bluuebunny/crossref_metadata_2025 huggingface dataset:
Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions
Authors: Nedialkova Lilia V. , Amat Miguel A. , Kevrekidis Ioannis G. , Hummer Gerhard
Published: September 2014

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.
Note: Longitudinally excited N2 laser with low beam divergence
Authors: Uno K. , Akitsu T. , Jitsuno T.
Published: September 2014

We developed a longitudinally excited N2 laser (337 nm) with low beam divergence without collimator lenses. The N2 laser consisted of a 30 cm long Pyrex glass tube with an inner diameter of 2.5 mm, a normal stable resonator formed by flat mirrors, and a simple, novel driver circuit. At a N2 gas pressure of 0.4 kPa and a repetition rate of 40 Hz, the N2 laser produced a circular beam with an output energy of 2.6 μJ and a low full-angle beam divergence of 0.29 mrad due to the uniform discharge formed by the longitudinal excitation scheme, the long cavity with the small aperture, and the low-input energy oscillation.
Calculation of positron binding energies using the generalized any particle propagator theory
Authors: Romero Jonathan , Charry Jorge A. , Flores-Moreno Roberto , Varella Márcio T. do N. , Reyes Andrés
Published: September 2014

We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.
GaAs1−y−zPyBiz, an alternative reduced band gap alloy system lattice-matched to GaAs
Authors: Forghani Kamran , Guan Yingxin , Losurdo Maria , Luo Guangfu , Morgan Dane , Babcock Susan E. , Brown April S. , Mawst Luke J. , Kuech T. F.
Published: September 2014

The growth and properties of alloys in the alternative quaternary alloy system GaAs1−y−zPyBiz were explored. This materials system allows simultaneous and independent tuning of lattice constant and band gap energy, Eg, over a wide range for potential near- and mid-infrared optoelectronic applications by adjusting y and z in GaAs1−y−zPyBiz. Highly tensile-strained, pseudomorphic films of GaAs1−yPy with a lattice mismatch strain of ∼1.2% served as the host for the subsequent addition of Bi. Lattice-matched alloy materials to GaAs were generated by holding y ∼ 3.3z in GaAs1−y−zPyBiz. Epitaxial films with both high Bi content, z ∼ 0.0854, and a smooth morphology were realized with measured band gap energies as low as 1.11–1.01 eV, lattice-matched to GaAs substrates. Density functional theory calculations are used to provide a predictive model for the band gap of GaAs1−y−zPyBiz lattice-matched to GaAs.
A 800 kV compact peaking capacitor for nanosecond generator
Authors: Jia Wei , Chen Zhiqiang , Tang Junping , Chen Weiqing , Guo Fan , Sun Fengrong , Li Junna , Qiu Aici
Published: September 2014

An extremely compact high voltage peaking capacitor is developed. The capacitor has a pancake structure with a diameter of 315 mm, a thickness of 59 mm, and a mass of 6.1 kg. The novel structural design endows the capacitor with a better mechanical stability and reliability under hundreds of kilovolts pulse voltage and an inner gas pressure of more than 1.5 MPa. The theoretical value of the capacitor self-inductance is near to 17 nH. Proved by series of electrical experiments, the capacitor can endure a high-voltage pulse with a rise time of about 20 ns, a half-width duration of around 25 ns, and an amplitude of up to 800 kV in a single shot model. When the capacitor was used in an electromagnetic pulse simulator as a peaking capacitor, the rise time of the voltage pulse can be reduced from 20 ns to less than 3 ns. The practical value of the capacitor's inductance deduced from the experimental date is no more than 25 nH.
Electrophoretic mobilities of counterions and a polymer in cylindrical pores
Authors: Singh Sunil P. , Muthukumar M.
Published: September 2014

We have simulated the transport properties of a uniformly charged flexible polymer chain and its counterions confined inside cylindrical nanopores under an external electric field. The hydrodynamic interaction is treated by describing the solvent molecules explicitly with the multiparticle collision dynamics method. The chain consisting of charged monomers and the counterions interact electrostatically with themselves and with the external electric field. We find rich behavior of the counterions around the polymer under confinement in the presence of the external electric field. The mobility of the counterions is heterogeneous depending on their location relative to the polymer. The adsorption isotherm of the counterions on the polymer depends nonlinearly on the electric field. As a result, the effective charge of the polymer exhibits a sigmoidal dependence on the electric field. This in turn leads to a nascent nonlinearity in the chain stretching and electrophoretic mobility of the polymer in terms of their dependence on the electric field. The product of the electric field and the effective polymer charge is found to be the key variable to unify our simulation data for various polymer lengths. Chain extension and the electrophoretic mobility show sigmoidal dependence on the electric field, with crossovers from the linear response regime to the nonlinear regime and then to the saturation regime. The mobility of adsorbed counterions is nonmonotonic with the electric field. For weaker and moderate fields, the adsorbed counterions move with the polymer and at higher fields they move opposite to the polymer's direction. We find that the effective charge and the mobility of the polymer decrease with a decrease in the pore radius.
The effects of plasma diffusion and viscosity on turbulent instability growth
Authors: Haines Brian M. , Vold Erik L. , Molvig Kim , Aldrich Charles , Rauenzahn Rick
Published: September 2014

We perform two-dimensional simulations of strongly–driven compressible Rayleigh–Taylor and Kelvin–Helmholtz instabilities with and without plasma transport phenomena, modeling plasma species diffusion, and plasma viscosity in order to determine their effects on the growth of the hydrodynamic instabilities. Simulations are performed in hydrodynamically similar boxes of varying sizes, ranging from 1 μm to 1 cm in order to determine the scale at which plasma effects become important. Our results suggest that these plasma effects become noticeable when the box size is approximately 100 μm, they become significant in the 10 μm box, and dominate when the box size is 1 μm. Results suggest that plasma transport may be important at scales and conditions relevant to inertial confinement fusion, and that a plasma fluid model is capable of representing some of the kinetic transport effects.
Indirect determination of the electric field in plasma discharges using laser-induced fluorescence spectroscopy
Authors: Vaudolon J. , Mazouffre S.
Published: September 2014

The evaluation of electric fields is of prime interest for the description of plasma characteristics. In this work, different methods for determining the electric field profile in low-pressure discharges using one- and two-dimensional Laser-Induced Fluorescence (LIF) measurements are presented and discussed. The energy conservation, fluid, and kinetic approaches appear to be well-suited for the electric field evaluation in this region of the plasma flow. However, the numerical complexity of a two-dimensional kinetic model is penalizing due to the limited signal-to-noise ratio that can be achieved, making the computation of the electric field subject to large error bars. The ionization contribution which appears in the fluid model makes it unattractive on an experimental viewpoint. The energy conservation and 1D1V kinetic approaches should therefore be preferred for the determination of the electric field when LIF data are used.
An interface facet driven Rayleigh instability in high-aspect-ratio bimetallic nanolayered composites
Authors: Zheng Shijian , Carpenter John S. , Wang Jian , Mara Nathan A. , Beyerlein Irene J.
Published: September 2014

One limitation hindering the structural and electrical applications of nanostructured metals is the loss of their nanostructure and strength under elevated temperatures. Nanostructured metals often have grain structures that contain a high density of triple junctions, where thermally induced instabilities commonly initiate. Prior work has resulted in fabrication of nanolayered two-phase composites that possess high-aspect ratio grains, a scarcity of triple junctions, and a thermally stable microstructure. In this work, transmission electron microscopy is used to investigate how these composites could eventually breakdown during heating. We reveal an unconventional thermal instability mechanism in this class of materials, which operates without the assistance of triple junctions. The mechanism can be rationalized by that thermally induced pinch off occurs as the result of bimetal interface faceting and can trigger a classic Rayleigh instability.
Phase-integral method for the radial Dirac equation
Authors: Linnæus Staffan
Published: September 2014

A phase-integral (WKB) solution of the radial Dirac equation is calculated up to the third order of approximation, retaining perfect symmetry between the two components of the wave function and introducing no singularities except at the zeroth-order transition points. The potential is allowed to be of scalar, vector, or tensor type, or any combination of these. The connection problem is investigated in detail. Explicit formulas are given for single-turning-point phase shifts and single-well energy levels.
Probe diagnostics of electron distributions in plasma with spatial and angular resolution
Authors: Demidov V. I. , Kudryavtsev A. A.
Published: September 2014

This paper discusses the spatial resolution that is required to study inhomogeneous, low-temperature plasmas and is based on a review of low-temperature plasma electron kinetics and methods for probe measurements of electron energy distribution functions (EEDFs). It is stated that EEDFs can be extracted from probe measurements by applying an appropriate probe theory. The Druyvesteyn formula is most commonly used for this extraction and has been used in numerous publications, but more general theory can be used for a wider range of gas pressures. It is demonstrated that the Druyvesteyn formula can be obtained from the general theory as a limiting case. This paper justifies the application of wall probes in plasma studies of an energetic part of EEDFs. This justification is made for an idealized probe. We briefly review the methods for studying anisotropic plasmas and their usefulness in plasma research. It is demonstrated that to determine anisotropic electron energy distribution functions, a planar, one-sided probe is most convenient.
Origin of superstructures in (double) perovskite thin films
Authors: Shabadi V. , Major M. , Komissinskiy P. , Vafaee M. , Radetinac A. , Baghaie Yazdi M. , Donner W. , Alff L.
Published: September 2014

We have investigated the origin of superstructure peaks as observed by X-ray diffraction of multiferroic Bi(Fe0.5Cr0.5)O3 thin films grown by pulsed laser deposition on single crystal SrTiO3 substrates. The photon energy dependence of the contrast between the atomic scattering factors of Fe and Cr is used to rule out a chemically ordered double perovskite Bi2FeCrO6 (BFCO). Structural calculations suggest that the experimentally observed superstructure occurs due to unequal cation displacements along the pseudo-cubic [111] direction that mimic the unit cell of the chemically ordered compound. This result helps to clarify discrepancies in the correlations of structural and magnetic order reported for Bi2FeCrO6. The observation of a superstructure in itself is not a sufficient proof of chemical order in double perovskites.
A powerful reflector in relativistic backward wave oscillator
Authors: Cao Yibing , Sun Jun , Teng Yan , Zhang Yuchuan , Zhang Lijun , Shi Yanchao , Ye Hu , Chen Changhua
Published: September 2014

An improved TM021 resonant reflector is put forward. Similarly with most of the slow wave structures used in relativistic backward wave oscillator, the section plane of the proposed reflector is designed to be trapezoidal. Compared with the rectangular TM021 resonant reflector, such a structure can depress RF breakdown more effectively by weakening the localized field convergence and realizing good electrostatic insulation. As shown in the high power microwave (HPM) generation experiments, with almost the same output power obtained by the previous structure, the improved structure can increase the pulse width from 25 ns to over 27 ns and no obvious surface damage is observed even if the generated HPM pulses exceed 1000 shots.
Thermally stable perpendicular magnetic anisotropy features of Ta/TaOx/Ta/CoFeB/MgO/W stacks via TaOx underlayer insertion
Authors: Yang SeungMo , Lee JaBin , An GwangGuk , Kim JaeHong , Chung WooSeong , Hong JinPyo
Published: September 2014

We report that a TaOx underlayer enhances the stability of perpendicular magnetic anisotropy (PMA) in TaOx/Ta/CoFeB/MgO stacks during annealing; control of oxygen content in the TaOx layer is critical. X-ray photoelectron spectroscopy observations revealed clear suppression of Ta atom diffusion towards the CoFeB/MgO interface or MgO regions. The TaOx underlayer possibly served as a diffusion sponge, permitting some thermally activated Ta atoms to impregnate the TaOx underlayer via a diffusion path, such as grain boundaries. We propose a possible mechanism for enhanced PMA stability based on diffusion of thermally activated Ta atoms.
Understanding the electronic structure of CdSe quantum dot-fullerene (C60) hybrid nanostructure for photovoltaic applications
Authors: Sarkar Sunandan , Rajbanshi Biplab , Sarkar Pranab
Published: September 2014

By using the density-functional tight binding method, we studied the electronic structure of CdSe quantum dot(QD)-buckminsterfullerene (C60) hybrid systems as a function of both the size of the QD and concentration of the fullerene molecule. Our calculation reveals that the lowest unoccupied molecular orbital energy level of the hybrid CdSeQD-C60 systems lies on the fullerene moiety, whereas the highest occupied molecular orbital (HOMO) energy level lies either on the QD or the fullerene depending on size of the CdSe QD. We explored the possibility of engineering the energy level alignment by varying the size of the CdSe QD. With increase in size of the QD, the HOMO level is shifted upward and crosses the HOMO level of the C60-thiol molecule resulting transition from the type-I to type-II band energy alignment. The density of states and charge density plot support these types of band gap engineering of the CdSe-C60 hybrid systems. This type II band alignment indicates the possibility of application of this nanohybrid for photovoltaic purpose.
A simple and clean source of low-energy atomic carbon
Authors: Krasnokutski S. A. , Huisken F.
Published: September 2014

A carbon source emitting low-energy carbon atoms from a thin-walled, sealed tantalum tube via thermal evaporation has been constructed. The tube is made from a 0.05 mm thick tantalum foil and filled with 12C or 13C carbon powder. After being sealed, it is heated by direct electric current. The solvated carbon atoms diffuse to the outer surface of the tube and, when the temperature rises over 2200 K, the evaporation of atomic carbon from the surface of the tantalum tube is observed. As the evaporated species have low energy they are well-suited for the incorporation into liquid helium droplets by the pick-up technique. Mass analysis of the incorporated species reveals the dominant presence of atomic carbon and very low abundances of C2 and C3 molecules (<1%). This is in striking contrast to the thermal evaporation of pure carbon, where C3 molecules are found to be the dominant species in the gas phase. Due to the thermal evaporation and the absence of high-energy application required for the dissociation of C2 and C3 molecules, the present source provides carbon atoms with rather low energy.
Thermal stability and in situ SiN passivation of InAlN/GaN high electron mobility heterostructures
Authors: Lugani L. , Carlin J.-F. , Py M. A. , Grandjean N.
Published: September 2014

We investigate the thermal stability of nearly lattice-matched InAlN layers under metal organic vapor phase epitaxy conditions for temperatures >800 °C and show that they are not fully stable. In particular, InAlN top layers undergo degradation during high temperature annealing due to a surface related process, which causes the loss of crystal quality. This strongly impacts the transport properties of InAlN/GaN HEMT heterostructures; in particular, the mobility is significantly reduced. However, we demonstrate that high thermal stability can be achieved by capping with a GaN layer as thin as 0.5 nm. Those findings enabled us to realize in situ passivated HEMT heterostructures with state of the art transport properties.
Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services
Authors: Lamarque Pénélope , Lavorel Sandra , Mouchet Maud , Quétier Fabien
Published: September 2014

Significance

The sustainable management of the supply of ecosystem services (ESs) in a context of global change is of major importance to sustain human livelihoods. Doing sustainable management requires us to understand and to quantify the effects and mechanisms of changes in driving variables on multiple ESs. However, few studies to date have analyzed ES scenarios, and even fewer have adopted a mechanistic approach. This study presents a unique approach to examine not only the direct effects of climate on multiple ESs, but also its indirect effects through its consequences for land management and for plant functional traits. The framework was tested in an alpine grassland system using ES models based on land use, plant functional traits, and soil data.
Temperature drives global patterns in forest biomass distribution in leaves, stems, and roots
Authors: Reich Peter B. , Luo Yunjian , Bradford John B. , Poorter Hendrik , Perry Charles H. , Oleksyn Jacek
Published: September 2014

Significance

Do forests in cold or dry climate zones distribute more resources in roots to enhance uptake of water and nutrients, which are scarce in such climates? Despite its importance to forest ecology and global carbon cycle modeling, this question is unanswered at present. To answer this question, we compiled and analyzed a large dataset (>6,200 forests, 61 countries) and determined that the proportion of total forest biomass in roots is greater and in foliage is smaller in increasingly cold climates. Surprisingly, allocation to roots or foliage was unrelated to aridity. These findings allow, for the first time to our knowledge, biogeographically explicit mapping of global root carbon pools, which will be useful for assessing climate change impacts on forest carbon dynamics and sequestration.
Biogeography of time partitioning in mammals
Authors: Bennie Jonathan J. , Duffy James P. , Inger Richard , Gaston Kevin J.
Published: September 2014

Significance

The majority of mammal species are nocturnal, but many are diurnal (active during the day), crepuscular (active mostly during twilight), or cathemeral (active during hours of daylight and darkness). These different strategies for regulating activity over a 24-h cycle are associated with suites of adaptations to light or semidarkness. The biogeography of these time partitioning strategies is, however, poorly understood. We show that global patterns in mammal diversity with different diel activity patterns are constrained by the duration of time that is both (i) illuminated by daylight, moonlight, and/or twilight and (ii) between thermal limits suitable for mammal activity.
A fully traits-based approach to modeling global vegetation distribution
Authors: van Bodegom Peter M. , Douma Jacob C. , Verheijen Lieneke M.
Published: September 2014

Significance

Models on vegetation dynamics are indispensable for our understanding of climate change impacts. These models contain variables describing vegetation attributes, so-called traits. However, the direct impacts of trait variation on global vegetation distribution are unknown. We derived global trait maps based on information on environmental drivers. Subsequently, we characterized nine globally representative vegetation types based on their trait combinations and could make valid predictions of their global occurrence probabilities based on trait maps. This study provides a proof of concept for the link between plant traits and vegetation types, stimulating enhanced application of trait-based approaches in vegetation modeling. We envision that our approach, our observation-driven trait maps, and vegetation maps may inspire a new generation of powerful traits-based vegetation models.
Gaining trust as well as respect in communicating to motivated audiences about science topics
Authors: Fiske Susan T. , Dupree Cydney
Published: September 2014

Expertise is a prerequisite for communicator credibility, entailing the knowledge and ability to be accurate. Trust also is essential to communicator credibility. Audiences view trustworthiness as the motivation to be truthful. Identifying whom to trust follows systematic principles. People decide quickly another’s apparent intent: Who is friend or foe, on their side or not, or a cooperator or competitor. Those seemingly on their side are deemed warm (friendly, trustworthy). People then decide whether the other is competent to enact those intents. Perception of scientists, like other social perceptions, involves inferring both their apparent intent (warmth) and capability (competence). To illustrate, we polled adults online about typical American jobs, rated as American society views them, on warmth and competence dimensions, as well as relevant emotions. Ambivalently perceived high-competence but low-warmth, “envied” professions included lawyers, chief executive officers, engineers, accountants, scientists, and researchers. Being seen as competent but cold might not seem problematic until one recalls that communicator credibility requires not just status and expertise but also trustworthiness (warmth). Other research indicates the risk from being enviable. Turning to a case study of scientific communication, another online sample of adults described public attitudes toward climate scientists specifically. Although distrust is low, the apparent motive to gain research money is distrusted. The literature on climate science communicators agrees that the public trusts impartiality, not persuasive agendas. Overall, communicator credibility needs to address both expertise and trustworthiness. Scientists have earned audiences’ respect, but not necessarily their trust. Discussing, teaching, and sharing information can earn trust to show scientists’ trustworthy intentions.
The cultural side of science communication
Authors: Medin Douglas L. , Bang Megan
Published: September 2014

The main proposition of this paper is that science communication necessarily involves and includes cultural orientations. There is a substantial body of work showing that cultural differences in values and epistemological frameworks are paralleled with cultural differences reflected in artifacts and public representations. One dimension of cultural difference is the psychological distance between humans and the rest of nature. Another is perspective taking and attention to context and relationships. As an example of distance, most (Western) images of ecosystems do not include human beings, and European American discourse tends to position human beings as being apart from nature. Native American discourse, in contrast, tends to describe humans beings as a part of nature. We trace the correspondences between cultural properties of media, focusing on children’s books, and cultural differences in biological cognition. Finally, implications for both science communication and science education are outlined.
Functional trait space and the latitudinal diversity gradient
Authors: Lamanna Christine , Blonder Benjamin , Violle Cyrille , Kraft Nathan J. B. , Sandel Brody , Šímová Irena , Donoghue John C. , Svenning Jens-Christian , McGill Brian J. , Boyle Brad , Buzzard Vanessa , Dolins Steven , Jørgensen Peter M. , Marcuse-Kubitza Aaron , Morueta-Holme Naia , Peet Robert K. , Piel William H. , Regetz James , Schildhauer Mark , Spencer Nick , Thiers Barbara , Wiser Susan K. , Enquist Brian J.
Published: September 2014

Significance

We present a conceptual framework for testing theories for the latitudinal gradient of species richness in terms of variation in functional diversity at the alpha, beta, and gamma scales. We compared ecological community theory with large-scale observational data of tree species richness and functional diversity. We found that the patterns of functional trait diversity are not consistent with any one theory of species diversity. These conflicting results indicate that none of the broad classes of biodiversity theory considered here is alone able to explain the latitudinal gradient of species diversity in terms of functional trait space.
Hypothesized link between Neoproterozoic greening of the land surface and the establishment of an oxygen-rich atmosphere
Authors: Kump Lee R.
Published: September 2014

Significance

The evolution of the biota and of atmospheric composition have been tightly coupled throughout Earth history. Of key importance has been the establishment of an oxygen-rich atmosphere, and this has apparently occurred in two major steps. The second step occurred during the Neoproterozoic, at the time when various lines of evidence suggest a significant expansion of terrestrial life and soil development. The present paper links these two events in a unique way, not through increased oxygen production on land, but through increased consumption in biotic soils that until compensated by higher atmospheric oxygen levels, restricted the supply of oxygen to the weathering environment.
Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems
Authors: Westengen Ola T. , Okongo Mark Atam , Onek Leo , Berg Trygve , Upadhyaya Hari , Birkeland Siri , Kaur Khalsa Siri Dharma , Ring Kristoffer H. , Stenseth Nils C. , Brysting Anne K.
Published: September 2014

Significance

This paper shows that cultural factors play a key role in shaping the genetic structure in sorghum. We present molecular evidence of close associations between sorghum population structure and the distribution of ethnolinguistic groups in Africa. We show that traditional seed-management practices, which have played an important role for survival and expansion of agropastoral groups in the past, still are remarkably resilient to threats to human security. We argue that efforts to strengthen African sorghum seed systems are more likely to be successful when building on, rather than seeking to replace, existing traditional seed systems and landraces.
Phylogenetic analysis of beak and feather disease virus across a host ring-species complex
Authors: Eastwood Justin R. , Berg Mathew L. , Ribot Raoul F. H. , Raidal Shane R. , Buchanan Katherine L. , Walder Ken R. , Bennett Andrew T. D.
Published: September 2014

Significance

The roles of disease and species hybridization in maintaining biodiversity are of wide interest, yet are rarely studied simultaneously in wild populations. Using genomic analysis of beak and feather disease virus in an avian ring-species complex,
Platycercus elegans
, to our knowledge we find viral phylogenetic structure analogous to Mayr’s ring-species hypothesis for the first time in any pathogen. Across 8 y, the host’s viral prevalence and infection load was lower in hybrid birds and in phenotypically intermediate subspecies. Viral genetic variation did not explain host prevalence or infection load, supporting conclusions that the evolved host response is more important. We show how host–species complexes and viral genomic analyses can provide insight into maintenance of biodiversity.
Pulque production from fermented agave sap as a dietary supplement in Prehispanic Mesoamerica
Authors: Correa-Ascencio Marisol , Robertson Ian G. , Cabrera-Cortés Oralia , Cabrera-Castro Rubén , Evershed Richard P.
Published: September 2014

Significance

This research provides the earliest direct chemical evidence for the production of alcoholic beverage pulque in Mesoamerica, based on organic residues recovered from pottery vessels from Teotihuacan. A novel bacterial lipid biomarker approach is reported, which provides a new means of documenting the consumption of bacterially fermented alcoholic beverages in antiquity worldwide. At Teotihuacan, we have evidence that pulque was stored in distinctive amphorae vessels sealed with pine resin, as well as in other, less specialized vessels. Direct evidence of pulque production provides new insights into how the nutritional requirements of Teotihuacanos were sustained in a region in which the diet was largely based on plants and crop failures, due to drought and frost damage, which resulted in frequent shortfalls in staples.
Ultradian corticosterone pulses balance glutamatergic transmission and synaptic plasticity
Authors: Sarabdjitsingh Ratna Angela , Jezequel Julie , Pasricha Natasha , Mikasova Lenka , Kerkhofs Amber , Karst Henk , Groc Laurent , Joëls Marian
Published: September 2014

Significance

A pulse of the adrenal hormone corticosterone (CORT) changes hippocampal glutamate transmission for many hours. CORT is normally released in hourly pulses, with a steeply rising amplitude just before awakening. How organisms can be prepared for imminent danger if the first high-amplitude pulse of CORT would lastingly change glutamate transmission—thus potentially deadlocking the system—has remained an enigma. We show that exposure of hippocampal cells to a second high-amplitude CORT pulse completely normalizes all aspects of glutamate transmission (including synaptic plasticity), thus lifting the potential deadlock caused by a first pulse. This ensures that the system remains fully responsive to any stressful event that requires encoding of information, an important principle that promotes survival of individuals.
Early origin of parental care in Mesozoic carrion beetles
Authors: Cai Chen-Yang , Thayer Margaret K. , Engel Michael S. , Newton Alfred F. , Ortega-Blanco Jaime , Wang Bo , Wang Xiang-Dong , Huang Di-Ying
Published: September 2014

Significance

We report on the unique discovery of Jurassic and Cretaceous carrion beetles (Silphidae) from China and Myanmar, early relatives of one of the most protected of beetle species in North America, and which clearly preserve evidence indicative of complex parental care. This finding represents the earliest evidence of parental care, a behavioral repertoire that is the first step in the development of truly social behavior and one that is intensely studied by ecologists, ethologists, and evolutionary biologists alike. Our fossils clearly span the origins of parent–offspring communication and allow us to provide a robust estimate of the time of origin for this complex behavior.
Mathematical model of renal interstitial fibrosis
Authors: Hao Wenrui , Rovin Brad H. , Friedman Avner
Published: September 2014

Significance

This paper deals with fibrosis of the kidney, a disease caused by inflammation, and so far there has been no way to diagnose and monitor the disease’s progression with noninvasive methods (the only way to determine the disease state is by biopsy, which cannot be frequently repeated). For this reason we developed a mathematical model of progression of renal fibrosis and validated it with biomarkers that were obtained from patients’ urine samples. We then used the model to show how antifibrosis drugs that are currently being developed for nonrenal fibrosis can be used to treat renal fibrosis.
The emergence and promise of functional biogeography
Authors: Violle Cyrille , Reich Peter B. , Pacala Stephen W. , Enquist Brian J. , Kattge Jens
Published: September 2014

Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.
Cellular redox regulation, signaling, and stress response in plants
Authors: Shigeoka Shigeru , Maruta Takanori
Published: September 2014

Cellular and organellar redox states, which are characterized by the balance between oxidant and antioxidant pool sizes, play signaling roles in the regulation of gene expression and protein function in a wide variety of plant physiological processes including stress acclimation. Reactive oxygen species (ROS) and ascorbic acid (AsA) are the most abundant oxidants and antioxidants, respectively, in plant cells; therefore, the metabolism of these redox compounds must be strictly and spatiotemporally controlled. In this review, we provided an overview of our previous studies as well as recent advances in (1) the molecular mechanisms and regulation of AsA biosynthesis, (2) the molecular and genetic properties of ascorbate peroxidases, and (3) stress acclimation via ROS-derived oxidative/redox signaling pathways, and discussed future perspectives in this field.
Transcriptional response machineries of Bacillus subtilis conducive to plant growth promotion
Authors: Hirooka Kazutake
Published: September 2014

Bacillus subtilis collectively inhabits the rhizosphere, where it contributes to the promotion of plant growth, although it does not have a direct symbiotic relationship to plants as observed in the case of rhizobia between leguminous plants. As rhizobia sense the flavonoids released from their host roots through the NodD transcriptional factor, which triggers transcription of the nod genes involved in the symbiotic processes, we supposed that B. subtilis utilizes certain flavonoids as signaling molecules to perceive and adapt to the rhizospheric environment that it is in. Our approaches to identify the flavonoid-responsive transcriptional regulatory system from B. subtilis resulted in the findings that three transcriptional factors (LmrA/QdoR, YetL, and Fur) are responsive to flavonoids, with the modes of action being different from each other. We also revealed a unique regulatory system by two transcriptional factors, YcnK and CsoR, for copper homeostasis in B. subtilis. In this review, we summarize the molecular mechanisms of these regulatory systems with the relevant information and discuss their physiological significances in the mutually beneficial interaction between B. subtilis and plants, considering the possibility of their application for plant cultivation.
Fish protein intake induces fast-muscle hypertrophy and reduces liver lipids and serum glucose levels in rats
Authors: Kawabata Fuminori , Mizushige Takafumi , Uozumi Keisuke , Hayamizu Kohsuke , Han Li , Tsuji Tomoko , Kishida Taro
Published: September 2014

In our previous study, fish protein was proven to reduce serum lipids and body fat accumulation by skeletal muscle hypertrophy and enhancing basal energy expenditure in rats. In the present study, we examined the precise effects of fish protein intake on different skeletal muscle fiber types and metabolic gene expression of the muscle. Fish protein increased fast-twitch muscle weight, reduced liver triglycerides and serum glucose levels, compared with the casein diet after 6 or 8 weeks of feeding. Furthermore, fish protein upregulated the gene expressions of a fast-twitch muscle-type marker and a glucose transporter in the muscle. These results suggest that fish protein induces fast-muscle hypertrophy, and the enhancement of basal energy expenditure by muscle hypertrophy and the increase in muscle glucose uptake reduced liver lipids and serum glucose levels. The present results also imply that fish protein intake causes a slow-to-fast shift in muscle fiber type.
The female human heart at rest and during exercise: A review
Authors: Nio Amanda Q. X. , Stöhr Eric J. , Shave Rob
Published: September 2014

Sexual dimorphism exists in numerous aspects of exercise physiology. One area that has long been debated is the potential of sex differences in cardiac structure and function. Anthropometric differences exist between males and females, and the relationship between absolute body size and cardiac structure dictate that men typically have larger hearts than women. However, increasing evidence suggests that males and females may also demonstrate different cardiac structure and function independent of body size, and it is likely that female sex hormones play a role in these differences. The purpose of this review is to draw together and examine the literature that has compared cardiac structure and function in men and women at rest and during exercise. We make specific reference to the influence of female sex hormones, and discuss the confounding effects of age and training status. Wherever possible, we provide conclusive remarks. Due to the paucity of data in this field, and general lack of consensus, the review concludes by making recommendations for future work.
The importance of internal facial features in learning new faces
Authors: Longmore Christopher A. , Liu Chang Hong , Young Andrew W.
Published: September 2014

For familiar faces, the internal features (eyes, nose, and mouth) are known to be differentially salient for recognition compared to external features such as hairstyle. Two experiments are reported that investigate how this internal feature advantage accrues as a face becomes familiar. In Experiment 1, we tested the contribution of internal and external features to the ability to generalize from a single studied photograph to different views of the same face. A recognition advantage for the internal features over the external features was found after a change of viewpoint, whereas there was no internal feature advantage when the same image was used at study and test. In Experiment 2, we removed the most salient external feature (hairstyle) from studied photographs and looked at how this affected generalization to a novel viewpoint. Removing the hair from images of the face assisted generalization to novel viewpoints, and this was especially the case when photographs showing more than one viewpoint were studied. The results suggest that the internal features play an important role in the generalization between different images of an individual's face by enabling the viewer to detect the common identity-diagnostic elements across non-identical instances of the face.
Default spacing is the optimal spacing for word reading
Authors: van den Boer Madelon , Hakvoort Britt E.
Published: September 2014

Increased interletter spacing is thought to reduce crowding effects and to enhance fluent reading. Several studies have shown beneficial effects of increased interletter spacing on reading speed and accuracy, especially in poor readers. Therefore, increased interletter spacing appears to be a relatively easy way to enhance reading performance. However, in adult readers reading speed was shown to be impeded with increased interletter spacing. Thus, findings on interletter spacing are still inconclusive. In the current study we examined the effect of a range of interletter spacings (−0.5, default, 0.5, 1, 1.5, 2) on naming fluency of monosyllabic and bisyllabic words in beginning (Grade 2) and more advanced (Grade 4) readers. Additionally we tested the effects of spacing in a subsample of poor readers. In contrast to previous findings, neither beginning nor advanced readers benefited from an increase in interletter spacing. However, they did show reduced reading fluency when letter spacing was smaller than the default spacing, which may be indicative of a crowding effect. Poor readers showed a similar pattern. We conclude that an increase in interletter spacing has no effect on word naming fluency.
Sustained attention in language production: An individual differences investigation
Authors: Jongman Suzanne R. , Roelofs Ardi , Meyer Antje S.
Published: September 2014

Whereas it has long been assumed that most linguistic processes underlying language production happen automatically, accumulating evidence suggests that these processes do require some form of attention. Here we investigated the contribution of sustained attention: the ability to maintain alertness over time. In Experiment 1, participants’ sustained attention ability was measured using auditory and visual continuous performance tasks. Subsequently, employing a dual-task procedure, participants described pictures using simple noun phrases and performed an arrow-discrimination task while their vocal and manual response times (RTs) and the durations of their gazes to the pictures were measured. Earlier research has demonstrated that gaze duration reflects language planning processes up to and including phonological encoding. The speakers’ sustained attention ability correlated with the magnitude of the tail of the vocal RT distribution, reflecting the proportion of very slow responses, but not with individual differences in gaze duration. This suggests that sustained attention was most important after phonological encoding. Experiment 2 showed that the involvement of sustained attention was significantly stronger in a dual-task situation (picture naming and arrow discrimination) than in simple naming. Thus, individual differences in maintaining attention on the production processes become especially apparent when a simultaneous second task also requires attentional resources.
Exhaustion of bacteria-specific CD4 T cells and microbial translocation in common variable immunodeficiency disorders
Authors: Perreau Matthieu , Vigano Selena , Bellanger Florence , Pellaton Céline , Buss Guillaume , Comte Denis , Roger Thierry , Lacabaratz Christine , Bart Pierre-Alexandre , Levy Yves , Pantaleo Giuseppe
Published: September 2014

In the present study, we have investigated the functional profile of CD4 T cells from patients with common variable immunodeficiency (CVID), including production of cytokines and proliferation in response to bacteria and virus-derived antigens. We show that the functional impairment of CD4 T cells, including the reduced capacity to proliferate and to produce IFN-γ and IL-2, was restricted to bacteria-specific and not virus-specific CD4 T cells. High levels of endotoxins were found in the plasma of patients with CVID, suggesting that CD4 T cell dysfunction might be caused by bacterial translocation. Of note, endotoxemia was associated with significantly higher expression of programmed death 1 (PD-1) on CD4 T cells. The blockade of the PD-1–PD-L1/2 axis in vitro restored CD4 T cell proliferation capacity, thus indicating that PD-1 signaling negatively regulates CD4 T cell functions. Finally, we showed that intravenous immunoglobulin G (IVIG) treatment significantly reduced endotoxemia and the percentage of PD-1+ CD4 T cells, and restored bacteria-specific CD4 T cell cytokine production and proliferation. In conclusion, the present study demonstrates that the CD4 T cell exhaustion and functional impairment observed in CVID patients is associated with bacterial translocation and that IVIG treatment resolves bacterial translocation and restores CD4 T cell functions.