bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep traps in AlGaN/GaN heterostructures studied by deep level transient spectroscopy: Effect of carbon concentration in GaN buffer layers
Authors: Fang Z.-Q. , Claflin B. , Look D. C. , Green D. S. , Vetury R.
Published: September 2010

Electrical properties, including leakage currents, threshold voltages, and deep traps, of AlGaN/GaN heterostructure wafers with different concentrations of carbon in the GaN buffer layer, have been investigated by temperature dependent current-voltage and capacitance-voltage measurements and deep level transient spectroscopy (DLTS), using Schottky barrier diodes (SBDs). It is found that (i) SBDs fabricated on the wafers with GaN buffer layers containing a low concentration of carbon (low-[C] SBD) or a high concentration of carbon (high-[C] SBD) have similar low leakage currents even at 500 K; and (ii) the low-[C] SBD exhibits a larger (negative) threshold voltage than the high-[C] SBD. Detailed DLTS measurements on the two SBDs show that (i) different trap species are seen in the two SBDs: electron traps Ax (0.9 eV), A1 (0.99 eV), and A2 (1.2 eV), and a holelike trap H1 (1.24 eV) in the low-[C] SBD; and electron traps A1, A2, and A3 (∼1.3 eV), and a holelike trap H2 (>1.3 eV) in the high-[C] SBD; (ii) for both SDBs, in the region close to GaN buffer layer, only electron traps can be detected, while in the AlGaN/GaN interface region, significant holelike traps appear; and iii) all of the deep traps show a strong dependence of the DLTS signal on filling pulse width, which indicates they are associated with extended defects, such as threading dislocations. However, the overall density of electron traps is lower in the low-[C] SBD than in the high-[C] SBD. The different traps observed in the two SBDs are thought to be mainly related to differences in microstructure (grain size and threading dislocation density) of GaN buffer layers grown at different pressures.
Broken ergodicity in two-dimensional homogeneous magnetohydrodynamic turbulence
Authors: Shebalin John V.
Published: September 2010

Two-dimensional (2D) homogeneous magnetohydrodynamic (MHD) turbulence has many of the same qualitative features as three-dimensional (3D) homogeneous MHD turbulence. These features include several ideal (i.e., nondissipative) invariants along with the phenomenon of broken ergodicity (defined as nonergodic behavior over a very long time). Broken ergodicity appears when certain modes act like random variables with mean values that are large compared to their standard deviations, indicating a coherent structure or dynamo. Recently, the origin of broken ergodicity in 3D MHD turbulence that is manifest in the lowest wavenumbers was found. Here, we study the origin of broken ergodicity in 2D MHD turbulence. It will be seen that broken ergodicity in ideal 2D MHD turbulence can be manifest in the lowest wavenumbers of a finite numerical model for certain initial conditions or in the highest wavenumbers for another set of initial conditions. The origins of broken ergodicity in an ideal 2D homogeneous MHD turbulence are found through an eigenanalysis of the covariance matrices of the probability density function and by an examination of the associated entropy functional. When the values of ideal invariants are kept fixed and grid size increases, it will be shown that the energy in a few large modes remains constant, while the energy in any other mode is inversely proportional to grid size. Also, as grid size increases, we find that broken ergodicity becomes manifest at more and more wavenumbers.
Trapping-related recombination of charge carriers in silicon
Authors: Harder N. P. , Gogolin R. , Brendel R.
Published: September 2010

We present experimental evidence and theoretical explanation for simultaneous occurrence of trapping related increased apparent carrier lifetime and decreased actual recombination lifetime in low injection. This correlation is not describable by the common Hornbeck and Haynes [Phys. Rev. 97, 311 (1955)] trapping model. McIntosh, Paudyal, and Macdonald [J. Appl. Phys. 104, 084503 (2008)] recently used Shockley–Read–Hall (SRH) recombination statistics [Phys. Rev. 87, 835 (1952)] for describing the temperature dependence of trapping. Our study shows that these SRH statistics for traps also explain a causal connection between trapping-related increased apparent charge carrier lifetime and reduced actual lifetime in low injection.
Two-subband conduction in a gated high density InAlN/AlN/GaN heterostructure
Authors: Cheng H. , Kurdak Ç. , Leach J. H. , Wu M. , Morkoç H.
Published: September 2010

Magnetotransport measurements on an In0.16Al0.84N/AlN/GaN gated Hall bar sample have been performed at 0.28 K. By the application of a gate voltage we were able to vary the total two-dimensional electron gas density from 1.83×1013 to 2.32×1013 cm−2. Two frequency Shubnikov–de Haas oscillations indicate occupation of two subbands by electrons. The density of electrons in the first and second sublevels are found to increase linearly with gate voltage with a slope of 2.01×1012 cm−2/V and 0.47×1012 cm−2/V, respectively. And the quantum lifetimes for the first and second subbands ranged from 0.55 to 0.95×10−13 s and from 1.2 to 2.1×10−13 s.
Kinetics controlled aging effect of ferroelectricity in Al-doped and Ga-doped BaTiO3
Authors: Guo Y. Y. , Qin M. H. , Wei T. , Wang K. F. , Liu J.-M.
Published: September 2010

Our experiments on ferroelectric aging of Al3+- and Ga3+-doped BaTiO3 ceramics reveal the crucial role of migration kinetics of point defects (oxygen vacancies) besides the thermodynamic driving force based on the symmetry conforming short-range ordering scenario. The doping with Ga3+ or tiny Al3+ ions shows the clear aging effect, while the high-level Al3+-doping suppresses the aging effect. The suppression is mainly attributed to the kinetically limited migration of oxygen vacancies due to the lattice shrinkage, while the other mechanisms may also make sense.
Deep level transient spectroscopy in plasma-assisted molecular beam epitaxy grown Al0.2Ga0.8N/GaN interface and the rapid thermal annealing effect
Authors: Park Young S. , Lee Minyoung , Jeon Kiyoung , Yoon Im T. , Shon Yoon , Im Hyunsik , Park C. J. , Cho Hoon Y. , Han Myung-Soo
Published: September 2010

We investigated deep-level traps formed in Al0.2Ga0.8N/GaN heterostructures grown using plasma-assisted molecular beam epitaxy and by performing deep level transient spectroscopy (DLTS). Two electron traps with activation energies of Ec−150 meV and Ec−250 meV were observed, and their capture cross-sections (σT) were estimated to be 2.0×10−18 cm2 and 1.1×10−17 cm2, respectively. Different behaviors in the dependence of DLTS on filling pulse length confirm that the traps originated from N vacancies and dislocations. The amplitude of the dislocation-induced DLTS signal was reduced significantly by high-temperature rapid thermal annealing under N2 ambient after hydrogen treatment due to the reduction in dislocation density.
Integrating fuel treatment into ecosystem management: a proposed project planning process
Authors: Stockmann Keith D. , Hyde Kevin D. , Jones J. Greg , Loeffler Dan R. , Silverstein Robin P.
Published: September 2010

Concern over increased wildland fire threats on public lands throughout the western United States makes fuel reduction activities the primary driver of many management projects. This single-issue focus recalls a management planning process practiced frequently in recent decades – a least-harm approach where the primary objective is first addressed and then plans are modified to mitigate adverse effects to other resources. In contrast, we propose a multiple-criteria process for planning fuel-treatment projects in the context of ecosystem management. This approach is consistent with policies that require land management activities be designed to meet multiple-use and environmental objectives, while addressing administrative and budget constraints, and reconciling performance measures from multiple policy directives. We present the process borrowing from the Trapper Bunkhouse Land Stewardship Project example to show the logic for conducting an integrated assessment of ecological and natural resource issues related to multiple management scenarios. The effects and trade-offs of the no-action scenario and proposed action alternatives are evaluated relative to silviculture, disturbance processes (including fire behaviour), wildlife habitat, noxious weeds, water quality, recreation and aesthetics, and economic contributions. Advantages and challenges of this project planning approach are also discussed.
Effect of drying temperature on fuel moisture content measurements
Authors: Matthews Stuart
Published: September 2010

Oven-drying of fuel samples is often used to determine fuel moisture content. In this study, laboratory measurements are used to demonstrate that drying temperature has a significant effect on the oven-dry mass of dead grass, pine and eucalyptus fuels. Differences between oven-dry masses of fuels dried at 60 and 105°C of up to 3.5% were measured. This is a large enough difference to have a significant effect on fire behaviour predictions. Samples should be dried at 105°C.
Prescribed burning of thinning slash in regrowth stands of jarrah (Eucalyptus marginata) following bauxite mining in south-west Australia
Authors: Grigg Andrew H. , Norman Melanie A. , Grant Carl D.
Published: September 2010

Prescribed burning of regrowth jarrah stands established after bauxite mining is key to their integration into standard jarrah forest management, but fire management in thinned regrowth stands has not been studied. Fuel loads in 10- to 13-year-old thinned regrowth increased exponentially with thinning intensity, doubling from 18 t ha–1 in untreated stands (1500–2500 stems ha–1) to 37.4 t ha–1 in the heaviest treatment (400 stems ha–1 retained); however, litter and standing dead vegetation were concentrated within 60 cm of the ground. Intensities of subsequent autumn prescribe-burns increased with increasing fuel loads, but all burns were typically of low to moderate intensity <1800 kW m–1. Three months post-burn, total fuel loads averaged 5 t ha–1, recovering after 4.5 years to 75% of pre-burn levels across all thinning treatments owing mostly to dense understorey regeneration. Where no burning occurred after thinning, total fuel loads declined to be comparable to the unthinned control after 4.5 years, averaging 20 t ha–1. Prescribed burns in autumn following thinning are not recommended because a dense well-aerated and elevated fuel layer is reinstated, posing a future fire risk. Burning 1–2 years before thinning may be an appropriate alternative strategy.
Methods to determine the impact of rainfall on fuels and burned area in southern African savannas
Authors: Archibald S. , Nickless A. , Scholes R. J. , Schulze R.
Published: September 2010

In southern African savannas, grass production, and therefore the annual extent of fire, is highly dependent on rainfall. This response has repeatedly been noted in the literature but authors used different input variables and modelling approaches and the results are not comparable. Using long-term fire occurrence data from six protected areas in southern Africa we tested various methods for determining the relationship between antecedent rainfall and burned area. The types of regression model, the most appropriate index of accumulated rainfall, and the period over which to calculate annual burned area were all investigated. The importance of accumulating rainfall over more than one growing season was verified in all parks – improving the accuracy of the models by up to 30% compared with indices that only used the previous year’s rainfall. Up to 56% of the variance in burned area between years could be explained by an 18-month accumulated rainfall index. Linear models and probit models performed equally well. The method suggested in this paper can be applied across southern Africa. This will improve our understanding of the drivers of interannual variation in burned area in this globally important fire region.
Fuel loading and flammability in the Mediterranean Basin woody species with different post-fire regenerative strategies
Authors: Saura-Mas S. , Paula S. , Pausas J. G. , Lloret F.
Published: September 2010

The flammability and combustibility of plant communities are determined by species features related to growth-form, structure and physiology. In some ecosystems, such as the Mediterranean ones, these characteristics may contribute to the existence of fire-prone species. We measured several parameters associated with the flammability and fuel loading of dominant woody species with different post-fire regenerative strategies (seeders and non-seeders) in shrublands in the western Mediterranean Basin. Overall, seeder species show lower fuel load but are more prone to burning owing to a higher dead-to-live fuel ratio, live fine-fuel proportion and dead fine-fuel proportion. Moreover, they burst into flame at lower temperatures than non-seeders. In the Mediterranean Basin, most seeder species emerged mainly during the Quaternary, under a highly fluctuating Mediterranean climate and during recurrent fires. We propose that properties related to the combustibility and flammability of seeders may be the result of selective pressures associated with both fire and climate. These results suggest that ecosystems dominated by seeder species are more susceptible to fire risk than those dominated by non-seeder species in the Mediterranean Basin. Therefore, the proportion of these types of species resulting from previous fire or management history is likely to determine the characteristics of future fire events.
Minimal effectiveness of native and non-native seeding following three high-severity wildfires
Authors: Stella Ken A. , Sieg Carolyn H. , Fulé Pete Z.
Published: September 2010

The rationale for seeding following high-severity wildfires is to enhance plant cover and reduce bare ground, thus decreasing the potential for soil erosion and non-native plant invasion. However, experimental tests of the effectiveness of seeding in meeting these objectives in forests are lacking. We conducted three experimental studies of the effectiveness of seeding with non-native and native species following three Arizona wildfires. Seeding treatments were largely ineffective in increasing vegetative cover or decreasing exposed bare ground. At one treatment at one fire, wheat seeding at the Warm Fire, senesced seeded annuals increased litter cover and resulted in lower bare ground values than unseeded controls. Only on one fire, the Warm Fire, did seeded non-native annuals establish well, resulting in 20–29% vegetative cover. On the other two fires, seeded cereal grains accounted for <3% cover. At all fires, native seeded species contributed between <1 and ∼12% vegetative cover. Vegetative cover on all treatments, including unseeded treatments, was at or near 40% the first year following fire, at all three study sites. Non-native species richness and abundance did not differ among treatments at any fire. This study adds to growing evidence that post-fire seeding is ineffective in enhancing post-fire plant cover and reducing invasive non-native plants.
Ancient class of translocated oomycete effectors targets the host nucleus
Authors: Schornack Sebastian , van Damme Mireille , Bozkurt Tolga O. , Cano Liliana M. , Smoker Matthew , Thines Marco , Gaulin Elodie , Kamoun Sophien , Huitema Edgar
Published: September 2010

Pathogens use specialized secretion systems and targeting signals to translocate effector proteins inside host cells, a process that is essential for promoting disease and parasitism. However, the amino acid sequences that determine host delivery of eukaryotic pathogen effectors remain mostly unknown. The Crinkler (CRN) proteins of oomycete plant pathogens, such as the Irish potato famine organism
Phytophthora infestans
, are modular proteins with predicted secretion signals and conserved N-terminal sequence motifs. Here, we provide direct evidence that CRN N termini mediate protein transport into plant cells. CRN host translocation requires a conserved motif that is present in all examined plant pathogenic oomycetes, including the phylogenetically divergent species
Aphanomyces euteiches
that does not form haustoria, specialized infection structures that have been implicated previously in delivery of effectors. Several distinct CRN C termini localized to plant nuclei and, in the case of CRN8, required nuclear accumulation to induce plant cell death. These results reveal a large family of ubiquitous oomycete effector proteins that target the host nucleus. Oomycetes appear to have acquired the ability to translocate effector proteins inside plant cells relatively early in their evolution and before the emergence of haustoria. Finally, this work further implicates the host nucleus as an important cellular compartment where the fate of plant–microbe interactions is determined.
Decisive factors affecting plasma resistance and roughness formation in ArF photoresist
Authors: Jinnai Butsurin , Uesugi Takuji , Koyama Koji , Kato Keisuke , Yasuda Atsushi , Maeda Shinichi , Momose Hikaru , Samukawa Seiji
Published: September 2010

Low plasma resistance and roughness formation in an ArF photoresist are serious issues in plasma processes. To resolve these issues, we investigated several factors that affect the roughness formation and plasma resistance in an ArF photoresist. We used our neutral beam process to categorize the effects of species from the plasma on the ArF photoresist into physical bombardment, chemical reactions and ultraviolet/vacuum ultraviolet (UV/VUV) radiation. The UV/VUV radiation drastically increased the etching rates of the ArF photoresist films, and, in contrast, chemical reactions increased the formation of surface roughness. FTIR analysis indicated that the UV/VUV radiation preferentially dissociates C–H bonds in the ArF photoresist, rather than C=O bonds, because of the dissociation energies of the bonds. This indicated that the etching rates of the ArF photoresist are determined by the UV/VUV radiation because this radiation can break C–H bonds, which account for the majority of structures in the ArF photoresist. In contrast, FTIR analysis showed that chemical species such as radicals and ions were likely to react with C=O bonds, in particular C=O bonds in the lactone groups of the ArF photoresist, due to the structural and electronic effects of the lactone groups. As a result, the etching rates of the ArF photoresist can vary in different bond structures, leading to increased surface roughness in the ArF photoresist.
Effects of annealing atmosphere on ZnO− ions-implanted silica glass: synthesis of Zn and ZnO nanoparticles
Authors: Kuiri P K , Mahapatra D P
Published: September 2010

The effects of annealing atmosphere (argon or oxygen) on Zn nanoparticles (NPs), embedded in silica glass, synthesized by implanting 50 keV ZnO− ions to a fluence of 7 × 1016 cm−2 have been studied. Optical absorption (OA) measurements carried out on the as-implanted samples have been found to result in a surface plasmon resonance (SPR) band centred at ∼255 nm due to the presence of Zn NPs in the silica glass. An increase in SPR peak intensity with a corresponding reduction of its full width at half maximum have been seen in the OA spectrum taken from the as-implanted sample following annealing in Ar ambient at 700 °C for 2 h, indicating a growth in the size of Zn NPs. However, annealing the as-implanted sample in O2 gas at 700 °C for 2 h has been found to result in a steep absorption edge at ∼364 nm in the OA spectrum which indicates the formation of ZnO NPs. These ZnO NPs show quantum confinement effects due to their small sizes. No observable photoluminescence (PL) emission has been seen from Zn NPs, whereas an excitonic band at ∼368 nm and three deep-level PL emission bands at ∼453 nm, ∼521 nm and ∼650 nm, respectively, have been seen from ZnO NPs. It was argued that the deep-level PLs were due to the singly ionized oxygen vacancies located at ZnO NPs' surfaces. These observations suggest that ZnO NPs were formed due to oxidation of Zn NPs via interaction with the indiffusing O2 molecules during annealing in O2 ambient, but not with the interaction of the implanted oxygen in silica glass.
Epitaxially stabilized TiN/(Ti,Fe,Co)N multilayer thin films in (pseudo-)fcc crystal structure by sequential magnetron sputter deposition
Authors: Klever C , Seemann K , Stüber M , Ulrich S , Brunken H , Ludwig A , Leiste H
Published: September 2010

Multilayer thin films were grown by non-reactive sequential magnetron sputter deposition from ceramic TiN and metallic FeCo targets addressing a combination of wear resistance and sensoric functionality. Coatings with bilayer period values ranging from 449 nm down to 2.6 nm were grown with the total amount of either material maintained constant. The multilayer thin films were post-annealed ex situ at 600 °C for 60 min in vacuum.

X-ray diffraction results imply the multilayer thin films undergo significant changes in their crystalline structure when the bilayer period is decreased. Using high-resolution transmission electron microscopy as well as selected-area electron diffraction it is shown that in the case of multilayer thin films with bilayer periods of several tens of nanometres and higher, FeCo layers and TiN layers in their respective common CsCl- and NaCl-type crystal structures alternate. In contrast, in the multilayer thin films with bilayer periods of only a few nanometres, grain growth across the interfaces between the individual layers takes place and a strongly textured microstructure is formed which features columns in (pseudo-)fcc crystal structure grown in heteroepitaxial growth mode.

It is suggested that the experimental findings imply the latter multilayer thin films to be alternately composed of TiN layers and (Ti,Fe,Co)N solid solution layers which have been formed by a solid-state reaction during the deposition process. As a consequence, heteroepitaxially stabilized columnar grains in strongly textured (pseudo-)fcc crystal structure are formed. This crystal structure is preserved after the annealing procedure which qualifies these coatings for use in applications where temperatures of up to 600 °C are reached.
Analysis of the electromagnetic radiation generated by a multipactor discharge occurring within a microwave passive component
Authors: Jiménez M , Gimeno B , Miquel-Espanya C , Raboso D , Anza S , Vicente C , Gil J , Quesada F , Álvarez A , Taroncher M , Reglero M , Boria V E
Published: September 2010

Multipactoring is a non-linear phenomenon that appears in high-power microwave equipment operating under vacuum conditions and causes several undesirable effects. In this paper, a theoretical and experimental study of the RF spectrum radiated by a multipactor discharge, occurring within a realistic microwave component based on rectangular waveguides, is reported. The electromagnetic coupling of a multipactor current to the fundamental propagative mode of a uniform waveguide has been analysed in the context of the microwave network theory. The discharge produced under a single-carrier RF voltage regime has been approached as a shunt current source exciting such a mode in a transmission-line gap region. By means of a simple equivalent circuit, this model allows prediction of the harmonics generated by the discharge occurring in a realistic passive waveguide component. Power spectrum radiated by a third-order multipactor discharge has been measured in an E-plane silver-plated waveguide transformer, thus validating qualitatively the presented theory to simulate the noise generated by a single-carrier multipactor discharge.
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape
Authors: Pentchev Konstantin , Ono Keiichiro , Herwig Ralf , Ideker Trey , Kamburov Atanas
Published: September 2010

Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.

Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site (http://cpdb.molgen.mpg.de).

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  kamburov@molgen.mpg.de
Combined prediction of Tat and Sec signal peptides with hidden Markov models
Authors: Bagos Pantelis G. , Nikolaou Elisanthi P. , Liakopoulos Theodore D. , Tsirigos Konstantinos D.
Published: September 2010

Motivation: Computational prediction of signal peptides is of great importance in computational biology. In addition to the general secretory pathway (Sec), Bacteria, Archaea and chloroplasts possess another major pathway that utilizes the Twin-Arginine translocase (Tat), which recognizes longer and less hydrophobic signal peptides carrying a distinctive pattern of two consecutive Arginines (RR) in the n-region. A major functional differentiation between the Sec and Tat export pathways lies in the fact that the former translocates secreted proteins unfolded through a protein-conducting channel, whereas the latter translocates completely folded proteins using an unknown mechanism. The purpose of this work is to develop a novel method for predicting and discriminating Sec from Tat signal peptides at better accuracy.

Results: We report the development of a novel method, PRED-TAT, which is capable of discriminating Sec from Tat signal peptides and predicting their cleavage sites. The method is based on Hidden Markov Models and possesses a modular architecture suitable for both Sec and Tat signal peptides. On an independent test set of experimentally verified Tat signal peptides, PRED-TAT clearly outperforms the previously proposed methods TatP and TATFIND, whereas, when evaluated as a Sec signal peptide predictor compares favorably to top-scoring predictors such as SignalP and Phobius. The method is freely available for academic users at http://www.compgen.org/tools/PRED-TAT/.

Contact:  pbagos@ucg.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of hydrogen peroxide production-related genes in Streptococcus sanguinis and their functional relationship with pyruvate oxidase
Authors: Chen Lei , Ge Xiuchun , Dou Yuetan , Wang Xiaojing , Patel Jenishkumar R. , Xu Ping
Published: September 2010

Hydrogen peroxide (H2O2), an important substance produced by many members of the genus Streptococcus, plays important roles in virulence and antagonism within a microbial community such as oral biofilms. The spxB gene, which encodes pyruvate oxidase, is involved in H2O2 production in many streptococcal species. However, knowledge about its regulation and relation with other genes putatively involved in the same pathway is limited. In this study, three genes – ackA, spxR and tpk – were identified as contributing to H2O2 production in Streptococcus sanguinis by screening mutants for opaque colony appearance. Mutations in all three genes resulted in significant decreases in H2O2 production, with 16–31 % of that of the wild-type. H2O2 production was restored in the complemented strains. Antagonism against Streptococcus mutans by these three S. sanguinis mutants was reduced, both on plates and in liquid cultures, indicating the critical roles of these three genes for conferring the competitive advantage of S. sanguinis. Analysis by qPCR indicated that the expression of spxB was decreased in the ackA and spxR mutants and significantly increased in the tpk mutant.
Acetaldehyde/alcohol dehydrogenase-2 (EhADH2) and clathrin are involved in internalization of human transferrin by Entamoeba histolytica
Authors: Reyes-López Magda , Bermúdez-Cruz Rosa María , Avila Eva E. , de la Garza Mireya
Published: September 2010

Transferrin (Tf) is a host glycoprotein capable of binding two ferric-iron ions to become holotransferrin (holoTf), which transports iron in to all cells.Entamoeba histolyticais a parasitic protozoan able to use holoTf as a sole iron sourcein vitro. The mechanism by which this parasite scavenges iron from holoTf is unknown. AnE. histolyticaholoTf-binding protein (EhTfbp) was purified by using an anti-human transferrin receptor (TfR) monoclonal antibody.EhTfbp was identified by MS/MS analysis and database searches asE. histolyticaacetaldehyde/alcohol dehydrogenase-2 (EhADH2), an iron-dependent enzyme. BothEhTfbp andEhADH2 bound holoTf and were recognized by the anti-human TfR antibody, indicating that they correspond to the same protein. It was found that the amoebae internalized holoTf through clathrin-coated pits, suggesting that holoTf endocytosis could be important for the parasite during colonization and invasion of the intestinal mucosa and liver.
Metabolomics as a tool for target identification in strain improvement: the influence of phenotype definition
Authors: Braaksma Machtelt , Bijlsma Sabina , Coulier Leon , Punt Peter J. , van der Werf Mariët J.
Published: September 2010

For the optimization of microbial production processes, the choice of the quantitative phenotype to be optimized is crucial. For instance, for the optimization of product formation, either product concentration or productivity can be pursued, potentially resulting in different targets for strain improvement. The choice of a quantitative phenotype is highly relevant for classical improvement approaches, and even more so for modern systems biology approaches. In this study, the information content of a metabolomics dataset was determined with respect to different quantitative phenotypes related to the formation of specific products. To this end, the production of two industrially relevant products by Aspergillus niger was evaluated: (i) the enzyme glucoamylase, and (ii) the more complex product group of secreted proteases, consisting of multiple enzymes. For both products, six quantitative phenotypes associated with activity and productivity were defined, also taking into account different time points of sampling during the fermentation. Both linear and nonlinear relationships between the metabolome data and the different quantitative phenotypes were considered. The multivariate data analysis tool partial least-squares (PLS) was used to evaluate the information content of the datasets for all the different quantitative phenotypes defined. Depending on the product studied, different quantitative phenotypes were found to have the highest information content in specific metabolomics datasets. A detailed analysis of the metabolites that showed strong correlation with these quantitative phenotypes revealed that various sugar derivatives correlated with glucoamylase activity. For the reduction of protease activity, mainly as-yet-unidentified compounds correlated.
Identification of Vibrio campbellii isolated from diseased farm-shrimps from south India and establishment of its pathogenic potential in an Artemia model
Authors: Haldar Soumya , Chatterjee Shruti , Sugimoto Norihiko , Das Surajit , Chowdhury Nityananda , Hinenoya Atsushi , Asakura Masahiro , Yamasaki Shinji
Published: September 2010

Shrimp diseases are frequently reported to be caused by closely related vibrios, and in many cases they are tentatively but inaccurately identified as Vibrio harveyi and related vibrios. In the present study, 28 biochemically identified V. harveyi-related strains isolated from diseased shrimps were randomly selected for further characterization by molecular tools. Twenty-six strains were identified as Vibrio campbellii and two as V. harveyi by sequence analysis of 16S rRNA and uridylate kinase genes. Haemolysin-gene-based species-specific multiplex PCR also confirmed these results. Experimental challenge studies using Artemia as a model showed that eight isolates were highly pathogenic, three were moderately pathogenic and the remaining 17 were non-pathogenic. Ribotyping with BglI clearly distinguished V. campbellii from V. harveyi, but it failed to separate pathogenic and non-pathogenic clusters. Artemia nauplii challenged with a fluorescently labelled highly pathogenic strain (IPEY54) showed patches in the digestive tract. However, no patches were observed for a non-pathogenic strain (IPEY41). Direct bacterial counts also supported colonization potential for the highly pathogenic strain. To our knowledge, this is the first report on the isolation and accurate identification of large numbers of V. campbellii associated with shrimp disease in aquacultural farms. V. campbellii has long been considered to be non-pathogenic and classified with V. harveyi-related bacteria. However, we show that this species may be an emerging aquaculture pathogen. This study will help to formulate suitable strategies to combat this newly identified pathogen.
Exceptionalism and Internationalism: The Origins of American Social Science Reconsidered
Authors: Goldman Lawrence
Published: September 2010

This paper examines the international context in which American social science was institutionalized in the generation after the Civil War, following the foundation of the American Social Science Association in 1865. The ASSA was modelled on an influential British forum, founded eight years previously, the National Association for the Promotion of Social Science. A comparison of these two organisations from the 1860s to the 1880s allows consideration of British intellectual and political influences on the first American social scientists. It also helps in the identification of the social and political attitudes of the well‐born, cosmopolitan, and high‐minded American reformers attracted to social science at this time. The theme of American exceptionalism has recently been emphasized when considering the motives and intentions of early social science in the United States. It is argued here that the replication in America of models of the new discipline which were first developed in Britain, is indicative also of a self‐conscious internationalism among the American social‐scientific community of this period. In addition to an institutional comparison, the article examines the careers and ideas of several representative figures in this process of Anglo‐American liberal transference, among them the physician Dr. Edward Jarvis, the feminist Caroline Healey Dall, the jurist David Dudley Field, and the famed British interpreter of American experience, James Bryce.
Gender and Compulsory Sterilization Programs in America: 1907–1950
Authors: Carey Allison C.
Published: September 2010

Current scholarship on compulsory sterilization and gender focuses almost exclusively on women as the targets of these programs. As Philip Reilly (1991:98) indicates, however, there occurred a "dramatic change" in the gender of those targeted for compulsory sterilizations in America. Prior to 1928 men were more likely to be sterilized, but, after 1928, women became far more likely to be sterilized. I use this shift as a focal point in examining the changing role of gender. First, I show the ways in which rationales for sterilization differed by gender. Then, turning to analyze the shift, I argue that the medical and legal professions criticized the rationales for male sterilization, yet these professions and others tended to be more supportive of female sterilization, imagining sterilization to have many advantages for society and women. Superintendents, simultaneously responding to external pressure and shaping sterilization to meet their own interests, transformed sterilization into a program which focused largely upon women.
The Renewed Search for Social Trusteeship: Cohen and Fitch on Social Justice and the City
Authors: Cowen M.P. , Shenton R.W.
Published: September 2010

It has become a commonplace to argue that in the face of a discredited Marxism, socialism must find an alternative basis for a renewed project. This article investigates two of these claims by Gerald Cohen and Bob Fitch. It does so with particular reference to the attempt by these authors to re‐invoke, both wittingly and unwittingly, David Ricardo, John Stuart Mill, Henry George, and Auguste Comte among others as the source of a renewed left project. It takes as its special concern the way in which the supposed need to revivify "industry" in the late twentieth century parallels the often voiced need to revivify "agriculture" in the late nineteenth century as a means of staving off "underdevelopment."
Ethnography, Cultural Change and Local Power
Authors: Zárate Hernández José Eduardo
Published: September 2010

The author argues that despite the declaration for the end of ethnography by some North American scholars, ethnography is precisely what is needed for a more nuanced and complex understanding of cultural change. Using snippets of ethnographic observation from the Mexican state of Michoacan, the argument is made that neither "modernization" nor "globalization" are imposed from above, but are woven together with local processes to create institutions and practices which synthesize both the "traditional" and the "modern" in previously unimagined ways. Local people and processes are thus conceived of as dynamic partners in cultural change rather than passive subjects. Ethnography, then, is a fruitful means for uncovering how and the extent to which this is so.
Politics of Displacement in Guatemala
Authors: Stepputat Finn
Published: September 2010

This article examines the processes and effects of displacement during the armed conflict in Guatemala. The analytical approach emphasizes the relations between space, power and culture and draws upon writers like Henry Lefebvre, Michel Foucault, de Certeau and the French army officer, Roger Trinquier. The article argues that the army, through the massive displacement of population and the organization of civil patrols, produced a dichotomous space of “villages” and “wilderness,” and that the reorganization of space enabled the army to control the conflict. The spatial reorganization increased the state's capacity for surveillance, but the article also shows how displacement and the struggles over modes of reinclusion of the displaced population had wider effects on the body politic and produced new political subjects in Guatemala.
Why were the 1980s “millenarian”? Style, repertoire, space and authority in South Africa’s black cities
Authors: Bozzoli Belinda
Published: September 2010

This paper argues that some of the key determinants of the style and repertoire of the South African township revolts of the mid‐eighties lie in the changing configurations of race, class and authority within townships over a long period of time. One major and pivotal change in these relationships is identified, and the paper employs ideal‐typical constructions of the nature of townships in the two crucial eras concerned: what could broadly be described as the era of “welfare paternalism” and succeeding it after a period of complex change, the equally broadly characterized era of “racial modernism”. Though both eras were racist, exploitative, and engendered class and community struggles they differed from one another in important stylistic and spatial ways. This paper suggests that the move from the one era to the other constitutes the move from a mode of “governability” to one of “ungovernability”, and highlights the form, repertoire and style of rebellion.
Do Other Firms Matter in Oligopolies?
Authors: Haskel Jonathan , Scaramozzino Pasquale
Published: September 2010

This paper examines how firms interact with their rivals. The main novelty of our approach is that we let conjectural variations depend on the actual ability of other firms to react, which we measure by both the physical capacity and financial status of firms. Our main findings are twofold. First, physical and financial capacity significantly affect conjectures. Second, we recover the implied conjectural variations and reject homogeneous conjectures. We generally find that leaders expect aggressive responses, and followers are Cournot players.
Minimum Quality Standards and Collusion
Authors: Ecchia Giulio , Lambertini Luca
Published: September 2010

We model the introduction of a minimum quality standard in a vertically differentiated duopoly. We extend the literature by determining the standard endogenously, showing that the maximisation of social welfare entails an increase in the surplus accruing to consumers served by the low quality firm and a decrease in the surplus of the remaining consumers. Then, we consider the effects of the standard on the stability of price collusion, proving that the standard makes it more difficult for firms to collude if consumers are sufficiently rich.
On Strategic Quantity Bidding in Multiple Unit Auctions
Authors: Tenorio Rafael
Published: September 2010

Standard studies of multiple unit auctions generally overlook the strategic role of bidders' quantity decisions. Using a simple equilibrium model of bidding I analyze bidders' incentives to choose quantities in discriminatory and competitive auctions. The main result is that bidders have a stronger strategic incentive to bid for fewer units in competitive auctions. Since under competition a bidder pays the lowest accepted price for each unit she gets, she may benefit from dropping her quantity to let lower‐valuing bidders enter the set of winners. This prediction is consistent with empirical observations from foreign currency and spectrum auctions.
Looking at the Cost Side of “Monopoly”
Authors: Aiginger Karl , Pfaffermayr Michael
Published: September 2010

Welfare loss under oligopoly is defined as that part of consumer surplus which is lost and not regained by higher profits. In a model with asymmetric firms, this implies that the total welfare loss consists of the deadweight loss triangle plus a cost side inefficiency effect, due to the fact that in imperfect markets not all firms utilize the lowest cost technique. Using a flexible CV‐model we calculate these effects empirically for two relatively homogeneous industries (pulp/paper and cement). The deadweight loss triangles are shown to be smaller than the cost difference effect (“the staircase”) for these industries.
The Differentiation Triangle
Authors: Canoy Marcel , Peitz Martin
Published: September 2010

The paper formalizes the observation that submarkets for high‐quality and low‐quality variants are markedly different from each other. We study a simple model where variants of low quality cannot be horizontally differentiated, whereas customers disagree about the value of variants in the high‐quality range. We determine the outcome under price competition in the differentiation triangle with sequential entry when each firm can develop the vertical product line or decide to follow a niche strategy, i.e. to develop only one variant.
The Competitive Effects of Price‐Floors
Authors: Bhaskar V.
Published: September 2010

Using Hotelling's model of locational competition, we show that a moderate price‐floor destroys the maximal differentiation equilibrium, resulting in minimum differentiation. Equilibrium prices are lower than prices in the absence of a floor. A low price‐floor can lead to multiple equilibria, with both minimum and maximum differentiation as possible outcomes.
The Access Pricing Problem with Deregulation: A Note
Authors: Armstrong Mark , Vickers John
Published: September 2010

This note extends the analysis of Armstrong, Doyle and Vickers [1996] to the case of retail price deregulation. It is shown (i) that the optimal access price may be above, below, or (in the linear case) equal to marginal cost, (ii) that optimal regulation of the margin between the retail price and the access price entails the ECPR, and (iii) that welfare and entrant profit are higher when the level of the access price, rather than the margin, is regulated.
The Control of Technology Alliances: An Empirical Analysis of the Biotechnology Industry
Authors: Lerner Josh , Merges Robert P.
Published: September 2010

We examine the determinants of control rights in biotechnology alliances through three case studies and a quantitative analysis. Aghion and Tirole [1994] argue that control rights will be assigned so as to maximize the value of the final output, as long as the R&D firm has sufficient financial resources. Consistent with this framework, the allocation of control rights to the R&D firm increases with the firm’s financial resources. The empirical evidence regarding the relationship between control rights and the stage of the project at the time the alliance is signed is more ambiguous.
Absorptive Capacity, Coauthoring Behavior, and the Organization of Research in Drug Discovery
Authors: Cockburn Iain M. , Henderson Rebecca M.
Published: September 2010

We examine the interface between for‐profit and publicly funded research in pharmaceuticals. Firms access upstream basic research through investments in absorptive capacity in the form of in‐house basic research and ‘pro‐publication’ internal incentives. Some firms also maintain extensive connections to the wider scientific community, which we measure using data on coauthorship of scientific papers between pharmaceutical company scientists and publicly funded researchers. ‘Connectedness’ is significantly correlated with firms’ internal organization, as well as their performance in drug discovery. The estimated impact of ‘connectedness’ on private research productivity implies a substantial return to public investments in basic research.
Environmental Regulation, Investment Timing, and Technology Choice
Authors: Gray Wayne B. , Shadbegian Ronald J.
Published: September 2010

We test whether environmental regulation affects investment decisions, using Census data for individual paper mills. New mills in states with strict environmental regulations choose cleaner production technologies, with differences in air and water pollution regulation also influencing technology choice. Examining investment allocation across existing plants, we find that abatement and productive investment tend to be scheduled together. However, plants with high abatement investment over the entire period spend significantly less on productive capital. This seems to reflect both environmental investment ‘crowding out’ productive investment within a plant, and firms shifting investment towards plants facing less stringent abatement requirements.
Takeover Risk and Dividend Strategy: A Study of UK Firms
Authors: Dickerson Andrew P. , Gibson Heather D. , Tsakalotos Euclid
Published: September 2010

We investigate the relationship between a company’s dividend strategy and its risk of takeover. Our results from a large panel of UK quoted companies suggest that higher dividend payments are associated with a significantly lower conditional probability (hazard) of takeover. Moreover, firms which wish to avoid takeover would be better to distribute the marginal £1 of earnings in dividends rather than investing it in the company. We consider two explanations for these findings. We suggest that the presence of an active market for corporate control could encourage firms to raise dividends to maintain shareholder loyalty.