bluuebunny/crossref_metadata_2025 huggingface dataset:
Extreme driven ion acoustic waves
Authors: Friedland L. , Shagalov A. G.
Published: August 2017

The excitation of large amplitude, strongly nonlinear ion acoustic waves from trivial equilibrium by a chirped frequency drive is discussed. Under certain conditions, after passage through the linear resonance in this system, the nonlinearity and the variation of parameters work in tandem to preserve the phase-locking with the driving wave via excursion of the excited ion acoustic wave in its parameter space, yielding controlled growth of the wave amplitude. We study these autoresonant waves via a fully nonlinear warm fluid model and predict the formation of sharply peaked (extreme) ion acoustic excitations with local ion density significantly exceeding the unperturbed plasma density. The driven wave amplitude is bound by the kinetic wave-breaking, as the local maximum fluid velocity of the wave approaches the phase velocity of the drive. The Vlasov-Poisson simulations are used to confirm the results of the fluid model, and Whitham's averaged variational principle is applied for analyzing the evolution of autoresonant ion acoustic waves.
Dynamical pruning of the multiconfiguration time-dependent Hartree (DP-MCTDH) method: An efficient approach for multidimensional quantum dynamics
Authors: Larsson H. R. , Tannor D. J.
Published: August 2017

We present two strategies for combining dynamical pruning with the multiconfiguration time-dependent Hartree (DP-MCTDH) method, where dynamical pruning means on-the-fly selection of relevant basis functions. The first strategy prunes the primitive basis that represents the single-particle functions (SPFs). This is useful for smaller systems that require many primitive basis functions per degree of freedom, as we will illustrate for NO2. Furthermore, this allows for higher-dimensional mode combination and partially lifts the sum-of-product-form requirement onto the structure of the Hamiltonian, as we illustrate for nonadiabatic 24-dimensional pyrazine. The second strategy prunes the set of configurations of SPF at each time step. We show that this strategy yields significant speed-ups with factors between 5 and 50 in computing time, making it competitive with the multilayer MCTDH method.
Multiscale time-dependent density functional theory: Demonstration for plasmons
Authors: Jiang Jiajian , Abi Mansour Andrew , Ortoleva Peter J.
Published: August 2017

Plasmon properties are of significant interest in pure and applied nanoscience. While time-dependent density functional theory (TDDFT) can be used to study plasmons, it becomes impractical for elucidating the effect of size, geometric arrangement, and dimensionality in complex nanosystems. In this study, a new multiscale formalism that addresses this challenge is proposed. This formalism is based on Trotter factorization and the explicit introduction of a coarse-grained (CG) structure function constructed as the Weierstrass transform of the electron wavefunction. This CG structure function is shown to vary on a time scale much longer than that of the latter. A multiscale propagator that coevolves both the CG structure function and the electron wavefunction is shown to bring substantial efficiency over classical propagators used in TDDFT. This efficiency follows from the enhanced numerical stability of the multiscale method and the consequence of larger time steps that can be used in a discrete time evolution. The multiscale algorithm is demonstrated for plasmons in a group of interacting sodium nanoparticles (15–240 atoms), and it achieves improved efficiency over TDDFT without significant loss of accuracy or space-time resolution.
The diffusion of a Ga atom on GaAs(001)β2(2 × 4): Local superbasin kinetic Monte Carlo
Authors: Lin Yangzheng , Fichthorn Kristen A.
Published: August 2017

We use first-principles density-functional theory to characterize the binding sites and diffusion mechanisms for a Ga adatom on the GaAs(001)β2(2 × 4) surface. Diffusion in this system is a complex process involving eleven unique binding sites and sixteen different hops between neighboring binding sites. Among the binding sites, we can identify four different superbasins such that the motion between binding sites within a superbasin is much faster than hops exiting the superbasin. To describe diffusion, we use a recently developed local superbasin kinetic Monte Carlo (LSKMC) method, which accelerates a conventional kinetic Monte Carlo (KMC) simulation by describing the superbasins as absorbing Markov chains. We find that LSKMC is up to 4300 times faster than KMC for the conditions probed in this study. We characterize the distribution of exit times from the superbasins and find that these are sometimes, but not always, exponential and we characterize the conditions under which the superbasin exit-time distribution should be exponential. We demonstrate that LSKMC simulations assuming an exponential superbasin exit-time distribution yield the same diffusion coefficients as conventional KMC.
A deformable plate interacting with a non-Newtonian fluid in three dimensions
Authors: Zhu Luoding , Yu Xijun , Liu Nansheng , Cheng Yongguang , Lu Xiyun
Published: August 2017

We consider a deformable plate interacting with a non-Newtonian fluid flow in three dimensions as a simple model problem for fluid-structure-interaction phenomena in life sciences (e.g., red blood cell interacting with blood flow). A power-law function is used for the constitutive equation of the non-Newtonian fluid. The lattice Boltzmann equation (the D3Q19 model) is used for modeling the fluid flow. The immersed boundary (IB) method is used for modeling the flexible plate and handling the fluid-plate interaction. The plate drag and its scaling are studied; the influences of three dimensionless parameters (power-law exponent, bending modulus, and generalized Reynolds number) are investigated.
Fabrication and characterization of abrupt TiO2–SiOx
core-shell nanowires by a simple heat treatment
Authors: Folger Alena , Kalb Julian , Schmidt-Mende Lukas , Scheu Christina
Published: August 2017

Three dimensional hierarchical metal oxide nanostructures, like TiO2 nanowire arrays, have attracted great attention for electrochemical energy conversion and storage applications. The functionality of such devices can be further enhanced by adding a nanowire shell with a different stoichiometry or composition compared to the core. Here, we report an approach with a facile heat treatment at 1050 °C, which allows the fabrication of rutile TiO2–SiOx core-shell nanowire arrays on silicon substrates. Our detailed electron microscopic investigation shows that this method is able to cover hydrothermally grown rutile TiO2 nanowires with a uniform shell of several nanometers in thickness. Moreover, the treatment improves the quality of the rutile TiO2 core by removing lattice defects, introduced from the hydrothermal growth. Electron energy loss spectroscopy reveals that the homogeneous shell around the TiO2 core consists of amorphous SiOx and does not form any intermediate phase with TiO2 at the interface. Thus, the properties of the TiO2 core are not affected by the shell, while the shell suppresses undesired electron back transfer. Latter leads to performance losses in many applications, e.g., dye sensitized solar cells, and is the main reason for a fast degradation of devices incorporating organic materials and TiO2.
Vortex motion around a circular cylinder above a plane
Authors: Vasconcelos G. L. , Moura M.
Published: August 2017

The study of vortex flows around solid obstacles is of considerable interest from both a theoretical and practical perspective. One geometry that has attracted renewed attention recently is that of vortex flows past a circular cylinder placed above a plane wall, where a stationary recirculating eddy can form in front of the cylinder, in contradistinction to the usual case (without the plane boundary) for which a vortex pair appears behind the cylinder. Here we analyze the problem of vortex flows past a cylinder near a wall through the lenses of the point-vortex model. By conformally mapping the fluid domain onto an annular region in an auxiliary complex plane, we compute the vortex Hamiltonian analytically in terms of certain special functions related to elliptic theta functions. A detailed analysis of the equilibria of the model is then presented. The location of the equilibrium in front of the cylinder is shown to be in qualitative agreement with recent experimental findings. We also show that a topological transition occurs in phase space as the parameters of the systems are varied.
Note: Single ion imaging and fluorescence collection with a parabolic mirror trap
Authors: Chou Chen-Kuan , Auchter Carolyn , Lilieholm Jennifer , Smith Kevin , Blinov Boris
Published: August 2017

Efficient fluorescence collection is the most challenging part in remote entangled ion qubit state generation. To address this issue, we developed an ion trap consisting of a reflective parabolic surface and a needle electrode. This parabolic trap design covers a solid angle of 2π steradians and allows precise ion placement at the focal point of the parabola. We measured (39 ± 3)% fluorescence collection from a single ion with this trap and analyzed the mirror optical performance. We observed single ion image spot size of 3.4 times diffraction limit, improved to 2.8 times diffraction limit with the help of an external deformable mirror. The micromotion of the ion is determined to be the limiting factor, and the result is consistent with theoretical calculation.
Flux amplification of a field-reversed configuration by double-sided plasmoid injection
Authors: Itagaki H. , Asai T. , Inomoto M. , Takahashi Ts.
Published: August 2017

Trapped magnetic flux in a field-reversed configuration (FRC) plasma was amplified by double-sided magnetized plasmoid injection. Since the magnetic energy in plasmoids was much less than that in the FRC, the FRC's magnetic flux was presumed to be enhanced by the increased diamagnetic current. The plasmoids supplied particles to the FRC from the both ends and increased the peak pressure as well as the pressure gradient in the vicinity of the separatrix.
Noise refocusing in a five-blade neutron interferometer
Authors: Nsofini J. , Sarenac D. , Ghofrani K. , Huber M. G. , Arif M. , Cory D. G. , Pushin D. A.
Published: August 2017

We provide a quantum information description of a proposed five-blade neutron interferometer geometry and show that it is robust against low-frequency mechanical vibrations and dephasing due to the dynamical phase. The extent to which the dynamical phase affects the contrast in a neutron interferometer is experimentally shown. In our model, we consider the coherent evolution of a neutron wavepacket in an interferometer crystal blade and simulate the effect of mechanical vibrations and momentum spread of the neutron through the interferometer. The standard three-blade neutron interferometer is shown to be immune to dynamical phase noise but prone to noise from mechanical vibrations, and the decoherence free subspace four-blade neutron interferometer is shown to be immune to mechanical vibration noise but prone to noise from the dynamical phase. Here, we propose a five-blade neutron interferometer and show that it is immune to both low-frequency mechanical vibration noise and dynamical phase noise.
Particle and surfactant interactions effected polar and dispersive components of interfacial energy in nanocolloids
Authors: Harikrishnan A. R. , Das Sarit K. , Agnihotri Prabhat K. , Dhar Purbarun
Published: August 2017

We segregate and report experimentally for the first time the polar and dispersive interfacial energy components of complex nanocolloidal dispersions. In the present study, we introduce a novel inverse protocol for the classical Owens Wendt method to determine the constitutive polar and dispersive elements of surface tension in such multicomponent fluidic systems. The effect of nanoparticles alone and aqueous surfactants alone are studied independently to understand the role of the concentration of the dispersed phase in modulating the constitutive elements of surface energy in fluids. Surfactants are capable of altering the polar component, and the combined particle and surfactant nanodispersions are shown to be effective in modulating the polar and dispersive components of surface tension depending on the relative particle and surfactant concentrations as well as the morphological and electrostatic nature of the dispersed phases. We observe that the combined surfactant and particle colloid exhibits a similar behavior to that of the particle only case; however, the amount of modulation of the polar and dispersive constituents is found to be different from the particle alone case which brings to the forefront the mechanisms through which surfactants modulate interfacial energies in complex fluids. Accordingly, we are able to show that the observations can be merged into a form of quasi-universal trend in the trends of polar and dispersive components in spite of the non-universal character in the wetting behavior of the fluids. We analyze the different factors affecting the polar and dispersive interactions in such complex colloids, and the physics behind such complex interactions has been explained by appealing to the classical dispersion theories by London, Debye, and Keesom as well as by Derjaguin-Landau-Verwey-Overbeek theory. The findings shed light on the nature of wetting behavior of such complex fluids and help in predicting the wettability and the degree of interfacial interaction with a substrate in such multicomponent nanocolloidal systems.
Newly generated thick amorphous oxide layer at electrode/sol-gel film interface under strong external electric field
Authors: Peng Yong , Yao Manwen , Xiao Ruihua , Yao Xi
Published: August 2017

SrTiO3/nano-Al2O3 composite films have been prepared using a sol-gel spin-coating method. When external electric fields were previously applied to the films with Al electrodes, the dielectric properties were strongly correlated with the applied field: both the dielectric constant and the dielectric loss decreased gradually with an increase in the previously applied voltage. For the films with Al electrodes, a superior dielectric strength of 507 MV/m was achieved; more importantly, the leakage current remained on the same order, i.e., microamperes; the results were ascribed to the Al electrode/film interface-reactions. The interface-reactions were experimentally confirmed by the cross-sectional transmission electron microscopy images and theoretically determined by Faraday's laws. The anodic oxidation reactions dominate the interface-reactions. The newly generated aluminum oxide originating from the interface-reactions contributes to the electric properties of the films.
Manipulation of anisotropic magnetoresistance and domain configuration in Co/PMN-PT (011) multiferroic heterostructures by electric field
Authors: Zhou Weiping , Ma Chunlin , Gan Zhixing , Zhang Zhengming , Wang Xiaoxiong , Tan Weishi , Wang Dunhui
Published: August 2017

The electric field manipulation of magnetic anisotropy and domain configuration has been investigated in the artificial multiferroic Co/PMN-PT (011) heterostructure at room temperature. A uniaxial magnetic anisotropy is induced with the application of an electric field, which leads to an electrically switched anisotropic magnetoresistance with tunability as large as ∼29%. Furthermore, the magnetic domain structures of Co films are investigated by magnetic force microscopy under an in situ electric field, which exhibits direct evidence for electric field control of magnetism at the mesoscale. The converse magnetoelectric effect demonstrated in this multiferroic heterostructure has potential to be utilized in magnetoelectric devices with low power consumption.
Hyperpolarized
13
C MR metabolic imaging can detect neuroinflammation in vivo in a multiple sclerosis murine model
Authors: Guglielmetti Caroline , Najac Chloé , Didonna Alessandro , Van der Linden Annemie , Ronen Sabrina M. , Chaumeil Myriam M.
Published: August 2017

Significance

Cells from the innate immune system, namely microglia and macrophages (mononuclear phagocytes, MPs), play a central role in the progression of neurological disorders such as multiple sclerosis. Such cells can contribute to lesion formations (proinflammatory) or participate in remyelinating processes (neuroprotective). When differentiated to a proinflammatory phenotype, MPs experience metabolic reprogramming leading to increased glycolysis and production of lactate. In this study we showed that a new metabolic imaging method, namely
13
C magnetic resonance spectroscopic imaging (MRSI) of hyperpolarized pyruvate, can detect increased lactate production from proinflammatory MPs, a mechanism mediated by pyruvate dehydrogenase kinase 1 upregulation, in a preclinical model of multiple sclerosis. These findings validate the potential of
13
C MRSI of hyperpolarized pyruvate for in vivo detection of neuroinflammation.
Empirical prediction intervals improve energy forecasting
Authors: Kaack Lynn H. , Apt Jay , Morgan M. Granger , McSharry Patrick
Published: August 2017

Significance

While many forecasters are moving toward generating probabilistic predictions, energy forecasts typically still consist of point projections and scenarios without associated probabilities. Empirical density forecasting methods provide a probabilistic amendment to existing point forecasts. Here we lay the groundwork for evaluating the performance of these methods in the data-scarce setting of long-term forecasts. Results can give policy analysts and other users confidence in estimating forecast uncertainties with empirical methods.
Metal-mediated diradical tuning for DNA replication arrest via template strand scission
Authors: Porter Meghan R. , Lindahl Sarah E. , Lietzke Anne , Metzger Erin M. , Wang Quan , Henck Erik , Chen Chun-Hsing , Niu Hengyao , Zaleski Jeffrey M.
Published: August 2017

Significance

Pharmaceuticals often act within a lock-and-key model whereby molecules bind their targets nearly irreversibly, either stalling or initiating biological processes. Here, the agent itself performs no chemical transformation on its target but rather triggers an event or cascade. However, unwanted side effects become more likely as the reactivity of these molecules increases. In contrast, molecular compounds may irreversibly damage biological targets using metal-mediated radical chemistry, but controlling the onset and extent of reaction is challenging. Even so, multiple examples of metal-containing or metal-radical paradigms have been used clinically for imaging and chemotherapy. Within this framework we report a class of metal-mediated radical generators that attack DNA, outcompete DNA polymerase, and are cytotoxic in short times and modest concentrations.
Quantitative time-resolved chemoproteomics reveals that stable
O
-GlcNAc regulates box C/D snoRNP biogenesis
Authors: Qin Wei , Lv Pinou , Fan Xinqi , Quan Baiyi , Zhu Yuntao , Qin Ke , Chen Ying , Wang Chu , Chen Xing
Published: August 2017

Significance

In mammalian cells, more than 1,000 intracellular proteins are posttranslationally modified with
O
-linked GlcNAc (
O
-GlcNAc), which regulates many important biological processes. The
O
-GlcNAc modification has been found to dynamically cycle on and off the modified proteins. How
O
-GlcNAc affects protein stability remains to be investigated at the proteome level. In this work, we developed a quantitative time-resolved proteomic strategy to analyze the turnover dynamics of
O
-GlcNAcylated proteins. We discovered that not all protein
O
-GlcNAcylation events were reversible and that a subset of
O
-GlcNAcylated proteins exhibited minimal removal of
O
-GlcNAc or degradation of protein backbones. Our work reveals stable
O
-GlcNAc as an important regulatory mechanism for stabilizing proteins, such as core proteins of box C/D small nucleolar ribonucleoprotein complexes.
Factor-dependent archaeal transcription termination
Authors: Walker Julie E. , Luyties Olivia , Santangelo Thomas J.
Published: August 2017

Significance

Proper transcription regulation is necessary for timely and accurate gene expression underlying growth and development. Transcription is regulated at each stage of the transcription cycle—initiation, elongation, and termination—and it is critical to define the factors and sequences regulating RNA polymerase activity. Many studies have investigated the mechanisms used by transcription factors involved in regulation of transcription initiation and elongation, but a mechanistic understanding of transcription termination has been slower to emerge. Here we characterize the first archaeal transcription termination factor, termed euryarchaeal termination activity (Eta). The mechanisms of Eta-mediated termination provide the first understanding of archaeal factor-dependent termination and provide insight into and contrast with the mechanisms used for factor-dependent termination in extant life.
Engineering the lutein epoxide cycle into
Arabidopsis thaliana
Authors: Leonelli Lauriebeth , Brooks Matthew D. , Niyogi Krishna K.
Published: August 2017

Significance

Optimizing the balance between light harvesting and photoprotection holds great promise for improving photosynthetic efficiency and ultimately crop yields. The switch between these two states is regulated by xanthophyll cycling, which occurs in response to changing light conditions. Two xanthophyll cycles have been described in vascular plants: the violaxanthin cycle and the lutein epoxide cycle. The contribution of the lutein epoxide cycle to photosynthesis has been difficult to dissect because the violaxanthin cycle often functions in parallel and responds more rapidly. The introduction of the lutein epoxide cycle into
Arabidopsis thaliana
creates a model system in which to study this ecologically significant but less well-characterized xanthophyll cycle and reveals its role in modulating a rapidly reversible component of nonphotochemical quenching of chlorophyll
a
fluorescence in response to light.
Atypical fracture with long-term bisphosphonate therapy is associated with altered cortical composition and reduced fracture resistance
Authors: Lloyd Ashley A. , Gludovatz Bernd , Riedel Christoph , Luengo Emma A. , Saiyed Rehan , Marty Eric , Lorich Dean G. , Lane Joseph M. , Ritchie Robert O. , Busse Björn , Donnelly Eve
Published: August 2017

Significance

Since the first reports of atypical femoral fractures (AFFs), a clinical phenomenon in which patients experience catastrophic brittle fractures of the femoral shaft with minimal trauma, the risk associated with bisphosphonates, the most widely prescribed pharmaceuticals for osteoporosis, has become increasingly well-established. However, the underlying cause of AFFs and their causal relationship to bisphosphonates is unknown. Here we examine bone tissue from women with AFFs and show that long-term bisphosphonate treatment degrades the fracture-resistance toughening mechanisms that are inherent to healthy bone. Our work resolves the apparent paradox of AFFs as a side effect of the most common osteoporosis treatment by clarifying the differing effects of bisphosphonates on bone tissue structure and mechanical properties across multiple length scales.
PUM1 is a biphasic negative regulator of innate immunity genes by suppressing LGP2
Authors: Liu Yonghong , Qu Linlin , Liu Yuanyuan , Roizman Bernard , Zhou Grace Guoying
Published: August 2017

Significance

We report that PUM1, a protein linked to control of translation of mRNAs carrying a cognate sequence, is a negative regulator of LGP2. In turn LGP2 emerged as a biphasic master activator of numerous innate immunity genes leading to production of interferon. The studies traced in real-time the changes in innate immune responses following transfection of siPUM1 RNA. This approach enabled the discovery that innate immune genes analyzed in this report were activated sequentially in a cascade fashion. The studies were done in uninfected cells in the absence of viral gene products that could affect the expression of cellular genes. This report seeds the possibility of systemic engagement of innate immune responses following life-threatening viral infections by suppressing PUM1 function.
Elevated auxin biosynthesis and transport underlie high vein density in C
4
leaves
Authors: Huang Chi-Fa , Yu Chun-Ping , Wu Yeh-Hua , Lu Mei-Yeh Jade , Tu Shih-Long , Wu Shu-Hsing , Shiu Shin-Han , Ku Maurice S. B. , Li Wen-Hsiung
Published: August 2017

Significance

Elevated leaf vein density is a key step in the evolution from C
3
to C
4
plants. We hypothesized that high vein density in C
4
leaves is due to elevated auxin biosynthesis and transport in developing leaves. We found higher expression levels of genes promoting auxin biosynthesis and higher auxin content in developing C
4
leaves than in developing C
3
leaves. We also found higher auxin content and vein density in loss-of-function mutants of
MYC2
, an auxin biosynthesis suppressor. Moreover, treatment with an auxin biosynthesis or transport inhibitor reduced vein density in new leaves. Finally, mutations that reduce auxin efflux or influx reduce vein density. These observations support our hypothesis and provide a molecular basis for high vein density in C
4
leaves.
Habitat Use by Telemetered Alabama Shad During the Spawning Migration in the Lower Flint River, Georgia
Authors: Kern A. I. , Sammons S. M. , Ingram T. R.
Published: August 2017

The Alabama Shad Alosa alabamae is an anadromous clupeid that lives in the northern Gulf of Mexico and ascends freshwater rivers in spring to spawn. Populations have experienced substantial range-wide declines due to habitat alteration. The largest known population of Alabama Shad is found in the Apalachicola River in northwest Florida. To assess their movement during the spawning migration, 250 Alabama Shad were fitted with acoustic or radio transmitters, depending on year, and transported upstream from Jim Woodruff Lock and Dam during 2010–2014. The 153 relocations from 126 individual fish revealed congregation areas that were suspected to be spawning locations. Alabama Shad selected limerock boulder substrate, avoided limerock fine and rocky substrates and used sandy substrate in the same proportion as its availability. Alabama Shad upstream movement was greatest during April through mid-May. Movements ≥ 20 km were generally clustered together over a period of a few days, with ~90% of such movements occurring following periods of increased river discharge. All limerock boulder substrate areas on the lower Flint River were identified to focus future efforts to determine exact spawning locations.
Induction of IAPP amyloid deposition and associated diabetic abnormalities by a prion-like mechanism
Authors: Mukherjee Abhisek , Morales-Scheihing Diego , Salvadores Natalia , Moreno-Gonzalez Ines , Gonzalez Cesar , Taylor-Presse Kathleen , Mendez Nicolas , Shahnawaz Mohammad , Gaber A. Osama , Sabek Omaima M. , Fraga Daniel W. , Soto Claudio
Published: August 2017

Although a large proportion of patients with type 2 diabetes (T2D) accumulate misfolded aggregates composed of the islet amyloid polypeptide (IAPP), its role in the disease is unknown. Here, we show that pancreatic IAPP aggregates can promote the misfolding and aggregation of endogenous IAPP in islet cultures obtained from transgenic mouse or healthy human pancreas. Islet homogenates immunodepleted with anti-IAPP–specific antibodies were not able to induce IAPP aggregation. Importantly, intraperitoneal inoculation of pancreatic homogenates containing IAPP aggregates into transgenic mice expressing human IAPP dramatically accelerates IAPP amyloid deposition, which was accompanied by clinical abnormalities typical of T2D, including hyperglycemia, impaired glucose tolerance, and a substantial reduction on β cell number and mass. Finally, induction of IAPP deposition and diabetic abnormalities were also induced in vivo by administration of IAPP aggregates prepared in vitro using pure, synthetic IAPP. Our findings suggest that some of the pathologic and clinical alterations of T2D might be transmissible through a similar mechanism by which prions propagate in prion diseases.
Some comments on motivic nilpotence
Authors: Hornbostel Jens
Published: August 2017

We discuss some results and conjectures related to the existence of the non-nilpotent motivic maps

η
\eta

and

μ
9

\mu _9

. To this purpose, we establish a theory of power operations for motivic

H

∞

H_{\infty }

-spectra. Using this, we show that the naive motivic analogue of the unstable Kahn-Priddy theorem fails. Over the complex numbers, we show that the motivic

T
T

-spectrum

S
[

η

−
1

,

μ
9

−
1

]

S[\eta ^{-1},\mu _9^{-1}]

is closely related to higher Witt groups, where

S
S

is the motivic sphere spectrum and

η
\eta

and

μ
9

\mu _9

are explicit elements in

π

∗
∗

(
S
)

\pi _{**}(S)

.
Actions on semigroups and an infinitary Gowers–Hales–Jewett Ramsey theorem
Authors: Lupini Martino
Published: August 2017

We introduce the notion of (Ramsey) action on a (filtered) semigroup. We then prove in this setting a general result providing a common generalization of the infinitary Gowers Ramsey theorem for multiple tetris operations, the infinitary Hales–Jewett theorems (for both located and nonlocated words), and the Farah–Hindman–McLeod Ramsey theorem for layered actions on partial semigroups. We also establish a polynomial version of our main result, recovering the polynomial Milliken–Taylor theorem of Bergelson–Hindman–Williams as a particular case. We present applications of our Ramsey-theoretic results to the structure of recurrence sets in amenable groups.
Consumers’ Willingness to Pay for Health Benefits in Food Products: A Meta‐Analysis
Authors: Dolgopolova Irina , Teuber Ramona
Published: August 2017

This article analyzes the existing literature on consumers’ marginal willingness to pay (MWTP) for health benefits in food products. Results indicate that the presence of a health claim does not only increase MWTP for health benefits in foods but also reduces heterogeneity among MWTP estimates. Hypothetical methods significantly positively affect MWTP. The most popular product category “dairy” negatively influences MWTP. The popular health claim of “lowering cholesterol” has a significantly positive influence on MWTP. In addition, our review highlights that existing studies significantly differ in their setup, which renders the inference of clear‐cut conclusions rather problematic.
LRCstats, a tool for evaluating long reads correction methods
Authors: La Sean , Haghshenas Ehsan , Chauve Cedric
Published: August 2017

Motivation

Third-generation sequencing (TGS) platforms that generate long reads, such as PacBio and Oxford Nanopore technologies, have had a dramatic impact on genomics research. However, despite recent improvements, TGS reads suffer from high-error rates and the development of read correction methods is an active field of research. This motivates the need to develop tools that can evaluate the accuracy of noisy long reads correction tools.

Results

We introduce LRCstats, a tool that measures the accuracy of long reads correction tools. LRCstats takes advantage of long reads simulators that provide each simulated read with an alignment to the reference genome segment they originate from, and does not rely on a step of mapping corrected reads onto the reference genome. This allows for the measurement of the accuracy of the correction while being consistent with the actual errors introduced in the simulation process used to generate noisy reads. We illustrate the usefulness of LRCstats by analyzing the accuracy of four hybrid correction methods for PacBio long reads over three datasets.

Availability and implementation

https://github.com/cchauve/lrcstats

Supplementary information

Supplementary data are available at Bioinformatics online.
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data
Authors: Sun Zhe , Wang Ting , Deng Ke , Wang Xiao-Feng , Lafyatis Robert , Ding Ying , Hu Ming , Chen Wei
Published: August 2017

Motivation

Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct counting of transcript copies using Unique Molecular Identifier (UMI). Despite the technology advances, statistical methods and computational tools are still lacking for analyzing droplet-based scRNA-Seq data. Particularly, model-based approaches for clustering large-scale single cell transcriptomic data are still under-explored.

Results

We developed DIMM-SC, a Dirichlet Mixture Model for clustering droplet-based Single Cell transcriptomic data. This approach explicitly models UMI count data from scRNA-Seq experiments and characterizes variations across different cell clusters via a Dirichlet mixture prior. We performed comprehensive simulations to evaluate DIMM-SC and compared it with existing clustering methods such as K-means, CellTree and Seurat. In addition, we analyzed public scRNA-Seq datasets with known cluster labels and in-house scRNA-Seq datasets from a study of systemic sclerosis with prior biological knowledge to benchmark and validate DIMM-SC. Both simulation studies and real data applications demonstrated that overall, DIMM-SC achieves substantially improved clustering accuracy and much lower clustering variability compared to other existing clustering methods. More importantly, as a model-based approach, DIMM-SC is able to quantify the clustering uncertainty for each single cell, facilitating rigorous statistical inference and biological interpretations, which are typically unavailable from existing clustering methods.

Availability and implementation

DIMM-SC has been implemented in a user-friendly R package with a detailed tutorial available on www.pitt.edu/∼wec47/singlecell.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
ComplexViewer: visualization of curated macromolecular complexes
Authors: Combe Colin W , Sivade Marine (Dumousseau) , Hermjakob Henning , Heimbach Joshua , Meldal Birgit H M , Micklem Gos , Orchard Sandra , Rappsilber Juri
Published: August 2017

Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex.

Availability and implementation

freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js.
Motif independent identification of potential RNA G-quadruplexes by G4RNA screener
Authors: Garant Jean-Michel , Perreault Jean-Pierre , Scott Michelle S
Published: August 2017

Motivation

G-quadruplex structures in RNA molecules are known to have regulatory impacts in cells but are difficult to locate in the genome. The minimal requirements for G-quadruplex folding in RNA (G≥3N1-7 G≥3N1-7 G≥3N1-7 G≥3) is being challenged by observations made on specific examples in recent years. The definition of potential G-quadruplex sequences has major repercussions on the observation of the structure since it introduces a bias. The canonical motif only describes a sub-population of the reported G-quadruplexes. To address these issues, we propose an RNA G-quadruplex prediction strategy that does not rely on a motif definition.

Results

We trained an artificial neural network with sequences of experimentally validated G-quadruplexes from the G4RNA database encoded using an abstract definition of their sequence. This artificial neural network, G4NN, evaluates the similarity of a given sequence to known G-quadruplexes and reports it as a score. G4NN has a predictive power comparable to the reported G richness and G/C skewness evaluations that are the current state-of-the-art for the identification of potential RNA G-quadruplexes. We combined these approaches in the G4RNA screener, a program designed to manage and evaluate the sequences to identify potential G-quadruplexes.

Availability and implementation

G4RNA screener is available for download at http://gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener.

Supplementary information

Supplementary data are available at Bioinformatics online.
‘A woman’s place…’: community-based approaches to gender-based violence in Malawi
Authors: Gaynor Niamh , Cronin Máirtín
Published: August 2017

One in five women has experienced gender-based violence (GBV) in Malawi and its incidence is reported to be increasing. The importance of cultural norms, practices, discourses and behaviours in both driving and addressing such violence is now well recognized. So too is the attendant need to involve men as well as women in community interventions to address this. In this context, this article draws on field research conducted in 2016 in two districts in Northern and Southern Malawi exploring the successes and challenges posed by community-based approaches (CBAs) to tackling GBV. We find that CBAs have yielded a number of successes – notably a reported reduction in GBV as communications between couples have improved and economic stresses within households reduced. However, we also find that these same CBAs have raised a number of challenges. These centre around resource distribution; the impact on local power dynamics; and CBA’s ability to challenge and interrogate dominant norms, ideologies, identities and practices. Overall, we argue that, while CBAs appear successful in transmitting the message to both women and men that GBV is unlawful and wrong, their impacts on the principal underlying causal factors remain weak.
Assessment of Efficacy and Safety of Arterolane Maleate–Piperaquine Phosphate Dispersible Tablets in Comparison With Artemether-Lumefantrine Dispersible Tablets in Pediatric Patients With Acute Uncomplicated Plasmodium falciparum Malaria: A Phase 3, Randomized, Multicenter Trial in India and Africa
Authors: Toure Offianan Andre , Mwapasa Victor , Sagara Issaka , Gaye Oumar , Thompson Ricardo , Maheshwar Aishwarya V , Mishra Pitabas , Behra Narendra , Tshefu Antoinette K , Das Rashmi R , Anvikar Anupkumar R , Sharma Pradeep , Roy Arjun , Sharma Sanjay K , Nasa Amit , Jalali Rajinder K , Valecha Neena ,   for the Arterolane Maleate-Piperaquine Phosphate (AM-PQP) Study Team, Beatrice Toure N , Valery Kouame N’Goran , Karim Tuo , Tiacoh Landry , Kigninma Ouattara , Sibale Naomi , Kaneka Kelvin , Machilika Mercy , Mabote Sheila , Bonzela Juvencio , Lourenceo Carlos , Dieudonneée Bidashimwa , Kasonga Paulin , Ndiaye Jean-Louis , Diop Modou , Sidibe Bouran , Coulibaly Moctar , Fofana Bakary , Toure Sekou , Panigrahy Ankita , Patro Debasis , Biswas Tapan Kumar , Panigrahy Preetish Kumar , Jana Saibal , Hota Debasish , Behera Bijayini , Mohanty Akshaya , Patel Goutam
Published: August 2017

Background

Administration of artemisinin-based combination therapy (ACT) to infant and young children can be challenging. A formulation with accurate dose and ease of administration will improve adherence and compliance in children. The fixed-dose combination dispersible tablet of arterolane maleate (AM) 37.5 mg and piperaquine phosphate (PQP) 187.5 mg can make dosing convenient in children.

Methods

This multicenter (India and Africa), comparative, parallel-group trial enrolled 859 patients aged 6 months to 12 years with Plasmodium falciparum malaria. Patients were randomized in a ratio of 2:1 to AM-PQP (571 patients) once daily and artemether-lumefantrine (AL) (288 patients) twice daily for 3 days and followed for 42 days.

Results

The cure rate (ie, polymerase chain reaction–corrected adequate clinical and parasitological response) in the per-protocol population at day 28 was 100.0% and 98.5% (difference, 1.48% [95% confidence interval {CI}, .04%–2.91%]) in the AM-PQP and AL arms, respectively, and 96.0% and 95.8% (difference, 0.14% [95% CI, –2.68% to 2.95%]) in the intention-to-treat (ITT) population. The cure rate was comparable at day 42 in the ITT population (AM-PQP, 94.4% vs AL, 93.1%). The median parasite clearance time was 24 hours in both the arms. The median fever clearance time was 6 hours in AM-PQP and 12 hours in the AL arm. Both the treatments were found to be safe and well tolerated. Overall, safety profile of both the treatments was similar.

Conclusions

The efficacy and safety of fixed-dose combination of AM and PQP was comparable to AL for the treatment of uncomplicated P. falciparum malaria in pediatric patients.

Clinical Trials Registration

CTRI/2014/07/004764.
Regional-scale patterns in harbour porpoise occupancy of tidal stream environments
Authors: Waggitt James J , Dunn Holly K , Evans Peter G H , Hiddink Jan Geert , Holmes Laura J , Keen Emma , Murcott Ben D , Piano Marco , Robins P E , Scott Beth E , Whitmore Jenny , Veneruso Gemma
Published: August 2017

As harbour porpoises Phocoena phocoena are abundant within tidal stream environments, mitigating population-level impacts from tidal stream energy extraction is considered a conservation priority. An understanding of their spatial and temporal occupancy of these habitats at a regional-scale will help steer installations towards locations which maximize energy returns but reduce the potential for interactions with populations. This study quantifies and compares relationships between the presence of harbour porpoise and several hydrodynamic characteristics across four tidal stream environments in Anglesey, UK—a region that has been earmarked for extensive industrial development. Within sites (0.57–1.13 km2), encounters with animals were concentrated in small areas (<200 m2) and increased during certain tidal states (ebb vs. flood). In sites showing relatively high maximum current speeds (2.67–2.87 ms−1), encounters were strongly associated with the emergence of shear-lines. In sites with relatively low maximum current speeds (1.70–2.08 ms−1), encounters were more associated with areas of shallow water during peak current speeds. The overall probability of encounters was higher in low current sites. It is suggested that the likelihood of interactions could be reduced by restricting developments to sites with high maximum current speeds (>2.5 ms−1), and placing turbines in areas of laminar currents therein. This study shows that a combination of local and regional hydrodynamic characteristics can partially explain variations in occupancy patterns across tidal-stream environments. However, it was found that such hydrodynamic characteristics could not comprehensively explain these occupancy patterns. Further studies into the biophysical mechanisms creating foraging opportunities within these habitats are needed to identify alternative explanatory variables that may have universal applications.
Surface instability of imperfectly bonded multi-layered curved films under van der Waals forces
Authors: Wang Xu , Schiavone Peter
Published: August 2017

Using a linear stability analysis and the transfer matrix method, we investigate the surface instability of an imperfectly bonded multi-layered curved film interacting with a curved rigid contactor, another imperfectly bonded multi-layered curved film or an imperfectly bonded multi-layered simply-supported cylindrical shell in each case through the action of attractive van der Waals forces. The imperfect interface is modelled as a linear spring layer with vanishing thickness characterized by normal and tangential imperfect interface parameters. Detailed numerical results are presented to demonstrate the resulting analytical solutions.
Dissociation
Authors: Carrión Victor G. , Turner John A. , Weems Carl F.
Published: August 2017

Dissociation is a neurological state of acute disconnection with the reality of a situation or the self, and is often observed in PTSD. Because of its broad definition, diverse expression, and frequent comorbidity with other disorders, dissociation remains a challenging phenomenon to research and treat. The current chapter reviews the small amount of preclinical literature that has laid the groundwork of our understanding of the physiological underpinnings of dissociation, including theories of its mechanization of the endogenous opioid system. The challenges and importance of assessing dissociation are discussed, and the current instruments available for this assessment are reviewed. The experience of childhood sexual abuse has been specifically linked to the development of dissociative symptoms in PTSD. Future directions, including suggestions for categorical approaches to the identification and treatment of dissociative symptoms, are discussed.
Prevalence and Underrecognition of Body Dysmorphic Disorder
Authors: Hartmann Andrea S. , Buhlmann Ulrike
Published: August 2017

Large epidemiologic studies across Western countries that used DSM-IV and DSM-5 diagnostic criteria have found a point prevalence rate of body dysmorphic disorder (BDD) of 1.7% to 2.9%. The prevalence of BDD is higher in clinical samples. Gender ratios in epidemiologic studies show a slight preponderance of females, which is confirmed in most convenience and clinical samples. Prevalence rates appear to be highest in younger (adolescent) subsamples. Other demographic correlates include a lower likelihood of being in a committed relationship, less education, lower household income, and higher unemployment rates. Key clinical correlates from epidemiologic studies are greater depression, anxiety, and somatoform symptoms and more frequent suicidal ideation and suicide attempts. Reasons for the underrecognition of BDD include shame, fear of not being understood by the clinician, lack of readiness for treatment, skepticism about treatment or belief in the superiority of other forms of treatment (such as cosmetic treatment), and lack of financial coverage for treatment.
Muscle Dysmorphia
Authors: Sreshta Nina , Pope Harrison G. , Hudson James I. , Kanayama Gen
Published: August 2017

This chapter discusses muscle dysmorphia (“bigorexia”), including its historical context, diagnostic features, epidemiology, associated psychiatric and medical conditions, and potential treatment approaches. Muscle dysmorphia is a specifier (subtype) of body dysmorphic disorder (BDD) characterized by pathologic preoccupation with muscularity and fear or anxiety about not being big or muscular enough, despite having an objectively normal or muscular body—or even a very muscular build. It is most often seen in males; average age at onset is before the end of the second decade. This preoccupation with body image often compromises social and occupational functioning, in part because of compulsive and meticulous exercise and dietary regimens. Individuals may avoid bodily exposure because of shame associated with perceived small body build. There is significant comorbid medical, social, and psychological disease burden, including disordered eating, other forms of BDD, anxiety, and substance use disorders (often steroid abuse). Treatment is challenging, as many patients do not present to a clinician.