bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability of Word-Retrieval Errors With the AphasiaBank Stimuli
Authors: Boyle Mary
Published: July 2015

Purpose

This study examined the test–retest reliability of select measures of word-retrieval errors in narrative discourses of individuals with aphasia assessed with the AphasiaBank stimuli.

Method

Ten participants with aphasia were video recorded during 2 sessions producing narratives elicited with pictures. Discourses were transcribed and coded using AphasiaBank procedures, then analyzed for the stability of rates of phonological errors, semantic errors, false starts, time fillers, and repetitions per minute. Values for correlation coefficients and the minimal detectable change score were used to assess stability for research and clinical decision making.

Results

There was poor test–retest reliability when the discourses were analyzed by each narrative subgenre. When the narrative discourses were combined for analysis, several measures appeared to be sufficiently stable across sessions for use in group studies, and 1 could be adequately stable for making clinical decisions about an individual.

Conclusions

Because the short speech samples yielded by the subgenre narrative analyses demonstrated poor test–retest reliability, it is recommended that all of the picture-based narrative discourse tasks be combined for analysis of word-retrieval impairments when the AphasiaBank stimuli are used. However, the confidence intervals associated with the reliability coefficients obtained in this study suggest caution in using the measures if they are based on performance in a single session. More investigations of the test–retest reliability of measures used to study language impairment in discourse contexts are essential.
Understanding Image Resolution and Quality in Videofluoroscopy
Authors: Peladeau-Pigeon Melanie , Steele Catriona
Published: July 2015

Current best practice recommendations for videofluoroscopic swallowing studies (VFSS) suggest that fluoroscopy should be performed either on a continuous setting or at 30 pulses per second (pps). Image capture should likewise be set to maximum resolution (i.e., 30 frames per second [fps]). In this article, we discuss choices in technical settings that may result in the output of fewer than 30 unique images per second or result in image distortions. We also describe a test that can be used to confirm image capture quality and rate using an analog metronome. Clinicians and researchers need to be aware of these issues and the limitations they bring to videofluoroscopy review and analysis.
Revisiting Swallowing Function Following Contemporary Surgical Interventions for Oral/Oropharyngeal Cancer: Key Underlying Issues
Authors: Goldsmith Tessa , Jacobson Marlene Carno
Published: July 2015

There has been resurgence in surgical interventions for oral cavity and oropharyngeal cancer in tandem with technological advances in reconstructive and ablative procedures. This paper considers the mechanisms of impact of these surgical techniques on swallow function and patient outcomes especially in light of the shifting demographics of human papilloma virus (HPV) associated oropharyngeal cancer. We present a framework for considering physiologic impairment within the context of a holistic approach to patient care based on a series of key underlying considerations.
Running wavelet archetype: time–frequency ensemble averaging requiring no fiducial points
Authors: Addison P.S.
Published: July 2015

A novel method of signal averaging within the wavelet transform time–frequency plane is presented. This running wavelet archetype technique uses the inherent scale‐dependent periodicity of the wavelet function within the averaging process, thus removing the requirement for the identification of fiducial points which is often the main cause of errors in traditional methods. The technique is illustrated using a synthetic signal and in its application to the detection of a cardiac pulse component in a noisy photoplethysmographic signal.
Efficient implementation of effective core potential integrals and gradients on graphical processing units
Authors: Song Chenchen , Wang Lee-Ping , Sachse Torsten , Preiß Julia , Presselt Martin , Martínez Todd J.
Published: July 2015

Effective core potential integral and gradient evaluations are accelerated via implementation on graphical processing units (GPUs). Two simple formulas are proposed to estimate the upper bounds of the integrals, and these are used for screening. A sorting strategy is designed to balance the workload between GPU threads properly. Significant improvements in performance and reduced scaling with system size are observed when combining the screening and sorting methods, and the calculations are highly efficient for systems containing up to 10 000 basis functions. The GPU implementation preserves the precision of the calculation; the ground state Hartree-Fock energy achieves good accuracy for CdSe and ZnTe nanocrystals, and energy is well conserved in ab initio molecular dynamics simulations.
Complementary cavity-enhanced spectrometers to investigate the OH + CH combination band in trans-formic acid
Authors: Golebiowski D. , Földes T. , Vanfleteren T. , Herman M. , Perrin A.
Published: July 2015

We have used continuous-wave cavity ring-down and femto-Fourier transform-cavity-enhanced absorption spectrometers to record the spectrum of the OH-stretching + CH-stretching (ν1 + ν2) combination band in trans-formic acid, with origin close to 6507 cm−1. They, respectively, allowed resolving and simplifying the rotational structure of the band near its origin under jet-cooled conditions (Trot = 10 K) and highlighting the overview of the band under room temperature conditions. The stronger B-type and weaker A-type subbands close to the band origin could be assigned, as well as the main B-type Q branches. The high-resolution analysis was hindered by numerous, severe perturbations. Rotational constants are reported with, however, limited physical meaning. The ν1 + ν2 transition moment is estimated from relative intensities to be 24° away from the principal b-axis of inertia.
Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface
Authors: Nagayama Gyoko , Takematsu Masaki , Mizuguchi Hirotaka , Tsuruta Takaharu
Published: July 2015

The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.
Design of in-flight fragment separator using high-power primary beams in the energy of a few hundred MeV/u
Authors: Kim J. Y. , Kim J. W. , Wan W.
Published: July 2015

An in-flight fragment separator usually requires large acceptance and high momentum resolution to minimize the loss of a rare isotope beam of interest produced at a thin target, which is especially important when 238U fission reactions in the energy of 200 MeV/u are used. The production target and beam dump are located in the pre-separator, where a beam power of up to 400 kW is dissipated. The area is surrounded by thick radiation shielding walls, which result in long drift spaces between adjacent magnetic components at various locations and an asymmetrical layout. Efforts have been made to minimize non-linear effects in the pre-separator beam optics with trials of different separator configurations and correction schemes using COSY Infinity and GICOSY. The main separator is configured to be mirror symmetric such that correction with hexapole and octupole coils can be more readily applied. The separator configuration was finalized to allow the facility design to proceed and the key components including superconducting magnets have been designed and prototyped. In addition, the separator design has been evaluated using LISE++ including a set of wedge degraders at dispersive focal planes to improve the yield and purity of selected isotope beam.
Microwave induced plasma discharge in multi-cell superconducting radio-frequency cavity
Authors: Ahmed Shahid , Mammosser John D.
Published: July 2015

A R&D effort for in situ cleaning of 1.5 GHz Superconducting Radio Frequency (SRF) cavities at room temperature using the plasma processing technique has been initiated at Jefferson Lab. This is a step toward the cleaning of cryomodules installed in the Continuous Electron Beam Accelerator Facility (CEBAF). For this purpose, we have developed an understanding of plasma discharge in a 5-cell CEBAF-type SRF cavity having configurations similar to those in the main accelerator. The focus of this study involves the detailed investigations of developing a plasma discharge inside the cavity volume and avoids the breakdown condition in the vicinity of the ceramic RF window. A plasma discharge of the gas mixture Ar–O2 (90%:10%) can be established inside the cavity volume by the excitation of a resonant 4π/5 TM010-mode driven by a klystron. The absence of any external magnetic field for generating the plasma is suitable for cleaning cavities installed in a complex cryomodule assembly. The procedures developed in these experimental investigations can be applied to any complex cavity structure. Details of these experimental measurements and the observations are discussed in the paper.
United polarizable multipole water model for molecular mechanics simulation
Authors: Qi Rui , Wang Lee-Ping , Wang Qiantao , Pande Vijay S. , Ren Pengyu
Published: July 2015

We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.
Mixed quantum/classical approach to OH-stretch inelastic incoherent neutron scattering spectroscopy for ambient and supercooled liquid water and ice Ih
Authors: Shi L. , Skinner J. L.
Published: July 2015

OH-stretch inelastic incoherent neutron scattering (IINS) has been measured to determine the vibrational density of states (VDOS) in the OH-stretch region for liquid water, supercooled water, and ice Ih, providing complementary information to IR and Raman spectroscopies about hydrogen bonding in these phases. In this work, we extend the combined electronic-structure/molecular-dynamics (ES/MD) method, originally developed by Skinner and co-workers to simulate OH-stretch IR and Raman spectra, to the calculation of IINS spectra with small k values. The agreement between theory and experiment in the limit k → 0 is reasonable, further validating the reliability of the ES/MD method in simulating OH-stretch spectroscopy in condensed phases. The connections and differences between IINS and IR spectra are analyzed to illustrate the advantages of IINS over IR in estimating the OH-stretch VDOS.
General criteria for determining rotation or oscillation in a two-dimensional axisymmetric system
Authors: Koyano Yuki , Yoshinaga Natsuhiko , Kitahata Hiroyuki
Published: July 2015

A self-propelled particle in a two-dimensional axisymmetric system, such as a particle in a central force field or confined in a circular region, may show rotational or oscillatory motion. These motions do not require asymmetry of the particle or the boundary, but arise through spontaneous symmetry breaking. We propose a generic model for a self-propelled particle in a two-dimensional axisymmetric system. A weakly nonlinear analysis establishes criteria for determining rotational or oscillatory motion.
Optical and electron transport properties of rock-salt Sc1−xAlxN
Authors: Deng Ruopeng , Zheng P. Y. , Gall D.
Published: July 2015

Epitaxial single-crystal Sc1−xAlxN ternary alloy layers deposited by magnetron co-sputtering on MgO(001) substrates at 950 °C exhibit a solid solution rock-salt phase for x = 0–0.2 without decomposition. Optical absorption indicates a linear increase in the optical gap from 2.51 eV for ScN to 3.05 eV for Sc0.8Al0.2N and, after correction due to the Moss-Burstein shift, a direct X point interband transition energy Eg(X) = 2.15 + 2.75 x (eV). Correspondingly, the direct transition at the zone center increases with Al concentration according to Eg(Γ) = 3.80 + 1.45 x (eV), as determined from a feature in the reflection spectra. All layers are degenerate n-type semiconductors with a room temperature mobility that decreases from 22 to 6.7 to 0.83 cm2/V s as x increases from 0 to 0.11 to 0.20. The corresponding carrier densities are 9.2 × 1020, 7.9 × 1020, and 0.95 × 1020 cm−3 as determined from Hall measurements and consistent with optical free carrier absorption below photon energies of 1 eV. Temperature dependent transport measurements indicate metallic conduction for ScN, but weak localization that leads to a resistivity minimum at 85 and 210 K for x = 0.051 and 0.15, respectively, and a negative temperature coefficient over the entire measured 4–300 K range for Sc0.8Al0.2N. The decreasing mobility is attributed to alloy scattering at randomly distributed Al atoms on cation sites, which also cause the weak localization. The carrier density is primarily due to unintentional F doping from the Sc target and decreases strongly for x > 0.15, which is attributed to trapping in defect states due to the deterioration of the crystalline quality, as evidenced by the x-ray diffraction peak width that exhibits a minimum of 0.14° for x = 0.11 but increases to 0.49° for x = 0.20. This is consistent with asymmetric x-ray diffraction analyses, indicating a relaxed lattice constant that decreases from 4.511 ± 0.005 to 4.411 ± 0.004 Å for x = 0–0.2, and a biaxial in-plane compressive strain that decreases from −1.1% to −0.2% as x increases from 0 to 0.11, which is attributed to the higher Al adatom mobility, but increases again to −1.8% for x = 0.20, as x approaches the critical composition for phase separation, which causes structural instability and a higher defect density.
Photodissociation of D2+ induced by linearly chirped laser pulses
Authors: Csehi András , Halász Gábor J. , Cederbaum Lorenz S. , Vibók Ágnes
Published: July 2015

Recently, it has been revealed that so-called light-induced conical intersections (LICIs) can be formed both by standing or by running laser waves even in diatomic molecules. Due to the strong nonadiabatic couplings, the existence of such LICIs has significant impact on the dynamical properties of a molecular system. In our former studies, the photodissociation process of the D2+ molecule was studied initiating the nuclear dynamics both from individual vibrational levels and from the superposition of all the vibrational states produced by ionizing D2. In the present work, linearly chirped laser pulses were used for initiating the dissociation dynamics of D2+. In contrast to the constant frequency (transform limited) laser fields, the chirped pulses give rise to LICIs with a varying position according to the temporal frequency change. To demonstrate the impact of these LICIs on the dynamical properties of diatomics, the kinetic energy release spectra, the total dissociation probabilities, and the angular distributions of the D2+ photofragments were calculated and discussed.
Wave drag on a submerged sphere
Authors: Benusiglio Adrien , Chevy Frédéric , Raphaël Élie , Clanet Christophe
Published: July 2015

We measure the wave drag acting on fully submerged spheres as a function of their depth and velocity, with an apparatus that measures only the component of the drag due to the proximity of the free surface. We observe that close to the surface the wave drag is of the order of the hydrodynamic drag. In our range of study, the measured force is more than one order smaller than predictions based on linear response. In order to investigate this discrepancy, we measure the amplitude of the waves at the origin of the wave drag, comparing the measurement with a theoretical model. The model captures the measurements at “large depth” but the wave’s amplitude saturates at “small depth,” an effect that partially accounts for the difference between the predicted and measured wave drag.
Spark discharge coupled laser multicharged ion source
Authors: Shaim Md. Haider A. , Elsayed-Ali Hani E.
Published: July 2015

A spark discharge is coupled to a laser multicharged ion source to enhance ion generation. The laser plasma triggers a spark discharge with electrodes located in front of the ablated target. For an aluminum target, the spark discharge results in significant enhancement in the generation of multicharged ions along with higher charge states than observed with the laser source alone. When a Nd:YAG laser pulse (wavelength 1064 nm, pulse width 7.4 ns, pulse energy 72 mJ, laser spot area on target 0.0024 cm2) is used, the total multicharged ions detected by a Faraday cup is 1.0 nC with charge state up to Al3+. When the spark amplification stage is used (0.1 μF capacitor charged to 5.0 kV), the total charge measured increases by a factor of ∼9 with up to Al6+ charge observed. Using laser pulse energy of 45 mJ, charge amplification by a factor of ∼13 was observed for a capacitor voltage of 4.5 kV. The spark discharge increases the multicharged ion generation without increasing target ablation, which solely results from the laser pulse. This allows for increased multicharged ion generation with relatively low laser energy pulses and less damage to the surface of the target.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
Authors: White Alexander J. , Gorshkov Vyacheslav N. , Tretiak Sergei , Mozyrsky Dmitry
Published: July 2015

Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Grain-size-dependent spontaneous relaxor-to-ferroelectric phase transition in (Bi1/2K1/2)TiO3 ceramics
Authors: Hagiwara Manabu , Fujihara Shinobu
Published: July 2015

Dense and phase-pure (Bi1/2K1/2)TiO3 (BKT) ceramics with various average grain sizes from 0.18 to 1.01 μm were prepared from a hydrothermally synthesized powder and their phase transition behaviors were studied by means of dielectric measurements. A drastic increase of the maximum dielectric permittivity (εm) with increasing the grain size was found in the temperature dependence of permittivity. The sample with the largest grain size clearly showed both a frequency dependence of dielectric maximum temperature (Tm) and a dielectric anomaly with a strong thermal hysteresis at a temperature below Tm, demonstrating that the BKT ceramic is intrinsically a material exhibiting a spontaneous relaxor to normal ferroelectric (R-nFE) phase transition. On the other hand, the suppression of the R-nFE transition was observed in the sample with the smallest grain size, which was explained as an effect of avoiding the internal stress development caused by the volume increase occurring with the phase transition.
Oxidation of Zn nanoparticles probed by online optical spectroscopy during nanosecond pulsed laser ablation of a Zn plate in H2O
Authors: Camarda P. , Vaccaro L. , Messina F. , Cannas M.
Published: July 2015

We report online UV-Visible absorption and photoluminescence measurements carried out during and after pulsed laser ablation of a zinc plate in water, which clarify the events leading to the generation of ZnO nanoparticles. A transient Zn/ZnO core-shell structure is revealed by the coexistence of the resonance absorption peak around 5.0 eV due to Zn surface plasmon resonance and the edge at 3.5 eV of ZnO. The growth kinetics of ZnO, selectively probed by the exciton luminescence at 3.3 eV, begins only after a ∼30 s delay from the onset of laser ablation. We also detect the luminescence at 2.3 eV of ZnO oxygen vacancies, yet rising with an even longer delay (∼100 s). These results show that the oxidation of Zn nanoparticles mainly occurs out of the ablation plume region and proceeds as a sequence of two stages: the earliest oxidation is only superficial and forms a defect-free ZnO shell around a Zn core, whereas core oxidation is driven by comparatively slower diffusion of water through the ZnO shell and leaves behind a defective ZnO material rich of oxygen vacancies.
Modulation of superconducting critical temperature in niobium film by using all-solid-state electric-double-layer transistor
Authors: Tsuchiya Takashi , Moriyama Satoshi , Terabe Kazuya , Aono Masakazu
Published: July 2015

An all-solid-state electric-double-layer transistor (EDLT) was fabricated for electrical modulation of the superconducting critical temperature (Tc) of Nb film epitaxially grown on α-Al2O3 (0001) single crystal. In an experiment, Tc was modulated from 8.33 to 8.39 K while the gate voltage (VG) was varied from 2.5 to −2.5 V. The specific difference of Tc for the applied VG was 12 mK/V, which is larger than that of an EDLT composed of ionic liquid. A Tc enhancement of 300 mK was found at the Li4SiO4/Nb film interface and is attributed to an increase in density of states near the Fermi level due to lattice constant modulation. This solid electrolyte gating method should enable development of practical superconducting devices highly compatible with other electronic devices.
2-Aryl-1,3-dimethylbenzimidazolines as Effective Electron and Hydrogen Donors in Photoinduced Electron-Transfer Reactions
Authors: Hasegawa Eietsu , Takizawa Shin-ya
Published: July 2015

2-Aryl-1,3-dimethylbenzimidazolines (DMBIHs) have been applied to photoinduced electron-transfer reductions of various organic substrates. Either direct or indirect electron transfer between the substrates and DMBIHs is utilized to promote the desired transformations. Photoexcitation of the substrates using light above 280 nm was carried out in the former protocol whereas a photosensitization method using materials such as substituted pyrenes, ruthenium and iridium complexes that absorb longer-wavelength light was employed in the latter. In these reactions, DMBIHs undergo initial electron transfer and subsequent proton or hydrogen atom transfer.
Developmental potential of 2n/3n mixoploid mouse embryos produced by fusion of individual second polar bodies and blastomeres of 2-cell embryos
Authors: Hino Toshiaki , Tateno Hiroyuki
Published: July 2015

Using 2n/3n mixoploid mouse embryos produced by fusion of individual second polar bodies (PB2s) with individual blastomeres of 2-cell embryos, the dynamics of PB2 nuclei in the host blastomeres during mitosis were examined and the fate of the 3n cell line in the mixoploid embryos was followed. Most of the PB2 nuclei were synchronised with the cell cycle of the host blastomeres and all chromosomes were incorporated into a single mitotic spindle. The majority of the mixoploid embryos developed to blastocysts with 3n cells. In conceptuses at Day 11.5 and Day 18.5 of gestation, 3n cells were recognised in both of the embryonic/fetal and placental tissues. When green fluorescent protein (GFP)-transgenic mice were used as a donor of PB2, GFP-positive 3n cells were found in more than 40% of morulae and blastocysts, indicating that the PB2 genome can be reactivated during the pre-implantation stage. GFP-positive 3n cells were non-randomly allocated in trophectoderm in blastocysts. These findings may explain the production mechanism of 2n/3n mixoploid human embryos, that is, a PB2 is incorporated into one daughter blastomere during the early cleavage period.
Conserved regulatory mechanism controls the development of cells with rooting functions in land plants
Authors: Tam Thomas Ho Yuen , Catarino Bruno , Dolan Liam
Published: July 2015

Significance

This work describes the discovery of an ancient genetic mechanism that was used to build rooting systems when plants colonized the relatively dry continental surfaces >470 million years ago. We demonstrate that a group of basic helix–loop–helix transcription factors—the LOTUS JAPONICUS ROOTHAIRLESS1-LIKE proteins—is part of a conserved auxin-regulated gene network that controls the development of tip-growing cells with rooting functions among extant land plants. This result suggests that this mechanism was active in the common ancestor of most land plants and facilitated the development of early land plant filamentous rooting systems, crucial for the successful colonization of the land by plants.
Climatic controls on ecosystem resilience: Postfire regeneration in the Cape Floristic Region of South Africa
Authors: Wilson Adam M. , Latimer Andrew M. , Silander John A.
Published: July 2015

Significance

The rate at which ecosystems recover from disturbance can greatly influence their resilience to environmental change. We used more than a decade of satellite data to model how the extraordinarily biodiverse shrublands of South Africa recover following fire and how recovery rates vary with temperature and precipitation across the region. We found that climate strongly affects how quickly plant communities can recover after fire. We also used global climate models to project ecosystem recovery into the future and found that warmer winter temperatures will likely speed up postfire recovery unless precipitation declines as temperature increases (as some models project).
Insular neural system controls decision-making in healthy and methamphetamine-treated rats
Authors: Mizoguchi Hiroyuki , Katahira Kentaro , Inutsuka Ayumu , Fukumoto Kazuya , Nakamura Akihiro , Wang Tian , Nagai Taku , Sato Jun , Sawada Makoto , Ohira Hideki , Yamanaka Akihiro , Yamada Kiyofumi
Published: July 2015

Significance

Patients with addiction have a greater tendency to engage in risk-taking behavior. However, the neural substrates responsible for these deficits remain unknown. Here we demonstrated that chronic methamphetamine-treated rats preferred high-risk/high-reward actions and assigned higher value to high returns, indicative of altered decision-making. Pharmacological studies revealed that the insular neural system controls decision-making in both healthy and methamphetamine-treated rats. We further confirmed the role of the insular cortex in decision-making using designer receptor exclusively activated by designer drug technology. Because decision-making is a cognitive process that influences many aspects of daily living and both mental and physical health, the findings of this study have broader implications.
Twentieth century surge of excess adult male mortality
Authors: Beltrán-Sánchez Hiram , Finch Caleb E. , Crimmins Eileen M.
Published: July 2015

Significance

Female life expectancy now exceeds that of males in all countries. Although this gender difference has become accepted as normal, it is a relatively recent demographic phenomenon that emerged with the reduction of infections and the increase in the share of adult mortality attributed to cancer and cardiovascular disease. Heart disease is the main condition associated with increased excess male mortality, making the strongest contributions in birth cohorts of 1900–1935. Smoking behavior accounts for about 30% of male excess mortality at ages 50–70 for those born in 1900–1935. The remaining excess male mortality may be explained by underlying traits of vulnerability to cardiovascular disease that emerged with the reduction of infections and changes in diet and other lifestyle factors.
Measuring selective constraint on fertility in human life histories
Authors: Jones James Holland , Tuljapurkar Shripad
Published: July 2015

Significance

Trade-offs, or constraints, play a substantial role in shaping the ability of organisms to respond adaptively to selection. We derive a simple means for measuring constraints in demographic rates like fertility and survival that builds on commonly used evolutionary demographic measures. We apply this measure to a hypothesized trade-off between fertility and infant survival and show that a 1% reduction in infant mortality would have to be balanced by an approximately 20% increase in fertility to be favored by selection. Our paper should have an important impact on shaping future empirical studies of human life histories and parental investment as it identifies key measures that we expect should be quite variable with respect to ecology, technology, and social systems.
Inferring influenza dynamics and control in households
Authors: Lau Max S.Y. , Cowling Benjamin J. , Cook Alex R. , Riley Steven
Published: July 2015

Significance

Traditionally, the efficacy of household-based nonpharmaceutical interventions against influenza is measured by the household secondary attack rate based on observed individual epidemiological data. We present an alternative measure of intervention efficacy that accounts for unobserved transmission using Bayesian techniques. We apply our methods to data from a study of household interventions (face masks and improved hand hygiene) in Hong Kong. This paper describes advances in our understanding of an important disease system and also our statistical ability to synthesize modern data streams.
Biased Brownian motion as a mechanism to facilitate nanometer-scale exploration of the microtubule plus end by a kinesin-8
Authors: Shin Yongdae , Du Yaqing , Collier Scott E. , Ohi Melanie D. , Lang Matthew J. , Ohi Ryoma
Published: July 2015

Significance

The cellular distributions of kinesins are defined in part by their intrinsic biophysical properties. The well-characterized kinesin-8s, for example, translocate exceptionally long distances on a microtubule track, concentrating them at plus ends of long, stable microtubules. Kif18B, a little-studied kinesin-8, targets the plus ends of fast-growing, short-lived microtubules by binding the plus-end tracking protein EB1. Whether ultraprocessivity is conserved among kinesin-8s is thus unclear. Here, we show that Kif18B is not ultraprocessive and that the motor switches frequently between diffusive and directed modes of motility. Our work identifies properties of Kif18B that may have optimized the motor to explore the ∼1-μm domain of microtubule plus ends and show that biophysical motor properties cannot be generalized within any one kinesin subfamily.
Superresolution fluorescence mapping of single-nanoparticle catalysts reveals spatiotemporal variations in surface reactivity
Authors: Zhang Yuwei , Lucas J. Matthew , Song Ping , Beberwyck Brandon , Fu Qiang , Xu Weilin , Alivisatos A. Paul
Published: July 2015

Significance

Here we use time-lapsed superresolution mapping of single-molecule catalysis events on individual nanoparticle surface to observe time-varying changes in the spatial distribution of catalysis events on Sb-doped TiO
2
nanorods and Au triangle nanoplates. The ability to measure both the spatial- and time-resolved activity of different types of active sites on single-nanoparticle surface leads to a more comprehensive understanding of reactivity patterns and may enable the design of new and more productive heterogeneous catalysts.
Randomization and resilience of brain functional networks as systems-level endophenotypes of schizophrenia
Authors: Lo Chun-Yi Zac , Su Tsung-Wei , Huang Chu-Chung , Hung Chia-Chun , Chen Wei-Ling , Lan Tsuo-Hung , Lin Ching-Po , Bullmore Edward T.
Published: July 2015

Significance

Using network analysis of resting-state functional MRI data, we demonstrate that significant randomization of global network metrics, and greater resilience to targeted attack on network hubs, was replicably demonstrable in Chinese patients with schizophrenia, and was also demonstrated for the first time in their nonpsychotic first-degree relatives. These results support the hypothesis that functional networks are abnormally randomized and resilient in schizophrenia and indicate that network randomization/resilience may be an endophenotype, or marker of familial risk, for schizophrenia. We suggest that the greater randomization of the brain network endophenotype of schizophrenia may confer advantages in terms of greater resilience to pathological attack that may explain the selection and persistence of risk genes for schizophrenia in the general population.
Rapid and widespread de novo evolution of kin discrimination
Authors: Rendueles Olaya , Zee Peter C. , Dinkelacker Iris , Amherd Michaela , Wielgoss Sébastien , Velicer Gregory J.
Published: July 2015

Significance

Relatedness-dependent behavior modification is common among social organisms and has been a major feature of social evolution theory for decades. However, the evolutionary causes of kin discrimination are often unclear. Here, we document many spontaneous origins of kin discrimination in a social microbe that appear to arise as indirect byproducts of adaptation at other traits and we show that kin discrimination evolves by diverse genetic mechanisms.
Quantification of biological aging in young adults
Authors: Belsky Daniel W. , Caspi Avshalom , Houts Renate , Cohen Harvey J. , Corcoran David L. , Danese Andrea , Harrington HonaLee , Israel Salomon , Levine Morgan E. , Schaefer Jonathan D. , Sugden Karen , Williams Ben , Yashin Anatoli I. , Poulton Richie , Moffitt Terrie E.
Published: July 2015

Significance

The global population is aging, driving up age-related disease morbidity. Antiaging interventions are needed to reduce the burden of disease and protect population productivity. Young people are the most attractive targets for therapies to extend healthspan (because it is still possible to prevent disease in the young). However, there is skepticism about whether aging processes can be detected in young adults who do not yet have chronic diseases. Our findings indicate that aging processes can be quantified in people still young enough for prevention of age-related disease, opening a new door for antiaging therapies. The science of healthspan extension may be focused on the wrong end of the lifespan; rather than only studying old humans, geroscience should also study the young.
Structure and mechanism of the ATPase that powers viral genome packaging
Authors: Hilbert Brendan J. , Hayes Janelle A. , Stone Nicholas P. , Duffy Caroline M. , Sankaran Banumathi , Kelch Brian A.
Published: July 2015

Significance

Many viruses use a molecular motor to pump DNA into a preformed protein shell called the capsid, a process that is essential for the formation of infectious virus particles. The ATPase machine powering this process is the strongest known biological motor. However, the structure and mechanism of this motor are unknown. Here, we derive a structural model of the ATPase assembly using a combination of X-ray crystallography, small-angle X-ray scattering, molecular modeling, and biochemical data. We identify residues critical for ATP hydrolysis and DNA binding, and derive a mechanistic model for the translocation of DNA into the viral capsid. Our studies introduce a model for ATPase assembly and illustrate how DNA is pumped with high force.
Sequential ubiquitination and deubiquitination enzymes synchronize the dual sensor and effector functions of TRIM21
Authors: Fletcher Adam J. , Mallery Donna L. , Watkinson Ruth E. , Dickson Claire F. , James Leo C.
Published: July 2015

Significance

Tripartite motif (TRIM) proteins are a large family of E3 ubiquitin (Ub) ligases, with many members having important roles in innate immunity. TRIM21 is a cytosolic antibody receptor that recognizes the Fc portion of antibodies bound to incoming virions. On binding to these immune complexes, TRIM21 triggers the catastrophic disassembly of viral capsids at the proteasome, terminating viral infection. Simultaneously, TRIM21 “senses” the presence of the virus and provokes signaling cascades that activate the transcription factor NF-κB, ultimately alerting surrounding cells to the infection. Here, we uncover the stepwise ubiquitination mechanism catalyzed by TRIM21, as well as the various cofactors required, that allows these two antiviral activities to occur synchronously at the proteasome.
Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters
Authors: Montiel Daniel , Kang Hahk-Soo , Chang Fang-Yuan , Charlop-Powers Zachary , Brady Sean F.
Published: July 2015

Significance

A rapidly growing number of cryptic natural product biosynthetic gene clusters have been identified in bacterial DNA sequencing datasets. The metabolites encoded by most of these gene clusters remain uncharacterized because they are not readily activated using monoculture fermentation methods. The development of generic gene cluster activation strategies is needed to access molecules encoded by this rapidly growing collection of sequenced gene clusters. The promoter engineering platform outlined here provides a simple, cost-effective, and potentially scalable tool for the characterization of molecules encoded by gene clusters found in sequenced microbial (meta)genomes. We believe that this gene cluster activation platform will accelerate the discovery of biomedically relevant metabolites using (meta)genomics-driven natural products discovery methods.
Intergenerational neural mediators of early-life anxious temperament
Authors: Fox Andrew S. , Oler Jonathan A. , Shackman Alexander J. , Shelton Steven E. , Raveendran Muthuswamy , McKay D. Reese , Converse Alexander K. , Alexander Andrew , Davidson Richard J. , Blangero John , Rogers Jeffrey , Kalin Ned H.
Published: July 2015

Significance

According to the World Health Organization, anxiety and depressive disorders are a leading source of disability, affecting hundreds of millions of people. Children can inherit an extremely anxious temperament, which is a prominent risk factor for the later development of anxiety, depression, and comorbid substance abuse. This study uses high-resolution functional and structural imaging in our well-established developmental nonhuman primate model to identify the heritable neural substrate that underlies extreme childhood anxious temperament. Using a large multigenerational family pedigree, genetic correlation analyses revealed a tripartite neural circuit where metabolism likely shares a genetic substrate with early-life dispositional anxiety. Interestingly, we found that brain function—not structure—is the critical intermediary between genetics and the childhood risk to develop stress-related psychopathology.
What the fly’s nose tells the fly’s brain
Authors: Stevens Charles F.
Published: July 2015

Significance

This work is significant for three reasons. First, a new way the brain represents information is identified, one in which the information present in a large population of neurons can be gotten from a small subset of any neurons rather that from a subset of certain specific neurons. Second, the nature of the combinatorial code used to specify odor identity is identified, and this same type of code may be used in other contexts. Third, the way fly olfaction works can potentially provide a model for understanding the function of important vertebrate brain regions that appear to share the same neural circuit architecture.
Spectrum of power laws for curved hand movements
Authors: Huh Dongsung , Sejnowski Terrence J.
Published: July 2015

Significance

In curved hand movements around ellipses, the speed tends to scale inversely with the curvature with a power law having an exponent of −1/3. We examined whether this well-known regularity in motor planning holds for more general shapes. Using an optimality principle, we identified a set of basis shapes, each with a single characteristic angular frequency, which subjects drew with power laws whose exponents ranged from 0 to −2/3. More general movements exhibited linear mixtures of power laws. The speed of arbitrary doodling movements with a broad spectrum of frequencies could also be predicted from the curvature with high accuracy.
Statistical energy conservation principle for inhomogeneous turbulent dynamical systems
Authors: Majda Andrew J.
Published: July 2015

Significance

Understanding the complexity of anisotropic turbulent processes over a wide range of spatiotemporal scales in engineering shear turbulence as well as climate atmosphere ocean science is a grand challenge of contemporary science with important societal impact. In such inhomogeneous turbulent dynamical systems, there is a large dimensional phase space with a large dimension of unstable directions where a large-scale ensemble mean and the turbulent fluctuations exchange energy and strongly influence each other. These complex features strongly impact practical prediction and uncertainty quantification. A systematic energy conservation principle is developed here in a
Theorem
that precisely accounts for the statistical energy exchange between the mean flow and the related turbulent fluctuations.
EGFR inhibition evokes innate drug resistance in lung cancer cells by preventing Akt activity and thus inactivating Ets-1 function
Authors: Phuchareon Janyaporn , McCormick Frank , Eisele David W. , Tetsu Osamu
Published: July 2015

Significance

Lung cancer is the leading cause of cancer death worldwide. About 10% harbor mutations in epidermal growth factor receptor (EGFR). Despite remarkable progress in treatment with EGFR inhibitors, only 5% of patients achieve tumor reduction >90%, even though all of those treated have EGFR mutations. Our study addressed this discrepant response by investigating the mechanism of innate drug resistance, i.e. resistance inherent in the tumor cells even before treatment begins and not acquired over its course. Because overcoming innate resistance will increase the primary response, our findings may provide an opportunity to develop new therapies to reduce the probability of emergent resistance to EGFR inhibitors.
ALDH2(E487K) mutation increases protein turnover and promotes murine hepatocarcinogenesis
Authors: Jin Shengfang , Chen Jiang , Chen Lizao , Histen Gavin , Lin Zhizhong , Gross Stefan , Hixon Jeffrey , Chen Yue , Kung Charles , Chen Yiwei , Fu Yufei , Lu Yuxuan , Lin Hui , Cai Xiujun , Yang Hua , Cairns Rob A. , Dorsch Marion , Su Shinsan M. , Biller Scott , Mak Tak W. , Cang Yong
Published: July 2015

Significance

About 40% of East Asians and over 500 million people worldwide carry a specific polymorphism, ALDH2*2, and exhibit “Asian flush” after alcohol drinking. We generated a mouse strain with this engineered polymorphism and demonstrated its resemblance to human carriers in terms of defective alcohol metabolism. With this model, we show that murine ALDH2*2 increases ALDH2 protein turnover and promotes chemical-induced liver tumor development. Importantly, ALDH2 is unstable in ALDH2*2 human liver samples and is significantly down-regulated in human liver tumors. Data from our mouse and clinical studies suggest that ALDH2 is a liver tumor suppressor and the ALDH2*2 polymorphism is a risk factor for liver cancer.
Measuring dynamic cell–material interactions and remodeling during 3D human mesenchymal stem cell migration in hydrogels
Authors: Schultz Kelly M. , Kyburz Kyle A. , Anseth Kristi S.
Published: July 2015

Significance

Scaffolds that serve as synthetic mimics of the extracellular matrix have applications in wound healing, tissue engineering, and stem cell expansion. When cells are cultured in these tunable matrices, little is known about local microenvironmental changes during degradation and remodeling. Methods that provide quantitative and predictable information about cell-mediated remodeling could significantly improve the biomaterial design process. We use passive microrheology, a technique that measures rheological properties from Brownian motion of embedded particles, to characterize remodeling of a cell-laden peptide-functionalized poly(ethylene glycol) hydrogel that degrades in response to cell-secreted enzymes. Results show microenvironmental changes at multiple time and size scales, and reveal an interesting degradation gradient, as mesenchymal stem cells attach, spread, and move through these synthetic extracellular matrix mimics.