bluuebunny/crossref_metadata_2025 huggingface dataset:
A Paradigmatic Analysis of Digital Application Marketplaces
Authors: Ghazawneh Ahmad , Henfridsson Ola
Published: May 2015

This paper offers a paradigmatic analysis of digital application marketplaces for advancing information systems research on digital platforms and ecosystems. We refer to the notion of digital application marketplace, colloquially called ‘appstores,’ as a platform component that offers a venue for exchanging applications between developers and end users belonging to a single or multiple ecosystems. Such marketplaces exhibit diversity in features and assumptions, and we propose that examining this diversity, and its ideal types, will help us to further understand the relationship between application marketplaces, platforms, and platform ecosystems. To this end, we generate a typology that distinguishes four kinds of digital application marketplaces: closed, censored, focused, and open marketplaces. The paper also offers implications for actors wishing to make informed decisions about their relationship to a particular digital application marketplace.
Thermometry and thermal management of carbon nanotube circuits
Authors: Mayle Scott , Gupta Tanuj , Davis Sam , Chandrasekhar Venkat , Shafraniuk Serhii
Published: May 2015

Monitoring of the intrinsic temperature and the thermal management is discussed for the carbon nanotube nano-circuits. The experimental results concerning fabricating and testing of a thermometer able to monitor the intrinsic temperature on nanoscale are reported. We also suggest a model which describes a bi-metal multilayer system able to filter the heat flow, based on separating the electron and phonon components one from another. The bi-metal multilayer structure minimizes the phonon component of the heat flow, while retaining the electronic part. The method allows one to improve the overall performance of the electronic nano-circuits due to minimizing the energy dissipation.
Gas-phase study on uridine: Conformation and X-ray photofragmentation
Authors: Itälä Eero , Kooser Kuno , Rachlew Elisabeth , Levola Helena , Ha Dang Trinh , Kukk Edwin
Published: May 2015

Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.
Defect topologies in chiral liquid crystals confined to mesoscopic channels
Authors: Schlotthauer Sergej , Skutnik Robert A. , Stieger Tillmann , Schoen Martin
Published: May 2015

We present Monte Carlo simulations in the grand canonical and canonical ensembles of a chiral liquid crystal confined to mesochannels of variable sizes and geometries. The mesochannels are taken to be quasi-infinite in one dimension but finite in the two other directions. Under thermodynamic conditions chosen and for a selected value of the chirality coupling constant, the bulk liquid crystal exhibits structural characteristics of a blue phase II. This is established through the tetrahedral symmetry of disclination lines and the characteristic simple-cubic arrangement of double-twist helices formed by the liquid-crystal molecules along all three axes of a Cartesian coordinate system. If the blue phase II is then exposed to confinement, the interplay between its helical structure, various anchoring conditions at the walls of the mesochannels, and the shape of the mesochannels gives rise to a broad variety of novel, qualitative disclination-line structures that are reported here for the first time.
Structure and morphology of a triple point
Authors: Hekiri H. , Emanuel G.
Published: May 2015

A comprehensive analytical/numerical treatment of triple points is based on over 5 × 103 parametric solutions. The approach is applicable to triple points in steady or unsteady, three-dimensional flow with a variable freestream. The analysis is for a perfect gas with three different ratios of specific heat values and an upstream Mach number that ranges from an onset value to 10. The structure and morphology of the solution manifold is extensively discussed. This includes solution type, solution overlap, double, triple, and split solutions, shock wave and slipstream angular orientations, the strength of the shocks, etc. Both the reflected and Mach stem shocks can be normal shocks. The occurrence, conditions, and parametric results for these normal shocks are provided.
Quantum confinement of excitons in wurtzite InP nanowires
Authors: Pemasiri K. , Jackson H. E. , Smith L. M. , Wong B. M. , Paiman S. , Gao Q. , Tan H. H. , Jagadish C.
Published: May 2015

Exciton resonances are observed in photocurrent spectra of 80 nm wurtzite InP nanowire devices at low temperatures, which correspond to transitions between the A, B, and C valence bands and the lower conduction band. Photocurrent spectra for 30 nm WZ nanowires exhibit shifts of the exciton resonances to higher energy, which are consistent with finite element calculations of wavefunctions of the confined electrons and holes for the various bands.
Estimation of viscous dissipation in nanodroplet impact and spreading
Authors: Li Xin-Hao , Zhang Xiang-Xiong , Chen Min
Published: May 2015

The developments in nanocoating and nanospray technology have resulted in the increasing importance of the impact of micro-/nanoscale liquid droplets on solid surface. In this paper, the impact of a nanodroplet on a flat solid surface is examined using molecular dynamics simulations. The impact velocity ranges from 58 m/s to 1044 m/s, in accordance with the Weber number ranging from 0.62 to 200.02 and the Reynolds number ranging from 0.89 to 16.14. The obtained maximum spreading factors are compared with previous models in the literature. The predicted results from the previous models largely deviate from our simulation results, with mean relative errors up to 58.12%. The estimated viscous dissipation is refined to present a modified theoretical model, which reduces the mean relative error to 15.12% in predicting the maximum spreading factor for cases of nanodroplet impact.
Influence of vortex dynamics and structure on turbulence statistics at large scales
Authors: Yoshimatsu Katsunori , Anayama Koujiro , Kaneda Yukio
Published: May 2015

The question whether the vortex dynamics and structure at small scales have significant influence on the statistics at large scales is addressed on the basis of quantitative comparison of two turbulent fields. One is a reference field generated by direct numerical simulation of turbulence of an incompressible fluid obeying the Navier-Stokes (NS) equation in a periodic box. The other is an artificial field in which the coherent vortical structures at small scales (∼η) that could be formed by the NS dynamics in the reference field are destroyed by an artificial computational operation, where η is the Kolmogorov micro-length scale. The comparison of the two fields suggests that the statistics at larger scale (≫η) are not sensitive to the exact vortex dynamics and structure, at least in the case studied here.
Model reduction for networks of coupled oscillators
Authors: Gottwald Georg A.
Published: May 2015

We present a collective coordinate approach to describe coupled phase oscillators. We apply the method to study synchronisation in a Kuramoto model. In our approach, an N-dimensional Kuramoto model is reduced to an n-dimensional ordinary differential equation with n≪N, constituting an immense reduction in complexity. The onset of both local and global synchronisation is reproduced to good numerical accuracy, and we are able to describe both soft and hard transitions. By introducing two collective coordinates, the approach is able to describe the interaction of two partially synchronised clusters in the case of bimodally distributed native frequencies. Furthermore, our approach allows us to accurately describe finite size scalings of the critical coupling strength. We corroborate our analytical results by comparing with numerical simulations of the Kuramoto model with all-to-all coupling networks for several distributions of the native frequencies.
Wave propagation in reconfigurable magneto-elastic kagome lattice structures
Authors: Schaeffer Marshall , Ruzzene Massimo
Published: May 2015

The paper discusses the wave propagation characteristics of two-dimensional magneto-elastic kagome lattices. Mechanical instabilities caused by magnetic interactions are exploited in combination with particle contact to bring about changes in the topology and stiffness of the lattices. The analysis uses a lumped mass system of particles, which interact through axial and torsional elastic forces as well as magnetic forces. The propagation of in-plane waves is predicted by applying Bloch theorem to lattice unit cells with linearized interactions. Elastic wave dispersion in these lattices before and after topological changes is compared, and large differences are highlighted.
Spatially and momentum resolved energy electron loss spectra from an ultra-thin PrNiO3 layer
Authors: Kinyanjui M. K. , Benner G. , Pavia G. , Boucher F. , Habermeier H.-U. , Keimer B. , Kaiser U.
Published: May 2015

We present an experimental approach which allows for the acquisition of spectra from ultra-thin films at high spatial, momentum, and energy resolutions. Spatially and momentum (q) resolved electron energy loss spectra have been obtained from a 12 nm ultra-thin PrNiO3 layer using a nano-beam electron diffraction based approach which enabled the acquisition of momentum resolved spectra from individual, differently oriented nano-domains and at different positions of the PrNiO3 thin layer. The spatial and wavelength dependence of the spectral excitations are obtained and characterized after the analysis of the experimental spectra using calculated dielectric and energy loss functions. The presented approach makes a contribution towards obtaining momentum-resolved spectra from nanostructures, thin film, heterostructures, surfaces, and interfaces.
Nano-rheology measurements reveal that the hydration layer of enzymes partially controls conformational dynamics
Authors: Alavi Zahra , Ariyaratne Amila , Zocchi Giovanni
Published: May 2015

For a typical (20 kD, 4 nm size) monomeric enzyme, more than 50% of the residues are at the surface. The mechanics of these soft, heterogeneous nanoparticles was recently shown to be viscoelastic. Here, we explore the contribution of the enzyme's surface to the mechanics of the molecule. Nano-rheology provides sub-Å resolution measurements of the reversible deformation of the enzyme subject to an oscillatory mechanical stress. We perturb the surface of the enzyme by adding small amounts of DMSO (dimethyl sulfoxide), believed to affect ordering of the enzyme–water interface. We observe a dramatic though reversible change in the mechanics of the enzyme, which becomes more viscous. On the other hand, the catalytic speed is unaffected, while at higher DMSO concentrations (>1 %) it even increases.
Si/ZnO nanorods/Ag/AZO structures as promising photovoltaic plasmonic cells
Authors: Placzek-Popko E. , Gwozdz K. , Gumienny Z. , Zielony E. , Pietruszka R. , Witkowski B. S. , Wachnicki Ł. , Gieraltowska S. , Godlewski M. , Jacak W. , Chang Liann-Be
Published: May 2015

The test structures for photovoltaic (PV) applications based on zinc oxide nanorods (NRs) that were grown using a low-temperature hydrothermal method on p-type silicon substrates (100) covered with Ag nanoparticles (NPs) were studied. The NPs of three different diameters, i.e., 5–10 nm, 20-30 nm, and 50–60 nm, were deposited using a sputtering method. The morphology and crystallinity of the structures were confirmed by scanning electron microscopy and Raman spectroscopy. It was found that the nanorods have a hexagonal wurtzite structure. An analysis of the Raman and photoluminescence spectra permitted the identification of the surface modes at 476 cm−1 and 561 cm−1. The presence of these modes is evidence of nanorods oriented along the wurtzite c-axis. The NRs with Ag NPs were covered with a ZnO:Al (AZO) layer that was grown using the low-temperature atomic layer deposition technique. The AZO layer served as a transparent ohmic contact to the ZnO nanorods. The applicability of the AZO layer for this purpose and the influence of the Ag nanoparticles on the effectiveness of light acquisition by such prepared PV cells were checked by reflectance and transmittance measurements of the AZO/glass and AZO/NPs/glass reference structures. Based on these studies, the high-energy transmittance edge was assigned to the ZnO energy gap, although it is blueshifted with respect to the bulk ZnO energy gap because of Al doping. It was also shown that the most optimal PV performance is obtained from a structure containing Ag nanoparticles with a diameter of 20–30 nm. This result is confirmed by the current-voltage measurements performed with 1-sun illumination. The structures show a plasmonic effect within the short wavelength range: the PV response for the structure with Ag nanoparticles is twice that of the structure without the nanoparticles. However, the influence of the Ag nanoparticle diameters on the plasmonic effect is ambiguous.
Extreme stress gradient effects on microstructural fatigue crack propagation rates in Ni microbeams
Authors: Sadeghi-Tohidi F. , Pierron O. N.
Published: May 2015

The fatigue crack propagation behavior of microstructurally small cracks growing under extreme stress gradients was investigated in Ni microbeams under fully reversed cyclic loading. A technique to calculate the crack growth rates in microbeams with two different normalized stress gradients (17% and 50% μm−1) is developed and validated. Decreasing crack propagation rates are observed over the first 2 μm, and the rates are more than 1 order of magnitude slower for the devices with 50% μm−1 stress gradients. This fundamental knowledge is critical to predict the fatigue reliability of advanced metallic microcomponents under bending such as in microelectromechanical systems or flexible/stretchable electronics.
Defect evaluation in InGaAs field effect transistors with HfO2 or Al2O3 dielectric
Authors: Roll G. , Mo J. , Lind E. , Johansson S. , Wernersson L.-E.
Published: May 2015

The performance of InGaAs metal oxide semiconductor field effect transistors with Al2O3 or HfO2 as gate oxide is evaluated and compared. The Al2O3 transistors show the lowest subthreshold slope and mid gap Dit, however, the HfO2 transistors reach a higher maximum transconductance (gmax) due to the higher oxide capacitance. Both high-κ dielectrics show a gm-frequency dispersion due to tunneling into border traps with a negligible activation energy as determined from temperature dependent measurements. The total amount of trapped charge at border traps is lower in the HfO2 devices. Scaling the HfO2 thickness further reduces the gm-frequency dispersion, possibly due to detrapping to the gate electrode.
Aromatic poly(arylene ether urea) with high dipole moment for high thermal stability and high energy density capacitors
Authors: Cheng Zhaoxi , Lin Minren , Wu Shan , Thakur Yash , Zhou Yue , Jeong Dae-Yong , Shen Qundong , Zhang Q. M.
Published: May 2015

Developing dielectric polymers with higher dielectric constant without sacrificing loss and thermal stability is of great importance for next generation of high energy density capacitors. We show here that by replacing the CH2 group in the aromatic polyurea (ArPU) with the polar ether group, thus raising the dipole moment of the molecular unit, poly(arylene ether urea) (PEEU) shows an increased dielectric constant of 4.7, compared with 4.2 of ArPU. Moreover, PEEU maintains the low dielectric loss and is thermally stable up to 250 °C. As a result, the polymer delivers 13 J/cm3 discharged energy density at room temperature and 9 J/cm3 at 120 °C. The high quality films perform well in terms of both breakdown strength (at 700 MV/m at room temperature) and leakage current from room temperature to elevated temperature. At 120 °C, the breakdown strength is 600 MV/m and the conductivity is 1.58 × 10−14 S/cm measured under 100 MV/m.
Mechanochemical approaches to employ silicon as a lithium-ion battery anode
Authors: Shimoi Norihiro , Qiwu Zhang , Bahena-Garrido Sharon , Tanaka Yasumitsu
Published: May 2015

Silicon is essential as an active material in lithium-ion batteries because it provides both high-charge and optimal cycle characteristics. The authors attempted to realize a composite by a simple mechanochemical grinding approach of individual silicon (Si) particles and copper monoxide (CuO) particles to serve as an active material in the anode and optimize the charge-discharge characteristics of a lithium-ion battery. The composite with Si and CuO allowed for a homogenous dispersion with nano-scale Si grains, nano-scale copper-silicon alloy grains and silicon monoxide oxidized the oxide from CuO. The authors successfully achieved the synthesis of an active composite unites the structural features of an active material based on silicon composite as an anode in Li-ion battery with high capacity and cyclic reversible charge properties of 3256 mAh g−1 after 200 cycles.
Multilayer-graphene-based amplifier of surface acoustic waves
Authors: Yurchenko Stanislav O. , Komarov Kirill A. , Pustovoit Vladislav I.
Published: May 2015

The amplification of surface acoustic waves (SAWs) by a multilayer graphene (MLG)-based amplifier is studied. The conductivity of massless carriers (electrons or holes) in graphene in an external drift electric field is calculated using Boltzmann’s equation. At some carrier drift velocities, the real part of the variable conductivity becomes negative and MLG can be employed in SAW amplifiers. Amplification of Blustein’s and Rayleigh’s SAWs in CdS, a piezoelectric hexagonal crystal of the symmetry group C6v, is considered. The corresponding equations for SAW propagation in the device are derived and can be applied to other substrate crystals of the same symmetry. The results of the paper indicate that MLG can be considered as a perspective material for SAW amplification and related applications.
Relaxed germanium-tin P-channel tunneling field-effect transistors fabricated on Si: impacts of Sn composition and uniaxial tensile strain
Authors: Han Genquan , Wang Yibo , Liu Yan , Wang Hongjuan , Liu Mingshan , Zhang Chunfu , Zhang Jincheng , Cheng Buwen , Hao Yue
Published: May 2015

In this work, relaxed GeSn p-channel tunneling field-effect transistors (pTFETs) with various Sn compositions are fabricated on Si. Enhancement of on-state current ION with the increase of Sn composition is observed in transistors, due to the reduction of direct bandgap EG. Ge0.93Sn0.07 and Ge0.95Sn0.05 pTFETs achieve 110% and 75% enhancement in ION, respectively, compared to Ge0.97Sn0.03 devices, at VGS - VTH = VDS = - 1.0 V. For the first time, ION enhancement in GeSn pTFET utilizing uniaxial tensile strain is reported. By applying 0.14% uniaxial tensile strain along [110] channel direction, Ge0.95Sn0.05 pTFETs achieve 12% ION improvement, over unstrained control devices at VGS - VTH = VDS = - 1.0 V. Theoretical study demonstrates that uniaxial tensile strain leads to the reduction of direct EG and affects the reduced tunneling mass, which bring the GBTBT rising, benefiting the tunneling current enhancement in GeSn TFETs.
Hybrid improper ferroelectricity in Ruddlesden-Popper Ca3(Ti,Mn)2O7 ceramics
Authors: Liu X. Q. , Wu J. W. , Shi X. X. , Zhao H. J. , Zhou H. Y. , Qiu R. H. , Zhang W. Q. , Chen X. M.
Published: May 2015

The hybrid improper ferroelectricity (HIF) has been proposed as a promising way to create multiferroic materials with strong magnetoelectric coupling by the first-principle calculation, and the experimental evidences of HIF in Ruddlesden-Poper Ca3(Ti1−xMnx)2O7 (x = 0, 0.05, 0.1, and 0.15) ceramics have been shown in the present work. The room temperature ferroelectric hysteresis loops are observed in these ceramics, and a polar orthorhombic structure with two oxygen tilting modes has been confirmed by the X-ray powder diffraction. A first-order phase transition around 1100 K in Ca3Ti2O7 was evidenced, and the temperatures of phase transitions decrease linearly with increasing of the contents of Mn4+ ions. Based on the result of first-principle calculations, the polarization should be reversed by switching through the mediated Amam phase in Ca3Ti2O7 ceramics.
Intrinsic spin polarized electronic structure of CrO2 epitaxial film revealed by bulk-sensitive spin-resolved photoemission spectroscopy
Authors: Fujiwara Hirokazu , Sunagawa Masanori , Terashima Kensei , Kittaka Tomoko , Wakita Takanori , Muraoka Yuji , Yokoya Takayoshi
Published: May 2015

We have performed bulk-sensitive spin-resolved photoemission spectroscopy in order to clarify the intrinsic spin-resolved electronic states of half-metallic ferromagnet CrO2. We used CrO2 epitaxial films on TiO2(100), which shows a peak at 1 eV with a clear Fermi edge, consistent with the bulk-sensitive PES spectrum for CrO2. In spin-resolved spectra at 40 K, while the Fermi edge was observed in the spin up (majority spin) state, no states at the Fermi level (EF) with an energy gap of 0.5 eV below EF were observed in the spin down (minority spin) state. At 300 K, the gap in the spin down state closes. These results are consistent with resistivity measurements and magnetic hysteresis curves of the fabricated CrO2 film, constituting spectroscopic evidence for the half-metallicity of CrO2 at low temperature and reducing the spin polarization at room temperature. We also discuss the electron correlation effects of Cr 3d.
Synthesis and Properties of Amphipathic Poly(D,L-lactide-co-glycolide)-polyethylene glycol-poly(D,L-lactide-co-glycolide) Triblock Copolymers
Authors: Zhen Wenyao , Zhu Yannan , Wang Weiping , Hou Zhaosheng
Published: May 2015

In this paper, amphipathic poly(d,l-lactide-co-glycolide)-polyethylene glycol-poly(d,l-lactide-co-glycolide) (PLGA-PEG-PLGA) triblock copolymers were synthesized via bulk ring-opening polymerization with d,l-lactide (d,l-LA), glycolide (GA), and polyethylene glycol (PEG) as raw materials and tin(ii) bis(2-ethylhexanoate) (Sn(Oct)2) as catalyst. The synthesis and purification processes were free from organic solvent. The chemical structure of PLGA-PEG-PLGA was characterized by Fourier transform infrared spectroscopy, 1H NMR, gel permeation chromatography, differential scanning calorimetry, and thermo gravimetric analysis. The thermo-sensitivity of PLGA-PEG-PLGA aqueous solution was examined, and the results showed that the copolymers concentration, mass ratio of d,l-LA/GA, and molecular weight of PEG played important parts in controlling the sol–gel transition temperature. The sol–gel transition occurred at lower temperatures with higher copolymer concentrations and mass ratios of d,l-LA/GA. In contrast, the sol–gel transition temperature increased with higher molecular weights of PEG. In vitro drug release studies were carried out using ceftibuten as a model drug. The results indicated that PLGA-PEG-PLGA prepared with 30 wt-% PEG1500 and 70 wt-% PLGA (mass ratio of d,l-LA/GA = 2 : 1) was an effective system for achieving long-sustained controlled release. The drug release from the hydrogel showed a higher initial release followed by a slower pattern up to 120 h, and the mean retention time was ~50 h.
Two-tiered coupling between flowing actin and immobilized
N
-cadherin/catenin complexes in neuronal growth cones
Authors: Garcia Mikael , Leduc Cécile , Lagardère Matthieu , Argento Amélie , Sibarita Jean-Baptiste , Thoumine Olivier
Published: May 2015

Significance

Using state-of-the-art micropatterning technology and single-molecule imaging, we revisited a prevalent paradigm in cell locomotion, the molecular clutch, which states that the intracellular actin motile machinery is dynamically coupled to transmembrane adhesion, allowing cells to move forward by applying forces on the substrate. We combined primary neuronal cultures on micropatterned substrates to trigger selective micron-scale
N
-cadherin adhesions, with single-molecule mapping of actin,
N
-cadherin, and α-catenin at the ventral surface of growth cones using photoconvertible fluorescent proteins. We demonstrate that actin filaments transit on a time scale of seconds between a flowing state and a state bound to immobilized
N
-cadherin/catenin complexes. These transient connections represent the first direct evidence for an intrinsic molecular clutch mechanism underlying growth cone locomotion.
Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening
Authors: La Jennifer , Latham Catherine F. , Tinetti Ricky N. , Johnson Adam , Tyssen David , Huber Kelly D. , Sluis-Cremer Nicolas , Simpson Jamie S. , Headey Stephen J. , Chalmers David K. , Tachedjian Gilda
Published: May 2015

Significance

In this study, we demonstrate a strategy using a combination of NMR-based binding and functional assays to screen a library of low-molecular-weight compounds known as fragments to identify new drug precursors that target HIV-1 reverse transcriptase (RT). Using this approach, we have discovered three fragments that inhibit HIV-1 RT and clinically relevant drug-resistant mutants. Enzyme assays demonstrate that at least two of these inhibitors are mechanistically distinct from HIV-1 RT drugs used clinically. One of these fragments inhibits HIV-1 replication in cell-based assays. The small size, hydrophilic nature, and excellent ligand efficiency of these fragments make them good starting points for the development of new classes of RT drugs for HIV-1 prevention or treatment.
Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance
Authors: Moreno-Gamez Stefany , Hill Alison L. , Rosenbloom Daniel I. S. , Petrov Dmitri A. , Nowak Martin A. , Pennings Pleuni S.
Published: May 2015

Significance

The evolution of drug resistance is a major health threat. In chronic infections with rapidly mutating pathogens—including HIV, tuberculosis, and hepatitis B and C viruses—multidrug resistance can cause even aggressive combination drug treatment to fail. Oftentimes, individual drugs within a combination do not penetrate equally to all infected regions of the body. Here we present a mathematical model suggesting that this imperfect penetration can dramatically increase the chance of treatment failure by creating regions where only one drug from a combination reaches a therapeutic concentration. The resulting single-drug compartments allow the pathogen to evolve resistance to each drug sequentially, rapidly causing multidrug resistance. More broadly, our model provides a quantitative framework for reasoning about trade-offs between aggressive and moderate drug therapies.
Using homology relations within a database markedly boosts protein sequence similarity search
Authors: Tong Jing , Sadreyev Ruslan I. , Pei Jimin , Kinch Lisa N. , Grishin Nick V.
Published: May 2015

Significance

In the field of protein structure prediction, identifying homology to known folds offers the most successful and practically useful strategy to provide protein spatial structure models. For protein sequence targets without closely related structures, even very distant homologs can provide reasonable templates for modeling. Despite significant progress in the field, remote sequence similarity search is far from perfection and fresh ideas are needed to extend detection limits. In computer science, the concept of utilizing internal relations within a database to improve similarity search was key to the success of search engines such as Google. Here, we show that similar consideration of the homology network within a protein database of structure templates can dramatically improve the accuracy of homology search.
Identification of an epithelial cell receptor responsible for
Clostridium difficile
TcdB-induced cytotoxicity
Authors: LaFrance Michelle E. , Farrow Melissa A. , Chandrasekaran Ramyavardhanee , Sheng Jinsong , Rubin Donald H. , Lacy D. Borden
Published: May 2015

Significance

Clostridium difficile
is a toxin-producing bacterium that is a frequent cause of hospital-acquired and antibiotic-associated diarrhea. The incidence, severity, and costs associated with
C. difficile
infection (CDI) are increasing, making
C. difficile
an important public health concern. As a toxin-mediated disease, there is significant interest in understanding the receptors that mediate the cellular entry and function of these toxins. The targeted disruption of toxin-receptor interactions could provide novel therapeutic strategies that can either augment or replace the need for antibiotic therapies in the treatment of CDI.
Assessing the role of static length scales behind glassy dynamics in polydisperse hard disks
Authors: Russo John , Tanaka Hajime
Published: May 2015

Significance

The origin of dynamical slowing down toward glass transition is a fundamental unsolved problem in condensed matter physics. A crucial question is whether this slowing down has a structural origin. Recently, a method to detect hidden order within the fluid was proposed, based on the idea that freezing a fraction of the particles in a system causes a transition akin to glass transition. Here, we show that a glass former, polydisperse hard disks, has a strong increase of structural order, well correlated with slow dynamics, which goes undetected by the pinning method. This casts doubt on the order-agnostic qualities of the pinning length scale and keeps static length scales in the race for plausible explanations of the glass transition problem.
Biotic interactions mediate soil microbial feedbacks to climate change
Authors: Crowther Thomas W. , Thomas Stephen M. , Maynard Daniel S. , Baldrian Petr , Covey Kristofer , Frey Serita D. , van Diepen Linda T. A. , Bradford Mark A.
Published: May 2015

Significance

The land carbon–climate feedback is incorporated into the earth system models that inform current Intergovernmental Panel on Climate Change projections. This feedback is driven by increases in soil microbial decomposition and carbon loss from soils under global change scenarios. The present study shows how trophic interactions in soil can mediate microbial responses to combined global change factors. As soil nitrogen deposition increases, the limitations on fungal growth are alleviated, stimulating total enzyme activity and decomposition rates. However, this process also affects the grazing activity of soil invertebrates. In the absence of nutrient limitation, top-down control by grazing isopods emerges as a dominant control, limiting any increases in fungal activity and carbon cycling.
Uncoupling protein 1 binds one nucleotide per monomer and is stabilized by tightly bound cardiolipin
Authors: Lee Yang , Willers Chrissie , Kunji Edmund R. S. , Crichton Paul G.
Published: May 2015

Significance

Uncoupling protein 1 (UCP1) is a mitochondrial carrier protein responsible for thermogenesis in brown adipose tissue, and a putative therapeutic target for the treatment of obesity and related diseases. It is widely accepted that the protein is dimeric and regulated by binding one nucleotide per dimer, and unlike other mitochondrial carriers, functions independently of the lipid cardiolipin. Here, we have developed novel methods to purify UCP1 from native sources, and demonstrate that the protein is in fact monomeric, binding nucleotide in a 1:1 stoichiometry. Each protein also binds three cardiolipin molecules, which confer stability. These findings put in place the true composition of UCP1, overturning a paradigm, which is crucial to resolve the controversial mechanism of this important membrane protein.
Selfish third parties act as peacemakers by transforming conflicts and promoting cooperation
Authors: Halevy Nir , Halali Eliran
Published: May 2015

Significance

Six experiments show that the mere possibility of third-party intervention increases cooperation in interpersonal and intergroup interactions, that third parties often fail to increase collective gains by withholding intervention, and that reducing the risk associated with intervention significantly increases peacemaking by self-interested third parties. These findings highlight the interdependence between disputants and third parties, thereby complementing existing models that solely focus on unidirectional influence of third parties on disputants. These findings underscore the role self-interest plays in shaping third parties’ intervention decisions and demonstrate that selfish third parties can promote peaceful conflict resolution by literally changing the game disputants are playing. Overall, we explain why, how, and when self-interested third parties intervene in others’ conflicts, to everyone’s benefit.
Stop-loss order for forage fish fisheries
Authors: Pikitch Ellen K.
Published: May 2015

Recent literature has highlighted the exceptional importance of forage fish, which include some of the largest fisheries in the world and produce a sizeable share of the global wild marine fish catch (1). Forage species play an essential and valuable supporting role within marine ecosystems by serving as prey for larger species (2, 3). These findings underscore the importance of (
i
) furthering understanding of the determinants of forage fish collapses, and (
ii
) of devising exploitation strategies that will maintain their crucial ecological and economic roles. Essington et al. (4) significantly advance understanding on both counts, applying novel methods to uncover fishing’s fingerprint in regulating population fluctuations and demonstrating the effectiveness of a simple remedy to prevent collapses.
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference
Authors: MacCallum Justin L. , Perez Alberto , Dill Ken A.
Published: May 2015

Significance

Modeling Employing Limited Data (MELD) is a method of integrative structural biology. It serves to determine protein structures by a Bayesian approach combining physical models with experimental data that are only semireliable, by virtue of being either too sparse, too ambiguous, or too uncertain. For eight proteins for which both the correct native structure and semireliable data were available, MELD gives excellent structures.
Efficient and selective molecular catalyst for the CO
2
-to-CO electrochemical conversion in water
Authors: Costentin Cyrille , Robert Marc , Savéant Jean-Michel , Tatin Arnaud
Published: May 2015

Significance

CO
2
-to-CO electrochemical conversion is a key step in the production of liquid fuels through dihydrogen-reductive Fischer–Tropsch chemistry. Among molecular catalysts, iron porphyrins reduced electrochemically to the Fe(0) state are particularly efficient and led to a deeper understanding of mechanisms involving coupled bond-breaking proton–electron transfer processes. The replacement of nonaqueous solvents by water should make the CO
2
-to-CO half-cell reaction much more attractive for applications, particularly because it would allow association with a water-oxidation anode through a proton-exchange membrane. Here it is demonstrated that electrochemical CO production catalyzed by a water-soluble iron porphyrin can occur with high catalytic efficiency. Manipulation of pH and buffering then allows conversions from those involving complete CO selectivity to ones with prescribed CO–H
2
mixtures.
A survey of human brain transcriptome diversity at the single cell level
Authors: Darmanis Spyros , Sloan Steven A. , Zhang Ye , Enge Martin , Caneda Christine , Shuer Lawrence M. , Hayden Gephart Melanie G. , Barres Ben A. , Quake Stephen R.
Published: May 2015

Significance

The brain comprises an immense number of cells and cellular connections. We describe the first, to our knowledge, single cell whole transcriptome analysis of human adult cortical samples. We have established an experimental and analytical framework with which the complexity of the human brain can be dissected on the single cell level. Using this approach, we were able to identify all major cell types of the brain and characterize subtypes of neuronal cells. We observed changes in neurons from early developmental to late differentiated stages in the adult. We found a subset of adult neurons which express major histocompatibility complex class I genes and thus are not immune privileged.
Exploring the potential impact of an expanded genetic code on protein function
Authors: Xiao Han , Nasertorabi Fariborz , Choi Sei-hyun , Han Gye Won , Reed Sean A. , Stevens Raymond C. , Schultz Peter G.
Published: May 2015

Significance

We describe a general strategy that begins to allow us to address the question of whether an expanded genetic code provides an evolutionary advantage to an organism. A large library of β-lactamase variants with distinct noncanonical amino acids substituted randomly at single sites throughout the protein was generated and then subjected to an antibiotic growth-based screen to identify mutants with enhanced catalytic activity. We show that a unique noncanonical mutation in the enzyme β-lactamase significantly increases catalytic activity by unexpected mechanisms. These effects cannot be recapitulated by other canonical amino acids at this site, suggesting that an expanded set of building blocks beyond the canonical 20 may offer unique solutions to organisms in the evolution of new functions.
Selection and characterization of Euglena anabaena var. minor as a new candidate Euglena species for industrial application
Authors: Suzuki Kengo , Mitra Sharbanee , Iwata Osamu , Ishikawa Takahiro , Kato Sueo , Yamada Koji
Published: May 2015

Euglena gracilis is a microalgae used as a model organism. Recently, mass cultivation of this species has been achieved for industrial applications. The genus Euglena includes more than 200 species that share common useful features, but the potential industrial applications of other Euglena species have not been evaluated. Thus, we conducted a pilot screening study to identify other species that proliferate at a sufficiently rapid rate to be used for mass cultivation; we found that Euglena anabaena var. minor had a rapid growth rate. In addition, its cells accumulated more than 40% weight of carbohydrate, most of which is considered to be a euglenoid specific type of beta-1-3-glucan, paramylon. Carbohydrate is stored in E. anabaena var. minor cells during normal culture, whereas E. gracilis requires nitrogen limitation to facilitate paramylon accumulation. These results suggest the potential industrial application of E. anabaena var. minor.
Identification of matrix metalloproteinase inhibitors by chemical arrays
Authors: Kawatani Makoto , Fukushima Yukako , Kondoh Yasumitsu , Honda Kaori , Sekine Tomomi , Yamaguchi Yoshiki , Taniguchi Naoyuki , Osada Hiroyuki
Published: May 2015

Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that degrade many extracellular matrix components and that have been implicated in the pathogenesis of various human diseases including cancer metastasis. Here, we screened MMP-9 inhibitors using photo-cross-linked chemical arrays, which can detect small-molecule ligand–protein interactions on a chip in a high-throughput manner. The array slides were probed sequentially with His-MMP-9, anti-His antibody, and a Cy5-labeled secondary antibody and then scanned with a microarray scanner. We obtained 27 hits among 24,275 compounds from the NPDepo library; 2 of the identified compounds (isoxazole compound 1 and naphthofluorescein) inhibited MMP-9 enzyme activity in vitro. We further explored 17 analogs of 1 and found that compound 18 had the strongest inhibitory activity. Compound 18 also inhibited other MMPs, including MMP-2, MMP-12, and MMP-13 and significantly inhibited cell migration in human fibrosarcoma HT1080 cells. These results suggest that 18 is a broad-spectrum MMP inhibitor.
Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
Authors: Mansouri Larry , Sutton Lesley-Ann , Ljungström Viktor , Bondza Sina , Arngården Linda , Bhoi Sujata , Larsson Jimmy , Cortese Diego , Kalushkova Antonia , Plevova Karla , Young Emma , Gunnarsson Rebeqa , Falk-Sörqvist Elin , Lönn Peter , Muggen Alice F. , Yan Xiao-Jie , Sander Birgitta , Enblad Gunilla , Smedby Karin E. , Juliusson Gunnar , Belessi Chrysoula , Rung Johan , Chiorazzi Nicholas , Strefford Jonathan C. , Langerak Anton W. , Pospisilova Sarka , Davi Frederic , Hellström Mats , Jernberg-Wiklund Helena , Ghia Paolo , Söderberg Ola , Stamatopoulos Kostas , Nilsson Mats , Rosenquist Richard
Published: May 2015

NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis.
Seeing Feeling: Queer Voyeurism in
À la recherche du temps perdu
Authors: Soldin Adeline
Published: May 2015

This article examines the constitutive pattern created by the Proustian narrator's repeated performance as a peeping Tom. Drawing on psychoanalysis, queer studies, visual culture, and affect and performance theories, this study expands the repertoire that has heretofore been limited to homosexual primal scenes by focusing on queer elements linking a number of voyeuristic moments in
À la recherche du temps perdu
. As unconventional primal scenes, these passages serve to break down heterosexual/homosexual and man/woman dichotomies through the inclusion of multiple participants of all genders and sexualities. That is, the repetition and authorization of such scenarios function as a performative discourse that advocates for queer sexualities in the novel. In addition to analysis dedicated to the implications of these erotic performances, significant attention is given to the protagonist's role as voyeur. By highlighting the pleasure that the narrator experiences as a peeping Tom, this article argues that, rather than endeavour to label the Proustian narrator as homosexual or heterosexual, a more productive approach would be to avoid such strict binaries and focus more on his erotic experiences; namely, to view his voyeurism of men and women of various sexual leanings as representative of his sexual preferences.
Contribution of Esophagram to the Evaluation of Complicated Pediatric Eosinophilic Esophagitis
Authors: Menard‐Katcher Calies , Swerdlow Mathew P. , Mehta Pooja , Furuta Glenn T. , Fenton Laura Z.
Published: May 2015

Objectives:

In contrast to peptic strictures, clinically significant strictures in patients with eosinophilic esophagitis (EoE) may be subtle and go unrecognized at the time of endoscopy. We aimed to identify how often stricture was identified by endoscopy as compared with contrast esophagram.

Methods:

We retrospectively reviewed esophagram and endoscopy examinations of all of the patients with EoE with esophageal stricture seen at a tertiary care pediatric hospital over a 6‐year period who had both procedures completed within a 3‐month time frame. Medical charts were reviewed for clinicopathologic information including age, duration of symptoms, histology, and treatment.

Results:

Twenty‐two children with EoE‐associated stricture completed both esophagram and endoscopic assessments. Esophageal strictures were identified by esophagram, and not endoscopy, in 55% of these children. Patients with stricture identified at esophagram alone had a shorter duration of symptoms (2.1 years duration vs 5.4 years duration, P = 0.03) than the group identified by endoscopy. Preoperative radiographic identification of a stricture was associated with dilation more often being performed.

Conclusions:

Esophagram is a valuable test to assess esophageal anatomy in children with complicated EoE. Esophagram may be able to detect subtle fibrostenosis earlier in the natural history of the disease than endoscopy.
Electrolyte and Mineral Homeostasis After Optimizing Early Macronutrient Intakes in VLBW Infants on Parenteral Nutrition
Authors: Senterre Thibault , Abu Zahirah Ibrahim , Pieltain Catherine , de Halleux Virginie , Rigo Jacques
Published: May 2015

Objectives:

The aim of the present study was to evaluate electrolyte and mineral homeostasis in very‐low‐birth‐weight (VLBW) infants who received high protein and energy intakes with a unique standardized parenteral nutrition solution containing electrolytes and minerals from birth onward.

Methods:

Prospective cohort study in 102 infants with birth weight <1250 g. The evolution of plasma biochemical parameters was described during the first 2 weeks of life.

Results:

During the first 3 days of life, mean parenteral intakes were 51 ± 8 kcal · kg−1 · day−1 with 2.7 ± 0.4 g · kg−1 · day−1 of protein, 1.1 ± 0.2 mmol · kg−1 · day−1 of sodium and potassium, and 1.3 ± 0.2 mmol · kg−1 · day−1 of calcium and phosphorus. Afterwards, most nutritional intakes (parenteral and enteral) met growth requirements. No infant developed a hyperkalemia >7 mmol/L, and a hypernatremia >150 mmol/L occurred only in 15.7% of the infants. In contrast, hyponatremia <130 mmol/L and hypokalemia <3 mmol/L occurred in 30.4% and 8.8% of the infants, respectively. The initial neonatal metabolic acidosis rapidly resolved in most infants and only 2.0% developed a base deficit >10 mmol/L after day 3 of life. Early hypocalcemia <1.8 mmol/L occurred in 13.7% of the infants. In contrast, hypophosphatemia <1.6 mmol/L occurred in 37.3% and hypercalcemia >2.8 mmol/L occurred in 12.7% of the infants.

Conclusions:

Increasing early protein and energy intakes in VLBW infants in the first week of life improves electrolyte homeostasis. It also increases the phosphorus requirements with a calcium‐to‐phosphorus ratio ≤1.0 (mmol/mmol) and the potassium and sodium requirements to avoid the development of a refeeding‐like syndrome. These data suggest that the parenteral nutrition guidelines for VLBW infants for the first week of life need to be revised.