bluuebunny/crossref_metadata_2025 huggingface dataset:
SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. IV. Linear-scaling second-order explicitly correlated energy with pair natural orbitals
Authors: Pavošević Fabijan , Pinski Peter , Riplinger Christoph , Neese Frank , Valeev Edward F.
Published: April 2016

We present a formulation of the explicitly correlated second-order Møller-Plesset (MP2-F12) energy in which all nontrivial post-mean-field steps are formulated with linear computational complexity in system size. The two key ideas are the use of pair-natural orbitals for compact representation of wave function amplitudes and the use of domain approximation to impose the block sparsity. This development utilizes the concepts for sparse representation of tensors described in the context of the domain based local pair-natural orbital-MP2 (DLPNO-MP2) method by us recently [Pinski et al., J. Chem. Phys. 143, 034108 (2015)]. Novel developments reported here include the use of domains not only for the projected atomic orbitals, but also for the complementary auxiliary basis set (CABS) used to approximate the three- and four-electron integrals of the F12 theory, and a simplification of the standard B intermediate of the F12 theory that avoids computation of four-index two-electron integrals that involve two CABS indices. For quasi-1-dimensional systems (n-alkanes), the ON DLPNO-MP2-F12 method becomes less expensive than the conventional ON5 MP2-F12 for n between 10 and 15, for double- and triple-zeta basis sets; for the largest alkane, C200H402, in def2-TZVP basis, the observed computational complexity is N∼1.6, largely due to the cubic cost of computing the mean-field operators. The method reproduces the canonical MP2-F12 energy with high precision: 99.9% of the canonical correlation energy is recovered with the default truncation parameters. Although its cost is significantly higher than that of DLPNO-MP2 method, the cost increase is compensated by the great reduction of the basis set error due to explicit correlation.
Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures
Authors: Caskey Christopher M. , Holder Aaron , Shulda Sarah , Christensen Steven T. , Diercks David , Schwartz Craig P. , Biagioni David , Nordlund Dennis , Kukliansky Alon , Natan Amir , Prendergast David , Orvananos Bernardo , Sun Wenhao , Zhang Xiuwen , Ceder Gerbrand , Ginley David S. , Tumas William , Perkins John D. , Stevanovic Vladan , Pylypenko Svitlana , Lany Stephan , Richards Ryan M. , Zakutayev Andriy
Published: April 2016

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.
The local projection in the density functional theory plus U approach: A critical assessment
Authors: Wang Yue-Chao , Chen Ze-Hua , Jiang Hong
Published: April 2016

Density-functional theory plus the Hubbard U correction (DFT + U) method is widely used in first-principles studies of strongly correlated systems, as it can give qualitatively (and sometimes, semi-quantitatively) correct description of energetic and structural properties of many strongly correlated systems with similar computational cost as local density approximation or generalized gradient approximation. On the other hand, the DFT + U approach is limited both theoretically and practically in several important aspects. In particular, the results of DFT + U often depend on the choice of local orbitals (the local projection) defining the subspace in which the Hubbard U correction is applied. In this work we have systematically investigated the issue of the local projection by considering typical transition metal oxides, β-MnO2 and MnO, and comparing the results obtained from different implementations of DFT + U. We found that the choice of the local projection has significant effects on the DFT + U results, which are more significant for systems with stronger covalent bonding (e.g., MnO2) than those with more ionic bonding (e.g., MnO). These findings can help to clarify some confusion arising from the practical use of DFT + U and may also provide insights for the development of new first-principles approaches beyond DFT + U.
Varying stopping and self-focusing of intense proton beams as they heat solid density matter
Authors: Kim J. , McGuffey C. , Qiao B. , Wei M. S. , Grabowski P. E. , Beg F. N.
Published: April 2016

Transport of intense proton beams in solid-density matter is numerically investigated using an implicit hybrid particle-in-cell code. Both collective effects and stopping for individual beam particles are included through the electromagnetic fields solver and stopping power calculations utilizing the varying local target conditions, allowing self-consistent transport studies. Two target heating mechanisms, the beam energy deposition and Ohmic heating driven by the return current, are compared. The dependences of proton beam transport in solid targets on the beam parameters are systematically analyzed, i.e., simulations with various beam intensities, pulse durations, kinetic energies, and energy distributions are compared. The proton beam deposition profile and ultimate target temperature show strong dependence on intensity and pulse duration. A strong magnetic field is generated from a proton beam with high density and tight beam radius, resulting in focusing of the beam and localized heating of the target up to hundreds of eV.
Diffusion mechanisms in Li0.5CoO2—A computational study
Authors: Bunjaku Teutë , Pedersen Andreas , Luisier Mathieu
Published: April 2016

An atomistic study of the order-effect occurring in LixCoO2 at x = 0.5 is presented, and an explanation for the experimentally observed dip in the Li diffusivity is proposed. Configurations where a single half-filled Li-layer arranged in either a linear or a zig-zag pattern are simulated. It is found that the lowest energy phase is the zig-zag pattern rather than the linear arrangement that is currently assumed to be of lowest energy. Atomic interactions are modeled at the density-functional theory level of accuracy, and energy barriers for Li-ion diffusion are determined from searches for first order saddle points on the resulting potential energy surface. The determined saddle points reveal that the barriers for diffusion parallel and perpendicular to the zig-zag phase differ significantly and explain the observed dip in diffusivity.
Precise measurement of single carbon nanocoils using focused ion beam technique
Authors: Nakamura Yasushi , Suda Yoshiyuki , Kunimoto Ryuji , Iida Tamio , Takikawa Hirofumi , Ue Hitoshi , Shima Hiroyuki
Published: April 2016

We have developed a precise resistivity measurement system for quasi-one-dimensional nanomaterials using a focused ion beam. The system enables the resistivity of carbon nanocoils (CNCs) to be measured and its dependence on coil geometry to be elucidated. At room temperature, the resistivity of CNCs tended to increase with coil diameter, while that of artificially graphitized CNCs remained constant. These contrasting behaviors indicate coil-diameter-induced enhancement in structural disorder internal to CNCs. Low-temperature resistivity measurements performed on the CNCs revealed that electron transport through the helical axis is governed by the variable range hopping mechanism. The characteristic temperature in variable range hopping theory was found to systematically increase with coil diameter, which supports our theory that the population of sp2-domains in CNCs decreases considerably with coil diameter.
Communication: Control of the fragment state distributions produced upon decay of an isolated resonance state
Authors: García-Vela A.
Published: April 2016

Control of the fragment state distributions produced upon decay of a resonance state is achieved by using a weak laser field consisting of two pulses with a varying time delay between them. It is shown that specific product fragment states can be significantly favored or quenched. The efficiency and flexibility of the control method are found to increase with increasing resonance width. The control scheme is completely independent of the specific system to which it is applied, which makes its applicability universal.
Investigation of particle inertial migration in high particle concentration suspension flow by multi-electrodes sensing and Eulerian-Lagrangian simulation in a square microchannel
Authors: Zhao Tong , Yao Jiafeng , Liu Kai , Takei Masahiro
Published: April 2016

The inertial migration of neutrally buoyant spherical particles in high particle concentration (αpi > 3%) suspension flow in a square microchannel was investigated by means of the multi-electrodes sensing method which broke through the limitation of conventional optical measurement techniques in the high particle concentration suspensions due to interference from the large particle numbers. Based on the measured particle concentrations near the wall and at the corner of the square microchannel, particle cross-sectional migration ratios are calculated to quantitatively estimate the migration degree. As a result, particle migration to four stable equilibrium positions near the centre of each face of the square microchannel is found only in the cases of low initial particle concentration up to 5.0 v/v%, while the migration phenomenon becomes partial as the initial particle concentration achieves 10.0 v/v% and disappears in the cases of the initial particle concentration αpi ≥ 15%. In order to clarify the influential mechanism of particle-particle interaction on particle migration, an Eulerian-Lagrangian numerical model was proposed by employing the Lennard-Jones potential as the inter-particle potential, while the inertial lift coefficient is calculated by a pre-processed semi-analytical simulation. Moreover, based on the experimental and simulation results, a dimensionless number named migration index was proposed to evaluate the influence of the initial particle concentration on the particle migration phenomenon. The migration index less than 0.1 is found to denote obvious particle inertial migration, while a larger migration index denotes the absence of it. This index is helpful for estimation of the maximum initial particle concentration for the design of inertial microfluidic devices.
Role of spinodal-like wrinkling as a prenucleation process in crystallization of sol-gel derived thin films
Authors: Valant Matjaz , Fanetti Mattia , Luin Uros
Published: April 2016

Studies of crystallization of a sol-gel derived alumina thin film showed on a critical role of spinodal-like wrinkling. The wrinkling that depends on a humidity gradient in the film provides nucleation sites with high supersaturation located at the top of topological islands that occur as a result of the wrinkling. Nucleation of crystal nuclei takes place at these sites at a significantly lower temperature as it would be the case for homogenous nucleation. The crystal growth continues through different supersaturation regimes that are defined by the wrinkling topology. We showed how the crystallization can be efficiently suppressed to higher temperatures by minimizing the humidity gradient in the dip-coated film by controlled drying.
Second-harmonic microscopy of strain fields around through-silicon-vias
Authors: Cho Yujin , Shafiei Farbod , Mendoza B. S. , Lei Ming , Jiang Tengfei , Ho P. S. , Downer M. C.
Published: April 2016

Through-Silicon-Vias (TSVs)—10 μm-diameter conducting rods that connect vertically stacked silicon layers—provide three dimensional circuit integration, but introduce strain in the surrounding silicon when thermally cycled. Here, we noninvasively probe strain fields around Cu TSVs in Si(001) using optical second-harmonic generation (SHG) microscopy. Results are compared with micro-Raman spectra of the strained regions. We find that SHG probes strain fields more quickly than Raman spectroscopy, while maintaining comparable sensitivity and spatial resolution, and avoiding the need for spectral analysis. Moreover, SHG is selectively sensitive to axial shear components uiz (i = x, y) of the strain tensor that are often neglected in Raman analysis. Thus, SHG complements Raman spectroscopy.
New advanced method and cost-based indices applied to probabilistic forecasting of photovoltaic generation
Authors: Bracale Antonio , Carpinelli Guido , De Falco Pasquale , Rizzo Renato , Russo Angela
Published: April 2016

The ability to forecast the production of power by photovoltaic (PV) systems accurately and reliably is of major importance for the appropriate management of future electrical distribution systems. Several forecasting methods have been proposed in the relevant literature, and many indices have been used to quantify the quality of the forecasts. The methods can provide either deterministic or probabilistic forecasts; the latter seem to be the most appropriate to take into account the unavoidable uncertainties of PV power production. Similarly, indices were used to quantify the quality of both deterministic and probabilistic forecasting methods, but they usually do not account for the economic consequences of forecasting errors. In this paper, two advanced probabilistic forecasting approaches based on the Bayesian inference method are applied to the short-term forecasting of PV power production. Moreover, new probabilistic indices were proposed with the aim of comparing the probabilistic forecasting methods in such way that the value of the forecast is not included only by the users in their decision-making process; instead, it is partially anticipated by the forecasters in their quality-assessment process. Numerical applications also are presented to provide evidence of the performances of the Bayesian-based approaches and the probabilistic indices that were considered.
An open-chamber flow-focusing device for focal stimulation of micropatterned cells
Authors: Cheng Jonathan W. , Chang Tim C. , Bhattacharjee Nirveek , Folch Albert
Published: April 2016

Microfluidic devices can deliver soluble factors to cell and tissue culture microenvironments with precise spatiotemporal control. However, enclosed microfluidic environments often have drawbacks such as the need for continuous culture medium perfusion which limits the duration of experiments, incongruity between microculture and macroculture, difficulty in introducing cells and tissues, and high shear stress on cells. Here, we present an open-chamber microfluidic device that delivers hydrodynamically focused streams of soluble reagents to cells over long time periods (i.e., several hours). We demonstrate the advantage of the open chamber by using conventional cell culture techniques to induce the differentiation of myoblasts into myotubes, a process that occurs in 7–10 days and is difficult to achieve in closed chamber microfluidic devices. By controlling the flow rates and altering the device geometry, we produced sharp focal streams with widths ranging from 36 μm to 187 μm. The focal streams were reproducible (∼12% variation between units) and stable (∼20% increase in stream width over 10 h of operation). Furthermore, we integrated trenches for micropatterning myoblasts and microtraps for confining single primary myofibers into the device. We demonstrate with finite element method (FEM) simulations that shear stresses within the cell trench are well below values known to be deleterious to cells, while local concentrations are maintained at ∼22% of the input concentration. Finally, we demonstrated focused delivery of cytoplasmic and nuclear dyes to micropatterned myoblasts and myofibers. The open-chamber microfluidic flow-focusing concept combined with micropatterning may be generalized to other microfluidic applications that require stringent long-term cell culture conditions.
Direct assessment of solid–liquid interface noise in ion sensing using a differential method
Authors: Zhang Da , Must Indrek , Netzer Nathan L. , Xu Xingxing , Solomon Paul , Zhang Shi-Li , Zhang Zhen
Published: April 2016

This letter presents a microelectrode cell dedicated to direct assessment of the solid–liquid interface noise without recourse to a reference electrode. In the present design, two identical TiN electrodes of various sizes are used for differential measurements in KCl-based electrolytes. Measured noise of the TiN|electrolyte system is found to be of thermal nature. Scaling inversely with electrode area, the noise is concluded to mainly arise from the solid–liquid interface. This noise is comparable to or larger than that of the state-of-the-art MOSFETs. Therefore, its influence cannot be overlooked for the design of future ion sensors.
Phenomenological theory of optical broadening in zero-dimensional systems applied to silicon nanocrystals
Authors: Nikolaev V. V. , Averkiev N. S. , Fujii Minoru
Published: April 2016

We develop a phenomenological theory of inhomogeneous broadening in zero-dimensional systems and apply it to study photoluminescence (PL) spectra of silicon nanocrystals measured at helium and room temperatures. The proposed approach allowed us to explain experimentally observed PL peak asymmetry, linear dependence of the peak width on its maximum, and anomalous alteration of spectral characteristics with temperature increase.
Simultaneous determination of the residual stress, elastic modulus, density and thickness of ultrathin film utilizing vibrating doubly clamped micro-/nanobeams
Authors: Stachiv Ivo , Kuo Chih-Yun , Fang Te-Hua , Mortet Vincent
Published: April 2016

Measurement of ultrathin film thickness and its basic properties can be highly challenging and time consuming due to necessity of using several very sophisticated devices. Here, we report an easy accessible resonant based method capable to simultaneously determinate the residual stress, elastic modulus, density and thickness of ultrathin film coated on doubly clamped micro-/nanobeam. We show that a general dependency of the resonant frequencies on the axial load is also valid for in-plane vibrations, and the one depends only on the considered vibrational mode. As a result, we found that the film elastic modulus, density and thickness can be evaluated from two measured in-plane and out-plane fundamental resonant frequencies of micro-/nanobeam with and without film under different prestress forces. Whereas, the residual stress can be determined from two out-plane (in-plane) measured consecutive resonant frequencies of beam with film under different prestress forces without necessity of knowing film and substrate properties and dimensions. Moreover, we also reveal that the common uncertainties in force (and thickness) determination have a negligible (and minor) impact on the determined film properties. The application potential of the present method is illustrated on the beam made of silicon and SiO2 with deposited 20 nm thick AlN and 40 nm thick Au thin films, respectively.
Neuropsychiatric pharmaceuticals and illicit drugs in wastewater treatment plants: a review
Authors: Asimakopoulos Alexandros G. , Kannan Kurunthachalam
Published: April 2016

Environmental contextNeuropsychiatric pharmaceuticals and illicit drugs in wastewaters are of increasing environmental concern. We compile the recent literature and evaluate the concentrations and profiles of various drugs and their removal efficiencies in wastewater treatment plants. The sewage epidemiology approach, used in the estimation of drug usage in communities, is discussed, and we make recommendations for future research in this area. AbstractNeuropsychiatric pharmaceuticals and illicit drugs encompass a broad range of compounds including opioids, amphetamine-type stimulants, cannabinoids, benzodiazepines, barbiturates, antipsychotics, anaesthetics, anti-epileptics and mood stabilisers, lysergic compounds, sympathomimetic amines and cocaine derivatives. In this article, we review studies on the occurrence and fate of these drugs in wastewater treatment plants. In general, among various drugs studied, the concentrations and detection frequencies of opioids and cocaine derivatives were the highest in wastewaters. The forensic analysis of wastewaters suggests that cocaine and opioids usage has increased. Given the fact that data on drug usage can be used for making regulatory decisions and policies, this review focuses on understanding the sources and environmental dynamics of neuropsychiatric and illicit drugs. There is a pressing need for more research on the magnitude and extent of illicit drug consumption. The ‘sewage epidemiology’ approach, currently applied in the estimation of illicit drug consumption in communities, is reviewed. The field of wastewater research has been advancing in multipronged paths, incorporating concepts in analytical chemistry, organic chemistry, environmental chemistry, biochemistry, sewage engineering, drug epidemiology and statistics. Future prospects with regard to the occurrence and environmental fate of illicit and psychoactive drugs are recommended.
Genetic relationships between landlocked and coastal populations of Lycengraulis grossidens (Engraulidae) in south-eastern South America: evidence for a continental colonisation route with secondary transitions to the coastal region
Authors: Mai Ana C. G. , Robe Lizandra J. , Marins Luis F. , Vieira João P.
Published: April 2016

The anchovies of the genus Lycengraulis are the product of an evolutionary transition from a marine to freshwater environment that occurred in South America during the Miocene epoch. Lycengraulis grossidens originated from freshwater lineages and is currently distributed in estuaries and coastal zones. Nevertheless, based on otolith chemistry, there are landlocked individuals in the Uruguay River. The aim of the present study was to investigate the spatiotemporal scenario by which these landlocked individuals reached their current distribution: whether through a north-to-south continental route based on the connection between basins or from the marine environment. To this end, a fragment of the mitochondrial (mt)DNA control region was analysed from individuals collected along freshwater, estuarine and marine environments. We found a significant genetic differentiation between freshwater and coastal (estuarine and marine) populations. Larger haplotype diversities and female effective population size values were found in the coastal population. Nevertheless, the outgroup rooting positioned some Uruguay River haplotypes as hypothetical ancestors in the directed network and as early offshoots in the phylogeny, suggesting the landlocked population as an ancestral lineage. Therefore, the phylogenetic history and biogeography are consistent with a north-to-south continental colonisation route putatively associated with ancient connections between the Amazon and Parana basins followed by new evolutionary transitions to the coastal region associated with Quaternary sea level oscillations.
Dominant hemisphere lateralization of cortical parasympathetic control as revealed by frontotemporal dementia
Authors: Guo Christine C. , Sturm Virginia E. , Zhou Juan , Gennatas Efstathios D. , Trujillo Andrew J. , Hua Alice Y. , Crawford Richard , Stables Lara , Kramer Joel H. , Rankin Katherine , Levenson Robert W. , Rosen Howard J. , Miller Bruce L. , Seeley William W.
Published: April 2016

Significance

Brain–body interactions are fundamental to physical and mental health. Here, we used a unique brain lesion model to elucidate the neural localization and lateralization of cerebro-cardiac control. Our data revealed that the salience network, an intrinsic connectivity network anchored by the anterior insula and cingulate, is crucial for maintaining basal parasympathetic outflow. Specifically, dominant hemisphere-predominant salience network damage undermined parasympathetic control of the heart. The findings suggest that balanced functional integrity of both hemispheres is vital to maintaining bodily homeostasis.
Echolocating bats use future-target information for optimal foraging
Authors: Fujioka Emyo , Aihara Ikkyu , Sumiya Miwa , Aihara Kazuyuki , Hiryu Shizuko
Published: April 2016

Significance

This study shows how an animal dynamically and rationally controls its sensing and navigates to capture multiple prey items. To perform this study, we extracted sonar attention and flight attention of foraging wild bats from both empirical data and mathematical modeling. We show that the bats directed their sonar and flight attention toward not only an immediate prey but also the next prey. In addition, numerical simulation shows a possibility that the bats select suitable flight paths for the consecutive capture. Hence, wild echolocating bats plan their flight paths by distributing their attention among multiple prey items, which means that the bats do not forage in a hit-or-miss fashion but rather spatially anticipate their future targets for optimum routing.
Function and regulation of TRPP2 ion channel revealed by a gain-of-function mutant
Authors: Arif Pavel Mahmud , Lv Caixia , Ng Courtney , Yang Lei , Kashyap Parul , Lam Clarissa , Valentino Victoria , Fung Helen Y. , Campbell Thomas , Møller Simon Geir , Zenisek David , Holtzman Nathalia G. , Yu Yong
Published: April 2016

Significance

Mutations in transient receptor potential polycystin 2 (TRPP2) and polycystin-1 account for autosomal dominant polycystic kidney disease (ADPKD). TRPP2 is a cation channel and plays a crucial role in coupling extracellular stimuli to cellular responses in cells. The activation mechanism of TRPP2 is unknown, which significantly limits its study. Here, we report a gain-of-function (GOF) mutation that causes constitutive activity of TRPP2. This mutant was applied to investigation of the TRPP2 channel properties, the functional effects of ADPKD pathogenic TRPP2 mutations, and the in vivo function of the GOF TRPP2 in zebrafish embryos. From our results, we conclude that the GOF TRPP2 is a powerful tool for TRPP2 study, and has potential therapeutic applications in ADPKD treatment.
Reversible host cell remodeling underpins deformability changes in malaria parasite sexual blood stages
Authors: Dearnley Megan , Chu Trang , Zhang Yao , Looker Oliver , Huang Changjin , Klonis Nectarios , Yeoman Jeff , Kenny Shannon , Arora Mohit , Osborne James M. , Chandramohanadas Rajesh , Zhang Sulin , Dixon Matthew W. A. , Tilley Leann
Published: April 2016

Significance

This study provides, to our knowledge, the first ultrastructural and dynamics analysis of the host red blood cell membrane of
Plasmodium falciparum
gametocytes, revealing reversible expansion of the spectrin–actin skeleton, accompanied by reversible modulation of skeletal coupling to the plasma membrane. We use the measured physical parameters to inform a computationally efficient coarse-grained model. This model shows that restructuring the skeletal meshwork can fully account for the observed deformability changes. We reveal a critical role for actin remodeling in driving this reversible biomechanical host cell subversion. This work provides fundamental insights into the molecular changes that underpin gametocyte survival in the circulation.
Emergent ultra–long-range interactions between active particles in hybrid active–inactive systems
Authors: Steimel Joshua P. , Aragones Juan L. , Hu Helen , Qureshi Naser , Alexander-Katz Alfredo
Published: April 2016

Significance

Particle–particle interactions determine the state of a system. Control over the range and magnitude of such interactions is critical for science and technology. Here, we show that active particles experience an emergent ultra–long-range attractive interaction in the presence of a passive medium. The range and magnitude of this interaction are controlled by the elasticity of the medium and the activity of the particles. For the conditions studied here, we have found the range to be as large as 20 particle diameters, which is much larger than the typical interaction range between colloids. This interaction may open up new routes of control between active objects in passive environments and help us to understand the emergent interactions in nonequilibrium (biological) systems.
Predictable evolution toward flightlessness in volant island birds
Authors: Wright Natalie A. , Steadman David W. , Witt Christopher C.
Published: April 2016

Significance

Predictable evolutionary trends illuminate mechanisms that affect the diversity of traits and species on the tree of life. We show that when birds colonize islands, they undergo predictable changes in body shape. Small-island bird populations evolve smaller flight muscles and longer legs. These shifts in investment from wings to legs, although often subtle, are qualitatively similar to changes that have occurred in flightless bird lineages. Islands with fewer predator species were associated with more dramatic shifts toward flightlessness, implicating reduced predation pressure as the most likely cause of this trend. These predictable evolutionary changes likely exacerbate the vulnerability of flighted island birds to introduced predators and reduce the potential for small-island species to give rise to subsequent radiations.
Implications of lemuriform extinctions for the Malagasy flora
Authors: Federman Sarah , Dornburg Alex , Daly Douglas C. , Downie Alexander , Perry George H. , Yoder Anne D. , Sargis Eric J. , Richard Alison F. , Donoghue Michael J. , Baden Andrea L.
Published: April 2016

Significance

Madagascar is a conservation priority because of its unique and threatened biodiversity. Lemurs, by acting as seed dispersers, are essential to maintaining healthy and diverse forests on the island. However, in the past few thousand years, at least 17 lemur species, many of which were inferred seed dispersers, have gone extinct. We outline the substantial impact that these extinctions have likely had on Malagasy forests by comparing the gape sizes and diets of living and extinct lemurs to identify large-seeded Malagasy plants that appear to be without extant animal dispersers. Additionally, we identify living lemurs that are endangered yet occupy unique and essential dispersal niches. This information can inform conservation initiatives targeting the protection and restoration of these vulnerable ecosystems.
Cofactor bypass variants reveal a conformational control mechanism governing cell wall polymerase activity
Authors: Markovski Monica , Bohrhunter Jessica L. , Lupoli Tania J. , Uehara Tsuyoshi , Walker Suzanne , Kahne Daniel E. , Bernhardt Thomas G.
Published: April 2016

Significance

Penicillin-binding proteins (PBPs) are the targets of penicillin and related beta-lactams, one of our oldest and most effective classes of antibiotics. These enzymes assemble the essential bacterial cell wall. Their structure and biochemical activities have been well-characterized in vitro. However, surprisingly little is known about how PBP activity is controlled in cells. Here, we investigate the mechanism of PBP activation in
Escherichia coli
by a lipoprotein cofactor located in the outer membrane. Our results suggest that activation proceeds via a conformational change in the PBP induced by lipoprotein binding. This information, as well as the nature of the PBP variants isolated, provides new insight into the function of these important drug targets.
Periodically microstructured composite films made by electric- and magnetic-directed colloidal assembly
Authors: Demirörs Ahmet Faik , Courty Diana , Libanori Rafael , Studart André R.
Published: April 2016

Significance

Combined magnetic and electric fields offer unprecedented control over the position and orientation of particles, enabling the formation of programmed colloidal assemblies and composite films with locally modulated mechanical properties. The amplitude of this modulation can be controlled to form polymer-based bioinspired films with reinforced islands. Strikingly, such mechanical modulation can be designed to improve considerably the wear resistance of composite films.
Conductance of P2X
4
purinergic receptor is determined by conformational equilibrium in the transmembrane region
Authors: Minato Yuichi , Suzuki Shiho , Hara Tomoaki , Kofuku Yutaka , Kasuya Go , Fujiwara Yuichiro , Igarashi Shunsuke , Suzuki Ei-ichiro , Nureki Osamu , Hattori Motoyuki , Ueda Takumi , Shimada Ichio
Published: April 2016

Significance

Partial agonists of ligand-gated ion channels reportedly offer clinical advantages over antagonists and full agonists in antidepressant and smoking-cessation treatment. In the cases of P2X purinergic receptors, the currents evoked by α,β-methylene ATP are lower than the currents evoked by ATP. Here, our NMR analyses revealed that the transmembrane region and the membrane side of the lower body exist in conformational equilibrium between the closed and open conformations, with slower exchange rates than the chemical shift difference (<100 s
-1
), and that the small population of the open conformation of zebrafish P2X
4
purinergic receptor causes the partial activation in the α,β-methylene ATP-bound state. These findings provide insights into the mechanism underlying the partial activation of P2X
4
receptors and other ligand-gated ion channels.
A descending dopamine pathway conserved from basal vertebrates to mammals
Authors: Ryczko Dimitri , Cone Jackson J. , Alpert Michael H. , Goetz Laurent , Auclair François , Dubé Catherine , Parent Martin , Roitman Mitchell F. , Alford Simon , Dubuc Réjean
Published: April 2016

Significance

In vertebrates, the contribution of dopamine neurons to locomotor control is traditionally attributed to their ascending projections to the basal ganglia that, in turn, project down to brainstem locomotor networks. We recently discovered in lampreys that brainstem networks receive a direct descending dopaminergic input that increases locomotor output. Here, we show that this descending dopaminergic pathway is conserved in higher vertebrates. We found that dopamine is released in salamander brainstem locomotor networks, together with reticulospinal cell activation, known to trigger locomotion. Dopamine is released in rat brainstem locomotor networks, and amphetamine potentiates dopamine release in vivo. Finally, brainstem locomotor networks in human tissue contain dopaminergic terminals. Our findings have important implications for understanding the locomotor role of dopamine in vertebrates.
Anthropogenic disturbances jeopardize biodiversity conservation within tropical rainforest reserves
Authors: Martínez-Ramos Miguel , Ortiz-Rodríguez Iván A. , Piñero Daniel , Dirzo Rodolfo , Sarukhán José
Published: April 2016

Significance

Human activities disrupt ecosystem functioning and jeopardize biodiversity, especially in the tropics. Increasing evidence shows this disturbance is happening even within reserves, but the underlying causative mechanisms are unclear. This paper provides a unique long-term (four decades) empirical, experimental, and modeling study showing how cascading effects of human disturbances affect the structure, dynamics, and functioning of a tropical rainforest reserve. In particular, we provide evidence of how fragmentation and defaunation, operating in synergy, stimulated the population explosion of a long-lived understory palm that, in turn, was followed by reductions in biodiversity and changes in some ecosystem properties.
Origins of the brain networks for advanced mathematics in expert mathematicians
Authors: Amalric Marie , Dehaene Stanislas
Published: April 2016

Significance

Our work addresses the long-standing issue of the relationship between mathematics and language. By scanning professional mathematicians, we show that high-level mathematical reasoning rests on a set of brain areas that do not overlap with the classical left-hemisphere regions involved in language processing or verbal semantics. Instead, all domains of mathematics we tested (algebra, analysis, geometry, and topology) recruit a bilateral network, of prefrontal, parietal, and inferior temporal regions, which is also activated when mathematicians or nonmathematicians recognize and manipulate numbers mentally. Our results suggest that high-level mathematical thinking makes minimal use of language areas and instead recruits circuits initially involved in space and number. This result may explain why knowledge of number and space, during early childhood, predicts mathematical achievement.
Molecular convergence of clock and photosensory pathways through PIF3–TOC1 interaction and co-occupancy of target promoters
Authors: Soy Judit , Leivar Pablo , González-Schain Nahuel , Martín Guiomar , Diaz Céline , Sentandreu Maria , Al-Sady Bassem , Quail Peter H. , Monte Elena
Published: April 2016

Significance

This study defines a molecular mechanism by which clock- and light-signaling pathways converge in Arabidopsis. The data reveal that Timing of CAB expression 1 (TOC1), an essential core component of the central oscillator, binds to and represses Phytochrome-interacting factor (PIF) transcriptional activators, which also are the direct molecular signaling partners of the phytochrome photosensory receptors. This finding shows that TOC1 functions as a clock output transducer, directly linking the core oscillator to a pleiotropically acting transcriptional network through repression of target genes. Collectively, in the plant, these components comprise a transcriptionally centered signaling hub that provides clock-imposed gating of PIF-mediated, photosensory-regulated diurnal growth patterns. These results provide a framework for future research aimed at understanding how circadian dynamics are integrated with other plant physiological processes important for optimal plant fitness.
Communicating about Screening, Brief Intervention, and Referral to Treatment: Messaging Strategies to Raise Awareness and Promote Voluntary Adoption and Implementation among New York School-Based Health Center Providers
Authors: Harris Brett R.
Published: April 2016

Background: School-based health centers (SBHCs) are satellite primary care clinics conveniently located within high-risk schools. Providing screening, brief intervention, and referral to treatment (SBIRT) in SBHCs has the potential to greatly increase identification and intervention among adolescents with problem substance use. Nevertheless, only 11% of New York State SBHC providers report the use of SBIRT. This study identifies strategies for communicating about SBIRT with the goal of raising awareness and promoting voluntary adoption and implementation among both SBHC program directors and clinicians. Methods: All 162 New York State SBHC program directors and clinicians serving middle and high school students were surveyed between May and June 2013 (40% response rate). Program directors were asked which factors were most important to them in their decision to adopt new practices, and both program directors and clinicians were asked to rank-order statements in 2 categories: (1) Substance use and its effects and (2) SBIRT integration and outcomes. Results: Student need was valued far more than any other factor in program directors’ decisions to adopt new practices. Both program directors and clinicians perceived the association between substance use and risky sexual behavior and the benefits and cost-effectiveness of SBIRT compared with other preventive health screenings as the strongest motivators to adopt and implement SBIRT. Conclusions: Findings from this study suggest that SBIRT awareness-raising strategies present the cost-effectiveness of SBIRT, highlight student need, particularly the connection between substance use and risky sexual behaviors, and should be communicated by state health departments and professional organizations.
Dual Cannabis and Alcohol use Disorders in Young Adults: Problems Magnified
Authors: Hayaki Jumi , Anderson Bradley J. , Stein Michael D.
Published: April 2016

Background: Alcohol and marijuana are the 2 most commonly used substances among young adults. The present study examines whether having 2 DSM-5 ( Diagnostic and Statistical Manual of Mental Disorders, 5th Edition) diagnoses (alcohol and cannabis) is associated with greater problems than having 1 (alcohol or cannabis) diagnosis. Methods: Participants were 307 young adults (18–25 years) from the community who met criteria for DSM-5 alcohol use disorder (AUD), cannabis use disorder (CUD), or both (dual use disorder [DUD]). Participants reported alcohol and marijuana use in the past 90 days (Timeline Follow-Back), alcohol problems (Short Inventory of Problems), and marijuana problems (Marijuana Problems Scale). Results: Eighty-four participants (27.4%) met criteria for AUD, 107 (34.9%) met criteria for CUD, and 116 (37.8%) met criteria for DUD. In multivariate analyses, the DUD group reported greater alcohol use frequency and more alcohol problems than the CUD-only group but not the AUD-only group. However, DUD individuals reported greater drinking intensity than singly diagnosed individuals. Those with DUD reported a greater proportion of marijuana consumption days than the AUD-only group but not the CUD-only group. However, DUD individuals reported more marijuana problems than both singly diagnosed groups. Conclusions: Results show that the concurrent presence of both DSM-5 AUD and CUD is associated with heavier drinking patterns and greater marijuana problems than disordered use of either substance alone, thus affirming the magnified severity of alcohol and marijuana use that accompanies dual DSM-5 alcohol and marijuana use disorders.
Generating hESCs with reduced immunogenicity by disrupting TAP1 or TAPBP
Authors: Cui Di , Wang Jinping , Zeng Yelin , Rao Lingjun , Chen Haide , Li Wenling , Li Yang , Li Hui , Cui Chun , Xiao Lei
Published: April 2016

Human embryonic stem cells (hESCs) are thought to be a promising resource for cell therapy, while it has to face the major problem of graft immunological rejection. Major histocompatibility complex (MHC) class I expressed on the cell surface is the major cause of graft rejection. Transporter associated with antigen presentation 1 (TAP1) and TAP-associated glycoprotein (TAPBP) play important roles in regulating MHC class I expression. In this study, we generated TAP1- and TAPBP-deficient hESC lines, respectively, using transcription activator-like effector nucleases technique. These cells showed deficient expression of MHC class I on the cell surface and reduced immunogenicity compared with wild types, but maintained normal pluripotency, karyotypes, and differentiation ability. Thus, our findings are instrumental in developing a universal cell resource with both pluripotency and hypo-immunogenicity for transplantation therapy in the future.
Anti-inflammatory activity of myricetin from Diospyros lotus through suppression of NF-κB and STAT1 activation and Nrf2-mediated HO-1 induction in lipopolysaccharide-stimulated RAW264.7 macrophages
Authors: Cho Byoung Ok , Yin Hong Hua , Park Sang Hyun , Byun Eui Baek , Ha Hun Yong , Jang Seon Il
Published: April 2016

Diospyros lotus is traditionally used for the treatment of diabetes, diarrhea, tumor, and hypertension. The purpose of this study was to investigate the anti-inflammatory effect and underlying molecular mechanisms of myricetin in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Myricetin dose-dependently suppressed the production of pro-inflammatory mediators (NO, iNOS, PGE2, and COX-2) in LPS-stimulated RAW264.7 macrophages. Myricetin administration decreased the production of NO, iNOS, TNF-α, IL-6, and IL-12 in mice. Myricetin decreased NF-κB activation by suppressing the degradation of IκBα, nuclear translocation of p65 subunit of NF-κB, and NF-κB DNA binding activity in LPS-stimulated RAW264.7 macrophages. Moreover, myricetin attenuated the phosphorylation of STAT1 and the production of IFN-β in LPS-stimulated RAW264.7 macrophages. Furthermore, myricetin induced the expression of HO-1 through Nrf2 translocation. In conclusion, these results suggest that myricetin inhibits the production of pro-inflammatory mediators through the suppression of NF-κB and STAT1 activation and induction of Nrf2-mediated HO-1 expression in LPS-stimulated RAW264.7 macrophages.
Increasing school autonomy in Western Europe: a comparative analysis of its causes and forms
Authors: Christ Claudia , Dobbins Michael
Published: April 2016

This article comparatively explores the driving forces behind and variations in the trend toward increasing school autonomy in England, Germany, Italy and Sweden. In a first step, we focus on the impact of processes of internationalization and the spread of post-materialist values. We hypothesize, on the one hand, that school autonomy may be a direct result of international policy promotion by transnational organizations and, on the other hand, that post-materialist values may lead to either an increase or decrease of school autonomy, depending on the specific form of school governance. In a second step, we examine the impact of partisan factors and explore the hypothesis that center-right and center-left parties pursue different objectives when introducing school autonomy policies. We assume that conservative parties will grant more extensive decision-making autonomy to schools in order to promote competition, accountability and efficiency, while leftist governments will use increased school autonomy as means of promoting political participation and democracy. In the empirical case studies we thus examine whether the partisan orientation of governing coalitions has brought about different school autonomy models in the four countries.