bluuebunny/crossref_metadata_2025 huggingface dataset:
Universal quantum state merging
Authors: Bjelaković I. , Boche H. , Janßen G.
Published: March 2013

We determine the optimal entanglement rate of quantum state merging when assuming that the state is unknown except for its membership in a certain set of states. We find that merging is possible at the lowest rate allowed by the individual states. Additionally, we establish a lower bound for the classical cost of state merging under state uncertainty. To this end we give an elementary proof for the cost in case of a perfectly known state which makes no use of the “resource framework.” As applications of our main result, we determine the capacity for one-way entanglement distillation if the source is not perfectly known. Moreover, we give another achievability proof for the entanglement generation capacity over compound quantum channels.
Magnetic and high frequency properties of nanogranular CoFe-TiO2 films
Authors: Wang Yicheng , Zhang Huaiwu , Wen Dandan , Zhong Zhiyong , Bai Feiming
Published: March 2013

A series of soft magnetic nanogranular CoFe-TiO2 films with different thicknesses were fabricated on Si substrates by co-sputtering CoFe and TiO2, and the magnetic and high frequency properties were studied in details. X-ray diffraction analysis confirmed that the films were nanocrystalline/amorphous composites. A saturation magnetization as high as 21 kGs and a ferromagnetic resonance (FMR) frequency above 3 GHz were obtained. It was found that the coercivity decreased steeply with the increase of film thickness and its minimum value was about 6 Oe. In addition, the variations of FMR peak broadness of the imaginary part and damping factor were also presented and discussed as functions of film thickness.
Hill's equation with small fluctuations: Cycle to cycle variations and stochastic processes
Authors: Adams Fred C. , Bloch Anthony M.
Published: March 2013

Hill's equations arise in a wide variety of physical problems, and are specified by a natural frequency, a periodic forcing function, and a forcing strength parameter. This classic problem is generalized here in two ways: (a) to Random Hill's equations which allow the forcing strength qk, the oscillation frequency λk, and the period (Δτ)k of the forcing function to vary from cycle to cycle, and (b) to Stochastic Hill's equations which contain (at least) one additional term that is a stochastic process ξ. This paper considers both random and stochastic Hill's equations with small parameter variations, so that pk = qk−⟨qk⟩, ℓk = λk−⟨λk⟩, and ξ are all \documentclass[12pt]{minimal}\begin{document}${\cal O}(\epsilon )$\end{document}O(ε), where ε ≪ 1. We show that random Hill's equations and stochastic Hill's equations have the same growth rates when the parameter variations pk and ℓk obey certain constraints given in terms of the moments of ξ. For random Hill's equations, the growth rates for the solutions are given by the growth rates of a matrix transformation, under matrix multiplication, where the matrix elements vary from cycle to cycle. Unlike classic Hill's equations where the parameter space (the λ-q plane) displays bands of stable solutions interlaced with bands of unstable solutions, random Hill's equations are generically unstable. We find analytic approximations for the growth rates of the instability; for the regime where Hill's equation is classically stable, and the parameter variations are small, the growth rate γ = \documentclass[12pt]{minimal}\begin{document}${\cal O}(p_k^2)$\end{document}O(pk2) = \documentclass[12pt]{minimal}\begin{document}${\cal O}(\epsilon ^2)$\end{document}O(ε2). Using the relationship between the (ℓk, pk) and the ξ, this result for γ can be used to find growth rates for stochastic Hill's equations.
Compact high-resolution gamma-ray computed tomography system for multiphase flow studies
Authors: Bieberle A. , Nehring H. , Berger R. , Arlit M. , Härting H.-U. , Schubert M. , Hampel U.
Published: March 2013

In this paper, a compact high-resolution gamma-ray Computed Tomography (CompaCT) measurement system for multiphase flow studies and tomographic imaging of technical objects is presented. Its compact and robust design makes it particularly suitable for studies on industrial facilities and outdoor applications. Special care has been given to thermal ruggedness, shock resistance, and radiation protection. Main components of the system are a collimated 137Cs isotopic source, a thermally stabilised modular high-resolution gamma-ray detector arc with 112 scintillation detector elements, and a transportable rotary unit. The CompaCT allows full CT scans of objects with a diameter of up to 130 mm and can be operated with any tilting angle from 0° (horizontal) to 90° (vertical).
Dependence of the magnetocaloric effect on the A-site ionic radius in isoelectronic manganites
Authors: Rocco D. L. , Coelho A. A. , Gama S. , Santos M. de C.
Published: March 2013

In this work, we explore the magnetocaloric and magnetic properties of isoelectronic manganites R0.6Sr0.4MnO3 (R = La, Pr, Nd, and Sm). Upon substitution of La3+ by smaller rare-earth ions, the average ionic radius 〈rA〉 of the A-site (A = (R, Sr)) elements systematically decreases. It is found that, with decreasing 〈rA〉, the magnetic-ordering temperature decreases from 341 K for La0.6Sr0.4MnO3 to 126 K for Sm0.6Sr0.4MnO3. Interestingly, the magnetic-entropy change increases with decreasing 〈rA〉, reaching ΔSM=−8.4 J/kg  K for ΔH=0−20  kOe for Sm0.6Sr0.4MnO3. For manganites, this is a high value of ΔSM, and it is related to the fact that the compound exhibits first-order magnetic transition. In contrast, the three other compounds exhibit a second order transition. The results indicate that the structural distortions caused by the decreasing 〈rA〉 couple the spin subsystem to the lattice, thus, inducing a first-order magnetic transition.
Production and evolution of A-centers in n-type Si1−xGex
Authors: Sgourou E. N. , Andrianakis A. , Londos C. A. , Chroneos A.
Published: March 2013

The vacancy-oxygen pair (VO or A-center) in n-type Si1−xGex crystals (x = 0, 0.025, 0.055) has been studied using infrared (IR) spectroscopy. It is determined that the VO production is suppressed in the case of n-type Si1−xGex as compared to Si. It is observed that the annealing temperature of the VO defect in Si1−xGex is substantially lower as compared to Si. The decay of the VO (830 cm−1) band, in the course of 20 min isochronal anneals, shows two stages: The onset of the first stage is at ∼180 °C and the decrease of the VO signal is accompanied in the spectra by the increase of the intensity of two bands at ∼834 and 839 cm−1. These bands appear in the spectra immediately after irradiation and were previously correlated with (VO-Ge) structures. The onset of the second stage occurs at ∼250 °C were the 830 cm−1 band of VO and the above two bands of (VO-Ge) decrease together in the spectra accompanied by the simultaneous growth of the 885 cm−1 band of the VO2 defect. Interestingly, the percentage of the VO pairs that are converted to VO2 defects is larger in the Si1−xGex samples with intermediate Ge content (x = 0.025) as compared with Si (x = 0) and with the high Ge content samples (x = 0.055). The results are discussed in view of the association of VO pairs with Ge.
Stabilization of the ceria ι-phase (Ce7O12) surface on Si(111)
Authors: Wilkens H. , Schuckmann O. , Oelke R. , Gevers S. , Schaefer A. , Bäumer M. , Zoellner M. H. , Schroeder T. , Wollschläger J.
Published: March 2013

In this work a 250 nm CeO2(111) film grown on a hex-Pr2O3(0001)/Si(111) system is annealed at 660 °C for 30 min to form the ι bulk phase of Ce7O12 as controlled by x-ray photoelectron spectroscopy. The (111) surface of the stabilized ι phase is characterized via high-resolution low-energy electron diffraction. The ι-phase surface exhibits a (7×7)R19.1° superstructure with two mirror domains. This structure is attributed to a periodic ordering of oxygen vacancies compared to the fluorite structure of CeO2.
The disintegration of GaSb/GaAs nanostructures upon capping
Authors: Martin Andrew J. , Hwang Jinyoung , Marquis Emmanuelle A. , Smakman Erwin , Saucer Timothy W. , Rodriguez Garrett V. , Hunter Allen H. , Sih Vanessa , Koenraad Paul M. , Phillips Jamie D. , Millunchick Joanna
Published: March 2013

Atom probe tomography and cross-sectional scanning tunneling microscopy show that GaSb/GaAs quantum dots disintegrate into ring-like clusters of islands upon capping. Band transition energies calculated using an 8-band k.p model of the capped dots with the observed dimensions are consistent with emission energies observed in photoluminescence data. These results emphasize the need for full three-dimensional characterization to develop an accurate understanding of the structure, and thus the optical properties, of buried quantum dots.
Low resistance GaN/InGaN/GaN tunnel junctions
Authors: Krishnamoorthy Sriram , Akyol Fatih , Park Pil Sung , Rajan Siddharth
Published: March 2013

Enhanced interband tunnel injection of holes into a p-n junction is demonstrated using p-GaN/InGaN/n-GaN tunnel junctions with a specific resistivity of 1.2 × 10−4 Ω cm2. The design methodology and low-temperature characteristic of these tunnel junctions are discussed, and insertion into a p-n junction device is described. Applications of tunnel junctions in III-nitride optoelectronics devices are explained using energy band diagrams. The lower bandgap and polarization fields reduce tunneling barrier, eliminating the need for ohmic contacts to p-type GaN. This demonstration of efficient tunnel injection of carriers in III-nitrides can lead to a replacement of existing resistive p-type contact material in light emitters with tunneling contact layers requiring very little metal footprint on the surface, resulting in enhanced light extraction.
Electronic structure disorder, vibronic coupling, and charge transfer excitons in poly(fluorene-alt-bithiophene):fullerene films
Authors: Riisness I. , Gordon M. J.
Published: March 2013

Charge transfer processes in conjugated polymer:fullerene blends play an important role in the operation of organic solar cells and organic light emitting diodes. Herein, near-infrared emission from poly-(9,9-dioctylfluorene-alt-bithiophene) (F8T2) and [6,6]-phenyl-C61-butyric acid methyl ester blends was studied and attributed to charge transfer exciton (CTX) recombination. Polymer and CTX emission were monitored via low-temperature/transient photoluminescence and absorbance to elucidate the effects of annealing and composition on donor-acceptor morphology. CTX emission decreased and F8T2 vibronic structure was partially restored due to lower fullerene dispersion and polymer realignment upon annealing. Differences in the temperature-dependent emissions of the polymer singlet vs. CTX were attributed to exciton diffusion in the polymer phase vs. enhanced quenching at the donor-acceptor interface, respectively.
Coupled vibrational modes in multiple-filled skutterudites and the effects on lattice thermal conductivity reduction
Authors: Guo L. , Xu X. , Salvador J. R. , Meisner G. P.
Published: March 2013

The influence of guest atoms on thermal conduction in filled skutterudites was studied using ultrafast reflectance spectroscopy. Different filling species cause coupled vibrational modes between the guest atoms and the host lattice at different frequencies, which scatter phonons in different spectral spans. Using a Debye model for the measured lattice thermal conductivity together with the measured vibration frequencies and scattering rates, it is shown that scattering due to the coupled vibrational modes has a considerable contribution to the suppression of lattice thermal conduction. This demonstrates that filling with multiple species can efficiently reduce the lattice thermal conductivity in skutterudites.
Prescribed fire in eucalypt woodlands: immediate effects on a microbat community of northern Australia
Authors: Inkster-Draper Tamara E. , Sheaves Marcus , Johnson Christopher N. , Robson Simon K. A.
Published: March 2013

Context
Fire is a major ecological factor in many landscapes. Prescribed fires are often used in the management of vegetation for ecological values, wildlife habitat and reduction of risk of wildfire. However, debate continues over whether active fire management is beneficial to flora and fauna. Although bats comprise ~20% of the world’s extant mammal fauna, they have been largely ignored in studies investigating ecosystem response to fire, especially in Australia.
Aims
In the present study, we aim to investigate the immediate responses of microbats to prescribed fires in a tropical eucalypt woodland.Methods
We used a replicated paired experimental design, consisting of burned and unburned treatment and control sites, to investigate how bat activity and community structure change following a prescribed fire.
Key results
Total bat activity increased significantly following fire. Fire also resulted in changes in the bat species assemblage. Changes in community structure were driven by the following five species: Saccolaimus spp., Chalinolobus nigrogriseus, Chaerephon jobensis, Rhinolophus megaphyllus and unidentified Species c35. Activity of C. nigrogriseus, Saccolaimus spp., C. jobensis and Species c35 increased in the burned sites, whereas changes in the activity of R. megaphyllus were uncorrelated with the effects of fire.
Conclusions
The effect of fire on these species is consistent with flight patterns and habitat use; species with higher wing aspect ratios, such as Saccolaimus spp., which are capable of fast flight but with limited manoeuvrability, became more active in the open conditions created by fire.
Implications
The results of the present study suggest that prescribed fire as an environmental management tool may be beneficial to bats, at least in the short term, because it increases habitat suitability for a wider range of species.
Removal control of the highly invasive fish Gambusia holbrooki and effects on its population biology: learning by doing
Authors: Ruiz-Navarro A. , Verdiell-Cubedo D. , Torralva M. , Oliva-Paterna F. J.
Published: March 2013

Context
For the success of future conservation and management programs, it is necessary to better understand the resilience mechanisms of invasive species and their invasive potential. In this sense, the study of the effects that management actions have on their biological traits is essential.

Aims
The present study aimed to assess the effects of removal control on the abundance and biology of an isolated population of the top invasive fish Gambusia holbrooki (eastern mosquitofish).

Methods
Experimental removal control with traps and handnets was carried out on a population of mosquitofish inhabiting a small semiarid stream in south-eastern Spain. Mosquitofish were periodically captured for more than 3 years. Temporal variations in abundance, fish somatic condition and reproductive investment, percentage of mature females, size at maturity and population recruitment were analysed.

Key results
Individuals of the 1+ age class increased their reproductive investment when population abundance was lower, thus increasing recruitment rate during the first months of the recruitment period. Individuals of the 0+ age class were responsible for expanding the reproductive period in conditions of low fish abundance.

Conclusions
The mosquitofish population showed variations of reproductive parameters that could indicate a compensatory density-dependent phenotypic response under diminished abundance conditions. However, its removal by the constant use of a combination of active and passive capture methods, reinforced by increased extraction effort according to its local biology, has led to an eradication of the population. The target mosquitofish population showed distinct ecological features that may have contributed to the effectiveness of local control, namely, low initial fish density, isolation in a headwater stretch and the prevalence of individuals in sunlit shallow ponds.

Implications
The compensatory mechanisms of this invasive species in low-density conditions should be considered in the design of management programs. Moreover, further research into removal control methods for mosquitofish or similar species is also needed.
Innervation is required for sense organ development in the lateral line system of adult zebrafish
Authors: Wada Hironori , Dambly-Chaudière Christine , Kawakami Koichi , Ghysen Alain
Published: March 2013

Superficial mechanosensory organs (neuromasts) distributed over the head and body of fishes and amphibians form the “lateral line” system. During zebrafish adulthood, each neuromast of the body (posterior lateral line system, or PLL) produces “accessory” neuromasts that remain tightly clustered, thereby increasing the total number of PLL neuromasts by a factor of more than 10. This expansion is achieved by a budding process and is accompanied by branches of the afferent nerve that innervates the founder neuromast. Here we show that innervation is essential for the budding process, in complete contrast with the development of the embryonic PLL, where innervation is entirely dispensable. To obtain insight into the molecular mechanisms that underlie the budding process, we focused on the terminal system that develops at the posterior tip of the body and on the caudal fin. In this subset of PLL neuromasts, bud neuromasts form in a reproducible sequence over a few days, much faster than for other PLL neuromasts. We show that wingless/int (Wnt) signaling takes place during, and is required for, the budding process. We also show that the Wnt activator R-spondin is expressed by the axons that innervate budding neuromasts. We propose that the axon triggers Wnt signaling, which itself is involved in the proliferative phase that leads to bud formation. Finally, we show that innervation is required not only for budding, but also for long-term maintenance of all PLL neuromasts.
Cell-to-cell propagation of infectious cytosolic protein aggregates
Authors: Hofmann Julia P. , Denner Philip , Nussbaum-Krammer Carmen , Kuhn Peer-Hendrik , Suhre Michael H. , Scheibel Thomas , Lichtenthaler Stefan F. , Schätzl Hermann M. , Bano Daniele , Vorberg Ina M.
Published: March 2013

Prions are self-templating protein conformers that replicate by recruitment and conversion of homotypic proteins into growing protein aggregates. Originally identified as causative agents of transmissible spongiform encephalopathies, increasing evidence now suggests that prion-like phenomena are more common in nature than previously anticipated. In contrast to fungal prions that replicate in the cytoplasm, propagation of mammalian prions derived from the precursor protein PrP is confined to the cell membrane or endocytic vesicles. Here we demonstrate that cytosolic protein aggregates can also behave as infectious entities in mammalian cells. When expressed in the mammalian cytosol, protein aggregates derived from the prion domain NM of yeast translation termination factor Sup35 persistently propagate and invade neighboring cells, thereby inducing a self-perpetuating aggregation state of NM. Cell contact is required for efficient infection. Aggregates can also be induced in primary astrocytes, neurons, and organotypic cultures, demonstrating that this phenomenon is not specific to immortalized cells. Our data have important implications for understanding prion-like phenomena of protein aggregates associated with human diseases and for the growing number of amyloidogenic proteins discovered in mammals.
The human gene connectome as a map of short cuts for morbid allele discovery
Authors: Itan Yuval , Zhang Shen-Ying , Vogt Guillaume , Abhyankar Avinash , Herman Melina , Nitschke Patrick , Fried Dror , Quintana-Murci Lluis , Abel Laurent , Casanova Jean-Laurent
Published: March 2013

High-throughput genomic data reveal thousands of gene variants per patient, and it is often difficult to determine which of these variants underlies disease in a given individual. However, at the population level, there may be some degree of phenotypic homogeneity, with alterations of specific physiological pathways underlying the pathogenesis of a particular disease. We describe here the human gene connectome (HGC) as a unique approach for human Mendelian genetic research, facilitating the interpretation of abundant genetic data from patients with the same disease, and guiding subsequent experimental investigations. We first defined the set of the shortest plausible biological distances, routes, and degrees of separation between all pairs of human genes by applying a shortest distance algorithm to the full human gene network. We then designed a hypothesis-driven application of the HGC, in which we generated a Toll-like receptor 3-specific connectome useful for the genetic dissection of inborn errors of Toll-like receptor 3 immunity. In addition, we developed a functional genomic alignment approach from the HGC. In functional genomic alignment, the genes are clustered according to biological distance (rather than the traditional molecular evolutionary genetic distance), as estimated from the HGC. Finally, we compared the HGC with three state-of-the-art methods: String, FunCoup, and HumanNet. We demonstrated that the existing methods are more suitable for polygenic studies, whereas HGC approaches are more suitable for monogenic studies. The HGC and functional genomic alignment data and computer programs are freely available to noncommercial users from
http://lab.rockefeller.edu/casanova/HGC
and should facilitate the genome-wide selection of disease-causing candidate alleles for experimental validation.
Molecular assembly of botulinum neurotoxin progenitor complexes
Authors: Benefield Desirée A. , Dessain Scott K. , Shine Nancy , Ohi Melanie D. , Lacy D. Borden
Published: March 2013

Botulinum neurotoxin (BoNT) is produced by
Clostridium botulinum
and associates with nontoxic neurotoxin-associated proteins to form high-molecular weight progenitor complexes (PCs). The PCs are required for the oral toxicity of BoNT in the context of food-borne botulism and are thought to protect BoNT from destruction in the gastrointestinal tract and aid in absorption from the gut lumen. The PC can differ in size and protein content depending on the
C. botulinum
strain. The oral toxicity of the BoNT PC increases as the size of the PC increases, but the molecular architecture of these large complexes and how they contribute to BoNT toxicity have not been elucidated. We have generated 2D images of PCs from strains producing BoNT serotypes A1, B, and E using negative stain electron microscopy and single-particle averaging. The BoNT/A1 and BoNT/B PCs were observed as ovoid-shaped bodies with three appendages, whereas the BoNT/E PC was observed as an ovoid body. Both the BoNT/A1 and BoNT/B PCs showed significant flexibility, and the BoNT/B PC was documented as a heterogeneous population of assembly/disassembly intermediates. We have also determined 3D structures for each serotype using the random conical tilt approach. Crystal structures of the individual proteins were placed into the BoNT/A1 and BoNT/B PC electron density maps to generate unique detailed models of the BoNT PCs. The structures highlight an effective platform that can be engineered for the development of mucosal vaccines and the intestinal absorption of oral biologics.
Rational reprogramming of fungal polyketide first-ring cyclization
Authors: Xu Yuquan , Zhou Tong , Zhou Zhengfu , Su Shiyou , Roberts Sue A. , Montfort William R. , Zeng Jia , Chen Ming , Zhang Wei , Lin Min , Zhan Jixun , Molnár István
Published: March 2013

Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the dihydroxyphenylacetic acid lactone dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal vs. bacterial folding mode difference is portable on creating hybrid enzymes, and we structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first-ring cyclizations will facilitate efforts to the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides.
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
Authors: Campbell James H. , O’Donoghue Patrick , Campbell Alisha G. , Schwientek Patrick , Sczyrba Alexander , Woyke Tanja , Söll Dieter , Podar Mircea
Published: March 2013

The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA
Gly
UCA
with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA
Gly
UCA
with glycine in vitro with similar activity compared with normal tRNA
Gly
UCC
. Coexpression of SR1 glycyl-tRNA synthetase and tRNA
Gly
UCA
in
Escherichia coli
yields significant β-galactosidase activity in vivo from a
lacZ
gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.
Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis
Authors: Starita Lea M. , Pruneda Jonathan N. , Lo Russell S. , Fowler Douglas M. , Kim Helen J. , Hiatt Joseph B. , Shendure Jay , Brzovic Peter S. , Fields Stanley , Klevit Rachel E.
Published: March 2013

Significance

Ubiquitin is a 76 residue protein that is attached to target proteins as a posttranslational modification. This modification is dependent on the successive activity of three enzymes, designated E1, E2, and E3. We developed a high-throughput mutagenesis strategy to probe the mechanism of E3-catalyzed transfer of ubiquitin from the E2 to the target protein. By scoring the effect of nearly 100,000 mutations in an E3, we identified mutations that affect direct and allosteric interactions between the E3 and the E2. These results highlight the general utility of high-throughput mutagenesis in delineating the molecular basis of enzyme activity.
Protein kinase C-theta (PKCθ) phosphorylates and inhibits the guanine exchange factor, GIV/Girdin
Authors: López-Sánchez Inmaculada , Garcia-Marcos Mikel , Mittal Yash , Aznar Nicolas , Farquhar Marilyn G. , Ghosh Pradipta
Published: March 2013

Gα-interacting, vesicle-associated protein (GIV/Girdin) is a multidomain signal transducer that enhances PI3K-Akt signals downstream of both G-protein–coupled receptors and growth factor receptor tyrosine kinases during diverse biological processes and cancer metastasis. Mechanistically, GIV serves as a non-receptor guanine nucleotide exchange factor (GEF) that enhances PI3K signals by activating trimeric G proteins, Gαi1/2/3. Site-directed mutations in GIV’s GEF motif disrupt its ability to bind or activate Gi and abrogate PI3K-Akt signals; however, nothing is known about how GIV’s GEF function is regulated. Here we report that PKCθ, a novel protein kinase C, down-regulates GIV’s GEF function by phosphorylating Ser(S)1689 located within GIV’s GEF motif. We demonstrate that PKCθ specifically binds and phosphorylates GIV at S1689, and this phosphoevent abolishes GIV’s ability to bind and activate Gαi. HeLa cells stably expressing the phosphomimetic mutant of GIV, GIV-S1689→D, are phenotypically identical to those expressing the GEF-deficient F1685A mutant: Actin stress fibers are decreased and cell migration is inhibited whereas cell proliferation is triggered, and Akt (a.k.a. protein kinase B, PKB) activation is impaired downstream of both the lysophosphatidic acid receptor, a G-protein–coupled receptor, and the insulin receptor, a receptor tyrosine kinase. These findings indicate that phosphorylation of GIV by PKCθ inhibits GIV's GEF function and generates a unique negative feedback loop for downregulating the GIV-Gi axis of prometastatic signaling downstream of multiple ligand-activated receptors. This phosphoevent constitutes the only regulatory pathway described for terminating signaling by any of the growing family of nonreceptor GEFs that modulate G-protein activity.
Another “strategic accession”? The EU and Serbia (2000–2010)
Authors: Stahl Bernhard
Published: March 2013

The South-eastern enlargement currently suffers from defections, compliance problems and blockades; the results of the European Union's policy since 1999 can be called mixed at best. The “Serbian question” – for instance – remains unsolved since Serbia still means a “problem child” of the international community. The thesis generated in this paper is that all of these problems are indicators of a basic identity conflict. This conflict stems from entirely different identities, i.e. world views, perception of the state, political cultures and the meaning of international politics. The EU's enlargement policy – in its ideal type – is precisely meant to overcome this conflict by “Europeanizing” the acceding states. Yet the argument here is that the EU also pursues goals beyond Europeanization – for instance “stabilization” – hence the EU might be interested in accessions despite the fact that the Copenhagen criteria have not been fulfilled. Such “strategic accessions”, as experienced with Romania, Greece and Cyprus, tend to hinder the EU's external governance and foster enlargement fatigue in the long run. The case of Serbia serves as an example for demonstrating that Serbia is not complying with the basic standards of EU integration and that the EU is not really enforcing compliance. As a result, we are heading towards a “strategic accession” in the Serbian case.
In vivo fate mapping identifies pre-TCRα expression as an intra- and extrathymic, but not prethymic, marker of T lymphopoiesis
Authors: Luche Hervé , Nageswara Rao Tata , Kumar Suresh , Tasdogan Alpaslan , Beckel Franziska , Blum Carmen , Martins Vera C. , Rodewald Hans-Reimer , Fehling Hans Jörg
Published: March 2013

Expression of the pre–T cell receptor α (pTα) gene has been exploited in previous studies as a molecular marker to identify tiny cell populations in bone marrow (BM) and blood that were suggested to contain physiologically relevant thymus settling progenitors (TSPs). But to what extent these cells genuinely contribute to thymopoiesis has remained obscure. We have generated a novel pTαiCre knockin mouse line and performed lineage-tracing experiments to precisely quantitate the contribution of pTα-expressing progenitors to distinct differentiation pathways and to the genealogy of mature hematopoietic cells under physiological in vivo conditions. Using these mice in combination with fluorescent reporter strains, we observe highly consistent labeling patterns that identify pTα expression as a faithful molecular marker of T lineage commitment. Specifically, the fate of pTα-expressing progenitors was found to include all αβ and most γδ T cells but, in contrast to previous assumptions, to exclude B, NK, and thymic dendritic cells. Although we could detect small numbers of T cell progenitors with a history of pTα expression in BM and blood, our data clearly exclude these populations as physiologically important precursors of thymopoiesis and indicate that they instead belong to a pathway of T cell maturation previously defined as extrathymic.
Classics and Cinema
Authors: Winkler Martin M.
Published: March 2013

“Let Dickens and the whole constellation of ancestors, who go as far back as Shakespeare or the Greeks, serve as superfluous reminders that Griffith and our cinema alike cannot claim originality for themselves, but have a vast cultural heritage; and this causes neither one any difficulty in advancing the great art of cinema, each at their moment of world history.” Thus wrote Sergei Eisenstein, the great Soviet filmmaker, theoretician of cinema, and one of the most influential artists in the history of film, in his 1942 essay “Dickens, Griffith and Ourselves.” Eisenstein regarded Charles Dickens as one of the 19th-century precursors of cinema and here examined his influence on D. W. Griffith, the American film pioneer. Griffith has often been credited with inventing most of the grammar of film language. Since the cinema’s birth in 1895, classical Antiquity has played a major part in the history of storytelling in moving images. Films either present their mythical, literary, and historical material in ancient settings or they transpose classical themes and historical or narrative archetypes to contemporary or even future times. For most of the 20th century, classical scholars and teachers neglected the presence of Greece and Rome on the screen, although there were some honorable exceptions. (Examples are cited under The Pioneers: Antiquity and Cinema.) Since the 1990s, however, classical scholarship has increasingly focused on this area of reception, which is now outpacing all others. Two statements published in The Classical Review, one of the profession’s foremost book review journals, illustrate the change that occurred in less than a decade. In 1999, a reviewer began with the following statement: “The combination of classics and film studies is not a common field of interdisciplinary research” (Classical Review, new ser., 49: 244–246). In 2005, a reviewer observed: “Successfully—and fruitfully—the study of classics and cinema has asserted itself as a leader in the field of reception studies” (Classical Review, new ser., 55: 688–690, at 688). Further evidence may be found in the fact that a highly regarded publisher—Edinburgh University Press—launched the book series “Screening Antiquity” in 2015, which has by now published nine volumes, distributed by Oxford University Press. The hope expressed in 1958 by Paul Leglise, that his approach to Virgil’s Aeneid (see The Pioneers: Antiquity and Cinema) would lead to future research of a comparable nature on other classical authors has now been fulfilled to a greater extent than he may have imagined. Nevertheless, the study of classics and cinema and related media (television, computer videos) is still evolving. It is a broad and demanding field that requires a double expertise from its practitioners: a sound knowledge of all aspects of the ancient cultures on the one hand; close familiarity with film history, technology, theory, aesthetics, and economics on the other. These are preconditions for all serious interpretive work on cinema and Antiquity.
Narratology and the Classics
Authors: Rengakos Antonios , Tsitsiou-Chelidoni Chrysanthe
Published: March 2013

Narratology (a term coined by Tzvetan Todorov in 1969), “a humanities discipline dedicated to the study of the logic, principles, and practices of narrative representation” (Jan Christoph Meister), has influenced classics mainly in its “classical”/structuralist version developed in the 1960s and 1970s in France by critics such as Roland Barthes, Todorov, Algirdas Greimas, Claude Julien Bremond, and Gérard Genette. A distinctive branch of German narratological studies (Erzähltheorie) represented by the works of Eberhard Lämmert, Käte Hamburger, or Franz Karl Stanzel had only a limited impact, almost exclusively on German-speaking classicists. The aim of this bibliography is to acquaint the reader with ancient authors whose study benefited from narratology, but it does not cover all narrative studies pertaining to Greek and Latin authors, though quite often in an inflationary use the term “narratology” is interchangeable with “narrative studies.”
Plato’s Apology of Socrates
Authors: Platter Charles
Published: March 2013

The Apology of Socrates takes its name from Plato’s version of the defense speech (Greek, apologia) given by Socrates at his trial. The date of its composition is unknown, but the work is generally believed to have been composed after the publication of Polycrates’s Accusation of Socrates (c. 393) but before Plato’s first voyage to Sicily (387). It consists of three parts: the defense proper (17a–35d), Socrates’s response to the guilty verdict (35e–38b), and a pair of speeches directed respectively at those who voted for the death penalty, and at those who voted against it (38c–42a). It is unique among Plato’s works because it is not a dialogue, and it exploits many of the conventions of Athenian forensic oratory. Despite its atypical form, the Apology is clearly important for understanding the significance of Socrates for Plato, and it has been remarked frequently that through him the work functions virtually as a foundation myth for the Western philosophical tradition. The Apology is alluded to frequently in the Platonic dialogues. It also serves as the pivot in a series of dialogues set in the last weeks of Socrates’s life. Two take place before the trial. At the end of Theaetetus (184d), Socrates leaves the discussion to attend a reading of the charges against him in the agora at King’s Stoa. At the conclusion of that hearing he meets Euthyphro, who has come to prosecute his father for the murder of a slave, and commences the dialogue named after him. A discussion of their respective circumstances (1a–2b) leads to the discussion of holiness that engages them for the rest of the dialogue. Two dialogues also are set after the Apology, and so implicitly offer a commentary on the trial. Crito takes place in the prison while Socrates awaits execution, and Phaedo on the last day of Socrates’s life. Plato’s decision to recall the trial of Socrates in so many works, probably written many years apart, attests strongly to the centrality of the Apology for his understanding of philosophy. Scholars have agreed. As a result, the bibliography related to the Apology, and to the trial of Socrates, is vast.
Bodhisattva
Authors: Apple James B.
Published: March 2013

A bodhisattva (Pāli bodhisatta; Tib. byang-chub sems-dpa’; Ch. pusa; Jpn. bosatsu) is generally considered to be a person (sattva) in pursuit of awakening (bodhi) to become a buddha. All Buddhist traditions acknowledge the figure of the bodhisattva, but they differ on its interpretation. Bodhisattvas in non-Mahayana forms of Buddhism are mainly considered to be the previous lives of Siddhārtha Gautama that are worthy of veneration. The bodhisattva in Mahayana forms of Buddhism is an ideal that all Buddhists may cultivate and that is committed to attaining awakening for the benefit of all beings. The manner in which bodhisattvas are understood in different Buddhist cultures, such as in Tibet or Southeast Asia, is dependent on the Buddhist literature that is accessible or acceptable to the particular culture and the interpretative attention and practices affiliated with that literature.
Women in Buddhism
Authors: Gutschow Kim
Published: March 2013

The very existence of a “Women and Buddhism” entry but no “Men in Buddhism” entry implies a set of methodological lacunae in Buddhist studies. On the one hand, Buddhist studies have often proceeded as if the history of men in Buddhism stands in for Buddhist history, with little effort made to mention or recover the significance of women. On the other hand, systematic methodological choices, such as the discounting of feminist analysis and the privileging of text over other sources of knowledge, have exacerbated the tendency to elide the role of women in Buddhism. This elision of women, or their marginalization, in Buddhist analyses where “man” or “male” is assumed to represent “human” has prompted a countersurge of analyses. These latter analyses have found ample evidence for the centrality of gender and women in shaping Buddhist society and soteriology. Although works are now available that cover the role of women and gender in most Buddhist eras or societies, these have only scratched the surface of an extraordinarily rich set of material and questions. It remains to be seen how well Buddhist scholarship can give gender and women their proper place in developing its central concerns.
Buddhism in India
Authors: Tribe Anthony
Published: March 2013

Buddhism in India comprises a vast array of traditions, institutions, doctrines, and literatures. It flourished on the Indian subcontinent for some 1,700 years, from its origins in the 5th century bce to its effective disappearance from most regions in the 13th century. The early tradition rapidly evolved monastic institutions, and during its first five or so centuries expanded from its birthplace in the north throughout much of the subcontinent. Within the schools and monastic culture of the Indian Buddhism of this period, and possibly as early as the 1st century bce, a number of movements developed that emphasized the importance of the bodhisattva and the scriptural authority of particular texts. Adopting the label Mahayana (Great Vehicle), these movements distinguished their emphases from those of the Buddhist mainstream (referred to as Mainstream Buddhism in modern scholarship). The Mahayana, apparently of marginal influence for a number of centuries, itself became progressively mainstream from the 5th or 6th century onward. By the end of the 7th century, tantric approaches to meditation and ritual emerged as a self-conscious tradition. Referring to itself as the Vajrayāna (Thunderbolt Vehicle), over the following centuries it increasingly came to dominate Indian Buddhist praxis. Scholarship on Buddhism in India almost matches the size and diversity of its subject. Recent research has been fascinated with issues of origins, whether of early Buddhist ideas and practices, the Mahayana, or tantric traditions. There has also been an emphasis on the importance of understanding the social, cultural, and historical contexts of texts and traditions, and a recognition of the value of epigraphic and archaeological sources of evidence. And, increasingly, studies are exploring the influence of the wider non-Buddhist religious, cultural, and political environments within which Buddhism in India was always embedded.
W. V. O. Quine
Authors: Kemp Gary
Published: March 2013

Willard Van Orman Quine (b. 1908–d. 2000) was the main agenda setter in post–World War II philosophy of language and related fields. He was also a highly active logician; if his views on formal and mathematical logic did not shape the field in quite the same way as his work on language, epistemology, and metaphysics, the latter largely sprang from his work on logic and the related domain of the foundations of mathematics. His doctoral thesis (“The Logic of Sequences,” 1933) attempted to clean up and generalize yet boil down the great Principia Mathematica of Bertrand Russell and Alfred North Whitehead (Cambridge, UK: Cambridge University Press, 1910, 1927). Quine’s subsequent works—including A System of Logistic (Cambridge, MA: Harvard University Press, 1934), Mathematical Logic (1940, 1951; Quine 1951, cited under Quine’s Monographs), “New Foundations for Mathematical Logic” (1937, 1953, 1961; Quine 1961, cited under Logic and Set Theory), and Set Theory and Its Logic (1963, 1969; Quine 1969, cited under Quine’s Textbooks)—developed more refined and original ideas on largely the same topics. In philosophy he is known most generally for his commitment to extensionalism, which, for scientific purposes, rules out as inadmissible that two expressions could have the same truth-value or extension or refer to the same object yet not be interchangeable in containing sentences without affecting the truth-values of the containing sentences. Closely related are his celebrated criticisms of the unexplicated reliance on the concepts “meaning,” the “a priori,” and “analyticity” among empiricist philosophers; pressed harder, Quine believed, those notions cannot support the edifices empiricists had envisaged. A scientifically rigorous attitude toward language shows that the notion of the meaning of a sentence, in the intuitive sense that sustains the idea that two correct translations of a given foreign sentence must be in some clear sense be equivalent, must be discarded; meaning in that sense is “indeterminate.” In metaphysics, specifically ontology, he is celebrated for formulating a clear and seemingly rigorous test for ontological commitment in his “On What There Is” (1948; Quine 1961, cited under Ontology): existence is equated with being the value of variable in the first-order predicate calculus. Less well known but equally interesting are his later views concerning the question of what exists; he held that certain considerations undermine the idea that there is a single answer to the question “What is there?” Finally, the notion that epistemology should be “naturalized” and more generally that philosophy itself should be thought of as taking its place within natural science has caused considerable commentary and indeed controversy.