening of children for familial hypercholesterolaemia may be highly effective at the time of immunization if combined with reverse cascade testing of adult family members, who have a more immediate risk of a coronary event. Alerts on laboratory reports and the application of bioinformatics to electronic health records may also be useful for identifying familial hypercholesterolaemia in community settings. Effective detection, diagnosis, and codification of familial hypercholesterolaemia are essential for the development of registries.

Although the cost-effectiveness of screening programs for familial hypercholesterolaemia in childhood remains to be established, combining universal and reverse cascade screening, complemented by opportunistic identification of individuals in high-risk settings, use of laboratory alerts, and screening of electronic health records are likely to have a high yield in the detection of familial hypercholesterolaemia in the community.
Interrater and Test-Retest Reliability of the Beery Visual-Motor Integration in Schoolchildren
Authors: Harvey Erin M. , Leonard-Green Tina K. , Mohan Kathleen M. , Kulp Marjean Taylor , Davis Amy L. , Miller Joseph M. , Twelker J. Daniel , Campus Irene , Dennis Leslie K.
Published: April 2017

Purpose

To assess interrater and test-retest reliability of the 6th Edition Beery-Buktenica Developmental Test of Visual-Motor Integration (VMI) and test-retest reliability of the VMI Visual Perception Supplemental Test (VMIp) in school-age children.

Methods

Subjects were 163 Native American third- to eighth-grade students with no significant refractive error (astigmatism <1.00 D, myopia <0.75 D, hyperopia <2.50 D, anisometropia <1.50 D) or ocular abnormalities. The VMI and VMIp were administered twice, on separate days. All VMI tests were scored by two trained scorers, and a subset of 50 tests was also scored by an experienced scorer. Scorers strictly applied objective scoring criteria. Analyses included interrater and test-retest assessments of bias, 95% limits of agreement, and intraclass correlation analysis.

Results

Trained scorers had no significant scoring bias compared with the experienced scorer. One of the two trained scorers tended to provide higher scores than the other (mean difference in standardized scores = 1.54). Interrater correlations were strong (0.75 to 0.88). VMI and VMIp test-retest comparisons indicated no significant bias (subjects did not tend to score better on retest). Test-retest correlations were moderate (0.54 to 0.58). The 95% limits of agreement for the VMI were −24.14 to 24.67 (scorer 1) and −26.06 to 26.58 (scorer 2), and the 95% limits of agreement for the VMIp were −27.11 to 27.34.

Conclusions

The 95% limit of agreement for test-retest differences will be useful for determining if the VMI and VMIp have sufficient sensitivity for detecting change with treatment in both clinical and research settings. Further research on test-retest reliability reporting 95% limits of agreement for children across different age ranges is recommended, particularly if the test is to be used to detect changes due to intervention or treatment.
Comparative Analysis of Multicolor Flow Cytometry and Immunohistochemistry for the Detection of Disseminated Tumor Cells
Authors: Szánthó Eszter , Kárai Bettina , Ivády Gergely , Bedekovics Judit , Szegedi István , Petrás Miklós , Ujj György , Ujfalusi Anikó , Kiss Csongor , Kappelmayer János , Hevessy Zsuzsanna
Published: April 2017

Disseminating cells of a primary solid tumor may represent the origin of metastases and relapses. We aimed at comparing the diagnostic efficacy of multicolor flow cytometry (MFC) and morphology/immunohistochemistry (IHC) in the detection of disseminated tumor cells in the bone marrow (BM) and body fluids of patients with solid tumors, and in pediatric neuroblastoma cases. We investigated 72 samples retrospecively from 50 patients by MFC. Morphology/IHC data were available in 48 cases. In the first cohort, 36 samples derived from 34 patients with various forms of suspected and proven solid tumors and in the second cohort, 36 samples of 16 children with suspected and proven neuroblastoma were analyzed at diagnosis or during follow-up in a 4-color setting by MFC, and the results were compared with those obtained by IHC. In the group of various solid tumors, we found 91% concordance between IHC and MFC, and it was 65% in the neuroblastoma group, and 77% overall. Detection of disseminated tumor cells was found to be more effective by MFC in de novo neuroblastoma samples (100% vs. 86%). The advantage of MFC was even more pronounced when minimal residual disease was evaluated (efficacy, 92% vs. 68%). In contrast, efficacy of IHC was 100% in the group of various solid tumors, whereas it was 91% for MFC. We conclude that MFC and IHC are both essential tools for examining infiltration of BM and body fluids by disseminating solid tumor cells. In the case of neuroblastoma, however, minimal residual disease detection by MFC in a hypoplastic/aplastic BM environment was more effective than IHC, as considerably more cells could be analyzed.