bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid determination of nanowires electrical properties using a dielectrophoresis-well based system
Authors: Constantinou Marios , Hoettges Kai F. , Krylyuk Sergiy , Katz Michael B. , Davydov Albert , Rigas Grigorios-Panagiotis , Stolojan Vlad , Hughes Michael P. , Shkunov Maxim
Published: March 2017

The use of high quality semiconducting nanomaterials for advanced device applications has been hampered by the unavoidable growth variability of electrical properties of one-dimensional nanomaterials, such as nanowires and nanotubes, thus highlighting the need for the characterization of efficient semiconducting nanomaterials. In this study, we demonstrate a low-cost, industrially scalable dielectrophoretic (DEP) nanowire assembly method for the rapid analysis of the electrical properties of inorganic single crystalline nanowires, by identifying key features in the DEP frequency response spectrum from 1 kHz to 20 MHz in just 60 s. Nanowires dispersed in anisole were characterized using a three-dimensional DEP chip (3DEP), and the resultant spectrum demonstrated a sharp change in nanowire response to DEP signal in 1–20 MHz frequency range. The 3DEP analysis, directly confirmed by field-effect transistor data, indicates that nanowires of higher quality are collected at high DEP signal frequency range above 10 MHz, whereas lower quality nanowires, with two orders of magnitude lower current per nanowire, are collected at lower DEP signal frequencies. These results show that the 3DEP platform can be used as a very efficient characterization tool of the electrical properties of rod-shaped nanoparticles to enable dielectrophoretic selective deposition of nanomaterials with superior conductivity properties.
Synchrotron radiation from a curved plasma channel laser wakefield accelerator
Authors: Palastro J. P. , Kaganovich D. , Hafizi B. , Chen Y.-H. , Johnson L. A. , Peñano J. R. , Helle M. H. , Mamonau A. A.
Published: March 2017

A laser pulse guided in a curved plasma channel can excite wakefields that steer electrons along an arched trajectory. As the electrons are accelerated along the curved channel, they emit synchrotron radiation. We present simple analytical models and simulations examining laser pulse guiding, wakefield generation, electron steering, and synchrotron emission in curved plasma channels. For experimentally realizable parameters, a ∼2 GeV electron emits 0.1 photons per cm with an average photon energy of multiple keV.
Prediction of irradiation induced microstructures using a multiscale method coupling atomistic and phase field modeling: Application to the AgCu model alloy
Authors: Demange G. , Lunéville L. , Pontikis V. , Simeone D.
Published: March 2017

Microstructure patterning using the ion beam mixing process results from the competition between thermal diffusion and ballistic disordering induced by impinging ions. Although microstructure patterning under irradiation is now qualitatively understood, so far, no study could quantitatively estimate irradiation conditions leading to patterning. In this work, a new multiscale approach based on phase field was developed to simulate the microstructure evolution, and the occurrence of patterning due to ion irradiation in a silver-copper alloy, from atomic to microstructural scale. For that purpose, an efficient numerical scheme was developed to simulate the microstructure dynamics, within the framework of phase field. Equilibrium parameters of AgCu were computed using a mixed Monte Carlo-molecular dynamics approach. Ballistic effects induced by krypton ion irradiation, and point defect recreation leading to irradiation enhanced diffusion, were estimated using the binary collision approximation framework. As a result, we predicted the range of temperatures and irradiation fluxes leading to the formation of patterned microstructures in the AgCu alloy under krypton ion irradiation. Results were summarized in a pseudo phase diagram in the temperature-flux plane. Our model was in good agreement with a previous diffraction experimental study.
Carrier capture in InGaN/GaN quantum wells: Role of electron-electron scattering
Authors: Vallone Marco , Goano Michele , Bertazzi Francesco , Ghione Giovanni
Published: March 2017

The competition of electron-electron interband scattering (ee) and longitudinal optical phonon emission (e-ph) as electron capture mechanisms is theoretically investigated in III-nitride quantum wells. The non-trivial separation of their scattering probabilities is discussed, and compact expressions for capture time are obtained in the framework of the quantum many-body formalism. At the typical operating conditions of light emitting diodes (LEDs), the model predicts an increasing importance of ee scattering as a capture mechanism with increasing carrier density. Verifications against recent experiments are presented to support this finding and confirm the need for population-dependent capture time expressions including both ee and e-ph mechanisms for an accurate description of LED carrier dynamics and efficiency.
Analogue of ultra-broadband and polarization-independent electromagnetically induced transparency using planar metamaterial
Authors: Hu Sen , Liu Dan , Lin Hai , Chen Jiao , Yi Yuanyuan , Yang Helin
Published: March 2017

In this paper, a classical analogue of electromagnetically induced transparency (EIT) metamaterial is numerically and experimentally demonstrated. The unit cell of our proposed structure is composed of two identical and orthogonal double-end fork (DEF) metallic resonators. Under the excitation of the normally incident waves, each of the two DEFs exhibits different frequency of electric dipole response, which leads to the ultra-broadband and polarization-independent EIT-like effect. The resonant feature of the EIT-like effect has been qualitatively analyzed from the surface current distributions and quantitatively by the “two-oscillator” coupling model. In addition, the large group index is extracted to verify the slow light property within the transmission window. The EIT metamaterial structure with the above-mentioned characteristics may have potential applications in some areas, such as sensing, slow light, and filtering devices.
Mass spectrometric investigations of plasma chemical reactions in a radiofrequency discharge with Ar/C2H2 and Ar/C2H2/O2 gas mixtures
Authors: Herrendorf Ann-Pierra , Sushkov Vladimir , Hippler Rainer
Published: March 2017

Plasma chemical reactions in complex Ar/C2H2 and Ar/C2H2/O2 radiofrequency plasmas with formation of nano-particles are investigated. Growing nano-particles cause a growth instability, which leads to temporal variations and a cyclic behaviour of plasma properties. Mass spectrometric observations show the consumption of C2H2 and the formation of polyacetylene C2nH2 molecules which increases with acetylene gas flow. The cycle frequency is a decreasing function of acetylene consumption. The addition of oxygen to the discharge reduces the cycle frequency and the formation of nano-particles and leads to the formation of CO and CO2 molecules presumably through the oxidation of C2H radicals which are formed in the discharge.
Description and stability analysis of nonlinear transmission line type metamaterials using nonlinear dynamics theory
Authors: Elnaggar Sameh Y. , Milford Gregory N.
Published: March 2017

Nonlinear metamaterials offer a potential technology to realize applications at microwave, terahertz, and optical frequencies. However, due to the strong and controlled nonlinearity, the wave interactions can be quite complex. In the current article, a framework based on nonlinear dynamics theory is developed to describe such complex interactions. This is demonstrated for the case of a harmonically pumped nonlinear left handed transmission line through the use of bifurcation theory, stability analysis, and linearization about the limit cycle to calculate the autonomously generated frequencies and their spatial distributions. Higher order parametric interactions, which can be mediated by the strong nonlinearity, are automatically included in the model. It is demonstrated that autonomous components can be visualized in both the phase and the set of solution spaces. The framework is general in terms of the transmission line configuration, the nature and strength of the nonlinearity, and the number of stages. It also provides accurate results when the autonomous frequencies are in the vicinity of the Bragg frequency.
Nonadiabatic ab initio molecular dynamics study of photoisomerization in N-salicilydenemethylfurylamine (SMFA)
Authors: Gao Ai-Hua , Wang Mei-Shan
Published: March 2017

The photoisomerization mechanisms of N-salicilydenemethylfurylamine upon excitation to the first singlet state are investigated by means of surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Due to different orientations of the methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring, various stable structures are obtained in the optimization. The enol isomer, S0-ENOL-5a, is the most stable conformer. An ultrafast excited-state intramolecular proton transfer is observed after photoexcitation of the most stable enol conformer and then the molecule reaches the excited-state minimum. After the internal conversion around a conical intersection, the system relaxes to either the cis-keto or trans-keto region in the ground state. The potential energy profiles of the ground and the first excited singlet state are also calculated. According to full-dimensional nonadiabatic dynamics simulations and potential energy profiles, the trans-keto and cis-keto photoproducts can be responsible for the photochromic effect of N-salicilydenemethylfurylamine.
Eu-doping effects on the structural and multiferroic properties of YMn0.5Cr0.5O3
Authors: Xie Xiangnan , Hao Lin , Wang Haoru , Lin Guankai , Zhu Hong
Published: March 2017

Y1−xEuxMn0.5Cr0.5O3 (x = 0.1–1.0) oxides were synthesized in a polycrystalline form by a conventional solid-state reaction method. X-ray diffraction patterns revealed that the whole series of compounds featured a simple distorted perovskite structure with the orthorhombic space group Pbnm. With increasing Eu content, the shorter a and c axes increased, while the longest b axis changed little. The ferrimagnetic transition temperature TN increased gradually to x = 0.8 before declining with a further increase in x. A clear correlation between TN and the negative molecular field coefficient within the Cr3+ sublattice indicated that an antiferromagnetic exchange interaction between the Cr3+ cations plays a dominant role in the magnetic ordering. By reversing the sign of the poling field, the occurrence of electric polarization reversal at temperatures around TN implied a possible multiferroic state in the samples. From the dielectric point of view, the disappearance of the dielectric constant anomaly at TN might be related to the high AC conductivity of the samples, which is a common feature of orthochromites.
Cobalt substitution induced magnetodielectric enhancement in multiferroic Bi2Fe4O9
Authors: Mohapatra S. R. , Vishwakarma P. N. , Kaushik S. D. , Choudhary R. J. , Mohapatra N. , Singh A. K.
Published: March 2017

Antiferromagnetic Bi2Fe4O9 (BFO) lightly substituted by cobalt is studied for magnetodielectricity. The substitution causes a substantial decrease in the Néel temperature (TN) from 250 K (in the parent sample, BFO) to 152 K (in the 2% Co substituted sample). At the same time, the substituted samples display a pronounced irreversibility in the zero field cooled-field cooled magnetization data for T < 370 K and opening of hysteresis in the M-H plot, thus signifying the onset of weak ferromagnetism and magnetic glassiness. The induced magnetic glassiness is found to slow down the dynamics such that the magnetization decay follows M(t)∝ exp[−(t)1−p]. The dielectric measurement in the same temperature window shows the unusual oppression in ε′ for T ∼ TN and the contrasting nature of tan loss for temperatures above and below TN, thus hinting a plausible coupling between the magnetic and electric order parameters. A confirmation to this coupling is seen in the magnetodielectric (MD) results, in which it is found that the substitution induces an additional component in the MD, apart from the usual components in BFO. This additional component of MD is found to obey ∝exp (ω)n behaviour, with the “n” values being comparable to “1-p” of magnetization. The temperature variation of MD also shows a contrasting behaviour for the parent and 2% Co substituted samples with an enhancement of two times in the MD value. In summary, our study shows that magnetoelectric coupling introduced by the magnetic glassiness and its behaviour is very much different from the intrinsic one.
A549 and MRC-5 cell aggregation in a microfluidic Lab-on-a-chip system
Authors: Zuchowska A. , Jastrzebska E. , Zukowski K. , Chudy M. , Dybko A. , Brzozka Z.
Published: March 2017

In this paper, we present a culture of A549 and MRC-5 spheroids in a microfluidic system. The aim of our work was to develop a good lung cancer model for the evaluation of drug cytotoxicity. Our research was focused on determining the progress of cell aggregation depending on such factors as the depth of culture microwells in the microdevices, a different flow rate of the introduced cell suspensions, and the addition of collagen to cell suspensions. We showed that these factors had a significant influence on spheroid formation. It was found that both MRC-5 and A549 cells exhibited higher aggregation in 500 μm microwells. We also noticed that collagen needs to be added to A549 cells to form the spheroids. Optimizing the mentioned parameters allowed us to form 3D lung tissue models in the microfluidic system during the 10-day culture. This study indicates how important an appropriate selection of the specified parameters is (e.g., geometry of the microwells in the microsystem) to obtain the spheroids characterized by high viability in the microfluidic system.
Introduction to Focus Issue: Complex network perspectives on flow systems
Authors: Donner Reik V. , Hernández-García Emilio , Ser-Giacomi Enrico
Published: March 2017

During the last few years, complex network approaches have demonstrated their great potentials as versatile tools for exploring the structural as well as dynamical properties of dynamical systems from a variety of different fields. Among others, recent successful examples include (i) functional (correlation) network approaches to infer hidden statistical interrelationships between macroscopic regions of the human brain or the Earth's climate system, (ii) Lagrangian flow networks allowing to trace dynamically relevant fluid-flow structures in atmosphere, ocean or, more general, the phase space of complex systems, and (iii) time series networks unveiling fundamental organization principles of dynamical systems. In this spirit, complex network approaches have proven useful for data-driven learning of dynamical processes (like those acting within and between sub-components of the Earth's climate system) that are hidden to other analysis techniques. This Focus Issue presents a collection of contributions addressing the description of flows and associated transport processes from the network point of view and its relationship to other approaches which deal with fluid transport and mixing and/or use complex network techniques.
Parametric decay of plasma waves near the upper-hybrid resonance
Authors: Dodin I. Y. , Arefiev A. V.
Published: March 2017

An intense X wave propagating perpendicularly to dc magnetic field is unstable with respect to a parametric decay into an electron Bernstein wave and a lower-hybrid wave. A modified theory of this effect is proposed that extends to the high-intensity regime, where the instability rate γ ceases to be a linear function of the incident-wave amplitude. An explicit formula for γ is derived and expressed in terms of cold-plasma parameters. Theory predictions are in reasonable agreement with the results of the particle-in-cell simulations presented in a separate publication.
Attainment of a stable, fully detached plasma state in innovative divertor configurations
Authors: Umansky M. V. , LaBombard B. , Brunner D. , Rensink M. E. , Rognlien T. D. , Terry J. L. , Whyte D. G.
Published: March 2017

A computational study of long-legged tokamak divertor configurations is performed with the edge transport code UEDGE. Several divertor configurations are considered, with radially or vertically extended, tightly baffled, outer divertor legs and with or without a secondary X-point in the divertor leg volume. For otherwise identical conditions, a scan of the input power from the core plasma is performed. As the power is reduced to a threshold value, the plasma in the outer leg transitions to a fully detached state, which defines the upper limit on the power for detached divertor operation. Reducing the power further results in the detachment front shifting upstream but remains stable. At low power, the detachment front eventually moves all the way to the primary X-point, which is usually associated with degradation of the core plasma, and this defines the lower limit on the power for the detached divertor operation. For the studied parameters, for long-legged divertors, the detached operation window is quite large, in particular, for the X-point target configuration using a secondary X-point in the divertor leg volume, allowing a factor of 5–10 variations in the input power. For the same parameters, for the standard divertor configuration, the detached operation window is very small or even non-existent. The present modeling results suggest the possibility of stable fully detached divertor operation for a tokamak with tightly baffled extended divertor legs.
Magneto-optical Kerr spectroscopy of (Ga,Mn)(As,P) ferromagnetic layers: Experiments and k.p theory
Authors: Yahyaoui M. , Riahi H. , Maaref M. A. , Boujdaria K. , Lemaître A. , Thevenard L. , Gourdon C.
Published: March 2017

We present a theoretical and experimental study of the magneto-optical properties of thin (Ga,Mn)(As,P) layers on GaAs substrates with varying phosphorus fractions. Using a 40-band k.p model as well as an antiferromagnetic (s, p)-d exchange interaction, we calculate the dielectric tensor, the Kerr rotation angle, and the ellipticity in the interband transition region. Our calculations are validated through a set of accurate comparisons with experimental results. The Kerr ellipticity peak is found to be 2 to 3 times larger than the Kerr rotation angle both experimentally and theoretically. This work will enable to optimize the magneto-optical effects in these layers for maximum sensitivity in ultra-fast magnetization dynamics and domain microscopy experiments.
Investigation of factors affecting electrical contacts on single germanium nanowires
Authors: Sett Shaili , Das K. , Raychaudhuri A. K.
Published: March 2017

We report an experimental investigation of the quality of electrical contacts made on single Germanium nanowires (grown using Au catalyst from vapor) using Cr/Au contact pads. The nanowires are single crystalline and have a thin layer of oxide on them. We find that a low specific contact resistivity of 10−6 Ω cm2 can be obtained in nanowires with low resistance and the contact resistance enhances almost linearly with the nanowire resistivity. The metal semiconductor junction shows an ideality factor close to unity. A low barrier height of 0.15 eV can be obtained in nanowires of lower resistivities which increase to nearly 0.3 eV for nanowires of higher resistivity. The experiments were carried down to 10 K, and junction characteristics as a function of temperature were evaluated. The specific contact resistance increases on cooling but the barrier shows suppression as the nanowire is cooled, along with an enhancement of the ideality factor. We analyze the temperature dependence of these parameters using a model that assumes a Gaussian distribution of barrier heights in the contact region. The temperature dependence predicted by the model was observed, and the relevant parameters were obtained from the data.
Systematic modulation of negative-differential transconductance effects for gated p+-i-n+ silicon ultra-thin body transistor
Authors: Kim Changmin , Lee Youngmin , Lee Sejoon
Published: March 2017

We demonstrate the precise control of the negative-differential transconductance (NDT) effects on a gated p+-i-n+ Si ultra-thin body transistor. The device clearly displays the N-shape transfer characteristic (i.e., NDT effect) at room temperature, and the NDT behavior is fully based on the gate-modulation of the electrostatic junction characteristics. The position and the current level of the peak in the NDT region are systematically controllable when modulating the potential profile at the channel-source junction. Namely, the NDT effect can be systematically modulated through modifying the band-to-band tunneling condition by controlling both gate- and drain-bias voltages. In-depth analyses on the transport characteristics and transport mechanisms are discussed.
Solution-processed high-mobility neodymium-substituted indium oxide thin-film transistors formed by facile patterning based on aqueous precursors
Authors: Lin Zhenguo , Lan Linfeng , Sun Sheng , Li Yuzhi , Song Wei , Gao Peixiong , Song Erlong , Zhang Peng , Li Meiling , Wang Lei , Peng Junbiao
Published: March 2017

Solution-processed neodymium-substituted indium oxide (InNdO) thin-film transistors (TFTs) based on gel-like aqueous precursors were fabricated with a surface-selective deposition technique associated with ultraviolet irradiation. The Nd concentration can be easily tuned by changing the ratio of Nd2O3 to In2O3 precursors. It was found that Nd played roles of suppressing grain growth, suppressing oxygen vacancy formation, and increasing the electrical stability of TFTs. The InNdO TFT with a Nd:In ratio of 0.02:1 exhibited a mobility of as high as 15.6 cm2 V−1 s−1 with improved stability under gate-bias stress.
Communication: Enthalpy relaxation in a metal-organic zeolite imidazole framework (ZIF-4) glass-former
Authors: Xu Di , Liu Yingdan , Tian Yongjun , Wang Li-Min
Published: March 2017

Amorphization in metal-organic framework materials initiated by the collapsed crystal offers new access to glasses; however, the understanding of such glasses remains to be clarified. Here, we studied the glass transition thermodynamics and kinetics in a zeolitic imidazolate framework ZIF-4 utilizing enthalpy relaxation measurements. The calorimetric glass transition profile and relaxation behaviors in ZIF-4 are found to reproduce the basic features and correlations manifested by conventional melt-quenched glasses. A comparison with various melt-quenched glasses suggests that the low fragility of ZIF-4 is ascribed to the low thermal-pressure coefficient due to the directional tetrahedral bond, partly leading to the low vibrational entropy in the melt-crystal entropy difference.
Origin of anomalous cryogenic magnetic behavior in a Ni-Mn-based magnetic shape memory alloy
Authors: Sun X. M. , Cong D. Y. , Liss K.-D. , Qu Y. H. , Ma L. , Suo H. L. , Wang Y. D.
Published: March 2017

The origin of the anomalous low-temperature staircase-like magnetization behavior in magnetic shape memory alloys, which has been commonly observed in a large variety of materials, has been remaining a mystery since it was discovered. Here, we elucidate the underlying mechanism for such anomalous magnetic behavior via tracing the structural evolution during applying magnetic fields at 4 K in an archetypal Ni-Mn-based magnetic shape memory alloy, by in-situ neutron diffraction technique. We found that it is the magnetic-field-induced structural transformation occurring at this extremely low temperature (far below martensitic transformation temperature) that is responsible for the anomalous low-temperature magnetic behavior. It is believed that this transformation proceeds by a succession of discrete steps, accounting for the abrupt jumps on the magnetization curve. The present study provides deep insights into the interplay between magnetism and structure in magnetic shape memory alloys, and it is also instructive for understanding the anomalous staircase-like magnetization behavior in other materials undergoing a magnetostructural transition.
Influence of dislocation density on internal quantum efficiency of GaN-based semiconductors
Authors: Yu Jiadong , Hao Zhibiao , Li Linsen , Wang Lai , Luo Yi , Wang Jian , Sun Changzheng , Han Yanjun , Xiong Bing , Li Hongtao
Published: March 2017

By considering the effects of stress fields coming from lattice distortion as well as charge fields coming from line charges at edge dislocation cores on radiative recombination of exciton, a model of carriers’ radiative and non-radiative recombination has been established in GaN-based semiconductors with certain dislocation density. Using vector average of the stress fields and the charge fields, the relationship between dislocation density and the internal quantum efficiency (IQE) is deduced. Combined with related experimental results, this relationship is fitted well to the trend of IQEs of bulk GaN changing with screw and edge dislocation density, meanwhile its simplified form is fitted well to the IQEs of AlGaN multiple quantum well LEDs with varied threading dislocation densities but the same light emission wavelength. It is believed that this model, suitable for different epitaxy platforms such as MOCVD and MBE, can be used to predict to what extent the luminous efficiency of GaN-based semiconductors can still maintain when the dislocation density increases, so as to provide a reasonable rule of thumb for optimizing the epitaxial growth of GaN-based devices.
Oviposition periodicity, egg morphology and life history of large cabbage moth Crocidolomia pavonana population in Samoa
Authors: Sulifoa John B. , Fangupo Sateki , Kant Rashmi
Published: March 2017

A study on the biology and behaviour of the Samoan population of Crocidolomia pavonana was carried out through a series of experiments. The study showed that C. pavonana completes its life cycle in 24-35 days. Female emerge, mate and oviposit (as egg mass) during the scotophase. The average size of egg mass was 9.0 ± 0.48 mm2 and the mean number of eggs oviposited were significantly (PC. pavonana oviposits small egg masses. This information could be used to develop effective pest management using the recently identified egg parasitoid Trichogramma chilonis.
Climate change both facilitates and inhibits invasive plant ranges in New England
Authors: Merow Cory , Bois Sarah Treanor , Allen Jenica M. , Xie Yingying , Silander John A.
Published: March 2017

Significance

Invasive species are often expected to benefit from novel conditions encountered with global change. Our range models based on demography show that invasive
Alliaria petiolata
(garlic mustard) may have much lower establishment in New England under future climate, despite prolific success under current climate, whereas other invasive and native plants may expand their ranges. Forecasts suggest that management should focus on inhibiting northward spread of
A. petiolata
into unoccupied areas and understanding source–sink population dynamics and how community dynamics might respond to loss of
A. petiolata
(it modifies soil properties). Our methods illustrate inadequacy of current approaches to forecasting invasions in progress, which are based on correlations between species’ occurrence and environment and illustrate critical need for mechanistic studies.
Why the US science and engineering workforce is aging rapidly
Authors: Blau David M. , Weinberg Bruce A.
Published: March 2017

Significance

The science and engineering workforce has aged rapidly, both absolutely and relative to the workforce, which is a concern if the large number of older scientists crowds out younger scientists. Moreover, scientists are believed to be most creative earlier in their careers, so the aging of the workforce may slow the pace of scientific progress. We study the causes of this aging, showing that a substantial majority is a result of the aging of the large baby boom cohort of scientists, but the elimination of mandatory retirement in universities in 1994 was also an important factor. Strikingly, current patterns imply a steady-state mean age 2.3 y higher than the 2008 level of 48.6.
Form and function of topologically associating genomic domains in budding yeast
Authors: Eser Umut , Chandler-Brown Devon , Ay Ferhat , Straight Aaron F. , Duan Zhijun , Noble William Stafford , Skotheim Jan M.
Published: March 2017

Significance

In metazoans, topological domains are regions in the genome that more frequently associate with themselves than with neighboring regions. These domains are important for regulating transcription and replication. However, topological domains were thought to be absent in budding yeast. Thus, we did not know the degree of conservation of topological organization and its associated functions. Herein, we describe the existence of topologically associating domains in budding yeast and show that these domains regulate replication timing so that origins within a domain fire synchronously. Our work showing conservation in budding yeast sets the stage to use yeast genetics to interrogate the molecular basis of the topological domains defining genome architecture.
Myosin-1E interacts with FAK proline-rich region 1 to induce fibronectin-type matrix
Authors: Heim Joel B. , Squirewell Edwin J. , Neu Ancilla , Zocher Georg , Sominidi-Damodaran Sindhuja , Wyles Saranya P. , Nikolova Ekaterina , Behrendt Nille , Saunte Ditte M. , Lock-Andersen Jorgen , Gaonkar Krutika S. , Yan Huihuang , Sarkaria Jann N. , Krendel Mira , van Deursen Jan , Sprangers Remco , Stehle Thilo , Böttcher Ralph T. , Lee Jeong-Heon , Ordog Tamas , Meves Alexander
Published: March 2017

Significance

Focal adhesion kinase (FAK) is an intensely studied protein involved in many medically relevant biological processes, including cancer. Despite the large interest in FAK, a promising strategy to target FAK therapeutically is elusive. Here, we show that a region within the FAK protein that contains autophosphorylation site tyrosine (Y) 397 is essential for FAK activity in vivo. Myosin-1E (MYO1E), an actin-dependent molecular motor protein, directly interacts with FAK to induce Y397 autophosphorylation, which, in turn, causes changes in gene expression commonly observed in aggressive cancer. Our findings are significant because they further delineate FAK function in vivo and identify the MYO1E–FAK interaction as a possible Achilles’ heel for cancer.
Evolution of the early Antarctic ice ages
Authors: Liebrand Diederik , de Bakker Anouk T. M. , Beddow Helen M. , Wilson Paul A. , Bohaty Steven M. , Ruessink Gerben , Pälike Heiko , Batenburg Sietske J. , Hilgen Frederik J. , Hodell David A. , Huck Claire E. , Kroon Dick , Raffi Isabella , Saes Mischa J. M. , van Dijk Arnold E. , Lourens Lucas J.
Published: March 2017

Significance

The Antarctic ice cap waxed and waned on astronomical time scales throughout the Oligo-Miocene time interval. We quantify geometries of Antarctic ice age cycles, as expressed in a new climate record from the South Atlantic Ocean, to track changing dynamics of the unipolar icehouse climate state. We document numerous ∼110-thousand-year-long oscillations between a near-fully glaciated and deglaciated Antarctica that transitioned from being symmetric in the Oligocene to asymmetric in the Miocene. We infer that distinctly asymmetric ice age cycles are not unique to the Late Pleistocene or to extremely large continental ice sheets. The patterns of long-term change in Antarctic climate interpreted from this record are not readily reconciled with existing CO
2
records.
Live imaging of root–bacteria interactions in a microfluidics setup
Authors: Massalha Hassan , Korenblum Elisa , Malitsky Sergey , Shapiro Orr H. , Aharoni Asaph
Published: March 2017

Significance

Microbial interactions in the rhizosphere, the microenvironment surrounding plant roots, are a major research area for both plant biologists and microbial ecologists. A significant obstacle in this field is the difficulty in studying root–bacteria interactions in real time. Here, we developed a microfluidics-based device that allows dynamic imaging of root–bacterial interactions at previously unattainable spatiotemporal resolutions. The intimate interaction of
Bacillus subtilis
with plant roots is accurately traced in high resolution to the root elongation zone. We further reveal how bacterial behavior leads to rapid root colonization and exclusion of competing bacteria. Hence, this approach has the potential to transform our understanding of root–bacteria interactions and the modulation of bacterial communities colonizing the root surface.
Mechanism of transcription initiation and promoter escape by
E
.
coli
RNA polymerase
Authors: Henderson Kate L. , Felth Lindsey C. , Molzahn Cristen M. , Shkel Irina , Wang Si , Chhabra Munish , Ruff Emily F. , Bieter Lauren , Kraft Joseph E. , Record M. Thomas
Published: March 2017

Significance

The enzyme RNA polymerase (RNAP) transcribes DNA genetic information into RNA. Regulation of transcription occurs largely in initiation; these regulatory mechanisms must be understood. Lifetimes of transcription-capable RNAP-promoter open complexes (OCs) vary greatly, dictated largely by the DNA discriminator region, but the significance of OC lifetime for regulation was unknown. We observe that a significantly longer RNA:DNA hybrid is synthesized before RNAP escapes from long-lived λP
R
-promoter OCs as compared with shorter-lived T7A1 promoter OCs. We quantify the free energy needed to overcome OC stability and allow escape from the promoter and elongation of the nascent RNA, and thereby predict escape points for ribosomal (rrnB P1) and lacUV5 promoters. Longer-lived OCs produce longer abortive RNAs, which likely have specific regulatory roles.
Optical visualization and quantification of enzyme activity using dynamic droplet lenses
Authors: Zarzar Lauren D. , Kalow Julia A. , He Xinping , Walish Joseph J. , Swager Timothy M.
Published: March 2017

Significance

A nonfluorescence-based technology is introduced that can lead to visual detection of enzyme activity. These results represent a dramatically different paradigm for creating sensors based on dynamic liquid lenses with general utility.
Origins of house mice in ecological niches created by settled hunter-gatherers in the Levant 15,000 y ago
Authors: Weissbrod Lior , Marshall Fiona B. , Valla François R. , Khalaily Hamoudi , Bar-Oz Guy , Auffray Jean-Christophe , Vigne Jean-Denis , Cucchi Thomas
Published: March 2017

Significance

Decreases in hunter-gatherer mobility during the Late Pleistocene altered relationships with animal communities and led to domestication. Little is known, however, about how selection operated in settlements of varying duration. This study of mice in modern African mobile settlements and ancient Levantine sites demonstrates competitive advantages for commensal mice when human mobility is low and niche partitioning with noncommensal wild mice when mobility increases. Changing mice molar shapes in a 200,000-y-long sequence from the Levant reveal that mice first colonized settlements of relatively settled hunter-gatherers 15,000 y ago. The first long-term hunter-gatherer settlements transformed ecological interactions and food webs, allowing commensal house mice to outcompete wild mice and establish durable populations that expanded with human societies.
Complement modulation in the retinal pigment epithelium rescues photoreceptor degeneration in a mouse model of Stargardt disease
Authors: Lenis Tamara L. , Sarfare Shanta , Jiang Zhichun , Lloyd Marcia B. , Bok Dean , Radu Roxana A.
Published: March 2017

Significance

The complement system, a key component of innate immunity, is necessary to maintain tissue homeostasis. In the eye, the retinal pigment epithelium (RPE) plays a major role in controlling the immune response through expression of various complement negative regulatory proteins (CRPs). Here we identify that inappropriate activation of the complement cascade plays a role in the pathogenesis of recessive Stargardt disease (STGD1). Using the STGD1 mouse model, we show that overexpression of the complement receptor 1-like protein y, a major murine CRP, reduces complement attack on the RPE and rescues both bisretinoid accumulation and photoreceptor degeneration. Our data demonstrate that STGD1 presents with dysregulation of the complement system as also has been proposed for age-related macular degeneration, supporting a common etiologic pathway.
Quantification of circulating
Mycobacterium tuberculosis
antigen peptides allows rapid diagnosis of active disease and treatment monitoring
Authors: Liu Chang , Zhao Zhen , Fan Jia , Lyon Christopher J. , Wu Hung-Jen , Nedelkov Dobrin , Zelazny Adrian M. , Olivier Kenneth N. , Cazares Lisa H. , Holland Steven M. , Graviss Edward A. , Hu Ye
Published: March 2017

Significance

Active
Mycobacterium tuberculosis
(
Mtb
) infections represent a significant global health threat, but can be difficult to diagnose and manage owing to the nonquantitative nature and relatively poor performance of current frontline sputum-based diagnostic assays, which can be further degraded by certain
Mtb
manifestations. This study describes the development of a rapid and quantitative blood-based assay with high sensitivity and specificity for active
Mtb
infections that can be used to monitor responses to antimycobacterial therapy. Our method combines antibody-labeled, energy-focusing nanodisks with high-throughput mass spectrometry to enhance the detection of
Mtb
-specific peptides in digested serum samples, and should allow rapid clinical translation. This approach also should be applicable to other infectious diseases, particularly those for which conventional immunoassays exhibit suboptimal performance.
In situ characterization of cofacial Co(IV) centers in Co
4
O
4
cubane: Modeling the high-valent active site in oxygen-evolving catalysts
Authors: Brodsky Casey N. , Hadt Ryan G. , Hayes Dugan , Reinhart Benjamin J. , Li Nancy , Chen Lin X. , Nocera Daniel G.
Published: March 2017

Significance

The Co-OEC (oxygen-evolving catalyst) is an exemplary OEC that has provided a wealth of kinetics information on the proton-coupled electron transfer mechanism of O–O bond formation. Whereas electrochemical kinetics studies establish a high-valent Co(IV)
2
oxidation state as a prerequisite for catalysis, this species cannot be spectroscopically examined in thin-film Co-OECs owing to its short lifetime and dilution against a largely Co(III) background. A molecular model of this high-valent active species is provisioned in the form of a doubly oxidized Co(III)
2
(IV)
2
cubane. In situ X-ray absorption spectroscopic examination of this high-valent state of the cubane provides direct insights into the electronic structure of a Co(IV)
2
site and into its role in the mechanism of O–O bond formation.
The transcription factor Foxo1 controls germinal center B cell proliferation in response to T cell help
Authors: Inoue Takeshi , Shinnakasu Ryo , Ise Wataru , Kawai Chie , Egawa Takeshi , Kurosaki Tomohiro
Published: March 2017

Germinal center (GC) B cells cycle between two states, the light zone (LZ) and the dark zone (DZ), and in the latter they proliferate and hypermutate their immunoglobulin genes. How this functional transition takes place is still controversial. In this study, we demonstrate that ablation of Foxo1 after GC development led to the loss of the DZ GC B cells and disruption of the GC architecture, which is consistent with recent studies. Mechanistically, even upon provision of adequate T cell help, Foxo1-deficient GC B cells showed less proliferative expansion than controls. Moreover, we found that the transcription factor BATF was transiently induced in LZ GC B cells in a Foxo1-dependent manner and that deletion of BATF similarly led to GC disruption. Thus, our results are consistent with a model where the switch from the LZ to the DZ is triggered after receipt of T cell help, and suggest that Foxo1-mediated BATF up-regulation is at least partly involved in this switch.
CXCR1 remodels the vascular niche to promote hematopoietic stem and progenitor cell engraftment
Authors: Blaser Bradley W. , Moore Jessica L. , Hagedorn Elliott J. , Li Brian , Riquelme Raquel , Lichtig Asher , Yang Song , Zhou Yi , Tamplin Owen J. , Binder Vera , Zon Leonard I.
Published: March 2017

The microenvironment is an important regulator of hematopoietic stem and progenitor cell (HSPC) biology. Recent advances marking fluorescent HSPCs have allowed exquisite visualization of HSPCs in the caudal hematopoietic tissue (CHT) of the developing zebrafish. Here, we show that the chemokine cxcl8 and its receptor, cxcr1, are expressed by zebrafish endothelial cells, and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization. Single-cell tracking experiments demonstrated that this is a result of increases in HSPC–endothelial cell “cuddling,” HSPC residency time within the CHT, and HSPC mitotic rate. Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression. Finally, using parabiotic zebrafish, we show that cxcr1 acts HSPC nonautonomously to improve the efficiency of donor HSPC engraftment. This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation.
Living in an adaptive world: Genomic dissection of the genus Homo and its immune response
Authors: Quach Hélène , Quintana-Murci Lluis
Published: March 2017

More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
Long-term photometric behavior of the eclipsing cataclysmic variable V729 Sagittarii
Authors: Han Zhong-Tao , Qian Sheng-Bang , Fernández-Lajús Eduardo , Voloshina Irina , Zhu Li-Ying
Published: March 2017

We present the analysis results of an eclipsing cataclysmic variable (CV) V729 Sgr, based on our observations and American Association of Variable Star Observers data. Some outburst parameters are determined, such as outburst amplitude (An) and recurrence time (Tn), and then the relationship between An and Tn is discussed. A cursory examination of the long-term light curves reveals that there are small-amplitude outbursts and dips present, which is similar to the behavior seen in some novalike CVs (NLs). More detailed inspection suggests that the outbursts in V729 Sgr may be Type A (outside-in) with a rise time ∼1.76 d. Further analysis also shows that V729 Sgr is an intermediate between dwarf nova and NLs, and we constrain its mass transfer rate to $1.59\times 10^{-9}<\skew5\dot{M}_{2}<5.8\times 10^{-9}\,M_{\odot }\:$yr−1 by combining the theory for Z Cam type stars with observations. Moreover, the rapid oscillations in V729 Sgr were detected and analyzed for the first time. Our results indicate that the oscillation at ∼25.5 s is a true dwarf nova oscillation (DNO), being associated with the accretion events. The classification of the oscillations at ∼136 and 154 s as longer-period DNOs (lpDNOs) is based on the relation between PlpDNOs and PDNOs. Meanwhile, quasi-periodic oscillations with periods of hundreds of seconds are also detected.
Extraction and Film Properties of Kafirin from Coarse Sorghum and Sorghum DDGS by Percolation
Authors: Muhiwa Peter J. , Taylor Janet , Taylor John R. N.
Published: March 2017

The high cost of kafirin and zein restricts their use for bioplastic and food applications. Effective, simple, and rapid kafirin/zein isolation processes are required. Here a percolation‐type aqueous ethanol solvent extraction process from coarse meals (grits) and coarse sorghum distillers dried grains and solubles (DDGS) for kafirin and zein isolation employing a low ratio of extractant to meal (2.5:1) was investigated, which is potentially applicable in the grain bioethanol industry. Postextraction filtration times were more than twice as fast using coarse meals compared with fine flours. Washing the meals prior to extraction to remove starch improved protein preparation purity to 73–85% compared with 68–72% for unwashed meals. Hence, no subsequent filtration or centrifugation step is required to clean up the kafirin/zein solution prior to solvent evaporation. With a single extraction step, kafirin/zein yields were 48% (protein basis) for DDGS and 53–70% for washed sorghum/maize meals. Cast films were used as a model bioplastic system to evaluate extracted kafirin/zein functional properties. DDGS kafirin films had rough surfaces but had the lowest water uptake and in vitro digestibility, owing to heat‐induced disulfide crosslinking during DDGS processing. Extraction by percolation using coarse meal/DDGS has potential to improve kafirin/zein viability.
Delayed Referral Results in Missed Opportunities for Organ Donation After Circulatory Death
Authors: Krmpotic Kristina , Payne Clare , Isenor Cynthia , Dhanani Sonny
Published: March 2017

Objectives:

Rates of organ donation and transplantation have steadily increased in the United States and Canada over the past decade, largely attributable to a notable increase in donation after circulatory death. However, the number of patients awaiting solid organ transplantation continues to remain much higher than the number of organs transplanted each year. The objective of this study was to determine the potential to increase donation rates further by identifying gaps in the well-established donation after circulatory death process in Ontario.

Design:

Retrospective cohort study.

Setting:

Provincial organ procurement organization.

Patients:

Patients who died in designated donation hospitals within the province of Ontario, Canada between April 1, 2013, and March 31, 2015.

Interventions:

None.

Measurements and Main Results:

Of 1,407 patient deaths following planned withdrawal of life-sustaining therapy, 54.0% (n = 760) were medically suitable for donation after circulatory death. In 438 cases where next of kin was approached, consent rates reached 47.5%. A total of 119 patients became actual organ donors. Only 66.2% (n = 503) of suitable patients were appropriately referred, resulting in 251 missed potential donors whose next of kin could not be approached regarding organ donation because referral occurred after initiation of withdrawal of life-sustaining therapy or not at all.

Conclusions:

The number of medically suitable patients who die within 2 hours of planned withdrawal of life-sustaining therapy is nearly six times higher than the number of actual organ donors, with the greatest loss of potential due to delayed referral until at the time of or after planned withdrawal of life-sustaining therapy. Intensive care teams are not meeting their ethical responsibility to recognize impending death and appropriately refer potential organ donors to the local organ procurement organization. In cases where patients had previously registered their consent decision, they were denied a healthcare right.