bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences between CAFs and their paired NCF from adjacent colonic mucosa reveal functional heterogeneity of CAFs, providing prognostic information
Authors: Berdiel-Acer Mireia , Sanz-Pamplona Rebeca , Calon Alexandre , Cuadras Daniel , Berenguer Antoni , Sanjuan Xavier , Paules Maria José , Salazar Ramon , Moreno Victor , Batlle Eduard , Villanueva Alberto , Molleví David G.
Published: May 2014

Little is known about the difference in gene expression between carcinoma‐associated fibroblasts (CAFs) and paired normal colonic fibroblasts (NCFs) in colorectal cancer. Paired CAFs and NCFs were isolated from eight primary human colorectal carcinoma specimens. In culture conditions, soluble factors secreted by CAFs in the conditioned media increased clonogenicity and migration of epithelial cancer cells lines to a greater extent than did NCF. In vivo, CAFs were more competent as tumour growth enhancers than paired NCFs when co‐inoculated with colorectal cell lines. Gene expression analysis of microarrays of CAF and paired NCF populations enabled us to identify 108 deregulated genes (38 upregulated and 70 downregulated genes). Most of those genes are fibroblast‐specific. This has been validated in silico in dataset GSE39396 and by qPCR in selected genes. GSEA analysis revealed a differential transcriptomic profile of CAFs, mainly involving the Wnt signallingsignalling pathway, focal adhesion and cell cycle. Both deregulated genes and biological processes involved depicted a considerable degree of overlap with deregulated genes reported in breast, lung, oesophagus and prostate CAFs. These observations suggest that similar transcriptomic programs may be active in the transition from normal fibroblast in adjacent tissues to CAFs, independently of their anatomic demarcation. Additionally NCF already depicted an activated pattern associated with inflammation.

The deregulated genes signature score seemed to correlate with CAF tumour promoter abilities in vitro, suggesting a high degree of heterogeneity between CAFs, and it has also prognostic value in two independent datasets.

Further characterization of the roles these biomarkers play in cancer will reveal how CAFs provide cancer cells with a suitable microenvironment and may help in the development of new therapeutic targets for cancer treatment.
A relative sea-level history for Arviat, Nunavut, and implications for Laurentide Ice Sheet thickness west of Hudson Bay
Authors: Simon Karen M. , James Thomas S. , Forbes Donald L. , Telka Alice M. , Dyke Arthur S. , Henton Joseph A.
Published: May 2014

Thirty-six new and previously published radiocarbon dates constrain the relative sea-level history of Arviat on the west coast of Hudson Bay. As a result of glacial isostatic adjustment (GIA) following deglaciation, sea level fell rapidly from a high-stand of nearly 170 m elevation just after 8000 cal yr BP to 60 m elevation by the mid Holocene (~ 5200 cal yr BP). The rate of sea-level fall decreased in the mid and late Holocene, with sea level falling 30 m since 3000 cal yr BP. Several late Holocene sea-level measurements are interpreted to originate from the upper end of the tidal range and place tight constraints on sea level. A preliminary measurement of present-day vertical land motion obtained by repeat Global Positioning System (GPS) occupations indicates ongoing crustal uplift at Arviat of 9.3 ± 1.5 mm/yr, in close agreement with the crustal uplift rate inferred from the inferred sea-level curve. Predictions of numerical GIA models indicate that the new sea-level curve is best fit by a Laurentide Ice Sheet reconstruction with a last glacial maximum peak thickness of ~ 3.4 km. This is a 30–35% thickness reduction of the ICE-5G ice-sheet history west of Hudson Bay.
Open Sourcing the Colonial Archive – A Digital Montage of the History of Fernando Pó and the Bight of Biafra
Authors: Martino Enrique
Published: May 2014

The archival sources gathered for my PhD research have all been posted to a blog,www.opensourceguinea.org. Among other things, the sources trace the migrants and laborers in and around the plantation island of Fernando Pó, moving through numerous empires and societies in Equatorial Guinea, Nigeria, Cameroon and Gabon for most of the twentieth century. Having sources “speak for themselves” to the “public” and even “amongst themselves” contributes not only to an expansionary information commons, but also to a methodological reorganization and pluralization. When a multiplicity of sources are displayed and interlinked as hypertext, the static conceptual lenses of traditional social and cultural history dissolve.
Writing Eritrea: History and Representation in a Bad Neighborhood
Authors: Reid Richard
Published: May 2014

This paper reflects on the ways in which Eritrea has been written about since circa 2001, the point at which the country entered a new phase of heightened authoritarianism and increased international isolation. It considers the ways in which Eritrea has been seen largely in “presentist” terms, due in no small way to the Eritrean government’s own intrinsic hostility to independent historical research, with an overwhelming fixation on its dire human rights and governance record, and on the nature of the Eritrean People’s Liberation Front (EPLF), which governs in all but name. The paper urges a more historical approach, beginning with the critical three decades that preceded the emergence of the EPLF in the early 1970s.
A shear instability mechanism for the pulsations of Rayleigh–Taylor unstable model flames
Authors: Hicks E. P.
Published: May 2014

Previous studies have shown that the behaviour of Rayleigh–Taylor (RT) unstable flames depends on the boundary conditions. If the boundary conditions at the domain walls are impermeable/adiabatic or reflecting then the flame assumes a stable parabolic shape. On the other hand, periodic boundary conditions can produce unstable pulsating solutions. In this paper, we explore why periodic boundary conditions allow unstable solutions by showing the results of two-dimensional direct numerical simulations of model flames. We show that RT unstable premixed model flames pulsate at low gravity because of a shear instability of the vorticity layers behind the flame front. The resulting vortex shedding is controlled by a region of absolute-like instability which moves closer to the flame front as gravity is increased, ultimately disturbing the flame and leading to pulsations. We demonstrate that this region is ‘absolutely unstable’ by showing that the wake is dominated by pure frequency oscillations. In addition, the shear instability can be described by the Landau equation and can be represented dynamically by a Hopf bifurcation. The applicability of the Landau equation allows the apparently complex spatio-temporal behaviour of the vortex shedding to be described by a simple temporal model with only a secondary spatial dependence. We show that the flame behaviour is analogous to the initial instability downstream of a circular cylinder, which leads to the von Kármán vortex street for large enough values of the Reynolds number.
Effect of plasma-β on the onset of plasmoid instability in Sweet–Parker current sheets
Authors: Baty H.
Published: May 2014

A numerical study of magnetic reconnection in two-dimensional resistive magnetohydrodynamics for Sweet–Parker current sheets that are subject to plasmoid instability is carried out. The effect of the initial upstream plasma-β on the critical Lundquist number Sc for the onset of plasmoid instability is studied. Our results indicate a weak dependence, with a value of Sc ≃ 1.5 × 104 in the limit of zero β, and a value of Sc ≃ 1 × 104 in the opposite high β regime (β ≫ 1). A similar dependence was previously obtained (Ni et al. 2012 Phys. Plasm. 19, 072902), but with a somewhat much larger variation, that can be largely attributed to the different configuration setup used in their study, and also to the definition of the Lundquist number. This conclusion does not depend significantly on the equilibrium used, i.e. both initial configurations with either plasma density or temperature spatial variations lead to very similar results. Finally, we show that the inner plasmoid structure appears as an under-dense hotted magnetic island, with a local temperature increase that is noticeably strengthened for low β cases.
Danish non-specific free relatives
Authors: Bjerre Anne
Published: May 2014

Within the Head-driven Phrase Structure Grammar (HPSG) community, one part of the Base Hypothesis concerning free relatives proposed by Bresnan & Grimshaw (1978) has gained wide support, namely that free relatives are headed by the wh-phrase. The second part of the hypothesis is that the wh-phrase is base-generated, and this has not gained support. In this paper, we will consider a subset of free relative constructions, i.e. non-specific free relatives, and provide support for this second part, restated in HPSG terms as a claim that there is no filler–gap relation between a free relative pronoun filler and a gap in the sister clause of the free relative pronoun.
Variation in Faroese and the development of a spoken standard: In search of corpus evidence
Authors: Knooihuizen Remco
Published: May 2014

Although Faroese exhibits extensive linguistic variation and rapid social change, the language is near-uncharted territory in variationist sociolinguistics. This article discusses some recent social changes in Faroese society in connection with language change, focusing in particular on the development of a de facto spoken standard, Central Faroese. Demographic mobility, media and education may be contributing to this development in different ways. Two linguistic variables are analysed as a first step towards uncovering the respective roles of standardisation, dialect levelling and dialect spread as contributing processes in the formation of Central Faroese: morphological variation in -stendings and phonological variation in -irand -urendings. The analysis confirms previously described patterns of geographically constrained variation, but no generational or stylistic differences indicative of language change are found, nor are there clear signs that informants use Central Faroese. The results may in part be due to the structure of the corpus used.
Note from the Editors
Authors: Hansson Gunnar Ólafur , Miestamo Matti , Ringen Catherine , Vikner Sten , Westergaard Marit
Published: May 2014

This is the first issue of volume 37 of the Nordic Journal of Linguistics. NJL is the journal of the Nordic Association of Linguists. Individuals may subscribe to the Journal by joining the Nordic Association of Linguists. The NAL membership form can be found on the Cambridge University Press web site of NJL, http://journals.cambridge.org/NJL, as well as on the NAL web site, http://www.uef.fi/nal.
Neonatal events, such as androgenization and postnatal overfeeding, modify the response to ghrelin
Authors: Novelle Marta G. , Vázquez María J. , Martinello Kátia D. , Sanchez-Garrido Miguel A. , Tena-Sempere Manuel , Diéguez Carlos
Published: May 2014

It is currently accepted that ambient, non-genetic factors influence perinatal development and evoke structural and functional changes that may persist throughout life. Overfeeding and androgenization after birth are two of these key factors that could result in “metabolic imprinting” of neuronal circuits early in life and, thereby, increase the body weight homeostatic “set point”, stimulate appetite and result in obesity. Our aim was to determine the influence of these obesogenic factors on the response to ghrelin. We observed the expected orexigenic effect of ghrelin regardless of the nutritional or hormonal manipulations to which the animals were subjected to at early postnatal development and this effect remained intact at later stages of development. In fact, ghrelin responses increased significantly when the animals were subjected to one of the two manipulations, but not when both were combined. An increased response to ghrelin could explain the obese phenotype displayed by individuals with modified perinatal environment.
Validated simultaneous determination of antipyrine and benzocaine HCl in the presence of benzocaine HCl degradation product
Authors: Merey Hanan A. , Zaazaa Hala E.
Published: May 2014

Two validated, sensitive and highly selective stability-indicating methods were adopted for the simultaneous quantitative determination of antipyrine (ANT) and benzocaine HCl (BEN) in the presence of the degradation product of benzocaine HCl [p-aminobenzoic acid (PABA)].
Towards chromate-free corrosion inhibitors: structure–property models for organic alternatives
Authors: Winkler D. A. , Breedon M. , Hughes A. E. , Burden F. R. , Barnard A. S. , Harvey T. G. , Cole I.
Published: May 2014

Progressive restrictions on the use of toxic chromate-based corrosion inhibitors present serious technical challenges.
Combined1H-NMR and1H–13C HSQC-NMR to improve urinary screening in autism spectrum disorders
Authors: Nadal-Desbarats Lydie , Aïdoud Nacima , Emond Patrick , Blasco Hélène , Filipiak Isabelle , Sarda Pierre , Bonnet-Brilhault Frédérique , Mavel Sylvie , Andres Christian R.
Published: May 2014

Improvement of urinary screening by combining1H and 2D HSQC NMR data in metabolomics: application in ASD.
A simple, label-free optical method for studies on the G-quadruplex/duplex competition inside duplex DNAs using a G-quadruplex-specific probe—TMPipEOPP
Authors: Zhu Li-Na , Huo Yan-Fang , Wu Bin
Published: May 2014

A label-free optical method was developed to probe G-quadruplex/duplex competition embedded in flanking duplex DNAs by using a G-quadruplex-specific optical probe, and some information on G-quadruplex/duplex competition was obtained.
pH dependent isotropic to nematic phase transitions in graphene oxide dispersions reveal droplet liquid crystalline phases
Authors: Tkacz Rachel , Oldenbourg Rudolf , Mehta Shalin B. , Miansari Morteza , Verma Amitabh , Majumder Mainak
Published: May 2014

The existence of a droplet liquid crystalline phase of graphene oxide (GO) is reported.
Glycine homopeptides: the effect of the chain length on the crystal structure and solid state reactivity
Authors: Smith Aaron J. , Ali Farukh I. , Soldatov Dmitriy V.
Published: May 2014

A series of linear oligoglycines has been studied to reveal the trends in their crystal structure, molecular conformation and thermally induced reactions.
Ab initio calculations on the1O2quenching mechanism by trans-resveratrol
Authors: Mazzone Gloria , Alberto Marta E. , Russo Nino , Sicilia Emilia
Published: May 2014

Computational exploration of possible reaction mechanisms oftrans-resveratrol with singlet molecular oxygen shows benzaldehydes as the most probable products.
Preparation of a ternary Pd–Rh–P amorphous alloy and its catalytic performance in selective hydrogenation of alkynes
Authors: Ren Mengrui , Li Changming , Chen Jiale , Wei Min , Shi Shuxian
Published: May 2014

Palladium–rhodium–phosphorus amorphous alloy nanoparticles were prepared via a facile one-pot synthesis method, exhibiting excellent catalytic behaviour in selective hydrogenation of alkynes.
Boron doped diamond biotechnology: from sensors to neurointerfaces
Authors: Hébert C. , Scorsone E. , Bendali A. , Kiran R. , Cottance M. , Girard H. A. , Degardin J. , Dubus E. , Lissorgues G. , Rousseau L. , Mailley P. , Picaud S. , Bergonzo P.
Published: May 2014

Boron doped nanocrystalline diamond is known as a remarkable material for the fabrication of sensors, taking advantage of its biocompatibility, electrochemical properties, and stability. Sensors can be fabricated to directly probe physiological species from biofluids (e.g. blood or urine), as will be presented. In collaboration with electrophysiologists and biologists, the technology was adapted to enable structured diamond devices such as microelectrode arrays (MEAs), i.e. common electrophysiology tools, to probe neuronal activity distributed over large populations of neurons or embryonic organs. Specific MEAs can also be used to build neural prostheses or implants to compensate function losses due to lesions or degeneration of parts of the central nervous system, such as retinal implants, which exhibit real promise as biocompatible neuroprostheses for in vivo neuronal stimulations. New electrode geometries enable high performance electrodes to surpass more conventional materials for such applications.
Improved light absorption and charge transport for perovskite solar cells with rough interfaces by sequential deposition
Authors: Zheng Lingling , Ma Yingzhuang , Chu Saisai , Wang Shufeng , Qu Bo , Xiao Lixin , Chen Zhijian , Gong Qihuang , Wu Zhaoxin , Hou Xun
Published: May 2014

A rougher interface between perovskite and HTM was introduced, resulting in simultaneous enhancements ofJscand PCE.
Free-standing electrochemical electrode based on Ni(OH)2/3D graphene foam for nonenzymatic glucose detection
Authors: Zhan Beibei , Liu Changbing , Chen Huaping , Shi Huaxia , Wang Lianhui , Chen Peng , Huang Wei , Dong Xiaochen
Published: May 2014

A facile method is developed for the one-pot preparation of hexagonal Ni(OH)2 nanosheets deposited on a 3DGF surface, which shows superior electrochemical performance for nonenzymatic glucose detection.
Impact of mono- and disubstitution on the colorimetric dynamic covalent switching chalcone/flavanone scaffold
Authors: Muller Brian M. , Mai Jesse , Yocum Reid A. , Adler Marc J.
Published: May 2014

The impact of substitution on a novel colorimetric dynamic covalent switching scaffold was investigated using UV/Vis and NMR spectroscopy.
Frustrated Lewis pair chemistry of carbon, nitrogen and sulfur oxides
Authors: Stephan Douglas W. , Erker Gerhard
Published: May 2014

Frustrated Lewis pairs have been used to activate a variety of small molecules.
Molybdenum carbide–carbon nanocomposites synthesized from a reactive template for electrochemical hydrogen evolution
Authors: Alhajri Nawal S. , Anjum Dalaver H. , Takanabe Kazuhiro
Published: May 2014

Active Mo2C–C nanocomposites were synthesized using an mpg-C3N4 template and demonstrated as active electrocatalysts for the hydrogen evolution reaction.
High performance of microtubular solid oxide fuel cells using Nd2NiO4+δ-based composite cathodes
Authors: Laguna-Bercero Miguel A. , Hanifi Amir R. , Monzón Hernán , Cunningham Joshua , Etsell Thomas H. , Sarkar Partha
Published: May 2014

Cathodes of porous YSZ supports infiltrated with Nd2NiO4+δ nanoparticles are offered as an alternative solution for IT-SOFC cathodes, presenting maximum power densities of 0.4 W cm−2 at 600 °C.
Substitution degree engineering the crystal packing and optoelectronic properties of benzofuranvinyl-substituted benzene-cored derivatives
Authors: Qiu Jin-Xing , Li Ye-Xin , Yang Xiao-Feng , Nie Yong , Zhang Zhen-Wei , Chen Zhong-He , Sun Guo-Xin
Published: May 2014

The molecular shape exerts remarkable effects on solubility, polymorphism, crystal packing and optoelectronic properties – searching for 3D organic semiconductors.
Simultaneous achievement of low efficiency roll-off and stable color in highly efficient single-emitting-layer phosphorescent white organic light-emitting diodes
Authors: Liu Baiquan , Wang Lei , Xu Miao , Tao Hong , Xia Xingheng , Zou Jianhua , Su Yueju , Gao Dongyu , Lan Linfeng , Peng Junbiao
Published: May 2014

Low efficiency roll-off, stable color and highly efficient single-EML phosphorescent WOLEDs are realized.
A Transactional Model of Spoken Vocabulary Variation in Toddlers With Intellectual Disabilities
Authors: Woynaroski Tiffany , Yoder Paul J. , Fey Marc E. , Warren Steven F.
Published: May 2014

Purpose

The authors examined (a) whether dose frequency of milieu communication teaching (MCT) affects children's canonical syllabic communication and (b) whether the relation between early canonical syllabic communication and later spoken vocabulary is mediated by parental linguistic mapping in children with intellectual disabilities (ID).

Method

The authors drew on extant data from a recent differential treatment intensity study in which 63 toddlers with ID were randomly assigned to receive either five 1-hr MCT sessions per week (i.e., daily treatment) or one 1-hr MCT session per week (i.e., weekly treatment) for 9 months. Children's early canonical syllabic communication was measured after 3 months of treatment, and later spoken vocabulary was measured at posttreatment. Midpoint parental linguistic mapping was measured after 6 months of treatment.

Results

A moderate-sized effect in favor of daily treatment was observed on canonical syllabic communication. The significant relation between canonical syllabic communication and spoken vocabulary was partially mediated by linguistic mapping.

Conclusions

These results suggest that canonical syllabic communication may elicit parental linguistic mapping, which may in turn support spoken vocabulary development in children with ID. More frequent early intervention boosted canonical syllabic communication, which may jump-start this transactional language-learning mechanism. Implications for theory, research, and practice are discussed.
One Step Back and Two Steps Up and Forward: The Superior Movements of Research Defining the Utility of the Mendelsohn Maneuver for Improving UES Function
Authors: McCullough Gary H.
Published: May 2014

The Mendelsohn maneuver has been used as both a compensatory strategy and a rehabilitation exercise since it was first described in the mid-1980s. Its purpose has been widely agreed upon: to improve hyolaryngeal movement and, consequently, opening of the upper esophageal sphincter during deglutition. Reports of success with the maneuver in isolation and as part of a larger regimen of treatments have been published. New technologies and research are clarifying the ways in which the Mendelsohn maneuver, as well as other treatments and strategies, impact swallowing musculature and bolus flow and provide improved understanding of the impact of various exercise protocols.
Mode matching pursuit for estimating dominant modes in bulk power grid
Authors: Jiang Tao , Jia Hongjie , Zhao Jinli , Ledwich Gerard , Wang Dan , Zhang Jinan , Qiu Lulu
Published: May 2014

This study presents a general approach to identify dominant oscillation modes in bulk power system by using wide‐area measurement system. To automatically identify the dominant modes without artificial participation, spectral characteristic of power system oscillation mode is applied to distinguish electromechanical oscillation modes which are calculated by stochastic subspace method, and a proposed mode matching pursuit is adopted to discriminate the dominant modes from the trivial modes, then stepwise‐refinement scheme is developed to remove outliers of the dominant modes and the highly accurate dominant modes of identification are obtained. The method is implemented on the dominant modes of China Southern Power Grid which is one of the largest AC/DC paralleling grids in the world. Simulation data and field‐measurement data are used to demonstrate high accuracy and better robustness of the dominant modes identification approach.
Is Theory King?: Questioning the Theory Fetish in Information Systems
Authors: Avison David , Malaurent Julien
Published: May 2014

This paper suggests that there is too much emphasis on the requirement for theory use and theory building in qualitative research published in our leading journals. We discuss six concerns that we have that relate to this high status of theory in such papers. We argue for what we refer to as ‘theory light’ papers where theory plays no significant part in the paper and the contribution lies elsewhere, for example, new arguments, facts, patterns or relationships. Some examples of theory light papers (and research) are provided from other disciplines and one exemplar information systems paper is studied in depth. We see these papers as equally worthy as those which demonstrate the applicability and predictive qualities of theory use as well as the potential of theory building. We propose a list of 10 questions that authors and reviewers might ask themselves when writing or reviewing such theory light papers. The more demanding role of the reader is also discussed along with the requirement for editorial teams to adapt. We suggest that the requirement for a contribution to theory would be replaced with the requirement that any journal paper has a high potential for stimulating research that will impact on information systems theory and/or practice.
Comparison of bifurcation dynamics of turbulent transport models for the L-H transition
Authors: Weymiens W. , Paquay S. , de Blank H. J. , Hogeweij G. M. D.
Published: May 2014

In more than three decades, a large amount of models and mechanisms have been proposed to describe a very beneficial feature of magnetically confined fusion plasmas: the L-H transition. Bifurcation theory can be used to compare these different models based on their dynamical transition structure. In this paper, we employ bifurcation theory to distinguish two fundamentally different descriptions of the interaction between turbulence levels and sheared flows. The analytic bifurcation analysis characterises the parameter space structure of the transition dynamics. Herewith, in these models three dynamically different types of transitions are characterised, sharp transitions, oscillatory transitions, and smooth transitions. One of the two models has a very robust transition structure and is therefore likely to be more accurate for such a robust phenomenon as the L-H transition. The other model needs more fine-tuning to get non-oscillatory transitions. These conclusions from the analytic bifurcation analysis are confirmed by dedicated numerical simulations, with the newly developed code Bifurcator.
Robotic calibration of the motional Stark effect diagnostic on Alcator C-Mod
Authors: Mumgaard Robert T. , Scott Steven D. , Ko Jinseok
Published: May 2014

The capability to calibrate diagnostics, such as the Motional Stark Effect (MSE) diagnostic, without using plasma or beam-into-gas discharges will become increasingly important on next step fusion facilities due to machine availability and operational constraints. A robotic calibration system consisting of a motorized three-axis positioning system and a polarization light source capable of generating arbitrary polarization states with a linear polarization angle accuracy of <0.05° has been constructed and has been used to calibrate the MSE diagnostic deployed on Alcator C-Mod. The polarization response of the complex diagnostic is shown to be fully captured using a Fourier expansion of the detector signals in terms of even harmonics of the input polarization angle. The system's high precision robotic control of position and orientation allow it to be used also to calibrate the geometry of the instrument's view. Combined with careful measurements of the narrow bandpass spectral filters, this system fully calibrates the diagnostic without any plasma discharges. The system's high repeatability, flexibility, and speed has been exploited to quantify several systematics in the MSE diagnostic response, providing a more complete understanding of the diagnostic performance.
Numerical investigations of shock wave interactions with a supersonic turbulent boundary layer
Authors: Jammalamadaka Avinash , Li Zhaorui , Jaberi Farhad
Published: May 2014

Direct numerical simulations (DNS) are conducted for a Mach 2.75 turbulent boundary layer interacting with an impinging shock at three different shock incidence angles. The accuracies of DNS calculations are established by checking the convergence of flow statistics for various grids, by comparing the generated results with those in the literature and also by the balance of contributing terms in the turbulent kinetic energy equation. Instantaneous flow visualizations show the significant effect of shock on turbulence structure in the shock-boundary layer interaction zone and also in the flow downstream of the interaction region. The separation bubbles exhibit highly unsteady and three-dimensional behavior and are larger for stronger shocks but the maximum probability of flow separation is found to be independent of the shock strength. The differences between Reynolds- and Favre-averaged quantities are also observed to be small and largely independent of the shock intensity. The turbulent kinetic energy is amplified across the shock, mainly by the production term in the turbulent kinetic energy equation. The amplification of enstrophy across the shock zone is found to be due to the vortex stretching term in the enstrophy transport equation. A detailed examination of the terms in the turbulent kinetic equation shows a strong coupling between the mean and turbulent fields in the interaction region with energy being continuously exchanged from one field to another. However, the compressibility-related terms in the transport equations for turbulent kinetic energy and enstrophy are found to be small for the simulated flows.
New insights on boundary plasma turbulence and the quasi-coherent mode in Alcator C-Mod using a Mirror Langmuir Probe
Authors: LaBombard B. , Golfinopoulos T. , Terry J. L. , Brunner D. , Davis E. , Greenwald M. , Hughes J. W. ,   Alcator C-Mod Team
Published: May 2014

A new “Mirror Langmuir Probe” diagnostic, combined with a double-coil scanning magnetic probe, is used to interrogate Alcator C-Mod's quasi-coherent mode (QCM) with unprecedented detail. In ohmic EDA H-modes, the QCM is found to reside in a region of positive radial electric field, with a radial width (∼3 mm) that spans open and closed field line regions. Large amplitude, in-phase sinusoidal bursts (∼100 kHz) in density, electron temperature, and plasma potential are observed, with potential lagging density by ∼16°, producing an outward radial transport velocity of ∼10 m/s. Mode propagation corresponds to the sum of local E × B and electron diamagnetic drift velocities. Poloidal magnetic field fluctuations project to current filaments carrying peak current densities of ∼25 A/cm2. An evaluation of parallel electron force balance (Ohm's law) over a fluctuation cycle indicates a significant electromotive component. Interchange drive is also a contributor in the current continuity (vorticity) equation. Thus, the QCM is primarily a separatrix-spanning electron drift-wave with interchange and electromagnetic contributions.
Vascular design for reducing hot spots and stresses
Authors: Rocha L. A. O. , Lorente S. , Bejan A.
Published: May 2014

This paper is a proposal to embed tree-shaped vasculatures in a wall designed such that the wall withstands without excessive hot spots and peak stresses the intense heating and pressure that impinge on it. The vasculature is a quilt of square-shaped panels, each panel having a tree vasculature that connects the center with the perimeter. The vascular designs for volumetric cooling can be complemented by the shaping and distributing of channels for maximum strength and thermal performance at the same time. Numerical simulations of heat flow and thermal stresses in three directions show that it is possible to determine the optimal geometric features of configurations with radial channels and trees with radial and one level of bifurcations. The global performance is evaluated in terms of the overall thermal resistance and peak von Mises stresses. The dendritic design is superior under the studied thermal condition.
Performance of solid oxide fuel cells approaching the two-dimensional limit
Authors: Kerman K. , Ramanathan S.
Published: May 2014

We model electrochemical kinetics and physical conduction mechanisms for carrier transport in electrolyte membranes to determine the limits of dimensionality reduction (down to 1 nm) on maximum power output of solid oxide fuel cells with symmetric Pt electrodes. Using Y-doped ZrO2, we find a minimum thickness of ∼6 nm to realize near ideal chemical potential in such fuel cells, which is limited by electronic breakdown when approaching the dielectric breakdown strength. For larger electrolyte thicknesses, the greatest source of electronic leakage influencing power loss is from Ohmic transport of minority carriers and emission of trapped carriers. For porous metallic electrodes, an ideal microstructure with the particle size comparable to particle spacing dimensions is found to accurately model experimental results. The role of electronic trap states in the electrolyte band gap on power density characteristics is highlighted.
Active control of thermoacoustic amplification in a thermo-acousto-electric engine
Authors: Olivier Come , Penelet Guillaume , Poignand Gaelle , Lotton Pierrick
Published: May 2014

In this paper, a new approach is proposed to control the operation of a thermoacoustic Stirling electricity generator. This control basically consists in adding an additional acoustic source to the device, connected through a feedback loop to a reference microphone, a phase-shifter, and an audio amplifier. Experiments are performed to characterize the impact of the feedback loop (and especially that of the controlled phase-shift) on the overall efficiency of the thermal to electric energy conversion performed by the engine. It is demonstrated that this external forcing of thermoacoustic self-sustained oscillations strongly impacts the performance of the engine, and that it is possible under some circumstances to improve the efficiency of the thermo-electric transduction, compared to the one reached without active control. Applicability and further directions of investigation are also discussed.
Field effect of in-plane gates with different gap sizes on the Fermi level tuning of graphene channels
Authors: Lin Meng-Yu , Chen Yen-Hao , Wang Cheng-Hung , Su Chen-Fung , Chang Shu-Wei , Lee Si-Chen , Lin Shih-Yen
Published: May 2014

Tuning of the Fermi level is investigated in graphene channels using two in-plane gates with significantly different-sized isolating gaps. While the n-type tuning was achievable in both schemes, the wide-gap device had an enhanced minimum drain current and less prominent current modulation than the narrow-gap device. In addition, further p-type tuning was not observed in the wide-gap device at negative gate biases. These phenomena indicated that both devices had distinct field-strength dependences and Fermi level tuning effects, which may be critical for the practical design of devices.
Coevolution can reverse predator–prey cycles
Authors: Cortez Michael H. , Weitz Joshua S.
Published: May 2014

Significance

The abundances of predators and their prey can oscillate in time. Mathematical theory of predator–prey systems predicts that in predator–prey cycles, peaks in prey abundance precede peaks in predator abundance. However, these models do not consider how the evolution of predator and prey traits related to offense and defense will affect the ordering and timing of peaks. Here we show that predator–prey coevolution can effectively reverse the ordering of peaks in predator–prey cycles, i.e., peaks in predator abundance precede peaks in prey abundance. We present examples from three distinct systems that exhibit reversed cycles, suggesting that coevolution may be an important driver of cycles in those systems.
Bet-hedging during bacterial diauxic shift
Authors: Solopova Ana , van Gestel Jordi , Weissing Franz J. , Bachmann Herwig , Teusink Bas , Kok Jan , Kuipers Oscar P.
Published: May 2014

Significance

More than 70 years ago, Monod described the phenomenon of diauxic growth of bacteria, the observation that in the presence of two alternative sugars, cells first use one of them and then, after a short lag phase, switch to the other. Until now it had been assumed that all cells in a population engage in the outgrowth on the second sugar after major metabolic adaptation of enzymatic composition has occurred, which takes time (hence the lag phase in growth). Here, we show that actually only a subpopulation is fit enough to partake in the second growth phase and present an evolutionary model, suggesting that this phenomenon might entail a bet-hedging strategy that helps bacteria adapt to the unexpectedly changing environment.
NLRX1 prevents mitochondrial induced apoptosis and enhances macrophage antiviral immunity by interacting with influenza virus PB1-F2 protein
Authors: Jaworska Joanna , Coulombe François , Downey Jeffrey , Tzelepis Fanny , Shalaby Karim , Tattoli Ivan , Berube Julie , Rousseau Simon , Martin James G. , Girardin Stephen E. , McCullers Jonathan A. , Divangahi Maziar
Published: May 2014

Significance

Apoptosis refers to the ability of a cell to undergo programmed cell death under normal physiological conditions or in response to stress signals. During infection, influenza A viruses have the capacity to induce early apoptosis of immune cells, thereby preventing them from performing their antiviral function. In this study, we identified that a host innate immune sensor [NLRX1 (nucleotide-binding oligomerization domain-like receptor X1)] has the capacity to bind a small death-inducing protein from influenza A virus [PB1-F2 (polymerase basic protein 1-frame 2)] and defend immune cells against virus-driven apoptosis. This phenomenon allows the immune cells to survive longer and effectively restrict viral replication, protecting the host against the detrimental consequences of influenza.
Location of the unique integration site on an
Escherichia coli
chromosome by bacteriophage lambda DNA in vivo
Authors: Tal Asaf , Arbel-Goren Rinat , Costantino Nina , Court Donald L. , Stavans Joel
Published: May 2014

Significance

Viral infection and integration is fundamental in the generation of genetic diversity in prokaryotes. After entering an
Escherichia coli
cell, bacteriophage λ DNA must locate a unique site among ∼5 million possible sites on the bacterial genome, with high efficiency and within physiological times, to integrate and establish lysogeny. How does it do it? We show that λ DNA does not carry out an active search. Instead, it remains confined at its entry point where it undergoes limited diffusion, while the process of bacterial DNA replication conveys the bacterial site close to the λ DNA. This mechanism adds to the list of profligate use of host functions by λ, brought about by coevolution of host−phage processes.
Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity
Authors: Meekins David A. , Raththagala Madushi , Husodo Satrio , White Cory J. , Guo Hou-Fu , Kötting Oliver , Vander Kooi Craig W. , Gentry Matthew S.
Published: May 2014

Significance

Starch is the main carbohydrate storage molecule in plants and is ubiquitous in human life. Reversible starch phosphorylation is the key regulatory event in starch catabolism. Starch Excess4 (SEX4) preferentially dephosphorylates the C6 position of starch glucose and its absence results in a dramatic accumulation of leaf starch. We present the structure of SEX4 bound to a phosphoglucan product, define its mechanism of specific activity, and reverse its specificity to the C3 position via mutagenesis. The ability to control starch phosphorylation has direct applications in agriculture and industrial uses of starch. These insights into SEX4 structure and function provide a foundation to control reversible phosphorylation and produce designer starches with tailored physiochemical properties and potentially widespread impacts.
Intrasperm vertical symbiont transmission
Authors: Watanabe Kenji , Yukuhiro Fumiko , Matsuura Yu , Fukatsu Takema , Noda Hiroaki
Published: May 2014

Significance

Diverse organisms are commonly associated with bacterial endosymbionts, which often affect hosts’ biology and phenotypes in a variety of ways. The majority of these symbionts are generally present in the host cell cytoplasm and maternally transmitted through host generations. Here, however, this conventional knowledge is countered by our discovery of intrasperm vertical transmission of nuclear-targeting bacterial symbiont (
Rickettsia
) in an insect (leafhopper
Nephotettix cincticeps
), which potentially erodes the nuclear-cytoplasmic conflict that governs the majority of endosymbiotic associations. The molecular and cellular mechanisms underlying the sperm head infection without disturbing sperm functioning are of not only basic but also applied interest, which may provide insights into the development of sperm-mediated genetic transformation and/or material delivery technologies.
Caspase-8 mediates caspase-1 processing and innate immune defense in response to bacterial blockade of NF-κB and MAPK signaling
Authors: Philip Naomi H. , Dillon Christopher P. , Snyder Annelise G. , Fitzgerald Patrick , Wynosky-Dolfi Meghan A. , Zwack Erin E. , Hu Baofeng , Fitzgerald Louise , Mauldin Elizabeth A. , Copenhaver Alan M. , Shin Sunny , Wei Lei , Parker Matthew , Zhang Jinghui , Oberst Andrew , Green Douglas R. , Brodsky Igor E.
Published: May 2014

Significance

Pathogenic organisms express virulence factors that can inhibit immune signaling pathways. Thus, the immune system is faced with the challenge of eliciting an effective inflammatory response to pathogens that actively suppress inflammation. The mechanisms that regulate this response are largely undefined. The
Yersinia
virulence factor YopJ blocks NF-κB and MAPK signaling, resulting in reduced cytokine production and target cell death. Here, we find that caspase-8, RIPK1, and FADD are required for YopJ-induced cell death and show that mice lacking caspase-8 are severely susceptible to
Yersinia
infection and have defective proinflammatory cytokine production. These findings highlight a possible mechanism of immune defense that can overcome pathogen inhibition of cell-intrinsic proinflammatory immune responses.
Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes
Authors: Mazor Ronit , Eberle Jaime A. , Hu Xiaobo , Vassall Aaron N. , Onda Masanori , Beers Richard , Lee Elizabeth C. , Kreitman Robert J. , Lee Byungkook , Baker David , King Chris , Hassan Raffit , Benhar Itai , Pastan Ira
Published: May 2014

Significance

Recombinant immunotoxins have produced complete remissions in leukemia patients where many doses can be given but are less active in patients with solid tumors because their immune system makes antidrug antibodies, which inactivate the immunotoxin. To suppress the immune response, we have identified and largely silenced the T-cell epitopes responsible for the immune response. A redesigned immunotoxin with T-cell epitope mutations is highly cytotoxic to cell lines and to cells isolated from cancer patients and produces complete remissions in mice with human cancer xenografts. The approach described can be applied to deimmunize other therapeutically useful foreign proteins.
Projected land-use change impacts on ecosystem services in the United States
Authors: Lawler Joshua J. , Lewis David J. , Nelson Erik , Plantinga Andrew J. , Polasky Stephen , Withey John C. , Helmers David P. , Martinuzzi Sebastián , Pennington Derric , Radeloff Volker C.
Published: May 2014

Significance

Land-use change affects the provision of ecosystem services and wildlife habitat. We project land-use change from 2001 to 2051 for the contiguous United States under two scenarios reflecting continuation of 1990s trends and high crop demand more reflective of the recent past. These scenarios result in large differences in land-use trajectories that generate increases in carbon storage, timber production, food production from increased yields (even with declines in cropland area), and >10% decreases in habitat for one-quarter of modeled species. We analyzed three policy alternatives that provide incentives to maintain and expand forest cover, conserve natural habitats, and limit urban sprawl. Policy interventions need to be aggressive to significantly alter underlying land-use trends and shift the trajectory of ecosystem service provision.
Mutation of mouse
Samd4
causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling
Authors: Chen Zhe , Holland William , Shelton John M. , Ali Aktar , Zhan Xiaoming , Won Sungyong , Tomisato Wataru , Liu Chen , Li Xiaohong , Moresco Eva Marie Y. , Beutler Bruce
Published: May 2014

Significance

Whereas many heritable obesity phenotypes are known, lean phenotypes are comparatively uncommon. Yet they can reveal critical checkpoints regulating energy balance. During a large-scale random germ-line mutagenesis project, we identified mice with a lean phenotype, myopathy, excessive energy expenditure despite diminished cage activity, and impaired glucose tolerance. This phenotype, termed “
supermodel,
” was strictly recessive and was ascribed to a missense mutation in
Sterile alpha motif domain containing protein 4
(
Samd4
), a gene encoding an RNA-binding protein with no previously known function in mammals. This study provides evidence that Samd4 modulates the activities of the mechanistic target of rapamycin complex 1, a master regulator of metabolism.
Antisense-mediated
FLC
transcriptional repression requires the P-TEFb transcription elongation factor
Authors: Wang Zhi-Wei , Wu Zhe , Raitskin Oleg , Sun Qianwen , Dean Caroline
Published: May 2014

Significance

Noncoding transcripts are found in high complexity but low abundance in most genomes, but their functional relevance is unclear. We investigate the function of a set of antisense transcripts expressed from an important floral repressor gene in
Arabidopsis
. Different polyadenylated forms of the antisense transcripts correlate with high or low expression states of the floral repressor gene. We now identify a mutation in a conserved transcription elongation factor that specifically disrupts the antisense transcription. The direct reduction of antisense transcription releases a repression mechanism that indirectly increases expression of both the floral repressor gene and antisense expression. This study reveals tight interplay between sense and antisense transcription and a mechanism that could have a widespread role in quantitative gene regulation.
Hypoxia-inducible factor-dependent signaling between triple-negative breast cancer cells and mesenchymal stem cells promotes macrophage recruitment
Authors: Chaturvedi Pallavi , Gilkes Daniele M. , Takano Naoharu , Semenza Gregg L.
Published: May 2014

Significance

The recruitment of host stromal cells, such as macrophages and mesenchymal stem cells (MSCs), to the primary tumor is a critical step toward cancer malignancy. We have identified signals that are exchanged between breast cancer cells (BCCs) and MSCs. This signaling increases the recruitment of both MSCs and macrophages to primary tumors and increases metastasis of BCCs to lymph nodes and lungs. Reduced oxygen levels (hypoxia) in breast cancers are associated with increased risk of metastasis and decreased patient survival. We show that hypoxia stimulates signaling between BCCs and MSCs due to the activity of hypoxia-inducible factors (HIFs). Drugs that block HIF activity prevent signaling and macrophage recruitment, which suggests that they may be useful additions to breast cancer therapy.
Drosophila Valosin-Containing Protein
is required for dendrite pruning through a regulatory role in mRNA metabolism
Authors: Rumpf Sebastian , Bagley Joshua A. , Thompson-Peer Katherine L. , Zhu Sijun , Gorczyca David , Beckstead Robert B. , Jan Lily Yeh , Jan Yuh Nung
Published: May 2014

Significance

The ubiquitin–proteasome system (UPS) is required for
Drosophila
class IV dendritic arborization neuron dendrite pruning. We found that mutants in the ubiquitylation machinery, the ubiquitin-dependent chaperone
Valosin-Containing Protein
(
VCP
), and the 19S regulatory particle of the proteasome—but not the 20S core particle—showed defects in pruning gene expression and mislocalization or overexpression of specific mRNA-binding proteins. In the case of
VCP
inhibition, we were able to detect a specific change in the splicing pattern of a pruning gene that likely contributes to pruning defects. A link between
VCP
and mRNA-binding proteins had been observed in the context of human neurodegenerative disease. This study implicates a specific function of
VCP
and ubiquitin in mRNA metabolism.