bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimal acidulated phosphate fluoride gel etching time for surface treatment of feldspathic porcelain: on shear bond strength to resin composite
Authors: Kukiattrakoon Boonlert , Thammasitboon Kewalin
Published: October 2019

Objectives: This in vitro study evaluated the shear bond strength (SBS) of resin composite to feldspathic porcelain after acidulated phosphate fluoride (APF) gel treatment over different periods of time

Methods: One hundred and fifty-six feldspathic specimens were divided into 12 groups. Group C received no treatment (control group). Groups APF1 through APF10, ten experimental groups, were treated with 1.23% APF gel. Each group obtained 1 to 10 minutes of etching time in 1 minute increments, respectively. Group HF2 was treated with 9.6% hydrofluoric acid (HF) for 2 minutes. All specimens were then bonded to a resin composite cylinder using Adper Scotchbond Multi-purpose (3M ESPE) after silane (Monobond-S, Ivoclar Vivadent AG) application. Specimens were stored at 37ºC for 24 hours before the SBS was performed and were recorded in MPa at fracture. Data were analyzed using one-way ANOVA and Tukey’s test (α=.05)

Results: HF etching yielded the highest SBS (18.0 ± 1.5 MPa), which was not significantly different from APF gel etching for 6 to 10 minutes (16.0 ± 2.1 to 17.2 ± 1.6 MPa) (P>.05)

Conclusions: APF gel etching for 6 minutes might be used as an alternative etchant to HF acid for bonding resin composite to silanized feldspathic porcelain. (Eur J Dent 2012;6:63-69)
Effect of cavity preparation techniques and different preheating procedures on microleakage of class V resin restorations
Authors: Karaarslan Emine Sirin , Usumez Aslihan , Ozturk Bora , Cebe Mehmet Ata
Published: October 2019

Objectives: This study aimed to evaluate the extent of microleakage of a single type of composite resin (Clearfil Majesty Posterior, Kuraray, Osaka, Japan) following different preheating procedures in Class V cavities prepared with a diamond bur or Er:YAG (erbium: yttrium aluminum garnet) laser

Methods: The study randomly divided 72 permanent molar teeth divided into eight groups (n = 9): G1: Diamond bur–unheated composite resin (room temperature-24 ºC); G2: Diamond bur–composite preheated to 37 ºC; G3: Diamond bur–composite preheated to 54 ºC; G4: Diamond bur–composite preheated to 68 ºC; G5: Er:YAG laser–unheated composite resin (room temperature-24 ºC); G6: Er:YAG laser–composite preheated to 37 ºC; G7: Er:YAG laser–composite preheated to 54 ºC; and G8: Er:YAG laser–composite preheated to 68 ºC. The specimens were subjected to a thermal cycling regimen of 5000 cycles between 5 and 55 ºC; then they were immersed in a solution of 0.5% basic fuchsin dye for 24 hours. The dyed specimens were sectioned in the buccolingual direction and dye penetration was scored in a blinded manner using a five-point qualitative scale. Microleakage scores were analyzed with the Kruskall-Wallis, Mann-Whitney U, and Wilcoxon tests

Results: There were no statistically significant differences between the microleakages of composite applied to cavities prepared by either the Er:YAG laser or diamond bur (P>05). Statistical analysis revealed significant differences between the enamel and dentin in all restorations (P<.001). However, there were no significant differences among the preheated groups (P>05)

Conclusions: For all groups, microleakage values were higher at gingival margins than at occlusal margins. The use of the Er:YAG laser at different preheating procedures did not influence the marginal sealing in Class V composite resin restorations. (Eur J Dent 2012;6:87-94)
Evaluation of marginal fit of two allceramic copings with two finish lines
Authors: Subasi Gulce , Ozturk Nilgun , Ozgur Inan , Bozogullari Nalan
Published: October 2019

Objectives: This in-vitro study investigated the marginal fit of two all-ceramic copings with 2 finish line designs

Methods: Forty machined stainless steel molar die models with two different margin designs (chamfer and rounded shoulder) were prepared. A total of 40 standardized copings were fabricated and divided into 4 groups (n=10 for each finish line-coping material). Coping materials tested were IPS e.max Press and Zirkonzahn; luting agent was Variolink II. Marginal fit was evaluated after cementation with a stereomicroscope (Leica MZ16). Two-way analysis of variance and Tukey-HSD test were performed to assess the influence of each finish line design and ceramic type on the marginal fit of 2 all-ceramic copings (α =.05)

Results: Two-way analysis of variance revealed no statistically significant differences for marginal fit relative to finish lines (P=.362) and ceramic types (P=.065)

Conclusion: Within the limitations of this study, both types of all-ceramic copings demonstrated that the mean marginal fit was considered acceptable for clinical application (≤120 μm). (Eur J Dent 2012;6:163-168)
Some exact results on quantum Newtonian cosmology
Authors: Vieira H. S. , Bezerra V. B. , Muniz C. R. , Cunha M. S.
Published: October 2019

We obtain the wave functions associated with the quantum Newtonian universe with a cosmological constant which is described by the Schrödinger equation and discuss some aspects of its dynamics for all forms of energy density, namely, matter, radiation, vacuum, dark energy, and quintessence. These wave functions of the quantum Newtonian universe are obtained in terms of Heun’s functions and the respective energy levels are shown. We use these solutions to investigate the expansion of the universe and found that the asymptotic behavior for the scale factor is R ∼ et for whatever the form of energy density is. We also analyze the behavior of the universe at early stages.
Results of the DCMIX1 experiment on measurement of Soret coefficients in ternary mixtures of hydrocarbons under microgravity conditions on the ISS
Authors: Galand Quentin , Van Vaerenbergh Stéfan , Köhler Werner , Khlybov Oleg , Lyubimova Tatyana , Mialdun Aliaksandr , Ryzhkov Ilya , Shevtsova Valentina , Triller Thomas
Published: October 2019

The Soret coefficients of a set of ternary systems of 1,2,3,4-tetrahydronaphthalene (THN), isobutylbenzene (IBB), and n-dodecane (nC12) at 298.15 K were measured under microgravity condition aboard the International Space Station in the frame of the DCMIX1 experiment. The present work includes a comprehensive study of possible data processing sequences for the interpretation of interferometric Soret experiments in ternary systems. Several data processing methodologies are discussed. A significant concentration dependence of the Soret coefficients is observed. In the present study, we have obtained large and positive values for THN and negative ones for IBB in all investigated systems. A linear relation between the Soret coefficients of two components is derived for each system and allows validating experimentally the coefficients measured in other experiments.
First-principles study of interfacial energy between alpha-zirconium and zirconium hydride
Authors: Huang Gui-Yang , Wirth Brian D.
Published: October 2019

The interfacial energies among α-Zr, ζ-, γ′-, γ-, and δ-phase zirconium hydride have been calculated via first-principles calculations. Hydrogen biplane configurations of ζ and γ′ are confirmed by binding energy calculations. Based on binding energy calculations and convex hull plots, the ζ phase is not a local stable configuration, and ZrH0.4 is more stable. ζ can be viewed as composed of α and γ′, as well as α∣γ′ interfaces with a 65 mJ/m2 interfacial energy. Thus, ζ is less stable than γ′, assuming no hcp-fct/fcc transformation occurred. Based on the calculated convex hull plots, γ is more stable than δ. The negative interfacial energy between ζ (or γ′) and δ may promote the δ hydride formation.
Intersubband resonant enhancement of second order-nonlinear susceptibility in asymmetric AlxGa1−xN/GaN double quantum wells
Authors: Saidi Imen
Published: October 2019

The present work aims at investigating the second-harmonic generation theoretically in asymmetric AlxGa1−xN/GaN double quantum wells based on a compact density-matrix formalism and a self-consistent approach. Calculations have been made using two- and three-level quantum well models. For this purpose, the electronic subbands and their related wave functions as well as the Fermi energy are computed in asymmetric AlxGa1−xN/GaN double quantum well heterostructures within the effective mass and Hartree approximations. From the given results, it was concluded as follows: (i) The susceptibility exhibits multiple peak structures originating from the intersubband and their corresponding virtual transitions. (ii) The second-order susceptibility strongly depends on the aluminum composition and on the planar-doping design in the barriers as well. (iii) The optimization of electron wave functions' overlaps considerably improved the second-harmonic generation. (iv) Double quantum well systems are revealed to be the most appropriate to generate the second harmonic with an efficient intensity at the suitable resonance frequency. Theoretically, the obtained results would make a useful contribution for experimental studies. From an applied viewpoint, they can open up new opportunities for AlxGa1−xN/GaN optoelectronic devices.
Linear instability of a charged non-Newtonian liquid jet under an axial electric field
Authors: Wang Xin-Tao , Ning Zhi , Lü Ming
Published: October 2019

A theoretical model is established to study the breakup of a charged power law liquid jet, which is moving in stationary air. Furthermore, the effect of a uniform axial electric field is considered in this mathematical model. The liquid non-Newtonian behavior is explained by the power law model, which is assumed to be a Taylor–Melcher leaky dielectric material in this case. The corresponding dispersion relation is derived through a linear analysis. Besides, the effects of the axial electric field with a low and a high density of surface charge, the asymmetric disturbances, and relaxation time on the charged power law liquid jet instability are investigated. Results show that the effects of the axial electric field intensity on the charged power law liquid jet are different when the density of charge on the liquid surface is set as low and high. Besides, the asymmetric disturbances dominate the jet instability when the charge density is set as low, and the axisymmetric disturbance dominates the jet instability when the surface charge density is set as high. The flow model in this paper can be used for designing and operating the electrospraying and spinning systems.
Interface engineering towards enhanced exchange interaction between Fe and FeO in Fe/MgO/FeO epitaxial heterostructures
Authors: Kozioł-Rachwał A. , Janus W. , Szpytma M. , Dróżdż P. , Ślęzak M. , Matlak K. , Gajewska M. , Ślęzak T. , Korecki J.
Published: October 2019

In our study, we examined the chemical and magnetic properties of FeO in an epitaxial Fe/MgO(dMgO)/FeO trilayer for different MgO thicknesses, dMgO. Analysis of the chemical structure revealed a stoichiometry improvement in the FeO layer in Fe/MgO/FeO in comparison with a Fe/FeO bilayer. Furthermore, we showed that deposition of a subtle MgO layer at the Fe/FeO interface results in an enhanced exchange interaction between Fe and FeO. For dMgO = 1.4 Å, we noted a 200% enhancement in the exchange bias in Fe/MgO/FeO compared to that in Fe/FeO.
Influence of distributed heavy-gas injection on stability and transition of supersonic boundary-layer flow
Authors: Lysenko V. I. , Gaponov S. A. , Smorodsky B. V. , Yermolaev Y. G. , Kosinov A. D.
Published: October 2019

This study performed a joint theoretical and experimental investigation of the influence of distributed normal-to-the-surface and inclined heavy-gas injection into the near-wall sublayer of a boundary layer through a permeable wall on the laminar-turbulent transition (LTT). Sulfur hexafluoride (SF6) is used as a foreign gas for injection into the boundary layer. It also assessed stability in relation to both natural and artificial (controlled) disturbances of a supersonic flat-plate boundary layer at a free-stream Mach number (M) of 2. It is established, theoretically, that the action of a large molecular weight gas injection on the boundary layer is similar to the action of wall cooling and leads to an increase in boundary layer stability and LTT delay. The influence of injection on the position of transition is estimated by means of the eN method. Principally, the analysis shows the possibility of increasing the transition Reynolds number by means of SF6 injection. Controlled disturbances are introduced in the model boundary layer by means of a point harmonic glow-discharge disturbance generator and are measured by using a hot-wire anemometer. For the first time, it is shown experimentally that distributed injection of the heavy SF6 gas leads to boundary layer stabilization. This is mostly due to the reduction in growth rates of disturbances at higher frequencies, while the LTT shifted to higher Reynolds number values. Good qualitative agreement is achieved between the experimental data obtained with artificially generated disturbances and computations based on linear stability theory.
Analytical energy gradient for the embedded cluster density approximation
Authors: Huang Chen
Published: October 2019

We recently developed the embedded cluster density approximation (ECDA), which is a local correlation method for scaling up Kohn-Sham (KS) density functional theory calculations using high-level exchange-correlation (XC) functionals. In ECDA, a system’s XC energy is obtained by patching locally calculated, high-level XC energy densities over the entire system. Our previous formulation of ECDA is not variational, making it difficult to derive the analytical energy gradient. In this work, we present a fully variational formulation of ECDA and derive the analytical energy gradient. The challenge for making ECDA a variational method is that both partitioning the system’s density and solving the system’s XC potential are the optimized effective potential (OEP) problems. Simply regularizing these two OEP equations makes ECDA a nonvariational method. We show how to regularize these two OEP problems while still keeping ECDA variational. KS linear responses are involved in the calculations of the system’s XC potential and the analytical energy gradients, but are not explicitly constructed. The terms involving the KS linear responses are calculated by solving the Sternheimer equation. The analytical energy gradients are validated with a Si2H6 molecule and are used to relax the geometry of Si6H10. In both examples, the exact exchange is used as the high-level XC functional and is patched over the molecules.
Holographic scanning confocal microscopy for both reflected light and fluorescence light imaging
Authors: Kalita Ranjan , Saikia Anindita , Bhuyan A. C. , Boruah Bosanta R.
Published: October 2019

In this paper, we propose a holographic scanning based confocal microscope that works in both the reflection and fluorescence modes. Here, the illumination beam is scanned using a reconfigurable binary hologram instead of a usual galvanometer mirror scanner. The reconfigurable hologram is implemented using a liquid crystal spatial light modulator. Two different lasers are used for fluorescence and reflection mode imaging with the phase profile of the illumination beam, derived from each laser, described by the holograms. We demonstrate the working of our microscope in both the modes by imaging a section of tooth specimen stained with a fluorescent dye.
Assessing a growth anomaly in ion-beam sputtered non-stoichiometric NiOx
Authors: Becker M. , Riedl P. , Kaupe J. , Michel F. , Polity A. , Mitić S.
Published: October 2019

Nonstoichiometric NiOx thin films were grown on single crystal substrates of c-plane (0001) sapphires by ion-beam sputter-deposition (IBSD) of a Ni metal target in a mixed argon and oxygen atmosphere. Structural characterization was carried out by X-ray diffraction and scanning electron microscopy. All samples grew (111)-oriented out-of-plane and with a defined in-plane orientation relationship relative to the crystalline substrate. The chemical bonding information of the films was examined by X-ray photoelectron spectroscopy showing that the composition x could be varied by adjusting the oxygen-to-argon ratio in the IBSD process. However, a growth anomaly was detected for a certain range of synthesis parameters, standing out due to an enhanced growth rate, nickel excess, and unusually elongated surface structures. With joint solid-state and plasma diagnostic tools, the underlying processes on the atomic scale were studied. An increased proportion of atomic oxygen species in the intermediate range of the oxygen-to-argon gas flux ratio was identified to be responsible for an enhanced generation of NiOx species. Optical emission spectroscopy was found to be a tool especially well-suited, since the in situ examination of various locations of interest (plasma, ion beam, and vicinity of the target) is feasible nonintrusively.
Thermoelectric properties and stability of nanostructured chromium disilicide CrSi2
Authors: Khalil M. , Moll A. , Godfroy M. , Letrouit-Lebranchu A. , Villeroy B. , Alleno E. , Viennois R. , Beaudhuin M.
Published: October 2019

CrSi2 alloy presents a strong interest for thermoelectric applications; however, its thermal conductivity is still too high and limits strongly its figure of merit. By combining experiment and modeling, we show that the nanostructuring of CrSi2 leads to a strong decrease in the thermal conductivity without affecting much the electronic transport properties. The thermal conductivity of nanostructured CrSi2 (∼45 nm) has also been determined as a function of the density. We predict that it would be about 5.5 W/mK at RT for a 100% dense sample, i.e., twice smaller than in bulk samples. We also give for the first time, a prediction of the effect of alloying on the thermal conductivity using the Callaway-Klemens model. To consider final applications, it is necessary to also investigate the thermal stability of nanostructured compounds. We show that grain coarsening of nanostructured CrSi2, even if it remains limited, happens above 1073 K and will deserve further attention.
Ferroelectric ordering and energy storage capacity in lead-free Ba(Zr0.2Ti0.8)O3 nanoscale film capacitors fabricated using pulsed laser deposition technique
Authors: Instan Alvaro A. , Mishra Karuna K. , Katiyar Ram S.
Published: October 2019

Dielectric thin film capacitors, storing large charge density, are useful in electric energy storing devices. Highly oriented lead-free BaZr0.20Ti0.80O3 (BZT20) thin films were grown on a conducting bottom layer La0.7Sr0.3MnO3 deposited on a MgO (100) substrate under an oxygen atmosphere using a pulsed laser deposition technique. X-ray diffraction studies indicate that BZT20 films were stabilized in a (100) oriented tetragonal phase. Microstructural studies on thin films indicate a smooth film (a roughness of ∼1.25 nm) with a thickness of around 320 nm. The structural sensitive A1(TO2) Raman band exhibits a discontinuous change across the tetragonal-cubic phase transition temperature Tc ∼ 275 K. The appearance of the broad Raman band in the cubic (Pm−3m) phase at an elevated temperature suggests the activation of symmetry forbidden Raman active bands. The temperature dependent band frequency and integrated intensity of the structural sensitive A1(TO2) band show anomaly across Tc. Temperature dependent dielectric studies (100–650 K) carried out in a wide range of frequencies 102–106 Hz on a fabricated Pt/BZT20/LSMO metal-insulator-metal capacitor suggest a broad dispersive peak of around 290 K. The polarization relaxation follows the Vogel-Fulcher relation with an activation energy of Ea = 0.047 eV and a freezing temperature of Tf = 246 K. The slim polarization P-E loops with a remanent polarization of ∼89.6 μC/cm2 and an EC value of ∼0.29 MV/cm were observed, suggesting its local ferroelectric ordering in corroboration with Raman and dielectric findings. From the P-E loop analysis, a large energy storage density of 31.9 J/cm3 and an energy storage efficiency of 56% were obtained. Our experimental results revealed that the BZT20 thin film capacitors have potential for energy storage device applications.
Effect of tantalum doping on SnO2 electron transport layer via low temperature process for perovskite solar cells
Authors: Liu Qi , Zhang Xin , Li Chongyuan , Lu Haizhou , Weng Zhenhua , Pan Yiyi , Chen Wei , Hang Xiao-Chun , Sun Zhengyi , Zhan Yiqiang
Published: October 2019

The electron transport layer (ETL) plays an important role in determining the device performance of perovskite solar cells (PSCs). Recently, SnO2 has been used extensively as an ETL due to its many outstanding optoelectronic properties. Herein, we develop Ta doped SnO2 (Ta-SnO2) as an ETL grown by chemical bath deposition, allowing the fabrication of low-temperature PSCs. In contrast to pristine SnO2, the I-V curve and transmittance spectra show a significant conductivity improvement of Ta-SnO2 without declining the light transmittance property. Meanwhile, Ta-doping could accelerate the electron transfer and decrease the recombination probability at the SnO2/perovskite interface, as well as passivate the electron traps, leading to the improvement in the PSC performance. Through a series of optimization methods, the champion device shows a power conversion efficiency of 20.80%, with an open-circuit voltage of 1.161 V, a short-circuit current density of 22.79 mA/cm2, and a fill factor of 0.786. SnO2 with a suitable Ta content is a promising candidate as an ETL for fabricating high-efficiency PSCs via the low-temperature process.
Dynamic behavior of helium bubbles at high temperature in Si studied by in situ TEM, STEM-EELS, and TDS
Authors: Ono K. , Miyamoto M. , Kurata H. , Haruta M. , Yatomi A.
Published: October 2019

We demonstrated, using in situ transmission electron microscopy (TEM), the random motion of helium bubbles formed by irradiation with helium ions in an FZ (011)Si specimen at high temperatures. Analysis of the random motion yielded the bubble diffusivity, which was dependent on the bubble size and the annealing temperature. The helium density in individual bubbles, measured using scanning transmission electron microscopy-electron energy loss spectroscopy, was as high as 70 ± 14 He/nm3. It was dependent on the irradiation temperature, beam flux, and annealing temperature but was independent of the bubble size. The bubbles retained a high density of helium atoms at around 800 K, but a significant reduction of the helium density within individual bubbles took place after annealing above about 970 K. Thermal desorption of helium from the specimen, measured using thermal desorption spectroscopy, occurred at temperatures between 650 K and 1100 K, centering at around 890 K. TEM revealed the corresponding microstructure. On the basis of these results, the thermal desorption profile was discussed in terms of the release of helium at lower temperatures from migrating and coalescing overpressurized bubbles and bubbles migrating to the specimen surface, and at higher temperatures from stationary large bubbles.
The theory and application of Navier-Stokeslets (NSlets)
Authors: Chadwick E.
Published: October 2019

Consider a closed body moving in an unbounded fluid that decays to rest in the far-field and governed by the incompressible Navier-Stokes equations. By considering a translating reference frame, this is equivalent to a uniform flow past the body. A velocity representation is given as an integral distribution of Green’s functions of the Navier-Stokes equations which we shall call NSlets. The strength of the NSlets is the same as the force distribution over the body boundary. An expansion for the NSlet is given with the leading-order term being the Oseenlet. To test the theory, the following three two-dimensional steady flow benchmark applications are considered. First, consider uniform flow past a circular cylinder for three cases: low Reynolds number, high Reynolds number, and also intermediate Reynolds numbers at values 26 and 36. These values are chosen because the flow is still steady and has not yet become unsteady. For the low Reynolds number, approximate the NSlet by the leading order Oseenlet term. For the high Reynolds number, approximate the NSlet by the Eulerlet which is the leading order Oseenlet in the high Reynolds number limit. For the intermediate Reynolds numbers, approximate the NSlet by an Eulerlet close to its origin and an Oseenlet further away. Second, consider uniform flow past a slender body with elliptical cross section with Reynolds number Re ∼ 106 and approximate the NSlet by the Eulerlet. Finally, consider the Blasius problem of uniform flow past a semi-infinite flat plate and consider the first three terms in the NSlet approximation.
Investigating the effect of different impurities on plasma detachment in linear plasma machine Magnum-PSI
Authors: Perillo R. , Chandra R. , Akkermans G. R. A. , Classen I. G. J. , Korving S. Q. ,   Magnum-PSI Team
Published: October 2019

To achieve a tolerable heat and particle flux to the divertor target of fusion reactors, the so-called plasma detachment is essential to be set up and controlled. Impurity seeding facilitates the achievement of such a regime, mostly due to the enhanced plasma radiation led by the excitation-relaxation cycle of such species. Little is known about the impurity-induced plasma chemical processes occurring in the divertor region during detachment operation. In this work, the influence of three different impurities, i.e., N2, Ar, and He, on detachment performance is studied. To do so, experimental campaigns on the linear plasma machine Magnum-PSI have been carried out. Results highlight the beneficial role of N2 + H2 seeding, decreasing the plasma pressure in front of the target, leading to a reduced heat load compared to the pure H2 seeding case. An opposite trend has been found concerning He and Ar puffing. In fact, injection of H2 + He and H2 + Ar gas mixtures led to an increased heat flux. To address the importance of different plasma-chemical reaction paths, global plasma models have been used. The resulting reduced reaction schemes for Ar + H2, He + H2, and N2 + H2 have been implemented in B2.5-Eunomia, a coupled code consisting of a Monte Carlo code treating the transport of neutrals and a fluid code solving plasma equations. Simulation results qualitatively reproduce the favorable effect of N2, while confirming the deteriorating effect of He and Ar on a detachedlike hydrogen plasma. We point the synergetic role of H2 + N2 to be due to molecular-driven ion recombination, i.e., N-molecular-assisted recombination (MAR). A direct comparison of the collision frequency between N-MAR and MAR is showed, highlighting the crucial importance of the former in reducing the ion and heat flux to the target plate.
Temperature-driven anion migration in gradient halide perovskites
Authors: Scheidt Rebecca A. , Kamat Prashant V.
Published: October 2019

Cesium lead halide perovskite films with a systematic change in the halide composition of CsPbBr3−xIx, in which iodide concentration varies from x = 0 to x = 3, provide a built-in gradient band structure. Such a gradient structure allows for the integrated capture of visible photons and directs them to the energetically low-lying iodide rich region. Annealing gradient halide perovskite films at temperatures ranging from 50 °C to 90 °C causes the films to homogenize into mixed halide perovskites. The movement of halide ions during the homogenization process was elucidated using UV-Visible absorbance and X-ray photoelectron spectroscopy. The halide ion movement in CsPbBr3−xIx gradient films was tracked via absorbance changes in the visible region of the spectrum that enabled us to measure the temperature dependent rate constant and energy of activation (74.5 kJ/mol) of halide ion homogenization. Excited state processes of both gradient and homogenized films probed through transient absorption spectroscopy showed the direct flow of charge carriers and charge recombination in both films.
The road taken
Authors: Porter Anne Marie , White Susan
Published: October 2019

Survey data show that PhD physicists find satisfaction in a wide range of careers, from academia to government to industry.
Mistletoes of Southern Australia
Authors: Watson David
Published: October 2019

Mistletoes are an enigmatic group of plants. Lacking roots and depending on other plants for their livelihood, they have inspired a range of beliefs throughout the world. Some people regard them as being endowed with magical properties, others as destructive weeds that devalue native habitats, and still others as beautiful native plants that support wildlife.
This second edition of Mistletoes of Southern Australia is the definitive authority on these intriguing native plants. With specially commissioned watercolours by artist Robyn Hulley and more than 130 colour photographs, it provides detailed species accounts for all 47 species found in the region. It is fully updated throughout, with new distribution maps and new sections on fire, climate change and mistletoes in urban areas. It also describes the ecology, life history and cultural significance of mistletoes, their distribution in Australia and around the world, and practical advice on their management.
A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales
Authors: Marcovitz Amir , Turakhia Yatish , Chen Heidi I. , Gloudemans Michael , Braun Benjamin A. , Wang Haoqing , Bejerano Gill
Published: October 2019

Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (
q
-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
Multiple modes of convergent adaptation in the spread of glyphosate-resistant
Amaranthus tuberculatus
Authors: Kreiner Julia M. , Giacomini Darci Ann , Bemm Felix , Waithaka Bridgit , Regalado Julian , Lanz Christa , Hildebrandt Julia , Sikkema Peter H. , Tranel Patrick J. , Weigel Detlef , Stinchcombe John R. , Wright Stephen I.
Published: October 2019

The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, or geographic spread of adaptive alleles through gene flow. Glyphosate-resistant
Amaranthus tuberculatus
poses one of the most significant threats to crop yields in the Midwestern United States, with both agricultural populations and herbicide resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the
A. tuberculatus
genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals from Canada and the United States. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically nonagricultural. Moreover, resistance on these local, nonagricultural backgrounds appears to have occurred predominantly through the partial sweep of a single haplotype. In contrast, resistant haplotypes arising from the Midwestern United States show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable species-wide diversity of
A. tuberculatus
has facilitated geographic parallel adaptation of glyphosate resistance, more recently established agricultural populations are limited to adaptation in a more mutation-limited framework.
Gray Matter Age Prediction as a Biomarker for Risk of Dementia
Authors: Wang Johnny , Knol Maria J. , Tiulpin Aleksei , Dubost Florian , de Bruijne Marleen , Vernooij Meike W. , Adams Hieab H. H. , Ikram M. Arfan , Niessen Wiro J. , Roshchupkin Gennady V.
Published: October 2019

Significance

The difference between brain age estimated from MRI and chronological age is thought to serve as an important biomarker reflecting pathological processes in the brain. Several recent studies showed the relation between accelerated brain aging and various disorders. However, until now, the utility of such an age difference for preclinical screening using longitudinal studies was absent. To fill this gap, we first built a deep learning model using brain MRI from a population-based study including 5,496 participants. And then, using follow-up information, we observed that this age difference was significantly associated with the risk of dementia. Therefore, our study shows that the difference between MRI-brain predicted and chronological age is potentially a biomarker for early dementia risk screening.
Empirical measures of mutational effects define neutral models of regulatory evolution in
Saccharomyces cerevisiae
Authors: Hodgins-Davis Andrea , Duveau Fabien , Walker Elizabeth A. , Wittkopp Patricia J.
Published: October 2019

Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast
Saccharomyces cerevisiae
by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and are inconsistent with normality. For example, all 10 distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.
GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture
Authors: Yano Kenji , Morinaka Yoichi , Wang Fanmiao , Huang Peng , Takehara Sayaka , Hirai Takaaki , Ito Aya , Koketsu Eriko , Kawamura Mayuko , Kotake Kunihiko , Yoshida Shinya , Endo Masaki , Tamiya Gen , Kitano Hidemi , Ueguchi-Tanaka Miyako , Hirano Ko , Matsuoka Makoto
Published: October 2019

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of
OsSPY
associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.
Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole
Authors: Rodriguez-Furlan Cecilia , Domozych David , Qian Weixing , Enquist Per-Anders , Li Xiaohui , Zhang Chunhua , Schenk Rolf , Winbigler Holly Saulsbery , Jackson William , Raikhel Natasha V. , Hicks Glenn R.
Published: October 2019

Significance

In plants, the retromer complex (VPS35, VPS29, VPS26) has been implicated in retrograde traffic from the endosomes back to the
trans
-Golgi network. Nevertheless, vps35 mutants exhibit impaired anterograde traffic toward the vacuole (synthetic, endocytic, and autophagic). This paradox remains an open question. We show that the small molecule endosidin17 (ES17) targets VPS35, which disrupts its association with RABG3f. This, in turn, impairs retromer complex membrane anchoring, producing vps35 mutant-like phenotypes. Using ES17, we found that VPS35–RABG3f binding precedes the release of RABG3f–GTP to interact with the vacuolar homotypic fusion and vacuole protein sorting (HOPS) complex, which is required for fusion of late compartments with the tonoplast. Thus, VPS35–RABG3f interaction constitutes a checkpoint before proceeding with membrane fusion.
Structural basis of light-induced redox regulation in the Calvin–Benson cycle in cyanobacteria
Authors: McFarlane Ciaran R. , Shah Nita R. , Kabasakal Burak V. , Echeverria Blanca , Cotton Charles A. R. , Bubeck Doryen , Murray James W.
Published: October 2019

Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin–Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential CB-cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco. PRK consumes ATP to produce the Rubisco substrate ribulose bisphosphate (RuBP). GAPDH catalyzes the reduction step of the CB cycle with NADPH to produce the sugar glyceraldehyde 3-phosphate (GAP), which is used for regeneration of RuBP and is the main exit point of the cycle. GAPDH and PRK are coregulated by the redox state of a conditionally disordered protein CP12, which forms a ternary complex with both enzymes. However, the structural basis of CB-cycle regulation by CP12 is unknown. Here, we show how CP12 modulates the activity of both GAPDH and PRK. Using thermophilic cyanobacterial homologs, we solve crystal structures of GAPDH with different cofactors and CP12 bound, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide preorders CP12 prior to binding the PRK active site, which is resolved in complex with CP12. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our structural and biochemical data explain how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.
HMGB1–C1q complexes regulate macrophage function by switching between leukotriene and specialized proresolving mediator biosynthesis
Authors: Liu Tianye , Xiang Alec , Peng Travis , Doran Amanda C. , Tracey Kevin J. , Barnes Betsy J. , Tabas Ira , Son Myoungsun , Diamond Betty
Published: October 2019

Significance

Monocyte to macrophage differentiation is critical to inflammation and resolution of inflammation and can be regulated by high-mobility group box 1 (HMGB1) and HMGB1 plus C1q, respectively. These are 2 evolutionarily old and highly conserved molecules. While HMGB1 causes a positive-feedback loop between the proinflammatory lipid mediator leukotriene B4 (LTB4) and IRF5, an important regulator of inflammatory macrophage polarization, HMGB1 plus C1q increases production of specialized proresolving lipid mediators (SPMs) lipoxin A4, resolvin D1, and resolvin D2, which prevent IRF5 transcription. As nonresolving inflammation is a common condition, we designed an HMGB1–C1q mimetic peptide that can polarize monocytes to an antiinflammatory phenotype in vitro and in vivo.
Paternal knockout of
Slc38a4
/SNAT4 causes placental hypoplasia associated with intrauterine growth restriction in mice
Authors: Matoba Shogo , Nakamuta Shoko , Miura Kento , Hirose Michiko , Shiura Hirosuke , Kohda Takashi , Nakamuta Nobuaki , Ogura Atsuo
Published: October 2019

The placenta is critical in mammalian embryonic development because the embryo’s supply of nutrients, including amino acids, depends solely on mother-to-embryo transport through it. However, the molecular mechanisms underlying this amino acid supply are poorly understood. In this study, we focused on system A amino acid transporters
Slc38a1
/SNAT1,
Slc38a2
/SNAT2, and
Slc38a4
/SNAT4, which carry neutral, short-side-chain amino acids, to determine their involvement in placental or embryonic development. A triple-target CRISPR screen identified
Slc38a4
/SNAT4 as the critical amino acid transporter for placental development in mice. We established mouse lines from the CRISPR founders with large deletions in
Slc38a4
and found that, consistent with the imprinted paternal expression of
Slc38a4
/SNAT4 in the placenta, paternal knockout (KO) but not maternal KO of
Slc38a4
/SNAT4 caused placental hypoplasia associated with reduced fetal weight. Immunostaining revealed that SNAT4 was widely expressed in differentiating cytotrophoblasts and maturing trophoblasts at the maternal–fetal interface. A blood metabolome analysis revealed that amino acid concentrations were globally reduced in
Slc38a4
/SNAT4 mutant embryos. These results indicated that SNAT4-mediated amino acid transport in mice plays a major role in placental and embryonic development. Given that expression of
Slc38a4
in the placenta is conserved in other species, our
Slc38a4
/SNAT4 mutant mice could be a promising model for the analysis of placental defects leading to intrauterine growth restriction in mammals.
Genetic ablation of purine salvage in
Cryptosporidium parvum
reveals nucleotide uptake from the host cell
Authors: Pawlowic Mattie C. , Somepalli Mastanbabu , Sateriale Adam , Herbert Gillian T. , Gibson Alexis R. , Cuny Gregory D. , Hedstrom Lizbeth , Striepen Boris
Published: October 2019

The apicomplexan parasite
Cryptosporidium
is a leading global cause of severe diarrheal disease and an important contributor to early-childhood mortality. Waterborne outbreaks occur frequently, even in countries with advanced water treatment capabilities, and there is currently no fully effective treatment. Nucleotide pathways are attractive targets for antimicrobial development, and several laboratories are designing inhibitors of these enzymes as potential treatment for
Cryptosporidium
infections. Here we take advantage of newly available molecular genetics for
Cryptosporidium parvum
to investigate nucleotide biosynthesis by directed gene ablation. Surprisingly, we found that the parasite tolerates the loss of classical targets including dihydrofolate reductase-thymidylate synthase (DHFR-TS) and inosine monophosphate dehydrogenase (IMPDH). We show that thymidine kinase provides a route to thymidine monophosphate in the absence of DHFR-TS. In contrast, only a single pathway has been identified for
C. parvum
purine nucleotide salvage. Nonetheless, multiple enzymes in the purine pathway, as well as the adenosine transporter, can be ablated. The resulting mutants are viable under normal conditions but are hypersensitive to inhibition of purine nucleotide synthesis in their host cell.
Cryptosporidium
might use as-yet undiscovered purine transporters and salvage enzymes; however, genetic and pharmacological experiments led us to conclude that
Cryptosporidium
imports purine nucleotides from the host cell. The potential for ATP uptake from the host has significant impact on our understanding of parasite energy metabolism given that
Cryptosporidium
lacks oxidative phosphorylation and glycolytic enzymes are not constitutively expressed throughout the parasite life cycle.
Measurements of the self-assembly kinetics of individual viral capsids around their RNA genome
Authors: Garmann Rees F. , Goldfain Aaron M. , Manoharan Vinothan N.
Published: October 2019

Significance

Self-assembly is a process in which functional nanoscale structures build themselves, driven by Brownian motion and interactions between components. The term was originally coined to describe the formation of a viral capsid, the protein shell that protects the genome of a virus. Despite decades of study, how capsids self-assemble has remained a mystery, because there were no methods to measure the assembly kinetics of individual capsids. We surmount this obstacle using a sensitive microscopy technique based on laser interferometry. The measurements show that a small nucleus of proteins must form on the viral RNA before the capsid assembles. These results might help researchers design strategies to stop the assembly of pathogenic viruses or to build synthetic nanostructures.
Rapid increase in Asian bottles in the South Atlantic Ocean indicates major debris inputs from ships
Authors: Ryan Peter G. , Dilley Ben J. , Ronconi Robert A. , Connan Maëlle
Published: October 2019

Significance

Many oceanic islands suffer high levels of stranded debris, particularly those near subtropical gyres where floating debris accumulates. During the last 3 decades, plastic drink bottles have shown the fastest growth rate of all debris types on remote Inaccessible Island. During the 1980s, most bottles drifted to the island from South America, carried 3,000 km by the west wind drift. Currently, 75% of bottles are from Asia, with most from China. The recent manufacture dates indicate that few bottles could have drifted from Asia, and presumably are dumped from ships, in contravention of International Convention for the Prevention of Pollution from Ships regulations. Our results question the widely held assumption that most plastic debris at sea comes from land-based sources.