bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of questionable occlusal carious lesions using an electrical bioimpedance method with fractional electrical model
Authors: Morais A. P. , Pino A. V. , Souza M. N.
Published: August 2016

This in vitro study evaluated the diagnostic performance of an alternative electric bioimpedance spectroscopy technique (BIS-STEP) detect questionable occlusal carious lesions. Six specialists carried out the visual (V), radiography (R), and combined (VR) exams of 57 sound or non-cavitated occlusal carious lesion teeth classifying the occlusal surfaces in sound surface (H), enamel caries (EC), and dentinal caries (DC). Measurements were based on the current response to a step voltage excitation (BIS-STEP). A fractional electrical model was used to predict the current response in the time domain and to estimate the model parameters: Rs and Rp (resistive parameters), and C and α (fractional parameters). Histological analysis showed caries prevalence of 33.3% being 15.8% hidden caries. Combined examination obtained the best traditional diagnostic results with specificity = 59.0%, sensitivity = 70.9%, and accuracy = 60.8%. There were statistically significant differences in bioimpedance parameters between the H and EC groups (p = 0.016) and between the H and DC groups (Rs, p = 0.006; Rp, p = 0.022, and α, p = 0.041). Using a suitable threshold for the Rs, we obtained specificity = 60.7%, sensitivity = 77.9%, accuracy = 73.2%, and 100% of detection for deep lesions. It can be concluded that BIS-STEP method could be an important tool to improve the detection and management of occlusal non-cavitated primary caries and pigmented sites.
An FPGA-based bolometer for the MAST-U Super-X divertor
Authors: Lovell Jack , Naylor Graham , Field Anthony , Drewelow Peter , Sharples Ray ,   JET Contributors
Published: August 2016

A new resistive bolometer system has been developed for MAST-Upgrade. It will measure radiated power in the new Super-X divertor, with millisecond time resolution, along 16 vertical and 16 horizontal lines of sight. The system uses a Xilinx Zynq-7000 series Field-Programmable Gate Array (FPGA) in the D-TACQ ACQ2106 carrier to perform real time data acquisition and signal processing. The FPGA enables AC-synchronous detection using high performance digital filtering to achieve a high signal-to-noise ratio and will be able to output processed data in real time with millisecond latency. The system has been installed on 8 previously unused channels of the JET vertical bolometer system. Initial results suggest good agreement with data from existing vertical channels but with higher bandwidth and signal-to-noise ratio.
Optimisation of amorphous zinc tin oxide thin film transistors by remote-plasma reactive sputtering
Authors: Niang K. M. , Cho J. , Heffernan S. , Milne W. I. , Flewitt A. J.
Published: August 2016

The influence of the stoichiometry of amorphous zinc tin oxide (a-ZTO) thin films used as the semiconducting channel in thin film transistors (TFTs) is investigated. A-ZTO has been deposited using remote-plasma reactive sputtering from zinc:tin metal alloy targets with 10%, 33%, and 50% Sn at. %. Optimisations of thin films are performed by varying the oxygen flow, which is used as the reactive gas. The structural, optical, and electrical properties are investigated for the optimised films, which, after a post-deposition annealing at 500 °C in air, are also incorporated as the channel layer in TFTs. The optical band gap of a-ZTO films slightly increases from 3.5 to 3.8 eV with increasing tin content, with an average transmission ∼90% in the visible range. The surface roughness and crystallographic properties of the films are very similar before and after annealing. An a-ZTO TFT produced from the 10% Sn target shows a threshold voltage of 8 V, a switching ratio of 108, a sub-threshold slope of 0.55 V dec−1, and a field effect mobility of 15 cm2 V−1 s−1, which is a sharp increase from 0.8 cm2 V−1 s−1 obtained in a reference ZnO TFT. For TFTs produced from the 33% Sn target, the mobility is further increased to 21 cm2 V−1 s−1, but the sub-threshold slope is slightly deteriorated to 0.65 V dec−1. For TFTs produced from the 50% Sn target, the devices can no longer be switched off (i.e., there is no channel depletion). The effect of tin content on the TFT electrical performance is explained in the light of preferential sputtering encountered in reactive sputtering, which resulted in films sputtered from 10% and 33% Sn to be stoichiometrically close to the common Zn2SnO4 and ZnSnO3 phases.
An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion
Authors: Yu Hua-Gen
Published: August 2016

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH4 and H2CO are given, together with a comparison with previous results.
Fluid dynamic design and experimental study of an aspirated temperature measurement platform used in climate observation
Authors: Yang Jie , Liu Qingquan , Dai Wei , Ding Renhui
Published: August 2016

Due to the solar radiation effect, current air temperature sensors inside a thermometer screen or radiation shield may produce measurement errors that are 0.8 °C or higher. To improve the observation accuracy, an aspirated temperature measurement platform is designed. A computational fluid dynamics (CFD) method is implemented to analyze and calculate the radiation error of the aspirated temperature measurement platform under various environmental conditions. Then, a radiation error correction equation is obtained by fitting the CFD results using a genetic algorithm (GA) method. In order to verify the performance of the temperature sensor, the aspirated temperature measurement platform, temperature sensors with a naturally ventilated radiation shield, and a thermometer screen are characterized in the same environment to conduct the intercomparison. The average radiation errors of the sensors in the naturally ventilated radiation shield and the thermometer screen are 0.44 °C and 0.25 °C, respectively. In contrast, the radiation error of the aspirated temperature measurement platform is as low as 0.05 °C. This aspirated temperature sensor allows the radiation error to be reduced by approximately 88.6% compared to the naturally ventilated radiation shield, and allows the error to be reduced by a percentage of approximately 80% compared to the thermometer screen. The mean absolute error and root mean square error between the correction equation and experimental results are 0.032 °C and 0.036 °C, respectively, which demonstrates the accuracy of the CFD and GA methods proposed in this research.
The Landau–de Gennes free energy expansion of a melt of V-shaped polymer molecules
Authors: Aliev M. A. , Ugolkova E. A. , Kuzminyh N. Yu.
Published: August 2016

The phase behavior of a monodisperse melt of polymer molecules consisting of two rod-like segments joined at an angle α has been inspected within the Landau theory of phase transitions. The interactions between monomer units were assumed to be of the Maier-Saupe form. The Landau–de Gennes expansion of the free energy of the melt has been obtained up to the sixth order in powers of the nematic order parameter, the coefficients of this expansion have been calculated from the microscopic model of polymer molecule. The phase diagram contains the regions of stability of isotropic, prolate uniaxial, oblate uniaxial, and biaxial nematic phases. The isotropic-uniaxial nematic and uniaxial-biaxial nematic transitions are of the first and second order, respectively. We found two Landau points in the phase diagram at which continuous transition from biaxial nematic state to isotropic phase occurs.
From Euler’s elastica to the mKdV hierarchy, through the Faber polynomials
Authors: Matsutani Shigeki , Previato Emma
Published: August 2016

The modified Korteweg-de Vries hierarchy (mKdV) is derived by imposing isometry and isoenergy conditions on a moduli space of plane loops. The conditions are compared to the constraints that define Euler’s elastica. Moreover, the conditions are shown to be constraints on the curvature and other invariants of the loops which appear as coefficients of the generating function for the Faber polynomials.
Effects of cation on electrical responses of ionic polymer-metal composite sensors at various ambient humidities
Authors: Zhu Zicai , Horiuchi Tetsuya , Takagi Kentaro , Takeda Jun , Chang Longfei , Asaka Kinji
Published: August 2016

In this study, we investigated the effects of various cations on the electrical responses of ionic polymer–metal composite (IPMC) sensors at various ambient humidities. Four typical Au–Nafion IPMC samples were prepared with H+, Li+, Na+, and K+ cations. The voltage and current responses of the IPMCs were investigated under static and dynamic bending displacements. The orders of the voltage and current amplitudes were generally Li+ > Na+ > K+ > H+ and depended on the cation transport properties and the water content. The static voltage response first increased to a peak and then slowly decreased to a steady state. A negative steady-state voltage was initially observed for the IPMC with H+ cations under near saturation conditions. The voltage amplitude increased monotonously with increasing frequency from 0.1 to 10 Hz at a high relative humidity (RH, ∼90%), first increased and then decreased at moderate humidity (RH, ∼50%), and decreased continuously at low humidity (RH, ∼20%). The static current response first rapidly increased to a peak and then quickly decayed. During current decay, free oscillation decay occurred at high humidity and attenuated with decreasing humidity. This was confirmed to be the result of cation movement in the IPMC. There are three necessary conditions for oscillation: sufficient migrated cations, high cation mobility, and high stiffness of the polymer network. For the dynamic current response, the amplitude increased with increasing frequency (0.1–10 Hz) and showed good linearity. The underlying physics, mainly involving cation forward migration and back diffusion caused by mechano-chemo-electrical coupling, was clarified.
Robust ferromagnetism in Mn-doped MoS2 nanostructures
Authors: Wang Jieqiong , Sun Fan , Yang Sen , Li Yitong , Zhao Chuan , Xu Minwei , Zhang Yin , Zeng Hao
Published: August 2016

Layered transition metal dichalcogenides (TMDs) have attracted extensive attention due to their interesting properties originating from an effective honeycomb lattice and strong spin-orbit coupling, and have potential applications in catalysis, lithium batteries, photonic, electronic, and valleytronic devices. Introducing magnetism in the TMDs can lead to the interesting functionalities such as magnetic order and carrier spin polarization with potential applications in spintronics. Here, we demonstrate an effective approach to induce robust ferromagnetism in MoS2 nanostructures by transition metal doping. After doping with a few percent Mn2+, the magnetism of MoS2 nanostructures is enhanced dramatically. Moreover, the magnetic properties are strongly temperature dependent, which is clearly different from the behavior of defect-induced magnetism. Our approach opens up the possibility for tuning the spin and magnetic properties in two-dimensional nanostructures.
Light-induced structural changes in a monomeric bacteriophytochrome
Authors: Takala Heikki , Niebling Stephan , Berntsson Oskar , Björling Alexander , Lehtivuori Heli , Häkkänen Heikki , Panman Matthijs , Gustavsson Emil , Hoernke Maria , Newby Gemma , Zontone Federico , Wulff Michael , Menzel Andreas , Ihalainen Janne A. , Westenhoff Sebastian
Published: August 2016

Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes.
III/V nano ridge structures for optical applications on patterned 300 mm silicon substrate
Authors: Kunert B. , Guo W. , Mols Y. , Tian B. , Wang Z. , Shi Y. , Van Thourhout D. , Pantouvaki M. , Van Campenhout J. , Langer R. , Barla K.
Published: August 2016

We report on an integration approach of III/V nano ridges on patterned silicon (Si) wafers by metal organic vapor phase epitaxy (MOVPE). Trenches of different widths (≤500 nm) were processed in a silicon oxide (SiO2) layer on top of a 300 mm (001) Si substrate. The MOVPE growth conditions were chosen in a way to guarantee an efficient defect trapping within narrow trenches and to form a box shaped ridge with increased III/V volume when growing out of the trench. Compressively strained InGaAs/GaAs multi-quantum wells with 19% indium were deposited on top of the fully relaxed GaAs ridges as an active material for optical applications. Transmission electron microcopy investigation shows that very flat quantum well (QW) interfaces were realized. A clear defect trapping inside the trenches is observed whereas the ridge material is free of threading dislocations with only a very low density of planar defects. Pronounced QW photoluminescence (PL) is detected from different ridge sizes at room temperature. The potential of these III/V nano ridges for laser integration on Si substrates is emphasized by the achieved ridge volume which could enable wave guidance and by the high crystal quality in line with the distinct PL.
Highly photoresponsive charge-sensitive infrared phototransistors with a dynamically controlled optical gate
Authors: Xu Jie , Yang Le , Yu Haochi , Weng Qianchun , Chen Pingping , Zhang Bo , Kang Tingting , Komiyama Susumu , Lu Wei , An Zhenghua
Published: August 2016

Charge-sensitive infrared phototransistors (CSIPs) with a built-in field-effect-induced amplification mechanism have much higher infrared photoresponsivity (≥103 A/W) than conventional detectors, which is often restricted by background black-body radiation induced saturation. Here, we report that dynamically controlling the electrostatic potential of the photosensitive floating gate of a CSIP can counterbalance this background-induced saturation effect. As a result, the CSIP photoresponsivity can be improved by about one order of magnitude, reaching as high as ∼1.2×104 A/W to external blinking light. Our work suggests that time-domain manipulation could be an agile degree of freedom in optimizing the CSIP performance and provide insight into operating more general phototransistors for a wide variety of optoelectronic applications.
Photoluminescence and electroluminescence from Ge/strained GeSn/Ge quantum wells
Authors: Lin Chung-Yi , Huang Chih-Hsiung , Huang Shih-Hsien , Chang Chih-Chiang , Liu C. W. , Huang Yi-Chiau , Chung Hua , Chang Chorng-Ping
Published: August 2016

Ge/strained GeSn/Ge quantum wells are grown on a 300 mm Si substrate by chemical vapor deposition. The direct bandgap emission from strained GeSn is observed in the photoluminescence spectra and is enhanced by Al2O3/SiO2 passivation due to the field effect. The electroluminescence of the direct bandgap emission of strained GeSn is also observed from the Ni/Al2O3/GeSn metal-insulator-semiconductor tunneling diodes. Electroluminescence is a good indicator of GeSn material quality, since defects in GeSn layers degrade the electroluminescence intensity significantly. At the accumulation bias, the holes in the Ni gate electrode tunnel to the strained n-type GeSn layer through the ultrathin Al2O3 and recombine radiatively with electrons. The emission wavelength of photoluminescence and electroluminescence can be tuned by the Sn content.
Band gap tuning of amorphous Al oxides by Zr alloying
Authors: Canulescu S. , Jones N. C. , Borca C. N. , Piamonteze C. , Rechendorff K. , Gudla V. C. , Bordo K. , Nielsen L. P. , Hoffmann S. V. , Almtoft K. P. , Ambat R. , Schou J.
Published: August 2016

The optical band gap and electronic structure of amorphous Al-Zr mixed oxides with Zr content ranging from 4.8 to 21.9% were determined using vacuum ultraviolet and X-ray absorption spectroscopy. The light scattering by the nano-porous structure of alumina at low wavelengths was estimated based on the Mie scattering theory. The dependence of the optical band gap of the Al-Zr mixed oxides on the Zr content deviates from linearity and decreases from 7.3 eV for pure anodized Al2O3 to 6.45 eV for Al-Zr mixed oxides with a Zr content of 21.9%. With increasing Zr content, the conduction band minimum changes non-linearly as well. Fitting of the energy band gap values resulted in a bowing parameter of ∼2 eV. The band gap bowing of the mixed oxides is assigned to the presence of the Zr d-electron states localized below the conduction band minimum of anodized Al2O3.
Cross-section imaging and p-type doping assessment of ZnO/ZnO:Sb core-shell nanowires by scanning capacitance microscopy and scanning spreading resistance microscopy
Authors: Wang Lin , Sallet Vincent , Sartel Corinne , Brémond Georges
Published: August 2016

ZnO/ZnO:Sb core-shell structured nanowires (NWs) were grown by the metal organic chemical vapor deposition method where the shell was doped with antimony (Sb) in an attempt to achieve ZnO p-type conduction. To directly investigate the Sb doping effect in ZnO, scanning capacitance microscopy (SCM) and scanning spreading resistance microscopy (SSRM) were performed on the NWs' cross-sections mapping their two dimensional (2D) local electrical properties. Although no direct p-type inversion in ZnO was revealed, a lower net electron concentration was pointed out for the Sb-doped ZnO shell layer with respect to the non-intentionally doped ZnO core, indicating an evident compensating effect as a result of the Sb incorporation, which can be ascribed to the formation of Sb-related acceptors. The results demonstrate SCM/SSRM investigation being a direct and effective approach for characterizing radial semiconductor one-dimensional (1D) structures and, particularly, for the doping study on the ZnO nanomaterial towards its p-type realization.
Effect of different forage types and concentrate levels on energy conversion, enteric methane production, and animal performance of Holstein × Zebu heifers
Authors: Silva F. A. S. , Filho S. C. Valadares , Detmann E. , Santos S. A. , Godoi L. A. , Silva B. C. , Pacheco M. V. C. , Alhadas H. M. , Rotta P. P.
Published: August 2016

The aim of this study was to evaluate the effect of diets containing corn silage (CS) or sugarcane (SC) with 300 or 500 g/kg of concentrate (on a DM basis) on energy conversion, enteric methane (CH4) production, and the animal performance of Holstein × Zebu heifers. An experiment was conducted while using comparative slaughter. Twenty Holstein × Zebu heifers with an average age of 12 ± 1.0 months and an average bodyweight of 218 ± 36.5 kg were used. Four heifers were assigned to a baseline group, whereas the remaining 16 heifers were distributed in a completely randomised design using a 2 × 2 factorial scheme (n = 4), with two types of roughage (CS or SC) and two levels of concentrate (300 or 500 g/kg) on a DM basis of the diet over the course of 112 days. For the evaluation of the apparent total-tract digestibility of diets and energy losses, a digestibility assay was performed by using the total collection of faeces and urine over three consecutive days. The enteric CH4 production was quantified by continuous analysis of regular samples of air excreted by the animals throughout the day. The greatest (P < 0.05) average daily gain was observed for heifers that were fed CS-based diets or with 500 g/kg of concentrate. Greater (P < 0.05) daily CH4 emissions were observed for heifers that were fed 500 g/kg of concentrate; CH4 production as a function of DM intake was greater (P < 0.05) for heifers that were fed SC-based diets. The efficiency of the conversion from digestible energy (DE) to metabolisable energy (ME) was not influenced (P > 0.05) by variables that were analysed in this study. However, the mean value that was observed in the present study was above those values proposed by the main evaluation systems of feedstuffs and nutrient requirements of ruminants. Therefore, we concluded that CS-based diets allow for better animal performance of Holstein × Zebu heifers in relation to SC-based diets. Also, the increased concentrate improves the performance of growing heifers. A greater inclusion of concentrate in SC-based diets can allow for a reduction of CH4 emissions per consumed unit and per gain unit. The mean suggested value for the ME : DE ratio based on this study is 0.86. However, more studies are necessary to validate this result.
Analysis of antimony species – lessons learnt from more than two decades of environmental research
Authors: Daus Birgit , Hansen Helle Rüsz
Published: August 2016

Environmental contextThe environmental behaviour and toxicological effects of antimony depend strongly on the specific form of the element, and thus methods have been developed for measuring the various forms of antimony. These methods, applicable to quite clean samples, often fail when applied to more complex environmental samples. We discuss some of the pitfalls in determining environmental antimony forms and the resulting risk of getting the bigger picture wrong regarding antimony pollution.
AbstractThe major findings of ~20 years of research on the analysis of antimony species in environmental samples are summarised in this paper. The complex chemistry of antimonite (SbIII) as well as of antimonate (SbV) plays a major role in chromatographic speciation of these species. For simple matrices, like surface or ground-water samples, antimony redox speciation has become a routine analysis and is robust and highly reproducible, if certain aspects are taken into consideration. These aspects are the formation of a stable complex of SbIII and complex formation kinetics. Then the antimony redox species can be separated on an anion-exchange column and detected with a suitable element detector (inductively coupled plasma–mass spectrometry (ICP-MS) or hydride generation–atomic fluorescence spectrometry (HG-AFS)) for trace analysis. The influence of complexing agents in the sample matrix, or in the eluent, on the formation of SbIII and SbV complexes and possible corruption of chromatography is discussed. This ability of antimony to form rather stable complexes also increases the risk of artefact formation during extraction of solid samples.
Transport characteristics of heavy metals, metalloids and pesticides through major agricultural soils of Bangladesh as determined by TDR
Authors: Mojid M. A. , Hossain A. B. M. Z. , Cappuyns V. , Wyseure G. C. L.
Published: August 2016

The transport parameters of soluble chemicals through soils are needed to assess the pollution risks of soil and groundwater resources. The transport parameters of seven heavy metal/metalloid compounds (NaAsO2, Cd(NO3)2, Pb(NO3)2, Ni(NO3)2, ZnCl2, CuSO4 and Co(NO3)2), two pesticides (cartap and carbendazim) and an inert salt (CaCl2) were determined in repacked columns of eight agricultural soils of Bangladesh. The relationships between physicochemical properties of the soils and solutes and the solute-transport parameters were investigated by time-domain reflectometry (TDR) using bulk soil electrical conductivity as a proxy. The transport velocity (V) of the solutes decreased linearly with the increasing clay content of the soils. Of the nine reactive solutes, cartap and As moved with the largest and smallest V values, respectively. Dispersivity of the solutes decreased with increasing clay content linearly but following power law with increasing median grain diameter of the soils. It also increased significantly (P<0.05) with the increasing length of travel path. The solute retardation factor (R) increased with increasing clay content following power law, implying that clay content is a determining factor for heavy metal retention in soils. Parameter R increased non-linearly with increasing travel length except for cadmium, for which the increase was linear. Based on R, the general adsorption affinity of the solutes in the soils was As>Co>Cd>carbendazim>Pb>Cu>cartap>Zn>Ni>Ca. In some soils, however, Cd and carbendazim showed a lower adsorption than Pb and Co, and Zn and cartap were more strongly adsorbed than Ni. The relationships between physicochemical properties of the soils and solutes and the solute transport parameters contribute to the improved interpretation of TDR data as a preliminary assessment of pollutant mobility in soils with different textures.
The shapes of collocation
Authors: Baker Paul
Published: August 2016

The toolGraphColl(Brezina et al. 2015) allows collocational networks to be identified within corpora, enabling corpus analysis to go beyond two-way collocation. This paper aims to illustrate the types of linguistic relationships that can appear when more than two words are considered, using graph theory to account for the different types of collocational “shapes” that can be formed withinGraphCollnetworks. Using the reference corpus, the BE06, examples of different types of graphs were obtained and analysed in order to form an understanding of the sorts of relationships between words that occur in particular shapes. The analysis indicates that concepts from graph theory can be usefully integrated into corpus analysis of collocation as well as showing the potential for a more sophisticated understanding of the company that words keep.
Literal versus exaggeratedalwaysandnever
Authors: Lindley Jori
Published: August 2016

In this cross-genre study of the literal versus exaggerated meanings of the frequency adverbsalwaysandnever, I analyze three data sets: written and spoken language (academic speech, unscripted TV/radio dialog, and casual speech); local, national, and international news articles; and humanities, science-technology, and medical articles. For each genre, I calculate what I call the ‘Exaggeration Quotient’ (instances ofalwaysandneverdivided by instances ofoftenorfrequentlyandrarelyorinfrequently, respectively) and the rate of negation ofalways. Large Exaggeration Quotients and low negation rates were associated with informality, a pattern explicable in terms of specific aspects of informal language that motivate exaggeration, including perceived accountability for accuracy. In other words, formality is a proxy for certain features, goals, and expectations which are associated with certain genres and which affect how we use and understandalwaysandnever. This analysis supports a cognitive-functional, encyclopedic view of meaning.
Taking meaning in hand
Authors: Lepic Ryan , Börstell Carl , Belsitzman Gal , Sandler Wendy
Published: August 2016

Traditionally in sign language research, the issue of whether a lexical sign is articulated with one hand or two has been treated as a strictly phonological matter. We argue that accounting for two-handed signs also requires considering meaning as a motivating factor. We report results from a Swadesh list comparison, an analysis of semantic patterns among two-handed signs, and a picture-naming task. Comparing four unrelated languages, we demonstrate that the two hands are recruited to encode various relationship types in sign language lexicons. We develop the general principle that inherently “plural” concepts are straightforwardly mapped onto our paired human hands, resulting in systematic use of the two hands across sign languages. In our analysis, “plurality” subsumes four primary relationship types —interaction,location,dimension, andcomposition— and we predict that signs with meanings that encompass these relationships — such as ‘meet’, ‘empty’, ‘large’, or ‘machine’ — will preferentially be two-handed in any sign language.
Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton
Authors: Herawati Elisa , Taniguchi Daisuke , Kanoh Hatsuho , Tateishi Kazuhiro , Ishihara Shuji , Tsukita Sachiko
Published: August 2016

Multiciliated cells (MCCs) promote fluid flow through coordinated ciliary beating, which requires properly organized basal bodies (BBs). Airway MCCs have large numbers of BBs, which are uniformly oriented and, as we show here, align linearly. The mechanism for BB alignment is unexplored. To study this mechanism, we developed a long-term and high-resolution live-imaging system and used it to observe green fluorescent protein–centrin2–labeled BBs in cultured mouse tracheal MCCs. During MCC differentiation, the BB array adopted four stereotypical patterns, from a clustering “floret” pattern to the linear “alignment.” This alignment process was correlated with BB orientations, revealed by double immunostaining for BBs and their asymmetrically associated basal feet (BF). The BB alignment was disrupted by disturbing apical microtubules with nocodazole and by a BF-depleting Odf2 mutation. We constructed a theoretical model, which indicated that the apical cytoskeleton, acting like a viscoelastic fluid, provides a self-organizing mechanism in tracheal MCCs to align BBs linearly for mucociliary transport.
Reassessing the mechanics of parasite motility and host-cell invasion
Authors: Tardieux Isabelle , Baum Jake
Published: August 2016

The capacity to migrate is fundamental to multicellular and single-celled life. Apicomplexan parasites, an ancient protozoan clade that includes malaria parasites (Plasmodium) and Toxoplasma, achieve remarkable speeds of directional cell movement. This rapidity is achieved via a divergent actomyosin motor system, housed within a narrow compartment that lies underneath the length of the parasite plasma membrane. How this motor functions at a mechanistic level during motility and host cell invasion is a matter of debate. Here, we integrate old and new insights toward refining the current model for the function of this motor with the aim of revitalizing interest in the mechanics of how these deadly pathogens move.
Richard Cheney: Life on the move
Authors: Jordan Shawn
Published: August 2016

Cheney’s work focuses on the molecular basis of cell movement.
Pyroptosis triggers pore-induced intracellular traps (PITs) that capture bacteria and lead to their clearance by efferocytosis
Authors: Jorgensen Ine , Zhang Yue , Krantz Bryan A. , Miao Edward A.
Published: August 2016

Inflammasomes activate caspase-1 in response to cytosolic contamination or perturbation. This inflammatory caspase triggers the opening of the GSDMD pore in the plasma membrane, resulting in lytic cell death called pyroptosis. We had previously assumed that pyroptosis releases intracellular bacteria to the extracellular space. Here, we find that viable bacteria instead remain trapped within the cellular debris of pyroptotic macrophages. This trapping appears to be an inevitable consequence of how osmotic lysis ruptures the plasma membrane, and may also apply to necroptosis and some forms of nonprogrammed necrosis. Although membrane tears release soluble cytosolic contents, they are small enough to retain organelles and bacteria. We call this structure the pore-induced intracellular trap (PIT), which is conceptually parallel to the neutrophil extracellular trap (NET). The PIT coordinates innate immune responses via complement and scavenger receptors to drive recruitment of and efferocytosis by neutrophils. Ultimately, this secondary phagocyte kills the bacteria. Hence, caspase-1–driven pore-induced cell death triggers a multifaceted defense against intracellular bacteria facilitated by trapping the pathogen within the cellular debris. Bona fide intracellular bacterial pathogens, such as Salmonella, must prevent or delay pyroptosis to avoid being trapped in the PIT and subsequently killed by neutrophils.
Extracellular matrix protein Matrilin-4 regulates stress-induced HSC proliferation via CXCR4
Authors: Uckelmann Hannah , Blaszkiewicz Sandra , Nicolae Claudia , Haas Simon , Schnell Alexandra , Wurzer Stephan , Wagener Raimund , Aszodi Attila , Essers Marieke Alida Gertruda
Published: August 2016

During homeostasis, hematopoietic stem cells (HSCs) are mostly kept in quiescence with only minor contribution to steady-state hematopoiesis. However, in stress situations such as infection, chemotherapy, or transplantation, HSCs are forced to proliferate and rapidly regenerate compromised hematopoietic cells. Little is known about the processes regulating this stress-induced proliferation and expansion of HSCs and progenitors. In this study, we identified the extracellular matrix (ECM) adaptor protein Matrilin-4 (Matn4) as an important negative regulator of the HSC stress response. Matn4 is highly expressed in long-term HSCs; however, it is not required for HSC maintenance under homeostasis. In contrast, Matn4 is strongly down-regulated in HSCs in response to proliferative stress, and Matn4 deficiency results in increased proliferation and expansion of HSCs and progenitors after myelosuppressive chemotherapy, inflammatory stress, and transplantation. This enhanced proliferation is mediated by a transient down-regulation of CXCR4 in Matn4−/− HSCs upon stress, allowing for a more efficient expansion of HSCs. Thus, we have uncovered a novel link between the ECM protein Matn4 and cytokine receptor CXCR4 involved in the regulation of HSC proliferation and expansion under acute stress.
Thermodynamic analysis questions claims of improved cardiac efficiency by dietary fish oil
Authors: Loiselle Denis S. , Han June-Chiew , Goo Eden , Chapman Brian , Barclay Christopher J. , Hickey Anthony J.R. , Taberner Andrew J.
Published: August 2016

Studies in the literature describe the ability of dietary supplementation by omega-3 fish oil to increase the pumping efficiency of the left ventricle. Here we attempt to reconcile such studies with our own null results. We undertake a quantitative analysis of the improvement that could be expected theoretically, subject to physiological constraints, by posing the following question: By how much could efficiency be expected to increase if inefficiencies could be eliminated? Our approach utilizes thermodynamic analyses to investigate the contributions, both singly and collectively, of the major components of cardiac energetics to total cardiac efficiency. We conclude that it is unlikely that fish oils could achieve the required diminution of inefficiencies without greatly compromising cardiac performance.
Dual regulation of the native ClC-K2 chloride channel in the distal nephron by voltage and pH
Authors: Pinelli Laurent , Nissant Antoine , Edwards Aurélie , Lourdel Stéphane , Teulon Jacques , Paulais Marc
Published: August 2016

ClC-K2, a member of the ClC family of Cl− channels and transporters, forms the major basolateral Cl− conductance in distal nephron epithelial cells and therefore plays a central role in renal Cl− absorption. However, its regulation remains largely unknown because of the fact that recombinant ClC-K2 has not yet been studied at the single-channel level. In the present study, we investigate the effects of voltage, pH, Cl−, and Ca2+ on native ClC-K2 in the basolateral membrane of intercalated cells from the mouse connecting tubule. The ∼10-pS channel shows a steep voltage dependence such that channel activity increases with membrane depolarization. Intracellular pH (pHi) and extracellular pH (pHo) differentially modulate the voltage dependence curve: alkaline pHi flattens the curve by causing an increase in activity at negative voltages, whereas alkaline pHo shifts the curve toward negative voltages. In addition, pHi, pHo, and extracellular Ca2+ strongly increase activity, mainly because of an increase in the number of active channels with a comparatively minor effect on channel open probability. Furthermore, voltage alters both the number of active channels and their open probability, whereas intracellular Cl− has little influence. We propose that changes in the number of active channels correspond to them entering or leaving an inactivated state, whereas modulation of open probability corresponds to common gating by these channels. We suggest that pH, through the combined effects of pHi and pHo on ClC-K2, might be a key regulator of NaCl absorption and Cl−/HCO3− exchange in type B intercalated cells.
Socioeconomic and Demographic Determinants of the Nutritional Content of National School Lunch Program Entrée Selections
Authors: Peckham Janet G. , Kropp Jaclyn D. , Mroz Thomas A. , Haley‐Zitlin Vivian , Granberg Ellen M. , Hawthorne Nicole
Published: August 2016

New National School Lunch Program (NSLP) guidelines aim to reduce sodium and saturated fats, limit calories, and eliminate trans‐fat and whole milk. This paper provides a novel approach to understanding how the healthfulness of NSLP participants’ entrée selections varies across socioeconomic and demographic groups. Unlike previous studies that rely on dietary recalls, we use a mixed logit model to examine students’ entrée choices in a school cafeteria. We estimate the likelihood that an entrée is selected from the available lunch choices as a function of the entrée's nutrients (fat, carbohydrate, protein, and sodium) and entrée's taste profile characteristics (e.g., Mexican, Pizza‐like), as well as the student's socio‐economic and demographic characteristics. Using these estimates, we examine how changing the nutritional content of an offering impacts the probability of selecting each of the offerings. Free lunch recipients are more likely to choose entrées higher in fat but lower in sodium than other students. Full‐price lunch recipients are the most responsive to changes in nutritional content of the offerings and are most likely to respond to changes in the nutritional content of the offered entrées by substituting a lunch brought from home for the school‐purchased lunch. Replacing less healthy menu items with popular but healthier items reduces the selection of total calories, calories from fat, and sodium by approximately 4%, 18%, and 8%, respectively, over the study period. The new guidelines should be effective at improving the nutrition of school‐age children, and potentially reducing childhood obesity, provided NSLP participation does not decline appreciably.
Resilient Provision of Ecosystem Services from Agricultural Landscapes: Trade‐offs Involving Means and Variances of Water Quality Improvements
Authors: Rabotyagov Sergey S. , Valcu‐Lisman Adriana M. , Kling Catherine L.
Published: August 2016

We assess the trade‐offs and synergies involved in reducing agriculture‐generated nutrient loads with different levels of resilience. We optimize the selection of least‐cost patterns of agricultural conservation practices for both the expected performance of the conservation actions and its variance. Securing nutrient loads with a higher level of resilience is costly, with marginal costs of resilience generally declining with lower loads. We find that the main trade‐off dimension is between cost of conservation investments and ecosystem service objectives, as opposed to pronounced mean‐variance or between‐nutrient objectives trade‐offs. We find relative synergies in agricultural conservation investments aimed at nutrient reductions.
Variation in high-priority drug-drug interaction alerts across institutions and electronic health records
Authors: McEvoy Dustin S , Sittig Dean F , Hickman Thu-Trang , Aaron Skye , Ai Angela , Amato Mary , Bauer David W , Fraser Gregory M , Harper Jeremy , Kennemer Angela , Krall Michael A , Lehmann Christoph U , Malhotra Sameer , Murphy Daniel R , O’Kelley Brandi , Samal Lipika , Schreiber Richard , Singh Hardeep , Thomas Eric J , Vartian Carl V , Westmorland Jennifer , McCoy Allison B , Wright Adam
Published: August 2016

Objective: The United States Office of the National Coordinator for Health Information Technology sponsored the development of a “high-priority” list of drug-drug interactions (DDIs) to be used for clinical decision support. We assessed current adoption of this list and current alerting practice for these DDIs with regard to alert implementation (presence or absence of an alert) and display (alert appearance as interruptive or passive).

Materials and methods: We conducted evaluations of electronic health records (EHRs) at a convenience sample of health care organizations across the United States using a standardized testing protocol with simulated orders.

Results: Evaluations of 19 systems were conducted at 13 sites using 14 different EHRs. Across systems, 69% of the high-priority DDI pairs produced alerts. Implementation and display of the DDI alerts tested varied between systems, even when the same EHR vendor was used. Across the drug pairs evaluated, implementation and display of DDI alerts differed, ranging from 27% (4/15) to 93% (14/15) implementation.

Discussion: Currently, there is no standard of care covering which DDI alerts to implement or how to display them to providers. Opportunities to improve DDI alerting include using differential displays based on DDI severity, establishing improved lists of clinically significant DDIs, and thoroughly reviewing organizational implementation decisions regarding DDIs.

Conclusion: DDI alerting is clinically important but not standardized. There is significant room for improvement and standardization around evidence-based DDIs.
Fire Blight Symptomatic Shoots and the Presence of Erwinia amylovora in Asymptomatic Apple Budwood
Authors: Tancos K. A. , Borejsza-Wysocka E. , Kuehne S. , Breth D. , Cox Kerik D.
Published: August 2016

Erwinia amylovora, the causal agent of fire blight, causes considerable economic losses in young apple plantings in New York on a yearly basis. Nurseries make efforts to only use clean budwood for propagation, which is essential, but E. amylovora may be present in trees that appear to have no apparent fire blight symptoms at the time of collection. We hypothesized that the use of infected budwood, especially by commercial nursery operations, could be the cause, in part, of fire blight outbreaks that often occur in young apple plantings in New York. Our goal was to investigate the presence of E. amylovora in asymptomatic budwood from nursery source plantings as it relates to trees with fire blight symptoms. From 2012 to 2015, apple budwood was collected from two commercial budwood source plantings of ‘Gala’ and ‘Topaz’ at increasing distances from visually symptomatic trees. From these collections, internal contents of apple buds were analyzed for the presence of E. amylovora. E. amylovora was detected in asymptomatic budwood in trees more than 20 m from trees with fire blight symptoms. In some seasons, there were significant (P ≤ 0.05) differences in the incidence of E. amylovora in asymptomatic budwood collected from symptomatic trees and those up to 20 m from them. In 2014 and 2015, the mean E. amylovora CFU per gram recovered from budwood in both the Gala and Topaz plantings were significantly lower in budwood collected 20 m from symptomatic trees. Further investigation of individual bud dissections revealed that E. amylovora was within the tissue beneath the bud scales containing the meristem. Results from the study highlight the shortcomings of current budwood collection practices and the need to better understand the factors that lead to the presence of E. amylovora in bud tissues to ensure the production of pathogen-free apple trees.
Comparative Evaluation of Disease Induced by Three Strains of Tobacco etch virus in Capsicum annuum L.
Authors: Murphy John F. , Morawo Tolulope
Published: August 2016

Tobacco etch virus (TEV; genus Potyvirus) strains HAT, Mex21, and N were evaluated comparatively for their pathogenicity and effects on growth of Capsicum annuum L. ‘Calwonder’. Each TEV strain induced an initial systemic symptom of vein-clearing but subsequent disease symptoms ranged from mild (HAT) to moderate (Mex21) to severe (N). Effects on plant growth parameters closely reflected disease symptoms induced by each TEV strain. HAT-infected Calwonder plants did not differ from the healthy control for plant height, internode lengths, and aboveground fresh weight of shoots. Root dry weight, however, was less for HAT-infected plants than for the healthy control. Mex21 affected plants more severely, with significantly shorter plant height (at 20, 30, and 40 days postinoculation), reduced root dry weight, and shortened internodes compared with HAT and healthy control treatments. Aboveground fresh weight of Mex21-infected plants was significantly less than for the healthy control. N induced significant negative effects relative to each of the other treatments for plant height, aboveground shoot fresh weight, root dry weight, and internode lengths. The effects on Calwonder fruit production mimicked disease severity and effects on plant growth for the respective TEV strains.
Population Genetic Structure of Rhizoctonia oryzae-sativae from Rice in Latin America and Its Adaptive Potential to Emerge as a Pathogen on Urochloa Pastures
Authors: Pereira Danilo A. dos Santos , Ceresini Paulo C. , Castroagudín Vanina L. , Ramos-Molina Lina M. , Chavarro-Mesa Edisson , Negrisoli Matheus Mereb , Campos Samara Nunes , Pegolo Mauro E. S. , Takada Hélio Minoru
Published: August 2016

The fungus Rhizoctonia oryzae-sativae is an important pathogen that causes the aggregated sheath spot disease on rice. In this study, we investigated the genetic structure of rice-adapted populations of R. oryzae-sativae sampled from traditional rice-cropping areas from the Paraíba Valley, São Paulo, Brazil, and from Meta, in the Colombian Llanos, in South America. We used five microsatellite loci to measure population differentiation and infer the pathogen’s reproductive system. Gene flow was detected among the three populations of R. oryzae-sativae from lowland rice in Brazil and Colombia. In contrast, a lack of gene flow was observed between the lowland and the upland rice populations of the pathogen. Evidence of sexual reproduction including low clonality, Hardy-Weinberg equilibrium within loci and gametic equilibrium between loci, indicated the predominance of a mixed reproductive system in all populations. In addition, we assessed the adaptive potential of the Brazilian populations of R. oryzae-sativae to emerge as a pathogen to Urochloa spp. (signalgrass) based on greenhouse aggressiveness assays. The Brazilian populations of R. oryzae-sativae were probably only incipiently adapted as a pathogen to Urochloa spp. Comparison between RST and QST showed the predominance of diversifying selection in the divergence between the two populations of R. oryzae-sativae from Brazil.