bluuebunny/crossref_metadata_2025 huggingface dataset:
Safe and efficient membrane permeabilizing polymers based on PLLA for antibacterial applications
Authors: Li Zibiao , Chee Pei Lin , Owh Cally , Lakshminarayanan Rajamani , Loh Xian Jun
Published: March 2016

Highly active antibacterial poly(N,N-dimethylaminoethyl methacrylate)-block-poly(l-lactic acid)-block-poly(N,N-dimethylaminoethyl methacrylate) conjugated with poly(ethylene glycol) (D-PLLA-D@PEG) copolymers were synthesized.
Diketopyrrolopyrrole-based polymer with a semi-fluorinated side chain for high-performance organic thin-film transistors
Authors: Miao Kangjian , Chae Gil Jo , Wu Xiaoxue , Shu Qinghai , Zhu Xin , Sun Bangjin , Fan Jian , Cho Shinuk
Published: March 2016

A semi-fluorinated DPP based polymer showed hole mobility about 3 times higher than did its non-fluorinated analogue.
Investigation of a stripline transmission line structure for gyromagnetic nonlinear transmission line high power microwave sources
Authors: Reale D. V. , Parson J. M. , Neuber A. A. , Dickens J. C. , Mankowski J. J.
Published: March 2016

A stripline gyromagnetic nonlinear transmission line (NLTL) was constructed out of yttrium iron garnet ferrite and tested at charge voltages of 35 kV–55 kV with bias fields ranging from 10 kA/m to 20 kA/m. Typically, high power gyromagnetic NLTLs are constructed in a coaxial geometry. While this approach has many advantages, including a uniform transverse electromagnetic (TEM) mode, simple interconnection between components, and the ability to use oil or pressurized gas as an insulator, the coaxial implementation suffers from complexity of construction, especially when using a solid insulator. By moving to a simpler transmission line geometry, NLTLs can be constructed more easily and arrayed on a single substrate. This work represents a first step in exploring the suitability of various transmission line structures, such as microstrips and coplanar waveguides. The resulting high power microwave (HPM) source operates in ultra high frequency (UHF) band with an average bandwidth of 40.1% and peak rf power from 2 MW to 12.7 MW.
Experimental investigation of defect-assisted and intrinsic water vapor permeation through ultrabarrier films
Authors: Kim Hyungchul , Singh Ankit Kumar , Wang Cheng-Yin , Fuentes-Hernandez Canek , Kippelen Bernard , Graham Samuel
Published: March 2016

In the development of ultrabarrier films for packaging electronics, the effective water vapor transmission rate is a combination of permeation through pinhole defects and the intrinsic permeation through the actual barrier film. While it is possible to measure the effective permeation rate through barriers, it is important to develop a better understanding of the contribution from defects to the overall effective barrier performance. Here, we demonstrate a method to investigate independently defect-assisted permeation and intrinsic permeation rates by observing the degradation of a calcium layer encapsulated with a hybrid barrier film, that is, prepared using atomic layer deposition (ALD) and plasma enhanced deposition (PECVD). The results are rationalized using an analytical diffusion model to calculate the permeation rate as a function of spatial position within the barrier. It was observed that a barrier film consisting of a PECVD SiNx layer combined with an ALD Al2O3/HfOx nanolaminate resulted in a defect-assisted water vapor transmission rate (WVTR) of 4.84 × 10−5 g/m2 day and intrinsic WVTR of 1.41 × 10−4 g/m2 day at 50 °C/85% RH. Due to the low defect density of the tested barrier film, the defect-assisted WVTR was found to be three times lower than the intrinsic WVTR, and an effective (or total) WVTR value was 1.89 × 10−4 g/m2 day. Thus, improvements of the barrier performance should focus on reducing the number of defects while also improving the intrinsic barrier performance of the hybrid layer.
Influence of electron-spin interaction on the electrostatic space-charge wave in a cylindrical waveguide quantum plasma
Authors: Hong Woo-Pyo , Jung Young-Dae
Published: March 2016

The influence of electron spin-interaction on the propagation of the electrostatic space-charge quantum wave is investigated in a cylindrically bounded quantum plasma. The dispersion relation of the space-charge quantum electrostatic wave is derived including the influence of the electron spin-current in a cylindrical waveguide. It is found that the influence of electron spin-interaction enhances the wave frequency for large wave number regions. It is shown that the wave frequencies with higher-solution modes are always smaller than those with lower-solution modes in small wave number domains. In addition, it is found that the wave frequency increases with an increase of the radius of the plasma cylinder as well as the Fermi wave number. We discuss the effects due to the quantum and geometric on the variation of the dispersion properties of the space-charge plasma wave.
A theoretical investigation of symmetry-origin unidirectional energy gradient in light-harvesting dendrimers
Authors: Koda Shin-ichi
Published: March 2016

We theoretically investigate a possibility that the symmetry of the repetitively branched structure of light-harvesting dendrimers creates the energy gradient descending toward inner generations (layers of pigment molecules) of the dendrimers. In the first half of this paper, we define a model system using the Frenkel exciton Hamiltonian that focuses only on the topology of dendrimers and numerically show that excitation energy tends to gather at inner generations of the model system at a thermal equilibrium state. This indicates that an energy gradient is formed in the model system. In the last half, we attribute this result to the symmetry of the model system and propose two symmetry-origin mechanisms creating the energy gradient. The present analysis and proposition are based on the theory of the linear chain (LC) decomposition [S. Koda, J. Chem. Phys. 142, 204112 (2015)], which equivalently transforms the model system into a set of one-dimensional systems on the basis of the symmetry of dendrimers. In the picture of the LC decomposition, we find that energy gradient is formed both in each linear chain and among linear chains, and these two mechanisms explain the numerical results well.
Faraday rotation, band splitting, and one-way propagation of plasmon waves on a nanoparticle chain
Authors: Pike N. A. , Stroud D.
Published: March 2016

We calculate the dispersion relations of plasmonic waves propagating along a chain of semiconducting or metallic nanoparticles in the presence of both a static magnetic field B and a liquid crystalline host. The dispersion relations are obtained using the quasistatic approximation and a dipole-dipole approximation to treat the interaction between surface plasmons on different nanoparticles. For plasmons propagating along a particle chain in a nematic liquid crystalline host with both B and the director parallel to the chain, we find a small, but finite, Faraday rotation angle. For B perpendicular to the chain, but director still parallel to the chain, the field couples the longitudinal and one of the two transverse plasmonic branches. This coupling is shown to split the two branches at the zero field crossing by an amount proportional to |B|. In a cholesteric liquid crystal host and an applied magnetic field parallel to the chain, the dispersion relations for left- and right-moving waves are found to be different. For some frequencies, the plasmonic wave propagates only in one of the two directions.
Modified Dirac Hamiltonian for efficient quantum mechanical simulations of micron sized devices
Authors: Habib K. M. Masum , Sajjad Redwan N. , Ghosh Avik W.
Published: March 2016

Representing massless Dirac fermions on a spatial lattice poses a potential challenge known as the Fermion Doubling problem. Addition of a quadratic term to the Dirac Hamiltonian provides a possible way to circumvent this problem. We show that the modified Hamiltonian with the additional term results in a very small Hamiltonian matrix when discretized on a real space square lattice. The resulting Hamiltonian matrix is considerably more efficient for numerical simulations without sacrificing on accuracy and is several orders of magnitude faster than the atomistic tight binding model. Using this Hamiltonian and the non-equilibrium Green's function formalism, we show several transport phenomena in graphene, such as magnetic focusing, chiral tunneling in the ballistic limit, and conductivity in the diffusive limit in micron sized graphene devices. The modified Hamiltonian can be used for any system with massless Dirac fermions such as Topological Insulators, opening up a simulation domain that is not readily accessible otherwise.
Orbital spectrum analysis of non-axisymmetric perturbations of the guiding-center particle motion in axisymmetric equilibria
Authors: Zestanakis P. A. , Kominis Y. , Anastassiou G. , Hizanidis K.
Published: March 2016

The presence of non-axisymmetric perturbations in an axisymmetric magnetic field equilibrium renders the Guiding Center (GC) particle motion non-integrable and may result in particle, energy, and momentum redistribution, due to resonance mechanisms. We analyse these perturbations in terms of their spectrum, as observed by the particles in the frame of unperturbed GC motion. We calculate semi-analytically the exact locations and strength of resonant spectral components of multiple perturbations. The presented Orbital Spectrum Analysis method is based on an exact Action-Angle transform that fully takes into account Finite Orbit Width effects. The method provides insight into the particle dynamics and enables the prediction of the effect of any perturbation to all different types of particles and orbits in a given, analytically or numerically calculated, axisymmetric equilibrium.
Virtual anode effect in the propagation of positive streamers
Authors: Robledo-Martinez A. , Garcia-Villareal L. A.
Published: March 2016

Experiments made in a parallel-plate arrangement, where one of the plates is the ground plane and the other a positively charged dielectric sheet, show that at low air pressure the dielectric injects streamers onto the surrounding air. The similarities and differences between the streamers thus produced and those emitted from electrodes are discussed. The streamers here obtained were found to have diameters and speeds that are clearly dependent on pressure. Often the streamers were seen to decelerate markedly to the point of coming to a complete stop and on occasions even returning back to the dielectric they came from. The deceleration and the reflection of the streamers are attributed to a virtual anode created by the electrostatic image of the head's charge behind the ground plane. Field calculations performed corroborate this hypothesis. Through the use of an equation of motion of the positive head, it is then possible to obtain an estimate of the magnitude of its charge. The charge thus obtained was found to be in the 2.5–26 nC range.
Acceleration and evolution of a hollow electron beam in wakefields driven by a Laguerre-Gaussian laser pulse
Authors: Zhang Guo-Bo , Chen Min , Schroeder C. B. , Luo Ji , Zeng Ming , Li Fei-Yu , Yu Lu-Le , Weng Su-Ming , Ma Yan-Yun , Yu Tong-Pu , Sheng Zheng-Ming , Esarey E.
Published: March 2016

We show that a ring-shaped hollow electron beam can be injected and accelerated by using a Laguerre-Gaussian laser pulse and ionization-induced injection in a laser wakefield accelerator. The acceleration and evolution of such a hollow, relativistic electron beam are investigated through three-dimensional particle-in-cell simulations. We find that both the ring size and the beam thickness oscillate during the acceleration. The beam azimuthal shape is angularly dependent and evolves during the acceleration. The beam ellipticity changes resulting from the electron angular momenta obtained from the drive laser pulse and the focusing forces from the wakefield. The dependence of beam ring radius on the laser-plasma parameters (e.g., laser intensity, focal size, and plasma density) is studied. Such a hollow electron beam may have potential applications for accelerating and collimating positively charged particles.
Perspective: Rapid synthesis of complex oxides by combinatorial molecular beam epitaxy
Authors: Bollinger A. T. , Wu J. , Božović I.
Published: March 2016

The molecular beam epitaxy (MBE) technique is well known for producing atomically smooth thin films as well as impeccable interfaces in multilayers of many different materials. In particular, molecular beam epitaxy is well suited to the growth of complex oxides, materials that hold promise for many applications. Rapid synthesis and high throughput characterization techniques are needed to tap into that potential most efficiently. We discuss our approach to doing that, leaving behind the traditional one-growth-one-compound scheme and instead implementing combinatorial oxide molecular beam epitaxy in a custom built system.
Dynamics of high quantum efficiency photoluminescence from N-Si-O bonding states in oxygenated amorphous silicon nitride films
Authors: Zhang Pengzhan , Chen Kunji , Lin Zewen , Tan Dameng , Dong Hengping , Li Wei , Xu Jun , Huang Xinfan
Published: March 2016

We have reported high internal quantum efficiency (IQE) (∼60%) of photoluminescence (PL) at 470 nm wavelength from oxygenated amorphous silicon nitride (a-SiNx:O) films. In this work, we explored the dynamics of high PL IQE from luminescent N-Si-O bonding states in a-SiNx:O films by using a combination of time resolved PL (TRPL) and temperature dependent PL (TDPL) measurements. The TRPL measurements include time integrated PL, microsecond range PL, and nanosecond range PL measurement modes. The a-SiNx:O films exhibit ns PL decay dynamics that is independent of pumping fluence (WPF) and uniform across the PL spectrum, which is different from the PL decay behavior in a-SiNx films. Particularly, we precisely monitored the temporal evolution of the PL spectra profile to verify that the luminescent N-Si-O bonding states are responsible for the observed blue PL with a radiative recombination rate of ∼108 s−1. Such very fast radiative recombination rate can be compared with that in direct band gap CdSe nanocrystals and can also help us to understand the high PL IQE in a-SiNx:O films. Moreover, by combining the TD-PL lifetimes with the PL IQE values, the temperature dependence of radiative and nonradiative lifetime can be determined.
Bifurcations and chaos of a vibration isolation system with magneto-rheological damper
Authors: Zhang Hailong , Zhang Ning , Min Fuhong , Yan Wei , Wang Enrong
Published: March 2016

Magneto-rheological (MR) damper possesses inherent hysteretic characteristics. We investigate the resulting nonlinear behaviors of a two degree-of-freedom (2-DoF) MR vibration isolation system under harmonic external excitation. A MR damper is identified by employing the modified Bouc-wen hysteresis model. By numerical simulation, we characterize the nonlinear dynamic evolution of period-doubling, saddle node bifurcating and inverse period-doubling using bifurcation diagrams of variations in frequency with a fixed amplitude of the harmonic excitation. The strength of chaos is determined by the Lyapunov exponent (LE) spectrum. Semi-physical experiment on the 2-DoF MR vibration isolation system is proposed. We trace the time history and phase trajectory under certain values of frequency of the harmonic excitation to verify the nonlinear dynamical evolution of period-doubling bifurcations to chaos. The largest LEs computed with the experimental data are also presented, confirming the chaotic motion in the experiment. We validate the chaotic motion caused by the hysteresis of the MR damper, and show the transitions between distinct regimes of stable motion and chaotic motion of the 2-DoF MR vibration isolation system for variations in frequency of external excitation.
Enhancemet of flow boiling heat transfer in pHEMA/pPFDA coated microtubes with longitudinal variations in wettability
Authors: Nedaei Masoumeh , Armagan Efe , Sezen Meltem , Ozaydin Ince Gozde , Kosar Ali
Published: March 2016

Flow boiling heat transfer was investigated in stainless steel hypodermic microtubes, whose surfaces were enhanced by gradient crosslinked polyhydroxyethylmethacrylate (pHEMA)/polyperfluorodecylacrylate (pPFDA) coatings thereby offering variations in wettability along the surface as well as high porosity. The initiated chemical vapor deposition (iCVD) method was implemented for coating the inner walls of the microtubes with an inner diameter of 502 μm, and deionized water was used as the working fluid. Experimental results were obtained from the coated microtubes, where one end corresponded to the pHEMA (hydrophilic) coated part and the other end was the most hydrophobic location with the pPFDA (hydrophobic) coating so that wettability varied along the length of the microtube. The results of both the hydrophobic and hydrophilic inlet cases were compared to their plain surface counterparts at the mass flux of 9500 kg/m2s. The experimental results showed a remarkable increase in boiling heat transfer with the coatings. The highest heat transfer coefficients were attained for the pHEMA coated (hydrophobic inlet and hydrophilic outlet) outlet case with a maximum heat transfer enhancement ratio of ∼64%. The reason for the enhanced heat transfer with the coated microtubes can be attributed to the increased nucleation site density and bubble release as well as enhanced convection and bubble motion near the surface due to the variation in wettability along the length. The results proved that gradient pHEMA/pPFDA coatings can be utilized as a viable surface enhancement method in microscale cooling applications.
Kinetic Studies of Gold Recovery from Diluted Chloride Aqueous Solutions Using Activated Carbon Organosorb 10 CO
Authors: Wojnicki Marek , Rudnik Ewa , Luty-Błocho Magdalena , Socha Robert P. , Pędzich Zbigniew , Fitzner Krzysztof , Mech Krzysztof
Published: March 2016

The kinetic studies of gold(iii) chloride complex ions recovery from acidic solution using activated carbon (AC) were carried out using spectrophotometry. AC samples were characterized in terms of surface area, porosity, and zeta potential. The surface functional groups were also identified. It was found that adsorption of AuCl4– onto AC was followed by reduction of the ions to the metallic form. The process obeyed the first order reaction model, but the reaction was controlled by diffusion. Arrhenius and Eyring–Polanyi equations were used for determination of the activation parameters. Distribution of gold across the AC pellets was also determined and discussed according to the porous material theory.
Solutions for soil fertility management to overcome the challenges of the Mediterranean organic agriculture: tomato plant case study
Authors: Cavoski Ivana , Al Chami Ziad , Jarrar Mohammad , Mondelli Donato
Published: March 2016

Regulation of organic farming allows the use of a limited range of fertilisers and soil amendments to meet nutritional needs of the plants. Before advocating alternative strategies for fertility management, performance should be evaluated. An open field experiment was conducted to study the effects of different fertilisation scenarios on tomato (Solanum lycopersicum Mill, cv. San Marzano) production and soil chemical properties. Fertilisation scenarios were based on combinations of amendments (composts and biochar) with organic and/or mineral fertilisers to balance plant nutrient requirements. Amendments were produced from agricultural and food-industry wastes available in the region. Most of the soil parameters did not vary by the end of experiment; only available phosphorus slightly increased in the treatments where organic fertilisers were applied. All treatments significantly increased yields over control and biochar alone. Different compost types showed promising results for tomato production and quality, whereas biochar did not. The study demonstrated that recycling of nutrients from on-farm or food-industry wastes might be a good strategy to increase productivity and sustainability of Mediterranean organic agriculture when integrated fertility management is adapted. However, more studies are needed to evaluate their effect in long-term experiments.
Carbon isotopes characterize rapid changes in atmospheric carbon dioxide during the last deglaciation
Authors: Bauska Thomas K. , Baggenstos Daniel , Brook Edward J. , Mix Alan C. , Marcott Shaun A. , Petrenko Vasilii V. , Schaefer Hinrich , Severinghaus Jeffrey P. , Lee James E.
Published: March 2016

Significance

Antarctic ice cores provide a precise, well-dated history of increasing atmospheric CO
2
during the last glacial to interglacial transition. However, the mechanisms that drive the increase remain unclear. Here we reconstruct a key indicator of the sources of atmospheric CO
2
by measuring the stable isotopic composition of CO
2
in samples spanning the period from 22,000 to 11,000 years ago from Taylor Glacier, Antarctica. Improvements in precision and resolution allow us to fingerprint CO
2
sources on the centennial scale. The data reveal two intervals of rapid CO
2
rise that are plausibly driven by sources from land carbon (at 16.3 and 12.9 ka) and two others that appear fundamentally different and likely reflect a combination of sources (at 14.6 and 11.5 ka).
Fiber networks amplify active stress
Authors: Ronceray Pierre , Broedersz Chase P. , Lenz Martin
Published: March 2016

Significance

Living organisms generate forces to move, change shape, and maintain their internal functions. These forces are typically produced by molecular motors embedded in networks of fibers. Although these motors are traditionally regarded as the defining elements of biological force generation, here we show that the surrounding network also plays a central role in this process. Indeed, rather than merely propagating forces like a simple elastic medium, fiber networks produce emergent, dramatically amplified stresses and can go so far as reversing small-scale extensile forces into large-scale contraction. Our theory quantitatively accounts for experimental measurements of contraction.
Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis
Authors: Méheust Raphaël , Zelzion Ehud , Bhattacharya Debashish , Lopez Philippe , Bapteste Eric
Published: March 2016

Significance

Endosymbiotic gene transfer from the plastid genome to the nucleus comprises the most significant source of horizontal gene transfer in photosynthetic eukaryotes. We investigated genomic data at the infragenic level to determine whether the cyanobacterial endosymbiont also contributed gene fragments (i.e., domains) to create novel nuclear-encoded proteins. We found 67 such gene families that are expressed as RNA and widely distributed among plants and algae. At least 23 genes are putatively involved in redox regulation and light response, namely the maintenance of a photodynamic organelle. Our results add a new layer of complexity to plastid integration and point to the role of fused proteins as key players in this process.
SARS-like WIV1-CoV poised for human emergence
Authors: Menachery Vineet D. , Yount Boyd L. , Sims Amy C. , Debbink Kari , Agnihothram Sudhakar S. , Gralinski Lisa E. , Graham Rachel L. , Scobey Trevor , Plante Jessica A. , Royal Scott R. , Swanstrom Jesica , Sheahan Timothy P. , Pickles Raymond J. , Corti Davide , Randell Scott H. , Lanzavecchia Antonio , Marasco Wayne A. , Baric Ralph S.
Published: March 2016

Significance

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV highlights the continued risk of cross-species transmission leading to epidemic disease. This manuscript describes efforts to extend surveillance beyond sequence analysis, constructing chimeric and full-length zoonotic coronaviruses to evaluate emergence potential. Focusing on SARS-like virus sequences isolated from Chinese horseshoe bats, the results indicate a significant threat posed by WIV1-CoV. Both full-length and chimeric WIV1-CoV readily replicated efficiently in human airway cultures and in vivo, suggesting capability of direct transmission to humans. In addition, while monoclonal antibody treatments prove effective, the SARS-based vaccine approach failed to confer protection. Together, the study indicates an ongoing threat posed by WIV1-related viruses and the need for continued study and surveillance.
Biphasic regulation of InsP
3
receptor gating by dual Ca
2+
release channel BH3-like domains mediates Bcl-x
L
control of cell viability
Authors: Yang Jun , Vais Horia , Gu Wenen , Foskett J. Kevin
Published: March 2016

Significance

Changes in Ca
2+
concentration in the cell play important roles in cell life and death decisions. Antiapoptotic Bcl-2 family proteins help protect cells from dying by interacting with proteins at mitochondria and endoplasmic reticulum. At the endoplasmic reticulum, antiapoptotic Bcl-2 proteins interact with InsP
3
R Ca
2+
channels that release Ca
2+
into the cytoplasm. However, it is controversial how they interact with the InsP
3
R, as well as the functional consequences of the interactions. We found that antiapoptotic Bcl-x
L
interacts with InsP
3
Rs by unique mechanisms that change the activity of the channel depending on its concentration. We also found that disrupting these interactions diminishes cell viability. Our results provide a unifying model of the effects of antiapoptotic Bcl-2 proteins on the InsP
3
R.
Artificial eye for scotopic vision with bioinspired all-optical photosensitivity enhancer
Authors: Liu Hewei , Huang Yinggang , Jiang Hongrui
Published: March 2016

Significance

Although biological eyes ingeniously adopt diverse optical approaches to improve their scotopic vision, enhancement of the photosensitivity in artificial imaging systems still clings to electronic methods. Here we present an all-optical strategy to significantly improve the low-light imaging capability of manmade sensors, which is inspired by the optical concept of superposition eyes and elephantnose fish eye. Besides showing an artificial eye whose scotopic vision is largely improved by a bioinspired photosensitivity enhancer, we also demonstrate a complete solution to acquire high-resolution images under low-light conditions with our device. More importantly, our purely optical approach can be used on top of other electronic technologies, which can boost the most state-of-the-art imaging sensor whose photosensitivity is gaining on the physical limitations.
Identification of tissue-specific cell death using methylation patterns of circulating DNA
Authors: Lehmann-Werman Roni , Neiman Daniel , Zemmour Hai , Moss Joshua , Magenheim Judith , Vaknin-Dembinsky Adi , Rubertsson Sten , Nellgård Bengt , Blennow Kaj , Zetterberg Henrik , Spalding Kirsty , Haller Michael J. , Wasserfall Clive H. , Schatz Desmond A. , Greenbaum Carla J. , Dorrell Craig , Grompe Markus , Zick Aviad , Hubert Ayala , Maoz Myriam , Fendrich Volker , Bartsch Detlef K. , Golan Talia , Ben Sasson Shmuel A. , Zamir Gideon , Razin Aharon , Cedar Howard , Shapiro A. M. James , Glaser Benjamin , Shemer Ruth , Dor Yuval
Published: March 2016

Significance

We describe a blood test for detection of cell death in specific tissues based on two principles: (
i
) dying cells release fragmented DNA to the circulation, and (
ii
) each cell type has a unique DNA methylation pattern. We have identified tissue-specific DNA methylation markers and developed a method for sensitive detection of these markers in plasma or serum. We demonstrate the utility of the method for identification of pancreatic β-cell death in type 1 diabetes, oligodendrocyte death in relapsing multiple sclerosis, brain cell death in patients after traumatic or ischemic brain damage, and exocrine pancreas cell death in pancreatic cancer or pancreatitis. The approach allows minimally invasive monitoring of tissue dynamics in humans in multiple physiological and pathological conditions.
Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface
Authors: Gorelik Maryna , Orlicky Stephen , Sartori Maria A. , Tang Xiaojing , Marcon Edyta , Kurinov Igor , Greenblatt Jack F. , Tyers Mike , Moffat Jason , Sicheri Frank , Sidhu Sachdev S.
Published: March 2016

Significance

The ubiquitin proteasome components are often misregulated in numerous diseases, encouraging the search for drug targets and inhibitors. E3 ligases that specify ubiquitination targets are of particular interest. Multimeric Skp1–Cul1–F-box (SCF) E3 ligases constitute one of the largest E3 families connected to every cellular process and multiple diseases; however, their characterization as therapeutic targets is impeded by functional diversity and poor characterization of its members. Herein we describe a strategy to inhibit SCF E3 ligases using engineered ubiquitin-based binders. We identify a previously uncharacterized inhibitory site and design ubiquitin-based libraries targeting this site. Our strategy to target SCF E3 ligases with small-molecule–like agents will have broad applications for basic research and drug development relating to SCF E3 ligase function.
Functional polymorphisms of macrophage migration inhibitory factor as predictors of morbidity and mortality of pneumococcal meningitis
Authors: Savva Athina , Brouwer Matthijs C. , Roger Thierry , Valls Serón Mercedes , Le Roy Didier , Ferwerda Bart , van der Ende Arie , Bochud Pierre-Yves , van de Beek Diederik , Calandra Thierry
Published: March 2016

Significance

Pneumococcal meningitis, the most frequent cause of bacterial meningitis in adults, is associated with substantial morbidity and mortality. In a prospective, nationwide cohort of patients with pneumococcal meningitis, macrophage migration inhibitory factor (MIF), a proinflammatory mediator, was identified as a previously unidentified genetic marker of patient’s outcome. High-expression
MIF
alleles were associated with disease severity and death, a finding consistent with the harmful consequences of robust proinflammatory cytokine responses on brain edema and neuronal damage in the course of bacterial meningitis. These results provide strong evidence that functional
MIF
polymorphisms are genetic predictors of morbidity and mortality of pneumococcal meningitis and suggest that MIF is a potential target for immune-modulating adjunctive therapies.
Bonobos (Pan paniscus) show an attentional bias toward conspecifics’ emotions
Authors: Kret Mariska E. , Jaasma Linda , Bionda Thomas , Wijnen Jasper G.
Published: March 2016

Significance

Applying well-established psychological paradigms to our closest relatives represents a promising approach for providing insight into similarities and differences between humans and apes. Numerous articles have been published on the dot-probe task, showing that humans have an attentional bias toward emotions, especially when threatening. For social species like primates, efficiently responding to others’ emotions has great survival value. Observational research has shown that, compared with humans and chimpanzees, bonobos excel in regulating their own and others’ emotions, thereby preventing conflicts from escalating. The present study is an initial effort to apply a psychological test to the bonobo, and demonstrates that they, like humans, have heightened attention to emotional—compared with neutral—conspecifics, but are mostly drawn toward protective and affiliative emotions.
Ultrahigh-pressure polyamorphism in GeO
2
glass with coordination number >6
Authors: Kono Yoshio , Kenney-Benson Curtis , Ikuta Daijo , Shibazaki Yuki , Wang Yanbin , Shen Guoyin
Published: March 2016

Significance

A new double-stage large-volume cell was developed to compress large GeO
2
glass samples to near 100 GPa and to conduct multiangle energy-dispersive X-ray diffraction measurement for in situ structure measurements. We find new experimental evidence of ultrahigh-pressure polyamorphism in GeO
2
glass with coordination number (CN) significantly >6. The structural change to CN higher than 6 is closely associated with the change in oxygen-packing fraction. Our results provide direct structural evidence for ultradense network-forming glasses and liquids. The observed ultrahigh-pressure polyamorphism may also exist in other network-forming glasses and liquids as well, such as SiO
2
and other silicate and germanate systems.
Inositol hexakisphosphate (IP6) generated by IP5K mediates cullin-COP9 signalosome interactions and CRL function
Authors: Scherer Paul C. , Ding Yan , Liu Zhiqing , Xu Jing , Mao Haibin , Barrow James C. , Wei Ning , Zheng Ning , Snyder Solomon H. , Rao Feng
Published: March 2016

Significance

The regulation of ubiquitylation is critical to maintain proteomic and cellular homeostasis. The cullin-RING E3 ubiquitin ligases (CRLs) mediate one-fifth of all ubiquitylation, but their regulation is largely unknown. Here, we describe how the generation of a small metabolite, inositol hexakisphosphate (IP6), locally switches two CRLs from their active to their inactive state by means of stabilizing their interaction with an inhibitor: the constitutive photomorphogenesis 9 signalosome. Furthermore, we demonstrate the physiologic consequences of IP6 depletion on CRL dysregulation, CRL substrate levels, and global cellular phenotypes. Targeting IP6 synthesis synergizes with the cytotoxic effect of CRL inhibition, which may have therapeutic relevance.
New tyrannosaur from the mid-Cretaceous of Uzbekistan clarifies evolution of giant body sizes and advanced senses in tyrant dinosaurs
Authors: Brusatte Stephen L. , Averianov Alexander , Sues Hans-Dieter , Muir Amy , Butler Ian B.
Published: March 2016

Significance

Tyrannosaurs—the iconic group of dinosaurian carnivores that includesTyrannosaurus rex—dominated latest Cretaceous ecosystems with their colossal sizes and sophisticated senses. A gap in the mid-Cretaceous fossil record between these giant apex predators and their older, smaller relatives makes it difficult to understand how the characteristic body size and ecological habits ofT.rexand kin developed. A new species from Uzbekistan fills this gap. This horse-sized animal shows that tyrannosaurs had yet to achieve huge size at this time but had already evolved key brain and sensory features of the gigantic latest Cretaceous species. Tyrannosaurs apparently developed giant body size rapidly, late in the Cretaceous, and their success may have been enabled by their early-evolving keen senses.
Human mesenchymal stromal cells reduce influenza A H5N1-associated acute lung injury in vitro and in vivo
Authors: Chan Michael C. W. , Kuok Denise I. T. , Leung Connie Y. H. , Hui Kenrie P. Y. , Valkenburg Sophie A. , Lau Eric H. Y. , Nicholls John M. , Fang Xiaohui , Guan Yi , Lee Jae W. , Chan Renee W. Y. , Webster Robert G. , Matthay Michael A. , Peiris J. S. Malik
Published: March 2016

Significance

Acute lung injury, including impaired alveolar fluid clearance, is a life-threatening complication of severe respiratory virus infection, and effective treatment is lacking. Understanding the mechanism of this complication may suggest novel therapies. Here, we found that, in vitro, influenza A/H5N1 infection impaired alveolar fluid clearance more than did seasonal virus, mimicking its greater severity in patients. We demonstrated that this impairment is mediated by the release of soluble factors from infected cells, leading to down-regulation of alveolar sodium and chloride transporters. Mesenchymal stromal cells prevented or reduced this effect in vitro and in vivo in A/H5N1-infected mice. These cells provide a potentially effective treatment for acute lung injury in severe influenza.
Mitochondrial calcium uniporter regulator 1 (MCUR1) regulates the calcium threshold for the mitochondrial permeability transition
Authors: Chaudhuri Dipayan , Artiga Daniel J. , Abiria Sunday A. , Clapham David E.
Published: March 2016

Significance

Cells injured by a variety of stressors feature a form of mitochondrial dysfunction termed the permeability transition. During this process, mitochondria swell and become disrupted, ultimately leading to cell death. In excitable cells such as cardiomyocytes or neurons, such injury is often triggered by calcium overload. By screening
Drosophila
cells, we have found a protein, mitochondrial calcium uniporter regulator 1 (MCUR1), that appears to regulate the amount of calcium required to induce the permeability transition. Modulating the function of this protein acutely may prove beneficial in limiting tissue damage during diseases that feature calcium overload.
Foraging ecology and occurrence of 7 sympatric babbler species (Timaliidae) in the lowland rainforest of Borneo and peninsular Malaysia
Authors: Styring Alison R. , Ragai Roslina , Zakaria Mohamed , Sheldon Frederick H.
Published: March 2016

Understanding foraging strategies of birds is essential to understanding mechanisms of their community assembly. To provide such information on a key Southeast Asian rainforest family, the babblers (Timaliidae), we evaluated foraging behavior and abundance in 7 morphologically and behaviorally similar sympatric species (Cyanoderma erythropterum, C. rufifrons, Stachyris maculata, S. nigricollis, S. poliocephala, Macronus ptilosus, and Mixornis gularis) in 5 habitats defined by structural complexity: (1) continuous native rainforest, (2) logged native rainforest fragments, (3) mature industrial tree plantation, (4) young industrial plantation, and (5) oil palm plantation. Enough data were obtained to compare abundance in all 7 species and foraging behavior in 5. All species were common in forest fragments and mature industrial tree plantations and less so in continuous rainforest and young industrial plantations; only M. gularis occurred in oil palm. In terms of foraging, M. gularis was the greatest generalist; C. rufifrons foraged mainly on live leaves in the forest midstory; and S. maculata, C. erythropterum, and M. ptilosus foraged mainly on dead leaves suspended in understory vegetation at significantly different heights. The dead-leaf substrate depends on a rich supply of falling leaves and extensive understory structure, conditions most common in native forest and old industrial plantations, and less so in mature forest, young plantations, and oil palm. Because of the importance of foraging data to understanding and managing biodiversity, we encourage the development of foraging fields in eBird (ebird.org), so that birdwatchers may help collect these relatively rare data.
A patient-centered system in a provider-centered world: challenges of incorporating post-discharge wound data into practice
Authors: Sanger Patrick C , Hartzler Andrea , Lordon Ross J , Armstrong Cheryl AL , Lober William B , Evans Heather L , Pratt Wanda
Published: March 2016

Objective The proposed Meaningful Use Stage 3 recommendations require healthcare providers to accept patient-generated health data (PGHD) by 2017. Yet, we know little about the tensions that arise in supporting the needs of both patients and providers in this context. We sought to examine these tensions when designing a novel, patient-centered technology – mobile Post-Operative Wound Evaluator (mPOWEr) – that uses PGHD for post-discharge surgical wound monitoring.

Materials and Methods As part of the iterative design process of mPOWEr, we conducted semistructured interviews and think-aloud sessions using mockups with surgical patients and providers. We asked participants how mPOWEr could enhance the current post-discharge process for surgical patients, then used grounded theory to develop themes related to conflicts and agreements between patients and providers.

Results We identified four areas of agreement: providing contextual metadata, accessible and actionable data presentation, building on existing sociotechnical systems, and process transparency. We identified six areas of conflict, with patients preferring: more flexibility in data input, frequent data transfer, text-based communication, patient input in provider response prioritization, timely and reliable provider responses, and definitive diagnoses.

Discussion We present design implications and potential solutions to the identified conflicts for each theme, illustrated using our work on mPOWEr. Our experience highlights the importance of bringing a variety of stakeholders, including patients, into the design process for PGHD applications.

Conclusion We have identified critical barriers to integrating PGHD into clinical care and describe design implications to help address these barriers. Our work informs future efforts to ensure the smooth integration of essential PGHD into clinical practice.
Urban Monumentality in Roman Britain
Authors: Revell Louise
Published: March 2016

This chapter investigates the character of the chartered towns in Roman Britain, their mature form in the late second/early third centuries, and the social use of urban space. It explores the activities fostered by the buildings within towns. The forum and the town are shown to be the centre of political organization, enabling the new system of elite magistracies. The religious structures of the towns allowed for varied forms of ritual experience engendered by the relationships between temple and urban layout. The buildings for leisure activities—theatres, amphitheatres, and baths—also formed an essential part of the urban existence. The final group of buildings to be considered are those for living and working in; these were an early part of urban construction and illustrate the continued investment throughout the Roman period. The chapter concludes by considering the nature of variability between the urban centres of the province.
Sinorhizobium meliloti Functionally Replaces 3-Oxoacyl-Acyl Carrier Protein Reductase (FabG) by Overexpressing NodG During Fatty Acid Synthesis
Authors: Mao Ya-Hui , Li Feng , Ma Jin-Cheng , Hu Zhe , Wang Hai-Hong
Published: March 2016

In Sinorhizobium meliloti, the nodG gene is located in the nodFEG operon of the symbiotic plasmid. Although strong sequence similarity (53% amino acid identities) between S. meliloti NodG and Escherichia coli FabG was reported in 1992, it has not been determined whether S. meliloti NodG plays a role in fatty acid synthesis. We report that expression of S. meliloti NodG restores the growth of the E. coli fabG temperature-sensitive mutant CL104 under nonpermissive conditions. Using in vitro assays, we demonstrated that NodG is able to catalyze the reduction of the 3-oxoacyl-ACP intermediates in E. coli fatty acid synthetic reaction. Moreover, although deletion of the S. meliloti nodG gene does not cause any growth defects, upon overexpression of nodG from a plasmid, the S. meliloti fabG gene encoding the canonical 3-oxoacyl-ACP reductase (OAR) can be disrupted without any effects on growth or fatty acid composition. This indicates that S. meliloti nodG encodes an OAR and can play a role in fatty acid synthesis when expressed at sufficiently high levels. Thus, a bacterium can simultaneously possess two or more OARs that can play a role in fatty acid synthesis. Our data also showed that, although SmnodG increases alfalfa nodulation efficiency, it is not essential for alfalfa nodulation.
Length of Efficacy for Control of Curly Top in Sugar Beet With Seed and Foliar Insecticides
Authors: Strausbaugh Carl A. , Wenninger Erik J. , Eujayl Imad A.
Published: March 2016

Curly top in sugar beet caused by Beet curly top virus (BCTV) is an important yield-limiting disease that can be reduced via neonicotinoid and pyrethroid insecticides. The length of efficacy of these insecticides is poorly understood; therefore, field experiments were conducted with the seed treatment Poncho Beta (clothianidin at 60 g a.i. + beta-cyfluthrin at 8 g a.i. per 100,000 seed) and foliar treatment Asana (esfenvalerate at 55.48 g a.i./ha). A series of four experiments at different locations in the same field were conducted in 2014 and repeated in a neighboring field in 2015, with four treatments (untreated check, Poncho Beta, Asana, and Poncho Beta + Asana) which were arranged in a randomized complete block design with eight replications. To evaluate efficacy, viruliferous (contain BCTV strains) beet leafhoppers were released 8, 9, 10, or 11weeks after planting for each experiment, which corresponded to 1, 2, 3, and 4 weeks after Asana application. Over both years, in 30 of 32 observation dates for treatments with Poncho Beta and 14 of 16 observation dates for Asana, visual curly top ratings decreased an average of 41 and 24%, respectively, with insecticide treatments compared with the untreated check. Over both years, in eight of eight experiments for treatments with Poncho Beta and six of eight experiments for Asana, root yields increased an average of 39 and 32%, respectively, with treatment compared with the untreated check. Over both years, the Poncho Beta treatments increased estimated recoverable sucrose (ERS) yield by 75% compared with the untreated check for weeks 8 and 9. By week 10, only the Poncho Beta + Asana treatment led to increases in ERS in both years, while the influence of increasing host resistance may have made other treatments more difficult to separate. When considering curly top symptoms, root yield, and ERS among all weeks and years, there was a tendency for the insecticides in the Poncho Beta + Asana treatment to complement each other to improve efficacy.
Mechanism of Action of the Benzimidazole Fungicide onFusarium graminearum: Interfering with Polymerization of Monomeric Tubulin But Not Polymerized Microtubule
Authors: Zhou Yujun , Xu Jianqiang , Zhu Yuanye , Duan Yabing , Zhou Mingguo
Published: March 2016

Tubulins are the proposed target of clinically relevant anticancer drugs, anthelmintic, and fungicide. β2-tubulin of the plant pathogen Fusarium graminearum was considered as the target of benzimidazole compounds by homology modeling in our previous work. In this study, α1-, α2-, and β2-tubulin of F. graminearum were produced in Escherichia coli. Three benzimidazole compounds (carbendazim, benomyl, and thiabendazole) interacted with the recombinant β2-tubulin and reduced the maximum fluorescence intensity of 2 μM β2-tubulin 47, 50, and 25%, respectively, at saturation of compound-tubulin complexes. Furthermore, carbendazim significantly inhibited the polymerization of α1-/β2-tubulins and α2-/β2-tubulins 90.9 ± 0.4 and 93.5 ± 0.05%, respectively, in vitro. A similar result appeared with benomyl on the polymerization of α1-/β2-tubulins and α2-/β2-tubulins at 89.9 ± 0.1% and 92.6 ± 1.2% inhibition ratios, respectively. In addition, thiabendazole inhibited 81.6 ± 1% polymerization of α1-/β2-tubulins, whereas it had less effect on α2-/β2-tubulin polymerization, with 20.1 ± 1.9% inhibition ratio. However, the three compounds cannot destabilize the polymerized microtubule. To illuminate the issue, mapping the carbendazim binding sites and β/α subunit interface on β/α-tubulin complexes by homology modeling showed that the two domains were closed to each other. Understanding the nature of the interaction between benzimidazole compounds and F. graminearum tubulin is fundamental for the development of tubulin-specific anti-F. graminearum compounds.