bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study of stratified turbulence forced with columnar dipoles
Authors: Augier P. , Billant P. , Negretti M. E. , Chomaz J.-M.
Published: April 2014

We present a novel experimental setup aimed at producing a forced strongly stratified turbulent flow. The flow is forced by an arena of 12 vortex pair generators in a large tank. The continuous interactions of the randomly produced vortex pairs give rise to a statistically stationary disordered flow in contrast to previous experiments where the stratified turbulence is decaying. The buoyancy frequency N is set to its highest value N = 1.7 rad/s using salt as stratifying agent so that the horizontal Froude number Fh = Ω/N is low, while the buoyancy Reynolds number \documentclass[12pt]{minimal}\begin{document}$\mathcal {R} = Re {F_h}^2$\end{document}R=ReFh2, where Re = Ωa2/ν is the classical Reynolds number, is as high as possible given the experimental constraints (Ω is the maximum angular velocity of the vortices, a their radius and ν the viscosity). PIV measurements show that the flow is not homogeneous in the horizontal plane and is organised into horizontal layers along the vertical. When \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}$\end{document}R is increased, we observe a progressive evolution from the viscosity dominated regime with smooth layers to a regime with small scales superimposed on the layers and for which the vertical Froude number is of order one. The latter regime resembles the strongly stratified turbulent regime with a downscale cascade that has been predicted for large \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}$\end{document}R. However, horizontal second order structure functions do not exhibit a clear inertial range for the largest \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}$\end{document}R achieved \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}=310$\end{document}R=310. In addition, the corresponding turbulent buoyancy Reynolds number \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}_t=P/(\nu N^2)$\end{document}Rt=P/(νN2) based on an estimation of the injection rate of energy P is only of order unity \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}_t \simeq 0.4$\end{document}Rt≃0.4 indicating that only the edge of the strongly stratified turbulent regime has been reached. However, these results suggest that sufficiently large turbulent buoyancy Reynolds numbers, \documentclass[12pt]{minimal}\begin{document}$\mathcal {R}_t \simeq 10$\end{document}Rt≃10, could be achieved experimentally by scaling up five times this novel set-up.
Vortex dynamics studies in supersonic flow: Merging of co-rotating streamwise vortices
Authors: Maddalena L. , Vergine F. , Crisanti M.
Published: April 2014

For air-breathing propulsion systems intended for flight at very high Mach numbers, combustion is carried out at supersonic velocities and the process is mixing limited. Substantial increase in mixing rates can be obtained by fuel injection strategies centered on generating selected modes of supersonic, streamwise vortex interactions. Despite the recognized importance, and potential of the role of streamwise vortices for supersonic mixing enhancement, only few fundamental studies on their dynamics and interactions have been conducted, leaving the field largely unexplored. A reduced order model that allows the dynamics of complex, interacting, supersonic vortical structures to be investigated, is presented in this work. The prediction of the evolution of mutually interacting streamwise vortices represents an enabling element for the initiation of an effective, systematic experimental study of selected cases of interest, and is an important step toward the design of new fuel injection strategies for supersonic combustors. The case presented in this work is centered on a merging process of co-rotating vortices, and the subsequent evolution of a system composed of two counter-rotating vortex pairs. This interaction was studied, initially, with the proposed model, and was chosen for the peculiarity of the resulting morphology of the vorticity field. These results were used to design an experimental investigation with the intent to target the same specific complex flow physics. The experiment revealed the same peculiar features encountered in the simulation.
Geometry of scale-to-scale energy and enstrophy transport in two-dimensional flow
Authors: Liao Yang , Ouellette Nicholas T.
Published: April 2014

Using filter-space techniques, we analyze the transport of energy and enstrophy between scales in an experimental quasi-two-dimensional weakly turbulent flow. By decomposing the scale-to-scale energy and enstrophy fluxes into three components that consist of distinct types of triad interactions, we find that different triads are responsible for forward and inverse flux. To understand this behavior, we analyze the geometric alignment between the turbulent stresses that drive scale-to-scale transfer and the large-scale velocity and vorticity gradients, and show that different triad interactions have distinct alignment signatures. Our results shed light on the role played by geometric alignment in the net behavior of triad interactions in turbulence.
On the extension of the eddy viscosity model to compressible flows
Authors: Germano M. , Abbà A. , Arina R. , Bonaventura L.
Published: April 2014

In the paper the authors examine the extension of the eddy viscosity modeling approach to compressible large eddy simulation. On the basis of formal algebraic relations among the generalized central moments and the filtered Favre terms, a new compressible eddy viscosity formulation is derived.
Dual operation characteristics of resistance random access memory in indium-gallium-zinc-oxide thin film transistors
Authors: Yang Jyun-Bao , Chang Ting-Chang , Huang Jheng-Jie , Chen Yu-Chun , Chen Yu-Ting , Tseng Hsueh-Chih , Chu Ann-Kuo , Sze Simon M.
Published: April 2014

In this study, indium-gallium-zinc-oxide thin film transistors can be operated either as transistors or resistance random access memory devices. Before the forming process, current-voltage curve transfer characteristics are observed, and resistance switching characteristics are measured after a forming process. These resistance switching characteristics exhibit two behaviors, and are dominated by different mechanisms. The mode 1 resistance switching behavior is due to oxygen vacancies, while mode 2 is dominated by the formation of an oxygen-rich layer. Furthermore, an easy approach is proposed to reduce power consumption when using these resistance random access memory devices with the amorphous indium-gallium-zinc-oxide thin film transistor.
Charge packets modeling in polyethylene
Authors: Baudoin F. , Laurent C. , Teyssedre G. , Le Roy S.
Published: April 2014

Charge packets in insulating polymers have been reported by many groups within the last two decades, especially in polyethylene-based materials. They consist in a pulse of net charge that remains in the form of a pulse as it crosses the insulation. In spite of a variety of characteristics depending on material properties and experimental conditions, one of the puzzling aspects of the packets is their repetitive character until they eventually die away. Several theories have been proposed to explain their formation and propagation. Two of them have the advantage of simplicity and of being physically based, being the existence of an hysteresis loop in the injection mechanism or a negative differential mobility of carriers with the electric field. Based on these descriptions, some progress has been done recently by discussing the shape of the packets during their propagation but none of the concepts has been incorporated into a transport model to describe the full evolution from the packet generation to their vanishing. Here, we used a simplified transport model featuring bipolar charge injection and transport coupled to specific conditions in charge injection or carrier mobility to reproduce experimental results. One of the salient features of the results is that both models are able to reproduce the repetitive character and the dying away of the packets that appear to be linked with the internal field distribution modulated by a bipolar space charge.
A new fast two-color interferometer at Alcator C-Mod for turbulence measurements and comparison with phase contrast imaging
Authors: Kasten C. P. , White A. E. , Irby J. H.
Published: April 2014

Accurately predicting the turbulent transport properties of magnetically confined plasmas is a major challenge of fusion energy research. Validation of transport models is typically done by applying so-called “synthetic diagnostics” to the output of nonlinear gyrokinetic simulations, and the results are compared to experimental data. As part of the validation process, comparing two independent turbulence measurements to each other provides the opportunity to test the synthetic diagnostics themselves; a step which is rarely possible due to limited availability of redundant fluctuation measurements on magnetic confinement experiments. At Alcator C-Mod, phase-contrast imaging (PCI) is a commonly used turbulence diagnostic. PCI measures line-integrated electron density fluctuations with high sensitivity and wavenumber resolution (1.6 cm−1≲|kR|≲11 cm−1). A new fast two-color interferometry (FTCI) diagnostic on the Alcator C-Mod tokamak measures long-wavelength (|kR|≲3.0 cm−1) line-integrated electron density fluctuations. Measurements of coherent and broadband fluctuations made by PCI and FTCI are compared here for the first time. Good quantitative agreement is found between the two measurements. This provides experimental validation of the low-wavenumber region of the PCI calibration, and also helps validate the low-wavenumber portions of the synthetic PCI diagnostic that has been used in gyrokinetic model validation work in the past. We discuss possibilities to upgrade FTCI, so that a similar comparison could be done at higher wavenumbers in the future.
Quantitative analysis of chemical interaction and doping of the Si(111) native oxide surface with tetrafluorotetracyanoquinodimethane
Authors: Yoshimoto Shinya , Furuhashi Masayuki , Koitaya Takanori , Shiozawa Yuichiro , Fujimaki Kazutaka , Harada Yosuke , Mukai Kozo , Yoshinobu Jun
Published: April 2014

The charge-transfer states and the carrier concentration of the native oxide Si(111) surface adsorbed with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) were investigated by X-ray photoelectron spectroscopy (XPS) and independently driven four-probe electrical conductivity measurements. The XPS results show that F4-TCNQ molecules are involved in charge transfer with the SiO2/Si(111) surface. The Si 2p XPS spectra and the surface photovoltage shift provide the evidences of (i) change in the oxidation states at the SiO2-Si(111) interface region and (ii) formation of a p-type space charge layer (SCL) with a hole concentration of 1.7 × 1010 cm−2, respectively. The four-probe I–V measurements also support the formation of the p-type SCL, and the estimated hole concentration of 2.0 × 1010 cm−2 agrees well with the XPS results. The estimated SCL hole concentrations were much smaller than the excess charge density in the F4-TCNQ layer, of the order of 1013 cm−2, suggesting that most of charges were localized as the oxidation states at the SiO2-Si(111) interface region. The present quantitative methods ensure precise determination of the doping concentration near the surface region.
Ab initio based understanding of diffusion mechanisms of hydrogen in liquid aluminum
Authors: Jakse N. , Pasturel A.
Published: April 2014

Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. We show that the hydrogen motion does not follow a Brownian motion caused by a broad distribution of spatial jumps that can exceed 15 times the interatomic AlH distance. This breakdown is also evidenced in the calculation of the self-part of the van Hove distribution function that is not the Gaussian expected for a Fickian process. We show that the hydrogen motion can be described well by a generalized continuous time random walk model leading to computed self-diffusion coefficients of H in liquid aluminum in good agreement with experimental ones. Finally, the impact of impurities and alloying elements is discussed.
Academic Research Strengths and Multinational Firms' Foreign R&D Location Decisions: Evidence from R&D Investments in European Regions
Authors: Belderbos Rene , Van Roy Vincent , Leten Bart , Thijs Bart
Published: April 2014

Although an expanding literature on university–industry linkages has suggested that proximity to academia can increase the innovative performance of firms, the role of academic research in the R&D location choices of multinational firms has received surprisingly little attention. In this paper we analyze the extent to which academic research in host regions of EU-15 countries attracts R&D investments by multinational firms. We analyze the determinants of the location of 394 multinational R&D projects in NUTS-1 regions of EU-15 countries during the period 2003–08. We construct precise measures of the academic research strengths of regions from annual publication data from Thomson Reuters Web of Science. University publications are counted at the level of regions and science fields, and measure academic research relevant for investing firms by linking science fields to the industries in which firms are active. We find that the probability of R&D projects being located in a host region is positively affected by the host region's academic strength—after controlling for industry agglomeration, the technological strength of the region, R&D tax incentives, and other characteristics of host locations. Our results further suggest that a major mechanism through which academic research attracts foreign R&D is the supply of PhD graduates.
Layering Spatial Identities: The Identity Discourses of New Regions
Authors: Terlouw Kees , van Gorp Bouke
Published: April 2014

The number and importance of regions are increasing at the same time as traditional regional identities are undermined through processes like globalisation and individualisation. Local and other administrations increasingly cooperate and create new regions which are too changeable for a distinct collective identity to develop. Nevertheless, a clear identity discourse helps administrators to justify their policies; to mobilise local stakeholders; to attract outside resources; and to get attention and funding from the central government. This paper studies how the identity discourses of these new regions are constructed by administrators and other stakeholders by using elements linked to the identity of more established spatial entities. Especially important are the selective downloading of characteristics from the nations and regions to which they belong and the uploading of specific qualities from the cities and areas within their boundaries. We analyse how in two areas in the Netherlands the identity discourses of new regions have been constructed through selective association with the complex layers of more established spatial identities nearby.
Politics of Urban Development and Wildfires in California and Turkey
Authors: Balaban Utku , Fu Albert S
Published: April 2014

While Turkey and California suffer similar wildfire risks, they have developed diametrically opposed fire-suppression strategies: the former adopted an increasingly centralized strategy, while the latter depends upon a highly decentralized system. This paper is a comparative analysis that relates the politics of land use in wildland–urban interfaces (WUIs) to this divergence in firefighting strategies. Our argument is that the evolution of the divergent fire-suppression strategies in California and Turkey are linked to two different types of rent-seeking behavior. Developers and landed interest seek absolute rent in Turkey and differential rent in California. The decentralized strategy in California allows property prices to be distinguished between areas of low and high protection, and commodifies safety as a form of investment regulating the market prices of land. In Turkey, the tendency toward centralization of firefighting is a part of the composite political strategy to open new land for development by completing the hitherto unfinished cadastral records of the WUIs. Thus, the centralized firefighting strategy leads indirectly to extensive commodification of the WUIs in Turkey and expands the national land market.
The Semantic Production of Space: Pervasive Computing and the Urban Landscape
Authors: Kelley Matthew James
Published: April 2014

This paper suggests that as pervasive computing technologies have gained purchase in urban space they have also become more implicitly blended with everyday life and more contingent on information that is inductively compiled from Internet-based data services. It is argued that existing theorizations of the technologically mediated production of urban must engage with the increasingly implicit nature of informational transactions as well as the emergent semantic structuring of information. Drawing on examples of ongoing pervasive computing projects, implicit computing procedures are explored in relation to the mediation of everyday urban life. Literatures from computing science and geographical theory are brought into conversation in order to examine the consequences of a convergence between implicit pervasive technologies and the spaces of everyday life.
The Social Dynamics of Suburbanization: Insights from a Qualitative Model
Authors: Reckien Diana , Luedeke Matthias K B
Published: April 2014

The authors contribute to the discussion on suburban developments by way of modeling the underlying social dynamics between suburban actors in two European suburban areas: the Wirral (Liverpool), UK and Leipzig, Germany. Data from questionnaires carried out in the two study areas are used to model social attraction and repulsion: that is, social segregation processes among socioeconomic groups. The model suggests that these social dynamics would, if other possible influences are ignored, lead to a situation of fluctuating residential in-migration and out-migration and to waves of suburbanization in the study regions. There are no persistent states: suburbanization would steadily continue until external—that is, not modeled—forces restrict movement, impact the spatial characteristics of the suburbs, or alter the social interactions among the actors. Suburban in-migration could only be reduced by strict planning regulations and/ or other external forces which impact actor-class constellations and interdependencies, for example, by measures to restrict migration to more distant suburban locations and to provide preferential housing in the inner urban areas. The analysis further indicates that suburbs develop into independent residential areas, separate from the urban centers, as the primary source of migration to suburbs is no longer the urban centers; the vast majority of moves occur within suburbs or into suburbs from outside the region.
The Resilience of South African Cities a Decade after Local Democracy
Authors: Turok Ivan
Published: April 2014

South Africa emerged from a cataclysm two decades ago to experience a stable democratic transition during which the local government system was transformed. The creation of large metropolitan municipalities was intended to accelerate socioeconomic development and urban restructuring in order to overcome the legacy of segregation and exclusion. This paper assesses their achievements, ten years on, using the concept of resilience as the analytical frame. Resilience helps to examine cities as interconnected systems open to external influences but with some capacity for self-organisation and learning. It is useful for exploring the coexistence of urban continuity and change. Evidence shows that the responses of South Africa city authorities to globalisation, urbanisation, and democracy have been circumscribed. Continuity and incremental change have been more evident than transformation and development. Hesitant progress exposes cities to the risk of greater social instability. Insights from resilience theory support the idea that enhanced municipal capabilities could facilitate a more enduring outcome.
The Dynamic Façade Pattern Grammar
Authors: Kotsopoulos Sotirios D , Carra Guglielmo , Graybill Wesley , Casalegno Federico
Published: April 2014

This paper presents a generative grammar producing a language of patterns for the south façade of a prototype sustainable house. The patterns are produced through the activation of the electrochromic material that is applied on the windowpanes of the façade. The class of the performatively effective configurations of the façade is approached as a visual language and the productive (generation), combinatorial (enumeration) and performative (verification) attributes of this language are examined. Random, performance driven, patterns could supply sufficient interior daylight without acknowledging the visual potential of façade pattern generation. The uniqueness of the chosen approach is that the shape grammar encodes the performative constraints pertaining to the generation of façade patterns in a visual manner by associating principles of two-dimensional pattern generation to levels of illuminance.
The Importance of Creative Participatory Planning in the Public Place-Making Process
Authors: Cilliers Elizelle J , Timmermans Wim
Published: April 2014

The idea of ‘place’ has long been central to the planning and design practice. Recent trends illustrate increased intervention in the ‘experience’ and ‘feeling’ of places, in order to influence and enhance community dynamics. While place-making is an important tool for experts to utilize in community planning, it should be accompanied by a thorough understanding of the contemporary social dynamics of place and the implications it has for the people who inhabit these places. In this sense, participatory planning forms an integral part of future place-making processes and planning thereof. In this paper, the first aim is to capture the importance of incorporating public perspective into the place-making process when considering future urban planning. The second is to stress the importance of the creative participatory processes to attract stakeholders and enhance their willingness to partake in the participatory planning processes. The third aim is to identify creative participatory planning tools that can be used to enhance participatory planning within the place-making process.
Unexpected Products from Mesoionic 1,3-Thiazinium and Oxazinium Olates: A Novel Access to 3,5-Diaryl-1,3-thiazine-2,4,6-trione and Alkoxy-3,5-diphenyl-3H-1,3-oxazine-2,6-dione Derivatives
Authors: Zahedifar Mahboobeh , Sheibani Hassan
Published: April 2014

The condensation of (chlorocarbonyl)ketenes 1 with N-phenylthiocarbamates 2 and N-phenylcarbamates 6 is postulated to lead to the formation of unstable mesoionic 1,3-thiazinium 4-olates I or 1,3-oxazinium 4-olates II, respectively. At room temperature, appropriately substituted mesoionic 1,3-thiazinium 4-olates I eliminated the corresponding alkene with generation of 3,5-diaryl-1,3-thiazine-2,4,6-trione derivatives 3. However, the methoxy-substituted compound 5 was stable at room temperature at least for several weeks. In the case of the mesoionic1,3-oxazinium 4-olates II an alkyl group migration affords 4-alkoxy-3,5-diphenyl-3H-1,3-oxazine-2,6-diones 7.
Hepatitis C virus triggers mitochondrial fission and attenuates apoptosis to promote viral persistence
Authors: Kim Seong-Jun , Syed Gulam H. , Khan Mohsin , Chiu Wei-Wei , Sohail Muhammad A. , Gish Robert G. , Siddiqui Aleem
Published: April 2014

Significance

Persistent hepatitis C virus (HCV) infection is associated with mitochondrial liver injury. Mitochondrial quality control is established as a physiological adaptation to mitochondrial injury. This study provides a new insight into how HCV disrupts mitochondrial dynamics and evades apoptosis and innate immunity to sustain persistent viral infection. HCV promoted dynamin-related protein 1-mediated mitochondrial fission, followed by mitophagy. Interference of HCV-induced mitochondrial fission and mitophagy led to the suppression of virus secretion, a decrease in glycolysis and ATP generation, an increase in interferon synthesis, and an increase in apoptotic death of infected cells via enhanced apoptotic signaling. These observations implicate the functional relevance of altered mitochondrial dynamics in the pathogenesis of chronic liver disease associated with HCV infection.
Younger Dryas deglaciation of Scotland driven by warming summers
Authors: Bromley Gordon R. M. , Putnam Aaron E. , Rademaker Kurt M. , Lowell Thomas V. , Schaefer Joerg M. , Hall Brenda , Winckler Gisela , Birkel Sean D. , Borns Harold W.
Published: April 2014

Significance

Resolving the full manifestation of past abrupt climate change is key to understanding the processes driving and propagating these events. As a principal component of global heat transport, the North Atlantic Ocean also is susceptible to rapid disruptions of meridional overturning circulation and thus widely invoked as a cause of abrupt climate variability in the Northern Hemisphere. We assess the impact of one such North Atlantic cold event—the Younger Dryas Stadial—on an adjacent ice mass and show that, rather than instigating a return to glacial conditions, this abrupt climate event was characterized by deglaciation. We suggest this pattern indicates summertime warming during the Younger Dryas, potentially as a function of enhanced seasonality in the North Atlantic.
Tetherin antagonism by Vpu protects HIV-infected cells from antibody-dependent cell-mediated cytotoxicity
Authors: Arias Juan F. , Heyer Lisa N. , von Bredow Benjamin , Weisgrau Kim L. , Moldt Brian , Burton Dennis R. , Rakasz Eva G. , Evans David T.
Published: April 2014

Significance

HIV-1 viral protein U (Vpu) facilitates virus release from infected cells by down-regulating and degrading tetherin, a transmembrane protein upregulated by IFN that impedes the detachment of enveloped viruses from infected cells. Here we show that this activity of Vpu protects HIV-infected cells from antibodies that are capable of directing their elimination by antibody-dependent cell-mediated cytotoxicity. A direct implication of these observations is that tetherin serves as a link between innate and adaptive immunity to enhance the susceptibility of virus-infected cells to antibodies. Thus, the antiviral activity of tetherin may be much greater than previously appreciated based on its ability to inhibit virus release in cell culture assays.
Stretched cell cycle model for proliferating lymphocytes
Authors: Dowling Mark R. , Kan Andrey , Heinzel Susanne , Zhou Jie H. S. , Marchingo Julia M. , Wellard Cameron J. , Markham John F. , Hodgkin Philip D.
Published: April 2014

Significance

Cell division is essential for an effective immune response. Estimates of rates of division are often based on DNA measurements interpreted with an appropriate model for internal cell cycle steps. Here we use time-lapse microscopy and single cell tracking of T and B lymphocytes from reporter mice to measure times spent in cell cycle phases. These data led us to a stretched cell cycle model, a novel and improved mathematical description of cell cycle progression for proliferating lymphocytes. Our model can be used to deduce cell cycle parameters for lymphocytes from DNA and BrdU labeling and will be useful when comparing the effects of different stimuli, or therapeutic treatments on immune responses, or to understand molecular pathways controlling cell division.
Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation
Authors: Agger Jane W. , Isaksen Trine , Várnai Anikó , Vidal-Melgosa Silvia , Willats William G. T. , Ludwig Roland , Horn Svein J. , Eijsink Vincent G. H. , Westereng Bjørge
Published: April 2014

Significance

Plant cell walls are recalcitrant copolymeric structures mainly comprising polysaccharides and lignin. Enzymatic degradation of the polysaccharides is a crucial step in biorefining of biomass. Recently, it was discovered that nature employs copper-dependent redox enzymes called lytic polysaccharide monoxoygenases (LPMOs) to promote degradation of the most recalcitrant and crystalline of these polysaccharides, cellulose. By carrying out oxidative cleavage of otherwise inaccessible cellulose chains, LPMOs create access points for classical hydrolytic enzymes such as cellulases. Intriguingly, the genomes of biomass degrading microorganisms encode a plethora of LPMOs (up to over 40). To our knowledge, we demonstrate for the first time that LPMOs act on hemicelluloses. This finding dramatically widens the scope of LPMOs and oxidative processes in plant cell wall degradation and biorefining.
Sea star tenacity mediated by a protein that fragments, then aggregates
Authors: Hennebert Elise , Wattiez Ruddy , Demeuldre Mélanie , Ladurner Peter , Hwang Dong Soo , Waite J. Herbert , Flammang Patrick
Published: April 2014

Significance

Sea stars are emblematic of the seashore. Despite this, their ability to pry open mussels and attach strongly but temporarily to rocks in their environments are poorly understood. Here we report, to our knowledge, the first sequence of a protein, Sea star footprint protein 1 (Sfp1), a primary constituent of the adhesive footprints secreted by sea star tube feet. Sfp1 is unusually large and complex compared with other marine adhesive proteins such as those of mussels. It is translated from a single mRNA and then fragmented into four subunits, which display specific domains that mediate interactions with other proteins present in the adhesive material and on the tube foot surface. After secretion, Sfp1 forms a structural scaffold and appears to provide footprints with cohesion.
Essential role for TrpC5-containing extracellular vesicles in breast cancer with chemotherapeutic resistance
Authors: Ma Xin , Chen Zhen , Hua Dong , He Dongxu , Wang Linjun , Zhang Peng , Wang Junqi , Cai Yanfei , Gao Caiji , Zhang Xiaodong , Zhang Fangfang , Wang Teng , Hong Tingting , Jin Linfang , Qi Xiaowei , Chen Shuxian , Gu Xiaoting , Yang Dangtong , Pan Qiongxi , Zhu Yifei , Chen Yun , Chen Daozhen , Jiang Liwen , Han Xiaofeng , Zhang Yanyun , Jin Jian , Yao Xiaoqiang
Published: April 2014

Significance

A critical challenge for chemotherapy is development of chemoresistance, but underlying molecular mechanisms remain unclear. In this study, we found that drug-resistant adriamycin-resistant human breast cancer cells possessed numerous transient receptor potential channel 5 (TrpC5) -containing extracellular vesicles (EVs) on the cell surface. Suppressing TrpC5 expression diminished the formation of EVs. Incubation of drug-sensitive recipient cells with EVs endowed recipients with drug-resistant properties. In both human samples and a mouse model of breast cancer, the expression of TrpC5 proteins was high in the tumor, and the levels of TrpC5-positive EVs were high in the circulation. These data suggest a critical role of TrpC5-containing EVs in the transfer of drug resistance. In the future, monitoring TrpC5-containing EVs in the circulation could potentially be used to predict the clinical outcome of chemotherapy.
Measurement of histidine pKavalues and tautomer populations in invisible protein states
Authors: Hansen Alexandar L. , Kay Lewis E.
Published: April 2014

Significance

Electrostatic interactions in proteins play significant roles in conferring stability and in dictating function. Histidine residues are particularly important because their side chains can serve as both acids and bases over the physiological pH range and as both hydrogen bond donors and acceptors. Solution NMR spectroscopy is a powerful method for studying these residues in highly populated ground-state conformers. Here we develop a strategy for extending such studies to sparsely populated, short-lived protein states that can also play a significant role in defining protein function. An application to an invisible folding intermediate of the Im7 protein is provided, where site-specific pKavalues of histidine residues have been determined that explain the strong pH-dependent stability differences between native and intermediate states.
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR
Authors: Lee Soon Goo , Krishnan Hari B. , Jez Joseph M.
Published: April 2014

Significance

Nitrogen nodules formed by the symbiosis of rhizobial microbes and legume roots are essential for fixation of nitrogen in the environment. As part of the symbiosis that leads to nodule formation, a series of changes in gene expression of the Rhizobium must occur. The protein NolR is a global regulator of rhizobial genes for symbiosis and nodulation. Here, we describe the three-dimensional structure of this transcription factor in unliganded and DNA bound forms. These structures show how NolR recognizes asymmetric DNA binding sites and reveal a previously unknown mechanism for conformational switching that alters the energetics of interaction to accommodate variable DNA sequences. Two models for the role of NolR in the regulation of nodulation and symbiosis genes are also proposed.
Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset
Authors: Veiseh Mandana , Kwon Daniel H. , Borowsky Alexander D. , Tolg Cornelia , Leong Hon S. , Lewis John D. , Turley Eva A. , Bissell Mina J.
Published: April 2014

Significance

Tumor heterogeneity is a poorly understood phenomenon. We lack biomarkers for identifying aggressive primary tumor subsets that give rise to metastases and impact early cancer detection and treatment. Many solid tumors are known to accumulate hyaluronan (HA), a glycosaminoglycan, which is also produced by the tumor cells themselves. We report a quantitative approach for uncovering breast cancer heterogeneity using fluorescent HA to detect differential binding patterns to CD44 and RHAMM/HMMR receptors. This approach permits identification of tumor-cell subsets that bind high levels of HA, and may be applicable to other ligands/receptors and disease models. Despite representing the invasive/metastatic subset of parental tumors, unexpectedly, the high HA-binding subset was slow-growing, and is thus likely to be a source of dormancy and relapse.
Evolutionary pathway to increased virulence and epidemic group A
Streptococcus
disease derived from 3,615 genome sequences
Authors: Nasser Waleed , Beres Stephen B. , Olsen Randall J. , Dean Melissa A. , Rice Kelsey A. , Long S. Wesley , Kristinsson Karl G. , Gottfredsson Magnus , Vuopio Jaana , Raisanen Kati , Caugant Dominique A. , Steinbakk Martin , Low Donald E. , McGeer Allison , Darenberg Jessica , Henriques-Normark Birgitta , Van Beneden Chris A. , Hoffmann Steen , Musser James M.
Published: April 2014

Significance

Epidemics of microbial infections are a considerable threat to human and animal health. Analysis of 3,615 genome sequences, coupled with virulence studies in animals, permitted us to delineate the nature and timing of molecular events that contributed to an ongoing global human epidemic of infections caused by group A
Streptococcus
, the “flesh-eating” pathogen. We clarified decades-long uncertainty about the timing and sequence of genomic alterations that underpinned the global epidemic. Analyses of this type are crucial for developing better strategies to predict and monitor strain emergence and epidemics, formulate effective protective public health maneuvers, and develop or modify vaccines.
(Finite) statistical size effects on compressive strength
Authors: Weiss Jérôme , Girard Lucas , Gimbert Florent , Amitrano David , Vandembroucq Damien
Published: April 2014

Significance

Large structures generally fail under stresses significantly lower than those of small ones. This is the size effect on strength, one of the oldest problems of engineering, already discussed by Leonardo da Vinci and Edmé Mariotte centuries ago. One classical explanation is the weakest-link hypothesis: The larger the “chain” is, the larger the probability to find a weak link whose breaking will set the failure of the whole chain. We show, however, that it is irrelevant in the case of compressive loading, a situation particularly crucial for, e.g., geotechnical problems. Interpreting compressive failure as a critical transition between an “intact” and a “failed” state, we quantitatively explain the size effects on compressive strength of materials such as concrete, rocks, coal, ice, or granular materials.
Prevention of influenza by targeting host receptors using engineered proteins
Authors: Connaris Helen , Govorkova Elena A. , Ligertwood Yvonne , Dutia Bernadette M. , Yang Lei , Tauber Sandra , Taylor Margaret A. , Alias Nadiawati , Hagan Robert , Nash Anthony A. , Webster Robert G. , Taylor Garry L.
Published: April 2014

Significance

We have developed a new class of host-targeted biologics to prevent influenza by engineering multivalent carbohydrate-binding modules that bind with high affinity to sialic acid, the critical component of the influenza virus cell surface receptor. Mouse studies reveal a remarkable efficacy: a single 1-μg dose of the lead biologic given 7 d before a lethal challenge with 2009 pandemic H1N1 influenza virus provides complete protection. This new approach has the potential to be a front-line defense against any current and future influenza virus, overcoming viral escape to vaccines and antivirals. In addition, the biologics may have broader application against other respiratory pathogens.
Training-free atomistic prediction of nucleosome occupancy
Authors: Minary Peter , Levitt Michael
Published: April 2014

Significance

Nucleosomes alter gene expression by preventing transcription factors from occupying binding sites along DNA. Conventional methods to predict nucleosome occupancy are trained on observed DNA sequence patterns. The method presented here uses physical principles and all-atom force fields to predict both nucleosome occupancy along genomic sequences as well as binding to known positioning sequences. Our method calculates the energy of both nucleosomal and linear DNA of the given sequence. Based on the DNA deformation energy, we accurately predict the in vitro occupancy profile observed experimentally for a 20,000-bp genomic region. DNA with all C bases methylated at the 5 position shows less variation of nucleosome binding: Strong binding is weakened and weak binding is strengthened compared with normal DNA.
Methylation protects microRNAs from an AGO1-associated activity that uridylates 5′ RNA fragments generated by AGO1 cleavage
Authors: Ren Guodong , Xie Meng , Zhang Shuxin , Vinovskis Carissa , Chen Xuemei , Yu Bin
Published: April 2014

Significance

This study, for the first time to the authors' knowledge, establishes HUA1 enhancer 1 (HEN1) suppressor 1 as a 5′ fragment uridyl transferase and shows that uridylation triggers the degradation of 5′ fragments. This study also demonstrates that HEN1 suppressor 1 interacts with Argonaute (AGO1) and is able to act on microRNA substrates in the AGO1 complex. Furthermore, this study reveals that methylation protects microRNAs from AGO1-associated uridylation activity in plants. Because methylation and uridylation are conserved processes in small RNA pathways in plants and animals, this study may have a broad effect in related fields.
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
Authors: Schweikhard Volker , Meng Cong , Murakami Kenji , Kaplan Craig D. , Kornberg Roger D. , Block Steven M.
Published: April 2014

Significance

In higher organisms, DNA is bound to proteins and tightly packed within the nucleus, leaving only certain regions accessible for gene expression. As the enzyme RNA polymerase II (RNAPII) travels along the DNA template synthesizing RNA, it must contend with forces generated by various obstacles, and some of these forces are known to produce transient pausing and even transcriptional arrest. How do organisms deal with such problems? Using optical-trapping technology, we performed a single-molecule study of RNAPII interactions with transcription factors TFIIS and TFIIF, which are involved in modulating and regulating transcriptional elongation. By applying controlled loads to RNAPII and combinations of these factors, we learned about the mechanisms by which pausing and arrest are overcome.
Conserved electron donor complex Dre2–Tah18 is required for ribonucleotide reductase metallocofactor assembly and DNA synthesis
Authors: Zhang Yan , Li Haoran , Zhang Caiguo , An Xiuxiang , Liu Lili , Stubbe JoAnne , Huang Mingxia
Published: April 2014

Significance

Ribonucleotide reductases (RNR) play a critical role in supplying cellular deoxynucleotide pools. Nucleotide reduction by class Ia RNR requires a diferric-tyrosyl radical cofactor, which is a target of anticancer agents. How this essential cofactor is assembled in vivo is not well understood. We show here that a conserved protein complex composed of the Fe-S–requiring Dre2 and the diflavin-requiring Tah18, previously shown to donate electrons for Fe-S cluster assembly for proteins found in the cytosol and nucleus, also is required for RNR cofactor assembly. Deficiency in this complex leads to activation of both the DNA-damage checkpoint and the iron regulon, linking iron homeostasis to maintenance of genome stability. These findings may provide new insights into development of RNR-targeted therapeutics.
British Prime Minister David Cameron’s apology for Bloody Sunday
Authors: Edwards Jason A. , Luckie Amber
Published: April 2014

In this essay, we examine British Prime Minister David Cameron’s apology for “Bloody Sunday.” This case study offers one possible theoretical re-conceptualization of the apology genre that Villadsen argued for earlier in this book. We provide a theoretical framework to examine these apologies, which are dedicated to rebuilding and strengthening communal bonds harmed by historical injustice caused by one collective against another.
The Bridge
Authors: Van Belle Hilde
Published: April 2014

Barack Obama’s early public speeches were inherently and totally ‘rhetorical’. Obama used to find the perfect balance between logos, ethos and pathos, and (re)created the dream of American people engaged in solving problems and creating a community. He appealed to the belief in change that can a.o. be achieved by the art of speaking well. In this paper, I will show how Obama’s biographer David Remnick presents his subject as a living example of the rhetor. I will also show how the biography is structured around the general idea of rhetoric as a humanistic project. I will discuss the strength and problems of this approach, along with Remnick’s romantic notion about the arc of civil rights history and his urge to report on the election of the first black president.
Learning to differ
Authors: Ornatowski Cezar M.
Published: April 2014

The essay describes how Polish members of parliament (MPs) reinvented the institution of parliament (conceived of in its essentially discursive character as parleyment) in the course of the political transition of 1989. The reinvention of “parliamentary democracy” and deliberation in the chamber involved four interrelated developments: rearticulation of the “people” and thereby providing new basis for parliamentary “representation” and for the rhetorical agency of MPs; redefinition and rearticulation of the relationship between parliament and other organs of state power, especially government; emergence of deliberation through the dialectic between identification and division; and refunctionalization of verbal and non-verbal behaviors to enable exercise of MPs’ rhetorical agency in the plural context. The essay suggests a perspective that sees argumentation and debate as both shaped by and constitutive of “institutions,” a perspective that complements the view of argument and debate in interpersonal terms.
Consequences of Air Exposure on the Physiology and Behavior of Caught-and-Released Common Carp in the Laboratory and under Natural Conditions
Authors: Rapp Tobias , Hallermann Jan , Cooke Steven J. , Hetz Stefan K. , Wuertz Sven , Arlinghaus Robert
Published: April 2014

Specialized anglers of Common Carp Cyprinus carpio in Europe and increasingly in North America usually release trophy-sized fish, often following retention in carp sacks, to facilitate photographic memories. This practice is associated with extended air exposure. We assessed the impact of air exposure for a period of 10 min after capture and after an additional 9 h of retention in carp sacks on the physiology of small carp at two water temperatures (12°C and 22°C) under laboratory conditions. In a complementary field experiment with large carp, we also assessed the effects of air exposure on their physiology and additionally assessed the effects on tissue damage, postrelease behavior (i.e., movement and time rested), and survival. In the laboratory, plasma lactate increased by 24% during air exposure following simulated capture, and blood pH dropped by 0.16 units relative to a capture-only situation. Other physiological variables were unaffected by the treatment. In the field, air exposure after capture did not affect any physiological variables or indicators of tissue damage. During retention in carp sacks, fish recovered from capture, but subsequent air exposure caused a plasma lactate rise of 358% in the laboratory and 89% in the field experiment, and blood pH dropped by 0.38 units in the laboratory relative to that for the retained fish. In the field experiment, postrelease movement was significantly reduced in air-exposed fish, but normalized within 12 h. No mortalities occurred within 2 months postrelease. From a fish welfare perspective, our results suggest that photography should be conducted directly following capture without further retention in carp sacks as this approach is less deleterious to the fish. However, there is no benefit in doing so for maintaining carp populations because no substantial mortalities are to be expected. Overall, Common Carp are highly resilient to even extended air exposure.

Received April 26, 2013; accepted October 8, 2013
Black Bass and Crappie Use of Installed Habitat Structures in Table Rock Lake, Missouri
Authors: Allen Michael J. , Bush Shane C. , Vining Ivan , Siepker Michael J.
Published: April 2014

Reservoirs are important resources utilized by millions of freshwater anglers annually, but as reservoirs age the quality of the habitat that they provide for fish deteriorates. In 2007, a large-scale habitat improvement project began on Table Rock Lake, Missouri, with the goal of supplementing existing fish habitat in this large reservoir. Over 2,000 habitat structures composed of cedar, pine, hardwoods, stumps, and rocks were installed between 2007 and 2013. By means of scuba surveys, we evaluated the use of these structures by black bass Micropterus spp. and crappies Pomoxis spp. to determine whether it varied among fish species, fish sizes, and structure types. Black bass were observed utilizing all structure types but appeared to utilize hardwoods most. Covariates such as water depth and visibility at the structure confounded our analysis of black bass use, however, limiting our ability to clearly document differences in use. Crappies never used rock structures, and more crappies were observed on cedar structures than any other type. In Table Rock Lake, black bass were attracted to all structure types and crappies were attracted to all structure types except rock. Since fish use is similar across nearly all habitat types, other factors such as cost and installation times should be considered when planning habitat enhancement projects on large reservoirs.

Received August 12, 2013; accepted October 30, 2013