bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting HER2‐positive cancer cells with receptor‐redirected anthrax protective antigen
Authors: McCluskey Andrew J. , Olive Andrew J. , Starnbach Michael N. , Collier R. John
Published: December 2012

Targeted therapeutics have emerged in recent years as an attractive approach to treating various types of cancer. One approach is to modify a cytocidal protein toxin to direct its action to a specific population of cancer cells. We created a targeted toxin in which the receptor‐binding and pore‐forming moiety of anthrax toxin, termed Protective Antigen (PA), was modified to redirect its receptor specificity to HER2, a marker expressed at the surface of a significant fraction of breast and ovarian tumors. The resulting fusion protein (mPA‐ZHER2) delivered cytocidal effectors specifically into HER2‐positive tumor cells, including a trastuzumab‐resistant line, causing death of the cells. No off‐target killing of HER2‐negative cells was observed, either with homogeneous populations or with mixtures of HER2‐positive and HER2‐negative cells. A mixture of mPA variants targeting different receptors mediated killing of cells bearing either receptor, without affecting cells devoid of these receptors. Anthrax toxin may serve as an effective platform for developing therapeutics to ablate cells bearing HER2 or other tumor‐specific cell‐surface markers.
Nonlinear Dynamic Analysis for FGM Circular Plates
Authors: Dai H.-L. , Yan X. , Yang L.
Published: December 2012

In the paper, nonlinear dynamic analysis of a circular plate composed of functionally graded material (FGM) is presented. Considering a transverse shear deformation and geometric nonlinearity, the von Karman geometric relation of the FGM circular plate is established. Based on the theory of the first-order shear deformation, a new set of equilibrium equations is developed by the principle of minimum total energy. Applying the finite difference method and Newmark scheme, the nonlinear transient problem is solved by the iterative method. To validate the presented method, the transient problem of the FGM circular plate is compared with those of the existed literature, and good agreement is observed. The effects of the volume fraction index, boundary conditions, mechanical load and the ratio of thickness to radius on the nonlinear transient problem of the FGM circular plate are investigated.
How do individuals reason in the Wason card selection task?
Authors: Wagenmakers Eric-Jan
Published: December 2012

The probabilistic approach to human reasoning is exemplified by the information gain model for the Wason card selection task. Although the model is elegant and original, several key aspects of the model warrant further discussion, particularly those concerning the scope of the task and the choice process of individuals.
Modern industrial policy and zoning: Chicago, 1910–1930
Authors: LEWIS ROBERT
Published: December 2012

Industrial policy has long been considered a federal responsibility. Indeed, most scholars date modern local economic development programmes as starting in the 1960s. Before that, in this view, industrial policy wasad hoc, unco-ordinated and fragmented. In this article, I argue that the origins of modern industrial policy initiated by the local state slowly emerged at the beginning of the twentieth century in Chicago. Using an assortment of sources, I show that a new type of industrial policy was forged in the conflict over the 1923 zoning ordinance. The city's real-estate, financial and political elites were able to mobilize information, science, funding, individuals and arguments to convince industrialists that zoning was to their advantage. In the process, the city's industrial interests were able to frame the new zoning ordinance to their ends.
From ‘the people’ to ‘the citizen’: the emergence of the Edwardian municipal park in Manchester, 1902–1912
Authors: O'REILLY CAROLE
Published: December 2012

This article argues that the Edwardian municipal park represents a significant transition from the highly regulated and formal space of the Victorian park. It takes as a case-study Heaton Park in Manchester purchased in late 1901 and suggests that this park represented a transition from a Victorian people's park to an Edwardian citizen's park in which each visitor accessed facilities and amenities appropriate to their individual or group leisure interests. It addresses the comparative neglect of the Edwardian park by urban historians and suggests the importance of the emerging concepts of citizenship and social responsibility.
Disputed transformations: deindustrialization and redevelopment of Cologne's Stollwerck factory, 1970–1980
Authors: HAUMANN SEBASTIAN
Published: December 2012

Urban development corresponds with economic shifts. In the second half of the twentieth century, when traditional forms of industrial production declined in many western cities, this posed new kinds of challenges. Cities were in need of a new economic base and at the same time had to cope with the abandonment of industrial sites. This article highlights the agency of local societies in shaping this process of deindustrialization and redevelopment. It interprets deindustrialization and redevelopment as a process of transformation which was open-ended and a matter of intense negotiation between diverging interests at the local level. In analysing the highly contentious case of the disused Stollwerck chocolate factory in Cologne, the article traces a complex set of site-specific factors of deindustrialization and redevelopment.
Gender effect on the relationship between stress hormones and panic-agoraphobic spectrum dimensions in healthy subjects
Authors: Dell'Osso Liliana , Marazziti Donatella , Da Pozzo Eleonora , Conversano Ciro , Baroni Stefano , Massimetti Gabriele , Martini Claudia , Carmassi Claudia
Published: December 2012

Introduction

Alterations of the hypothalamic-pituitary-adrenal (HPA) axis and of its peripheral indices have been reported in both normal and pathological anxiety with controversial findings. The aim of the present study was to investigate the possible correlations between serum cortisol and dehydroepiandrosterone-sulfate (DHEA-S) levels and DHEA-S/cortisol ratio, and panic-agoraphobic spectrum dimensions in a sample of healthy subjects.

Methods

Forty-two healthy subjects of both sexes, with no current or lifetime psychiatric disorders, were assessed by means of the Structured Clinical Interview for DSM-IV (SCID-I/P) and the so-called Panic Agoraphobic Spectrum-Self Report lifetime version (PAS-SR).

Results

Significant, negative correlations were found between cortisol levels and the total score of the separation sensitivity, panic-like symptoms, and medication/substance sensitivity PAS-SR domains. The PAS-SR total and the panic-like symptoms domain scores were positively related to the DHEAS/cortisol ratio. When the sample was divided in women and men, these correlations were present in women only.

Discussion

These findings, while indicating the presence of significant relationships between panic-agoraphobic traits and some indices of HPA axis functioning in healthy women, would suggest this as one of the factors explaining the greater vulnerability of women to cross the line between normal and pathological anxiety.

Conclusions

Further studies are needed to explore gender differences in the relationships between HPA axis alterations and the panic-agoraphobic spectrum dimensions.
Response to Matthew N. Beckmann's review of The Speaker of the House: A Study of Leadership
Authors: Green Matthew N.
Published: December 2012

Matthew Beckmann offers a penetrating, insightful, and eminently fair review of my book. Although I agree with most of his critiques, I offer my thoughts with respect to three questions that Beckmann says are not fully addressed by my study.
Response to Matthew N. Green's review of Pushing the Agenda: Presidential Leadership in U.S. Lawmaking, 1953–2004
Authors: Beckmann Matthew N.
Published: December 2012

In Pushing the Agenda, I sought to revisit the basic tenets of presidential coalition building on Capitol Hill. My hope was that tracing the White House's lobbying strategies would not only reveal how they are intended to work but also offer a better blueprint for assessing if they do. To those ends, I theorized that the White House has two basic lobbying strategies—an early game (agenda-centered) strategy aimed at shaping the legislative alternatives considered and an endgame (vote-centered) strategy aimed at determining which prevailed. Tests with a diverse assortment of original data—on the practice of lobbying, the results of key roll-call votes, and the passage of new laws—all corroborated a key point: presidential coalition building operates differently than scholars have thought, with effects greater than previously realized.
Response to Sharon Erickson Nepstad's review of Violence, Nonviolence, and the Palestinian National Movement
Authors: Pearlman Wendy
Published: December 2012

Sharon Erickson Nepstad's thoughtful review makes important points. I am gratified by what she describes as my contributions, and no less appreciative of her discussion of areas in which a stronger contribution might have been made. Many of these are questions that my book raises and that I hope future research will investigate.
Neoliberalism, Race, and the American Welfare State
Authors: Ernst Rose
Published: December 2012

Disciplining the Poor: Neoliberal Paternalism and the Persistent Power of Race.By Joe Soss, Richard C. Fording, and Sanford F. Schram. Chicago: University of Chicago Press, 2011. 368p. $75.00 cloth, $25.00 paper.

It is more than 15 years since the Personal Responsibility and Work Opportunity Act was passed in 1996, famously described by then-President Bill Clinton as “the end of welfare as we know it.” InDisciplining the Poor, Joe Soss, Richard Fording, and Sanford Schram analyze recent changes in US welfare policy as reflections of broader transformations of the “governance” of poverty, arguing that these transformations represent a new form of “neoliberal paternalism” in which race continues to be an important element. In this symposium, a diverse group of political scientists working on welfare issues have been asked to critically assess the book's account and to comment more broadly on the importance of the “governance of poverty” to the future of American politics.—Jeffrey C. Isaac, Editor
Improbable but Potentially Pivotal Oppositions: Privatization, Capitalists, and Political Contestation in the Post-Soviet Autocracies
Authors: Junisbai Barbara
Published: December 2012

Reflecting a chiefly economic approach to understanding political outcomes, a burgeoning literature on post-Soviet political economy finds a strong link between privatization and political pluralism in the region. To test whether the political promise of economic liberalization and the logic of modernization that underlies it hold true, I draw on existing and original data on privatization, pluralism, and opposition movements throughout the region from early independence to the present. The data reveal a fundamentally different formulation of the relationship between economics and politics than that found in the standard causal account. Contrary to approaches that stress the “the primacy of economics” in determining political outcomes, numerous cases of post-Soviet capitalist defection to the political opposition clearly point to “the primacy of politics”: the tangible ways that formal and informal institutions structure economic opportunities and ultimately impinge on individual calculations to comply with, oppose, or seek refuge from the regime.
From the EFPA Network of National News Correspondents
Authors: Polisenska Veronika
Published: December 2012

The first report from the Network of National News Correspondents (NNC) was published in European Psychologist 3 (2012) to keep readers informed of what is happening in the field of psychology in countries across Europe. We hope this second report proves just as informative. It includes news from Cyprus, Germany, Portugal, Slovenia, and Spain. Cyprus reports on legislation concerning professional psychologists and the provision of continued education. Germany provides news on the launch of EuroPsy and the release of an authorized translation of the International Test Commission (ITC) guidelines. Portugal describes a successful conference and the unemployment situation among psychologists. Slovenia announces the approval of its National Accreditation Committee for the EuroPsy. Spain reports on the cooperation agreements the Spanish Psychological Association (COP) has signed with the American Psychological Association (APA) and the Portuguese Psychologists’ Association (OPP), as well as on COP’s efforts in the field of active aging.
Morphological and spatial control of InP growth using closed-space sublimation
Authors: Kiriya Daisuke , Zheng Maxwell , Kapadia Rehan , Zhang Junjun , Hettick Mark , Yu Zhibin , Takei Kuniharu , Hank Wang Hsin-Hua , Lobaccaro Peter , Javey Ali
Published: December 2012

Scalable growth of high quality III-V semiconductor thin films on non-epitaxial substrates is of profound interest for photovoltaic applications. Here, we demonstrate growth of indium phosphide (InP) crystals directly on metal foils using closed-space sublimation (CSS) method. CSS allows effective transfer of source material to the substrate due to a small (∼2 mm gap between source and substrate) sublimation space. The crystallization kinetics are found to be dependent on the substrate temperature and pressure of the system. Importantly, experiments revealed that both InP nanowires and polycrystalline films could be obtained by tuning the growth conditions. Furthermore, utilizing a silicon dioxide mask, selective nucleation of InP on metal substrates was obtained. Photoluminescence measurements depict the high optical quality of the CSS grown InP.
Refractory two-dimensional hole gas on hydrogenated diamond surface
Authors: Hiraiwa Atsushi , Daicho Akira , Kurihara Shinichiro , Yokoyama Yuki , Kawarada Hiroshi
Published: December 2012

Use of two-dimensional hole gas (2DHG), induced on a hydrogenated diamond surface, is a solution to overcoming one of demerits of diamond, i.e., deep energy levels of impurities. This 2DHG is affected by its environment and accordingly needs a passivation film to get a stable device operation especially at high temperature. In response to this requirement, we achieved the high-reliability passivation forming an Al2O3 film on the diamond surface using an atomic-layer-deposition (ALD) method with an H2O oxidant at 450 °C. The 2DHG thus protected survived air annealing at 550 °C for an hour, establishing a stable high-temperature operation of 2DHG devices in air. In part, this achievement is based on high stability of C-H bonds up to 870 °C in vacuum and above 450 °C in an H2O-containing environment as in the ALD. Chemically, this stability is supported by the fact that both the thermal decomposition of C-H bonds and reaction between C-H bonds and H2O are endothermic processes. It makes a stark contrast to the instability of Si-H bonds, which decompose even at room temperature being exposed to atomic hydrogen. In this respect, the diamond 2DHG devices are also promising as power devices expectedly being free from many instability phenomena, such as hot carrier effect and negative-bias temperature instability, associated with Si devices. As to adsorbate, which is the other prerequisite for 2DHG, it desorbed in vacuum below 250 °C, and accordingly some new adsorbates should have adsorbed during the ALD at 450 °C. As a clue to this question, we certainly confirmed that some adsorbates, other than those at room temperature, adsorbed in air above 100 °C and remained at least up to 290 °C. The identification of these adsorbates is open for further investigation.
Plane waveguides with corners in the small angle limit
Authors: Dauge Monique , Raymond Nicolas
Published: December 2012

The plane waveguides with corners considered here are infinite V-shaped strips with constant thickness. They are parametrized by their sole opening angle. We study the eigenpairs of the Dirichlet Laplacian in such domains when this angle tends to 0. We provide multi-scale asymptotics for eigenpairs associated with the lowest eigenvalues. For this, we investigate the eigenpairs of a one-dimensional model which can be viewed as their Born-Oppenheimer approximation. We also investigate the Dirichlet Laplacian on triangles with sharp angles. The eigenvalue asymptotics involve powers of the cube root of the angle, while the eigenvector asymptotics include simultaneously two scales in the triangular part, and one scale in the straight part of the guides.
Long-range interactions in the ozone molecule: Spectroscopic and dynamical points of view
Authors: Lepers Maxence , Bussery-Honvault Béatrice , Dulieu Olivier
Published: December 2012

Using the multipolar expansion of the electrostatic energy, we characterized the asymptotic interactions between an oxygen atom O(3P) and an oxygen molecule \documentclass[12pt]{minimal}\begin{document}${\rm O}_2(\sideset{^3}{_{g}^{-}}{\Sigma})$\end{document}O2(Σg−3), both in their electronic ground state. We calculated the interaction energy induced by the permanent electric quadrupoles of O and O2 and the van der Waals energy. On one hand, we determined the 27 electronic potential energy surfaces including spin-orbit connected to the O(3P) + \documentclass[12pt]{minimal}\begin{document}${\rm O}_2(\sideset{^3}{_{g}^{-}}{\Sigma})$\end{document}O2(Σg−3) dissociation limit of the O–O2 complex. On the other hand, we computed the potential energy curves characterizing the interaction between O(3P) and a rotating \documentclass[12pt]{minimal}\begin{document}${\rm O}_2(\sideset{^3}{_{g}^{-}}{\Sigma})$\end{document}O2(Σg−3) molecule in its lowest vibrational level. Such curves are found adiabatic to a good approximation, namely, they are only weakly coupled to each other. These results represent a first step for modeling the spectroscopy of ozone bound levels close to the dissociation limit, as well as the low energy collisions between O and O2 thus complementing the knowledge relevant for the ozone formation mechanism.
Excitation of a slow wave structure
Authors: Zhang Peng , Hoff Brad , Lau Y. Y. , French D. M. , Luginsland J. W.
Published: December 2012

The Green's function on a slow wave structure is constructed. The Green's function includes all radial modes, and for each radial mode, all space harmonics. We compare the analytic solution of the frequency response on the slow wave structure with that obtained from a particle-in-cell code. Favorable comparison is obtained when the first few lower order modes are resonantly excited. This gives some confidence in the prediction of converting a pulse train into radiation using a slow wave structure.
A coarse-grained transport model for neutral particles in turbulent plasmas
Authors: Mekkaoui A. , Marandet Y. , Reiter D. , Boerner P. , Genesio P. , Rosato J. , Capes H. , Koubiti M. , Godbert-Mouret L. , Stamm R.
Published: December 2012

The transport of neutral particles in turbulent plasmas is addressed from the prospect of developing coarse-grained transport models which can be implemented in code suites like B2-EIRENE, currently used for designing the ITER divertor. The statistical properties of turbulent fluctuations are described by a multivariate Gamma distribution able to retain space and time correlations through a proper choice of covariance function. We show that in the scattering free case, relevant for molecules and impurity atoms, the average neutral particle density obeys a Boltzmann equation with an ionization rate renormalized by fluctuations. This result lends itself to a straightforward implementation in the EIRENE Monte Carlo solver for neutral particles. Special emphasis is put on the inclusion of time correlations, and in particular on the ballistic motion of coherent turbulent structures. The role of these time dependent effects is discussed for D2 molecules and beryllium atoms. The sensitivity of our results to the assumptions on the statistical properties of fluctuations is investigated.
Unipolar to ambipolar conversion in graphene field-effect transistors
Authors: Feng Tingting , Xie Dan , Lin Yuxuan , Tian He , Zhao Haiming , Ren Tianling , Zhu Hongwei
Published: December 2012

Unlike commonly observed ambipolar graphene field-effect transistors (GFETs) that show a V-shape transfer curve with hole and electron conduction region switching at the Dirac point, all our GFETs with graphene from chemical vapor deposition show p-type unipolar conduction under a wide range of back-gate voltage sweeping. After evaporating 3 nm-thick Al thin film on graphene surface, the unipolar characteristic was changed to ambipolar. The reason for this conversion might be that the as-prepared GFETs were p-type doped during the device fabrication process, while Al film has an n-type doping effect on graphene, thus restoring the intrinsic characteristics of GFETs.
Laser-induced effects on the electronic features of graphene nanoribbons
Authors: Calvo Hernán L. , Perez-Piskunow Pablo M. , Roche Stephan , Foa Torres Luis E. F.
Published: December 2012

We study the interplay between lateral confinement and photon-induced processes on the electronic properties of illuminated graphene nanoribbons. We find that by tuning the device setup (edges geometries, ribbon width, and polarization direction), a laser with frequency Ω may either not affect the electronic structure, or induce bandgaps or depletions at ±ℏΩ/2, and/or at other energies not commensurate with half the photon energy. Similar features are also observed in the dc conductance, suggesting the use of the polarization direction to switch on and off the graphene device. Our results could guide the design of novel types of optoelectronic nano-devices.
Ultrafast polarization modulation in vertical cavity surface emitting lasers with frequency dependent current injection
Authors: Barve A. V. , Zheng Y. , Johansson L. , Mehta A. , Husain A. , Coldren L.
Published: December 2012

We report on a polarization modulation in vertical cavity surface emitting lasers (VCSEL), based on RF electrical injection. Complex polarization dynamics in the single mode regime is studied as a function of RF frequency and power at different bias currents. It has been observed that the polarization state of the VCSEL can be altered by changing the frequency of RF current modulation. Time resolved measurements show that by injecting periodic bursts of RF modulation in the VCSEL, it is possible to change the dominant polarization between the two orthogonal modes at gigahertz rates.
Mode latching and self tuning of whispering gallery modes in a stand-alone silica microsphere
Authors: Agarwal Monica , Teraoka Iwao
Published: December 2012

Performance of whispering gallery mode resonators can be compromised by resonance wavelength fluctuations. Here, we employ a silica microsphere coupled with a pair of head-on, single-ended tapers to show that the resonator by itself can latch onto a specific mode when the wavelength of a high-power laser changes over many resonance peak widths in both directions. We also show that, at high power of pump-in laser, the resonator can self-tune its resonance to a fixed wavelength when the resonator temperature changes or the gas flow surrounding the resonator changes, but the resonance is easily lost when the power is low.
Measurement of polarization-induced electric fields in GaN/AlInN quantum wells
Authors: Zhou Lin , Gonschorek Marcus , Giraud Etienne , Feltin E. , Carlin J. F. , Grandjean Nicolas , Smith David J. , McCartney Martha R.
Published: December 2012

GaN(Si)/AlInN multiple quantum wells were grown on GaN/Al2O3 (0001) templates by metalorganic vapor-phase epitaxy. Transmission electron microscopy observations showed well-defined GaN quantum wells and AlInN barrier layers. Electrostatic potential profiles across the heterostructure have been measured using off-axis electron holography. A polarization-induced electric field with magnitude of ∼2.2 ± 0.1 MV/cm was measured across the GaN quantum wells, in reasonable agreement with simulated values. However, the measured fields across the AlInN barriers were considerably less than predicted from simulations: possible reasons are briefly discussed.
Mapping microwave field distributions via the spin Hall effect
Authors: Vlaminck Vincent , Schultheiss Helmut , Pearson John E. , Fradin Frank Y. , Bader Sam D. , Hoffmann Axel
Published: December 2012

The spatial variation of the spin pumping–inverse spin Hall effect was studied in a palladium/permalloy bilayer via a coplanar waveguide ferromagnetic resonance (CPW-FMR) broadband technique. The inverse spin Hall signal is both inhomogeneous and asymmetric with respect to both the position along the CPW and the excitation port. Based on this observation, we show how the inverse spin Hall effect can be used as a sensitive probe for mapping the microwave magnetic field distribution in the FMR frequency range.
Audiovisual Temporal Recalibration: Space-Based versus Context-Based
Authors: Yuan Xiangyong , Li Baolin , Bi Cuihua , Yin Huazhan , Huang Xiting
Published: December 2012

Recalibration of perceived simultaneity has been widely accepted to minimise delay between multisensory signals owing to different physical and neural conduct times. With concurrent exposure, temporal recalibration is either contextually or spatially based. Context-based recalibration was recently described in detail, but evidence for space-based recalibration is scarce. In addition, the competition between these two reference frames is unclear. Here, we examined participants who watched two distinct blob-and-tone couples that laterally alternated with one asynchronous and the other synchronous and then judged their perceived simultaneity and sequence when they swapped positions and varied in timing. For low-level stimuli with abundant auditory location cues space-based aftereffects were significantly more apparent (8.3%) than context-based aftereffects (4.2%), but without such auditory cues space-based aftereffects were less apparent (4.4%) and were numerically smaller than context-based aftereffects (6.0%). These results suggested that stimulus level and auditory location cues were both determinants of the recalibration frame. Through such joint judgments and the simple reaction time task, our results further revealed that criteria from perceived simultaneity to successiveness profoundly shifted without accompanying perceptual latency changes across adaptations, hence implying that criteria shifts, rather than perceptual latency changes, accounted for space-based and context-based temporal recalibration.
Refractive Error and Monocular Viewing Strengthen the Hollow-Face Illusion
Authors: Hill Harold , Palmisano Stephen , Matthews Harold
Published: December 2012

We measured the strength of the hollow-face illusion—the ‘flipping distance’ at which perception changes between convex and concave—as a function of a lens-induced 3 dioptre refractive error and monocular/binocular viewing. Refractive error and closing one eye both strengthened the illusion to approximately the same extent. The illusion was weakest viewed binocularly without refractive error and strongest viewed monocularly with it. This suggests binocular cues disambiguate the illusion at greater distances than monocular cues, but that both are disrupted by refractive error. We argue that refractive error leaves the ambiguous low-spatial-frequency shading information critical to the illusion largely unaffected while disrupting other, potentially disambiguating, depth/distance cues.
Dissecting Perceptual Processes with a New Tri-Stable Reversible Figure
Authors: Long Gerald M , Batterman Jared M
Published: December 2012

Five experiments are presented that examine observers' reports with a new tri-stable reversible figure using two measures of observers' experience with the figure: observers' initial percept upon figure presentation in the test period and the total number of reversals reported in the test period. Experiment 1 demonstrates the equiprobability of the three alternatives for the figure. Experiment 2 demonstrates the powerful effect of fixation location on observers' reported organization of the tri-stable figure. Experiment 3 demonstrates clear priming effects following brief presentation of particular components of the tri-stable figure. Experiment 4 demonstrates clear adaptation effects following prolonged presentation of the same components of the figure used in experiment 3 as well as the transient nature of this adaptation. Experiment 5 demonstrates observers' ability to “hold” each of the three percepts regardless of fixation location. The special sensitivity of the tri-stable figure to these manipulations even with naive subjects and small sample sizes is discussed, and the interplay of both bottom–up and top–down processes on figural reversal is emphasized.
The Okuma Illusion: A New Illusion of Leaning
Authors: Yasuda Takashi , Ueda Takashi , Shiina Kenpei
Published: December 2012

A new illusion demonstrating the perception of tilted objects is reported. Physically, all the objects in a rotated image should tilt at the same degree. We, however, found that the tilt of objects in a rotated frame is perceived differently. We tested several objects and found that this phenomenon is especially noticeable when an element in the image has a non-geometric shape. A possible mechanism for this illusion is proposed.
A Comparative Study of the Structural, Optical, and Electrochemical Properties of Squarate-Based Coordination Frameworks
Authors: Usov Pavel M. , Keene Tony D. , D'Alessandro Deanna M.
Published: December 2012

Systematic studies of the thermal expansion, optical, and redox properties of a series of six squarate-based frameworks, [MII(C4O4)(H2O)2] (MII = MnII, FeII, CoII, NiII, ZnII, CdII) have revealed that five members of the series exhibit cubic structures in which the squarate ligands are configured in an ‘eclipsed’ phase, while the CdII analogue exhibits a trigonal structure with a ‘staggered’ orientation of the ligands. The ‘eclipsed’ structures are characterised by a positive coefficient of thermal expansion, while the CdII analogue exhibits zero thermal expansion. Ultraviolet-visible-near infrared (UV-Vis-NIR) spectra and electrochemical measurements indicate that electron delocalisation across the dianionic squarate bridge is absent.
An optimised protocol for barcoding museum collections of decapod crustaceans: a case-study for a 10 - 40-years-old collection
Authors: Zuccon Dario , Brisset Julien , Corbari Laure , Puillandre Nicolas , Utge José , Samadi Sarah
Published: December 2012

The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection’s crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of the specimens (58%, n = 1920). We hypothesised that this failure may have been due to incompatible mismatches between the crustaceans targeted and the Folmer primer sequences and/or the amount of degradation of the DNA extracted from museum specimens. The comparison of the Folmer primers against the COI sequences from GenBank complete decapod mitochondrial genomes revealed that the annealing regions were, in fact, rather conserved, suggesting that the amplification failures were due more likely to the low quality of the DNA isolated. Using an alignment of all available decapod sequences we designed two internal primers in the middle of the barcoding COI region and also selected two additional external primers to be used as alternative to the standard Folmer primers. Using a two-overlapping-fragments amplification strategy and different primer combinations, our new protocol significantly increased the amplification success rate of the collection material from 42% with the Folmer primers to 84%, recovering an additional 364 complete barcodes and 443 minibarcodes (i.e. fragments of less than 400 base pairs), and expanding the species coverage from 254 to 397 barcoded crustaceans.
DNA barcodes and morphology reveal a hybrid hawkmoth in Tahiti (Lepidoptera : Sphingidae)
Authors: Rougerie R. , Haxaire Jean , Kitching Ian J. , Hebert Paul D. N.
Published: December 2012

Interspecific hybridisation is a rare but widespread phenomenon identified as a potential complicating factor for the identification of species through DNA barcoding. Hybrids can, however, also deceive morphology-based taxonomy, resulting in the description of invalid species based on hybrid specimens. As the result of an unexpected case of discordance between barcoding results and current morphology-based taxonomy, we discovered an example of such a hybrid ‘species’ in hawkmoths. By combining barcodes, morphology and a nuclear marker, we show that Gnathothlibus collardi Haxaire, 2002 is actually an F1 hybrid between two closely related species that co-occur on Tahiti. In accordance with the International Code of Zoological Nomenclature, the taxon G. collardi is thus invalid as a species. This study demonstrates the potential of DNA barcodes to detect overlooked hybrid taxa. With the growth of sequence libraries, we anticipate that more unsuspected hybrid species will be detected, particularly among those taxa that are very rare, such as those known from only the type specimen.
What happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded?
Authors: Janzen Daniel H. , Hallwachs Winnie , Harvey Donald J. , Darrow Karolyn , Rougerie Rodolphe , Hajibabaei Mehrdad , Smith M. Alex , Bertrand Claudia , Gamboa Isidro Chacon , Espinoza Bernardo , Sullivan J. Bolling , Decaens Thibaud , Herbin Daniel , Chavarria Luis Felipe , Franco Ruth , Cambronero Hazel , Rios Sergio , Quesada Freddy , Pereira Guillermo , Vargas Johan , Guadamuz Adrian , Espinoza Roberto , Hernandez Jorge , Rios Lucia , Cantillano Elieth , Moraga Roster , Moraga Calixto , Rios Petrona , Rios Manuel , Calero Ricardo , Martinez Dinia , Briceño Duvalier , Carmona Minor , Apu Edwin , Aragon Keiner , Umaña Cirilo , Perez Jose , Cordoba Ana , Umaña Pablo , Sihezar Gloria , Espinoza Osvaldo , Cano Carolina , Araya Elda , Garcia Dunia , Ramirez Harry , Pereira Manuel , Cortez Jose , Pereira Mariano , Medina Waldy , Hebert Paul D. N.
Published: December 2012

Biodiversity of tropical Saturniidae, as measured through traditionally described and catalogued species, strongly risks pooling cryptic species under one name. We examined the DNA barcodes, morphology, habitus and ecology of 32 ‘well known’ species of dry forest saturniid moths from Area de Conservacion Guanacaste (ACG) in north-western Costa Rica and found that they contain as many as 49 biological entities that are probably separate species. The most prominent splitting of traditional species – Eacles imperialis, Automeris zugana, Automeris tridens, Othorene verana, Hylesia dalina, Dirphia avia, Syssphinx molina, Syssphinx colla, and Syssphinx quadrilineata – is where one species was believed to breed in dry forest and rain forest, but is found to be two biological entities variously distinguishable by DNA barcodes and morphology, habitus, and/or microecological distribution. This implies that ‘standard’ biological information about each traditional species may be an unconscious mix of interspecific information, and begs renewed DNA barcoding, closer attention to so-called intraspecific variation, and increased museum collection and curation of specimens from more individual and ecologically characterised sites – as well as eventually more species descriptions. Simultaneously, this inclusion of sibling species as individual entities in biodiversity studies, rather than pooled under one traditional name, reduces the degree of ecological and evolutionary generalisation perceived by the observer.
Migration of cells in a social context
Authors: Vedel Søren , Tay Savaş , Johnston Darius M. , Bruus Henrik , Quake Stephen R.
Published: December 2012

In multicellular organisms and complex ecosystems, cells migrate in a social context. Whereas this is essential for the basic processes of life, the influence of neighboring cells on the individual remains poorly understood. Previous work on isolated cells has observed a stereotypical migratory behavior characterized by short-time directional persistence with long-time random movement. We discovered a much richer dynamic in the social context, with significant variations in directionality, displacement, and speed, which are all modulated by local cell density. We developed a mathematical model based on the experimentally identified “cellular traffic rules” and basic physics that revealed that these emergent behaviors are caused by the interplay of single-cell properties and intercellular interactions, the latter being dominated by a pseudopod formation bias mediated by secreted chemicals and pseudopod collapse following collisions. The model demonstrates how aspects of complex biology can be explained by simple rules of physics and constitutes a rapid test bed for future studies of collective migration of individual cells.
Atomic model of the human cardiac muscle myosin filament
Authors: AL-Khayat Hind A. , Kensler Robert W. , Squire John M. , Marston Steven B. , Morris Edward P.
Published: December 2012

Of all the myosin filaments in muscle, the most important in terms of human health, and so far the least studied, are those in the human heart. Here we report a 3D single-particle analysis of electron micrograph images of negatively stained myosin filaments isolated from human cardiac muscle in the normal (undiseased) relaxed state. The resulting 28-Å resolution 3D reconstruction shows axial and azimuthal (no radial) myosin head perturbations within the 429-Å axial repeat, with rotations between successive 132 Å-, 148 Å-, and 149 Å-spaced crowns of heads close to 60°, 35°, and 25° (all would be 40° in an unperturbed three-stranded helix). We have defined the myosin head atomic arrangements within the three crown levels and have modeled the organization of myosin subfragment 2 and the possible locations of the 39 Å-spaced domains of titin and the cardiac isoform of myosin-binding protein-C on the surface of the myosin filament backbone. Best fits were obtained with head conformations on all crowns close to the structure of the two-headed myosin molecule of vertebrate chicken smooth muscle in the dephosphorylated relaxed state. Individual crowns show differences in head-pair tilts and subfragment 2 orientations, which, together with the observed perturbations, result in different intercrown head interactions, including one not reported before. Analysis of the interactions between the myosin heads, the cardiac isoform of myosin-binding protein-C, and titin will aid in understanding of the structural effects of mutations in these proteins known to be associated with human cardiomyopathies.
ATP-independent diffusion of double-stranded RNA binding proteins
Authors: Koh Hye Ran , Kidwell Mary Anne , Ragunathan Kaushik , Doudna Jennifer A. , Myong Sua
Published: December 2012

The proteins harboring double-stranded RNA binding domains (dsRBDs) play diverse functional roles such as RNA localization, splicing, editing, export, and translation, yet mechanistic basis and functional significance of dsRBDs remain unclear. To unravel this enigma, we investigated transactivation response RNA binding protein (TRBP) consisting of three dsRBDs, which functions in HIV replication, protein kinase R(PKR)–mediated immune response, and RNA silencing. Here we report an ATP-independent diffusion activity of TRBP exclusively on dsRNA in a length-dependent manner. The first two dsRBDs of TRBP are essential for diffusion, whereas the third dsRBD is dispensable. Two homologs of TRBP, PKR activator and R3D1-L, displayed the same diffusion, implying a universality of the diffusion activity among this protein family. Furthermore, a Dicer–TRBP complex on dsRNA exhibited dynamic diffusion, which was correlated with Dicer’s catalytic activity. These results implicate the dsRNA-specific diffusion activity of TRBP that contributes to enhancing siRNA and miRNA processing by Dicer.
Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in
Escherichia coli
Authors: Krishna Leela J. , Syeda Aisha H. , Anupama K. , Gowrishankar J.
Published: December 2012

Two pathways of transcription termination, factor-independent and -dependent, exist in bacteria. The latter pathway operates on nascent transcripts that are not simultaneously translated and requires factors Rho, NusG, and NusA, each of which is essential for viability of WT
Escherichia coli
. NusG and NusA are also involved in antitermination of transcription at the ribosomal RNA operons, as well as in regulating the rates of transcription elongation of all genes. We have used a bisulfite-sensitivity assay to demonstrate genome-wide increase in the occurrence of RNA-DNA hybrids (R-loops), including from antisense and read-through transcripts, in a
nusG
missense mutant defective for Rho-dependent termination. Lethality associated with complete deficiency of Rho and NusG (but not NusA) was rescued by ectopic expression of an R-loop-helicase UvsW, especially so on defined growth media. Our results suggest that factor-dependent transcription termination subserves a surveillance function to prevent translation-uncoupled transcription from generating R-loops, which would block replication fork progression and therefore be lethal, and that NusA performs additional essential functions as well in
E. coli
. Prevention of R-loop–mediated transcription-replication conflicts by cotranscriptional protein engagement of nascent RNA is emerging as a unifying theme among both prokaryotes and eukaryotes.
Making a difference in language learning: the role of sociocultural factors and of learner strategy instruction
Authors: Grenfell Michael , Harris Vee
Published: December 2012

There has been increasing concern over the poor performance and lack of interest in modern language learning among secondary‐school students. Although there is some evidence as to the under‐achievement of boys in modern languages (ML), there is less information as to the degree to which other factors such as social class, and bilingual or monolingual status play a role; the focus of much ML research being on individual rather than sociocultural differences in language learning. The present study took place in two London schools with 120 students aged 12–13 years learning French. Using multiple regression analysis, it brings together psychological and sociocultural perspectives to examine the role of these factors on performance and motivation. In addition, it explores if these same factors are also significant in terms of students' responses to explicit instruction to teach students the strategies they need to operate autonomously. Findings suggest that at this early stage in their language learning career, there was no significant difference in terms of gender on performance or motivation but all bilingual students, regardless of whether they were in the control or experimental classes, out‐performed their monolingual peers in listening comprehension; linguistic features of their home background appeared to provide some explanation. Furthermore, the strategy instruction was also a significant factor in determining progress. The 12–13 age range may be a critical time for students, when teaching them how to learn may reverse an otherwise downward spiral in achievement and motivation.
Production and Associated Economics of Fingerling-to-Stocker and Stocker-to-Grow-Out Modular Phases for Farming Channel Catfish in Commercial-Size Ponds
Authors: D’Abramo Louis R , Hanson Terrill R , Kingsbury Susan K , Steeby James A , Tucker Craig S
Published: December 2012

A 2-year study was conducted to evaluate two phases (phase 2: fingerling to stocker; phase 3: stocker to grow out) of a three-phase modular production system for Channel Catfish Ictalurus punctatus in commercial-scale ponds. Fingerlings (mean = 14.3 kg/1,000 fish; 11.9 cm TL) were stocked into each of six 1.62-ha earthen ponds at a density of 123,500 fish/ha and were fed a 35% crude protein floating feed daily to satiation. After 142 d, the mean weight of harvested stockers ranged from 108.9 to 158.8 g and survival ranged from 38.8% to 62.0%. These fish were subsequently stocked (at either 12,350 or 16,055 fish/ha) into 1.62-ha ponds for grow out to food-size fish (≥567.5 kg) and were fed a 35% crude protein floating feed to satiation. A partial (selective) harvest was conducted at 105–130 d poststocking by using an in-pond grader, and a final harvest was conducted at 207–245 d poststocking. Combined production means were 7,124 kg/ha for the 12,350-fish/ha treatment and 7,210 kg/ha for the 16,055-fish/ha treatment. Survival (range = 84.3–105.5%) and feed conversion ratios (range = 2.25–2.65) were not significantly different. Mean weight (659.5 g) and length (41.8 cm) of fish harvested from the 12,350-fish/ha treatment ponds were significantly greater than those of fish harvested from the 16,055-fish/ha treatment (474.8 g; 38.4 cm). Cost of producing a 142-g stocker was $0.409. For the economic analysis, phase-2 production area was based on producing sufficient stockers for all phase-3 ponds within a representative 445-ha operation. Enterprise budgets were developed for the 12,350- and 16,055-fish/ha treatments; the incomes above variable cost were $1,450 and $108 per hectare, respectively, and net returns to land were $399 and −$943 per hectare, respectively. Low survival in phase-2 stocker production reduced the returns. The three-phase modular system should provide additional management benefits that were not valued in this analysis.
Captive Volitional Spawning and Larval Rearing of Pigfish
Authors: DiMaggio Matthew A , Broach Jason S , Ohs Cortney L , Grabe Scott W
Published: December 2012

Pigfish Orthopristis chrysoptera have been identified as a species with potential for commercial production; however, lack of established culture protocols remain a major obstacle. To date, there is no scientific literature that adequately examines captive spawning and culture of this species. The purpose of this study was to evaluate volitional spawning and larval culture of Pigfish. Additionally, a preliminary larval feeding regime was investigated and growth and development of Pigfish larvae were documented. A fecundity of 1,147,149 eggs per female (2,959 eggs/g body weight) was calculated based on 58 recorded volitional spawning events. Larval survival ranged from 6.5% to 100% through 25-d posthatch (DPH). Larvae were observed to initiate swim bladder inflation by 9 DPH, and 100% percent of larvae exhibited notochord flexion by 19 DPH. An effective feeding regime was established that incorporated the nauplii of the copepod Pseudodiaptomus pelagicus, the rotifer Brachionus plicatilis, and Artemia. This study represents the first published report of repeated captive volitional spawning of Pigfish with successful protracted larval rearing.
Observing and Improving Hand Hygiene Compliance Implementation and Refinement of an Electronic-Assisted Direct-Observer Hand Hygiene Audit Program
Authors: Chen Luke F. , Carriker Charlene , Staheli Russell , Isaacs Pamela , Elliott Brandon , Miller Becky A. , Anderson Deverick J. , Moehring Rebekah W. , Vereen Sheila , Bringhurst Judie , Rhodes Lisa , Strittholt Nancy , Sexton Daniel J.
Published: December 2012

We implemented a direct-observer hand hygiene audit program that used trained observers, wireless data entry devices, and an intranet portal. We improved the reliability and utility of the data by standardizing audit processes, regularly retraining auditors, developing an audit guidance tool, and reporting weighted composite hand hygiene compliance scores.