bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-dimensional lift-up problem for a rigid porous bed
Authors: Chang Y. , Huang L. H. , Yang F. P. Y.
Published: May 2015

The present study analytically reinvestigates the two-dimensional lift-up problem for a rigid porous bed that was studied by Mei, Yeung, and Liu [“Lifting of a large object from a porous seabed,” J. Fluid Mech. 152, 203 (1985)]. Mei, Yeung, and Liu proposed a model that treats the bed as a rigid porous medium and performed relevant experiments. In their model, they assumed the gap flow comes from the periphery of the gap, and there is a shear layer in the porous medium; the flow in the gap is described by adhesion approximation [D. J. Acheson, Elementary Fluid Dynamics (Clarendon, Oxford, 1990), pp. 243-245.] and the pore flow by Darcy’s law, and the slip-flow condition proposed by Beavers and Joseph [“Boundary conditions at a naturally permeable wall,” J. Fluid Mech. 30, 197 (1967)] is applied to the bed interface. In this problem, however, the gap flow initially mainly comes from the porous bed, and the shear layer may not exist. Although later the shear effect becomes important, the empirical slip-flow condition might not physically respond to the shear effect, and the existence of the vertical velocity affects the situation so greatly that the slip-flow condition might not be appropriate. In contrast, the present study proposes a more general model for the problem, applying Stokes flow to the gap, the Brinkman equation to the porous medium, and Song and Huang’s [“Laminar poroelastic media flow,” J. Eng. Mech. 126, 358 (2000)] complete interfacial conditions to the bed interface. The exact solution to the problem is found and fits Mei’s experiments well. The breakout phenomenon is examined for different soil beds, mechanics that cannot be illustrated by Mei’s model are revealed, and the theoretical breakout times obtained using Mei’s model and our model are compared. The results show that the proposed model is more compatible with physics and provides results that are more precise.
Finding mechanochemical pathways and barriers without transition state search
Authors: Avdoshenko Stanislav M. , Makarov Dmitrii E.
Published: May 2015

In covalent mechanochemistry, precise application of mechanical stress to molecules of interest (“mechanophores”) is used to induce to promote desired reaction pathways. Computational prediction of such phenomena and rational mechanophore design involves the computationally costly task of finding relevant transition-state saddles on force-deformed molecular potential energy surfaces (PESs). Finding a transition state often requires an initial guess about the pathway by which the reaction will proceed. Unfortunately, chemical intuition often fails when predicting likely consequences of mechanical stress applied to molecular systems. Here, we describe a fully deterministic method for finding mechanochemically relevant transition states and reaction pathways. The method is based on the observation that application of a sufficiently high mechanical force will eventually destabilize any molecular structure. Mathematically, such destabilization proceeds via a “catastrophe” occurring at a critical force where the energy minimum corresponding to the stable molecular structure coalesces with a transition state. Catastrophe theory predicts the force-deformed PES to have universal behavior in the vicinity of the critical force, allowing us to deduce the molecular structure of the transition state just below the critical force analytically. We then use the previously developed method of tracking transition-state evolution with the force to map out the entire reaction path and to predict the complete force dependence of the reaction barrier. Beyond its applications in mechanochemistry, this approach may be useful as a general method of finding transition states using fictitious forces to target specific reaction mechanisms.
Understanding nuclear motions in molecules: Derivation of Eckart frame ro-vibrational Hamiltonian operators via a gateway Hamiltonian operator
Authors: Szalay Viktor
Published: May 2015

A new ro-vibrational Hamiltonian operator, named gateway Hamiltonian operator, with exact kinetic energy term, Tˆ, is presented. It is in the Eckart frame and it is of the same form as Watson’s normal coordinate Hamiltonian. However, the vibrational coordinates employed are not normal coordinates. The new Hamiltonian is shown to provide easy access to Eckart frame ro-vibrational Hamiltonians with exact Tˆ given in terms of any desired set of vibrational coordinates. A general expression of the Eckart frame ro-vibrational Hamiltonian operator is given and some of its properties are discussed.
Relaxation dynamics in a transient network fluid with competing gel and glass phases
Authors: Chaudhuri Pinaki , Hurtado Pablo I. , Berthier Ludovic , Kob Walter
Published: May 2015

We use computer simulations to study the relaxation dynamics of a model for oil-in-water microemulsion droplets linked with telechelic polymers. This system exhibits both gel and glass phases and we show that the competition between these two arrest mechanisms can result in a complex, three-step decay of the time correlation functions, controlled by two different localization lengthscales. For certain combinations of the parameters, this competition gives rise to an anomalous logarithmic decay of the correlation functions and a subdiffusive particle motion, which can be understood as a simple crossover effect between the two relaxation processes. We establish a simple criterion for this logarithmic decay to be observed. We also find a further logarithmically slow relaxation related to the relaxation of floppy clusters of particles in a crowded environment, in agreement with recent findings in other models for dense chemical gels. Finally, we characterize how the competition of gel and glass arrest mechanisms affects the dynamical heterogeneities and show that for certain combination of parameters these heterogeneities can be unusually large. By measuring the four-point dynamical susceptibility, we probe the cooperativity of the motion and find that with increasing coupling this cooperativity shows a maximum before it decreases again, indicating the change in the nature of the relaxation dynamics. Our results suggest that compressing gels to large densities produces novel arrested phases that have a new and complex dynamics.
Unraveling the roles of thermal annealing and off-time duration in magnetic properties of pulsed electrodeposited NiCu nanowire arrays
Authors: Haji jamali Z. , Almasi Kashi M. , Ramazani A. , Montazer A. H.
Published: May 2015

Magnetic alloy nanowires (ANWs) have long been studied owing to both their fundamental aspects and possible applications in magnetic storage media and magnetoresistance devices. Here, we report on the roles of thermal annealing and duration of off-time between pulses (toff) in crystalline characteristics and magnetic properties of arrays of pulsed electrodeposited NiCu ANWs (35 nm in diameter and a length of 1.2 μm), embedded in porous anodic alumina template. Increasing toff enabled us to increase the Cu content thereby fabricating NiCu ANWs with different crystallinity and alloy compositions. Although major hysteresis curve measurements showed no considerable change in magnetic properties before and after annealing, the first-order reversal curve (FORC) analysis provided new insights into the roles of thermal annealing and toff. In other words, FORC diagrams indicated the presence of low and high coercive field regions in annealed Ni-rich ANWs, coinciding with the increase in toff in as-deposited ANWs. The former has a small coercivity with strong demagnetizing magnetostatic interactions from neighboring NWs and may correspond to a soft magnetic phase. The latter has a greater coercivity with weak interactions, corresponding to a hard magnetic phase. On the other hand, for as-deposited and annealed Cu-rich NiCu ANWs, a mixed phase of the soft and hard segments could be found. Furthermore, a transition from the interacting Ni-rich to non-interacting Cu-rich ANWs took place with a magnetic field applied parallel to the NW axis. Thus, these arrays of ANWs with tunable magnetic phases and interactions may have potential applications in the nanoscale devices.
Algebraic geometrization of the Kuramoto model: Equilibria and stability analysis
Authors: Mehta Dhagash , Daleo Noah S. , Dörfler Florian , Hauenstein Jonathan D.
Published: May 2015

Finding equilibria of the finite size Kuramoto model amounts to solving a nonlinear system of equations, which is an important yet challenging problem. We translate this into an algebraic geometry problem and use numerical methods to find all of the equilibria for various choices of coupling constants K, natural frequencies, and on different graphs. We note that for even modest sizes (N ∼ 10–20), the number of equilibria is already more than 100 000. We analyze the stability of each computed equilibrium as well as the configuration of angles. Our exploration of the equilibrium landscape leads to unexpected and possibly surprising results including non-monotonicity in the number of equilibria, a predictable pattern in the indices of equilibria, counter-examples to conjectures, multi-stable equilibrium landscapes, scenarios with only unstable equilibria, and multiple distinct extrema in the stable equilibrium distribution as a function of the number of cycles in the graph.
Phase locking of moving magnetic vortices in bridge-coupled nanodisks
Authors: Zhu Qiyuan , Zheng Qi , Liu Xianyin , Wang Jianbo , Liu Qingfang
Published: May 2015

In this paper, phase locking dynamics of vortices induced by spin transfer torque in bridge-coupled nanodisks are studied by micromagnetic simulations. In the presence of the bridge coupling, the required time for the phase locking is dramatically reduced, and the phase difference between the two vortices keeps at a nonzero value after the phase locking. Moreover, the phase difference is affected significantly by bridge coupling, Oersted field distribution, nanodisk size, as well as in-plane bias magnetic field. In addition, the coupled gyrotropic frequency of vortices depends linearly on the perpendicular magnetic field. This systematic study of phase locking parameters, especially the phase difference, is important for the applications of vortex-based spin-torque nano-oscillators.
A new model for gas transport in fractal-like tight porous media
Authors: Li Xiao-Gang , Yi Liang-Ping , Yang Zhao-Zhong , Huang Xin
Published: May 2015

A new gas transport model for fractal-like tight porous media is proposed by simultaneously considering the microstructural complexity of real porous media, the compressibility of gas, and the gas slippage effect. This model clarifies the gas transport mechanisms in porous media: the total gas flow volume is governed by the weighted addition of viscous flow and slippage flow, and the distribution weighting factor depends on the capillary diameter and the mean free path of the gas. Based on the proposed model, a new permeability model was derived for gas transport in fractal-like tight porous media. The new permeability model does not have any empirical constants, and every parameter in the model has clear physical meaning. The predictions from the model were then compared with experimental data to show that the model is valid. Furthermore, the parameters influencing gas permeability were analyzed.
Photovoltaic action in a self-assembled monolayer of hemicyanine dyes on gold from dissociation of surface plasmons
Authors: Gholamrezaie Fatemeh , Vijayaraghavan Ratheesh K. , Meskers Stefan C. J.
Published: May 2015

Hemicyanine dye molecules, containing a thiol functionality, form a self-assembled monolayer (SAM) on thin films of gold. The combined SAM-gold layer system supports surface plasmons and can be converted into a diode using a liquid electrolyte top contact. Diodes fabricated on a quartz prism allow for incoupling of incident light to surface plasmons and show a spontaneous photocurrent under short-circuit conditions. Measurement of the short-circuit photocurrent as function of incident angle of the light shows that the photocurrent arises from dissociation of surface plasmons into pairs of charge carriers.
Spatial and spectral distributions of thermal radiation emitted by a semi-infinite body and absorbed by a flat film
Authors: Blandre Etienne , Chapuis Pierre-Olivier , Francoeur Mathieu , Vaillon Rodolphe
Published: May 2015

We analyze the radiative power emitted by a semi-infinite medium and absorbed by a flat film located in its vicinity. In the near-field regime, if the film is thin enough, the surface waves at the rear interface of the film can contribute to the heat transfer. As a result, the absorbed power can be enhanced farther from the front surface. In the near-to-far field transition regime, temporal coherence of thermal radiation and the associated interferences can be used to shape the spectrum of the transferred radiative heat flux by selecting approriate geometrical parameters. These results highlight possibilities to control both the location where the radiative power is absorbed in the film and the spectral distribution, which are of paramount importance for applications such as near-field thermophotovoltaics.
Potassium acceptor doping of ZnO crystals
Authors: Parmar Narendra S. , Corolewski Caleb D. , McCluskey Matthew D. , Lynn K. G.
Published: May 2015

ZnO bulk single crystals were doped with potassium by diffusion at 950°C. Positron annihilation spectroscopy confirms the filling of zinc vacancies and a different trapping center for positrons. Secondary ion mass spectroscopy measurements show the diffusion of potassium up to 10 μm with concentration ∼1 × 1016 cm−3. IR measurements show a local vibrational mode (LVM) at 3226 cm−1, at a temperature of 9 K, in a potassium doped sample that was subsequently hydrogenated. The LVM is attributed to an O–H bond-stretching mode adjacent to a potassium acceptor. When deuterium substitutes for hydrogen, a peak is observed at 2378 cm−1. The O-H peak is much broader than the O-D peak, perhaps due to an unusually low vibrational lifetime. The isotopic frequency ratio is similar to values found in other hydrogen complexes. Potassium doping increases the resistivity up to 3 orders of magnitude at room temperature. The doped sample has a donor level at 0.30 eV.
Effects of the inlet conditions and blood models on accurate prediction of hemodynamics in the stented coronary arteries
Authors: Jiang Yongfei , Zhang Jun , Zhao Wanhua
Published: May 2015

Hemodynamics altered by stent implantation is well-known to be closely related to in-stent restenosis. Computational fluid dynamics (CFD) method has been used to investigate the hemodynamics in stented arteries in detail and help to analyze the performances of stents. In this study, blood models with Newtonian or non-Newtonian properties were numerically investigated for the hemodynamics at steady or pulsatile inlet conditions respectively employing CFD based on the finite volume method. The results showed that the blood model with non-Newtonian property decreased the area of low wall shear stress (WSS) compared with the blood model with Newtonian property and the magnitude of WSS varied with the magnitude and waveform of the inlet velocity. The study indicates that the inlet conditions and blood models are all important for accurately predicting the hemodynamics. This will be beneficial to estimate the performances of stents and also help clinicians to select the proper stents for the patients.
Characterisation of microsatellite markers for fig-pollinating wasps in the Pleistodontes imperialis species complex
Authors: Sutton Timothy L. , Reuter Caroline , Riegler Markus , Cook James M.
Published: May 2015

We characterised a set of nine polymorphic microsatellite loci for Pleistodontes imperialis sp. 1, the pollinator wasp of Port Jackson fig (Ficus rubiginosa) in south-eastern Australia. Characterisation was performed on 30 female individuals collected from a population in Sydney, Australia. The average number of alleles per locus was 7.33, and eight loci were not in Hardy–Weinberg equilibrium. This was expected as fig wasps are known to be highly inbred. A test of genetic differentiation between two natural populations of P. imperialis sp. 1 (Sydney and Newcastle, Australia – some 120 km apart) yielded a very low FST value of 0.012, suggesting considerable gene flow. Bayesian clustering analysis using TESS 2.3.1, which does not assume Hardy–Weinberg equilibrium, however, indicated potential spatial substructuring between the Sydney and Newcastle populations, as well as within the Sydney population. The described loci were also characterised for two other species in the P. imperialis complex: P. imperialis sp. 2 (Townsville, Australia) and P. imperialis sp. 4 (Brisbane, Australia). Seven and six of the nine loci were polymorphic for P. imperialis sp. 2 and P. imperialis sp. 4, respectively.
Specific heat and sound velocity at the relevant competing phase of high-temperature superconductors
Authors: Varma Chandra M. , Zhu Lijun
Published: May 2015

Significance

A variety of experiments have supported the idea that high-temperature superconductivity is caused by the interaction of quantum mechanical zero-point fluctuations of a competing order with electrons. One of the strangest features of this order is that a transition to it appears to occur without a noticeable specific heat anomaly. We show unambiguously that a proposed order, in which currents spontaneously flow in close loops within each unit cell of the compound, is such that an unusual signature of transition to it is found in the sound velocity experiments but that it is unobservable in the specific heat measurements. Stringent conditions are provided by the analysis for other possible orders to be relevant to the fundamental physics of high-temperature superconductivity.
Bestrophin 1 is indispensable for volume regulation in human retinal pigment epithelium cells
Authors: Milenkovic Andrea , Brandl Caroline , Milenkovic Vladimir M. , Jendryke Thomas , Sirianant Lalida , Wanitchakool Potchanart , Zimmermann Stephanie , Reiff Charlotte M. , Horling Franziska , Schrewe Heinrich , Schreiber Rainer , Kunzelmann Karl , Wetzel Christian H. , Weber Bernhard H. F.
Published: May 2015

Significance

First insight into the molecular identity of volume-regulated anion channel (VRAC) emerged only recently by demonstrating a role for leucine-rich repeats containing 8A (LRRC8A) in channel activity. Our results now expand on VRAC biology, suggesting a model where VRAC subunit composition is cell type- or tissue-specific rather than a single ubiquitous channel formed solely by LRRC8A. Here, we show that bestrophin 1 (BEST1), but not LRCC8A, is crucial in cell volume regulation in retinal pigment epithelium (RPE) cells differentiated from human-induced pluripotent stem cells (hiPSCs). VRAC-mediated currents were strongly reduced in hiPSC-RPE from macular dystrophy patients with pathologic BEST1 mutations. Our model is further supported by in vivo effects of Best1 deficiency in the mouse that manifest as severe subfertility phenotype due to enhanced abnormal sperm morphology related to impaired volume regulation.
Extreme selective sweeps independently targeted the X chromosomes of the great apes
Authors: Nam Kiwoong , Munch Kasper , Hobolth Asger , Dutheil Julien Yann , Veeramah Krishna R. , Woerner August E. , Hammer Michael F. ,   Great Ape Genome Diversity Project, Mailund Thomas , Schierup Mikkel Heide , Prado-Martinez Javier , Sudmant Peter H. , Kidd Jeffrey M. , Li Heng , Kelley Joanna L. , Lorente-Galdos Belen , Veeramah Krishna R. , Woerner August E. , O’Connor Timothy D. , Santpere Gabriel , Cagan Alexander , Theunert Christoph , Casals Ferran , Laayouni Hafid , Munch Kasper , Hobolth Asger , Halager Anders E. , Malig Maika , Hernandez-Rodriguez Jessica , Hernando-Herraez Irene , Prüfer Kay , Pybus Marc , Johnstone Laurel , Lachmann Michael , Alkan Can , Twigg Dorina , Petit Natalia , Baker Carl , Hormozdiari Fereydoun , Fernandez-Callejo Marcos , Dabad Marc , Wilson Michael L. , Stevison Laurie , Camprubí Cristina , Carvalho Tiago , Ruiz-Herrera Aurora , Vives Laura , Mele Marta , Abello Teresa , Kondova Ivanela , Bontrop Ronald E. , Pusey Anne , Lankester Felix , Kiyang John A. , Bergl Richard A. , Lonsdorf Elizabeth , Myers Simon , Ventura Mario , Gagneux Pascal , Comas David , Siegismund Hans , Blanc Julie , Agueda-Calpena Lidia , Gut Marta , Fulton Lucinda , Tishkoff Sarah A. , Mullikin James C. , Wilson Richard K. , Gut Ivo G. , Gonder Mary Katherine , Ryder Oliver A. , Hahn Beatrice H. , Navarro Arcadi , Akey Joshua M. , Bertranpetit Jaume , Reich David , Mailund Thomas , Schierup Mikkel H. , Hvilsom Christina , Andrés Aida M. , Wall Jeffrey D. , Bustamante Carlos D. , Hammer Michael F. , Eichler Evan E. , Marques-Bonet Tomas
Published: May 2015

Significance

The X chromosome has a different inheritance pattern from the autosomes, direct interaction and potential conflict with the Y chromosome, and fewer copies than the autosomes. Natural selection may, therefore, act differently on the X chromosome. We analyze polymorphism patterns in 10 great ape species using 87 high-coverage whole genomes. We find that the X chromosome contains megabase-sized regions that are almost without variation in most species. No such regions are found on the autosomes. We suggest that independent and very strong selective sweeps are the only plausible explanation for these observations, and we hypothesize that the targets of these sweeps are multicopy testis-expressed genes in a genetic conflict with the Y chromosome for transmission to the next generation.
Limits to adaptation along environmental gradients
Authors: Polechová Jitka , Barton Nicholas H.
Published: May 2015

Significance

Why do species’ ranges often end when no obvious change in the environment suggests they should? Our theory explains that there is an inherent limit to adaptation arising in any (finite) natural population and identifies the key parameters that determine this limit to a species’ range. Two observable parameters describe the threshold when adaptation fails: (
i
) the loss of fitness due to dispersal to a different environment, and (
ii
) the efficacy of selection relative to stochastic effects in finite populations.
Symbolic bones and interethnic violence in a frontier zone, northwest Mexico, ca. 500–900 C.E.
Authors: Nelson Ben A. , Martin Debra L.
Published: May 2015

Significance

Persistent interethnic violence has affected some global regions for centuries. Recent research reveals that major outbreaks are often prevented or limited by creative social action. In the prehispanic Northern Frontier of Mesoamerica, approximately 500–900 C.E., people of different ethnic backgrounds struggled for standing in a shifting sociopolitical landscape. Evidence is consistent with long-term social violence, but also with the use of the dead to communicate a range of symbolic messages. Complex arrays of human skeletal material commemorated past physical conflicts, possibly discouraging their repetition, while also connecting the living symbolically with a metaphysical realm inhabited by ancestors and deities. This article highlights the postmortem agency of the dead and illustrates their roles in structuring social relations.
Specialization and integration of functional thalamocortical connectivity in the human infant
Authors: Toulmin Hilary , Beckmann Christian F. , O'Muircheartaigh Jonathan , Ball Gareth , Nongena Pumza , Makropoulos Antonios , Ederies Ashraf , Counsell Serena J. , Kennea Nigel , Arichi Tomoki , Tusor Nora , Rutherford Mary A. , Azzopardi Denis , Gonzalez-Cinca Nuria , Hajnal Joseph V. , Edwards A. David
Published: May 2015

Significance

We investigated the way in which the human thalamus and cortex are functionally connected at the time of normal birth. We found the functional parcellation of the thalamus to be a good facsimile of that found in adult studies. However, although primary cortical regions were almost entirely connected to specific thalamic regions, heteromodal cortex was more widely connected to multiple thalamic regions, giving the potential for an integrative role for these circuits. Development seemed to have been modulated by the experience of premature extrauterine life, with an increase in connectivity to primary sensory cortex, but reduced connectivity between areas of the thalamus and heteromodal cortex known to support higher cognitive functions.
The phototransduction machinery in the rod outer segment has a strong efficacy gradient
Authors: Mazzolini Monica , Facchetti Giuseppe , Andolfi Laura , Proietti Zaccaria Remo , Tuccio Salvatore , Treu Johannes , Altafini Claudio , Di Fabrizio Enzo M. , Lazzarino Marco , Rapp Gert , Torre Vincent
Published: May 2015

Significance

Phototransduction is now considered to be a quite thoroughly understood phenomenon. It is well known that new discs are continuously generated at the base of the outer segments (OSs) and old discs are shed at their tip, but the rod OSs are considered a well-stirred compartment with minor inhomogeneities. To verify this assumption and to better understand the machinery within the OS, we developed a new methodology to deliver highly localized lights. We found that, as the light stimulus is moved from the OS base toward its tip, the amplitude of saturating and single photon responses decreased by 5–10 times. This gradient of efficacy is attributed to a progressive loss of phosphodiesterase. Therefore, OSs are highly inhomogeneous compartments.
Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo
Authors: Onjiko Rosemary M. , Moody Sally A. , Nemes Peter
Published: May 2015

Significance

Spatiotemporal characterization of molecular expression during embryonic development is critical for understanding how cells become different and give rise to distinct tissues and organs. Technological advances enabled the measurement of RNAs and proteins in single cells of embryos, but there is very little information on small molecules, metabolites, that are the ultimate indication of the physiological state. To fill this knowledge gap, we developed and used a single-cell technology to find that embryonic cells that give rise to different tissues have characteristically different metabolic signatures that are not simply a reflection of cell pigmentation, yolk content, size, or position in the embryo, but also affect cell fate. This approach is likely to provide new mechanistic insights into early embryo development.
Lack of pairing during meiosis triggers multigenerational transgene silencing in
Caenorhabditis elegans
Authors: Leopold Luciana E. , Heestand Bree N. , Seong Soobin , Shtessel Ludmila , Ahmed Shawn
Published: May 2015

Significance

Transgenes can be permanently silenced in a single generation via a previously described small RNA-induced epigenetic silencing (RNAe) mechanism, which is promoted by the presence of a perfect Piwi-interacting RNA (piRNA) target site. In this study, we identify a previously unidentified mechanism capable of silencing single-copy transgenes that lack perfect piRNA target sites and that is triggered by a lack of chromosomal pairing during meiosis for multiple generations. Multigenerational RNAe can lead to reversible or permanent transgene silencing and may provide insight into variability in the expression of single-copy transgenes or single-copy genomic insertions, which are commonly used in experimental biology. Our analysis of “multigenerational RNAe” also offers new insights into potentially common epigenetic silencing events relevant to genome expression in the germline and embryo.
Rational design of self-assembly pathways for complex multicomponent structures
Authors: Jacobs William M. , Reinhardt Aleks , Frenkel Daan
Published: May 2015

Significance

Recent experiments have demonstrated that complex, three-dimensional nanostructures can be self-assembled out of thousands of short strands of preprogrammed DNA. However, the mechanism by which robust self-assembly occurs is poorly understood, and the same feat has not yet been achieved using any other molecular building block. Using a new theory of “addressable” self-assembly, we explain how the design of the target structure and the choice of interparticle interactions determine the self-assembly pathway, and, to our knowledge, for the first time predict that a time-dependent protocol, rather than merely a carefully tuned set of conditions, may be necessary to optimize the yield. With an understanding of these design principles, it should be possible to engineer addressable nanostructures using a much wider array of materials.
Differential effects of fructose versus glucose on brain and appetitive responses to food cues and decisions for food rewards
Authors: Luo Shan , Monterosso John R. , Sarpelleh Kayan , Page Kathleen A.
Published: May 2015

Significance

Fructose compared with glucose may be a weaker suppressor of appetite. Here we sought to determine the effects of fructose versus glucose on brain, hormone, and appetitive responses to food cues and food-approach behavior. We show that the ingestion of fructose compared with glucose resulted in smaller increases in plasma insulin levels and greater brain responses to food cues in the visual cortex and left orbital frontal cortex. Ingestion of fructose versus glucose also led to greater hunger and desire for food and a greater willingness to give up long-term monetary rewards to obtain immediate high-calorie foods. These findings suggest that ingestion of fructose relative to glucose activates brain regions involved in attention and reward processing and may promote feeding behavior.
Stable long-range interhemispheric coordination is supported by direct anatomical projections
Authors: Shen Kelly , Mišić Bratislav , Cipollini Ben N. , Bezgin Gleb , Buschkuehl Martin , Hutchison R. Matthew , Jaeggi Susanne M. , Kross Ethan , Peltier Scott J. , Everling Stefan , Jonides John , McIntosh Anthony R. , Berman Marc G.
Published: May 2015

Significance

We show that the functional coordination between the two hemispheres of the brain is maintained by strong and stable interactions of a specific subset of connections between homotopic regions. Our data suggest that the stability of those functional interactions is mediated in part by the direct anatomical projections of large, highly myelinated fibers that traverse the corpus callosum. These functional properties were evident in both humans and macaques, suggesting a preserved framework for interhemispheric communication despite an increase in functional lateralization in humans. These results contribute to our fundamental understanding of how dynamic functional interactions between the two hemispheres of the mammalian brain are supported by its underlying anatomical architecture.
Age-related changes in working memory and the ability to ignore distraction
Authors: McNab Fiona , Zeidman Peter , Rutledge Robb B. , Smittenaar Peter , Brown Harriet R. , Adams Rick A. , Dolan Raymond J.
Published: May 2015

Significance

We reveal a novel and highly significant change in how items are held in mind in healthy aging. Using smartphones, data were collected from 29,631 participants, between the ages of 18–69 y. We compare the ability to exclude distractors when items are entered into working memory (WM) (encoding distraction, ED) and when items are held in mind (delay distraction, DD). In older adults, WM in the absence of distraction was more similar to ED exclusion than DD exclusion. A greater reliance on focused attention during encoding may reflect compensation for the more pronounced deterioration we observed in DD exclusion in older age. This can inform other areas of cognition and strategies to ameliorate or manage debilitating age-related cognitive decline.
Elastocapillary interactions on nematic films
Authors: Liu Iris B. , Gharbi Mohamed A. , Ngo Victor L. , Kamien Randall D. , Yang Shu , Stebe Kathleen J.
Published: May 2015

Significance

In this research we demonstrate complementary roles for elastic and capillary interactions for particles on thin nematic liquid crystal films. A priori estimates would suggest that surface tension effects would dominate over those associated with bend, twist, or splay of nematic director fields. This work is the first to our knowledge to clearly demonstrate complementary roles for both effects and extends significantly the means for developing oriented anisotropic assemblies. Anisotropic particles create strong capillary interactions that can dictate assembly. These assemblies obey orientations dictated by director fields in oriented planar nematic films. Curved interfaces add another degree of freedom, because curvature capillary-driven alignment competes with elastic-driven orientations. Experimental results are supported by analysis.
Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis
Authors: Koch Miriam , Flür Sara , Kreutz Christoph , Ennifar Eric , Micura Ronald , Polacek Norbert
Published: May 2015

Significance

Translational GTPases are key players in ribosomal protein synthesis. Their intrinsic GTPase activity is low and is stimulated by ribosome association. Although it has been shown by structural and biochemical studies that the sarcin-ricin loop of ribosomal RNA (rRNA) closely approaches the supposedly catalytic His of elongation factor (EF)-G and EF-Tu and thereby may contribute to GTP hydrolysis, the exact mechanism of activation remains unclear and is a matter of controversial debate. Using the atomic mutagenesis approach that allows incorporation of nonnatural 23S rRNA nucleotides into 70S particles, we show that a nonbridging phosphate oxygen of rRNA is key for GTP hydrolysis of translational GTPases. To date, this is only the second rRNA backbone residue shown to be critical in ribosome function.
Malaria continues to select for sickle cell trait in Central Africa
Authors: Elguero Eric , Délicat-Loembet Lucrèce M. , Rougeron Virginie , Arnathau Céline , Roche Benjamin , Becquart Pierre , Gonzalez Jean-Paul , Nkoghe Dieudonné , Sica Lucas , Leroy Eric M. , Durand Patrick , Ayala Francisco J. , Ollomo Benjamin , Renaud François , Prugnolle Franck
Published: May 2015

Significance

Sickle cell disease (SCD) is a major cause of death for young children in Africa, which the World Health Organization has declared a public health priority. It is increasingly spreading outside of Africa because of population migrations, and, thus, it will become in the near future a global health concern. It is therefore important to understand how this genetic disorder is maintained in human populations. Although the association between
Plasmodium falciparum
malaria and SCD is well known, the strength of this association is far from known. Using an extensive cohort of 3,959 persons, distributed over the entire Gabonese Republic, this study shows that
P. falciparum
malaria continues to exert strong selective pressure in favor of the sickle cell allele.
Self-motion perception in autism is compromised by visual noise but integrated optimally across multiple senses
Authors: Zaidel Adam , Goin-Kochel Robin P. , Angelaki Dora E.
Published: May 2015

Significance

Descriptions of impaired coherent motion perception in autism spectrum disorder (ASD) underlie theories that individuals with ASD have difficulty integrating local “parts” into a global percept. This notion maintains widespread influence and motivates recent theories of defective multisensory integration in ASD. However, heightened sensitivity to sensory noise, used to manipulate task difficulty in predominant visual motion stimuli, may provide an alternative explanation for impaired performance. Here we indeed found increased sensitivity in ASD to sensory noise. Noiseless motion perception and multisensory integration (even with noise) were unimpaired. These findings question prevalent theories of global and multisensory integration deficits in ASD. Rather, they suggest increased reliance on—and sensitivity to—incoming sensory information and less use of prior knowledge in ASD.
Nitrogen emissions from animal agricultural systems and strategies to protect the environment.
Authors: Kohn R. A.
Published: May 2015

Animal production systems are among the largest contributors of reactive nitrogen to the environment. Nitrogen (N) is lost from animal agriculture through volatilization to the atmosphere (NH3, N2O, NO) and runoff and leaching to water resources (NH4+, NO3-, organic N). Most N losses from agriculture are in a form (NH4+, NH3, NO3-) that does not directly affect climate change. However, these compounds have serious environmental consequences of their own, including contributing to haze, acidity of rain, eutrophication of surface water bodies and damage to forests. In addition, a significant amount of nitrous oxide (N2O) emissions result from animal agriculture because the ammonium and nitrates from agriculture are converted to N2O during manure storage and crop production. N2O is a potent greenhouse gas. Although animals emit very little nitrogen directly to the air, animal excreta (urine and faeces) contains environmentally reactive nitrogen, which begins moving to the air and water from the moment it leaves the animal, unless it is incorporated into a crop or converted to molecular nitrogen (N2). Nitrogen is lost from the barn floor or pen, storage facility and from cropland during manure application and crop growth. Additional nitrogen is lost to the environment when producing feeds for animals using nitrogen fertilizer. Strategies to control or mitigate nitrogen losses must simultaneously consider multiple forms of losses (e.g. NH4+, NH3, N2O and NOx) in various media (e.g. air, water) for multiple processes (e.g. animal feeding, crop production, manure storage). Otherwise, management practices merely shift the losses from one form or source to another. Fortunately, process-based models assist with estimating emissions and optimizing management choices. Increased nutrient utilization efficiency of animals and crops has had the greatest impact on decreasing reactive nitrogen losses to the environment of all management strategies employed to date. Nonetheless, increased demand for animal products has continued to present environmental challenges.
Proteomics in studying the molecular mechanism of fibre degradation.
Authors: Singh N. K.
Published: May 2015

The degradation of plant cell walls by ruminants is of major economic importance in the developed as well as the developing world. Rumen fermentation and degradation of cell wall relies on the cooperation between the microorganisms that produce fibrolytic enzymes and the host animal, which provides an anaerobic fermentation chamber. From the 19th century, the efficiency with which the rumen microbiota degrades fibre has been the subject of extensive research. In this chapter, we will discuss various proteomic approaches such as protein fractionation (chromatography, isoelectric focusing), protein separation (two-dimensional gel electrophoresis, SDS polyacrylamide gel electrophoresis), in-gel digestion to peptides (matrix-assisted laser desorption ionization, mass spectrometry or electrospray mass spectrometry), peptide separation (two-dimensional liquid chromatography), complex protein solution digestion to peptides (electrospray ionization or MALDI-tandem MS) and proteomics of fibrolytic bacteria, which can be used to improve our knowledge of the functional framework of plant cell wall degradation in the rumen.
Indigenous livestock resources in a changing climate: Indian perspective.
Authors: Ahlawat S. P. S. , Pushpendra Kumar Pushpendra Kumar , Kush Shrivastava Kush Shrivastava , Sahoo N. R.
Published: May 2015

Biological diversity, the variability of life on earth, exists in the form of different species and breeds within the animal kingdom. This diversity is created in the process of molecular/biochemical/metabolic reactions, and acts as a critical measure of adaptation in changing climatic conditions. Indigenous breeds have adapted to climatic variations since time immemorial, and hence have acquired unique traits that make them suitable in given agroclimatic zones; for example, the Indian cattle breeds, Tharparkar and Sahiwal, are heat and tick resistant. Similar cases have also been observed worldwide in Asia, Africa, Europe, Latin America, North America and the south-west Pacific region, having a total of 1144, 1300, 345, 104 and 108 breeds of major livestock species, respectively. Native breeds, namely N'Dama cattle, Red Massai sheep, etc., have developed trypanosomiasis resistance and gastrointestinal nematode tolerance by continuous natural selection. The overwhelming majority of indigenous livestock around the world are bred locally and kept by small-scale livestock keepers; hence, there is a need to promote local indigenous livestock species, as they represent a genetic resource that is relatively resilient to climate variability.
Thermodynamic and kinetic control of methane emissions from ruminants.
Authors: Kohn R. A.
Published: May 2015

CH4 emissions occur directly from animal digestion (enteric) and from animal waste that is stored under anaerobic conditions. In both regards, CH4 emissions depends on kinetic and thermodynamic factors. With kinetic control, the profile of products formed depends on the relative rates of the different competing reactions. In turn, the rates of reactions depend on substrate concentrations and enzyme activities, and these enzyme activities depend on microbial growth or enzyme synthesis. With thermodynamic control, which pathway branches are available and the direction of metabolite flow depends on the concentrations of reactants and products. Biologists have focused on controlling the kinetic elements of fermentation such as enzyme function, microbial activity, gene expression or provision of substrates. However, fermentation is often controlled by thermodynamics. In chemistry, thermodynamics is quantified using Gibbs energy calculations. Whether or not a reaction can proceed spontaneously in the forward direction is represented by the change in Gibbs energy (ΔG), which can be calculated based on the ratio of products and reactants in the system. Using this calculation, a strongly negative ΔG indicates that a reaction could proceed strongly in the forward direction without the addition of energy to the system. A strongly positive value of ΔG indicates the reaction cannot proceed in the forward direction without the addition of energy to the system, and it may even run in the reverse direction. The analysis of thermodynamics in different situations in the rumen or manure storage facility can identify when CH4 may be controlled kinetically by affecting the rates of reactions, or thermodynamically by affecting substrate or product concentrations.
Feed-based approaches in enteric methane amelioration.
Authors: Malik P. K. , Bhatta R. , Soren N. M. , Sejian V. , Mech A. , Prasad K. S. , Prasad C. S.
Published: May 2015

Mitigation of methane (CH4) emissions from ruminants is necessary not only from the global warming point of view but also for saving dietary energy. Livestock being the significant contributors to the anthropogenic CH4 pool have remained the prime target of global research for the past two decades, in order to find suitable, sustainable and economical possibilities of reducing enteric CH4 emission. The adoption of a particular strategy by the stakeholders depends on the input cost, economic status, toxicity to host/inhabiting microbes, mitigation potential and persistency in long run. Among all the available options, feed-based intervention seems remarkable, and can be tried anywhere by making little alterations to the available feed resources and prevailing feeding practices. This chapter deliberates the pros and cons of various nutritional interventions, along with their future prospects to reduce enteric CH4 emission. Issues like necessity of methanogenesis in the rumen, the feasibility of reducing livestock numbers and cutting down emissions, and the expected reimbursements that arise from this practically feasible reduction, are well debated in the chapter.
Insect resistance to Bt toxins in Brazil and Latin America.
Authors: Monnerat R. , Martins E. , Queiroz P. , Praça L. , Soares C. M.
Published: May 2015

Bioinsecticides based on Bacillus thuringiensis (Bt) and transgenic plants expressing its toxins have been widely used to control insects in Latin America. In Brazil, during the season of 2013/14, 4 million ha were treated with Bt biopesticides, and the area of transgenic crops under cultivation reached 40.3 million ha. Countries such as Honduras, Guatemala, Costa Rica, Nicaragua and Brazil reported cases of resistance of Plutella xylostella to Bt biopesticides. Insect resistance to toxins expressed in Bt crops was reported in Puerto Rico and Brazil, and reports of low efficacy were also communicated from several regions of Brazil and Argentina. Faced to this scenario, it is important that companies providing technologies, extension services, farmers and the scientific community and governments of countries either using Bt as bioinsecticides or as Bt crops unite in their efforts to establish guidelines that will enable greater durability of Bt technology.
Mechanism of Cry1Ac resistance in cabbage loopers - a resistance mechanism selected in insect populations in an agricultural environment.
Authors: Wang P.
Published: May 2015

The development of resistance to Bacillus thuringiensis (Bt) in insect populations in agriculture not only depends on the level of resistance conferred by a selected resistance mechanism, but also on the fitness cost associated with the resistance mechanism under specific ecological and environmental conditions. Bt resistance in the cabbage looper (Trichoplusia ni), which was identified by Janmaat and Myers (2003), is a case of Bt resistance evolved in an agricultural system, and is used in this chapter to review and discuss the mechanism of Cry1Ac resistance that is selected in an agricultural environment.
Roles of ABC proteins in the mechanism and management of Bt resistance.
Authors: Heckel D. G.
Published: May 2015

Genetic studies of strains of insects that have developed resistance to pore-forming Cry toxins from Bacillus thuringiensis (Bt) have provided useful and unexpected insights into the mode of action of the toxin. Independent approaches in five species of Lepidoptera have converged on the same result: that mutations in a member of the superfamily of ABC transporters confer resistance to Cry toxins. These mutations range from a single amino acid insertion to truncations that delete most of the protein. This result is surprising, because since the first detection of the specific binding of Cry toxins to sites in the lepidopteran midgut in 1988, no studies had documented any sort of interaction between Cry toxins and ABC proteins. It is hypothesized that ABC transporters mediate the critical step of Cry pore insertion into the membrane. Heterologous expression of ABC proteins has recently shown that they can facilitate cell swelling by Cry toxins, which is indirect evidence of pore formation. It is suggested that the 'ATP-switch' mechanism of ABC proteins that drives the transport of small molecules across cell membranes might be exploited to potentiate Bt action and to guide the design of improved Cry toxins.