bluuebunny/crossref_metadata_2025 huggingface dataset:
The New Moses and the Wisdom of God: A Convergence of Themes in Matthew 11:25–30
Authors: Sharbaugh Patricia
Published: January 2014

This article focuses on the confluence of Wisdom and Mosaic themes in Matthew 11:25–30, asserting that the convergence of these two themes points to an association between wisdom traditions and salvation history that is often overlooked. The two traditions evolved as Israel, trying to live life in obedience to Torah, encountered sin, suffering, trial, mystery, and an often turbulent history. As Israel encountered new and often painful life experiences, they remembered and appealed to tensive metaphors and traditions in order to understand the new experience and to provide stability in the midst of changing history. Recognizing that God's revelation in Jesus is a mystery both transcending and occurring within human experience, Matthew uses traditional tensive metaphors in order to emphasize that while the revelation of God's salvation in Jesus Christ is new, it is grounded in and continuous with salvation history. At the same time, this mystery transcends former expression. By describing Jesus as both a new Moses and personified Wisdom, Matthew imaginatively combines the symbolic worlds evoked by these two metaphors. The convergence of these symbolic worlds assures that Christological reflection moves beyond the familiar and is open to the mystery of God's revelation in Christ.
Stokes waves in water with a non-flat bed
Authors: Constantin A.
Published: January 2014

We investigate the relevance of Stokes waves for the propagation of ocean swell in the absence of strong currents. By providing estimates for the depth of the near-surface layer to which the main effects of a Stokes flow are confined, we show that wind-generated uniform wave trains can be modelled as Stokes waves over a fictitious flat bed, immersed in the water. Throughout the lower parts of this layer the deviations of the flow from a pure current are negligible.
Altered Functional Organization within and between Resting-State Networks in Chronic Subcortical Infarction
Authors: Wang Caihong , Qin Wen , Zhang Jing , Tian Tian , Li Ying , Meng Liangliang , Zhang Xuejun , Yu Chunshui
Published: January 2014

This study aimed to investigate the changes in functional connectivity (FC) within each resting-state network (RSN) and between RSNs in subcortical stroke patients who were well recovered in global motor function. Eleven meaningful RSNs were identified via functional magnetic resonance imaging data from 25 subcortical stroke patients and 22 normal controls using independent component analysis. Compared with normal controls, stroke patients exhibited increased intranetwork FC in the sensorimotor (SMN), visual (VN), auditory (AN), dorsal attention (DAN), and default mode (DMN) networks; they also exhibited decreased intranetwork FC in the frontoparietal network (FPN) and anterior DMN. Stroke patients displayed a shift from no FC in controls to negative internetwork FC between the VN and AN as well as between the VN and SMN. Stroke patients also exhibited weakened positive (anterior and posterior DMN; posterior DMN and right FPN) or negative (AN and right FPN; posterior DMN and dorsal SMN) internetwork FC when compared with normal controls. We suggest that subcortical stroke may induce connectivity changes in multiple functional networks, affecting not only the intranetwork FC within RSNs but also the internetwork FC between these RSNs.
Self-sustaining reactions as a tool to study mechanochemical activation
Authors: Takacs L.
Published: January 2014

Ever since Faraday reported on the reduction of AgCl with Zn and Sn the “dry way”, the study of Mechanically induced Self-propagating Reactions (MSRs) has been an important area within mechanochemistry. An interesting phenomenon is the mutual suppression of ignition in some mixed metal–chalcogen systems, such as in (1 − x)(Sn + Se) + x(Zn + Se) powders. Here both the Sn + Se and Zn + Se mixtures react in a self-sustaining manner after some activation time, but when they are combined, the reaction is gradual in the middle of the concentration scale. Mechanically induced metal–chalcogen combination reactions were studied by Chakurov et al. in the 1980s, using a low-energy vibratory mill. Similar measurements were carried out in our laboratory using the more energetic SPEX 8000 shaker mill. The results show qualitative similarities, but the details are different. It is suggested that the loss of MSR in mixed systems is the consequence of the very different properties of the binary systems, so that either one of the components (Zn) or a product formed gradually without ignition (e.g. SnSe) can act as an inert component relative to the rest of the system. Several examples are presented and the effect of the milling conditions is discussed. Finding new systems with similar behaviour and detailed studies of the activated state are needed to understand MSR in these systems.
Unfolding a design rule for microparticle buffering and dropping in microring-resonator-based add-drop devices
Authors: Wang Jiawei , Poon Andrew W.
Published: January 2014

We propose and demonstrate a design rule for determining microparticle buffering and dropping in microring-resonator-based add-drop devices at cavity resonances.
A novel approach to synthesize polymers for potential photodynamic therapy: from benzenedinitrile to phthalocyanine
Authors: Wang Laibing , Li Jun , Zhang Weidong , Chen Gaojian , Zhang Wei , Zhu Xiulin
Published: January 2014

RAFT synthesized polymers with benzenedinitrile side chains were converted to phthalocyanine conveniently, providing a novel method for making PDT polymers.
Electrospun glycopolymer fibers for lectin recognition
Authors: Wang Lei , Williams Gareth R. , Nie Hua-li , Quan Jing , Zhu Li-min
Published: January 2014

Thermoresponsive glycopolymers have been prepared by a free radical polymerisation process, and subsequently processed into blended fibers with poly-l-lactide-co-ε-caprolactone (PLCL) using electrospinning.
Benzoate dioxygenase fromRalstonia eutrophaB9 – unusual regiochemistry of dihydroxylation permits rapid access to novel chirons
Authors: Griffen Julia A. , Kenwright Sarah J. , Abou-Shehada Sarah , Wharry Scott , Moody Thomas S. , Lewis Simon E.
Published: January 2014

Oxidation of benzoic acid by a microorganism expressing benzoate dioxygenase leads to the formation of an unusualipso,orthoarenecis-diol in sufficient quantities to be useful for synthesis.
Reactions of mono- and bicyclic enol ethers with the I2–hydroperoxide system
Authors: Terent'ev Alexander O. , Zdvizhkov Alexander T. , Kulakova Alena N. , Novikov Roman A. , Arzumanyan Ashot V. , Nikishin Gennady I.
Published: January 2014

Reactions of mono- and bicyclic enol ethers with I2–H2O2, I2–ButOOH, and I2–tetrahydropyranyl hydroperoxide systems possessing unique and unpredictable reactivity have been studied.
Evolution of excitation wavelength dependent photoluminescence in nano-CeO2 dispersed ferroelectric liquid crystals
Authors: Goel Puja , Arora Manju , Biradar A. M.
Published: January 2014

The optical properties of nano-ceria (nano-CeO2) particles dispersed in ferroelectric liquid crystals (FLCs) have been investigated by excitation wavelength dependent photoluminescence (PL) spectroscopy.
Layered polyaniline/graphene film from sandwich-structured polyaniline/graphene/polyaniline nanosheets for high-performance pseudosupercapacitors
Authors: Tong Zhongqiu , Yang Yongning , Wang Jiayu , Zhao Jiupeng , Su Bao-Lian , Li Yao
Published: January 2014

Binder-free layered graphene/polyaniline composite supercapacitor film was prepared by an environmentally friendly route. It exhibited 384 F g−1 at 0.5 A g−1 and 84% capacitance retention over 1000 cycles.
Fabrication of ordered mesoporous carbon hollow fiber membranes via a confined soft templating approach
Authors: Li Jiansheng , Qi Junwen , Liu Chao , Zhou Liang , Song Hao , Yu Chengzhong , Shen Jinyou , Sun Xiuyun , Wang Lianjun
Published: January 2014

A new method to prepare ordered mesoporous carbon (OMC) hollow fiber membranes through a confined soft templating route is developed. The gas permeance results indicate that the OMC hollow fiber membranes exhibit Knudsen diffusion behavior confirming their good quality.
Honeycomb-like single-wall carbon nanotube networks
Authors: Li Shisheng , Hou Peng-Xiang , Liu Chang , Liu Tianyuan , Li Wen-Shan , Li Jin-Cheng , Cheng Hui-Ming
Published: January 2014

A honeycomb-like single-wall carbon nanotube (SWCNT) network was constructed. Different from random SWCNT networks, the honeycomb-like network shows much higher conductivity, transparency and electrical response to chemical doping.
Hollow cathode plasma-assisted atomic layer deposition of crystalline AlN, GaN and AlxGa1−xN thin films at low temperatures
Authors: Ozgit-Akgun Cagla , Goldenberg Eda , Okyay Ali Kemal , Biyikli Necmi
Published: January 2014

The authors report on the use of hollow cathode plasma for low-temperature plasma-assisted atomic layer deposition (PA-ALD) of crystalline AlN, GaN and AlxGa1−xN thin films with low impurity concentrations.
Perspective: Structural dynamics in condensed matter mapped by femtosecond x-ray diffraction
Authors: Elsaesser T. , Woerner M.
Published: January 2014

Ultrashort soft and hard x-ray pulses are sensitive probes of structural dynamics on the picometer length and femtosecond time scales of electronic and atomic motions. Recent progress in generating such pulses has initiated new directions of condensed matter research, exploiting a variety of x-ray absorption, scattering, and diffraction methods to probe photoinduced structural dynamics. Atomic motion, changes of local structure and long-range order, as well as correlated electron motion and charge transfer have been resolved in space and time, providing a most direct access to the physical mechanisms and interactions driving reversible and irreversible changes of structure. This perspective combines an overview of recent advances in femtosecond x-ray diffraction with a discussion on ongoing and future developments.
Secondary flows in a laterally heated horizontal cylinder
Authors: Mercader Isabel , Sánchez Odalys , Batiste Oriol
Published: January 2014

In this paper we study the problem of thermal convection in a laterally heated, finite, horizontal cylinder. We consider cylinders of moderate aspect ratio (height/diameter ≈2) containing a small Prandtl number fluid (σ < 0.026) typical of molten metals and molten semiconductors. We use the Navier-Stokes and energy equations in the Boussinesq approximation to calculate numerically the basic steady states, analyze their linear stability, and compute some nonlinear secondary flows originated from the instabilities. All the calculated flows and the stability analysis are characterized by their symmetry properties. Due to the confined cylindrical geometry, -presence of lateral walls and lids-, all the flows are completely three dimensional even for the basic steady states. In the range of Prandtl numbers studied, we have identified four different types of instabilities, either oscillatory or stationary. The physical mechanisms, shear or buoyancy, of the corresponding flow transitions have been analyzed. As the value of the Prandtl number approaches σ = 0.026 the scenario of bifurcations becomes more complicated due to the existence of two different stable basic states originated in a saddle-node bifurcation; a fact that had been overlooked in previous works.
Electronic structure changes during the surface-assisted formation of a graphene nanoribbon
Authors: Bronner Christopher , Utecht Manuel , Haase Anton , Saalfrank Peter , Klamroth Tillmann , Tegeder Petra
Published: January 2014

High conductivity and a tunability of the band gap make quasi-one-dimensional graphene nanoribbons (GNRs) highly interesting materials for the use in field effect transistors. Especially bottom-up fabricated GNRs possess well-defined edges which is important for the electronic structure and accordingly the band gap. In this study we investigate the formation of a sub-nanometer wide armchair GNR generated on a Au(111) surface. The on-surface synthesis is thermally activated and involves an intermediate non-aromatic polymer in which the molecular precursor forms polyanthrylene chains. Employing angle-resolved two-photon photoemission in combination with density functional theory calculations we find that the polymer exhibits two dispersing states which we attribute to the valence and the conduction band, respectively. While the band gap of the non-aromatic polymer obtained in this way is relatively large, namely 5.25 ± 0.06 eV, the gap of the corresponding aromatic GNR is strongly reduced which we attribute to the different degree of electron delocalization in the two systems.
Analysis and comparison of two two-dimensional Halbach permanent magnet arrays for magnetically levitated planar motor
Authors: Zhang Lu , Kou Baoquan , Xing Feng , Zhang He
Published: January 2014

A novel 2-D Halbach permanent magnet array which can be used in magnetically levitated planar motor is proposed in this paper. The air-gap flux density distribution of the novel 2-D Halbach permanent magnet array is solved by the scalar magnetic potential equation. In order to compare with the well-known Halbach magnet array that was used by Jansen et al. [IEEE Trans. Ind. Appl. 44(4), 1108 (2008)], harmonic analysis of the x- and z- component of the air-gap flux density are carried out by Fourier decomposition. Comparison of Bx and Bz between the two 2-D Halbach magnet arrays are made. And it is verified that the performance of the new Halbach magnet array is superior to the existing Halbach magnet arrays, its higher magnetic flux density and lower high-order harmonics will help to improve the performance of the magnetically levitated planar motor.
Note: Low energy inverse photoemission spectroscopy apparatus
Authors: Yoshida Hiroyuki
Published: January 2014

An apparatus for the low-energy inverse photoemission spectroscopy is described. In this technique, low energy electron having kinetic energy below 4 eV is incident to the sample and detect the emitted photons in the near ultraviolet range (below 5 eV, longer than 250 nm) to investigate the unoccupied states of the solid materials. Compared with the prototype apparatus reported previously [H. Yoshida, Chem. Phys. Lett. 539–540, 180–185 (2012)], the collection efficiency of photons is improved by a factor of four and practically any conductive substrates can be used. The overall resolution is 0.27 eV.
Impacts of first-order phase transition and phase coexistence on the universal behavior of inverse magnetocaloric effect
Authors: Biswas Anis , Bingham N. S. , Phan T. L. , Dan N. H. , Yu S. C. , Phan M. H. , Srikanth H.
Published: January 2014

A systematic study of the inverse magnetocaloric effect (IMCE) in Ni50Mn35.8Sn14.2 and Pr0.5Sr0.5MnO3 has been performed to understand the impacts of first-order phase transition (FOPT) and phase coexistence on the universality of the temperature-dependent magnetic entropy change, ΔSM(T). We show that for Ni50Mn35.8Sn14.2—a system exhibiting IMCE associated with FOPT—it is possible to construct a universal master curve to describe ΔSM(T) in different applied fields without rescaling a temperature axis. However, the universality of IMCE does not hold for Pr0.5Sr0.5MnO3—a system with coexisting ferromagnetic and antiferromagnetic phases. The proposed universal curve provides a simple method for extrapolating ΔSM in a wide range of fields and temperatures, thus giving useful guidance to the design of magnetocaloric materials for active magnetic refrigeration technology.
Diffusion of In0.53Ga0.47As elements through hafnium oxide during post deposition annealing
Authors: Cabrera W. , Brennan B. , Dong H. , O'Regan T. P. , Povey I. M. , Monaghan S. , O'Connor É. , Hurley P. K. , Wallace R. M. , Chabal Y. J.
Published: January 2014

Diffusion of indium through HfO2 after post deposition annealing in N2 or forming gas environments is observed in HfO2/In0.53Ga0.47As stacks by low energy ion scattering and X-ray photo electron spectroscopy and found to be consistent with changes in interface layer thickness observed by transmission electron microscopy. Prior to post processing, arsenic oxide is detected at the surface of atomic layer deposition-grown HfO2 and is desorbed upon annealing at 350 °C. Reduction of the interfacial layer thickness and potential densification of HfO2, resulting from indium diffusion upon annealing, is confirmed by an increase in capacitance.
Analysis of and remedies for unphysical ground states of the multireference averaged coupled-pair functional
Authors: Krisiloff David B. , Oyeyemi Victor B. , Libisch Florian , Carter Emily A.
Published: January 2014

A Multireference Configuration Interaction (MRCI) wavefunction includes both static and dynamic electron correlation. MRCI's well-known flaw, a lack of size extensivity, can be ameliorated with the Multireference Averaged Coupled-Pair Functional (MRACPF). However, the original MRACPF is frequently unstable, sometimes producing unphysical results. The more Multireference Averaged Quadratic Coupled-Cluster and MRACPF2 functionals also occasionally exhibit unphysical behavior. We find that these instabilities are avoided crossings with unphysical solutions to the MRACPF equations. We present two approaches to avoid the undesirable unphysical solutions.
Comparison of direct numerical simulation databases of turbulent channel flow at Reτ = 180
Authors: Vreman A. W. , Kuerten J. G. M.
Published: January 2014

Direct numerical simulation (DNS) databases are compared to assess the accuracy and reproducibility of standard and non-standard turbulence statistics of incompressible plane channel flow at Reτ = 180. Two fundamentally different DNS codes are shown to produce maximum relative deviations below 0.2% for the mean flow, below 1% for the root-mean-square velocity and pressure fluctuations, and below 2% for the three components of the turbulent dissipation. Relatively fine grids and long statistical averaging times are required. An analysis of dissipation spectra demonstrates that the enhanced resolution is necessary for an accurate representation of the smallest physical scales in the turbulent dissipation. The results are related to the physics of turbulent channel flow in several ways. First, the reproducibility supports the hitherto unproven theoretical hypothesis that the statistically stationary state of turbulent channel flow is unique. Second, the peaks of dissipation spectra provide information on length scales of the small-scale turbulence. Third, the computed means and fluctuations of the convective, pressure, and viscous terms in the momentum equation show the importance of the different forces in the momentum equation relative to each other. The Galilean transformation that leads to minimum peak fluctuation of the convective term is determined. Fourth, an analysis of higher-order statistics is performed. The skewness of the longitudinal derivative of the streamwise velocity is stronger than expected (−1.5 at y+ = 30). This skewness and also the strong near-wall intermittency of the normal velocity are related to coherent structures.
Gelator-doped liquid-crystal phase grating with multistable and dynamic modes
Authors: Lin Hui-Chi , Yang Meng-Ru , Tsai Sheng-Feng , Yan Shih-Chiang
Published: January 2014

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.
Strong non-volatile voltage control of magnetism in magnetic/antiferroelectric magnetoelectric heterostructures
Authors: Zhou Z. , Zhang X. Y. , Xie T. F. , Nan T. X. , Gao Y. , Yang X. , Wang X. J. , He X. Y. , Qiu P. S. , Sun N. X. , Sun D. Z.
Published: January 2014

Strong magnetoelectric coupling was demonstrated in magnetic/antiferroelectric heterostructures of FeGaB/Pb(La,Sn,Zr,Ti)O3, which exhibited a voltage induced coercive field change of 7–10 Oe and ferromagnetic resonance field shifts by ∼80 Oe. Nonvolatile voltage induced magnetization switching and ferromagnetic resonance field shift in FeGaB were realized based on the ferroelectric-antiferroelectric phase transition in Pb(La,Sn,Zr,Ti)O3. The nonvolatile strong voltage control of magnetism in magnetic/antiferroelectric heterostructures has great implications in compact and power efficient spintronics and RF/microwave components.
3 μm aperture probes for near-field terahertz transmission microscopy
Authors: Macfaden Alexander J. , Reno John L. , Brener Igal , Mitrofanov Oleg
Published: January 2014

The transmission of electromagnetic waves through a sub-wavelength aperture is described by Bethe's theory. This imposes severe limitations on using apertures smaller than ∼1/100 of the wavelength for near-field microscopy at terahertz (THz) frequencies. Experimentally, we observe that the transmitted evanescent field within 1 μm of the aperture deviates significantly from the Bethe dependence of E ∝ a3. Using this effect, we realized THz near-field probes incorporating 3 μm apertures and we demonstrate transmission mode THz time-domain near-field imaging with spatial resolution of 3 μm, corresponding to λ/100 (at 1 THz).
A heterozygous mutation of
GALNTL5
affects male infertility with impairment of sperm motility
Authors: Takasaki Nobuyoshi , Tachibana Kouichi , Ogasawara Satoshi , Matsuzaki Hideki , Hagiuda Jun , Ishikawa Hiromichi , Mochida Keiji , Inoue Kimiko , Ogonuki Narumi , Ogura Atsuo , Noce Toshiaki , Ito Chizuru , Toshimori Kiyotaka , Narimatsu Hisashi
Published: January 2014

Significance

Polypeptide
N
-acetylgalactosaminyltransferase-like protein 5 (GALNTL5) belongs to the pp-GalNAc-T family, but its in vivo activity has not yet been identified. To investigate the functions of GALNTL5, we attempted to establish
Galntl5
-deficient mice and found that the heterozygous mutation of
Galntl5
causes infertility in male mice because of immotile sperm. In these mice, glycolytic enzymes required for sperm motility were decreased, their protein loading into acrosomes was disrupted, and aberrant localization of the ubiquitin–proteasome system was observed. We found a patient diagnosed with asthenozoospermia, poor sperm motility, who had a mutation of the
GALNTL5
gene in sperm and blood cells. Our data suggest that GALNTL5 is an essential functional molecule for sperm development, and the
GALNTL5
mutation may cause human asthenozoospermia.
What Happens Next?: How Ovarian Cancer Forces a Woman into a New Draft of Her Life Script
Authors: Carr Philippa
Published: January 2014

A diagnosis of ovarian cancer has an impact on many areas of a woman's life which define her identity and life story. Women are forced to reconsider the future ‘scenes’ of their life scripts as they deal with the loss of fertility, a challenge to plans and existential threat. This paper considers this experience within the theoretical framework of the Self-Memory System.

Alongside this theory, the author shares her use of dramatherapy tools applied to weekend residential courses run across the UK on four occasions to support women affected by ovarian cancer.
When the Child Proof Cap has Been Left off the Medicine Bottle – Dramatherapy with Young People Affected by Parental Drug and Alcohol Problems
Authors: Chown Toby
Published: January 2014

Young people affected by drug and alcohol use in their family face profound challenges. This paper looks at how young people are affected by their parents’ drug and alcohol problems and how dramatherapy can offer a space for them to engage with problems such as conflicted loyalties, neglect, abandonment, rage, isolation and premature responsibility. It draws on four years of experience offering individual and group dramatherapy to young people, and current approaches to the problem from psychology, social work, psychotherapy and the arts therapies. Each help to understand and illustrate the uses of a psychological and dramatic space to engage with the diverse problems parental drug and alcohol use create for a child.
Anticipation by basketball defenders: An explanation based on the three‐dimensional inverted pendulum model
Authors: Fujii Keisuke , Shinya Masahiro , Yamashita Daichi , Kouzaki Motoki , Oda Shingo
Published: January 2014

We previously estimated the timing when ball game defenders detect relevant information through visual input for reacting to an attacker's running direction after a cutting manoeuvre, called cue timing. The purpose of this study was to investigate what specific information is relevant for defenders, and how defenders process this information to decide on their opponents' running direction. In this study, we hypothesised that defenders extract information regarding the position and velocity of the attackers' centre of mass (CoM) and the contact foot. We used a model which simulates the future trajectory of the opponent's CoM based upon an inverted pendulum movement. The hypothesis was tested by comparing observed defender's cue timing, model‐estimated cue timing using the inverted pendulum model (IPM cue timing) and cue timing using only the current CoM position (CoM cue timing). The IPM cue timing was defined as the time when the simulated pendulum falls leftward or rightward given the initial values for position and velocity of the CoM and the contact foot at the time. The model‐estimated IPM cue timing and the empirically observed defender's cue timing were comparable in median value and were significantly correlated, whereas the CoM cue timing was significantly more delayed than the IPM and the defender's cue timings. Based on these results, we discuss the possibility that defenders may be able to anticipate the future direction of an attacker by forwardly simulating inverted pendulum movement.
The End of the Thermodynamics of Computation: A No-Go Result
Authors: Norton John D.
Published: January 2014

The thermodynamics of computation assumes that computational processes at the molecular level can be brought arbitrarily close to thermodynamic reversibility and that thermodynamic entropy creation is unavoidable only in data erasure or the merging of computational paths, in accord with Landauer’s principle. The no-go result shows that fluctuations preclude completion of thermodynamically reversible processes. Completion can be achieved only by irreversible processes that create thermodynamic entropy in excess of the Landauer limit.
Quantum Chemistry and Organic Theory
Authors: Goodwin William
Published: January 2014

In this essay I consider whether the theory of organic chemistry is reducible to the theory of quantum chemistry. Using philosophical machinery developed by James Woodward, I characterize the understanding provided by both theories. Then I argue that there are systematic reasons to suspect that quantum chemistry is incapable of supporting some of the significant explanations, predictions, and applications underwritten by an understanding of theoretical organic chemistry. Consequently, even should quantum chemistry be ‘reducible to’ quantum physics in some suitable sense, there are good reasons to doubt that many of the significant results of organic chemistry could be reproduced by quantum chemistry alone.
Understanding Nonmodular Functionality: Lessons from Genetic Algorithms
Authors: Kuorikoski Jaakko , Pöyhönen Samuli
Published: January 2014

Evolution is often characterized as a tinkerer creating efficient but messy solutions. We analyze the nature of the problems that arise when trying to explain and understand cognitive phenomena created by this haphazard design process. We present a theory of explanation and understanding and apply it to a case problem—solutions generated by genetic algorithms. By analyzing the nature of solutions that genetic algorithms present to computational problems, we show, first, that evolutionary designs are often hard to understand because they exhibit nonmodular functionality and, second, that breaches of modularity wreak havoc on our strategies of causal and constitutive explanation.
Rethinking Functional Reference
Authors: Scarantino Andrea
Published: January 2014

The theoretical construct of functional reference is the main tool used by animal communication researchers to explore how animals refer to the world in the absence of a language. Functionally referential signals are commonly defined as signals elicited by a specific class of stimuli and capable of causing behaviors adaptive to such stimuli in the absence of contextual cues. I will argue that this definition is conceptually flawed and propose an alternative definition according to which signals can functionally refer to things that rarely cause them while relying on the essential contribution of contextual cues.
An Epistemology of Causal Inference from Experiment
Authors: Zwier Karen R.
Published: January 2014

The manipulationist account of causation provides a framework for assessing causal claims and the experiments used to test them. But its pertinence to the more general class of scientific experiments—particularly those experiments not explicitly designed for testing causal claims—is less clear. I aim to show (1) that the set of causal inferences afforded by any experiment is determined solely on the basis of contrasting case structures that I call “experimental series” and (2) that the conditions that suffice for causal inference obtain quite commonly, even among “ordinary” scientific experiments not explicitly designed for the testing of causal claims.
The Evolution of Bayesian Updating
Authors: Okasha Samir
Published: January 2014

An evolutionary basis for Bayesian rationality is suggested, by considering how natural selection would operate on an organism’s ‘policy’ for choosing an action depending on an environmental signal. It is shown that the evolutionarily optimal policy, as judged by the criterion of maximal expected reproductive output, is the policy that, for each signal, picks an action that maximizes conditional expected output given that signal. This suggests a possible route by which Bayes-rational creatures might have evolved.
Colour–magnitude diagrams of transiting Exoplanets – I. Systems with parallaxes
Authors: Triaud Amaury H. M. J.
Published: January 2014

Broad-band flux measurements centred around [3.6 μm] and [4.5 μm] obtained with Spitzer during the occultation of seven extrasolar planets by their host stars have been combined with parallax measurements to compute the absolute magnitudes of these planets. Those measurements are arranged in two colour–magnitude diagrams. Because most of the targets have sizes and temperatures similar to brown dwarfs, they can be compared to one another. In principle, this should permit inferences about exoatmospheres based on knowledge acquired by decades of observations of field brown dwarfs and ultracool stars’ atmospheres. Such diagrams can assemble all measurements gathered so far and will provide help in the preparation of new observational programmes. In most cases, planets and brown dwarfs follow similar sequences. HD 2094589b and GJ 436b are found to be outliers, so is the night side of HD 189733b. The photometric variability associated with the orbital phase of HD 189733b is particularly revealing. The planet exhibits what appears like a spectral type and chemical transition between its day and night sides: HD 189733b straddles the L–T spectral class transition, which would imply different cloud coverage on each hemisphere. Methane absorption could be absent at its hotspot but present over the rest of the planet.
The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach
Authors: Gonzalez Diego , Kozdon Jennifer B. , McAdams Harley H. , Shapiro Lucy , Collier Justine
Published: January 2014

DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.
Modeling the Effects of Cloudy Weather on Regional Epidemics of Soybean Rust
Authors: Dias A. P. S. , Li X. , Yang X. B.
Published: January 2014

This study simulated daily development of soybean rust (SBR), caused by Phakopsora pachyrhizi, based on cloud cover conditions. Results from a previous study that determined the relationship between shading and apparent infection rates were applied in this study to simulate SBR progress on a regional scale using a semi-empirical logistic model parameterized according to the observed cloud cover conditions. Depending on local weather data availability, cloudy days were assumed to be either (i) the days with less than 2 h of full sun or (ii) the days with complete cloud cover as measured by three daily observations. Estimated disease progress and final estimates of epidemic intensity were verified by 30 reports of seasonal disease progress in 11 regions of Brazil and South Africa from 2002 to 2007. The model predicted final disease severity and the observed final severity fall into a linear relationship with correlation coefficient r = 0.96 and a slope close to 1. Severe SBR epidemics occurred when 19.5 or more cloudy days were recorded during the period from initial disease detection to the date of final disease assessment near the end of a growing season in Brazil and South Africa. Mild epidemics were observed with less than eight cloudy days in a season.
Nitrous Oxide–related Postoperative Nausea and Vomiting Depends on Duration of Exposure
Authors: Peyton Philip J. , Wu Christine Yx
Published: January 2014

Background

Inclusion of nitrous oxide in the gas mixture has been implicated in postoperative nausea and vomiting (PONV) in numerous studies. However, these studies have not examined whether duration of exposure was a significant covariate. This distinction might affect the future place of nitrous oxide in clinical practice.

Methods

PubMed listed journals reporting trials in which patients randomized to a nitrous oxide or nitrous oxide–free anesthetic for surgery were included, where the incidence of PONV within the first 24 postoperative hours and mean duration of anesthesia was reported. Meta-regression of the log risk ratio for PONV with nitrous oxide (lnRR PONVN2O) versus duration was performed.

Results

Twenty-nine studies in 27 articles met the inclusion criteria, randomizing 10,317 patients. There was a significant relationship between lnRR PONVN2O and duration (r

2
= 0.51, P = 0.002). Risk ratio PONV increased 20% per hour of nitrous oxide after 45 min. The number needed to treat to prevent PONV by avoiding nitrous oxide was 128, 23, and 9 where duration was less than 1, 1 to 2, and over 2 h, respectively. The risk ratio for the overall effect of nitrous oxide on PONV was 1.21 (CIs, 1.04–1.40); P = 0.014.

Conclusions

This duration-related effect may be via disturbance of methionine and folate metabolism. No clinically significant effect of nitrous oxide on the risk of PONV exists under an hour of exposure. Nitrous oxide–related PONV should not be seen as an impediment to its use in minor or ambulatory surgery.
Experimental perspective on fallback foods and dietary adaptations in early hominins
Authors: Scott Jeremiah E. , McAbee Kevin R. , Eastman Meghan M. , Ravosa Matthew J.
Published: January 2014

The robust jaws and large, thick-enameled molars of the Plio–Pleistocene hominins
Australopithecus
and
Paranthropus
have long been interpreted as adaptations for hard-object feeding. Recent studies of dental microwear indicate that only
Paranthropus robustus
regularly ate hard items, suggesting that the dentognathic anatomy of other australopiths reflects rare, seasonal exploitation of hard fallback foods. Here, we show that hard-object feeding cannot explain the extreme morphology of
Paranthropus boisei
. Rather, analysis of long-term dietary plasticity in an animal model suggests year-round reliance on tough foods requiring prolonged postcanine processing in
P. boisei
. Increased consumption of such items may have marked the earlier transition from
Ardipithecus
to
Australopithecus
, with routine hard-object feeding in
P. robustus
representing a novel behaviour.
Are thyroid hormones mediators of incubation temperature-induced phenotypes in birds?
Authors: DuRant S. E. , Carter A. W. , Denver R. J. , Hepp G. R. , Hopkins W. A.
Published: January 2014

Incubation temperature influences a suite of traits in avian offspring. However, the mechanisms underlying expression of these phenotypes are unknown. Given the importance of thyroid hormones in orchestrating developmental processes, we hypothesized that they may act as an upstream mechanism mediating the effects of temperature on hatchling phenotypic traits such as growth and thermoregulation. We found that plasma T3, but not T4concentrations, differed among newly hatched wood ducks (Aix sponsa) from different embryonic incubation temperatures. T4at hatching correlated with time spent hatching, and T3correlated with hatchling body condition, tarsus length, time spent hatching and incubation period. In addition, the T3: T4ratio differed among incubation temperatures at hatch. Our findings are consistent with the hypothesis that incubation temperature modulates plasma thyroid hormones which in turn influences multiple aspects of duckling phenotype.
A linear-encoding model explains the variability of the target morphology in regeneration
Authors: Lobo Daniel , Solano Mauricio , Bubenik George A. , Levin Michael
Published: January 2014

A fundamental assumption of today's molecular genetics paradigm is that complex morphology emerges from the combined activity of low-level processes involving proteins and nucleic acids. An inherent characteristic of such nonlinear encodings is the difficulty of creating the genetic and epigenetic information that will produce a given self-assembling complex morphology. This ‘inverse problem’ is vital not only for understanding the evolution, development and regeneration of bodyplans, but also for synthetic biology efforts that seek to engineer biological shapes. Importantly, the regenerative mechanisms in deer antlers, planarian worms and fiddler crabs can solve an inverse problem: their target morphology can be altered specifically and stably by injuries in particular locations. Here, we discuss the class of models that use pre-specified morphological goal states and propose the existence of a linear encoding of the target morphology, making the inverse problem easy for these organisms to solve. Indeed, many model organisms such asDrosophila, hydra andXenopusalso develop according to nonlinear encodings producing linear encodings of their final morphologies. We propose the development of testable models of regeneration regulation that combine emergence with a top-down specification of shape by linear encodings of target morphology, driving transformative applications in biomedicine and synthetic bioengineering.
The energy components of stacked chromatin layers explain the morphology, dimensions and mechanical properties of metaphase chromosomes
Authors: Daban Joan-Ramon
Published: January 2014

The measurement of the dimensions of metaphase chromosomes in different animal and plant karyotypes prepared in different laboratories indicates that chromatids have a great variety of sizes which are dependent on the amount of DNA that they contain. However, all chromatids are elongated cylinders that have relatively similar shape proportions (length to diameter ratio approx. 13). To explain this geometry, it is considered that chromosomes are self-organizing structures formed by stacked layers of planar chromatin and that the energy of nucleosome–nucleosome interactions between chromatin layers inside the chromatid is approximately 3.6 × 10−20J per nucleosome, which is the value reported by other authors for internucleosome interactions in chromatin fibres. Nucleosomes in the periphery of the chromatid are in contact with the medium; they cannot fully interact with bulk chromatin within layers and this generates a surface potential that destabilizes the structure. Chromatids are smooth cylinders because this morphology has a lower surface energy than structures having irregular surfaces. The elongated shape of chromatids can be explained if the destabilizing surface potential is higher in the telomeres (approx. 0.16 mJ m−2) than in the lateral surface (approx. 0.012 mJ m−2). The results obtained by other authors in experimental studies of chromosome mechanics have been used to test the proposed supramolecular structure. It is demonstrated quantitatively that internucleosome interactions between chromatin layers can justify the work required for elastic chromosome stretching (approx. 0.1 pJ for large chromosomes). The high amount of work (up to approx. 10 pJ) required for large chromosome extensions is probably absorbed by chromatin layers through a mechanism involving nucleosome unwrapping.
Fascicles from energy-storing tendons show an age-specific response to cyclic fatigue loading
Authors: Thorpe Chavaunne T. , Riley Graham P. , Birch Helen L. , Clegg Peter D. , Screen Hazel R. C.
Published: January 2014

Some tendons, such as the human Achilles and equine superficial digital flexor tendon (SDFT), act as energy stores, stretching and recoiling to increase efficiency during locomotion. Our previous observations of rotation in response to applied strain in SDFT fascicles suggest a helical structure, which may provide energy-storing tendons with a greater ability to extend and recoil efficiently. Despite this specialization, energy-storing tendons are prone to age-related tendinopathy. The aim of this study was to assess the effect of cyclic fatigue loading (FL) on the microstructural strain response of SDFT fascicles from young and old horses. The data demonstrate two independent age-related mechanisms of fatigue failure; in young horses, FL caused low levels of matrix damage and decreased rotation. This suggests that loading causes alterations to the helix substructure, which may reduce their ability to recoil and recover. By contrast, fascicles from old horses, in which the helix is already compromised, showed greater evidence of matrix damage and suffer increased fibre sliding after FL, which may partially explain the age-related increase in tendinopathy. Elucidation of helix structure and the precise alterations occurring owing to both ageing and FL will help to develop appropriate preventative and repair strategies for tendinopathy.
Thermo-poromechanics of a fluid-filled cavity in a fluid-saturated geomaterial
Authors: Selvadurai A. P. S. , Suvorov A. P.
Published: January 2014

In this paper, we examine the coupled thermo-poromechanical behaviour of a fluid-saturated porous medium of infinite extent bounded internally by a fluid-filled cavity. The mechanical behaviour of the porous skeleton can either be Hookean elastic or elasto-plastic, with a constitutive response corresponding to a modified Cam Clay plasticity model. The fluid within the cavity can be subjected simultaneously to a temperature rise and a pressure pulse. The paper presents analytical results for the spherically symmetric thermo-poroelasticity problem and these are used to validate the thermo-poroelasticity module of a computational code. We proceed to examine the thermo-poroelasto-plasticity problem. Results presented in the paper illustrate the interaction between thermal and mechanical phenomena and their influence on the cavity fluid pressure and the skeletal stresses at the cavity boundary. The paper presents solutions that will be of value in benchmarking exercises.
Meta-ecosystem dynamics and functioning on finite spatial networks
Authors: Marleau Justin N. , Guichard Frédéric , Loreau Michel
Published: January 2014

The addition of spatial structure to ecological concepts and theories has spurred integration between sub-disciplines within ecology, including community and ecosystem ecology. However, the complexity of spatial models limits their implementation to idealized, regular landscapes. We present a model meta-ecosystem with finite and irregular spatial structure consisting of local nutrient–autotrophs–herbivores ecosystems connected through spatial flows of materials and organisms. We study the effect of spatial flows on stability and ecosystem functions, and provide simple metrics of connectivity that can predict these effects. Our results show that high rates of nutrient and herbivore movement can destabilize local ecosystem dynamics, leading to spatially heterogeneous equilibria or oscillations across the meta-ecosystem, with generally increased meta-ecosystem primary and secondary production. However, the onset and the spatial scale of these emergent dynamics depend heavily on the spatial structure of the meta-ecosystem and on the relative movement rate of the autotrophs. We show how this strong dependence on finite spatial structure eludes commonly used metrics of connectivity, but can be predicted by the eigenvalues and eigenvectors of the connectivity matrix that describe the spatial structure and scale. Our study indicates the need to consider finite-size ecosystems in meta-ecosystem theory.
Horizontal gene transfer in the acquisition of novel traits by metazoans
Authors: Boto Luis
Published: January 2014

Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.