bluuebunny/crossref_metadata_2025 huggingface dataset:
Alveolar Hemorrhage in Vasculitis (Primary and Secondary)
Authors: Nasser Mouhamad , Cottin Vincent
Published: November 2018

Defined by the accumulation of red blood cells into the alveolar space, diffuse alveolar hemorrhage (DAH) is a severe and potentially fatal medical condition requiring careful attention. In contrast to simple extravasation of erythrocytes facilitated by impaired hemostasis or hemodynamic causes, DAH in vasculitis is due to capillaritis, that is, inflammation of capillaries. Dyspnea, hemoptysis, chest infiltrates, and abrupt fall of blood hemoglobin level represent the cardinal features of DAH; yet, hemoptysis is lacking in one-third of cases. Bronchoalveolar lavage, retrieving bright red fluid, is the best diagnostic clue, also excluding infection and other causes of hemoptysis. Although not recommended, lung biopsy is the gold standard for the diagnosis of DAH and pulmonary capillaritis. Pulmonary capillaritis may be primary as in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis or secondary to drugs (especially antithyroid drugs such as propylthiouracil), infections, connective tissue diseases especially systemic lupus erythematosus, or other small vessel vasculitides. Newer toxic causes of drugs of abuse may be difficult to diagnose. Granulomatosis with polyangiitis and microscopic polyangiitis are the most common causes of capillaritis and DAH, whereas DAH is extremely rare in eosinophilic granulomatosis with polyangiitis. When pulmonary capillaritis is not secondary to underlying systemic vasculitis, idiopathic pauci-immune pulmonary capillaritis may be considered, with or without ANCA. Supportive treatment strategy is mandatory in all cases of DAH. Mechanical ventilation and extracorporeal membrane oxygenation may be used in severe cases. Early identification and removal of the putative drug is crucial in drug-induced vasculitis/DAH and may obviate the need for immunosuppressive therapy. High-dose corticosteroids, intravenous cyclophosphamide, and recently rituximab are the mainstay of treatment in vasculitis. Plasma exchange is recommended in anti–glomerular basement membrane disease and in severe DAH associated with systemic lupus erythematosus and is used in selected cases in ANCA-associated vasculitis.
Musculoskeletal Radiology in the Middle East: Training Programs, Current Practice, and Future Directions
Authors: Ashkanani Ali , Alkhayat Abdullah
Published: November 2018

This article outlines the development of radiology training in the Middle East. It discusses the history of radiology in the region and current available pathways to subspecialize in musculoskeletal (MSK) radiology. Owing to the rapidly changing demographics and health indicators in the region, a major shift has occurred in the government's focus in directing more resources to advance the health care system. This in addition to intraregional initiatives, such as the establishment of many radiologic societies, has provided strong incentives toward developing radiology training programs in the region. There are profound differences in the region regarding the development of radiology, with only few countries offering structured radiology training programs and MSK radiology fellowships. To keep up with the explosion of information in imaging technology and hold clinical ground, current and future MSK radiologists must overcome certain challenges and change their approach to stay clinically relevant.
Apnea Threshold in Pediatric Brain Death: A Case with Variable Results Across Serial Examinations
Authors: Sosa Tina , Berrens Zachary , Conway Susan , Stalets Erika
Published: November 2018

Consensus guidelines currently exist for the evaluation of pediatric patients with suspected brain death. The guidelines include the requirement for two consistent examinations separated by an observation period and a threshold of 60 mm Hg for PaCO2 during apnea testing. We present a patient who met all prerequisites to perform brain death examination but had variability in examinations during apnea testing. We discuss our strategy in managing these unexpected findings, including the importance of open and ongoing communication with the family, and the implications for current guidelines for the determination of brain death in pediatric patients.
Design and optimization of the diamagnetic lateral force calibration method
Authors: Qu Cangyu , Liu Bingtong , Ma Ming , Zheng Quanshui
Published: November 2018

The lateral force calibration is a key procedure for applications of atomic force microscopes. Among different calibration methods, the diamagnetic lateral force calibration (DLFC) method has been widely used due to its ease of use as well as being able to estimate the cross talk conversion factor and achieve very small stiffness. The lateral stiffness of the system is the only parameter in the DLFC method; however, its dependence on the properties and parameters of the DLFC system remains unexplored. In this paper, a theoretical formulation of such dependence is developed and experimentally verified. These results provide a guidance to design and optimize future DLFC systems with better applicability and precision in calibrations. As an example, we optimized a DLFC system such that it is robust against normal load, which is previously assumed impossible.
Comprehensive numerical modeling of filamentary RRAM devices including voltage ramp-rate and cycle-to-cycle variations
Authors: Niraula Dipesh , Karpov Victor
Published: November 2018

The equilibrium ON and OFF states of resistive random access memory (RRAM) are due to formation and destruction of a conducting filament. The laws of thermodynamics dictate that these states correspond to the minimum of free energy. Here, we develop a numerical model that, through the minimization of free energy at a given voltage, determines the filament parameters and thus the electric current. Overall, it simulates the current-voltage (I-V) characteristics of RRAM. The model describes mutual transformations of RRAM states through SET (ON→OFF) and RESET (OFF→ON) processes. From the modeling perspectives, these states and processes constitute four programing modules constructed here in COMSOL multiphysics software tackling the electrodynamic and heat transfer equations and yielding RRAM energy and I-V. Our modeling uniquely reproduces the observed I-V varying with voltage ramp-rates. This is achieved by accounting for the ramp-rate dependent activation energy of conduction. The underlying mechanism is due to the deformation interaction caused by the double well atomic potentials universally present in amorphous materials and having exponentially broad distribution of relaxation times. As another unique feature, our modeling reproduces the observed cycle-to-cycle variations of RRAM parameters attributed to the lack of self-averaging in small ensembles of double well potentials and electronic states in geometrically small (nano-sized) RRAM structures.
Wavelength tunable soliton rains in a nanotube-mode locked Tm-doped fiber laser
Authors: Fu B. , Popa D. , Zhao Z. , Hussain S. A. , Flahaut E. , Hasan T. , Soavi G. , Ferrari A. C.
Published: November 2018

We report soliton rains in a tunable Tm-doped fiber laser mode locked by carbon nanotubes. We also detect their second- and third-harmonics. We achieve a tunability of over 56 nm, from 1877 to 1933 nm, by introducing a polarization-maintaining isolator and two in-line polarization controllers. This makes our system promising as a tunable filter for ultrafast spectroscopy.
Defect evaluation in strain-relaxed Ge0.947Sn0.053 grown on (001) Si
Authors: Gupta S. , Shimura Y. , Richard O. , Douhard B. , Simoen E. , Bender H. , Nakatsuka O. , Zaima S. , Loo R. , Heyns M.
Published: November 2018

Defects in Ge0.947Sn0.053 layers grown using molecular beam epitaxy on (001) Si substrates with 4.9% mismatch are investigated using optical, scanning, and transmission electron and atomic force microscopies. It is shown that the strain relaxation occurs via the introduction of 90° misfit dislocations of short length, at the Ge0.947Sn0.053/Si interface. An irregular morphology in the form of mounds is observed on the surface of epitaxial Ge1−xSnx (0.031 ≤ x ≤ 0.093) and is found to be associated with carbon impurities at the hetero-interface. A low-cost and fast defect selective wet etching technique is described to determine the etch pit density in epitaxial Ge1−xSnx with a low Sn content (≤5.3%). On the basis of etch pit morphology, different defects, e.g., dislocations, stacking faults, and crystal originated particles, are distinguished.
Electronic interactions do not affect electronic decoherence in the pure-dephasing limit
Authors: Gu Bing , Franco Ignacio
Published: November 2018

The relationship between electronic interactions and electronic decoherence is a fundamental problem in chemistry. Here we show that varying the electron-electron interactions does not affect the electronic decoherence in the pure-dephasing limit. In this limit, the effect of varying the electronic interactions is to rigidly shift in energy the diabatic potential energy surfaces without changing their shape, thus keeping the nuclear dynamics in these surfaces that leads to the electronic decoherence intact. This analysis offers a simple and intuitive understanding of previous theoretical and computational efforts to characterize the influence of electronic interactions on the decoherence and opens opportunities to study exact electronic decoherence with approximate electronic structure theories.
Dynamics of self-rewetting drop on an inclined uniformly heated substrate
Authors: Ye Xuemin , Zhang Xiangshan , Li Minglan , Li Chunxi
Published: November 2018

The dynamics of a self-rewetting drop on a uniformly heated, inclined substrate are considered. Based on the lubrication theory and Navier slip condition, an evolution equation for the drop thickness of a two-dimensional drop is established. The migration characteristics of the drop are investigated when the interfacial tension is positive and negative and in a quadratic functional relationship with temperature under the same wetting scenario. The effects of the inclination angle, capillary number, Bond number, and thermocapillary force on the drop migration are examined when the interfacial tension has a nonmonotonic dependence on temperature. Numerical results indicate that the direction of interfacial tension has a significant influence on drop spreading. When the conventional pure fluid drop and self-rewetting fluid drop have the same wettability, the self-rewetting drop spreads more rapidly and the fluid is more evenly distributed on the inclined substrate. The effect of gravity parallel to the wall is enhanced by the increase in the inclination angle, resulting in faster drop sliding velocity. The increase in Ca results in a delay of the contact line pinning state and prolonged pinning time; however, the increase in Bo leads to an advanced pinning state of the contact line and reduced pinning time. The thermocapillary force is important to the deformation of the drop. When the enhancement in the thermocapillary force overcomes the effect of the other forces, less fluid is driven to flow down the wall, resulting in a relatively uniform distribution of the fluid on the substrate.
Modeling and analysis of I-V hysteresis behaviors caused by defects in tin perovskite thin films
Authors: Noma Taishi , Taguchi Dai , Manaka Takaaki , Iwamoto Mitsumasa
Published: November 2018

We analyzed the I-V hysteresis behaviors of tin perovskite (MASnI3, MA: CH3NH3) thin films using impedance spectroscopy coupled with charge modulation spectroscopy (CMS). The capacitance-voltage (C-V) characteristics of the ITO/MASnI3/Al device showed hysteresis behaviors, in accordance with the trap filling process suggested by the I-V characteristics. The CMS measurement indicated the enlargement of the energy bandgap of the MASnI3. On the basis of these results, we proposed a model that trap states in the vicinity of the bottom of conduction band are filled, and concluded that the trap filling process occurring at Sn vacancies makes a significant contribution to the electrical properties of tin perovskite film and the hysteresis of the I-V and C-V characteristics of our device. The I-V hysteresis is suppressed with the decrease of defects such as Sn vacancies in MASnI3 films.
Growth of beryllium thin films on beryllium (0001) surface: Influence of incident energy and incident angle by molecular dynamics simulation
Authors: Zhu Xuegang , Lu Yuping
Published: November 2018

The morphology and microstructure of metallic thin films synthesized by magnetron sputtering deposition are sensitive to incident energy and incident angle. The role of incident energy and incident angle in films’ morphology evolution of the beryllium thin films’ growth on beryllium (0001) surface was studied by molecular dynamics simulations. The analytical bond order potential was used to represent the interatomic interactions, and the common neighbor analysis algorithm for crystal structures was used for the structural characterization of the simulated films. It is found that when the incident energy is between 1 eV and 20 eV, the increased incident energy is beneficial to grow uniform crystal films and, when the incident energy is greater than 15 eV, the interstitial atoms formed inside the films. Furthermore, under the small incident angle conditions, the morphology of a smooth surface was formed, which means that the vertical incident conditions are desired for the growth of high quality films. In short, vertically inserted atoms with hyperthermal energy (5–10 eV) are more propitious for the growth of perfect crystal Be thin films. The obtained results can be used to guide the experiment.
Structural evolution and bonding properties of BSin−/ (n = 4–12) clusters: Size-selected anion photoelectron spectroscopy and theoretical calculations
Authors: Lu Sheng-Jie , Xu Xi-Ling , Cao Guo-Jin , Xu Hong-Guang , Zheng Wei-Jun
Published: November 2018

Size-selected anion photoelectron spectroscopy and theoretical calculations were used to investigate the structural evolution and bonding properties of BSin−/0 (n = 4–12) clusters. The results showed that the B atom in BSi4–12−/0 prefers to occupy the high coordination sites to form more B–Si bonds. The lowest-lying isomers of BSi4–7−/0 primarily adopt bowl-shaped based geometries, while those of BSi8–12−/0 are mainly dominated by prismatic based geometries. For anionic clusters, BSi11− is the critical size of the endohedral structure, whereas BSin neutrals form the B-endohedral structure at n = 9. Interestingly, both anionic and neutral BSi11 have a D3h symmetric tricapped tetragonal antiprism structure with the B atom at the center and exhibit 3D aromaticity. The BSi11− anion possesses σ plus π doubly delocalized bonding characters. The natural population analysis charge distributions on the B atom are related with the structural evolution of BSin− and the B–Si interactions.
Oscillation of the shock train in an isolator with incident shocks
Authors: Li Nan , Chang Jun-Tao , Xu Ke-Jing , Yu Da-Ren , Bao Wen , Song Yan-Ping
Published: November 2018

The oscillation characteristics of the shock train in an isolator have been investigated in a direct-connect wind tunnel at Mach 2.7. High-speed schlieren imaging and high-resonance frequency pressure measurements were used to capture the flow features during the shock train movement. The oscillation features without the effects of incident shocks were analyzed first. As the shock train moved upstream, the low-frequency part of the oscillation was found to develop. The analysis was then extended to complex situations with incident shocks. It was revealed that the shock wave-boundary layer interactions considerably influence the shock train behavior. The interactions were classified into three patterns: (I) single interaction, (II) multi-interactions on the same side, and (III) multi-interactions on different sides. Experimental results indicated that the oscillation could be affected in temporal scale by pattern II and enhanced in spatial scale by pattern III. The data also showed that the pressure rise induced upstream propagates to the exit, causing phase offsets in the wall pressure histories and making the pressure distributions diverge from their stable state. This phenomenon suggested a possible physical mechanism for the oscillation during shock train movement, which was verified by additional tests with large backpressure rising rate. It was found that there exists a critical frequency which is related to the pressure ramping rate during the oscillation. If the dominant frequency of the backpressure varies beyond this critical frequency, the pressure distribution could be forced into a steady state before the oscillation was induced. Otherwise the oscillation could not be suppressed.
Detection of nanowatt microwave radiation by the photoluminescence of an ensemble of negatively charged nitrogen vacancies in diamond
Authors: Debus J. , Ivanov V. Yu. , Braukmann D. , Azamat D. V. , Glaser E. R. , Kennedy T. A. , Yakovlev D. R. , Bayer M.
Published: November 2018

We report on detecting continuous 60-GHz microwave radiation with powers in the nanowatt range by the photoluminescence of an ensemble of negatively charged nitrogen vacancy (NV−) centers in diamond at room temperature. The high contrast of the optically detected magnetic resonance and the efficient photon collection yield a magnetic field sensitivity of 86 nT/Hz for continuous-wave laser excitation with a photon energy of 2.33 eV and a power density of 93 W/cm2. The efficiency of the microwave-power-to-magnetic-field conversion amounts to 0.54 mT/W. The microwave excitation also enhances the degree of the linear polarization of NV− photoluminescence at magnetic resonance conditions, and for linearly co-polarized NV− photoluminescence and laser light, the magnetic field sensitivity is improved by about 7%.
Equation-of-motion coupled-cluster theory based on the 4-component Dirac–Coulomb(–Gaunt) Hamiltonian. Energies for single electron detachment, attachment, and electronically excited states
Authors: Shee Avijit , Saue Trond , Visscher Lucas , Severo Pereira Gomes André
Published: November 2018

We report in this paper an implementation of a 4-component relativistic Hamiltonian based Equation-of-Motion Coupled-Cluster with singles and doubles (EOM-CCSD) theory for the calculation of ionization potential, electron affinity, and excitation energy. In this work, we utilize the previously developed double group symmetry-based generalized tensor contraction scheme and also extend it in order to carry out tensor contractions involving non-totally symmetric and odd-ranked tensors. Several approximated spin-free and two-component Hamiltonians can also be accessed in this implementation. We have applied this method to the halogen monoxide (XO, X = Cl, Br, I, At, Ts) species, in order to assess the quality of a few other recent EOM-CCSD implementations, where spin-orbit coupling contribution has been approximated in different degrees. Besides, we have also studied various excited states of CH2IBr, CH2I2, and I3− (as well as single electron attachment and detachment electronic states of the same species) where comparison has been made with a closely related multi-reference coupled-cluster method, namely, Intermediate Hamiltonian Fock Space Coupled-Cluster singles and doubles theory.
Ground-state crystal structures of superconducting Nb3Al and the phase transformation under high pressures
Authors: Mao Jianjun , Chen Yue
Published: November 2018

Niobium aluminide Nb3Al, a typical A15 conventional superconductor, has been believed to adopt the cubic β-W type structure with a space group of Pm3¯n at ambient pressure since its discovery. Herein, we report a new crystal structure with a space group of C2/c, as predicted from the ab initio evolutionary algorithm, is energetically more favorable than the A15 phase at ambient pressure and low temperature. Phonon calculations indicate this phase is dynamically stable. The application of the Allen-Dynes modified McMillan equation to the C2/c phase yields a superconducting transition temperature Tc in the range of 17.44 – 19.48 K, which is in good agreement with experiments (18.8 K). A key difference between the A15 and C2/c crystal structures is the distortion of the Nb atomic chains, which are believed to be closely related to the superconducting behavior. Based on ab initio molecular dynamics simulations, we find that Nb3Al transforms from the newly discovered C2/c phase to the standard A15 phase as temperature increases. Furthermore, another new phase with a space group of Cmcm is found to become stable as a hydrostatic pressure is applied.
Dielectrophoretic separation with a floating-electrode array embedded in microfabricated fluidic networks
Authors: Jiang Tianyi , Ren Yukun , Liu Weiyu , Tang Dewei , Tao Ye , Xue Rui , Jiang Hongyuan
Published: November 2018

In this study, we proposed a high-throughput separation strategy of the binary colloid mixture by dielectrophoresis (DEP) induced around large-scale bipolar electrode arrays embedded in microfabricated fluidic networks via a thorough numerical investigation. The usage of a floating electrode (FE) eliminates the need of external Ohmic connection to individual array units, therefore potentially steering the faddish design of new microdevice structures. Diffuse charge dynamics within the induced double layer at opposite ends of every FE permit a sinusoidal electric field to penetrate throughout the whole device, as long as the imposed field frequency is beyond the reciprocal resistor-capacitor time constant at the electrode/electrolyte interface. In this special device configuration, FEs interconnect multiple microchannels arranged in parallel. Pockets embedded on the sidewalls of fluidic channels help create strong field gradients at the tip of FEs and sharp pocket/channel junctions, improving the trapping performance of incoming bioparticles subjected to positive-DEP (pDEP) force, while latex beads experiencing negative-DEP (nDEP) stress are electrically squeezed to the midchannel and finally exit as a series of co-flowing thin streams with unequal translatory velocity. Taking the synergy of DEP force, induced-charge electro-osmosis, alternating-current electrothermal streaming, pressure-driven flow, and buoyancy effect into consideration, a numerical model is established to account for motion trajectories of micro-entities in full-scale three-dimensional space using the Lagrange particle track algorithm, as well as testing the feasibility of the device design in separation of the binary mixture containing yeast cells and polystyrene beads. Applying suitable voltage parameters of frequency O(1) MHz and electric field strength O(10) V/mm, highly efficient DEP separation is theoretically achievable under inlet flow velocity on the order of O(1) mm/s, where most of incoming yeasts are captured by pDEP within these five parallel branching channels, while polystyrene spheres are repelled by nDEP away from the FE array to form slim beams co-flowing into the outlet according to the calculation results. The microfluidic separation device exploiting the FE array offers great potential to build up scalable electrokinetic platforms for high-throughput on-chip sample treatment.
Single Zn2GeO4 nanowire high-performance broadband photodetector
Authors: Tien Li-Chia , Yang Feng-Ming , Huang Shih-Chieh , Fan Zheng-Xuan , Chen Ruei-San
Published: November 2018

Broadband photodetectors have attracted considerable attention owing to their commercial and military applications. We report using a single Zn2GeO4 nanowire for high-performance broadband photodetectors. The Zn2GeO4 nanowires are stoichiometric, single crystal rhombohedral structure with a high concentration of intrinsic defects. The photodetector exhibits high photocurrent, high normalized gain, high detectivity, and a broad spectral response from UV to visible light. The photoresponsivities of 404 A W−1 at the UV wavelength of 325 nm, 505 A W−1 at the visible light of 405 nm, 606 A W−1 at 532 nm, and 336 A W−1 at 633 nm have been achieved. The detectivity of a device is ranging from 4.3 × 1011 to 1.2 × 1012 Jones in the spectral range from UV to visible. The broadband photoresponse characteristics of a single Zn2GeO4 nanowire photodetector are attributed to the high surface-to-volume ratio, wide bandgap, and defect-rich nature of Zn2GeO4 nanowire. In addition, the oxygen-sensitized photoconduction mechanism has been proposed. The results suggest that Zn2GeO4 nanowires are promising materials for a broadband flexible photodetector under harsh environments.
Extending the particle ellipsoidal statistical Bhatnagar-Gross-Krook method to diatomic molecules including quantized vibrational energies
Authors: Pfeiffer M.
Published: November 2018

The particle-based ellipsoidal statistical Bhatnagar-Gross-Krook (ESBGK) model is extended to diatomic molecules and compared with the Direct Simulation Monte Carlo (DSMC) method. For this, an efficient method is developed that optionally allows the handling of quantized vibrational energies. The proposed method is verified with a gas in an adiabatic box relaxing from a non-equilibrium state to an equilibrium. It is shown that the analytical Landau-Teller expression as well as DSMC results agrees very well with the new method. Furthermore, the method is compared with DSMC results and experimental measurements of a hypersonic flow around a 70° blunted cone. It is shown that the ESBGK compares very well with the DSMC results while saving up to a factor of ≈35.8 computational time for this low Knudsen number case.
Switching of binding site from nonpolar to polar ligands toward cationic benzonitrile revealed by infrared spectroscopy
Authors: Chatterjee Kuntal , Dopfer Otto
Published: November 2018

Noncovalent interactions of aromatic molecules in their various charge states with their surrounding environment are of fundamental importance in chemistry and biology. Herein, we analyze the infrared photodissociation spectra of mass-selected cationic clusters of benzonitrile (BN, cyanobenzene, C6H5CN) with L = Ar, N2, and H2O (W), in the CH and OH stretch range (2950-3800 cm−1) with the aid of density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level to probe the interaction of this fundamental aromatic cation in its 2B1 ground electronic state with nonpolar, quadrupolar, and dipolar solvent molecules. While Ar and N2 prefer π-stacking to the aromatic ring of BN+ strongly supported by dispersion forces, W forms a bifurcated CH⋯O ionic hydrogen bond to two adjacent CH groups stabilized by electrostatic forces. Comparison of the BN+-L dimers with related aromatic clusters reveals the effect of ionization, protonation, and substitution of functional groups on the type and strengths of the competing ligand binding motifs.
Subsurface imaging of cavities in liquid by higher harmonic atomic force microscopy
Authors: Zhang Weijie , Chen Yuhang , Liu Huarong , Zheng Lei
Published: November 2018

Subsurface imaging capability of liquid-environment higher-harmonic atomic force microscopy (AFM) was investigated using a reference artifact. A series of cylindrical cavities with pre-known dimensions were fabricated on a silicon substrate via electron beam lithography and then covered by a set of highly oriented pyrolytic graphite (HOPG) pieces with different thicknesses. Experiments on these structures demonstrated that the higher-harmonic amplitude sensitivity to the local stiffness in liquids was at least an order of magnitude larger than that in ambient air under the same parameter settings. The harmonic AFM in liquids could detect the cavities beneath over a 200 nm thick HOPG cover. Theoretical analyses based on the cantilever dynamics and the membrane mechanical properties well interpreted the experimental results. Furthermore, it was verified that the momentary excitation of the non-driven higher eigenmode in a low-Q environment could play a critical role in the enhanced subsurface imaging capability of harmonic AFM in liquids.
Specifics of the focused electron beam transport in the forevacuum range of pressure
Authors: Klimov A. S. , Zenin A. A. , Oks E. M. , Prech K.
Published: November 2018

We have investigated electron beam transport at an elevated forevacuum pressure of tens of Pascals of helium. The continuous electron beam (6–14 keV, 300 mA) is generated by a forevacuum-pressure plasma-cathode electron source utilizing a hollow-cathode discharge. A beam-plasma discharge is generated in the beam transport zone, which is characterized by increased plasma density in the region of the most intense beam-plasma interaction. We find that the location and distribution of the beam-plasma discharge depend on the electron beam energy and current density. Under certain conditions, we observe that the beam plasma is stratified, with a periodic variation of plasma density and luminosity along the direction of electron beam propagation.
Overexpression of a soybean 4-coumaric acid: coenzyme A ligase (GmPI4L) enhances resistance to Phytophthora sojae in soybean
Authors: Chen Xi , Fang Xin , Zhang Youyi , Wang Xin , Zhang Chuanzhong , Yan Xiaofei , Zhao Yuanling , Wu Junjiang , Xu Pengfei , Zhang Shuzhen
Published: November 2018

Phytophthora root and stem rot of soybean (Glycine max (L.) Merr.) caused by Phytophthora sojae is a destructive disease worldwide. The enzyme 4-coumarate: CoA ligase (4CL) has been extensively studied with regard to plant responses to pathogens. However, the molecular mechanism of the response of soybean 4CL to P. sojae remains unclear. In a previous study, a highly upregulated 4CL homologue was characterised through suppressive subtractive hybridisation library and cDNA microarrays, in the resistant soybean cultivar ‘Suinong 10’ after infection with P. sojae race 1. Here, we isolated the full-length EST, and designated as GmPI4L (P. sojae-inducible 4CL gene) in this study, which is a novel member of the soybean 4CL gene family. GmPI4L has 34–43% over all amino acid sequence identity with other plant 4CLs. Overexpression of GmPI4L enhances resistance to P. sojae in transgenic soybean plants. The GmPI4L is located in the cell membrane when transiently expressed in Arabidopsis protoplasts. Further analyses showed that the contents of daidzein, genistein, and the relative content of glyceollins are significantly increased in overexpression GmPI4L soybeans. Taken together, these results suggested that GmPI4L plays an important role in response to P. sojae infection, possibly by enhancing the content of glyceollins, daidzein, and genistein in soybean.
Ecoregions and stream types help us understand ecological variability in Neotropical reference streams
Authors: Agra Janaina Uchôa Medeiros , Ligeiro Raphael , Macedo Diego Rodrigues , Hughes Robert Mason , Callisto Marcos
Published: November 2018

Stream site classification is a fundamental step in defining reference conditions for freshwater bioassessments globally. Landscape regionalisation and stream typology approaches have both been used to determine classes that reduce inherent environmental variation and to show classes with ecological meaning. We evaluated the applicability of ecoregion and stream typology approaches in a river basin located between the Neotropical Savanna and the Atlantic Forest biomes in south-eastern Brazil. We delimited two ecoregions and assessed whether stream types within each ecoregion would further reduce environmental and macroinvertebrate assemblage variability. In addition, we determined indicator taxa for each of the reference condition classes. Our results confirm the importance of defining ecoregions a priori and for using a nested a posteriori stream typology approach for further explaining macroinvertebrate assemblage variation. Geology and natural vegetation physiognomy were the key ecoregion factors likely to influence macroinvertebrate assemblages, and stream dimension attributes best delimited meaningful stream types. Although stream classification is a very important step in any monitoring, management or restoration program, it has been widely neglected in many tropical regions. In this study we demonstrated how it can be conducted to determine macroinvertebrate assemblage potentials even with a relatively limited number of sites.
Agassiz’s desert tortoise (Gopherus agassizii) activity areas are little changed after wind turbine induced fires in California
Authors: Lovich Jeffrey E. , Agha Mickey , Ennen Joshua R. , Arundel Terence R. , Austin Meaghan
Published: November 2018

Wind turbine-induced fires at a wind energy facility in California, USA, provided an opportunity to study the before and after effects of fire on a population of protected Agassiz’s desert tortoises (Gopherus agassizii) in the Sonoran Desert, a species and ecosystem poorly adapted to fire. We compared annual activity areas (AAs) of tortoises in 2011 and 2013, before and after two 2012 fires, with those of tortoises in adjacent areas unaffected by the same fires. Tortoises in both AAs affected by fire or unaffected by fire occupied the same general AAs in 2013, after the fires, as they did in 2011, before the fires. Some tortoises had both their 2011 and 2013 AAs completely or almost completely within the areas burned by the 2012 fires, despite the proximity of unburned habitat. None of the tortoises with 2011 AAs subsequently unaffected by the 2012 fires shifted their AAs into burned habitat in 2013. For the fire-affected group of tortoises, the mean percentages of 2011 and 2013 AAs burned by the 2012 fires were not significantly different, showing fidelity to the burned areas. Tortoises in both groups generally occupied consistent AAs, even post fire, placing them at potential risk of exposure to unfavourable burned habitat.
NOXA genetic amplification or pharmacologic induction primes lymphoma cells to BCL2 inhibitor-induced cell death
Authors: Liu Yuxuan , Mondello Patrizia , Erazo Tatiana , Tannan Neeta Bala , Asgari Zahra , de Stanchina Elisa , Nanjangud Gouri , Seshan Venkatraman E. , Wang Shenqiu , Wendel Hans-Guido , Younes Anas
Published: November 2018

Significance

BCL2 selective inhibitors are promising agents currently under clinical investigation for treatment of BCL2-dependent cancers. However, the clinical activity of BCL2 inhibitors in patients with diffuse large B cell lymphoma (DLBCL) has been disappointing. In this study, we identified PMAIP1/NOXA gene amplification as a marker of sensitivity to BCL2 inhibitors in DLBCL. Cells lacking NOXA amplification were less sensitive to BCL2 inhibitors due to codependency on MCL1 and BCL2 proteins. We show that pharmacologic induction of NOXA by the HDAC inhibitor panobinostat primes DLBCL to BCL2 inhibitor-induced cell death by disrupting the codependency on BCL2 and MCL1, mimicking the biologic effects of NOXA genetic amplification. Our data provide a mechanistic rationale for combining HDAC inhibitors with BCL2 inhibitors in DLBCL.
Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
Authors: Yu Haoran , Dalby Paul A.
Published: November 2018

Significance

Incomplete understanding of the mechanisms of epistasis between two or more substitutions in a protein can hamper protein-engineering strategies. With
Escherichia coli
transketolase as a model, we explore the epistatic interactions between a set of stabilizing mutations from across two different domains within the protein structure. Surprisingly, not all pairwise effects between distant mutations from the surface and core regions of different domains were additive. Additionally, the epistatic behaviors observed were dependent on the type of stability measured. We found single mutations that altered local protein dynamics, which then induced correlated changes in the dynamics of a second domain of the same monomer. This mechanism mediated epistasis between distant mutations.
Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists
Authors: Liu Hongtao , Hofmann Josefa , Fish Inbar , Schaake Benjamin , Eitel Katrin , Bartuschat Amelie , Kaindl Jonas , Rampp Hannelore , Banerjee Ashutosh , Hübner Harald , Clark Mary J. , Vincent Sandra G. , Fisher John T. , Heinrich Markus R. , Hirata Kunio , Liu Xiangyu , Sunahara Roger K. , Shoichet Brian K. , Kobilka Brian K. , Gmeiner Peter
Published: November 2018

Significance

The development of selective antagonists for muscarinic acetylcholine receptors is challenging due to high homology in orthosteric binding sites among subtypes. Starting from a single amino acid difference in the orthosteric pockets in M2 muscarinic acetylcholine receptor (M2R) and M3R, we developed an M3R-selective antagonist using molecular docking and structure-based design. The resulting M3R antagonist showed up to 100-fold selectivity over the M2R in affinity and 1,000-fold selectivity in vivo. The docking-predicted geometry was further confirmed by a 3.1 Å crystal structure of M3R in complex with the selective antagonist. The potential of structure-based design to develop selective drugs with reduced off-target effects is supported by this study.
Evolution of weak cooperative interactions for biological specificity
Authors: Gao Ang , Shrinivas Krishna , Lepeudry Paul , Suzuki Hiroshi I. , Sharp Phillip A. , Chakraborty Arup K.
Published: November 2018

Significance

Functional specificity in biology is mediated by two classes of mechanisms, “lock–key” interactions and multivalent weak cooperative interactions (WCI). Despite growing evidence that WCI are widely prevalent in higher organisms, little is known about the selection forces that drove its evolution and repeated positive selection for mediating biological specificity in metazoa. We report that multivalent WCI for mediating biological specificity evolved as the number of tasks that organisms had to perform with functional specificity became large (e.g., multicellular organisms). We find that the evolution of multivalent WCI confer enhanced and robust evolvability to organisms, and thus it has been repeatedly positively selected. Thus, we provide insights on the evolution of WCI and, more broadly, on the evolution of evolvability.
Comparing introductory sections in city audio guides in Italian and English
Authors: Fina Maria Elisa
Published: November 2018

The aim of this paper is to analyse introductory sections in Italian, British/Irish and American city audio guides
from a contrastive perspective, in order to identify possible differences in the type and distribution of content. Three main
content types and their corresponding subtypes were identified in the introductions of fifty professional city audio guides and
were both quantitatively and qualitatively compared across the three groups. Differences between audio guides in Italian and in
English are identified and discussed in reference to Hall’s ‘contexting’ theory (1983,
1990), and the findings are then compared to existing guidelines for audio guides
production provided by scholars and professionals in the field. Finally, on the basis of the results, translation issues are
addressed by providing a list of aspects that could be taken into account when producing English versions of Italian audio
guides.
HGF-induced migration depends on the PI(3,4,5)P3-binding microexon-spliced variant of the Arf6 exchange factor cytohesin-1
Authors: Ratcliffe Colin D.H. , Siddiqui Nadeem , Coelho Paula P. , Laterreur Nancy , Cookey Tumini N. , Sonenberg Nahum , Park Morag
Published: November 2018

Differential inclusion or skipping of microexons is an increasingly recognized class of alternative splicing events. However, the functional significance of microexons and their contribution to signaling diversity is poorly understood. The Met receptor tyrosine kinase (RTK) modulates invasive growth and migration in development and cancer. Here, we show that microexon switching in the Arf6 guanine nucleotide exchange factor cytohesin-1 controls Met-dependent cell migration. Cytohesin-1 isoforms, differing by the inclusion of an evolutionarily conserved three-nucleotide microexon in the pleckstrin homology domain, display differential affinity for PI(4,5)P2 (triglycine) and PI(3,4,5)P3 (diglycine). We show that selective phosphoinositide recognition by cytohesin-1 isoforms promotes distinct subcellular localizations, whereby the triglycine isoform localizes to the plasma membrane and the diglycine to the leading edge. These data highlight microexon skipping as a mechanism to spatially restrict signaling and provide a mechanistic link between RTK-initiated phosphoinositide microdomains and Arf6 during signal transduction and cancer cell migration.
FAM92A1 is a BAR domain protein required for mitochondrial ultrastructure and function
Authors: Wang Liang , Yan Ziyi , Vihinen Helena , Eriksson Ove , Wang Weihuan , Soliymani Rabah , Lu Yao , Xue Yaxin , Jokitalo Eija , Li Jing , Zhao Hongxia
Published: November 2018

Mitochondrial function is closely linked to its dynamic membrane ultrastructure. The mitochondrial inner membrane (MIM) can form extensive membrane invaginations known as cristae, which contain the respiratory chain and ATP synthase for oxidative phosphorylation. The molecular mechanisms regulating mitochondrial ultrastructure remain poorly understood. The Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of diverse cellular processes related to membrane remodeling and dynamics. Whether BAR domain proteins are involved in sculpting membranes in specific submitochondrial compartments is largely unknown. In this study, we report FAM92A1 as a novel BAR domain protein localizes to the matrix side of the MIM. Loss of FAM92A1 caused a severe disruption to mitochondrial morphology and ultrastructure, impairing organelle bioenergetics. Furthermore, FAM92A1 displayed a membrane-remodeling activity in vitro, inducing a high degree of membrane curvature. Collectively, our findings uncover a role for a BAR domain protein as a critical organizer of the mitochondrial ultrastructure that is indispensable for mitochondrial function.
Can microtubule motors use every available track?
Authors: Avasthi Prachee
Published: November 2018

Flagellar assembly and function depend on cargo traveling via motors on microtubule doublets. Bertiaux, Mallet et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201805030) find that only a subset of available doublets are used for this transport in trypanosomes, leading to questions about how and why this is achieved.
PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia
Authors: Ariës Ingrid M. , Bodaar Kimberly , Karim Salmaan A. , Chonghaile Triona Ni , Hinze Laura , Burns Melissa A. , Pfirrmann Maren , Degar James , Landrigan Jack T. , Balbach Sebastian , Peirs Sofie , Menten Björn , Isenhart Randi , Stevenson Kristen E. , Neuberg Donna S. , Devidas Meenakshi , Loh Mignon L. , Hunger Stephen P. , Teachey David T. , Rabin Karen R. , Winter Stuart S. , Dunsmore Kimberly P. , Wood Brent L. , Silverman Lewis B. , Sallan Stephen E. , Van Vlierberghe Pieter , Orkin Stuart H. , Knoechel Birgit , Letai Anthony G. , Gutierrez Alejandro
Published: November 2018

The tendency of mitochondria to undergo or resist BCL2-controlled apoptosis (so-called mitochondrial priming) is a powerful predictor of response to cytotoxic chemotherapy. Fully exploiting this finding will require unraveling the molecular genetics underlying phenotypic variability in mitochondrial priming. Here, we report that mitochondrial apoptosis resistance in T cell acute lymphoblastic leukemia (T-ALL) is mediated by inactivation of polycomb repressive complex 2 (PRC2). In T-ALL clinical specimens, loss-of-function mutations of PRC2 core components (EZH2, EED, or SUZ12) were associated with mitochondrial apoptosis resistance. In T-ALL cells, PRC2 depletion induced resistance to apoptosis induction by multiple chemotherapeutics with distinct mechanisms of action. PRC2 loss induced apoptosis resistance via transcriptional up-regulation of the LIM domain transcription factor CRIP2 and downstream up-regulation of the mitochondrial chaperone TRAP1. These findings demonstrate the importance of mitochondrial apoptotic priming as a prognostic factor in T-ALL and implicate mitochondrial chaperone function as a molecular determinant of chemotherapy response.
In vitro reconstitution of DNA replication initiated by genetic recombination: a T4 bacteriophage model for a type of DNA synthesis important for all cells
Authors: Barry Jack , Wong, Mei Lie , Alberts Bruce
Published: November 2018

Using a mixture of 10 purified DNA replication and DNA recombination proteins encoded by the bacteriophage T4 genome, plus two homologous DNA molecules, we have reconstituted the genetic recombination–initiated pathway that initiates DNA replication forks at late times of T4 bacteriophage infection. Inside the cell, this recombination-dependent replication (RDR) is needed to produce the long concatemeric T4 DNA molecules that serve as substrates for packaging the shorter, genome-sized viral DNA into phage heads. The five T4 proteins that catalyze DNA synthesis on the leading strand, plus the proteins required for lagging-strand DNA synthesis, are essential for the reaction, as are a special mediator protein (gp59) and a Rad51/RecA analogue (the T4 UvsX strand-exchange protein). Related forms of RDR are widespread in living organisms—for example, they play critical roles in the homologous recombination events that can restore broken ends of the DNA double helix, restart broken DNA replication forks, and cross over chromatids during meiosis in eukaryotes. Those processes are considerably more complex, and the results presented here should be informative for dissecting their detailed mechanisms.
Network embedding in biomedical data science
Authors: Su Chang , Tong Jie , Zhu Yongjun , Cui Peng , Wang Fei
Published: November 2018

Owning to the rapid development of computer technologies, an increasing number of relational data have been emerging in modern biomedical research. Many network-based learning methods have been proposed to perform analysis on such data, which provide people a deep understanding of topology and knowledge behind the biomedical networks and benefit a lot of applications for human healthcare. However, most network-based methods suffer from high computational and space cost. There remain challenges on handling high dimensionality and sparsity of the biomedical networks. The latest advances in network embedding technologies provide new effective paradigms to solve the network analysis problem. It converts network into a low-dimensional space while maximally preserves structural properties. In this way, downstream tasks such as link prediction and node classification can be done by traditional machine learning methods. In this survey, we conduct a comprehensive review of the literature on applying network embedding to advance the biomedical domain. We first briefly introduce the widely used network embedding models. After that, we carefully discuss how the network embedding approaches were performed on biomedical networks as well as how they accelerated the downstream tasks in biomedical science. Finally, we discuss challenges the existing network embedding applications in biomedical domains are faced with and suggest several promising future directions for a better improvement in human healthcare.