bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-step dielectric anomalies coupled with structural phase transitions in a co-crystal of 1,4-diazabicyclo[2.2.2]octane and 4,4′-biphenol
Authors: Ning Wei-Hua , Zhai Lu , Ren Xiao-Ming
Published: July 2014

Two-step dielectric anomalies appear in co-crystal of 1,4-diazabicyclo[2.2.2]octane (DABCO) and 4,4′-biphenol which are coupled with structural phase transitions related to the disorder–order transformation of DABCO molecules.
Improvements in electrical and electrochemical properties of Nb-doped SnO2−δ supports for fuel cell cathodes due to aggregation and Pt loading
Authors: Senoo Yuichi , Kakinuma Katsuyoshi , Uchida Makoto , Uchida Hiroyuki , Deki Shigehito , Watanabe Masahiro
Published: July 2014

We found the specific activities of Pt/Sn0.96Nb0.04O2−δ for the oxygen reduction reaction increased with increasing conductivity of the support.
Efficient and scalable total synthesis of calcitroic acid and its 13C-labeled derivative
Authors: Meyer Daniel , Rentsch Lara , Marti Roger
Published: July 2014

Calcitroic acid and its 13C labeled derivative has been synthesized from Inhoffen-Lythgoe diol in 11 steps with an overall yield of 21%.
Fabrication of a core–shell–shell particle with a quarter-wave thick shell and its optical properties
Authors: Shibata Hiroki , Imakita Kenji , Fujii Minoru
Published: July 2014

In the present work, core–shell–shell particles with quarter-wave thick shells have been synthesized using chemical solution processes for the first time and the optical properties are discussed both theoretically and experimentally.
Uncovering divergent evolution of α/β-hydrolases: a surprising residue substitution needed to convert Hevea brasiliensis hydroxynitrile lyase into an esterase
Authors: Nedrud David M. , Lin Hui , Lopez Gilsinia , Padhi Santosh K. , Legatt Graig A. , Kazlauskas Romas J.
Published: July 2014

Although Glu79 does not contribute to esterase catalysis, it can block esterase catalysis by hydrogen bonding to the active site histidine.
Metal−organic framework encapsulated Pd nanoparticles: towards advanced heterogeneous catalysts
Authors: Chen Liyu , Chen Huirong , Luque Rafael , Li Yingwei
Published: July 2014

Palladium precursors were encapsulated through ligand design prior to the MOF assembly, achieving uniformly distributed Pd NPs inside the cavities of MOFs. The embedded Pd NPs exhibited significantly improved catalytic efficiencies as compared to those synthesized by traditional impregnation method, due to the nano-confinement and electron-donation effects offered by MOFs.
Effect of head group size on the photoswitching applications of azobenzene Disperse Red 1 analogues
Authors: Goulet-Hanssens Alexis , Corkery T. Christopher , Priimagi Arri , Barrett Christopher J.
Published: July 2014

We investigate the effect of the increased molecular bulk in the ‘head’ group for a class of newly synthesized azobenzene chromophores and demonstrate that motifs with larger free-volume changes during isomerization drive photoinduced macromolecular phenomena.
Fast one-step synthesis of N-doped carbon dots by pyrolyzing ethanolamine
Authors: Dong Xinwei , Su Yanjie , Geng Huijuan , Li Zhongli , Yang Chao , Li Xiaolin , Zhang Yafei
Published: July 2014

N-doped CDs can be obtained directly with high yield by pyrolyzing ethanolamine in air within just 7 minutes with the assistance of hydrogen peroxide.
Issues in Language Sample Collection and Analysis With Children Using AAC
Authors: Van Tatenhove Gail
Published: July 2014

Language sample analysis is considered one of the best methods of evaluating expressive language production in speaking children. However, the practice of language sample collection and analysis is complicated for speech-language pathologists working with children who use augmentative and alternative communication (AAC) devices. This article identifies six issues regarding use of language sample collection and analysis in clinical practice with children who use AAC devices. The purpose of this article is to encourage speech-language pathologists practicing in the area of AAC to utilize language sample collection and analysis as part of ongoing AAC assessment.
Triple‐step method to design non‐linear controller for rail pressure of gasoline direct injection engines
Authors: Chen Hong , Gong Xun , Liu Qifang , Hu Yunfeng
Published: July 2014

The precise control of rail pressure in gasoline direct injection (GDI) engines is considered as an important issue. This study presents a novel approach for rail pressure control of GDI engines. The control objective is to make the rail pressure track a given reference. Different from the existing non‐linear controller design methods, the proposed method can be formalised as a triple‐step procedure: (i) a steady‐state control is deduced, playing the similar role of the map‐based control strategy widely used in automotive control; (ii) a feed‐forward control is derived concerning the variation of the tracking reference; and (iii) the previous two steps result in an explicit and affine expression of the tracking error dynamics, based on that a non‐linear error feedback can be easily designed for enhancing the closed‐loop performance and rearranged into a state‐dependent PID. The structure of the designed non‐linear controller is concise and is comparable to those widely used in modern automotive control. In addition, this procedure provides a concise design process so that the derivation of the control law is simplified and straightforward. A guideline of the control parameters tuning is given based on robustness analysis. Finally, the simulation results in the environment of AMESim with a realistic common rail injection system model show the efficiency of the proposed approach.
Direct visualization of atomically precise nitrogen-doped graphene nanoribbons
Authors: Zhang Yi , Zhang Yanfang , Li Geng , Lu Jianchen , Lin Xiao , Du Shixuan , Berger Reinhard , Feng Xinliang , Müllen Klaus , Gao Hong-Jun
Published: July 2014

We have fabricated atomically precise nitrogen-doped chevron-type graphene nanoribbons by using the on-surface synthesis technique combined with the nitrogen substitution of the precursors. Scanning tunneling microscopy and spectroscopy indicate that the well-defined nanoribbons tend to align with the neighbors side-by-side with a band gap of 1.02 eV, which is in good agreement with the density functional theory calculation result. The influence of the high precursor coverage on the quality of the nanoribbons is also studied. We find that graphene nanoribbons with sufficient aspect ratios can only be fabricated at sub-monolayer precursor coverage. This work provides a way to construct atomically precise nitrogen-doped graphene nanoribbons.
A MATLAB-based finite-element visualization of quantum reactive scattering. I. Collinear atom-diatom reactions
Authors: Warehime Mick , Alexander Millard H.
Published: July 2014

We restate the application of the finite element method to collinear triatomic reactive scattering dynamics with a novel treatment of the scattering boundary conditions. The method provides directly the reactive scattering wave function and, subsequently, the probability current density field. Visualizing these quantities provides additional insight into the quantum dynamics of simple chemical reactions beyond simplistic one-dimensional models. Application is made here to a symmetric reaction (H+H2), a heavy-light-light reaction (F+H2), and a heavy-light-heavy reaction (F+HCl). To accompany this article, we have written a MATLAB code which is fast, simple enough to be accessible to a wide audience, as well as generally applicable to any problem that can be mapped onto a collinear atom-diatom reaction. The code and user's manual are available for download from http://www2.chem.umd.edu/groups/alexander/FEM.
Production of cold beams of ND3 with variable rotational state distributions by electrostatic extraction of He and Ne buffer-gas-cooled beams
Authors: Twyman Kathryn S. , Bell Martin T. , Heazlewood Brianna R. , Softley Timothy P.
Published: July 2014

The measurement of the rotational state distribution of a velocity-selected, buffer-gas-cooled beam of ND3 is described. In an apparatus recently constructed to study cold ion-molecule collisions, the ND3 beam is extracted from a cryogenically cooled buffer-gas cell using a 2.15 m long electrostatic quadrupole guide with three 90° bends. (2+1) resonance enhanced multiphoton ionization spectra of molecules exiting the guide show that beams of ND3 can be produced with rotational state populations corresponding to approximately \documentclass[12pt]{minimal}\begin{document}$T_\text{rot}$\end{document}Trot = 9–18 K, achieved through manipulation of the temperature of the buffer-gas cell (operated at 6 K or 17 K), the identity of the buffer gas (He or Ne), or the relative densities of the buffer gas and ND3. The translational temperature of the guided ND3 is found to be similar in a 6 K helium and 17 K neon buffer-gas cell (peak kinetic energies of 6.92(0.13) K and 5.90(0.01) K, respectively). The characterization of this cold-molecule source provides an opportunity for the first experimental investigations into the rotational dependence of reaction cross sections in low temperature collisions.
Tensor hypercontracted ppRPA: Reducing the cost of the particle-particle random phase approximation from O(r 6) to O(r 4)
Authors: Shenvi Neil , van Aggelen Helen , Yang Yang , Yang Weitao
Published: July 2014

In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combine the particle-particle random phase approximation with tensor hypercontraction to produce the tensor-hypercontracted particle-particle RPA (THC-ppRPA) algorithm. Unlike previous implementations of ppRPA which scale as O(r6), the THC-ppRPA algorithm scales asymptotically as only O(r4), albeit with a much larger prefactor than the traditional algorithm. We apply THC-ppRPA to several model systems and show that it yields the same results as traditional ppRPA to within mH accuracy. Our method opens the door to the development of post-Kohn Sham functionals based on ppRPA without the excessive asymptotic cost of traditional ppRPA implementations.
A magnetic particle time-of-flight (MagPTOF) diagnostic for measurements of shock- and compression-bang time at the NIF (invited)
Authors: Rinderknecht H. G. , Sio H. , Frenje J. A. , Magoon J. , Agliata A. , Shoup M. , Ayers S. , Bailey C. G. , Gatu Johnson M. , Zylstra A. B. , Sinenian N. , Rosenberg M. J. , Li C. K. , Sèguin F. H. , Petrasso R. D. , Rygg J. R. , Kimbrough J. R. , Mackinnon A. , Bell P. , Bionta R. , Clancy T. , Zacharias R. , House A. , Döppner T. , Park H. S. , LePape S. , Landen O. , Meezan N. , Robey H. , Glebov V. U. , Hohenberger M. , Stoeckl C. , Sangster T. C. , Li C. , Parat J. , Olson R. , Kline J. , Kilkenny J.
Published: July 2014

A magnetic particle time-of-flight (MagPTOF) diagnostic has been designed to measure shock- and compression-bang time using D3He-fusion protons and DD-fusion neutrons, respectively, at the National Ignition Facility (NIF). This capability, in combination with shock-burn weighted areal density measurements, will significantly constrain the modeling of the implosion dynamics. This design is an upgrade to the existing particle time-of-flight (pTOF) diagnostic, which records bang times using DD or DT neutrons with an accuracy better than ±70 ps [H. G. Rinderknecht et al., Rev. Sci. Instrum. 83, 10D902 (2012)]. The inclusion of a deflecting magnet will increase D3He-proton signal-to-background by a factor of 1000, allowing for the first time simultaneous measurements of shock- and compression-bang times in D3He-filled surrogate implosions at the NIF.
A system to measure isomeric state half-lives in the 10 ns to 10 μs range
Authors: Toufen D. L. , Allegro P. R. P. , Medina N. H. , Oliveira J. R. B. , Cybulska E. W. , Seale W. A. , Linares R. , Silveira M. A. G. , Ribas R. V.
Published: July 2014

The Isomeric State Measurement System (SISMEI) was developed to search for isomeric nuclear states produced by fusion-evaporation reactions. The SISMEI consists of 10 plastic phoswich telescopes, two lead shields, one NaI(Tl) scintillation detector, two Compton suppressed HPGe γ-ray detectors, and a cone with a recoil product catcher. The new system was tested at the 8 UD Pelletron tandem accelerator of the University of São Paulo with the measurement of two known isomeric states: 54Fe, 10+ state (E = 6527.1 (11) keV, T1/2 = 364(7) ns) and the 5/2+ state of 19F (E = 197.143 (4) keV, T1/2 = 89.3 (10) ns). The results indicate that the system is capable of identifying delayed transitions, of measuring isomeric state lifetimes, and of identifying the feeding transitions of the isomeric state through the delayed γ-γ coincidence method. The measured half-life for the 10+ state was T1/2 = 365(14) ns and for the 5/2+ state, 100(36) ns.
The dependence of homogeneous nucleation rate on supersaturation
Authors: Girshick Steven L.
Published: July 2014

The claim that classical nucleation theory (CNT) correctly predicts the dependence on supersaturation of the steady-state rate of homogeneous nucleation is reexamined in light of recent experimental studies of nucleation of a range of substances, including water, argon, nitrogen, and several 1-alcohols. Based on these studies (which include, for water, a compilation of nine different studies), it is concluded that the dependence of nucleation rate on supersaturation is not correctly predicted by CNT. It is shown that CNT's incorrect prediction of the supersaturation dependence of nucleation rate is due to its incorrect prediction of the Gibbs free energy change associated with formation of small clusters from the monomer vapor, evaluated at the substance's equilibrium vapor pressure, even though that free energy change is itself a function only of temperature.
An ionic concentration and size dependent dielectric permittivity Poisson-Boltzmann model for biomolecular solvation studies
Authors: Li Hanlin , Lu Benzhuo
Published: July 2014

By considering the influence of volume exclusion on the solvent dielectric, a variable dielectric Poisson-Boltzmann (VDPB) model is explored for molecular solvation studies by using a dielectric as an explicit function of ionic sizes and concentrations. A finite element method is adopted and an iterative strategy is introduced to numerically solve the VDPB equation. According to our computations, the current dielectric model can result in considerable differences compared with the traditional Poisson-Boltzmann (PB) solutions, especially for those systems with highly charged biomolecule and/or under high salt concentration condition. The model to certain extent captures the fact of dielectric decrement of electrolyte solutions, which is especially remarkable in the vicinity of molecules. Counter-ion concentration very near the molecular surface in VDPB calculation is found higher than that in PB. The new dielectric model may also influence the charge compensation behavior near biomolecular surface. For a spherical cavity solvated in a concentrated ionic solution, charge inversion is observed in VDPB, which does not occur with the traditional PB model. Besides, the solvation energy predicted by VDPB will always be greater than that by PB. Moreover, differing from PB, the VDPB also allows non-monotonous dependencies of solvation energy on ionic strength.
All optical method for investigation of spin and charge transport in semiconductors: Combination of spatially and time-resolved luminescence
Authors: Cadiz F. , Barate P. , Paget D. , Grebenkov D. , Korb J. P. , Rowe A. C. H. , Amand T. , Arscott S. , Peytavit E.
Published: July 2014

A new approach is demonstrated for investigating charge and spin diffusion as well as surface and bulk recombination in unpassivated doped semiconductors. This approach consists in using two complementary, conceptually related, techniques, which are time-resolved photoluminescence (TRPL) and spatially resolved microluminescence (μPL) and is applied here to p+ GaAs. Analysis of the sole TRPL signal is limited by the finite risetime. On the other hand, it is shown that joint TRPL and μPL can be used to determine the diffusion constant, the bulk recombination time, and the spin relaxation time. As an illustration, the temperature variation of these quantities is investigated for p+ GaAs.
Thermoelectric and transport properties of sintered n-type K8Ba16Ga40Sn96 with type-II clathrate structure
Authors: Koda Shota , Kishimoto Kengo , Akai Koji , Asada Hironori , Koyanagi Tsuyoshi
Published: July 2014

This clathrate had a maximum dimensionless figure-of-merit, ZT, of 0.93 at 637 K, which was slightly higher than that of 0.83 for the sintered type-VIII clathrate Ba8Ga16Sn30. We investigated the high-temperature thermoelectric properties, transport properties, electronic structures, and thermal stabilities of the clathrates. The type-II clathrate was found to be superior to the type-VIII clathrate as a thermoelectric material; it had a high thermal stability and melting point, 859 K, high mobility, 141 cm2V−1s−1 at 300 K, because of its low inertial mass, and low high-temperature lattice thermal conductivity, approximately 4 mW cm−1K−1, resulting from a larger unit cell and weaker bipolar thermal conduction. We discuss these properties in terms of the electronic structure and the differences between the two types of clathrate.
Near-infrared quantum-cutting luminescence and energy transfer properties of Ca3(PO4)2:Tm3+,Ce3+ phosphors
Authors: Dong S. L. , Lin H. H. , Yu T. , Zhang Q. Y.
Published: July 2014

The phosphors Ca3(PO4)2:Tm3+ by co-doping Ce3+ have been synthesized by conventional high-temperature solid-state reaction method. Their spectroscopic properties in the UV-VIS-NIR range have been investigated. The first 5d crystal field level location and stokes shift have been determined from the UV excitation and emission spectra of Ca3(PO4)2:Ce3+. The three-photon NIR quantum-cutting luminescence of Tm3+ assigned to the electronic transitions of 1G4→3H4, 3H4→3F4 and 3F4→3H6 is observed, whether in Ca3(PO4)2:Tm3+ or Ca3(PO4)2:Tm3+,Ce3+. The energy transfer from Ce3+ to Tm3+ takes place with energy-transfer efficiency up to 34.5% for the Ca3(PO4)2:Tm3+,Ce3+. A cross relaxation scheme using the 5d states of Ce3+ and f-f transition of Tm3+ is proposed. The mechanism is revealed from energy level and decay measurements. The results show that the broadband absorption of Ce3+ sensitizer not only extends the spectrum conversion in UV region but also greatly enhances the photoluminescence intensities of the three-photon quantum cutting luminescence of Tm3+ doped Ca3(PO4)2.
Nanocrystalline SiC formed by annealing of a-SiC:H on Si substrates: A study of dopant interdiffusion
Authors: Schnabel Manuel , Weiss Charlotte , Löper Philipp , Canino Mariaconcetta , Summonte Caterina , Wilshaw Peter R. , Janz Stefan
Published: July 2014

Nanocrystalline silicon carbide (nc-SiC) is an interesting material for electronics applications, both in its own right and as a host matrix for silicon quantum dots. When synthesized by annealing of a-SiC:H on Si substrates, interdiffusion of dopants occurs if either the a-SiC:H or the Si substrate is doped. Annealing a-SiC:H on highly boron-doped substrates at 1100 °C leads to a fairly homogeneous doping level of ≥4 × 1019 cm−3 throughout the nc-SiC film. An unexpected anomaly in secondary ion mass spectroscopy quantification is observed and a method to circumvent it is shown. The nanostructure of the nc-SiC is only weakly affected as most of the diffusion occurs after the onset of crystallization. Annealing of doped a-SiC:H on Si substrates at 1100 °C leads to strong free carrier absorption at infrared wavelengths. This is demonstrated to originate from dopants that have diffused from the a-SiC:H to the Si substrate, and a method is developed to extract from it the doping profile in the Si substrate. The detection limit of this method is estimated to be ≤6 × 1013 cm−2. Doping levels of (0.5–3.5) × 1019 cm−3 are induced at the Si substrate surface by both boron and phosphorus-doped a–SiC:H. When the Si substrate is doped opposite to the a-SiC:H p–n junctions are induced at a depth of 0.9–1.4 μm within the Si substrate for substrate resistivities of 1–10 Ω cm. Implications for different solar cell architectures are discussed. Dopant diffusion can be strongly reduced by lowering the annealing temperature to 1000 °C, albeit at the expense of reduced crystallinity.
Epitaxial polymorphism of La2O3 on Si(111) studied by in situ x-ray diffraction
Authors: Proessdorf A. , Niehle M. , Hanke M. , Grosse F. , Kaganer V. , Bierwagen O. , Trampert A.
Published: July 2014

The phase formation of La2O3 epitaxial films during growth on Si(111) is investigated by synchrotron-based in situ grazing incidence x-ray diffraction and high resolution transmission electron microscopy. We find that first a 2–4 nm thick cubic bixbyite La2O3 layer grows at the interface to Si(111) substrate, followed by a hexagonal La2O3 film. Hence, to keep a cubic on cubic heteroepitaxy and to achieve high quality epitaxial nanostructures or multi-layers, the thickness of the interfacial La2O3 layer has to be restricted to 2 nm. The larger formation energy of the cubic phase can only partially be compensated by the biaxial strain in the epitaxial film based on density functional perturbation theory. Hence, the stabilization of the cubic phase is not due to bulk strain but could be related to a lower surface or interface free energy, or to kinetic effects.
Dynamic grazing incidence fast atom diffraction during molecular beam epitaxial growth of GaAs
Authors: Atkinson P. , Eddrief M. , Etgens V. H. , Khemliche H. , Debiossac M. , Momeni A. , Mulier M. , Lalmi B. , Roncin P.
Published: July 2014

A Grazing Incidence Fast Atom Diffraction (GIFAD) system has been mounted on a commercial molecular beam epitaxy chamber and used to monitor GaAs growth in real-time. In contrast to the conventionally used Reflection High Energy Electron Diffraction, all the GIFAD diffraction orders oscillate in phase, with the change in intensity related to diffuse scattering at step edges. We show that the scattered intensity integrated over the Laue circle is a robust method to monitor the periodic change in surface roughness during layer-by-layer growth, with oscillation phase and amplitude independent of incidence angle and crystal orientation. When there is a change in surface reconstruction at the start of growth, GIFAD intensity oscillations show that there is a corresponding delay in the onset of layer-by-layer growth. In addition, changes in the relative intensity of different diffraction orders have been observed during growth showing that GIFAD has the potential to provide insight into the preferential adatom attachment sites on the surface reconstruction during growth.
Classical trajectory Monte Carlo simulations of particle confinement using dual levitated coils
Authors: Lane R. A. , Ordonez C. A.
Published: July 2014

The particle confinement properties of plasma confinement systems that employ dual levitated magnetic coils are investigated using classical trajectory Monte Carlo simulations. Two model systems are examined. In one, two identical current-carrying loops are coaxial and separated axially. In the second, two concentric and coplanar loops have different radii and carry equal currents. In both systems, a magnetic null circle is present between the current loops. Simulations are carried out for seven current loop separations for each system and at numerous values of magnetic field strength. Particle confinement is investigated at three locations between the loops at different distances from the magnetic null circle. Each simulated particle that did not escape the system exhibited one of four modes of confinement. Reduced results are given for both systems as the lowest magnetic field strength that exhibits complete confinement of all simulated particles for a particular loop separation.
A metallography and x-ray tomography study of spall damage in ultrapure Al
Authors: Qi M. L. , Bie B. X. , Zhao F. P. , Hu C. M. , Fan D. , Ran X. X. , Xiao X. H. , Yang W. G. , Li P. , Luo S. N.
Published: July 2014

We characterize spall damage in shock-recovered ultrapure Al with metallography and x-ray tomography. The measured damage profiles in ultrapure Al induced by planar impact at different shock strengths, can be described with a Gaussian function, and showed dependence on shock strengths. Optical metallography is reasonably accurate for damage profile measurements, and agrees within 10–25% with x-ray tomography. Full tomography analysis showed that void size distributions followed a power law with an exponent of γ = 1.5 ± 2.0, which is likely due to void nucleation and growth, and the exponent is considerably smaller than the predictions from percolation models.
Anomalous magnetic behavior at the graphene/Co interface
Authors: Mandal Sumit , Saha Shyamal K.
Published: July 2014

An intensive theoretical study on the interaction between graphene and transition metal atom has been carried out; however, its experimental verification is still lacking. To explore the theoretical prediction of antiferromagnetic coupling due to charge transfer between graphene and cobalt, epitaxial layer of cobalt is grown on graphene surface. Predicted antiferromagnetic interaction with Neel temperature (TN ∼ 32 K) which anomalously shifts to higher temperature (34 K) and becomes more prominent under application of magnetic field of 1 T is reported. Lowering of magnetoresistance as a consequence of this antiferromagnetic coupling at the interface is also observed.
Time resolved photoluminescence spectroscopy of narrow gap Hg1−xCdxTe/CdyHg1−yTe quantum well heterostructures
Authors: Morozov S. V. , Rumyantsev V. V. , Antonov A. V. , Kadykov A. M. , Maremyanin K. V. , Kudryavtsev K. E. , Mikhailov N. N. , Dvoretskii S. A. , Gavrilenko V. I.
Published: July 2014

Photoluminescence (PL) spectra and kinetics of narrow gap Hg1−xCdxTe/CdyHg1−yTe quantum well (QW) heterostructures grown by molecular beam epitaxy technique are studied. Interband PL spectra are observed from 18 K up to the room temperature. Time resolved studies reveal an additional PL line with slow kinetics (7 μs at 18 K) related to deep defect states in barrier layers. These states act as traps counteracting carrier injection into QWs. The decay time of PL signal from QW layers is about 5 μs showing that gain can be achieved at wavelengths 10–20 μm by placing such QWs in HgCdTe structures with waveguides.
Potential pharmacological chaperones targeting cancer-associated MCL-1 and Parkinson disease-associated α-synuclein
Authors: Oh Misook , Lee Ji Hoon , Wang Wei , Lee Hui Sun , Lee Woo Sirl , Burlak Christopher , Im Wonpil , Hoang Quyen Q. , Lim Hyun-Suk
Published: July 2014

Significance

Many complex diseases are caused by aberrant protein–protein interactions or protein misfolding, which present immense challenges for drug discovery. Here, we present the design, synthesis, and usage of a diverse library of potential pharmacological chaperones that could interfere with undesirable protein–protein interactions and prevent aggregation of misfolded proteins.
Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein
Authors: Amprazi Maria , Kotsifaki Dina , Providaki Mary , Kapetaniou Evangelia G. , Fellas Georgios , Kyriazidis Ioannis , Pérez Javier , Kokkinidis Michael
Published: July 2014

Significance

The ColE1 Rop protein is a paradigm of a canonical 4-α-helical bundle and an attractive model system for protein-folding studies. This work characterizes Rop and several of its loop mutants, focusing on their extreme structural plasticity. Plasticity gives rise to new helical bundle topologies and properties and establishes a variety of native-like and molten globule states that depend on nonnative disulfide bonds. This plasticity and the capacity of the Rop mutants to assemble a large variety of different hydrophobic cores add Rop to the list of proteins that are suitable for the engineering of bio-inspired materials. Additionally, our findings have implications for the theory of protein folding and for understanding certain pathogenic mechanisms and diseases.
A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion
Authors: Sampson Timothy R. , Napier Brooke A. , Schroeder Max R. , Louwen Rogier , Zhao Jinshi , Chin Chui-Yoke , Ratner Hannah K. , Llewellyn Anna C. , Jones Crystal L. , Laroui Hamed , Merlin Didier , Zhou Pei , Endtz Hubert P. , Weiss David S.
Published: July 2014

Significance

Increasing the integrity of the bacterial envelope is necessary to allow the successful survival of bacterial pathogens within the host and allow them to counteract damage caused by membrane-targeting antibiotics. We demonstrate that components of a clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) system, a prokaryotic defense against viruses and foreign nucleic acid, act to regulate the permeability of the bacterial envelope, ultimately providing these cells with the capability to resist membrane damage caused by antibiotics. This regulation further allows bacteria to resist detection by multiple host receptors to promote virulence. Overall, this study demonstrates the breadth of function of CRISPR-Cas systems in regulation, antibiotic resistance, innate immune evasion, and virulence.
Arrhythmias, elicited by catecholamines and serotonin, vanish in human chronic atrial fibrillation
Authors: Christ Torsten , Rozmaritsa Nadiia , Engel Andreas , Berk Emanuel , Knaut Michael , Metzner Katharina , Canteras Manuel , Ravens Ursula , Kaumann Alberto
Published: July 2014

Significance

Catecholamines and serotonin elicit arrhythmias in atrial trabeculae and arrhythmogenic diastolic Ca
2+
releases in myocytes from patients with normal sinoatrial rhythm (SR). Arrhythmic events are greatly blunted in the myocardium of patients with chronic atrial fibrillation (AF). The mediation by cyclic AMP-dependent protein kinase of L-type Ca
2+
-current (I
Ca,L
) responses to agonists, lusitropy, and protein phosphorylation are preserved in AF. The vanishing of agonist-evoked arrhythmias in AF is associated with the disappearance of an I
Ca,L
response, facilitated by Ca
2+
/calmodulin-dependent kinase II (CaMKII), in myocytes from patients with SR, and decreased phosphorylation of phospholamban, but not ryanodine, by this enzyme. The disappearance of arrhythmias and associated reduction of CaMKII functions questions the use of CaMKII inhibitors in AF, as has been proposed by other groups.
Object grouping based on real-world regularities facilitates perception by reducing competitive interactions in visual cortex
Authors: Kaiser Daniel , Stein Timo , Peelen Marius V.
Published: July 2014

Significance

A major challenge for visual perception is to select behaviorally relevant objects from scenes containing a large number of distracting objects that compete for limited processing resources. Here, we show that such competitive interactions in human visual cortex are reduced when distracters are positioned in commonly experienced configurations (e.g., a lamp above a dining table), leading to improved detection of target objects. This indicates that the visual system can exploit real-world regularities to group objects that typically co-occur; a plate flanked by a fork and a knife can be grouped into a dining set. This interobject grouping effectively reduces the number of competing objects and thus can facilitate the selection of targets in cluttered, but regular environments.
On the evolution of hoarding, risk-taking, and wealth distribution in nonhuman and human populations
Authors: Bergstrom Theodore C.
Published: July 2014

This paper applies the theory of the evolution of risk-taking in the presence of idiosyncratic and environmental risks to the example of food hoarding by animals and explores implications of the resulting theory for human attitudes toward risk.
Bargaining and fairness
Authors: Binmore Kenneth
Published: July 2014

The idea that human morality might be the product of evolution is not popular. The reason is partly that the moral principles that actually govern our day-to-day behavior have been idealized in a way that makes a natural origin seem impossible. This paper puts the case for a more down-to-earth assessment of human morality by arguing that the evolution of our sense of fairness can be traced to the practicalities of food-sharing. When animals share food, they can be seen as enjoying the fruits of an implicit bargain to ensure each other against hunger. The implications of this observation are explored using the tools of game theory. The arguments lead to a structure for fair bargains that closely resembles the structure proposed by John Rawls, the leading moral philosopher of the last century.
Culture-dependent strategies in coordination games
Authors: Jackson Matthew O. , Xing Yiqing
Published: July 2014

We examine different populations’ play in coordination games in online experiments with over 1,000 study participants. Study participants played a two-player coordination game that had multiple equilibria: two equilibria with highly asymmetric payoffs and another equilibrium with symmetric payoffs but a slightly lower total payoff. Study participants were predominantly from India and the United States. Study participants residing in India played the strategies leading to asymmetric payoffs significantly more frequently than study participants residing in the United States who showed a greater play of the strategy leading to the symmetric payoffs. In addition, when prompted to play asymmetrically, the population from India responded even more significantly than those from the United States. Overall, study participants’ predictions of how others would play were more accurate when the other player was from their own populations, and they coordinated significantly more frequently and earned significantly higher payoffs when matched with other study participants from their own population than when matched across populations.
Spatial interactions and cooperation can change the speed of evolution of complex phenotypes
Authors: Komarova Natalia L.
Published: July 2014

Complex traits arise from the interactions among multiple gene products. In the case where the complex phenotype is separated from the wild type by a fitness valley or a fitness plateau, the generation of a complex phenotype may take a very long evolutionary time. Interestingly, the rate of evolution depends in nontrivial ways on various properties of the underlying stochastic process, such as the spatial organization of the population and social interactions among cells. Here we review some of our recent work that investigates these phenomena in asexual populations. The role of spatial constraints is quite complex: there are realistic cases where spatial constrains can accelerate or delay evolution, or even influence it in a nonmonotonic fashion, where evolution works fastest for intermediate-range constraints. Social interactions among cells can be studied in the context of the division-of-labor games. Under a range of circumstances, cooperation among cells can lead to a relatively fast creation of a complex phenotype as an emerging (distributed) property. If we further assume the presence of cheaters, we observe the emergence of a fully mutated population of cells possessing the complex phenotype. Applications of these ideas to cancer initiation and biofilm formation in bacteria are discussed.
Microspatial gene expression patterns in the Amazon River Plume
Authors: Satinsky Brandon M. , Crump Byron C. , Smith Christa B. , Sharma Shalabh , Zielinski Brian L. , Doherty Mary , Meng Jun , Sun Shulei , Medeiros Patricia M. , Paul John H. , Coles Victoria J. , Yager Patricia L. , Moran Mary Ann
Published: July 2014

Significance

The microbial community of the Amazon River Plume determines the fate of the world’s largest input of terrestrial carbon and nutrients to the ocean. By benchmarking with internal standards during sample collection, we determined that each liter of plume seawater contains 1 trillion genes and 50 billion transcripts from thousands of bacterial, archaeal, and eukaryotic taxa. Gene regulation by taxa inhabiting distinct microenvironments provides insights into micron-scale patterns of transformations in the marine carbon, nitrogen, phosphorus, and sulfur cycles in this globally important ecosystem.
Policy folklists and evolutionary theory
Authors: O’Neill Barry
Published: July 2014

Policy folklists present a set of alleged historical facts seen as relevant to some social issue. Although the validity of these folklists is dubious, leaders and writers circulate them in the media, variants arise, and the lists continue on, sometimes for decades. Folklists are repeated because their messages are appealing and their users are credible. Because folklists are on the record, we can examine their origins and changes. This report draws an analogy with evolutionary theory and suggests that biological mechanisms of self-repair, boundary maintenance, plasticity, speciation, and predation have significant interpretations for folklists, and clarify how the lists win the credence of otherwise skeptical people.
Specific collagen XVIII isoforms promote adipose tissue accrual via mechanisms determining adipocyte number and affect fat deposition
Authors: Aikio Mari , Elamaa Harri , Vicente David , Izzi Valerio , Kaur Inderjeet , Seppinen Lotta , Speedy Helen E. , Kaminska Dorota , Kuusisto Sanna , Sormunen Raija , Heljasvaara Ritva , Jones Emma L. , Muilu Mikko , Jauhiainen Matti , Pihlajamäki Jussi , Savolainen Markku J. , Shoulders Carol C. , Pihlajaniemi Taina
Published: July 2014

Significance

A previously unrecognized role is described for collagen XVIII—a ubiquitous, structurally complex basement membrane proteoglycan—in supporting preadipocyte differentiation and the maintenance of this differentiated state, and hence the size and lipid-clearing/storage functions of white adipose tissue depots. Specific lack of medium and long isoforms of this nonfibrillar collagen in mice led to reduced adiposity, ectopic deposition of fat in liver, and elevated very low-density lipoprotein-triglyceride levels. The finding of a previously unidentified extracellular mechanism contributing to control of adipogenesis is expected to promote understanding of the molecular and functional bases of human hyperlipidemic syndromes associated with fatty liver.
Genetic information transfer promotes cooperation in bacteria
Authors: Dimitriu Tatiana , Lotton Chantal , Bénard-Capelle Julien , Misevic Dusan , Brown Sam P. , Lindner Ariel B. , Taddei François
Published: July 2014

Significance

Bacteria often cooperate through the production of public goods that change their environment. These processes can affect human health by increasing virulence or antibiotic resistance. Public good production is costly, making cooperation susceptible to invasion by nonproducing “cheater” individuals. Bacteria also readily share genes, even among distinct species. Our experiments and models converge to show that when both cheating and cooperative genes are transferred, cooperators win against cheaters because transfer increases assortment among alleles, favoring cooperation. This can explain why genes for cooperation are often mobile, and suggests that, in addition to reducing antibiotic resistance spread, preventing gene mobility could reduce cooperative virulence.
Effects of explicit atmospheric convection at high CO
2
Authors: Arnold Nathan P. , Branson Mark , Burt Melissa A. , Abbot Dorian S. , Kuang Zhiming , Randall David A. , Tziperman Eli
Published: July 2014

Significance

The representation of clouds and convection has an enormous impact on simulation of the climate system. This study addresses concerns that conventional parameterizations may bias the response of climate models to increased greenhouse gases. The broadly similar response of two models with parameterized and nonparameterized convection and clouds suggests that state-of-the-art predictions, based on parameterized climate models, may not necessarily be strongly biased in either direction (too strong or too weak warming). At the same time, large differences in simulated tropical variability and Arctic sea ice area suggest that improvement in convection and cloud representations remains essential.
Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium
Gemmata obscuriglobus
Authors: Gottshall Ekaterina Y. , Seebart Corrine , Gatlin Jesse C. , Ward Naomi L.
Published: July 2014

Significance

Eukaryotic (plant and animal) cells possess a nuclear membrane that separates the two stages of gene expression (transcription and translation), whereas prokaryotic (bacteria and archaea) cells lack the nuclear membrane barrier to colocated transcription and translation. However, cells of the bacterium
Gemmata obscuriglobus
possess extensive intracellular membranes, resulting in superficially eukaryote-like cellular complexity. We have found that a substantial amount of
G. obscuriglobus
translation is uncoupled from transcription, broadening our understanding of the spatial organization of bacterial gene expression, which currently is based entirely on a handful of model species. This broader understanding provides a useful background for consideration of the evolutionary development of eukaryotic cellular complexity and how it led to decoupled processes of gene expression in eukaryotes.
Dual inhibition of cyclooxygenase-2 and soluble epoxide hydrolase synergistically suppresses primary tumor growth and metastasis
Authors: Zhang Guodong , Panigrahy Dipak , Hwang Sung Hee , Yang Jun , Mahakian Lisa M. , Wettersten Hiromi I. , Liu Jun-Yan , Wang Yanru , Ingham Elizabeth S. , Tam Sarah , Kieran Mark W. , Weiss Robert H. , Ferrara Katherine W. , Hammock Bruce D.
Published: July 2014

Significance

Our study suggests that cyclooxygenase (COX)-2 and soluble epoxide hydrolase (sEH) pathways have potent synergistic antiangiogenic and anticancer activity. Dual pharmacological inhibition of COX-2 and sEH pathways may be useful in treating cancer with minimal toxicity associated with COX-2 inhibition.
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling
Authors: Wawer Mathias J. , Li Kejie , Gustafsdottir Sigrun M. , Ljosa Vebjorn , Bodycombe Nicole E. , Marton Melissa A. , Sokolnicki Katherine L. , Bray Mark-Anthony , Kemp Melissa M. , Winchester Ellen , Taylor Bradley , Grant George B. , Hon C. Suk-Yee , Duvall Jeremy R. , Wilson J. Anthony , Bittker Joshua A. , Dančík Vlado , Narayan Rajiv , Subramanian Aravind , Winckler Wendy , Golub Todd R. , Carpenter Anne E. , Shamji Alykhan F. , Schreiber Stuart L. , Clemons Paul A.
Published: July 2014

Significance

A large compound screening collection is usually constructed to be tested in many distinct assays, each one designed to find modulators of a different biological process. However, it is generally not known to what extent a compound collection actually contains molecules with distinct biological effects (or even any effect) until it has been tested for a couple of years. This study explores a cost-effective way of rapidly assessing the biological performance diversity of a screening collection in a single assay. By simultaneously measuring a large number of cellular features, unbiased profiling assays can distinguish compound effects with high resolution and thus measure performance diversity. We show that this approach could be used as a filtering strategy to build effective screening collections.
Chapter 1.1 A Multi-Dimensional analysis of regional variation in American English
Authors: Grieve Jack
Published: July 2014

This paper analyzes regional linguistic variation in a corpus of letters to the editor from across the United States. However, unlike most regional dialect studies, which analyze linguistic alternation variables, this study analyzes the relative frequency of parts-of-speech using a Multi-Dimensional approach, which allows for patterns of regional functional linguistic variation to be identified in this corpus. In particular, this analysis identifies three basic patterns of regional functional linguistic variation in American letters to the editor: letters from the East tend to exhibit an elaborate style, letters from the Central States tend to exhibit a narrative style, and letters from South tend to exhibit an opinionated style, when compared to letters originating from the rest of the United States.
Chapter 3.1 A Multi-Dimensional analysis of essay writing
Authors: Crossley Scott A. , Allen Laura K. , McNamara Danielle S.
Published: July 2014

This study applied the Multi-Dimensional analysis used by Biber (1988) to examine the functional parameters of essays. Co-occurrence patterns were identified within an essay corpus (n = 1529) using linguistic indices provided by Coh-Metrix. These patterns were used to identify essay groups that shared features based upon situational parameters. Results revealed that the linguistic features reliably co-occurred according to the parameters. Namely, four dimensions were interpreted and associated with essay quality, prompt, and grade level. Confirmatory analyses revealed that the dimensions reliably distinguished among the parameters. Results provide insight into the situational parameters that affect writing, and the extent to which essays vary among and between themselves. The results have important implications for composition pedagogy, writing assessment, and writing theory.
Chapter 3.2 A Multi-Dimensional analysis of advanced written L2 Spanish
Authors: Asención-Delaney Yuly
Published: July 2014

Written academic discourse in Spanish as a second language has been extensively described from a textual linguistic perspective. However, second-language researchers have not embraced corpus methodologies to analyze register variation in learner corpora. This study adds to our understanding of the types of discourse that advanced Spanish learners produce in academic writing through a Multi-Dimensional analysis of a corpus of L2 Spanish writing (998,686 words) from a graduate program for teaching Spanish. Results uncovered six significant factors that accounted for 56.76 percent of the variation. Dimension 1, the principal component, clustered 47 co-occurring features in expository discourse related to the instructional setting and to literary analysis. The remaining five dimensions were discursive variations of expository prose found in that particular context.
An interpersonal study of The Leading Hotels of the World. A systemic-functional social-semiotic approach
Authors: Moya-Guijarro Aresenio Jesús , González Lanza José María
Published: July 2014

Within the frameworks of Halliday’s SFL and Kress and Van Leeuwen’s Visual
Social Semiotics, the main aim of this chapter is to analyse how the verbal and
visual modes of ten tourist brochures, taken from The Leading Hotels of the
World guide (2009), are co-deployed to construct interpersonal meaning. The
use of declarative mood structures, the scarce presence of imperative clauses
and the lack of interrogative clauses demonstrate that the verbal component
accompanying the photographs does not encourage much interaction. However,
the middle-shots and essentially the medium angles utilised are evidence of
the engagement created between the visual readers and what is displayed in the
photographs. This analysis shows that words and images reinforce each other
to highlight the elitist characteristics of the facilities and services offered to the
potential clients.