bluuebunny/crossref_metadata_2025 huggingface dataset:
Donor–acceptor–acceptor (D–A–A) type 1,8-naphthalimides as non-fullerene small molecule acceptors for bulk heterojunction solar cells
Authors: Gautam Prabhat , Sharma Rahul , Misra Rajneesh , Keshtov M. L. , Kuklin S. A. , Sharma Ganesh D.
Published: November 2016

Donor–acceptor–acceptor (D–A–A) type 1,8-naphthalimide based small molecules SM1 and SM2 functionalized with tetracyanobutadiene (TCBD) and dicyanoquino-dimethane (DCNQ) modules, showing strong absorption in the visible and near-infrared (NIR) region are reported.
Selective anomeric acetylation of unprotected sugars in water
Authors: Lim David , Fairbanks Antony J.
Published: November 2016

Selective acetylation of only the anomeric hydroxyl group of unprotected sugars is possible in aqueous solution. This new one step route to glycosyl acetates may facilitate their use as donors for enzyme catalysed glycosylation.
MOF-templated nanorice–nanosheet core–satellite iron dichalcogenides by heterogeneous sulfuration for high-performance lithium ion batteries
Authors: Pang Huicong , Sun Weiwei , Lv Li-Ping , Jin Feiying , Wang Yong
Published: November 2016

The nanorice–nanosheet core–satellite structure of FeS2 synthesized by heterogeneous sulfuration from a MIL-88-Fe precursor achieves highly reversible larger-than-theoretical Li-storage capacities.
The Pull-Through Technique: A Viable Option for Preserving the Inferior Alveolar Nerve during Surgical Resection
Authors: Leite Gustavo Boehmer , Sartoretto Suelen Cristina , Lima Fernando César Amazonas , Calasans-Maia Mônica , Louro Rafael Seabra
Published: November 2016

The aim of this study was to present a new surgical technique used to remove benign mandibular tumors with minimal damage to the inferior alveolar nerve. The pull-through technique was shown using an ameloblastoma surgical resection as an example. This technique consisted in the reconstruction of the lower jaw associating the resection of the lesion with nerve repair at the same surgical time. The resection was performed using the pull-through technique and the inferior alveolar nerve was preserved. After 6 months, the patient presented a recovery of approximately 80% of sensory function. The surgical technique presented should be considered an important method by which to produce a higher functional outcome to remove benign mandibular tumors with minimal damage to the inferior alveolar nerve and allows the maintenance of quality of life for the patient, as the consequences of this type of surgery are minimized.
Minimum action transition paths connecting minima on an energy surface
Authors: Koehl Patrice
Published: November 2016

Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown that the structures along the RelaxPath trajectories remain protein-like. Open source versions of the two programs MinActionPath and RelaxPath are available by request.
UV excitations of halons
Authors: Stojanović Ljiljana , Alyoubi Abdulrahman O. , Aziz Saadullah G. , Hilal Rifaat H. , Barbatti Mario
Published: November 2016

In the present study, we examined the UV excitations of a newly introduced molecular set, Halons-9, composed of nine gaseous halon molecules. The performance of the density functional-based multi-reference configuration interaction method (DFT/MRCI) and time-dependent density functional theory with CAM-B3LYP functional (TD-CAM-B3LYP) in the computation of singlet and triplet excited states of this set was evaluated against coupled-cluster with singles and doubles (CCSD). Excited states up to the corresponding ionization limits, including both localized and delocalized excitations, have been benchmarked. TD-CAM-B3LYP significantly underestimates excitation energies of the higher mixed valence-Rydberg and Rydberg states, with computed mean absolute deviations from the equation of motion (EOM)-CCSD results 1.06 and 0.76 eV, respectively. DFT/MRCI gives a significantly better description of higher excited states, albeit still poor, compared to the TD-CAM-B3LYP. The mean absolute deviations of mixed valence-Rydberg and Rydberg states from the reference EOM-CCSD values are 0.66 and 0.47 eV, respectively. The performance of DFT/MRCI for description of strongly correlated states with valence-Rydberg mixing is still not satisfactory enough. On the other hand, oscillator strengths of most of singlet states obtained with both methods are close to the EOM-CCSD values. The largest deviations, occurring in the case of several high-lying multiconfigurational states, are of an order of magnitude.
Local and average structures of BaTiO3-Bi(Zn1/2Ti1/2)O3
Authors: Usher Tedi-Marie , Iamsasri Thanakorn , Forrester Jennifer S. , Raengthon Natthaphon , Triamnak Narit , Cann David P. , Jones Jacob L.
Published: November 2016

The complex crystallographic structures of (1−x)BaTiO3-xBi(Zn1/2Ti1/2)O3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. The results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). However, a box-car fitting analysis of the PDFs reveals variations at different length scales. For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 Å vs. 5 Å). When the longest distances are evaluated (r > 40 Å), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. For the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. Collectively, the results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.
The double-layer structure of overscreened surfaces by smeared-out ions
Authors: Frydel Derek
Published: November 2016

The present work focuses on the structure of a double-layer of overscreened charged surfaces by smeared-out charges and probes the link between the structure of a double-layer and the bulk properties of an electrolyte with special view to the role of the Kirkwood crossover. Just as the Kirkwood line divides a bulk solution into a fluid with monotonic and oscillatory decaying correlations, it similarly separates charge inversion into two broad domains, with and without oscillating charge density profile. As initially oscillations may appear like a far-field occurrence, eventually they develop into a full fledged layering of a charge density.
A phenomenological continuum model for force-driven nano-channel liquid flows
Authors: Ghorbanian Jafar , Celebi Alper T. , Beskok Ali
Published: November 2016

A phenomenological continuum model is developed using systematic molecular dynamics (MD) simulations of force-driven liquid argon flows confined in gold nano-channels at a fixed thermodynamic state. Well known density layering near the walls leads to the definition of an effective channel height and a density deficit parameter. While the former defines the slip-plane, the latter parameter relates channel averaged density with the desired thermodynamic state value. Definitions of these new parameters require a single MD simulation performed for a specific liquid-solid pair at the desired thermodynamic state and used for calibration of model parameters. Combined with our observations of constant slip-length and kinematic viscosity, the model accurately predicts the velocity distribution and volumetric and mass flow rates for force-driven liquid flows in different height nano-channels. Model is verified for liquid argon flow at distinct thermodynamic states and using various argon-gold interaction strengths. Further verification is performed for water flow in silica and gold nano-channels, exhibiting slip lengths of 1.2 nm and 15.5 nm, respectively. Excellent agreements between the model and the MD simulations are reported for channel heights as small as 3 nm for various liquid-solid pairs.
First-principles investigation on solar radiation shielding performance of rutile VO2 filters for smart windows
Authors: Xiao Lihua , Su Yuchang , Qiu Wei , Ran Jingyu , Liu Yike , Wu Jianming , Lu Fanghai , Shao Fang , Peng Ping
Published: November 2016

Vanadium dioxide (VO2) undergoing reversible metal-insulator phase transition could allow for the formation of an efficient thermochromic material for smart windows. However, solar radiation shielding performance is determined by transparent rutile VO2 filters, and the puzzling metal-insulator transition mechanism makes it challenging to explain the origin of the coexistence of strong near infrared absorption with high optical transparency. The band structure, the density of states, and the optical properties of rutile VO2 were calculated using the first-principles calculations. The calculated results of the structural and optical properties are in good agreement with the previously reported experimental findings. The calculated dielectric functions, electron energy-loss function and solar radiation shielding performance of the rutile VO2 filters indicate that rutile VO2 is a promising near-infrared absorption/reflectance material with the near-infrared radiation insulating abilities and a visible light transmittance. These properties arise from plasma oscillation and a collective oscillation (volume plasmons) of carrier electrons.
Theoretical study of the reaction kinetics and the detonation wave profile for 1,3,5-triamino-2,4,6-trinitrobenzene
Authors: Long Yao , Chen Jun
Published: November 2016

We simulate the reaction process of 1,3,5-triamino-2,4,6-trinitrobenzene in wide temperature and pressure ranges by molecular dynamics and evaluate the intermediate molecules, chemical reaction rates, and Hugoniot relations. Based on them, the leading shock wave, fast reaction zone, Chapman-Jouguet state, and slow reaction zone under detonation are investigated by different theoretical methods. A complete structure of the detonation wave is obtained. The calculated detonation velocity, detonation pressure, detonation products, and the length of the reaction zone are in agreement with the experiments and others' calculations. We find that some intermediate molecules play an important role in determining the reaction path of explosives but just remain a little after detonation, such as H2 and NH3.
Inverted organic light-emitting diodes with an electrochemically deposited zinc oxide electron injection layer
Authors: Takada Makoto , Furuta Suguru , Kobayashi Takashi , Nagase Takashi , Shinagawa Tsutomu , Izaki Masanobu , Naito Hiroyoshi
Published: November 2016

Electrical and optical properties of poly(dioctylfluorene-alt-benzothiadiazole) based inverted organic light-emitting diodes (iOLEDs) with electrochemically deposited ZnO electron-injecting layer (EIL) have been studied. The device characteristics of the iOLEDs fabricated in this work (8600 cd/m2, 1.5 cd/A at 6.0 V) are almost comparable to those of conventional iOLEDs with sputtered ZnO EIL, indicating that the electron injection properties of electrodeposited ZnO EIL are similar to those of sputtered ZnO EIL. Impedance spectroscopy reveals that the equivalent circuits of iOLEDs with electrochemically deposited ZnO EIL and with sputtered ZnO EIL are indistinguishable.
Development of multi-frequency ESR/EDMR system using a rectangular cavity equipped with waveguide window
Authors: Fukuda Kunito , Asakawa Naoki
Published: November 2016

A straightforward method for a variable frequency electron spin resonance/electrically detected magnetic resonance (ESR/EDMR) spectroscopy using a C-band microwave cavity equipped with waveguide windows is presented. The method enables us to perform quasi-continuous multiple resonance frequency (MF-ESR/EDMR) experiments for electronic devices. The C-band microwave circuitry was selected because of larger available sample volume than that for conventional X-band one. All the measurements were performed using a combined sample of 2,2-diphenyl-1-picrylhydrazyl/ pn-junction Si diode. The present simple MF-ESR/EDMR method will be useful for the characterization of electronic and optoelectronic devices.
Near perfect ultrasonic omnidirectional transducer using the optimal patterning of the zero-index acoustic metamaterials
Authors: Hyun Jaeyub , Wang Semyung
Published: November 2016

This study proposes the theoretical optimal patterning method based on the geometrical transformation acoustics to design an ultrasonic omnidirectional transducer system, which is composed of the designed near zero-index acoustic metamaterial (ZIAMM). The designed ZIAMM is made of circular rubber rods in water matrix. Meanwhile, the curved unit cell structure is necessary to arrange the designed ZIAMM effectively into the circular-shaped ultrasonic omnidirectional transducer system. To this end, we transform the square unit cell into the curved unit cell in the physical space, instead of starting from a homogeneous medium. Also the periodic boundary condition in the two-dimensional polar coordinate is proposed to calculate the dynamic characteristic (i.e., the effective material properties and the dispersion relation) according to the curvature of curved unit cell. The proposed optimal patterning method is verified through the ZIAMM-based ultrasonic omnidirectional transducer system. Especially the radiation performance of ZIAMM-based ultrasonic omnidirectional transducer system is greatly improved by this optimal patterning.
On the interplay between Si(110) epilayer atomic roughness and subsequent 3C-SiC growth direction
Authors: Khazaka Rami , Michaud Jean-François , Vennéguès Philippe , Nguyen Luan , Alquier Daniel , Portail Marc
Published: November 2016

In this contribution, we performed the growth of a 3C-SiC/Si/3C-SiC layer stack on a Si(001) substrate by means of chemical vapor deposition. We show that, by tuning the growth conditions, the 3C-SiC epilayer can be grown along either the [111] direction or the [110] direction. The key parameter for the growth of the desired 3C-SiC orientation on the Si(110)/3C-SiC(001)/Si(001) heterostructure is highlighted and is linked to the Si epilayer surface morphology. The epitaxial relation between the layers has been identified using X-ray diffraction and transmission electron microscopy (TEM). We showed that, regardless of the top 3C-SiC epilayer orientation, domains rotated by 90° around the growth direction are present in the epilayer. Furthermore, the difference between the two 3C-SiC orientations was investigated by means of high magnification TEM. The results indicate that the faceted Si(110) epilayer surface morphology results in a (110)-oriented 3C-SiC epilayer, whereas a flat hetero-interface has been observed between 3C-SiC(111) and Si(110). The control of the top 3C-SiC growth direction can be advantageous for the development of new micro-electro-mechanical systems.
Deriving idiolectal variation
Authors: Danckaert Lieven , D'Hulster Tijs , Haegeman Liliane
Published: November 2016

The focus of this paper is on apparent cases of subject-to-subject raising out of finite clauses in English, which are accepted as (fully) grammatical by a minority of native speakers. The basic pattern involves a bi-clausal structure in which a displaced subject triggers agreement in both the embedded and the matrix clause. Crucially, this ‘double agreement’ pattern is only acceptable when a subject is wh-moved. Our analysis builds on the criterial approach to subject extraction developed in Rizzi (2006) and Rizzi & Shlonsky (2006, 2007). We propose that the main ingredient of the wh-raising pattern is incorporation of a functional head in the embedded left periphery into the matrix V.
Communication in schizophrenia, between pragmatics, cognition, and social cognition
Authors: Bosia Marta , Arcara Giorgio , Buonocore Mariachiara , Bechi Margherita , Moro Andrea , Cavallaro Roberto , Bambini Valentina
Published: November 2016

We previously reported communication disruption in schizophrenia at the pragmatic level, i.e., in the ability to match language and context. Pragmatic abilities interact with a number of cognitive functions, from Theory of Mind to executive control, which in turn are known to be compromised in schizophrenia. This study aims to explore the relationship between communication-related skills, assessed through a newly developed pragmatic protocol, and neuropsychological measures, including Theory of Mind, in a sample of 39 patients with schizophrenia. Among all neuropsychological domains assessed, verbal short term memory and executive functions seem to especially correlate with the comprehension of the pragmatic aspects of language. Other cognitive and socio-cognitive domains seem to correlate in a task-specific fashion, i.e., depending on the pragmatic task under investigation. Our findings suggest that, while there is a cognitive platform for pragmatic abilities, communicative behavior is at least partially independent of the global cognitive profile. Also, the effect of Theory of Mind is likely to be mediated by more basic cognitive functions.
Effect of heat treatment on morphology of Fe-rich intermetallics in Al–Cu alloys
Authors: Lin B. , Zhang W. W.
Published: November 2016

The iron-rich intermetallics are considered to be stable in aluminium alloys and usually hard to dissolve into the matrix during solution heat treatment (SHT). Nevertheless, solid-state transformations between Fe-rich intermetallics may happen and will play a great role in breaking-up of the large Fe-rich intermetallics particle during hot deformation process. In this study, the solid-state phase transformation of the iron-rich intermetallics from AlmFe to β-Fe (Al7Cu2Fe) has been studied using SEM, XRD and deep-etched technique in a 2xxx Al–Cu cast alloy during SHT. The mechanism of solid-state transformation for the Fe-rich intermetallics was discussed, including the solid-state reaction, nucleation and growth of iron-rich intermetallics and Al phases.
Ion beam transport: modelling and experimental measurements on a large negative ion source in view of the ITER heating neutral beam
Authors: Veltri P. , Sartori E. , Agostinetti P. , Aprile D. , Brombin M. , Chitarin G. , Fonnesu N. , Ikeda K. , Kisaki M. , Nakano H. , Pimazzoni A. , Tsumori K. , Serianni G.
Published: November 2016

Neutral beam injectors are among the most important methods of plasma heating in magnetic confinement fusion devices. The propagation of the negative ions, prior to their conversion into neutrals, is of fundamental importance in determining the properties of the beam, such as its aiming and focusing at long-distances, so as to deposit the beam power in the proper position inside the confined plasma, as well as to avoid interaction with the material surfaces along the beam path. The final design of the ITER Heating Neutral Beam prototype has been completed at Consorzio RFX (Padova, Italy), in the framework of a close collaboration with European, Japanese and Indian fusion research institutes. The physical and technical rationales on which the design is based were essentially driven by numerical modelling of the relevant physical processes, and the same models and codes will be useful to design the DEMO neutral beam injector in the near future. This contribution presents a benchmark study of the codes used for this purpose, by comparing their results against the measures performed in an existing large-power device, hosted at the National Institute for Fusion Science, Japan. In particular, the negative ion formation and acceleration are investigated. A satisfactory agreement was found between codes and experiments, leading to an improved understanding of beam transport dynamics. The interpretation of the discrepancies identified in previous works, possibly related to the non-uniformity of the extracted negative ion current, is also presented.
Sensitivity, proximal extension and higher order almost automorphy
Authors: Ye Xiangdong , Yu Tao
Published: November 2016

Let

(
X
,
T
)

(X,T)

be a topological dynamical system, and

F

\mathcal {F}

be a family of subsets of

Z

+

\mathbb {Z}_+

.

(
X
,
T
)

(X,T)

is strongly

F

\mathcal {F}

-sensitive if there is

δ
>
0

\delta >0

such that for each non-empty open subset

U
U

there are

x
,
y
∈
U

x,y\in U

with

{
n
∈

Z

+

:
d
(

T
n

x
,

T
n

y
)
>
δ
}
∈

F

\{n\in \mathbb {Z}_+: d(T^nx,T^ny)>\delta \}\in \mathcal {F}

. Let

F

t

\mathcal {F}_t

(resp.

F

i
p

\mathcal {F}_{ip}

,

F

f
i
p

\mathcal {F}_{fip}

) consist of thick sets (resp. IP-sets, subsets containing arbitrarily long finite IP-sets).

The following Auslander-Yorke’s type dichotomy theorems are obtained: (1) a minimal system is either strongly

F

f
i
p

\mathcal {F}_{fip}

-sensitive or an almost one-to-one extension of its

∞
\infty

-step nilfactor; (2) a minimal system is either strongly

F

i
p

\mathcal {F}_{ip}

-sensitive or an almost one-to-one extension of its maximal distal factor; (3) a minimal system is either strongly

F

t

\mathcal {F}_{t}

-sensitive or a proximal extension of its maximal distal factor.
Specialization of nonsymmetric Macdonald polynomials at 𝑡=∞ and Demazure submodules of level-zero extremal weight modules
Authors: Naito Satoshi , Nomoto Fumihiko , Sagaki Daisuke
Published: November 2016

In this paper, we give a representation-theoretic interpretation of the specialization

E

w
∘

λ

(
q
,
∞
)

E_{w_\circ \lambda } (q,\infty )

of the nonsymmetric Macdonald polynomial

E

w
∘

λ

(
q
,
t
)

E_{w_\circ \lambda }(q,t)

at

t
=
∞

t=\infty

in terms of the Demazure submodule

V

w
∘

−

(
λ
)

V_{w_\circ }^- (\lambda )

of the level-zero extremal weight module

V
(
λ
)

V(\lambda )

over a quantum affine algebra of an arbitrary untwisted type. Here,

λ
\lambda

is a dominant integral weight, and

w
∘

w_\circ

denotes the longest element in the finite Weyl group

W
W

. Also, for each

x
∈
W

x \in W

, we obtain a combinatorial formula for the specialization

E

x
λ

(
q
,
∞
)

E_{x \lambda } (q, \infty )

at

t
=
∞

t=\infty

of the nonsymmetric Macdonald polynomial

E

x
λ

(
q
,
t
)

E_{x \lambda } (q,t)

and also a combinatorical formula for the graded character

gch
⁡

V

x

−

(
λ
)

\operatorname {gch} V_{x}^- (\lambda )

of the Demazure submodule

V

x

−

(
λ
)

V_{x}^- (\lambda )

of

V
(
λ
)

V(\lambda )

. Both of these formulas are described in terms of quantum Lakshmibai-Seshadri paths of shape

λ
\lambda

.
Is the higher mortality among men with hip fracture explained by sex-related differences in quality of in-hospital care? A population-based cohort study
Authors: Kristensen Pia Kjær , Johnsen Søren Paaske , Mor Anil , Thillemann Theis Muncholm , Pedersen Alma Becic
Published: November 2016

Background

mortality after hip fracture is two-fold higher in men compared with women. It is unknown whether sex-related differences in the quality of in-hospital care contribute to the higher mortality among men.

Objective

to examine sex-related differences in quality of in-hospital care, 30-day mortality, length of hospital stay and readmission among patients with hip fracture.

Design

population-based cohort study.

Measures

using prospectively collected data from the Danish Multidisciplinary Hip Fracture Registry, we identified 25,354 patients ≥65 years (29% were men). Outcome measures included quality of in-hospital care as reflected by seven process performance measures, 30-day mortality, length of stay (LOS) and readmission within 30 days after discharge. Data were analysed using multivariable regression techniques.

Results

in general, there were no substantial sex-related differences in quality of in-hospital care. The relative risk for receiving the individual process performance measure ranged from 0.91 (95% confidence interval (CI) 0.85–0.97) to 0.97 (95% CI 0.94–0.99) for men compared with women. The 30-day mortality was 15.9% for men and 9.3% for women corresponding to an adjusted odds ratio (OR) of 2.30 (95% CI 2.09–2.54). The overall readmission risk within 30 days after discharge was 21.6% for men and 16.4% for women (adjusted OR of 1.38 (95% CI 1.29–1.47)). No difference in LOS was observed between men and women.

Conclusions

sex differences in the quality of in-hospital care appeared not to explain the higher mortality and risk of readmission among men hospitalised with hip fracture.
Accelerating Bayesian inference for evolutionary biology models
Authors: Meyer Xavier , Chopard Bastien , Salamin Nicolas
Published: November 2016

Motivation

Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods.

Results

We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models. We show on a parameter-rich macroevolutionary model increases of the sampling speed up to 35 times with 32 processors when compared to a sequential M-H process. More importantly, our framework achieves up to a twentyfold faster convergence to estimate the posterior probability of phylogenetic trees using 32 processors when compared to the well-known software MrBayes for Bayesian inference of phylogenetic trees.

Availability and Implementation

https://bitbucket.org/XavMeyer/hogan

Supplementary information

Supplementary data are available at Bioinformatics online.
Expanding the toolkit for membrane protein modeling in Rosetta
Authors: Koehler Leman Julia , Mueller Benjamin K , Gray Jeffrey J
Published: November 2016

Motivation

A range of membrane protein modeling tools has been developed in the past 5–10 years, yet few of these tools are integrated and make use of existing functionality for soluble proteins. To extend existing methods in the Rosetta biomolecular modeling suite for membrane proteins, we recently implemented RosettaMP, a general framework for membrane protein modeling. While RosettaMP facilitates implementation of new methods, addressing real-world biological problems also requires a set of accessory tools that are used to carry out standard modeling tasks.

Results

Here, we present six modeling tools, including de novo prediction of single trans-membrane helices, making mutations and refining the structure with different amounts of flexibility, transforming a protein into membrane coordinates and optimizing its embedding, computing a Rosetta energy score, and visualizing the protein in the membrane bilayer. We present these methods with complete protocol captures that allow non-expert modelers to carry out the computations.

Availability and Implementation

The presented tools are part of the Rosetta software suite, available at www.rosettacommons.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
The asteroseismic surface effect from a grid of 3D convection simulations – I. Frequency shifts from convective expansion of stellar atmospheres
Authors: Trampedach Regner , Aarslev Magnus J. , Houdek Günter , Collet Remo , Christensen-Dalsgaard Jørgen , Stein Robert F. , Asplund Martin
Published: November 2016

We analyse the effect on adiabatic stellar oscillation frequencies of replacing the near-surface layers in 1D stellar structure models with averaged 3D stellar surface convection simulations. The main difference is an expansion of the atmosphere by 3D convection, expected to explain a major part of the asteroseismic surface effect, a systematic overestimation of p-mode frequencies due to inadequate surface physics. We employ pairs of 1D stellar envelope models and 3D simulations from a previous calibration of the mixing-length parameter, α. That calibration constitutes the hitherto most consistent matching of 1D models to 3D simulations, ensuring that their differences are not spurious, but entirely due to the 3D nature of convection. The resulting frequency shift is identified as the structural part of the surface effect. The important, typically non-adiabatic, modal components of the surface effect are not included in this analysis, but relegated to future papers. Evaluating the structural surface effect at the frequency of maximum mode amplitude, νmax , we find shifts from δν = −0.8 μHz for giants at log g = 2.2 to − 35 μHz for a (Teff = 6901 K, log g = 4.29) dwarf. The fractional effect δν(νmax )/νmax , ranges from −0.1 per cent for a cool dwarf (4185 K, 4.74) to −6 per cent for a warm giant (4962 K, 2.20).
Peanut-shaped metallicity distributions in bulges of edge-on galaxies: the case of NGC 4710
Authors: Gonzalez Oscar A. , Debattista Victor P. , Ness Melissa , Erwin Peter , Gadotti Dimitri A.
Published: November 2016

Bulges of edge-on galaxies are often boxy/peanut-shaped (B/PS), and unsharp masks reveal the presence of an X shape. Simulations show that these shapes can be produced by dynamical processes driven by a bar which vertically thickens the centre. In the Milky Way, which contains such a B/PS bulge, the X-shaped structure is traced by the metal-rich stars but not by the metal-poor ones. Recently, Debattista et al. interpreted this property as a result of the varying effect of the bar on stellar populations with different starting kinematics. This kinematic fractionation model predicts that cooler populations at the time of bar formation go on to trace the X shape, whereas hotter populations are more uniformly distributed. As this prediction is not specific to the Milky Way, we test it with Multi Unit Spectroscopic Explorer (MUSE) observations of the B/PS bulge in the nearby galaxy NGC 4710. We show that the metallicity map is more peanut-shaped than the density distribution itself, in good agreement with the prediction. This result indicates that the X-shaped structure in B/PS bulges is formed of relatively metal-rich stars that have been vertically redistributed by the bar, whereas the metal-poor stars have a more uniform, box-shaped distribution.
Impaired Pain Modulation in Fibromyalgia Patients in Response to Social Distress Manipulation
Authors: Canaipa Rita , Castro-Caldas Alexandre , Moreira João Manuel , Pimentel-Santos Fernando , Branco Jaime Cunha , Treister Roi
Published: November 2016

Objectives:

Fibromyalgia (FM), a chronic pain condition, is associated with abnormalities in pain modulation. A growing body of evidence has shown that social distress modulates pain sensitivity. The current study aimed to assess the effects of social distress manipulation on pain in FM patients compared with positive (rheumatoid arthritis, RA) and negative (pain-free) controls.

Materials and Methods:

FM, RA patients and pain-free controls (PFC) were recruited. Demographic, medical, and psychological data were collected. Each participant was exposed to 3 study conditions in a random order: the inclusion (positive social effects) and exclusion (negative social effects) conditions of Cyberball, a game that manipulates social distress, and a control condition. Pain sensitivity in response to nociceptive electrical and thermal (cold) stimuli was assessed before and during each study condition.

Results:

In response to electrical stimuli, pain decreased in both the inclusion and exclusion conditions in PFC and RA groups, whereas inclusion conditions significantly increased pain in the FM group. Social manipulation (inclusion or exclusion) did not affect pain sensitivity as measured in response to thermal stimulation.

Discussion:

These results are in line with previous studies demonstrating altered pain inhibition in FM patients, and suggest that unlike PFC or other non-“stress–related” chronic pain conditions, being socially included may increase pain perception in FM patients. Possible underlying mechanisms and clinical relevance are discussed.
Disparity in Outcomes for Adolescent and Young Adult Patients Diagnosed With Pediatric Solid Tumors Across 4 Decades
Authors: Chen Ishita , Pasalic Dario , Fischer-Valuck Benjamin , Frangoul Haydar , DeWees Todd , Shinohara Eric T. , Perkins Stephanie M.
Published: November 2016

Objective:

Cancer mortality is a leading cause of disease-related death in the adolescent and young adult (AYA) population. Compared with older and younger patients, AYA patients often experience worse cancer-specific outcomes. Here, we compare AYA and pediatric overall survival (OS) in the most common pediatric extracranial solid tumors.

Materials and Methods:

Using the US Surveillance, Epidemiology, and End Results database, we studied patients (age, 0 to 39 y) diagnosed with Ewing sarcoma, neuroblastoma, osteosarcoma, rhabdomyosarcoma, and Wilms tumor.

Results:

A total of 12,375 patients (age, 0 to 39 y) were diagnosed between 1973 and 2010 (8247 pediatric and 4128 AYA patients). AYA patients with rhabdomyosarcoma and Ewing sarcoma were more likely to present with metastatic disease. OS was significantly worse in the AYA cohort for all tumor types (P<0.001) with the exception of osteosarcoma (P=0.29). Across 2 treatment time periods (1973 to 1989 and 1990 to 2010), there was significant improvement in 5-year OS in all tumor types with the exception of rhabdomyosarcoma; however, AYA patients continued to experience worse OS in the modern treatment cohort with the exception of osteosarcoma patients. There was no improvement in OS among AYA patients with Ewing sarcoma, neuroblastoma, rhabdomyosarcoma, or Wilms tumor over the 2 treatment eras.

Conclusions:

For the most common pediatric extracranial solid tumors, AYA patients experience significantly worse OS compared with pediatric patients. Although improvements in therapy have led to gain in survival for pediatric patients, with the exception of osteosarcoma, AYA experienced no increase in survival over the study period. This investigation demonstrates the importance for further research in the AYA population.
Nontraditional Methods to Evaluate Wound Healing
Authors: Hasatsri Sukhontha , Aramwit Pornanong
Published: November 2016

BACKGROUND

Traditional evaluation of wound healing is sometimes subjective. It is necessary to develop qualitative and quantitative methods to enable more efficient and accurate evaluation of wounds. Recently, new techniques have been introduced and the correspondence between these techniques and clinician judgment is critical.

OBJECTIVE

Some nontraditional techniques that analyze wound healing were reviewed, which include measurements of the wound area, tissue color, skin barrier function, skin humidity, and keratinocyte morphology.

METHODS

This review article is based on medical research that focuses on the evaluation of wound healing.

RESULTS

Software-based and advanced device-based techniques generally provide more accurate and precise results than traditional ones, such as the ruler-based technique. Measurement of tissue color can also help to identify the type of tissue. Evaluation of skin barrier function can assist clinicians to analyze functional restoration of skin, whereas skin humidity demonstrates the exudate production status of the wound. In addition, keratinocyte morphology in the wound bed indicates quality of wound healing and side effects of treatment.

CONCLUSION

There is no gold standard method for qualitative and quantitative evaluation of wound healing. It is important to understand the type of wound, sample size, results obtained, advantages, and limitations of each technique.
Comprehensive management of hereditary hemorrhagic telangiectasia
Authors: Lupa Michael D. , Wise Sarah K.
Published: November 2016

Purpose of review

Hereditary hemorrhagic telangiectasia (HHT), or Osler Weber-Rendu disease, is a rare inherited disorder of fibrovascular tissue affecting various organs. Epistaxis is the most common symptom of HHT but as the disease affects multiple organs, a multisystem and multidisciplinary approach to management is required. The purpose of this article is to provide an overview of the multidisciplinary approach to HHT for the otolaryngologist and to discuss the current pharmacologic and procedural treatment options available for HHT-related epistaxis.

Recent findings

Multidisciplinary expert guidelines have better defined what screening tests are advised for the multisystem evaluation of the HHT patient. New pharmacologic therapies including bevacizumab (Avastin) used submucosally or topically have shown promise as in-office treatment modalities. Sclerotherapy of telangiectasia, including in-office applications, has recently proven safe and effective.

HHT remains a difficult disease to treat. Being aware of the common organ systems involved by the disease will help the practicing otolaryngologist to ensure the patient receives appropriate multidisciplinary care. For HHT-related epistaxis, new medical and surgical options allow for a wider range of treatments than were previously available.
The evidence for olfactory training in treating patients with olfactory loss
Authors: Patel Zara M.
Published: November 2016

Purpose of review

The purpose of this review is to go over the only therapy for olfactory loss supported by level 1a evidence that is currently available, which is olfactory training. This therapy is widely underutilized and has the potential to help many patients with olfactory dysfunction who are otherwise offered no management options.

Recent findings

We will review the rationale, clinical studies, and quality of the evidence regarding olfactory training, specifically the olfactory system's inherent ability to regenerate, the plasticity of the system, and the multiple protocols and modifications of protocols present in the literature.

Olfactory training is an effective therapy for some patients suffering from olfactory loss, and, while we do not yet know the optimal duration or number of odorants or exact patient population it may be most beneficial for, as an extremely easy, self-driven therapy with no significant side-effects, it should be consistently offered to this patient population.
Detangling the evolutionary developmental integration of dentate jaws: evidence that a p63 gene network regulates odontogenesis exclusive of mandible morphogenesis
Authors: Raj Muhammad T. , Boughner Julia C.
Published: November 2016

Vertebrate jaws and dentitions fit and function together, yet the genetic processes that coordinate cranial and dental morphogenesis and evolution remain poorly understood. Teeth but not jaws fail to form in the edentate p63−/− mouse mutant, which we used here to identify genes important to odontogenesis, but not jaw morphogenesis, and that may allow dentitions to change during development and evolution without necessarily affecting the jaw skeleton. With the working hypothesis that tooth and jaw development are autonomously controlled by discreet gene regulatory networks, using gene expression microarray assays validated by quantitative reverse‐transcription PCR we contrasted expression in mandibular prominences at embryonic days (E) 10–13 of mice with normal lower jaw development but either normal (p63+/−, p63+/+) or arrested (p63−/−) tooth development. The p63−/− mice showed significantly different expression (fold change ≥2, ≤−2; P ≤ 0.05) of several genes. Some of these are known to help regulate odontogenesis (e.g., p63, Osr2, Cldn3/4) and/or to be targets of p63 (e.g., Jag1/2, Fgfr2); other genes have no previously reported roles in odontogenesis or the p63 pathway (e.g., Fermt1, Cbln1, Pltp, Krt8). As expected, from E10 to E13, few genes known to regulate mandible morphogenesis differed in expression between mouse strains. This study newly links several genes to odontogenesis and/or to the p63 signaling network. We propose that these genes act in a novel odontogenic network that is exclusive of lower jaw morphogenesis, and posit that this network evolved in oral, not pharyngeal, teeth.
Am kürzeren Ende der Sonnenallee in 140 Characters or Less: Using Twitter as a Creative Approach to Literature in the Intermediate German Classroom
Authors: Steckenbiller Christiane
Published: November 2016

The advent of new and social media, and Twitter in particular, has not only revolutionized how we communicate with each other, but also how we learn and teach. Twitter is increasingly incorporated across the disciplines as a tool to engage with content. In the foreign‐language classroom, for instance, Twitter has been used to facilitate language learning, communicate with native speakers, and build community. This article describes how Twitter was initially introduced into an intermediate German classroom to improve communicative competence and foster student engagement. Yet its main focus is on how Twitter was used as the only method of instruction as part of the discussion of Thomas Brussig's 1999 novel Am kürzeren Ende der Sonnenallee. The first section explains the methodology behind using Twitter, and briefly charts the advantages and disadvantages of the social networking tool for honing communicative skills and building community. The second section outlines the classroom unit during which the students and the instructor communicated solely via Twitter. After a discussion of the session, and sample student assignments and reactions, the article concludes by highlighting the educational benefits of Twitter as a playful and motivating approach to teaching literature in the intermediate foreign‐language classroom.
“achJA, dann kenn ich das auch!” Managing Understanding and Knowledge: On Teaching Response Tokens in the German Language Classroom
Authors: Taleghani‐Nikazm Carmen
Published: November 2016

This paper offers an instructional unit on the response token achja in everyday German conversation. The paper first provides a description of achja and its distinctive prosodic features based on empirical research in conversation analysis. The goal of the paper is to provide instructors of German with information and guidance to integrate authentic and natural conversational data in their teaching and to provide their L2 learners with opportunities to examine, practice, compare, and reflect on some of the ways in which Germans manage and negotiate knowledge and information. In addition, this paper provides hands‐on materials for teaching language and pragmatics suitable for novice to intermediate students.
Transient Electrohydrodynamic Manipulation of Particles on the Surface of a Drop
Authors: Amah Edison C. , Fischer Ian S. , Singh Pushpendra
Published: November 2016

In our previous studies we have shown that particles adsorbed on the surface of a drop can be concentrated at its poles or equator by applying a uniform electric field. This happens even when the applied electric field is uniform; the electric field on the surface of the drop is nonuniform, and so particles adsorbed on the surface are subjected to dielectrophoretic (DEP) forces. In this study, we use leaky dielectric model to model the transient behavior of particles at low electric field frequencies. We show that the frequency of the electric field is an important control parameter that under certain conditions can be used to collect particles at the poles or the equator, and to move them from the poles to the equator. The speed with which particles move on the surface depends on the strength of the electrohydrodynamic flow which diminishes with increasing frequency.
CFD Modelling of the Dehydrogenation Reaction of Isobutane to Isobutylene in a Fixed Bed Reactor
Authors: Jamaleddine Tarek J. , Bunama Ramsey M.
Published: November 2016

The catalytic dehydrogenation reaction of isobutane to isobutylene is simulated in a commercial-scale heterogenous fixed bed reactor (FBR). The porous medium method in ANSYS Fluent combined with the reaction model capability was utilized to predict the flow behavior and species transport in a bed of spherical particles. Physical and material properties of a dehydrogenating catalyst of Chromium Oxide (Cr2O3) on Aluminum Oxide Support (Al2O3) were employed in the model. Several reaction models were implemented using a customized User-defined Function (UDF) subroutine. Simulation results were validated against literature data for a similar process. Good agreement was observed for the conversion of alkanes to alkenes within acceptable accuracy. It is concluded that the power-law model showed the least fit for the feed conversion and product selectivity compared to the other studied reaction models.