bluuebunny/crossref_metadata_2025 huggingface dataset:
Fabrication of FeOx thin films and the modulation of transport and magnetic properties by resistance switching in Au/α-Fe2O3/Pt heterostructure
Authors: Yun C. , Chen X. G. , Fu J. B. , Zhang Y. X. , Sun J. R. , Wang Y. F. , Zhang Y. , Liu S. Q. , Lian G. J. , Yang Y. C. , Wang C. S. , Yang J. B.
Published: March 2014

It was found that by using the same α-Fe2O3 target in fabrication process, an oxygen-deficient and an oxygen-sufficient atmosphere facilitated the formation of Fe3O4 and α-Fe2O3, respectively. The Au/α-Fe2O3/Pt heterostructure showed a memristive bipolar resistance switching. A clear difference was observed in the transport and magnetic properties between the two resistance states. The enhanced conductivity and magnetization in the Au/α-Fe2O3/Pt heterostructure are believed to result from an enhanced electron hopping between Fe3+-Fe2+ pairs and Fe3+-O-Fe2+ double exchange coupling effect. The enhanced Fe2+ comes from a redox transition between two phases (one behaves like Fe3O4 and the other like α-Fe2O3), due to the electrochemical migration of oxygen vacancies.
Conservation properties and potential systems of vorticity-type equations
Authors: Cheviakov Alexei F.
Published: March 2014

Partial differential equations of the form \documentclass[12pt]{minimal}\begin{document}$\mathop {\hbox{\rm div}}{{\bm N}} =0$\end{document}divN=0, \documentclass[12pt]{minimal}\begin{document}${{\bm N}}_t + \mathop {\hbox{\rm curl}}{{\bm M}}=0$\end{document}Nt+curlM=0 involving two vector functions in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3$\end{document}R3 depending on t, x, y, z appear in different physical contexts, including the vorticity formulation of fluid dynamics, magnetohydrodynamics (MHD) equations, and Maxwell's equations. It is shown that these equations possess an infinite family of local divergence-type conservation laws involving arbitrary functions of space and time. Moreover, it is demonstrated that the equations of interest have a rather special structure of a lower-degree (degree two) conservation law in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^4(t,x,y,z)$\end{document}R4(t,x,y,z). The corresponding potential system has a clear physical meaning. For the Maxwell's equations, it gives rise to the scalar electric and the vector magnetic potentials; for the vorticity equations of fluid dynamics, the potentialization inverts the curl operator to yield the fluid dynamics equations in primitive variables; for MHD equations, the potential equations yield a generalization of the Galas-Bogoyavlenskij potential that describes magnetic surfaces of ideal MHD equilibria. The lower-degree conservation law is further shown to yield curl-type conservation laws and determined potential equations in certain lower-dimensional settings. Examples of new nonlocal conservation laws, including an infinite family of nonlocal material conservation laws of ideal time-dependent MHD equations in 2+1 dimensions, are presented.
Isothermal dehydration of thin films of water and sugar solutions
Authors: Heyd R. , Rampino A. , Bellich B. , Elisei E. , Cesàro A. , Saboungi M.-L.
Published: March 2014

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.
Atomic resolution scanning tunneling microscopy in a cryogen free dilution refrigerator at 15 mK
Authors: den Haan A. M. J. , Wijts G. H. C. J. , Galli F. , Usenko O. , van Baarle G. J. C. , van der Zalm D. J. , Oosterkamp T. H.
Published: March 2014

Pulse tube refrigerators are becoming more common, because they are cost efficient and demand less handling than conventional (wet) refrigerators. However, a downside of a pulse tube system is the vibration level at the cold-head, which is in most designs several micrometers. We implemented vibration isolation techniques which significantly reduced vibration levels at the experiment. These optimizations were necessary for the vibration sensitive magnetic resonance force microscopy experiments at milli-kelvin temperatures for which the cryostat is intended. With these modifications we show atomic resolution scanning tunneling microscopy on graphite. This is promising for scanning probe microscopy applications at very low temperatures.
Collision dynamics of proton with formaldehyde: Fragmentation and ionization
Authors: Wang Jing , Gao Cong-Zhang , Calvayrac Florent , Zhang Feng-Shou
Published: March 2014

Using time-dependent density functional theory, applied to the valence electrons and coupled non-adiabatically to molecular dynamics of the ions, we study the ionization and fragmentation of formaldehyde in collision with a proton. Four different impact energies: 35 eV, 85 eV, 135 eV, and 300 eV are chosen in order to study the energy effect in the low energy region, and ten different incident orientations at 85 eV are considered for investigating the steric effect. Fragmentation ratios, single, double, and total electron ionization cross sections are calculated. For large impact parameters, these results are close to zero irrespective of the incident orientations due to a weak projectile-target interaction. For small impact parameters, the results strongly depend on the collision energy and orientation. We also give the kinetic energy releases and scattering angles of protons, as well as the cross section of different ion fragments and the corresponding reaction channels.
Self-replenishing ability of cross-linked low surface energy polymer films investigated by a complementary experimental-simulation approach
Authors: Esteves A. C. C. , Lyakhova K. , van Riel J. M. , van der Ven L. G. J. , van Benthem R. A. T. M. , de With G.
Published: March 2014

Nowadays, many self-healing strategies are available for recovering mechanical damage of bulk polymeric materials. The recovery of surface-dependent functionalities on polymer films is, however, equally important and has been less investigated. In this work we study the ability of low surface energy cross-linked poly(ester urethane) networks containing perfluorinated dangling chains to self-replenish their surface, after being submitted to repeated surface damage. For this purpose we used a combined experimental-simulation approach. Experimentally, the cross-linked films were intentionally damaged by cryo-microtoming to remove top layers and create new surfaces which were characterized by water Contact Angle measurements and X-Ray Photoelectron Spectroscopy. The same systems were simultaneously represented by a Dissipative Particles Dynamics simulation method, where the damage was modeled by removing the top film layers in the simulation box and replacing it by new “air” beads. The influence of different experimental parameters, such as the concentration of the low surface energy component and the molecular mobility span of the dangling chains, on the surface recovery is discussed. The combined approach reveals important details of the self-replenishing ability of damaged polymer films such as the occurrence of multiple-healing events, the self-replenishing efficiency, and the minimum “healing agent” concentration for a maximum recovery.
External-field-free magnetic biosensor
Authors: Li Yuanpeng , Wang Yi , Klein Todd , Wang Jian-Ping
Published: March 2014

In this paper, we report a magnetic nanoparticle (MNP) detection scheme without the presence of any external magnetic field. The proposed magnetic sensor uses a patterned groove structure within the sensor so that no external magnetic field is needed to magnetize the MNPs. An example is given based on a giant magnetoresistance (GMR) sensing device with a spin valve structure. For this structure, the detection of MNPs located inside the groove and near the free layer is demonstrated under no external magnetic field. Micromagnetic simulations are performed to calculate the signal to noise level of this detection scheme. A maximum signal to noise ratio (SNR) of 18.6 dB from one iron oxide magnetic nanoparticle with 8 nm radius is achieved. As proof of concept, this external-field-free GMR sensor with groove structure of 200 nm × 200 nm is fabricated using a photo and an electron beam integrated lithography process. Using this sensor, the feasibility demonstration of the detection SNR of 9.3 dB is achieved for 30 μl magnetic nanoparticles suspension (30 nm iron oxide particles, 1 mg/ml). This proposed external-field-free sensor structure is not limited to GMR devices and could be applicable to other magnetic biosensing devices.
Time-of-flight secondary ion mass spectrometry with transmission of energetic primary cluster ions through foil targets
Authors: Hirata K. , Saitoh Y. , Chiba A. , Yamada K. , Matoba S. , Narumi K.
Published: March 2014

We developed time-of-flight (TOF) secondary ion (SI) mass spectrometry that provides informative SI ion mass spectra without needing a sophisticated ion beam pulsing system. In the newly developed spectrometry, energetic large cluster ions with energies of the order of sub MeV or greater are used as primary ions. Because their impacts on the target surface produce high yields of SIs, the resulting SI mass spectra are informative. In addition, the start signals necessary for timing information on primary ion incidence are provided by the detection signals of particles emitted from the rear surface of foil targets upon transmission of the primary ions. This configuration allows us to obtain positive and negative TOF SI mass spectra without pulsing system, which requires precise control of the primary ions to give the spectra with good mass resolution. We also successfully applied the TOF SI mass spectrometry with energetic cluster ion impacts to the chemical structure characterization of organic thin film targets.
Theory of perturbative pulse train based coherent control
Authors: Grinev Timur , Brumer Paul
Published: March 2014

A theoretical description of coherent control of excited state dynamics using pulse trains in the perturbative regime, as carried out in recent experiments, is presented. Analytical expressions relating the excited state populations to the pulse train control parameters are derived. Numerical examples are provided for models of pyrazine and β-carotene, and the significant role of overlapping resonances is exposed.
The 2ν3 Raman overtone of sulfur hexafluoride: Absolute spectra, pressure effects, and polarizability properties
Authors: Chrysos M. , Rachet F. , Kremer D.
Published: March 2014

Of the six normal vibrations of SF6, ν3 has a key role in the mechanisms of radiative forcing. This vibration, though inactive in Raman, shows up through the transition 2ν3 allowing for a complementary view on the asymmetric stretch of the molecule. Here, we look back into this topic, which has already caught some interest in the past but with some points been left out. We make a systematic incoherent-light-scattering analysis of the overtone with the use of different gas pressures and polarization orientations for the incident beam. Absolute-scale isotropic and anisotropic spectra are reported along with natural and pressure-induced widths and shifts, and other spectral features such as the peaks corresponding to the (experimentally indistinguishable) interfering channels Eg and F2g hitherto seen solely as two-photon IR-absorption features. We make the first-ever prediction of the SF6 polarizability second derivative with respect to the ν3-mode coordinate and we develop a heuristic argument to explain why the superposition of the three degenerate stretching motions that are related to the ν3 mode cannot but generate a polarized Raman band.
Drift kinetic Alfvén wave in temperature anisotropic plasma
Authors: Naim Hafsa , Bashir M. F. , Murtaza G.
Published: March 2014

By using the gyrokinetic theory, the kinetic Alfvén waves (KAWs) are discussed to emphasize the drift effects through the density inhomogeneity and the temperature anisotropy on their dispersion characteristics. The dependence of stabilization mechanism of the drift-Alfvén wave instability on the temperature anisotropy is highlighted. The estimate of the growth rate and the threshold condition for a wide range of parameters are also discussed.
Interface scattering in polycrystalline thermoelectrics
Authors: Popescu Adrian , Haney Paul M.
Published: March 2014

We study the effect of electron and phonon interface scattering on the thermoelectric properties of disordered, polycrystalline materials (with grain sizes larger than electron and phonons' mean free path). Interface scattering of electrons is treated with a Landauer approach, while that of phonons is treated with the diffuse mismatch model. The interface scattering is embedded within a diffusive model of bulk transport, and we show that, for randomly arranged interfaces, the overall system is well described by effective medium theory. Using bulk parameters similar to those of PbTe and a square barrier potential for the interface electron scattering, we identify the interface scattering parameters for which the figure of merit ZT is increased. We find the electronic scattering is generally detrimental due to a reduction in electrical conductivity; however, for sufficiently weak electronic interface scattering, ZT is enhanced due to phonon interface scattering.
Advanced magnetorheological damper with a spiral channel bypass valve
Authors: McLaughlin G. , Hu W. , Wereley N. M.
Published: March 2014

Magnetorheological (MR) fluid has a yield stress that is readily controllable using an applied magnetic field. MR dampers adjust this yield stress in a magnetic valve to accommodate a wide range of shock or vibration loads. In this study, the performance of an MR damper with a spiral channel bypass valve is examined. Three bypass damper configurations, i.e., a spiral channel, a spiral channel with beads, and a straight channel with beads, are subject to sinusoidal forcing at constant amplitude, while varying frequency, and applied field (current). These configurations are characterized using tortuosity and porosity parameters. The spiral channel without beads had the largest porosity and smallest tortuosity, which produced the smallest damper force, but the widest controllable damping range. The spiral channel with beads had the smallest porosity, and a comparable tortuosity, which produced the largest damping force, but similar controllable damping range to the straight channel with beads.
In situ study on low-k interconnect time-dependent-dielectric-breakdown mechanisms
Authors: Boon Yeap Kong , Gall Martin , Liao Zhongquan , Sander Christoph , Muehle Uwe , Justison Patrick , Aubel Oliver , Hauschildt Meike , Beyer Armand , Vogel Norman , Zschech Ehrenfried
Published: March 2014

An in situ transmission-electron-microscopy methodology is developed to observe time-dependent dielectric breakdown (TDDB) in an advanced Cu/ultra-low-k interconnect stack. A test structure, namely a “tip-to-tip” structure, was designed to localize the TDDB degradation in small dielectrics regions. A constant voltage is applied at 25 °C to the “tip-to-tip” structure, while structural changes are observed at nanoscale. Cu nanoparticle formation, agglomeration, and migration processes are observed after dielectric breakdown. The Cu nanoparticles are positively charged, since they move in opposite direction to the electron flow. Measurements of ionic current, using the Triangular-Voltage-Stress method, suggest that Cu migration is not possible before dielectric breakdown, unless the Cu/ultra-low-k interconnect stacks are heated to 200 °C and above.
Communication: Different behavior of Young's modulus and fracture strength of CeO2: Density functional theory calculations
Authors: Sakanoi Ryota , Shimazaki Tomomi , Xu Jingxiang , Higuchi Yuji , Ozawa Nobuki , Sato Kazuhisa , Hashida Toshiyuki , Kubo Momoji
Published: March 2014

In this Communication, we use density functional theory (DFT) to examine the fracture properties of ceria (CeO2), which is a promising electrolyte material for lowering the working temperature of solid oxide fuel cells. We estimate the stress-strain curve by fitting the energy density calculated by DFT. The calculated Young's modulus of 221.8 GPa is of the same order as the experimental value, whereas the fracture strength of 22.7 GPa is two orders of magnitude larger than the experimental value. Next, we combine DFT and Griffith theory to estimate the fracture strength as a function of a crack length. This method produces an estimated fracture strength of 0.467 GPa, which is of the same order as the experimental value. Therefore, the fracture strength is very sensitive to the crack length, whereas the Young's modulus is not.
Topological Structure of Urban Street Networks from the Perspective of Degree Correlations
Authors: Jiang Bin , Duan Yingying , Lu Feng , Yang Tinghong , Zhao Jing
Published: March 2014

Many complex networks demonstrate a phenomenon of striking degree correlations: that is, a node tends to link to other nodes with similar (or dissimilar) degrees. From the perspective of degree correlations, in this paper we attempt to characterize topological structures of urban street networks. We adopted six urban street networks (three European and three North American), and converted them into network topologies in which nodes and edges represent individual streets and street intersections, respectively, and compared the network topologies with three reference network topologies (biological, technological, and social). The urban street network topologies (with the exception of Manhattan) showed a consistent pattern that distinctly differs from the three reference networks. The topologies of urban street networks lack striking degree correlations in general. Through reshuffling the network topologies towards, for example, maximum or minimum degree correlations while retaining the initial degree distributions, we found that all the surrogate topologies of the urban street networks, as well as the reference ones, tended to deviate from small-world properties. This implies that the initial degree correlations do not have any positive or negative effect on the networks' performance or functions.
Reaction of 2-Pyridylmethylthiourea Derivatives with [(en)2Co(OSO2CF3)2]+ Induces Hypodentate Coordination of an Ethylenediamine Ligand
Authors: Roecker Lee , Anderson Alison , Al-Haddad Aladdin , Engineer Cawas , Fetty Joan , Kiaza Charles , Noinaj Nicholas , Coker Nathan L. , Krause Jeanette , Parkin Sean
Published: March 2014

Pyridylmethylthiourea derivatives coordinate with [(en)2Co(OSO2CF3)2]+ in a tridentate manner resulting in the formation of a hypodentate ethylenediamine ligand. Four ligands were studied: N-(R)phenyl-N′-2-pyridylmethylthiourea (R = H (1a), CH3 (1b), OCH3 (1c)) and N-benzyl-N′-2-pyridylmethylthiourea (2). These bind through the sulfur, a deprotonated exo nitrogen, and the pyridyl nitrogen atoms forming four and five-membered rings, respectively. The ligand also coordinates in a bidentate manner through the sulfur and deprotonated endo or exo nitrogen atoms, forming two additional coordination isomers. The solid state structure (X-ray) of one of the bidentate isomers of Co-1b2+ (endo isomer) shows that the coordinated thiourea sulfur induces a structural trans effect of 0.035 Å on the trans Co–N bond while that of the tridentate isomer of Co-1a3+ confirms the coordination mode of the ligand and the presence of a protonated hypodentate ethylenediamine ligand as suggested by 1H and 13C NMR spectroscopy.
Quantum turbulence in superfluids with wall-clamped normal component
Authors: Eltsov Vladimir , Hänninen Risto , Krusius Matti
Published: March 2014

In Fermi superfluids, such as superfluid
3
He, the viscous normal component can be considered to be stationary with respect to the container. The normal component interacts with the superfluid component via mutual friction, which damps the motion of quantized vortex lines and eventually couples the superfluid component to the container. With decreasing temperature and mutual friction, the internal dynamics of the superfluid component becomes more important compared with the damping and coupling effects from the normal component. As a result profound changes in superfluid dynamics are observed: the temperature-dependent transition from laminar to turbulent vortex motion and the decoupling from the reference frame of the container at even lower temperatures.
SHP-2 deletion in postmigratory neural crest cells results in impaired cardiac sympathetic innervation
Authors: Lajiness Jacquelyn D. , Snider Paige , Wang Jian , Feng Gen-Sheng , Krenz Maike , Conway Simon J.
Published: March 2014

Significance

Initial heart development takes place independently of its innervation; however, impaired postnatal cardiac sympathetic innervation can result in deadly consequences. This study provides evidence that the signaling molecules SHP-2 and phosphorylated-extracellular signal-regulated kinase (pERK) are critical components in the development of cardiac sympathetic innervation. Interruption of this signaling cascade resulted in decreased sympathetic innervation and decreased heart rate. Genetic rescue of downstream pERK signaling restored both cardiac innervation and heart rate. Thus, this work lends mechanistic insight into clinical presentations of diseases associated with alterations in this signaling pathway such as LEOPARD syndrome as well as other ECG abnormalities resulting from disturbed pERK-dependent sympathetic innervation.
Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy
Authors: Dykeman Eric C. , Stockley Peter G. , Twarock Reidun
Published: March 2014

Significance

One of the important puzzles in virology is how viruses assemble protective protein containers for their genomes rapidly and efficiently during an infection. Recent advances in the field of RNA viruses suggests that multiple specific contacts between the genomic RNA and the proteins in these containers play crucial roles in this process, but the detailed molecular mechanisms by which this occurs are largely obscure. We describe here a mathematical model of virus assembly that incorporates these contacts and other details of real virus infections. It demonstrates how such contacts act collectively to reduce the complexity of virus formation, ensuring efficient and selective packaging of the viral genomes. These competitive advantages shed new light on viral assembly and evolution and open up unique avenues for antiviral therapy.
Preparedness of Americans for the Affordable Care Act
Authors: Barcellos Silvia Helena , Wuppermann Amelie C. , Carman Katherine Grace , Bauhoff Sebastian , McFadden Daniel L. , Kapteyn Arie , Winter Joachim K. , Goldman Dana
Published: March 2014

Significance

The ultimate success of the Affordable Care Act (ACA) depends on how well the health insurance exchanges can bring the benefits of private competition to individuals in the form of lower premiums. Doing so requires that individuals, when shopping for health insurance, correctly weigh the benefits and costs of various insurance options. Our work suggests that the overall population, and even more so those most likely affected by the ACA, is not well equipped to do so. We documented low levels of ACA and health insurance knowledge in the month preceding the introduction of the exchanges. We propose that simplified options, decision aids, and health insurance product design to address the limited understanding of health insurance contracts will be crucial for ACA’s success.
Readily releasable vesicles recycle at the active zone of hippocampal synapses
Authors: Schikorski Thomas
Published: March 2014

Significance

Nerve cells communicate via the release of a neurotransmitter that is stored in synaptic vesicles. The availability of synaptic vesicles is thus crucial for synaptic function. Availability of synaptic vesicles is ensured by vesicle retrieval after fusion with the plasma membrane; however, the underlying mechanisms of membrane retrieval at hippocampal synapses are still debated. Here we show that synaptic vesicles are retrieved at the active zone without the assistance of coated vesicles. Such a mechanism is similar to “kiss and run” but contradicts the classical pathway via clathrin-coated vesicles.
The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity
Authors: Angerer Heike , Radermacher Michael , Mańkowska Michalina , Steger Mirco , Zwicker Klaus , Heide Heinrich , Wittig Ilka , Brandt Ulrich , Zickermann Volker
Published: March 2014

Significance

Complex I is the largest membrane protein complex of the respiratory chain. In addition to 14 central subunits conserved from bacteria to man, the mitochondrial enzyme comprises some 30 so-called accessory subunits of largely unknown structure and function. We show that accessory subunit NB4M [human ortholog NDUFA6, LYR motif containing protein 6 (LYRM6)], a member of the LYR protein superfamily, anchors an acyl carrier protein to complex I, thus forming a structurally well-defined subdomain essential for complex I activity. Our study offers structural insights into the functional interplay of several central and accessory subunits that seem to be specifically involved in controlling the catalytic activity of mitochondrial complex I. This also provides the structural basis for human complex I inactivation in HIV-linked LYRM6 deficiency.
Protein phosphatase PP1/GLC7 interaction domain in yeast eIF2γ bypasses targeting subunit requirement for eIF2α dephosphorylation
Authors: Rojas Margarito , Gingras Anne-Claude , Dever Thomas E.
Published: March 2014

Significance

Phosphorylation of eukaryotic protein synthesis initiation factor 2α (eIF2α) is the principal mechanism cells use to regulate translation initiation. Specific kinases phosphorylate eIF2α to inhibit protein synthesis under stress conditions; however, eIF2α dephosphorylation is catalyzed by the general protein phosphatase PP1. In mammalian cells, specific
trans
-acting targeting subunits direct PP1 to dephosphorylate eIF2α and restore protein synthesis. However, these targeting subunits are missing in the yeast
Saccharomyces cerevisiae
. We show that a PP1-binding element in a region of the eIF2γ subunit that is unique to yeast functions to target PP1 to dephosphorylate eIF2α. Thus, yeast rely on the recruitment of PP1 in
cis
to the eIF2 complex to maintain eIF2α phosphorylation at levels appropriate for cellular homeostasis.
Glacial forcing of central Indonesian hydroclimate since 60,000 y B.P.
Authors: Russell James M. , Vogel Hendrik , Konecky Bronwen L. , Bijaksana Satria , Huang Yongsong , Melles Martin , Wattrus Nigel , Costa Kassandra , King John W.
Published: March 2014

Significance

Climate variability in the tropical western Pacific exerts enormous influence on global climate, yet its history remains poorly constrained. We present the region’s first continuous terrestrial sedimentary record of surface hydrology and vegetation spanning the last 60,000 y based upon geochemical data from Lake Towuti, Indonesia. Our data demonstrate that wet conditions and rainforest ecosystems present during the Holocene and during marine isotope stage 3 were interrupted by severe drying between ∼33,000 and 16,000 y B.P., when high-latitude ice sheets expanded and global temperatures cooled. These findings indicate an important role for glacial boundary conditions in pacing tropical western Pacific climate change, and highlight the potential for the western Pacific to amplify global climate change during glacial–interglacial cycles.
Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids
Authors: Woodhouse Margaret R. , Cheng Feng , Pires J. Chris , Lisch Damon , Freeling Michael , Wang Xiaowu
Published: March 2014

Significance

Ancient plant polyploids contain dissimilar subgenomes. Subgenomes that have lost fewer genes are subgenomes that tend to express their genes to higher mRNA levels: “genome dominance.” Genome dominance is heritable through multiple rounds of polyploidy and over tens of millions of years. Twenty-four–nucleotide RNA coverage of noncoding, transposon DNA upstream of genes marks the recessive subgenomes of
Brassica rapa
and
Arabidopsis
with only a small effect of gene expression. We hypothesize that the “diploid” parent of a tetraploidy with the lowest transposon load was to become the dominant subgenome. The balance of transposon position effects on genes is important for the regulation of quantity (and perhaps to solve the heterosis and C-value paradoxes).
Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells
Authors: Firth Amy L. , Dargitz Carl T. , Qualls Susan J. , Menon Tushar , Wright Rebecca , Singer Oded , Gage Fred H. , Khanna Ajai , Verma Inder M.
Published: March 2014

Significance

Pulmonary disease is the third highest cause for morbidity and mortality worldwide. Studies of human lung disease in vivo or in vitro are currently limited. Using induced pluripotent stem cells, we developed a step-wise differentiation protocol ending in an air–liquid interface to generate a pseudostratified polarized layer of endodermal-derived epithelial cells (forkhead box protein A2
+
and NK2 homeobox 1
+
). This layer includes Clara cells with Clara cell 10 kD-positive vesicles, mucin 5A/C-positive goblet cells, multiciliated cells, and isolated cells that have forskolin-induced chloride currents sensitive to cystic fibrosis transmembrane regulator inhibitor 172. The development of this model will enable the future study of many lung diseases (especially those where defective cilia are involved, such as primary ciliary dyskinesia) that have been difficult to study in human models from a developmental perspective.
Food for thought – or, what’s (in) a recipe?
Authors: Arendholz Jenny , Bublitz Wolfram , Kirner-Ludwig Monika , Zimmermann Iris
Published: March 2014

This paper focuses on the text type of cooking instructions, or recipes, from a chiefly diachronic point of view. After giving a brief overview on both the etymological origins and semantic developments of the notion recipe, we will compare two recipes with regard to formal and functional similarities and discrepancies: one Middle English recipe (“Beef y-Stywyd”, MS. Harl. 279 f. 6v) by an anonymous scribe with its Modern English online counterpart (“beef and ale stew”) by the British chef James ‘Jamie’ Oliver. Opposed to findings by e.g. Görlach (2004), particularly the functional comparison remains mostly obscure, as the medieval recipe escapes functional classification. However, remarkable text type specific parallels can be identified with regard to formal aspects, such as syntactic constructions and lexical codification.
Men eat for muscle, women eat for weight loss
Authors: Fuller Janet M. , Briggs Janelle , Dillon-Sumner Laurel
Published: March 2014

This chapter examines discourses about food in Women’s Health and Men’s Health magazines, and finds gendered ideologies about foodways. While the concept of “good food” is prevalent in both magazines, what is “good” depends on the gender of the target audience. Both magazines advocate controlled eating, but what this is varies. Eating for women is portrayed as having the goal of improving appearance, while for men it is more about improving performance. Further, women are portrayed as both more emotional and more in need of strict control over their actions. We show how these subtle differences in advertisements and articles aimed at women and at men are part of the construction of hegemonic femininity and masculinity.
Landscape embedded in language
Authors: Jett Stephen C.
Published: March 2014

Humans interact with landscape by classifying and labeling a select multitude of the landscape’s limitless individual areas and features. Studying place names reveals much about language, perception, values, beliefs, environment, economy, and history. Like place-naming among other Athabaskan speakers, Navajo toponymic practice overwhelmingly produces descriptive names for landscape features, reserving commemorative and activity place-naming largely for human-modified places. Athabaskan languages employ an unusual number of topological and directional affixes and verb forms, which can condense and convey much information within brief descriptive place names. Lexeme frequencies hint at what Navajos see or saw as significant in their natural landscape. Place-naming facilitated possessing/controlling landscapes. The Navajo attached the itineraries and activities of mythological protagonists to the land via a web of place names; the associated stories and their descriptive names served as mnemonic guides for far-traveling Navajos.
The diachrony of Ute case-marking
Authors: Givón T.
Published: March 2014

This paper deals with Ute case-marking and its reconstructed diachrony, demonstrating once again that synchronic data from a single language can serve, via Internal Reconstruction (IR) and a theoretically informed approach to grammaticalization, to reconstruct older diachronic states. The synchronic data of object and genitive marking in Ute yields sufficient clues to reconstruct two or even three layers of older object and/or genitive markin. The persistent connection between object and genitive points to several cycles of clausal (or VP) nominalization, a well-documented phenomenon in Northern Uto-Aztecan (Numic, Takic, Yaqui, Tarrahumara, Huichol). The post-positional markings of indirect objects in Ute are also surveyed, showing that the vast majority of them are verb-derived, through patterns that are consonant with serial-verb constructions elsewhere.
The voice of (White) reason
Authors: Meek Barbra A.
Published: March 2014

This chapter argues that the power of “covert racist discourses” lies in the obscurity of authorship and the interpellation of readership along with the tacit preconditions of their enunciation. Drawing on Jane H. Hill’s concern with the practices of enunciation (2008), this chapter explores the ways in which conceptualizations of difference and unity are enunciated beyond clearly defined institutional domains. It analyzes the semiotic elements deployed in electronically-circulating jokes with American Indian characters and shows how such jokes re-inscribe tropes of conquest. Furthermore, the discourse emanating from such characterizations maintain a particular type of citizen as quintessential and perpetuate the already difficult struggle people of color, especially American Indians, face with respect to recognition, legitimation, and citizenship in “White” domains.
Computation efficiency and feature inheritance in crash-proof syntax
Authors: Ouali Hamid
Published: March 2014

Frampton & Guttmann (2002) argue that a language design that assumes “crashing derivations” would seem to be less computationally efficient than a design which outputs only convergent derivations. Therefore, they advocate a “crash-proof” syntax which requires constraining all the computational operations. This paper makes a distinction between a fatal crash/strict crash and non-fatal crash/soft crash. I will argue that in a model with Feature Inheritance (Chomsky 2000, 2001 and 2004), a mechanism that supersedes Agree, seemingly non-convergent derivations can be salvaged as long every mechanism in the grammar that’s available is exhausted. I argue, given data from Tamazight Berber, that the three logical possibilities of Feature Inheritance namely DONATE, KEEP, and SHARE, proposed in Ouali (2006, 2008), and whose application is ranked with KEEP applying only if DONATE fails, and SHARE applying only of KEEP fails, despite requiring seemingly different derivations can be accounted for within a less strict crash-proof syntax.
Implications of grammatical gender for the theory of uninterpretable features
Authors: Carstens Vicki
Published: March 2014

I argue that grammatical gender is semantically empty but intrinsically valued, so the strict linkage between uninterpretable and unvalued in Chomsky (2001) cannot be correct. I then demonstrate that gender is infinitely reusable as an “ activity” feature; in contrast, abstract Case activates a DP for just one Agree relation. This asymmetry suggests that valuation via Agree causes goal deactivation, and that deactivation is not necessary for every uninterpretable feature (uF). I accordingly analyze deactivation as arising from PF illegibility of multiple values for a single feature. Agree relations value Case, but never value nominal gender, so the legibility problem does not arise. I demonstrate that in Bantu, adjunction of N to D makes gender accessible to all probes outside DP. This and the reusability of gender as an activity feature leads to a cluster of systematic contrasts between Bantu and Indo-European languages: Bantu DPs A-move much more freely than Indo-European DPs, and value iterating
subject agreement. The facts thus demonstrate that the internal syntax of DP impacts its feature matrix; it is not the case that a DP automatically inherits all f-features of its subparts, as syntactic theory generally assumes. Finally, I illustrate that Bantu C and T can agree with different expressions, casting doubt on the Feature Inheritance approach to uF in Chomsky (2007, 2008) and Richards (2007). The facts of grammatical gender argue that valued uF Transfer to the Conceptual-Intentional Interface without inducing crashes.
Uninterpretable features
Authors: Epstein Samuel David , Kitahara Hisatsugu , Seely T. Daniel
Published: March 2014

This paper consists of four sections. Section 1 identifies an important unclarity regarding the central concept “crash” and suggests a way to rectify it. Section 2 reveals a pervasive empirical problem confronting Chomsky’s (2007, 2008) attractively deductive valuation-transfer analysis. Section 3 offers a possible solution to this problem, reanalyzing the relation between uninterpretable features and Transfer. Section 4 presents a possible modification of a crash-proof aspect of the proposed model and briefly discusses a remaining question.
TAp73 is essential for germ cell adhesion and maturation in testis
Authors: Holembowski Lena , Kramer Daniela , Riedel Dietmar , Sordella Raffaella , Nemajerova Alice , Dobbelstein Matthias , Moll Ute M.
Published: March 2014

A core evolutionary function of the p53 family is to protect the genomic integrity of gametes. However, the role of p73 in the male germ line is unknown. Here, we reveal that TAp73 unexpectedly functions as an adhesion and maturation factor of the seminiferous epithelium orchestrating spermiogenesis. TAp73 knockout (TAp73KO) and p73KO mice, but not ΔNp73KO mice, display a “near-empty seminiferous tubule” phenotype due to massive premature loss of immature germ cells. The cellular basis of this phenotype is defective cell–cell adhesions of developing germ cells to Sertoli nurse cells, with likely secondary degeneration of Sertoli cells, including the blood–testis barrier, which leads to disruption of the adhesive integrity and maturation of the germ epithelium. At the molecular level, TAp73, which is produced in germ cells, controls a coordinated transcriptional program of adhesion- and migration-related proteins including peptidase inhibitors, proteases, receptors, and integrins required for germ–Sertoli cell adhesion and dynamic junctional restructuring. Thus, we propose the testis as a unique organ with strict division of labor among all family members: p63 and p53 safeguard germ line fidelity, whereas TAp73 ensures fertility by enabling sperm maturation.
Retrograde neurotrophin signaling through Tollo regulates synaptic growth in Drosophila
Authors: Ballard Shannon L. , Miller Daniel L. , Ganetzky Barry
Published: March 2014

Toll-like receptors (TLRs) are best characterized for their roles in mediating dorsoventral patterning and the innate immune response. However, recent studies indicate that TLRs are also involved in regulating neuronal growth and development. Here, we demonstrate that the TLR Tollo positively regulates growth of the Drosophila melanogaster larval neuromuscular junction (NMJ). Tollo mutants exhibited NMJ undergrowth, whereas increased expression of Tollo led to NMJ overgrowth. Tollo expression in the motoneuron was both necessary and sufficient for regulating NMJ growth. Dominant genetic interactions together with altered levels of phosphorylated c-Jun N-terminal kinase (JNK) and puc-lacZ expression revealed that Tollo signals through the JNK pathway at the NMJ. Genetic interactions also revealed that the neurotrophin Spätzle3 (Spz3) is a likely Tollo ligand. Spz3 expression in muscle and proteolytic activation via the Easter protease was necessary and sufficient to promote NMJ growth. These results demonstrate the existence of a novel neurotrophin signaling pathway that is required for synaptic development in Drosophila.
IL-17–induced CXCL12 recruits B cells and induces follicle formation in BALT in the absence of differentiated FDCs
Authors: Fleige Henrike , Ravens Sarina , Moschovakis Georgios Leandros , Bölter Jasmin , Willenzon Stefanie , Sutter Gerd , Häussler Susanne , Kalinke Ulrich , Prinz Immo , Förster Reinhold
Published: March 2014

Ectopic lymphoid tissue, such as bronchus-associated lymphoid tissue (BALT) in the lung, develops spontaneously at sites of chronic inflammation or during infection. The molecular mechanisms underlying the neogenesis of such tertiary lymphoid tissue are still poorly understood. We show that the type of inflammation-inducing pathogen determines which key factors are required for the formation and maturation of BALT. Thus, a single intranasal administration of the poxvirus modified vaccinia virus Ankara (MVA) is sufficient to induce highly organized BALT with densely packed B cell follicles containing a network of CXCL13-expressing follicular DCs (FDCs), as well as CXCL12-producing follicular stromal cells. In contrast, mice treated with P. aeruginosa (P.a.) develop BALT but B cell follicles lack FDCs while still harboring CXCL12-positive follicular stromal cells. Furthermore, in IL-17–deficient mice, P.a.-induced BALT largely lacks B cells as well as CXCL12-expressing stromal cells, and only loose infiltrates of T cells are present. We show that Toll-like receptor pathways are required for BALT induction by P.a., but not MVA, and provide evidence that IL-17 drives the differentiation of lung stroma toward podoplanin-positive CXCL12-expressing cells that allow follicle formation even in the absence of FDCs. Taken together, our results identify distinct pathogen-dependent induction and maturation pathways for BALT formation.
RNA editing in RHOQ promotes invasion potential in colorectal cancer
Authors: Han Sae-Won , Kim Hwang-Phill , Shin Jong-Yeon , Jeong Eun-Goo , Lee Won-Chul , Kim Keon Young , Park Sang Youn , Lee Dae-Won , Won Jae-Kyung , Jeong Seung-Yong , Park Kyu Joo , Park Jae-Gahb , Kang Gyeong Hoon , Seo Jeong-Sun , Kim Jong-Il , Kim Tae-You
Published: March 2014

RNA editing can increase RNA sequence variation without altering the DNA sequence. By comparing whole-genome and transcriptome sequence data of a rectal cancer, we found novel tumor-associated increase of RNA editing in ras homologue family member Q (RHOQ) transcripts. The adenosine-to-inosine (A-to-I) editing results in substitution of asparagine with serine at residue 136. We observed a higher level of the RHOQ RNA editing in tumor compared with normal tissue in colorectal cancer (CRC). The degree of RNA editing was associated with RhoQ protein activity in CRC cancer cell lines. RhoQ N136S amino acid substitution increased RhoQ activity, actin cytoskeletal reorganization, and invasion potential. KRAS mutation further increased the invasion potential of RhoQ N136S in vitro. Among CRC patients, recurrence was more frequently observed in patients with tumors having edited RHOQ transcripts and mutations in the KRAS gene. In summary, we show that RNA editing is another mechanism of sequence alteration that contributes to CRC progression.
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles
Authors: Aksoy Bülent Arman , Demir Emek , Babur Özgün , Wang Weiqing , Jing Xiaohong , Schultz Nikolaus , Sander Chris
Published: March 2014

Motivation: Somatic homozygous deletions of chromosomal regions in cancer, while not necessarily oncogenic, may lead to therapeutic vulnerabilities specific to cancer cells compared with normal cells. A recently reported example is the loss of one of the two isoenzymes in glioblastoma cancer cells such that the use of a specific inhibitor selectively inhibited growth of the cancer cells, which had become fully dependent on the second isoenzyme. We have now made use of the unprecedented conjunction of large-scale cancer genomics profiling of tumor samples in The Cancer Genome Atlas (TCGA) and of tumor-derived cell lines in the Cancer Cell Line Encyclopedia, as well as the availability of integrated pathway information systems, such as Pathway Commons, to systematically search for a comprehensive set of such epistatic vulnerabilities.

Results: Based on homozygous deletions affecting metabolic enzymes in 16 TCGA cancer studies and 972 cancer cell lines, we identified 4104 candidate metabolic vulnerabilities present in 1019 tumor samples and 482 cell lines. Up to 44% of these vulnerabilities can be targeted with at least one Food and Drug Administration-approved drug. We suggest focused experiments to test these vulnerabilities and clinical trials based on personalized genomic profiles of those that pass preclinical filters. We conclude that genomic profiling will in the future provide a promising basis for network pharmacology of epistatic vulnerabilities as a promising therapeutic strategy.

Availability and implementation : A web-based tool for exploring all vulnerabilities and their details is available at http://cbio.mskcc.org/cancergenomics/statius/ along with supplemental data files.

Contact : statius@cbio.mskcc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.