bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating Arrhenius parameters using temperature programmed molecular dynamics
Authors: Imandi Venkataramana , Chatterjee Abhijit
Published: July 2016

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.
Measurement of turbulent electron temperature fluctuations on the ASDEX Upgrade tokamak using correlated electron cyclotron emission
Authors: Freethy S. J. , Conway G. D. , Classen I. , Creely A. J. , Happel T. , Köhn A. , Vanovac B. , White A. E.
Published: July 2016

Turbulent temperature fluctuations are measured on the ASDEX Upgrade tokamak using pairs of closely spaced, narrow-band heterodyne radiometer channels and a standard correlation technique. The pre-detection spacing and bandwidth of the radiometer channel pairs is chosen such that they are physically separated less than a turbulent correlation length, but do not overlap. The radiometer has 4 fixed filter frequency channels and two tunable filter channels for added flexibility in the measurement position. Relative temperature fluctuation amplitudes are observed in a helium plasma to be δT/T = (0.76 ± 0.02)%, (0.67 ± 0.02)%, and (0.59 ± 0.03)% at normalised toroidal flux radius of ρtor = 0.82, 0.75, and 0.68, respectively.
A mass resolved, high resolution neutral particle analyzer for C-2U
Authors: Clary R. , Roquemore A. , Douglass J. , Jaramillo D. , Korepanov S. , Magee R. , Medley S. , Smirnov A.
Published: July 2016

C-2U is a high-confinement, advanced beam driven field-reversed configuration plasma experiment which sustains the configuration for >5 ms, in excess of typical MHD and fast particle instability times, as well as fast particle slowing down times. Fast particle dynamics are critical to C-2U performance and several diagnostics have been deployed to characterize the fast particle population, including neutron and proton detectors. To increase our understanding of fast particle behavior and supplement existing diagnostics, an E ∥ B neutral particle analyzer was installed, which simultaneously measures H0 and D0 flux with large dynamic range and high energy resolution. Here we report the commissioning of the E ∥ B analyzer, confirm the instrument has energy resolution ΔE/E≲0.1 and a dynamic range Emax/Emin∼30, and present measurements of initial testing on C-2U.
Chaotic processes using the two-parameter derivative with non-singular and non-local kernel: Basic theory and applications
Authors: Doungmo Goufo Emile Franc
Published: July 2016

After having the issues of singularity and locality addressed recently in mathematical modelling, another question regarding the description of natural phenomena was raised: How influent is the second parameter β of the two-parameter Mittag-Leffler function Eα,β(z), z∈ℂ? To answer this question, we generalize the newly introduced one-parameter derivative with non-singular and non-local kernel [A. Atangana and I. Koca, Chaos, Solitons Fractals 89, 447 (2016); A. Atangana and D. Bealeanu (e-print)] by developing a similar two-parameter derivative with non-singular and non-local kernel based on Eα,β(z). We exploit the Agarwal/Erdelyi higher transcendental functions together with their Laplace transforms to explicitly establish the Laplace transform's expressions of the two-parameter derivatives, necessary for solving related fractional differential equations. Explicit expression of the associated two-parameter fractional integral is also established. Concrete applications are done on atmospheric convection process by using Lorenz non-linear simple system. Existence result for the model is provided and a numerical scheme established. As expected, solutions exhibit chaotic behaviors for α less than 0.55, and this chaos is not interrupted by the impact of β. Rather, this second parameter seems to indirectly squeeze and rotate the solutions, giving an impression of twisting. The whole graphics seem to have completely changed its orientation to a particular direction. This is a great observation that clearly shows the substantial impact of the second parameter of Eα,β(z), certainly opening new doors to modeling with two-parameter derivatives.
Realization of consensus of multi-agent systems with stochastically mixed interactions
Authors: Sun Yongzheng , Li Wang , Zhao Donghua
Published: July 2016

In this paper, we propose a new consensus model in which the interactions among agents stochastically switch between attraction and repulsion. Such a positive-and-negative mechanism is described by the white-noise-based coupling. Analytic criteria for the consensus and non-consensus in terms of the eigenvalues of the noise intensity matrix are derived, which provide a better understanding of the constructive roles of random interactions. Specifically, we discover a positive role of noise coupling that noise can accelerate the emergence of consensus. We find that the converging speed of the multi-agent network depends on the square of the second smallest eigenvalue of its graph Laplacian. The influence of network topologies on the consensus time is also investigated.
Synthesis of self-organized TiO2 nanotube arrays: Microstructural, stereoscopic, and topographic studies
Authors: Quiroz Heiddy P. , Dussan A.
Published: July 2016

In this work, titanium dioxide nanotubes were prepared by using titanium foils via electrochemical anodization in ethylene glycol solutions containing different amounts of water and fluoride in the ranges of 1%–3% and 0.15%–0.5%, respectively, to determine their effects on morphology, optical, and crystalline structure properties. Annealing processes were performed on all samples in the range between 273 and 723 K. Morphology and structure properties of the samples were studied by scanning electron microscopy, X-ray diffraction (XRD), and transmission electron microscopy. Titanium dioxide (TiO2) nanotubes, through anodization method, are strongly influenced by conditions, like fluoride concentration and applied voltages. Tube lengths between 2 and 7 μm were obtained, exhibiting different diameters and wall thicknesses. When alternating voltage was applied, the outer surface of the nanotubes exhibited evenly spaced ring-shaped regions, while smooth tubes were observed when constant voltage was applied. Reflection peaks, corresponding to Brookite, Anatase, and Rutile, of TiO2 phases, were observed from the XRD pattern. These phases were corroborated via μXRD measurements, and the Ti3O5 phase was also observed in detail. Absorption coefficient (α), optical band gap (Eg), and extinction coefficient (ε) of TiO2 nanotubes were calculated by transmittance spectra in the UV–Vis range. Strong absorption was noted in the UV region from reflectance and absorbance measurements. A correlation between synthesis parameters and physical properties is presented.
Molecular shear heating and vortex dynamics in thermostatted two dimensional Yukawa liquids
Authors: Gupta Akanksha , Ganesh Rajaraman , Joy Ashwin
Published: July 2016

It is well known that two-dimensional macroscale shear flows are susceptible to instabilities leading to macroscale vortical structures. The linear and nonlinear fate of such a macroscale flow in a strongly coupled medium is a fundamental problem. A popular example of a strongly coupled medium is a dusty plasma, often modelled as a Yukawa liquid. Recently, laboratory experiments and molecular dynamics (MD) studies of shear flows in strongly coupled Yukawa liquids indicated the occurrence of strong molecular shear heating, which is found to reduce the coupling strength exponentially leading to the destruction of macroscale vorticity. To understand the vortex dynamics of strongly coupled molecular fluids undergoing macroscale shear flows and molecular shear heating, MD simulation has been performed, which allows the macroscopic vortex dynamics to evolve, while at the same time “removes” the microscopically generated heat without using the velocity degrees of freedom. We demonstrate that by using a configurational thermostat in a novel way, the microscale heat generated by shear flow can be thermostatted out efficiently without compromising the large scale vortex dynamics. In the present work, using MD simulations, a comparative study of shear flow evolution in Yukawa liquids in the presence and absence of molecular or microscopic heating is presented for a prototype shear flow, namely, Kolmogorov flow.
Electronic structure and magnetism of Mn-doped GaSb for spintronic applications: A DFT study
Authors: Seña N. , Dussan A. , Mesa F. , Castaño E. , González-Hernández R.
Published: July 2016

We have carried out first-principles spin polarized calculations to obtain comprehensive information regarding the structural, magnetic, and electronic properties of the Mn-doped GaSb compound with dopant concentrations: x = 0.062, 0.083, 0.125, 0.25, and 0.50. The plane-wave pseudopotential method was used in order to calculate total energies and electronic structures. It was found that the MnGa substitution is the most stable configuration with a formation energy of ∼1.60 eV/Mn-atom. The calculated density of states shows that the half-metallic ferromagnetism is energetically stable for all dopant concentrations with a total magnetization of about 4.0 μB/Mn-atom. The results indicate that the magnetic ground state originates from the strong hybridization between Mn-d and Sb-p states, which agree with previous studies on Mn-doped wide gap semiconductors. This study gives new clues to the fabrication of diluted magnetic semiconductors.
Surface acoustic wave regulated single photon emission from a coupled quantum dot–nanocavity system
Authors: Weiß M. , Kapfinger S. , Reichert T. , Finley J. J. , Wixforth A. , Kaniber M. , Krenner H. J.
Published: July 2016

A coupled quantum dot–nanocavity system in the weak coupling regime of cavity-quantumelectrodynamics is dynamically tuned in and out of resonance by the coherent elastic field of a fSAW ≃ 800 MHz surface acoustic wave. When the system is brought to resonance by the sound wave, light-matter interaction is strongly increased by the Purcell effect. This leads to a precisely timed single photon emission as confirmed by the second order photon correlation function, g(2). All relevant frequencies of our experiment are faithfully identified in the Fourier transform of g(2), demonstrating high fidelity regulation of the stream of single photons emitted by the system.
Enhanced transmission and beaming via a zero-index photonic crystal
Authors: Hajian Hodjat , Ozbay Ekmel , Caglayan Humeyra
Published: July 2016

Certain types of photonic crystals with Dirac cones at the Γ point of their band structure have a zero effective index of refraction at Dirac cone frequency. Here, by an appropriate design of the photonic structure, we obtain a strong coupling between modes around the Dirac cone frequency of an all-dielectric zero-index photonic crystal and the guided ones supported by a photonic crystal waveguide. Consequently, we experimentally demonstrate that the presence of the zero-index photonic crystal at the inner side of the photonic crystal waveguide leads to an enhancement in the transmission of some of the guided waves passing through this hybrid system. Moreover, those electromagnetic waves extracted from the structure with enhanced transmission exhibit high directional beaming due to the presence of the zero-index photonic crystal at the outer side of the photonic crystal waveguide.
Enhancement of the transverse magneto-optical Kerr effect via resonant tunneling in trilayers containing magneto-optical metals
Authors: Girón-Sedas J. A. , Mejía-Salazar J. R. , Moncada-Villa E. , Porras-Montenegro N.
Published: July 2016

We propose a way to enhance the transverse magneto-optical Kerr effect, by the excitation of resonant tunneling modes, in subwavelength trilayer structures featuring a dielectric slab sandwiched between two magneto-optical metallic layers. Depending on the magneto-optical layer widths, the proposed system may exhibit an extraordinary transverse magneto-optical Kerr effect, which makes it very attractive for the design and engineering of thin-film magneto-optical-based devices for future photonic circuits or fiber optical-communication systems.
Simultaneous enhancement of photovoltage and charge transfer in Cu2O-based photocathode using buffer and protective layers
Authors: Li Changli , Hisatomi Takashi , Watanabe Osamu , Nakabayashi Mamiko , Shibata Naoya , Domen Kazunari , Delaunay Jean-Jacques
Published: July 2016

Coating n-type buffer and protective layers on Cu2O may be an effective means to improve the photoelectrochemical (PEC) water-splitting performance of Cu2O-based photocathodes. In this letter, the functions of the buffer layer and protective layer on Cu2O are examined. It is found that a Ga2O3 buffer layer can form a buried junction with Cu2O, which inhibits Cu2O self-reduction as well as increases the photovoltage through a small conduction band offset between the two semiconductors. The introduction of a TiO2 thin protective layer not only improves the stability of the photocathode but also enhances the electron transfer from the photocathode surface into the electrolyte, thus resulting in an increase in photocurrent at positive potentials. These results show that the selection of overlayers with appropriate conduction band positions provides an effective strategy for obtaining a high photovoltage and high photocurrent in PEC systems.
Dual stratified mixed convection flow of Eyring-Powell fluid over an inclined stretching cylinder with heat generation/absorption effect
Authors: Rehman Khalil Ur , Malik M.Y. , Salahuddin T. , Naseer M.
Published: July 2016

Present work is made to study the effects of double stratified medium on the mixed convection boundary layer flow of Eyring-Powell fluid induced by an inclined stretching cylinder. Flow analysis is conceded in the presence of heat generation/absorption. Temperature and concentration are supposed to be higher than ambient fluid across the surface of cylinder. The arising flow conducting system of partial differential equations is primarily transformed into coupled non-linear ordinary differential equations with the aid of suitable transformations. Numerical solutions of resulting intricate non-linear boundary value problem are computed successfully by utilizing fifth order Runge-Kutta algorithm with shooting technique. The effect logs of physical flow controlling parameters on velocity, temperature and concentration profiles are examined graphically. Further, numerical findings are obtained for two distinct cases namely, zero (plate) and non-zero (cylinder) values of curvature parameter and the behaviour are presented through graphs for skin-friction coefficient, Nusselt number and Sherwood number. The current analysis is validated by developing comparison with previously published work, which sets a benchmark of quality of numerical approach.
A Biomimetic Synthetic Approach to the Frondosins
Authors: Kuan Kevin K. W. , Hirschvogel Aylin M. C. , George Jonathan H.
Published: July 2016

The frondosins are a family of five marine sponge-derived meroterpenoids. We propose that the 6–7 ring system common to each of the frondosins is biosynthesized via ring expansion of a 6–6 ring system. Compelling evidence in favour of this proposal was obtained in the form of a biomimetic synthesis of the frondosin 6–7 ring system, which features a highly stereo- and regio-selective ring expansion cascade reaction as the key step.
Modelling fire probability in the Brazilian Amazon using the maximum entropy method
Authors: Fonseca Marisa G. , Aragão Luiz Eduardo O. C. , Lima André , Shimabukuro Yosio E. , Arai Egidio , Anderson Liana O.
Published: July 2016

Fires are both a cause and consequence of important changes in the Amazon region. The development and implementation of better fire management practices and firefighting strategies are important steps to reduce the Amazon ecosystems’ degradation and carbon emissions from land-use change in the region. We extended the application of the maximum entropy method (MaxEnt) to model fire occurrence probability in the Brazilian Amazon on a monthly basis during the 2008 and 2010 fire seasons using fire detection data derived from satellite images. Predictor variables included climatic variables, inhabited and uninhabited protected areas and land-use change maps. Model fit was assessed using the area under the curve (AUC) value (threshold-independent analysis), binomial tests and model sensitivity and specificity (threshold-dependent analysis). Both threshold-independent (AUC = 0.919 ± 0.004) and threshold-dependent evaluation indicate satisfactory model performance. Pasture, annual deforestation and secondary vegetation are the most effective variables for predicting the distribution of the occurrence data. Our results show that MaxEnt may become an important tool to guide on-the-ground decisions on fire prevention actions and firefighting planning more effectively and thus to minimise forest degradation and carbon loss from forest fires in Amazonian ecosystems.
Protective responses to sublytic complement in the retinal pigment epithelium
Authors: Tan Li Xuan , Toops Kimberly A. , Lakkaraju Aparna
Published: July 2016

Significance

The complement system regulates immune defense and inflammation. Abnormal complement activation in the retina is associated with blinding macular degenerations, which have limited treatment options. The retinal pigment epithelium (RPE) is an initial site of injury in macular degenerations, but mechanisms that protect the RPE from complement-mediated damage are unclear. Here, we identify two critical responses to complement in the RPE: accelerated recycling of the complement inhibitor CD59 and lysosome-mediated membrane repair. We show that in models of macular degeneration, excess cholesterol impairs both defense mechanisms, resulting in mitochondrial damage. Drugs that decrease RPE cholesterol restore these mechanisms and help the RPE combat complement attack. Our studies identify promising drug targets to preserve RPE health and function in macular degenerations.
Fortnightly modulation of San Andreas tremor and low-frequency earthquakes
Authors: van der Elst Nicholas J. , Delorey Andrew A. , Shelly David R. , Johnson Paul A.
Published: July 2016

Significance

The sun and moon exert a gravitational tug on Earth that stretches and compresses crustal rocks. This cyclic stressing can promote or inhibit fault slip, particularly at the deep roots of faults. The amplitude of the solid Earth tide varies over a fortnightly (2-wk) cycle, as the sun and moon change their relative positions in the sky. In this study, we show that deep, small earthquakes on the San Andreas Fault are most likely to occur during the waxing fortnightly tide—not when the tidal amplitude is highest, as might be expected, but when the tidal amplitude most exceeds its previous value. The response of faults to the tidal cycle opens a window into the workings of plate tectonics.
Directed evolution of a sphingomyelin flippase reveals mechanism of substrate backbone discrimination by a P4-ATPase
Authors: Roland Bartholomew P. , Graham Todd R.
Published: July 2016

Significance

The asymmetric organization of cellular membranes is a critical determinant of cell and tissue physiology. Phospholipid flippases are principle regulators of this membrane asymmetry, and understanding their mechanics will be important for determining how deficiencies of these enzymes lead to several different diseases. The current study has identified a key structural mechanism for the exclusion of sphingomyelin as a flippase substrate. Understanding how these unique enzymes recognize and transport substrates can direct pharmacologic and therapeutic strategies for medical applications. Finally, the specificity of this designer enzyme represents a unique opportunity to modulate membrane biology intentionally through directed perturbations in phospholipid asymmetry.
Diversity of immune strategies explained by adaptation to pathogen statistics
Authors: Mayer Andreas , Mora Thierry , Rivoire Olivier , Walczak Aleksandra M.
Published: July 2016

Significance

Organisms possess many mechanisms for protecting themselves from pathogens. In addition to the well-studied innate and adaptive immune systems of vertebrates, recently discovered mechanisms such as CRISPR immunity in prokaryotes diversify the known modes of information processing used in immune protection. By classifying these different systems in terms of their rules of heritability and response to the environment, we propose a mathematical framework that recapitulates the observed natural diversity of immune systems. We show how the basic modes of immunity emerge as optimal strategies of a population adapting to a changing pathogenic environment. The proposed framework offers a unified view of immunity across species and helps rationalize the diversity of observed mechanisms.
Dynamic neural activity during stress signals resilient coping
Authors: Sinha Rajita , Lacadie Cheryl M. , Constable R. Todd , Seo Dongju
Published: July 2016

Significance

We live in a time of increasing terror, stress, and trauma, and yet humans show a remarkable ability to cope under high stress states. How the brain supports such active resilient coping is not well-understood. Findings showed high stress levels are accompanied by dynamic brain signals in circuits representing the stress reaction, adaptation, and behavioral control responses. In addition, a ventromedial prefrontal cortical region showed initial decreases in brain activation, but then mobilized with increased activation, and this dynamic change was correlated with active coping. Conversely, individuals who failed to show such “neuroflexibility” in this specific ventromedial prefrontal region reported higher maladaptive coping behaviors. Findings suggest that strategies to promote such neuroflexibility under stress may increase stress resilience in humans.
Root morphology and mycorrhizal symbioses together shape nutrient foraging strategies of temperate trees
Authors: Chen Weile , Koide Roger T. , Adams Thomas S. , DeForest Jared L. , Cheng Lei , Eissenstat David M.
Published: July 2016

Significance

Plant growth requires acquisition of soil nutrients in a patchy environment. Nutrient patches may be actively foraged by symbioses comprising roots and mycorrhizal fungi. Here, we show that thicker root tree species (e.g., tulip poplar, pine) respond weakly or not at all to nutrient heterogeneity. In contrast, thinner root tree species readily respond by selectively growing roots [arbuscular mycorrhizal trees (e.g., maple)] or mycorrhizal fungal hyphae [ectomycorrhizal trees (e.g., oak)] in nutrient-rich “hotspots.” Our results thus indicate predictable patterns of nutrient foraging among tree species with contrasting mycorrhiza types and root morphologies. These findings can pave the way for a more holistic understanding of root-microbial function, which is critical to plant growth and biogeochemical cycles in forested ecosystems.
Inferring responses to climate dynamics from historical demography in neotropical forest lizards
Authors: Prates Ivan , Xue Alexander T. , Brown Jason L. , Alvarado-Serrano Diego F. , Rodrigues Miguel T. , Hickerson Michael J. , Carnaval Ana C.
Published: July 2016

We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (
Anolis punctatus
,
Anolis ortonii
, and
Polychrus marmoratus
), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
Reticulation, divergence, and the phylogeography–phylogenetics continuum
Authors: Edwards Scott V. , Potter Sally , Schmitt C. Jonathan , Bragg Jason G. , Moritz Craig
Published: July 2016

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
The probability of monophyly of a sample of gene lineages on a species tree
Authors: Mehta Rohan S. , Bryant David , Rosenberg Noah A.
Published: July 2016

Monophyletic groups—groups that consist of all of the descendants of a most recent common ancestor—arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte.
Comparative phylogeography of oceanic archipelagos: Hotspots for inferences of evolutionary process
Authors: Shaw Kerry L. , Gillespie Rosemary G.
Published: July 2016

Remote island archipelagos offer superb opportunities to study the evolution of community assembly because of their relatively young and simple communities where speciation contributes to the origin and evolution of community structure. There is great potential for common phylogeographic patterns among remote archipelagos that originate through hotspot volcanism, particularly when the islands formed are spatially isolated and linearly arranged. The progression rule is characterized by a phylogeographic concordance between island age and lineage age in a species radiation. Progression is most likely to arise when a species radiation begins on an older island before the emergence of younger islands of a hotspot archipelago. In the simplest form of progression, colonization of younger islands as they emerge and offer appropriate habitat, is coincident with cladogenesis. In this paper, we review recent discoveries of the progression rule on seven hotspot archipelagos. We then discuss advantages that progression offers to the study of community assembly, and insights that community dynamics may offer toward understanding the evolution of progression. We describe results from two compelling cases of progression where the mosaic genome may offer insights into contrasting demographic histories that shed light on mechanisms of speciation and progression on remote archipelagos.
Geogenetic patterns in mouse lemurs (genus
Microcebus
) reveal the ghosts of Madagascar's forests past
Authors: Yoder Anne D. , Campbell C. Ryan , Blanco Marina B. , dos Reis Mario , Ganzhorn Jörg U. , Goodman Steven M. , Hunnicutt Kelsie E. , Larsen Peter A. , Kappeler Peter M. , Rasoloarison Rodin M. , Ralison José M. , Swofford David L. , Weisrock David W.
Published: July 2016

Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how the dynamic process of landscape change on Madagascar has shaped the distribution of a targeted clade of mouse lemurs (genus
Microcebus
) and, conversely, how phylogenetic and population genetic patterns in these small primates can reciprocally advance our understanding of Madagascar's prehuman environment. The degree to which human activity has impacted the natural plant communities of Madagascar is of critical and enduring interest. Today, the eastern rainforests are separated from the dry deciduous forests of the west by a large expanse of presumed anthropogenic grassland savanna, dominated by the Family Poaceae, that blankets most of the Central Highlands. Although there is firm consensus that anthropogenic activities have transformed the original vegetation through agricultural and pastoral practices, the degree to which closed-canopy forest extended from the east to the west remains debated. Phylogenetic and population genetic patterns in a five-species clade of mouse lemurs suggest that longitudinal dispersal across the island was readily achieved throughout the Pleistocene, apparently ending at ∼55 ka. By examining patterns of both inter- and intraspecific genetic diversity in mouse lemur species found in the eastern, western, and Central Highland zones, we conclude that the natural environment of the Central Highlands would have been mosaic, consisting of a matrix of wooded savanna that formed a transitional zone between the extremes of humid eastern and dry western forest types.
Loss of function mutation in
LOX
causes thoracic aortic aneurysm and dissection in humans
Authors: Lee Vivian S. , Halabi Carmen M. , Hoffman Erin P. , Carmichael Nikkola , Leshchiner Ignaty , Lian Christine G. , Bierhals Andrew J. , Vuzman Dana ,   Brigham Genomic Medicine, Mecham Robert P. , Frank Natasha Y. , Stitziel Nathan O. , Maas Richard , Sunyaev Shamil , Vuzman Dana , Krier Joel , Aday Aaron , Bodea Corneliu , Bjonnes Andrew , Carmichael Nikkola , Cassa Christopher , Frank Natasha Y. , Green Robert , Goessling Wolfram , Haghighi Alireza , Homsi Jason , Krieg Elizabeth , MacRae Calum , McDonough Barbara , Mohanty Anwoy , O’Leary Melanie , Raychaudhuri Soumya , Seidman Christine , Sutti Sheila , Valerius Jamie , Qiu Haiyan
Published: July 2016

Significance

The mechanical integrity of the arterial wall is dependent on a properly structured ECM. Elastin and collagen are key structural components of the ECM, contributing to the stability and elasticity of normal arteries. Lysyl oxidase (LOX) normally cross-links collagen and elastin molecules in the process of forming proper collagen fibers and elastic lamellae. Here, using whole-genome sequencing in humans and genome engineering in mice, we show that a missense mutation in
LOX
causes aortic aneurysm and dissection because of insufficient elastin and collagen cross-linking in the aortic wall. These findings confirm mutations in
LOX
as a cause of aortic disease in humans and identify LOX as a diagnostic and potentially therapeutic target.
Anatomically shaped tissue-engineered cartilage with tunable and inducible anticytokine delivery for biological joint resurfacing
Authors: Moutos Franklin T. , Glass Katherine A. , Compton Sarah A. , Ross Alison K. , Gersbach Charles A. , Guilak Farshid , Estes Bradley T.
Published: July 2016

Significance

Whereas some success has been realized treating isolated, focal defects or lesions of articular cartilage, the complete resurfacing of synovial joints remains an important challenge for the treatment of osteoarthritis. Here, we develop an anatomically shaped, functional cartilage construct based on a 3D woven scaffold that can provide for total joint resurfacing, with capabilities for tunable and inducible production of anticytokine therapy to protect diseased or injured joints from pathologic inflammation. An important advance of this work is the incorporation of a technique for scaffold-mediated viral gene delivery for overexpression of antiinflammatory molecules within the joint. This approach provides a foundation for total biological cartilage resurfacing to treat end-stage osteoarthritis for young patients, who currently have few therapeutic options.
Boosting medical diagnostics by pooling independent judgments
Authors: Kurvers Ralf H. J. M. , Herzog Stefan M. , Hertwig Ralph , Krause Jens , Carney Patricia A. , Bogart Andy , Argenziano Giuseppe , Zalaudek Iris , Wolf Max
Published: July 2016

Significance

Collective intelligence is considered to be one of the most promising approaches to improve decision making. However, up to now, little is known about the conditions underlying the emergence of collective intelligence in real-world contexts. Focusing on two key areas of medical diagnostics (breast and skin cancer detection), we here show that similarity in doctors’ accuracy is a key factor underlying the emergence of collective intelligence in these contexts. This result paves the way for innovative and more effective approaches to decision making in medical diagnostics and beyond, and to the scientific analyses of those approaches.
Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification
Authors: Zamudio Kelly R. , Bell Rayna C. , Mason Nicholas A.
Published: July 2016

Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes.
Plastidial metabolite MEcPP induces a transcriptionally centered stress-response hub via the transcription factor CAMTA3
Authors: Benn Geoffrey , Bjornson Marta , Ke Haiyan , De Souza Amancio , Balmond Edward I. , Shaw Jared T. , Dehesh Katayoon
Published: July 2016

Significance

A dual-function plastidial metabolite, methylerythritol cyclodiphosphate (MEcPP), an intermediate of the plastidial pathway for isoprenoids production and a retrograde signaling metabolite, transduces signals to activate general stress-response (GSR) genes by inducing a transcriptionally centered stress hub. Specifically, MEcPP mediates the induction of the rapidly and transiently stress-responsive functional
cis
-element
rapid stress response element
via the calmodulin-binding transcriptional activator CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 in a calcium-dependent manner. MEcPP-mediated induction of this hard-wired GSR circuitry is a prime example of the integration of this metabolite into transcriptional networks and, by extension, modulation of downstream responses such as protein-folding capacity. This finding provides a foundation for investigating mechanisms of biological responses to stress and the roles of metabolites beyond the expected classical biochemical pathways.
Evolutionary lessons from California plant phylogeography
Authors: Sork Victoria L. , Gugger Paul F. , Chen Jin-Ming , Werth Silke
Published: July 2016

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak,
Quercus lobata
, and the western North American lichen,
Ramalina menziesii
. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.
Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity
Authors: Dakin Roslyn , Fellows Tyee K. , Altshuler Douglas L.
Published: July 2016

Significance

Birds can steer a precise course at high speed, but little is known about how they avoid collisions with surrounding objects and the ground. We manipulated the visual environment of hummingbirds as they flew across a long chamber to evaluate how they use visual information for course control. We found that lateral course control is based on the vertical size of features, rather than the strategy observed in insects of regulating fore–aft image velocity. However, like insects, birds use image velocity in the vertical axis for altitude control. Our results suggest that in natural settings, birds may avoid collisions by monitoring the vertical size, expansion, and relative position of obstacles.
Regulation of transcriptional pausing through the secondary channel of RNA polymerase
Authors: Esyunina Daria , Agapov Aleksei , Kulbachinskiy Andrey
Published: July 2016

Significance

Tight and highly controlled transcriptional regulation is pivotal for cell survival under stress conditions. We demonstrate that Gre factor homolog (Gfh) proteins found in the
Deinococcus
/
Thermus
lineage of extremophilic bacteria affect multiple steps of transcription and may serve to halt transcription at specific genomic sites. These proteins bind within the secondary channel of RNA polymerase (RNAP) and dramatically increase site-specific transcriptional pausing in the presence of manganese ions, likely by stabilizing inactive enzyme conformation. Both Gfh expression and cellular manganese concentration are increased during stress response, thus providing an efficient way for transcription regulation. Similar mechanisms may be operating with other prokaryotic and eukaryotic factors acting through the secondary channel, which emerges as the central regulatory hub in the control of RNAP activities.
Physical cryptographic verification of nuclear warheads
Authors: Kemp R. Scott , Danagoulian Areg , Macdonald Ruaridh R. , Vavrek Jayson R.
Published: July 2016

Significance

We provide a method for potentially solving one of the central problems in arms control: proving the authenticity of a nuclear warhead without revealing information about its construction. The proposal is the first, to our knowledge, to be proof-theoretically sound (i.e., unspoofable) and information-theoretically secure. The method uses a tomography technique which can resolve the spatial distribution of mass with isotopic specificity. The soundness and security emerge from an integral-geometric transform that is able to uniquely map 3D geometries from zero-dimensional point measurements.
Viral binding-induced signaling drives a unique and extended intracellular trafficking pattern during infection of primary monocytes
Authors: Kim Jung Heon , Collins-McMillen Donna , Caposio Patrizia , Yurochko Andrew D.
Published: July 2016

Significance

Human cytomegalovirus (HCMV)-infected monocytes play a critical role in the hematogenous dissemination of the virus, establishment of persistence, and progression of HCMV-mediated diseases. Here we identify a unique HCMV nuclear translocation pathway in monocytes. HCMV moves from early endosomes to the trans-Golgi network, then to recycling endosomes before its nuclear translocation. Signaling (via c-Src) induced by viral binding of the gH/gL/UL128-131 complex to integrins triggers this unique pathway. Because HCMV is degraded without this signal, we suggest that this distinct signal-induced nuclear translocation functions as a viral evasion pathway in infected monocytes.
Sensing and signaling of oxidative stress in chloroplasts by inactivation of the SAL1 phosphoadenosine phosphatase
Authors: Chan Kai Xun , Mabbitt Peter D. , Phua Su Yin , Mueller Jonathan W. , Nisar Nazia , Gigolashvili Tamara , Stroeher Elke , Grassl Julia , Arlt Wiebke , Estavillo Gonzalo M. , Jackson Colin J. , Pogson Barry J.
Published: July 2016

Significance

Management of oxidative stress in plant chloroplasts involves signaling pathways to the nucleus that trigger stress response mechanisms. Yet, how oxidative stress is initially sensed in the chloroplast to activate accumulation of a stress signal remains enigmatic. We show that inactivation of a phosphatase, SAL1, by oxidative stress in chloroplasts controls accumulation of its substrate, as a plant stress signal. This regulatory mechanism is highly conserved across the plant kingdom and confers a second function to this metabolic enzyme as an oxidative stress sensor.
Superpriming of synaptic vesicles as a common basis for intersynapse variability and modulation of synaptic strength
Authors: Taschenberger Holger , Woehler Andrew , Neher Erwin
Published: July 2016

Significance

Short-term plasticity (STP) of synaptic connections underlies many basic signal processing capabilities of the brain, such as gain control, temporal filtering, and adaptation. Glutamatergic synapses, the predominant excitatory synapses in the brain, display large variability both in basal synaptic strength and in STP. We show that a small fraction of release-ready vesicles are released with much higher probability than other vesicles. The number of these “superprimed” vesicles is variable among synapses, but increases strongly after application of phorbol ester, an analogue of the second messenger diacylglycerol, and after inducing posttetanic potentiation. Thus, modulatory transmitter systems, acting through the phospholipase-C–diacylglycerol pathway, will be able to upregulate superprimed vesicles and thereby boost synaptic strength at the onset of burst-like activity.