bluuebunny/crossref_metadata_2025 huggingface dataset:
A coupled cluster theory with iterative inclusion of triple excitations and associated equation of motion formulation for excitation energy and ionization potential
Authors: Maitra Rahul , Akinaga Yoshinobu , Nakajima Takahito
Published: August 2017

A single reference coupled cluster theory that is capable of including the effect of connected triple excitations has been developed and implemented. This is achieved by regrouping the terms appearing in perturbation theory and parametrizing through two different sets of exponential operators: while one of the exponentials, involving general substitution operators, annihilates the ground state but has a non-vanishing effect when it acts on the excited determinant, the other is the regular single and double excitation operator in the sense of conventional coupled cluster theory, which acts on the Hartree-Fock ground state. The two sets of operators are solved as coupled non-linear equations in an iterative manner without significant increase in computational cost than the conventional coupled cluster theory with singles and doubles excitations. A number of physically motivated and computationally advantageous sufficiency conditions are invoked to arrive at the working equations and have been applied to determine the ground state energies of a number of small prototypical systems having weak multi-reference character. With the knowledge of the correlated ground state, we have reconstructed the triple excitation operator and have performed equation of motion with coupled cluster singles, doubles, and triples to obtain the ionization potential and excitation energies of these molecules as well. Our results suggest that this is quite a reasonable scheme to capture the effect of connected triple excitations as long as the ground state remains weakly multi-reference.
Effective colloidal interactions in rotating magnetic fields
Authors: Coughlan Anna C. H. , Bevan Michael A.
Published: August 2017

Non-equilibrium, steady-state effective pair potentials of micron-sized superparamagnetic particles in rotating magnetic fields are obtained vs. field frequency and amplitude. Trajectories of center-to-center distance between particle pairs from Brownian dynamic simulations, which were previously matched to experimental measurements, are analyzed to obtain local drift and diffusion coefficients. These coefficients are used to obtain effective interaction potentials from solving a one-dimensional Fokker-Planck equation. Biased sampling of the effective energy landscape was implemented by intermittent switching between the field of interest and a repulsive field. Our findings show how the shape and attractive well-depth of pair interactions can be tuned by changing field frequency and amplitude.
Tracking an electronic wave packet in the vicinity of a conical intersection
Authors: Qi Da-Long , Duan Hong-Guang , Sun Zhen-Rong , Miller R. J. Dwayne , Thorwart Michael
Published: August 2017

This work treats the impact of vibrational coherence on the quantum efficiency of a dissipative electronic wave packet in the vicinity of a conical intersection by monitoring the time-dependent wave packet projection onto the tuning and the coupling mode. The vibrational coherence of the wave packet is tuned by varying the strength of the dissipative vibrational coupling of the tuning and the coupling modes to their thermal baths. We observe that the most coherent wave packet yields a quantum efficiency of 93%, but with a large transfer time constant. The quantum yield is dramatically decreased to 50% for a strongly damped incoherent wave packet, but the associated transfer time of the strongly localized wave packet is short. In addition, we find for the strongly damped wave packet that the transfer occurs via tunneling of the wave packet between the potential energy surfaces before the seam of the conical intersection is reached and a direct passage takes over. Our results provide direct evidence that vibrational coherence of the electronic wave packet is a decisive factor which determines the dynamical behavior of a wave packet in the vicinity of the conical intersection.
Measurement of degenerate two-photon absorption spectra of a series of developed two-photon initiators using a dispersive white light continuum Z-scan
Authors: Ajami Aliasghar , Husinsky Wolfgang , Tromayer Maximilian , Gruber Peter , Liska Robert , Ovsianikov Aleksandr
Published: August 2017

To achieve efficient micro- and nanostructuring based on two-photon polymerization (2PP), the development and evaluation of specialized two-photon initiators (2PIs) are essential. Hence, a reliable method to determine the two-photon absorption (2PA) spectra of the synthesized 2PIs used for 2PP structuring is crucial. A technique by which absolute visible-to-near-infrared 2PA spectra of degenerate nature can be determined via performing a single dispersive white-light continuum (WLC) Z-scan has been realized. Using a dispersed white light beam containing 8 fs pulses at wavelengths ranging from 650 nm to 950 nm, the nonlinear transmittance as a function of the sample position can be measured for all spectral components by performing a single scan along the laser beam propagation direction. In this work, the 2PA spectrum of three different 2PIs was determined using this technique. 2PP structuring was also accomplished using the developed 2PIs at different wavelengths. Tuning the wavelength of the laser to match the peak of the 2PA spectra of the developed 2PIs resulted in lower intensity thresholds and facilitated higher structuring speeds. As an example, using M2CMK 2PI for 2PP, the scanning speed can be increased up to 5 folds when the laser wavelength is tuned to 760 nm (i.e., 2PA maximum) instead of the conventionally used 800 nm.
Drop impact on spherical soft surfaces
Authors: Chen Simeng , Bertola Volfango
Published: August 2017

The impact of water drops on spherical soft surfaces is investigated experimentally through high-speed imaging. The effect of a convex compliant surface on the dynamics of impacting drops is relevant to various applications, such as 3D ink-jet printing, where drops of fresh material impact on partially cured soft substrates with arbitrary shape. Several quantities which characterize the morphology of impacting drops are measured through image-processing, including the maximum and minimum spreading angles, length of the wetted curve, and dynamic contact angle. In particular, the dynamic contact angle is measured using a novel digital image-processing scheme based on a goniometric mask, which does not require edge fitting. It is shown that the surface with a higher curvature enhances the retraction of the spreading drop; this effect may be due to the difference of energy dissipation induced by the curvature of the surface. In addition, the impact parameters (elastic modulus, diameter ratio, and Weber number) are observed to significantly affect the dynamic contact angle during impact. A quantitative estimation of the deformation energy shows that it is significantly smaller than viscous dissipation.
Duality and conditional expectations in the Nakajima-Mori-Zwanzig formulation
Authors: Dominy Jason M. , Venturi Daniele
Published: August 2017

We develop a new operator algebraic formulation of the Nakajima-Mori-Zwanzig (NMZ) method of projections. The new theory is built upon rigorous mathematical foundations, and it can be applied to both classical and quantum systems. We show that a duality principle between the NMZ formulation in the space of observables and in the state space can be established, analogous to the Heisenberg and Schrödinger pictures in quantum mechanics. Based on this duality we prove that under natural assumptions, the projection operators appearing in the NMZ equation must be conditional expectations. The proposed formulation is illustrated in various examples.
Taylor-Couette flow with radial fluid injection
Authors: Wilkinson Nikolas , Dutcher Cari S.
Published: August 2017

Taylor-Couette cells have been shown to improve a number of industrial processes due to the wide variety of hydrodynamic flow states accessible. Traditional designs, however, limit the ability to introduce new fluids into the annulus during device operation due to geometric confinement and complexity. In this paper, a co- and counter-rotating Taylor-Couette cell with radial fluid injection has been constructed. The incorporation of 16 ports in the inner cylinder enables radial fluid injection during rotation of both cylinders. The design is also capable of continuous axial flow, enabling large injection volumes. The new inner cylinder design does not modify the critical Re for flow instabilities and can precisely inject a desired mass at a desired flow rate. A range of injection rates and masses were explored to quantify the effect of radial injection on the stability of the turbulent Taylor vortex structure. Only the highest injection rate and total mass studied (5.9 g/s, 100 g) modified the turbulent Taylor vortex structure after injection for a sustained period. The post-injection vortices remained larger than the pre-injection vortices, whereas at lower injection rates or masses, the vortex structure quickly returned to the pre-injection structure. This new system allows for in situ study of hydrodynamic effects on fluid-fluid (gas and liquid) mixing and multiphase complexation, growth, and structure. We demonstrated this new design’s potential for studying the flocculation of bentonite using cationic polyacrylamide for enhancing water treatment operations.
Size effect on interlayer shear between graphene sheets
Authors: Wang Shengtao , Chen Yuli , Ma Yong , Wang Zhou , Zhang Jianyu
Published: August 2017

Interlayer shear between graphene sheets plays an important role in graphene-based materials and devices, but the effect of in-plane deformation of graphene, which may depend on the graphene size, has not been fully understood. In this paper, the size effect on interlayer shear behavior between two graphene sheets is studied based on a non-linear shear-lag model with energy barrier analysis, in which both the lattice registry effect and the elastic deformation of graphene are taken into account, and molecular dynamics (MD) simulations are carried out to verify the model. Both theoretical prediction and MD simulations show that the maximum interlayer shear force of short graphene sheets increases with the graphene length and width. However, if the sheet length is beyond 20 nm, the maximum shear force cannot be further increased by increasing the graphene length due to the non-uniform relative displacement between graphene layers, which is caused by the in-plane deformation of graphene. The upper bound of the maximum shear force per unit graphene width is obtained analytically as a constant 5.6 N/m, suggesting that a small force can pull an infinite long graphene belt to slide on a graphene substrate. This study offers useful information for design and manufacture of graphene-based nano-devices and materials.
Symmetry and the geometric phase in ultracold hydrogen-exchange reactions
Authors: Croft J. F. E. , Hazra J. , Balakrishnan N. , Kendrick B. K.
Published: August 2017

Quantum reactive scattering calculations are reported for the ultracold hydrogen-exchange reaction and its non-reactive atom-exchange isotopic counterparts, proceeding from excited rotational states. It is shown that while the geometric phase (GP) does not necessarily control the reaction to all final states, one can always find final states where it does. For the isotopic counterpart reactions, these states can be used to make a measurement of the GP effect by separately measuring the even and odd symmetry contributions, which experimentally requires nuclear-spin final-state resolution. This follows from symmetry considerations that make the even and odd identical-particle exchange symmetry wavefunctions which include the GP locally equivalent to the opposite symmetry wavefunctions which do not. It is shown how this equivalence can be used to define a constant which quantifies the GP effect and can be obtained solely from experimentally observable rates. This equivalence reflects the important role that discrete symmetries play in ultracold chemistry and highlights the key role that ultracold reactions can play in understanding fundamental aspects of chemical reactivity more generally.
Genuine-multipartite entanglement criteria based on positive maps
Authors: Clivaz Fabien , Huber Marcus , Lami Ludovico , Murta Gláucia
Published: August 2017

Positive maps applied to a subsystem of a bipartite quantum state constitute a central tool in characterising entanglement. In the multipartite case, however, the direct application of a positive but not completely positive map cannot distinguish if a state is genuinely multipartite entangled or just entangled across some bipartition. We thus generalise this bipartite concept to the multipartite setting by introducing non-positive maps that are positive on the subset of biseparable states but can map to a non-positive element if applied to a genuine multipartite entangled state. We explicitly construct examples of multipartite non-positive maps, obtained from positive maps via a lifting procedure, that in this fashion can reveal genuine multipartite entanglement in a robust way.
Cooling rate effects in sodium silicate glasses: Bridging the gap between molecular dynamics simulations and experiments
Authors: Li Xin , Song Weiying , Yang Kai , Krishnan N. M. Anoop , Wang Bu , Smedskjaer Morten M. , Mauro John C. , Sant Gaurav , Balonis Magdalena , Bauchy Mathieu
Published: August 2017

Although molecular dynamics (MD) simulations are commonly used to predict the structure and properties of glasses, they are intrinsically limited to short time scales, necessitating the use of fast cooling rates. It is therefore challenging to compare results from MD simulations to experimental results for glasses cooled on typical laboratory time scales. Based on MD simulations of a sodium silicate glass with varying cooling rate (from 0.01 to 100 K/ps), here we show that thermal history primarily affects the medium-range order structure, while the short-range order is largely unaffected over the range of cooling rates simulated. This results in a decoupling between the enthalpy and volume relaxation functions, where the enthalpy quickly plateaus as the cooling rate decreases, whereas density exhibits a slower relaxation. Finally, we show that, using the proper extrapolation method, the outcomes of MD simulations can be meaningfully compared to experimental values when extrapolated to slower cooling rates.
Chip-scale white flip-chip light-emitting diode containing indium phosphide/zinc selenide quantum dots
Authors: Fan Bingfeng , Yan Linchao , Lao Yuqin , Ma Yanfei , Chen Zimin , Ma Xuejin , Zhuo Yi , Pei Yanli , Wang Gang
Published: August 2017

A method for preparing a quantum dot (QD)-white light-emitting diode (WLED) is reported. Holes were etched in the SiO2 layer deposited on the sapphire substrate of the flip-chip LED by inductively coupled plasma, and these holes were then filled with QDs. An ultraviolet-curable resin was then spin-coated on top of the QD-containing SiO2 layer, and the resin was cured to act as a protecting layer. The reflective sidewall structure minimized sidelight leakage. The fabrication of the QD-WLED is simple in preparation and compatible with traditional LED processes, which was the minimum size of the WLED chip-scale integrated package. InP/ZnS core-shell QDs were used as the converter in the WLED. A blue light-emitting diode with a flip-chip structure was used as the excitation source. The QD-WLED exhibited color temperatures from 5900 to 6400 K and Commission Internationale De L'Elcairage color coordinates from (0.315, 0.325) to (0.325, 0.317), under drive currents from 100 to 400 mA. The QD-WLED exhibited stable optoelectronic properties.
Microwave microscope unmasks, measures surface acoustic waves in ferroelectrics
Authors: Bello Mark
Published: August 2017

Tool may lead to all-in-one method for patterning and testing SAW devices integral to many communication technologies.
New Insights into the Origin of the cis-Configuration Preferences in 1,2-Dihaloethenes: The Importance of the Bonding Orbital Deviations
Authors: Tavanaei Leila , Nori-Shargh Davood
Published: August 2017

The origin of the preferences for the cis-configurations in 1,2-difluoroethene (1), 1,2-dichloroethene (2), and 1,2-dibromoethene (3) were explored by means of the G3MP2, LC-ωPBE and CCSD(T) methods with the 6–311+G** basis set on all atoms, and natural bond orbital interpretation. On the basis of the results obtained, the cis-configurations preferences decrease in going from compound 1 to compound 3. Effectively, the deletions of the hyperconjugative interactions from the Fock matrices of the cis- and trans-configurations of compound 1 lead to the increase of the trans-conformation stability (by ~6.11 kcal mol−1) compared with its corresponding cis-conformation. However, the Pauli exchange-type repulsion difference between the cis- and trans-configurations of compound 1 is in favour of the trans-configuration (by ~6.25 kcal mol−1), revealing that the stabilization energies associated with the hyperconjugative interactions do not compensate the destabilizations associated with the exchange component and dipole-dipole interactions. Importantly, the C=C bond paths in the cis-configuration of compound 1 are bent in essentially the same direction (towards the C–F bonds), leading to an increased overlap and a stronger C–C bond, whereas the C–C bond paths in the trans-configuration are bent in opposite directions. Accordingly, the co-operative stabilizations associated with the bending of the C=C bond paths (towards the C–F bonds) and total hyperconjugative generalized anomeric effect overcome the destabilizations associated with the exchange component and dipole–dipole interactions, leading to the preference of the cis-configuration in compound 1. The deletions of all the donor–acceptor electronic interactions from the Fock matrices of the cis- and trans-configurations of compounds 2 and 3 lead to the increase of the trans-conformation stabilities compared with their corresponding cis-conformations, revealing the determining impacts of the hyperconjugative interactions on the configurational preferences in compounds 2 and 3.
Conformational dynamics of 1-deoxy-
d
-xylulose 5-phosphate synthase on ligand binding revealed by H/D exchange MS
Authors: Zhou Jieyu , Yang Luying , DeColli Alicia , Freel Meyers Caren , Nemeria Natalia S. , Jordan Frank
Published: August 2017

Significance

We applied hydrogen–deuterium exchange MS to a study of full-length
Escherichia coli
1-deoxy-
d
-xylulose 5-phosphate synthase (DXPS), a key enzyme in the methylerythritol 4-phosphate pathway, to provide a snapshot of its conformational dynamics. The three regions displaying an EX1 (monomolecular) exchange behavior, two of which are absent in the X-ray structure, were shown to be dynamic. Open and closed conformations of those regions were revealed with no ligand bound; with substrate analogue bound, a closed conformation was favored, while addition of the second substrate
d
-glyceraldehyde 3-phosphate and product 1-deoxy-
d
-xylulose 5-phosphate induced the open conformation, suggesting crucial roles of conformational changes in the mechanism. Our findings revealed a role for active center loops on DXPS, a mechanistically unique thiamin diphosphate-dependent enzyme.
Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation
Authors: Leney Aneika C. , El Atmioui Dris , Wu Wei , Ovaa Huib , Heck Albert J. R.
Published: August 2017

Significance

Nearly all proteins are posttranslationally modified, a phenomenon known to alter protein function. Recently, multiple posttranslational modifications (PTMs) have been documented to exist on the same proteins, revealing an additional level of complexity (named “PTM crosstalk”) that, due to its dynamic nature, is challenging to predict. Here, we propose a motif for PTM crosstalk between two of the most common PTMs: phosphorylation and O-GlcNAcylation. Through the use of a kinetic-based high-resolution mass spectrometry assay, we highlight specific residues that, when phosphorylated, hamper O-GlcNAcylation at nearby sites. In addition, we show that the Ser/Thr residues in one of the most common kinase motifs, PX(S/T)P, cannot be O-GlcNAcylated, demonstrating that reciprocal PTM crosstalk does not occur with Pro-directed kinases.
Superior colliculus encodes visual saliency before the primary visual cortex
Authors: White Brian J. , Kan Janis Y. , Levy Ron , Itti Laurent , Munoz Douglas P.
Published: August 2017

Significance

Theories of visual attention postulate the existence of a saliency map that guides attention/gaze toward the most visually conspicuous stimuli in complex scenes. This study compared saliency coding in the two dominant visual gateways: the primary visual cortex (V1) and the evolutionarily older visual system that exists in the midbrain superior colliculus. Our results show that neurons in the superficial visual layers of the superior colliculus (SCs) encoded saliency earlier and more robustly than V1 neurons. This was surprising, because the dominant input to the SCs arises from V1. This result is in line with models that place a feature processing stage (V1) before the feature-agnostic saliency map in SCs.
Impact of catch shares on diversification of fishers’ income and risk
Authors: Holland Daniel S. , Speir Cameron , Agar Juan , Crosson Scott , DePiper Geret , Kasperski Stephen , Kitts Andrew W. , Perruso Larry
Published: August 2017

Significance

Catch share programs, which allocate a share of a fishery’s annual catch to fishers, are an increasingly popular management approach in the United States and around the world. While catch shares have been shown to increase efficiency, they may reduce diversification of individual fishers, which could increase income variation and financial risk. Shifts in the productivity and distribution of fisheries resulting from climate change may increase the importance of diversification. Our evaluation of 13 US fisheries is a large-scale study to evaluate whether catch shares do in fact lead to reduced diversification. We find that diversification was generally reduced after implementation of catch shares; however, in most cases, we found no significant change in income variation.
Reducing posttreatment relapse in cleft lip palatal expansion using an injectable estrogen–nanodiamond hydrogel
Authors: Hong Christine , Song Dayoung , Lee Dong-Keun , Lin Lawrence , Pan Hsin Chuan , Lee Deborah , Deng Peng , Liu Zhenqing , Hadaya Danny , Lee Hye-Lim , Mohammad Abdulaziz , Zhang Xinli , Lee Min , Wang Cun-Yu , Ho Dean
Published: August 2017

Patients with cleft lip and/or palate (CLP), who undergo numerous medical interventions from infancy, can suffer from lifelong debilitation caused by underdeveloped maxillae. Conventional treatment approaches use maxillary expansion techniques to develop normal speech, achieve functional occlusion for nutrition intake, and improve esthetics. However, as patients with CLP congenitally lack bone in the cleft site with diminished capacity for bone formation in the expanded palate, more than 80% of the patient population experiences significant postexpansion relapse. While such relapse has been a long-standing battle in craniofacial care of patients, currently there are no available strategies to address this pervasive problem. Estrogen, 17β-estradiol (E2), is a powerful therapeutic agent that plays a critical role in bone homeostasis. However, E2’s clinical application is less appreciated due to several limitations, including its pleiotropic effects and short half-life. Here, we developed a treatment strategy using an injectable system with photo–cross-linkable hydrogel (G) and nanodiamond (ND) technology to facilitate the targeted and sustained delivery of E2 to promote bone formation. In a preclinical expansion/relapse model, this functionalized E2/ND/G complex substantially reduced postexpansion relapse by nearly threefold through enhancements in sutural remodeling compared with unmodified E2 administration. The E2/ND/G group demonstrated greater bone volume by twofold and higher osteoblast number by threefold, compared with the control group. The E2/ND/G platform maximized the beneficial effects of E2 through its extended release with superior efficacy and safety at the local level. This broadly applicable E2 delivery platform shows promise as an adjuvant therapy in craniofacial care of patients.
Adaptive benefit of cross-modal plasticity following cochlear implantation in deaf adults
Authors: Anderson Carly A. , Wiggins Ian M. , Kitterick Pádraig T. , Hartley Douglas E. H.
Published: August 2017

Significance

Following sensory deprivation, the sensory brain regions can become colonized by the other intact sensory modalities. In deaf individuals, evidence suggests that visual language recruits auditory brain regions and may limit hearing restoration with a cochlear implant. This suggestion underpins current rehabilitative recommendations that deaf individuals undergoing cochlear implantation should avoid using visual language. However, here we show the opposite: Recruitment of auditory brain regions by visual speech after implantation is associated with better speech understanding with a cochlear implant. This suggests adaptive benefits of visual communication because visual speech may serve to optimize, rather than hinder, restoration of hearing following implantation. These findings have implications for both neuroscientific theory and the clinical rehabilitation of cochlear implant patients worldwide.
A p53-dependent response limits the viability of mammalian haploid cells
Authors: Olbrich Teresa , Mayor-Ruiz Cristina , Vega-Sendino Maria , Gomez Carmen , Ortega Sagrario , Ruiz Sergio , Fernandez-Capetillo Oscar
Published: August 2017

Significance

Haploidy is a critical advantage for studies on gene function, because only one allele needs to be mutated to yield a phenotype. That is why yeast has led genetic screenings in recent decades. All mammalian cells except germ cells contain two or more sets of chromosomes. Recently, several mammalian haploid cell lines have been obtained; however, the haploid state is unstable, and cultures become progressively enriched in diploid cells. Here we reveal that chromosome segregation takes longer in mammalian haploid cells than in their diploid counterparts, and is followed by an increase in spontaneous cell death. By deleting p53, we can rescue the viability of haploid cells and thereby stabilize the haploid state in mammalian somatic cells.
Prefrontal cortex modulates posterior alpha oscillations during top-down guided visual perception
Authors: Helfrich Randolph F. , Huang Melody , Wilson Guy , Knight Robert T.
Published: August 2017

Significance

Neural oscillations have been shown to support a range of cognitive abilities. Here we demonstrate that delta activity (2–4 Hz) in the prefrontal cortex tracked the current task context and modulated sensory processing in a top-down manner. We show that frontal delta and parietooccipital alpha (8–12 Hz) oscillations are functionally coupled and jointly guide visual perception to integrate sensory evidence with current task demands. We observed strong moment-to-moment behavioral fluctuations, which cycled at the rate of the endogenous prefrontal oscillatory brain activity. Our findings suggest that neuronal oscillations provide the functional basis for context-dependent visual perception.
Role of co-occurring competition and facilitation in plant spacing hydrodynamics in water-limited environments
Authors: Trautz Andrew C. , Illangasekare Tissa H. , Rodriguez-Iturbe Ignacio
Published: August 2017

Significance

Plant communities exist in a continual state of transition as the spacing between individuals in each successive generation changes in response to environmental conditions. We developed a conceptual model based on quantitative experimental data and established ecological theories to provide insight into plant performance and community spatial pattern development from a hydrodynamic perspective. We demonstrate that the roles of co-occurring competition for soil water and facilitation of abiotic stresses (i.e., microclimatic) vary with spacing distance between individual plants, impacting soil moisture patterns and local water availability. Our conceptual model can provide insight into the design of future field and modeling efforts focused on pertinent climatological and ecohydrological problems related to land–atmosphere fluxes, agricultural best practices, and ecosystem productivity and recovery.
Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen
Authors: Pallesen Jesper , Wang Nianshuang , Corbett Kizzmekia S. , Wrapp Daniel , Kirchdoerfer Robert N. , Turner Hannah L. , Cottrell Christopher A. , Becker Michelle M. , Wang Lingshu , Shi Wei , Kong Wing-Pui , Andres Erica L. , Kettenbach Arminja N. , Denison Mark R. , Chappell James D. , Graham Barney S. , Ward Andrew B. , McLellan Jason S.
Published: August 2017

Significance

Coronaviruses such as Middle East respiratory syndrome coronavirus (MERS-CoV) cause severe respiratory distress with high fatality rates. The spike (S) glycoprotein is a determinant of host range and is the target of neutralizing antibodies and subunit vaccine development. We describe an engineering strategy for stabilization of soluble S proteins in the prefusion conformation, which results in greatly increased expression, conformational homogeneity, and elicitation of potent antibody responses. Cryo-EM structures of the stabilized MERS-CoV S protein in complex with a stem-directed neutralizing antibody provide a molecular basis for host-cell protease requirements and identify a site of immune pressure. We also defined four conformational states of the trimer wherein each receptor-binding domain is either packed together at the membrane-distal apex or rotated into a receptor-accessible conformation.
Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion
Authors: Katava Marina , Stirnemann Guillaume , Zanatta Marco , Capaccioli Simone , Pachetti Maria , Ngai K. L. , Sterpone Fabio , Paciaroni Alessandro
Published: August 2017

Significance

In 1910 F. A. Lindemann introduced a practical criterion to predict the melting of crystals on the basis of the relative magnitude of thermal atomic fluctuations and the crystal lattice constant. The idea of a critical threshold for the local motions that would trigger melting also in disordered media like proteins has inspired important subsequent investigations. Here, a common scaling toward a constant value for the local fluctuations of a model protein in different environments is proved when approaching the unfolding temperature. This landmark result not only sheds unique light on the relationship between protein flexibility and stability, but also opens the possibility to predict protein unfolding in special environments (e.g., the cell interior) by following thermal local fluctuations.
Optimized strategy for in vivo Cas9-activation in
Drosophila
Authors: Ewen-Campen Ben , Yang-Zhou Donghui , Fernandes Vitória R. , González Delfina P. , Liu Lu-Ping , Tao Rong , Ren Xingjie , Sun Jin , Hu Yanhui , Zirin Jonathan , Mohr Stephanie E. , Ni Jian-Quan , Perrimon Norbert
Published: August 2017

Significance

Recently, a number of approaches have been developed to repurpose the CRISPR/Cas9 system as a sequence-specific transcriptional activator for gain-of-function experiments (CRISPR activators, or “CRISPRa”). While multiple CRISPRa strategies have been characterized in cell culture, little is known about their performance in vivo. We present an optimized strategy for generating a large-scale CRISPRa resource in
Drosophila
and show that this system has a high success rate and generates easily recognizable phenotypes in vivo. We describe a growing collection of transgenic fly lines to facilitate large-scale in vivo CRISPRa experiments.
Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria
Authors: Bar Eyal Leeat , Ranjbar Choubeh Reza , Cohen Eyal , Eisenberg Ido , Tamburu Carmen , Dorogi Márta , Ünnep Renata , Appavou Marie-Sousai , Nevo Reinat , Raviv Uri , Reich Ziv , Garab Győző , van Amerongen Herbert , Paltiel Yossi , Keren Nir
Published: August 2017

Significance

All photosynthetic organisms regulate efficiency of excitation energy transfer (EET) to fit energy supply to biochemical demands. For desiccation-tolerant desert crust cyanobacteria this ability is of the utmost importance. These organisms spend most of the daytime in the desiccated state whence absorbed energy is completely quenched. Based on our observations we propose a model where in the hydrated state the organized rod structure of the light-harvesting phycobilisome supports directional EET to reaction centers with minimal losses to thermal dissipation. In the desiccated state this structure gives way to more random aggregates. The resulting EET path exhibits increased coupling to the environment and enhanced quenching. This energy dissipation mechanism is completely reliant on changes in aggregation state of phycobilisome components.
Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C
e
3D)
Authors: Li Weizhe , Germain Ronald N. , Gerner Michael Y.
Published: August 2017

Significance

Major biological processes rely on the precise positioning of diverse cell types in specific anatomical locations. Existing techniques for studying cellular spatial positioning in tissues, especially with robust identification of densely packed cells, have substantial time, cost, resolution, and multiplexing limitations. Here, we describe an easy-to-use and inexpensive tissue clearing technique for attaining high-quality images of cells and diverse molecules of interest in substantial tissue volumes, enabling simultaneous quantitative analysis of 3D organ structure and fine-grained cellular composition. This technology will enhance our capacity for acquiring a quantitative understanding of the relationships between cells and their microenvironments in the context of broader tissue organization and is directly applicable to diverse biological disciplines as well as diagnostic medicine.
A protein complex regulates RNA processing of intronic heterochromatin-containing genes in
Arabidopsis
Authors: Duan Cheng-Guo , Wang Xingang , Zhang Lingrui , Xiong Xiansong , Zhang Zhengjing , Tang Kai , Pan Li , Hsu Chuan-Chih , Xu Huawei , Tao W. Andy , Zhang Heng , Zhu Jian-Kang
Published: August 2017

Significance

How heterochromatin affects RNA processing is unclear. The chromatin regulators ASI1 and EDM2 function in regulating alternative polyadenylation at genes with intronic heterochromatin. We found that ASI1 and EDM2 are associated in planta through interactions with a putative RNA-binding protein, AIPP1. Protein interaction assays suggest that the RNA Pol II C-terminal domain phosphatase CPL2 and two other proteins (AIPP2 and AIPP3) are associated with the ASI1-AIPP1-EDM2 complex. Like ASI1 and EDM2, AIPP1 also functions in promoting the expression of heterochromatin-containing genes. However, the function of CPL2, AIPP2, and AIPP3 is antagonistic to that of ASI1, EDM2, and AIPP1. Our discovery of the ASI1-AIPP1-EDM2 complex and associated proteins is important for understanding how heterochromatin regulates RNA processing.
A genome Tree of Life for the Fungi kingdom
Authors: Choi JaeJin , Kim Sung-Hou
Published: August 2017

Significance

Fungi belong to one of the largest and most diverse groups of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”) constructed using a small number of genes. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population, depending on the selection of the genes. We present whole-genome information-based trees (“genome trees”) using a variation of a computational algorithm developed to find plagiarism in two books, where we represent a whole-genomic information of an organism as a book of words without spaces.
DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion
Authors: McLennan Rebecca , Bailey Caleb M. , Schumacher Linus J. , Teddy Jessica M. , Morrison Jason A. , Kasemeier-Kulesa Jennifer C. , Wolfe Lauren A. , Gogol Madeline M. , Baker Ruth E. , Maini Philip K. , Kulesa Paul M.
Published: August 2017

Neural crest cells are both highly migratory and significant to vertebrate organogenesis. However, the signals that regulate neural crest cell migration remain unclear. In this study, we test the function of differential screening-selected gene aberrant in neuroblastoma (DAN), a bone morphogenetic protein (BMP) antagonist we detected by analysis of the chick cranial mesoderm. Our analysis shows that, before neural crest cell exit from the hindbrain, DAN is expressed in the mesoderm, and then it becomes absent along cell migratory pathways. Cranial neural crest and metastatic melanoma cells avoid DAN protein stripes in vitro. Addition of DAN reduces the speed of migrating cells in vivo and in vitro, respectively. In vivo loss of function of DAN results in enhanced neural crest cell migration by increasing speed and directionality. Computer model simulations support the hypothesis that DAN restrains cell migration by regulating cell speed. Collectively, our results identify DAN as a novel factor that inhibits uncontrolled neural crest and metastatic melanoma invasion and promotes collective migration in a manner consistent with the inhibition of BMP signaling.
Zebrafish earns its stripes for in vivo ASC speck dynamics
Authors: Bezbradica Jelena S. , Schroder Kate
Published: August 2017

Assembly of the ASC speck is critical for signaling by the inflammasome. In this issue, Kuri et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201703103) use live microscopy to track fluorescently tagged endogenous ASC in the zebrafish, describing the molecular domains driving ASC speck assembly and identifying a key role for macrophages in ASC speck removal in vivo.
IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Authors: Ito Takashi , Hirose Koichi , Saku Aiko , Kono Kenta , Takatori Hiroaki , Tamachi Tomohiro , Goto Yoshiyuki , Renauld Jean-Christophe , Kiyono Hiroshi , Nakajima Hiroshi
Published: August 2017

Previous studies have shown that IL-22, one of the Th17 cell–related cytokines, plays multiple roles in regulating allergic airway inflammation caused by antigen-specific Th2 cells; however, the underlying mechanism remains unclear. Here, we show that allergic airway inflammation and Th2 and Th17 cytokine production upon intratracheal administration of house dust mite (HDM) extract, a representative allergen, were exacerbated in IL-22-deficient mice. We also found that IL-22 induces Reg3γ production from lung epithelial cells through STAT3 activation and that neutralization of Reg3γ significantly exacerbates HDM-induced eosinophilic airway inflammation and Th2 cytokine induction. Moreover, exostatin-like 3 (EXTL3), a functional Reg3γ binding protein, is expressed in lung epithelial cells, and intratracheal administration of recombinant Reg3γ suppresses HDM-induced thymic stromal lymphopoietin and IL-33 expression and accumulation of type 2 innate lymphoid cells in the lung. Collectively, these results suggest that IL-22 induces Reg3γ production from lung epithelial cells and inhibits the development of HDM-induced allergic airway inflammation, possibly by inhibiting cytokine production from lung epithelial cells.
A conceptual framework for evaluating data suitability for observational studies
Authors: Shang Ning , Weng Chunhua , Hripcsak George
Published: August 2017

Objective

To contribute a conceptual framework for evaluating data suitability to satisfy the research needs of observational studies.

Materials and Methods

Suitability considerations were derived from a systematic literature review on researchers’ common data needs in observational studies and a scoping review on frequent clinical database design considerations, and were harmonized to construct a suitability conceptual framework using a bottom-up approach. The relationships among the suitability categories are explored from the perspective of 4 facets of data: intrinsic, contextual, representational, and accessible. A web-based national survey of domain experts was conducted to validate the framework.

Results

Data suitability for observational studies hinges on the following key categories: Explicitness of Policy and Data Governance, Relevance, Availability of Descriptive Metadata and Provenance Documentation, Usability, and Quality. We describe 16 measures and 33 sub-measures. The survey uncovered the relevance of all categories, with a 5-point Likert importance score of 3.9 ± 1.0 for Explicitness of Policy and Data Governance, 4.1 ± 1.0 for Relevance, 3.9 ± 0.9 for Availability of Descriptive Metadata and Provenance Documentation, 4.2 ± 1.0 for Usability, and 4.0 ± 0.9 for Quality.

Conclusions

The suitability framework evaluates a clinical data source’s fitness for research use. Its construction reflects both researchers’ points of view and data custodians’ design features. The feedback from domain experts rated Usability, Relevance, and Quality categories as the most important considerations.
Effects of β‐Glucan Content and Pearling of Barley in Diet‐Induced Obese Mice
Authors: Aoe Seiichiro , Ichinose Yasunori , Kohyama Noriko , Komae Kozo , Takahashi Asuka , Yoshioka Toji , Yanagisawa Takashi
Published: August 2017

The effects of the β‐glucan content and pearling of barley on abdominal obesity and the proinflammatory state were investigated in diet‐induced obese mice. Male C57BL/6J mice were randomly divided into four groups and fed either a high‐fat diet containing high‐β‐glucan barley (Beau Fiber [BF]) or a high‐fat diet containing β‐glucan‐free barley (Shikoku‐hadaka 84(bgl) [BGL]) as whole grain flour or 60% pearled flour for 12 weeks. The weights of mesenteric fat, serum total and low density lipoprotein cholesterol levels, serum insulin and fasting glucose levels, oral glucose tolerance test results, and messenger RNA (mRNA) expression of proinflammatory markers in epididymal fat in both BF groups were significantly lower than those of both BGL groups. The abundance of Bacteroides in both BF groups was significantly higher than that in both BGL groups, whereas the abundance of Clostridium clusters in both BF groups was significantly lower than that in both BGL groups. No significant differences between the whole grain and pearled flours were observed. These results suggest that high‐β‐glucan barley attenuates the progression of abdominal obesity and the proinflammatory state in diet‐induced obese mice compared with β‐glucan‐free barley, possibly by modifying insulin secretion and the microbiota.
Wheat breeding for quality: A historical review
Authors: Kiszonas Alecia M. , Morris Craig F.
Published: August 2017

Background and objectives

Wheat (Triticumspp. L.) is a leading cereal contributing to the nourishment of humankind. Since its domestication ca. 12,000 years ago, humans have profoundly influenced its evolution. In the more recent past, breeding via cross‐hybridization and the selection of progeny with superior end‐use quality have moved from solely phenotyping (e.g., bread baking quality), to a more detailed genetic approach of selecting genes, alleles, and whole‐genome structure for desirable traits.

Findings

The present review provides a brief historical summary of wheat improvement for end‐use quality. In the last ~150 years, wheat improvement has benefited from advances in genetics, chemistry and biotechnology. In the past couple decades, rapid advances inDNAand next‐generation sequencing technology have promised a revolution in wheat improvement. The various technologies are reviewed here.

Conclusions

The “future” of wheat improvement may involve the whole‐genome‐based analysis, “genomic selection.” However, to date, the plethora ofQTLgenerated over the recent years have largely remained unused.

Significance and novelty

Wheat is vital to the survival of humankind, and new cultivars must be continually developed. These cultivars should have high quality for processing and consumer products. An important means of breeding and selecting for high quality is through rapidly evolving genome‐based technologies.
Changes in the Functional Components of Barley Produced from Different Cultivars and Germination Periods
Authors: Lee Yoon Jeong , Jang Gwi Yeong , Li Meishan , Kim Min Young , Kim Eun Hee , Lee Mi Ja , Lee Junsoo , Jeong Heon Sang
Published: August 2017

This study investigated the changes in the functional components of three cultivars (Kunalbori, Dahan, and Hinchalssalbori) over a 6 day germination period; these cultivars were selected because of their varied characteristics and applications. Barley produced from the cultivars was subjected to 6 days of germination. Germinated barley was analyzed for total polyphenol, total flavonoid, hordenine, total arabinoxylan, soluble arabinoxylan, γ‐aminobutyric acid, and γ‐oryzanol contents. The total polyphenol content increased with germination period, corresponding to 1.47–3.83, 1.41–3.42, and 1.59–2.82 mg/g in barley produced from the three cultivars, respectively. The corresponding total flavonoid contents were 0.35–0.44, 0.31–0.48, and 0.22–0.37 mg/g. The hordenine contents in the barley produced from the three cultivars increased from not detected for nongerminated barley to 1.52, 1.09, and 1.34 mg/100 g, respectively, at germination day 6. The γ‐aminobutyric acid content significantly increased until germination day 4, followed by a decrease, and the highest content was observed for barley produced from the Kunalbori cultivar at germination day 4. The total arabinoxylan and soluble arabinoxylan contents increased with germination period. Results indicated that the germination period is crucial for increasing the functional components. These results are expected to be beneficial during food product manufacturing.
Reduced Field-of-View Diffusion-Weighted Magnetic Resonance Imaging of the Prostate at 3 Tesla: Comparison With Standard Echo-Planar Imaging Technique for Image Quality and Tumor Assessment
Authors: Tamada Tsutomu , Ream Justin M. , Doshi Ankur M. , Taneja Samir S. , Rosenkrantz Andrew B.
Published: August 2017

Objective

The purpose of this study was to compare image quality and tumor assessment at prostate magnetic resonance imaging (MRI) between reduced field-of-view diffusion-weighted imaging (rFOV-DWI) and standard DWI (st-DWI).

Methods

A total of 49 patients undergoing prostate MRI and MRI/ultrasound fusion–targeted biopsy were included. Examinations included st-DWI (field of view [FOV], 200 × 200 mm) and rFOV-DWI (FOV, 140 × 64 mm) using a 2-dimensional (2D) spatially-selective radiofrequency pulse and parallel transmission. Two readers performed qualitative assessments; a third reader performed quantitative evaluation.

Results

Overall image quality, anatomic distortion, visualization of capsule, and visualization of peripheral/transition zone edge were better for rFOV-DWI for reader 1 (P ≤ 0.002), although not for reader 2 (P ≥ 0.567). For both readers, sensitivity, specificity, and accuracy for tumor with a Gleason Score (GS) of 3 + 4 or higher were not different (P ≥ 0.289). Lesion clarity was higher for st-DWI for reader 2 (P = 0.008), although similar for reader 1 (P = 0.409). Diagnostic confidence was not different for either reader (P ≥ 0.052). Tumor-to-benign apparent diffusion coefficient ratio was not different (P = 0.675).

Conclusions

Potentially improved image quality of rFOV-DWI did not yield improved tumor assessment. Continued optimization is warranted.