bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic ordering of EuTe∕PbTe multilayers determined by x-ray resonant diffraction
Authors: Díaz B. , Granado E. , Abramof E. , Rappl P. H. O. , Chitta V. A. , Henriques A. B.
Published: June 2008

In this work we use resonant x-ray diffraction combined with polarization analysis of the diffracted beam to study the magnetic ordering in EuTe∕PbTe multilayers. The presence of satellites at the (12 12 12) magnetic reflection of a 50 repetition EuTe∕PbTe superlattice demonstrated the existence of magnetic correlations among the alternated EuTe layers. The behavior of the satellites intensity as T increases toward the Nèel temperature TN indicates that these correlations persist nearly up to TN and suggests the preferential decrease of the magnetic order parameter of external monolayers of each EuTe layer within the superlattice.
How to make sticky surfaces slippery: Contact angle hysteresis in electrowetting with alternating voltage
Authors: Li F. , Mugele F.
Published: June 2008

Contact angle hysteresis caused by random pinning forces is a major obstacle in moving small quantities of liquid on solid surfaces. Here, we demonstrate that the contact angle hysteresis for sessile drops in electrowetting almost disappears with increasing alternating voltage, whereas for direct voltage it remains constant. This observation is explained in terms of a balance of surface tension, pinning, and (time-dependent) electrostatic forces at the contact line.
The weak antilocalization and quantum scattering time in a two-dimensional electron gas in AlGaN∕GaN heterostructure
Authors: Olshanetsky E. B. , Kvon Z. D. , Sassine S. , Portal J. C. , Cho H. I. , Lee J. H.
Published: June 2008

In the present work, we report an experimental study of the low field magnetoresistance in two groups of AlGaN∕GaN samples with a two-dimensional electron gas. The characteristic transport parameters of the samples in these two groups are similar except for the value of the quantum scattering time, which is about three times larger in one group than in the other. In the magnetoresistance measured in the group of samples with a larger value of quantum scattering time, we find a well-pronounced weak antilocalization peak, whereas in the group with a smaller quantum scattering time only a weak localization is observed.
Effect of surface stress on the asymmetric yield strength of nanowires
Authors: Zhang Weixu , Wang Tiejun , Chen Xi
Published: June 2008

While it is widely known that nanowires show strong size dependence on their elastic modulus and yield strength, the study on the asymmetric tensile and compressive yield strengths is scarce. In particular, the effect of the surface stress needs to be clearly revealed. In this paper, a theoretical framework is proposed to study the effect of surface stress on the elastic property and yield strength of nanowires. Both the surface residual stress and surface elasticity are taken into account, and the constraint of surface stress in the transverse direction is incorporated. For a representative aluminum nanowire with the decrease in the nanowire radius, the surface elasticity causes both the Young’s modulus and Poisson’s ratio to increase, and the surface stress causes the tensile yield strength to increase and the magnitude of compressive yield strength to decrease, leading to tension-compression asymmetry. The effect of surface elasticity is relatively small whereas the effect of transverse surface stress is important.
Optical and electronic properties of metal doped thermoelectric Zn4Sb3
Authors: Litvinchuk A. P. , Nylén J. , Lorenz B. , Guloy A. M. , Häussermann U.
Published: June 2008

Optical and electronic properties of metal (Pb, Bi, Sn, and In) doped Zn4Sb3 are reported in the temperature range 80–300 K, which covers the β, α, and α′ structural phases of this thermoelectric material. Metal doping alters the subtle balance between Zn disorder and Zn deficiency present in β-Zn4Sb3 and changes its low temperature structural behavior. Analysis of infrared reflection data shows that the formation of ordered α′-Zn4Sb3 is accompanied by a substantial increase in the free charge-carrier concentration. In contrast, for samples where doping suppresses the occurrence of the low temperature α′-phase, the free charge-carrier concentration is only weakly temperature dependent. Different degrees of structural disorder in doped β-Zn4Sb3 and the ordering processes at low temperatures leading to α- and α′-Zn4Sb3 are also recognized in the charge-carrier dynamics.
Quasi-one-dimensional hopping conductivity of the spin-ladder CaCu2O3 single crystals: Influence of the cation and oxygen nonstoichiometry
Authors: Lisunov K. G. , Wizent N. , Waske A. , Werner J. , Tristan N. , Sekar C. , Krabbes G. , Behr G. , Arushanov E. , Büchner B.
Published: June 2008

The resistivity ρ(T) of the spin-ladder compound CaCu2O3 measured along the Cu–O–Cu leg (j∥b) exhibits a strongly activated character. It increases from ∼104 to ∼109 Ω m if T decreases from 350 to 100 K. The charge transfer above T∼200 K is governed by a quasi-one-dimensional (1D) nearest-neighbor hopping (NNH) conductivity mechanism characterized by the law ρ(T)∼exp(Ea/kT). Below 200 K a novel quasi-1D variable-range hopping (VRH) conductivity law ρ(T)∼exp[(T0/T)3/4] is observed, predicted recently by Fogler, Teber, and Shklovskii [Phys. Rev. B 69, 035413 (2004)]. The NNH activation energy Ea and the VRH characteristic temperature T0 exhibit high sensitivity to the cation (Ca, Cu) content, decreasing by 2.3–2.5 times and by 3.0–3.2 times, respectively, when the composition of Ca is changed from 0.854 to 0.786–0.798 and the composition of Cu from 2.039 to 2.159–2.163. The behavior of Ea and T0 can be attributed to a corresponding variation of the concentration of intrinsic defects associated with Cu vacancies. On the other hand, no direct dependence of Ea and T0 to the excess oxygen concentration is observed.
Effects of post-growth annealing on the structure and electro-optical properties of low-temperature grown GaAs
Authors: Youn Doo-Hyeb , Lee Seung-Hwan , Ryu Han-Cheol , Jung Se-Young , Kang Seung-Bum , Kwack Min-Hwan , Kim Sungil , Choi Sang-Kuk , Baek Mun-Cheol , Kang Kwang-Yong , Kim Chang-Seop , Yee Ki-Ju , Ji Young-Bin , Lee Eui-Su , Jeon Tae-In , Kim Seong-Jin , Kumar Sanjeev , Kim Gil-Ho
Published: June 2008

This paper investigates how postgrowth annealing affects the structure and the electro-optical properties of low-temperature grown GaAs (LT-GaAs). A systematic study of as-grown and annealed LT-GaAs revealed that the carrier lifetime is directly related to the density of the An duster and distance between As clusters. The Ga/As compositional ratio and the crystal structure of As clusters were observed for the first time. The As/Ga ratio of the As clusters is higher than that obtained from the LT-GaAs. The carrier lifetime of the annealed LT-GaAs increases as the annealing temperature increases from 400 (less than 30 fs) to 800 °C (824 fs). Under the annealing temperatures ranging from 600 to 700 °C for 90 s, we observed the emission of terahertz radiation using the annealed LT-GaAs grown at temperatures ranging from 260 to 320 °C.
Two-dimensional electron gas insulation by local surface thin thermal oxidation in AlGaN∕GaN heterostructures
Authors: Roccaforte Fabrizio , Giannazzo Filippo , Iucolano Ferdinando , Bongiorno Corrado , Raineri Vito
Published: June 2008

In this letter, the physical effects of the local surface thin thermal oxidation on the current transport in AlGaN∕GaN heterostructures are reported. Current-voltage measurements performed on appropriate test patterns demonstrated that a selective oxidation process at 900°C enables the suppression of the current flow through the two-dimensional electron gas. The electrical insulation was achieved even though structural analysis showed that the formed oxide did not reach the depth of the AlGaN∕GaN heterointerface. The combination of capacitance-voltage measurements with depth-resolved scanning capacitance microscopy enabled to correlate the electrical results to the doping and the compositional stability of the material during oxidation.
Predicting the hydrogen pressure to achieve ultralow friction at diamond and diamondlike carbon surfaces from first principles
Authors: Guo Haibo , Qi Yue , Li Xiaodong
Published: June 2008

Hydrogen atmosphere can significantly change the tribological behavior at diamond and diamondlike carbon (DLC) surfaces and the friction-reducing effect depends on the partial pressure of hydrogen. We combined density functional theory modeling and thermodynamic quantities to predict the equilibrium partial pressures of hydrogen at temperature T, PH2 (T), for a fully atomic hydrogen passivated diamond surface. Above the equilibrium PH2 (T), ultralow friction can be achieved at diamond and DLC surfaces. The calculation agrees well with friction tests at various testing conditions. We also show that PH2 (T) increases with temperature; therefore, the temperature effect observed in friction tests should first be treated as an equilibrium factor rather than a kinetic factor.
Nickel self-diffusion in silicon-rich Si–Ni melts
Authors: Pommrich A. I. , Meyer A. , Holland-Moritz D. , Unruh T.
Published: June 2008

The nickel self-diffusion coefficient in Si–Ni melts was measured for compositions up to 20at.% Ni in a temperature range from 270K below to 200K above the liquidus temperature by using quasielastic neutron scattering in combination with electromagnetic levitation. Ni self-diffusion coefficients are in the order of 10−8m2∕s, fairly independent of the Ni concentration. Diffusion coefficients calculated from viscosity data of pure liquid silicon via the Stokes–Einstein relation compare well with the Ni self-diffusion obtained here, indicating a strong correlation between the mobility of the silicon and nickel atoms.
Electronic structure and optical properties of Nb-doped anatase TiO2
Authors: Liu X. D. , Jiang E. Y. , Li Z. Q. , Song Q. G.
Published: June 2008

The electronic structure and optical properties of pure and Nb-doped TiO2 with anatase structure were calculated using local-density approximation based on the density-functional theory. For the undoped TiO2, the Fermi level locates in the band gap between the conduction band and valence band, while it moves into the conduction band and shows metal-like characteristic after Nb atom was introduced into the TiO2 supercell. The optical absorption coefficients for both compounds are very small in the visible light range. Our calculations provide electronic structure evidence that the Nb-doped anatase TiO2 is a new type transparent conducing metal.
Characterization of the disaggregation state of single-walled carbon nanotube bundles by dielectrophoresis and Raman spectroscopy
Authors: Kumatani A. , Warburton P. A.
Published: June 2008

We have used a combination of dielectrophoretic assembly and Raman spectroscopy to characterize the disaggregation state of bundles of single-walled carbon nanotubes. The presence of semiconducting nanotubes following assembly indicates incomplete disaggregation of the nanotubes in the surfactant/solvent. We show that this combined technique is a more sensitive measure of the aggregation state of nanotubes than either optical absorption measurement or Raman spectroscopy alone.
Atomic structure of Mn-rich nanocolumns probed by x-ray absorption spectroscopy
Authors: Rovezzi M. , Devillers T. , Arras E. , d’Acapito F. , Barski A. , Jamet M. , Pochet P.
Published: June 2008

In this letter, we have used the extended x-ray-absorption fine-structure (EXAFS) technique to investigate the structure of Mn-rich self-organized nanocolumns grown by low temperature molecular beam epitaxy. The EXAFS analysis has shown that Mn-rich nanocolumns exhibit a complex local structure that cannot be described by a simple substitutional model. Additional interatomic distances had to be considered in the EXAFS model which are in excellent agreement with the structure of a Ge–3Mn building block tetrahedron of Ge3Mn5.
Carrier scattering in graphene nanoribbon field-effect transistors
Authors: Ouyang Yijian , Wang Xinran , Dai Hongjie , Guo Jing
Published: June 2008

The elastic scattering mean free path (mfp) in a graphene nanoribbon (GNR) is characterized to be short. In the absence of other scattering mechanisms, elastic scattering has a large effect on the source-drain current of a GNR field-effect transistor due to its quasi-one-dimensional channel. In the presence of optical phonon scattering, the effect of elastic scattering is reduced. The coupling of inelastic, short-mfp optical phonon scattering to elastic scattering results in an increase rather than a decrease of the source-drain current. Improving the GNR edge quality promises significant on-current improvement.
Substrate grain boundary effect on residual stress distribution at micrometer scale in chromia oxide thin films
Authors: Kemdehoundja M. , Grosseau-Poussard J. L. , Dinhut J. F.
Published: June 2008

Residual stresses in chromia oxide films formed at 700°C on NiCr30 have been investigated with confocal Raman spectroscopy. The high lateral resolution allows us to determine stress distribution in the oxide growing above both substrate grains and grain boundaries. It is demonstrated that the magnitude of the equibiaxial compressive stress is related to local oxide microstructure evolution: during the initial oxidation, stress is smaller in the chromia located above substrate grain boundaries as compared to that above substrate grains. Subsequently, this gap in stress magnitude progressively vanishes due to the occurrence of oxide grains forming bridges across depressions in the oxide scale above substrate grain boundaries.
High gain in hybrid transistors with BAlq3∕Alq3 isotype heterostructure emitter
Authors: Yi Mingdong , Huang Jinying , Ma Dongge , Hümmelgen Ivo A.
Published: June 2008

We report the fabrication of permeable metal-base transistors based on bis(2-methyl-8-quinolinolato-N1,O8)-(1,1’-biphenyl-4-olato) aluminum (BAlq3)/tri(8-hydroxyquinoline) aluminum (Alq3) isotype heterostructure as emitter layer. In this transistor, n-Si was used as the collector, LiF∕Al as the emitter electrode, and Au∕Al bilayer metal as the base. We show that the leakage current is greatly reduced in Al∕n-Si∕Au∕Al∕BAlq3∕Alq3∕LiF∕Al devices with respect to Al∕n-Si∕Au∕Al∕Alq3∕LiF∕Al devices due to the utilization of BAlq3∕Alq3 isotype heterostructure emitter, leading to high common-base and common-emitter current gains at low driving voltages.
Equal mobility of constituent cations in BaTiO3
Authors: Yoo Han-Ill , Lee Chung-Eun , De Souza Roger A. , Martin Manfred
Published: June 2008

It is widely believed that in BaTiO3, Ba2+ cations are much more mobile than Ti4+ cations. Under a dc electric field, Ba cations are therefore expected at elevated temperatures to move at a faster rate to the cathode, leading to compositional demixing and eventually to decomposition of the BaTiO3. We have found that this is not the case. Overall mass transfer in BaTiO3 does occur but with no compositional demixing. This indicates that contrary to the general belief, Ba2+ and Ti4+ have the same electrochemical mobilities in BaTiO3. This suggests a common diffusion mechanism involving both cation sublattices.
Formation of an oxide-free Ge∕TiO2 interface by atomic layer deposition on brominated Ge
Authors: Ardalan Pendar , Pickett Evan R. , Harris James S. , Marshall Ann F. , Bent Stacey F.
Published: June 2008

Atomic layer deposition (ALD) of titanium dioxide (TiO2) high-κ dielectric films on brominated Ge substrates using titanium tetrachloride and water has been studied. A strong temperature dependence was observed for the TiO2 deposition rate. An accelerated growth rate was measured for the first 15 ALD cycles at 300°C; this effect is attributed to bromine desorption and resultant deposition on halide-free Ge. Results suggest that TiO2 films were deposited with no interfacial oxide layer at 300°C. The films were in a crystalline anatase phase at 300°C, and were amorphous when deposited at 100°C.
An analysis of 1.55μm InAs∕InP quantum dash lasers
Authors: Heck S. C. , Healy S. B. , Osborne S. , O’Reilly E. P. , Lelarge F. , Poingt F. , Accard A. , Pommereau F. , Le Gouezigou O. , Dagens B.
Published: June 2008

Calculations show that electron states are not confined in the dashes in 1.55μm InAs∕InP quantum dash-in-a-well laser structures. The combination of strain and three-dimensional confinement reduces the calculated density of states (DOS) near the valence band maximum, with the conduction and valence DOS then almost equal close to the band edges. Calculations and photoabsorption measurements show strongly polarized spontaneous emission and gain spectra. Experimental analysis shows the room temperature threshold current is dominated by nonradiative current paths.
Magneto-optical properties of transparent divalent iron phosphate glasses
Authors: Akamatsu Hirofumi , Fujita Koji , Murai Shunsuke , Tanaka Katsuhisa
Published: June 2008

We have prepared glasses having xFeO⋅(100−x)P2O5 (mol %) (x=50.0,54.0,57.1) compositions by melting under mild reducing condition and found that these glasses exhibit fairly high transmittance in the visible range and large Faraday effect at the wavelength of about 400nm. Fe57 Mössbauer spectra confirm that almost all the iron ions are present as Fe2+ in the glasses. A spin glass transition is observed at low temperatures in the temperature dependence of magnetic susceptibility. Intense optical absorption in the ultraviolet and infrared wavelength ranges occurs by the charge transfer transition from O2− to Fe2+ and the intra-atomic d-d transition, respectively. The analysis on the wavelength dependence of the Faraday rotation angle using the Van Vleck–Hebb theory has revealed that the charge transfer transition contributes more significantly to the Faraday effect owing to the large effective transition probability, which is comparable to those reported for glasses containing 4f rare-earth ions. The magneto-optical figure of merit shows a maximum at around 380nm.
Post-dispersal seed predation in Pinus halepensis and consequences on seedling establishment after fire
Authors: Broncano Maria José , Rodrigo Anselm , Retana Javier
Published: June 2008

In the present study, we analyse the spatiotemporal patterns of seed predation and the consequences of this predation in the establishment of new Pinus halepensis individuals. Rodents were the main predators of P. halepensis seeds in burned areas, while predation by ants was considerably lower. Concerning spatiotemporal patterns of seed predation, the results obtained indicate that, although there were some small differences among distances or among seasons, removal of P. halepensis seeds was consistently very high in all situations, whether close to or far from the unburned margins, in pine or mixed forests, in different sites and in all sampling periods throughout the year. We analysed the role of seed predation on the modulation of post-fire regeneration of P. halepensis. Just after fire, no differences in seedling density were found between plots with or without rodent exclusion, probably owing to the high density of seeds on the ground and the low density of rodents affected by fire. One year after fire, when rodent populations had recovered in burned areas and seeds were much less abundant, the combination of addition of seeds and rodent exclusion led to an increase in pine seedling establishment.
Mapping the severity of fire using object-based classification of IKONOS imagery
Authors: Mitri G. H. , Gitas I. Z.
Published: June 2008

Mapping fire severity is necessary in order (1) to locate areas in need of special or intense post-fire management; (2) to allow the study of fire impact and vegetation recovery; and (3) to validate fire risk and fire behaviour models. The present study aimed to develop a method to map the severity of fire by employing post-fire IKONOS imagery. The objective was to develop an object-oriented model that would distinguish between different degrees of fire severity and to assess the accuracy of the model by employing field-collected data. The work comprised five main consecutive steps, namely, field data collection, data preprocessing, image segmentation, image classification and accuracy assessment. An adapted version of the FIREMON (fire effects monitoring and inventory protocol) landscape assessment method was employed to quantitatively record fire severity in the field. As a result, two different datasets were used: one for training and developing the classification rules, and another one for assessing the accuracy of the classification. Separate and independent data were used for training and for accuracy assessment. Overall accuracy was estimated to be 83%, while the Kappa Index of Agreement obtained was 0.74. The main source of inaccuracy was the inability of IKONOS to penetrate the dense canopy of unburned vegetation. The main conclusion drawn from the present work was that object-based classification applied to IKONOS imagery has the potential to produce accurate maps of fire severity, especially in the case of the open Mediterranean forest.
Light-dependent regulation of structural flexibility in a photochromic fluorescent protein
Authors: Mizuno Hideaki , Mal Tapas Kumar , Wälchli Markus , Kikuchi Akihiro , Fukano Takashi , Ando Ryoko , Jeyakanthan Jeyaraman , Taka Junichiro , Shiro Yoshitsugu , Ikura Mitsuhiko , Miyawaki Atsushi
Published: June 2008

The structural basis for the photochromism in the fluorescent protein Dronpa is poorly understood, because the crystal structures of the bright state of the protein did not provide an answer to the mechanism of the photochromism, and structural determination of the dark state has been elusive. We performed NMR analyses of Dronpa in solution at ambient temperatures to find structural flexibility of the protein in the dark state. Light-induced changes in interactions between the chromophore and β-barrel are responsible for switching between the two states. In the bright state, the apex of the chromophore tethers to the barrel by a hydrogen bond, and an imidazole ring protruding from the barrel stabilizes the plane of the chromophore. These interactions are disrupted by strong illumination with blue light, and the chromophore, together with a part of the β-barrel, becomes flexible, leading to a nonradiative decay process.
A TCP domain transcription factor controls flower type specification along the radial axis of the
Gerbera
(Asteraceae) inflorescence
Authors: Broholm Suvi K. , Tähtiharju Sari , Laitinen Roosa A. E. , Albert Victor A. , Teeri Teemu H. , Elomaa Paula
Published: June 2008

Several key processes in plant development are regulated by TCP transcription factors. CYCLOIDEA-like (CYC-like) TCP domain proteins have been shown to control flower symmetry in distantly related plant lineages.
Gerbera hybrida
, a member of one of the largest clades of angiosperms, the sunflower family (Asteraceae), is an interesting model for developmental studies because its elaborate inflorescence comprises different types of flowers that have specialized structures and functions. The morphological differentiation of flower types involves gradual changes in flower size and symmetry that follow the radial organization of the densely packed inflorescence. Differences in the degree of petal fusion further define the distinct shapes of the
Gerbera
flower types. To study the role of TCP transcription factors during specification of this complex inflorescence organization, we characterized the CYC-like homolog GhCYC2 from
Gerbera
. The expression of
GhCYC2
follows a gradient along the radial axis of the inflorescence.
GhCYC2
is expressed in the marginal, bilaterally symmetrical ray flowers but not in the centermost disk flowers, which are nearly radially symmetrical and have significantly less fused petals. Overexpression of
GhCYC2
causes disk flowers to obtain morphologies similar to ray flowers. Both expression patterns and transgenic phenotypes suggest that
GhCYC2
is involved in differentiation among
Gerbera
flower types, providing the first molecular evidence that CYC-like TCP factors take part in defining the complex inflorescence structure of the Asteraceae, a major determinant of the family's evolutionary success.
Is an eclipse described in the Odyssey?
Authors: Baikouzis Constantino , Magnasco Marcelo O.
Published: June 2008

Plutarch and Heraclitus believed a certain passage in the 20th book of the Odyssey (“Theoclymenus's prophecy”) to be a poetic description of a total solar eclipse. In the late 1920s, Schoch and Neugebauer computed that the solar eclipse of 16 April 1178 B.C.E. was total over the Ionian Islands and was the only suitable eclipse in more than a century to agree with classical estimates of the decade-earlier sack of Troy around 1192–1184 B.C.E. However, much skepticism remains about whether the verses refer to this, or any, eclipse. To contribute to the issue independently of the disputed eclipse reference, we analyze other astronomical references in the Epic, without assuming the existence of an eclipse, and search for dates matching the astronomical phenomena we believe they describe. We use three overt astronomical references in the epic: to Boötes and the Pleiades, Venus, and the New Moon; we supplement them with a conjectural identification of Hermes's trip to Ogygia as relating to the motion of planet Mercury. Performing an exhaustive search of all possible dates in the span 1250–1115 B.C., we looked to match these phenomena in the order and manner that the text describes. In that period, a single date closely matches our references: 16 April 1178 B.C.E. We speculate that these references, plus the disputed eclipse reference, may refer to that specific eclipse.
Remodeling the exocrine pancreas at metamorphosis in
Xenopus laevis
Authors: Mukhi Sandeep , Mao Jinzhe , Brown Donald D.
Published: June 2008

At metamorphosis the
Xenopus laevis
tadpole exocrine pancreas remodels in two stages. At the climax of metamorphosis thyroid hormone (TH) induces dedifferentiation of the entire exocrine pancreas to a progenitor state. The organ shrinks to 20% of its size, and ≈40% of its cells die. The acinar cells lose their zymogen granules and ≈75% of their RNA. The mRNAs that encode exocrine-specific proteins (including the transcription factor Ptf1a) undergo almost complete extinction at climax, whereas
PDX-1
,
Notch-1
, and
Hes-1
, genes implicated in differentiation of the progenitor cells, are activated. At the end of spontaneous metamorphosis when the endogenous TH has reached a low level, the pancreas begins to redifferentiate. Exogenous TH induces the dedifferentiation phase but not the redifferentation phase. The tadpole pancreas lacks the mature ductal system that is found in adult vertebrate pancreases, including the frog. Exocrine pancreases of transgenic tadpoles expressing a dominant negative form of the TH receptor controlled by the elastase promoter are resistant to TH. They do not shrink when subjected to TH. Their acinar cells do not dedifferentiate at climax, nor do they down-regulate exocrine-specific genes or activate
Notch-1
and
Hes-1
. Even 2 months after metamorphosis these frogs have not developed a mature ductal system and the acinar cells are abnormally arranged. The TH-dependent dedifferentiation of the tadpole acinar cells at climax is a necessary step in the formation of a mature frog pancreas.
Ethiopia: Reforming Land Tenure
Authors: Crewett Wibke , Korf Benedikt
Published: June 2008

Land policy in Ethiopia has been controversial since the fall of the military socialist derg regime in 1991. While the current Ethiopian government has implemented a land policy that is based on state ownership of land (where only usufruct rights are given to land holders), many agricultural economists and international donor agencies have propagated some form of privatized land ownership. This article traces the antagonistic arguments of the two schools of thought in the land reform debate and how their antagonistic principles ‐ fairness vs. efficiency ‐ are played out. It then goes on to explore how these different arguments have trickled down in the formulation of the federal and regional land policies with a particular view on the new Oromia regional land policy as it is considered the most progressive (with regards to tenure security). We provide some empirical material on ongoing practices of implementing the Rural Land Use and Administration Proclamation of Oromia Region. Our analysis suggests that while the laws are conceptual hybrids that accommodate both fairness and efficiency considerations, regional bureaucrats have selectively implemented those elements of the proclamation that are considered to strengthen the regime’s political support in the countryside.
The ANC for Sale? Money, Morality & Business in South Africa
Authors: Southall Roger
Published: June 2008

The African National Congress (ANC) as a liberation movement drew much of its strength from its moral underpinnings as fighting for a just society. However, since its acquisition of political office in 1994, the ANC is widely perceived to have lost its moral compass. This demoralization needs to be located within the structural determinants of the South African transition. Against the background of the dilemmas faced by the ANC in its bid to promote its National Democratic Revolution (NDR), this paper explores how the party's need to secure funding has seen it complement official state funding by tapping corporate largesse, moving into business and accessing public monies. Meanwhile, the mutual interests of the new political power holders and established business have forged close connections across the public and private divide which at times have bordered on the criminal. Despite the ANC's declared intentions to address its moral rot by implementation of new ethical controls, the reciprocal needs of powerful business interests and party elites are likely to limit their effectiveness. Continued pressure for ‘revolutionary morality’ must therefore come from below and outside the ruling party.
Role of Sec61p in the ER-associated degradation of short-lived transmembrane proteins
Authors: Scott Daniel C. , Schekman Randy
Published: June 2008

Misfolded proteins in the endoplasmic reticulum (ER) are identified and degraded by the ER-associated degradation pathway (ERAD), a component of ER quality control. In ERAD, misfolded proteins are removed from the ER by retrotranslocation into the cytosol where they are degraded by the ubiquitin–proteasome system. The identity of the specific protein components responsible for retrotranslocation remains controversial, with the potential candidates being Sec61p, Der1p, and Doa10. We show that the cytoplasmic N-terminal domain of a short-lived transmembrane ERAD substrate is exposed to the lumen of the ER during the degradation process. The addition of N-linked glycan to the N terminus of the substrate is prevented by mutation of a specific cysteine residue of Sec61p, as well as a specific cysteine residue of the substrate protein. We show that the substrate protein forms a disulfide-linked complex to Sec61p, suggesting that at least part of the retrotranslocation process involves Sec61p.
CNI-1493 inhibits Aβ production, plaque formation, and cognitive deterioration in an animal model of Alzheimer's disease
Authors: Bacher Michael , Dodel Richard , Aljabari Bayan , Keyvani Kathy , Marambaud Philippe , Kayed Rakez , Glabe Charles , Goertz Nicole , Hoppmann Anne , Sachser Norbert , Klotsche Jens , Schnell Susanne , Lewejohann Lars , Al-Abed Yousef
Published: June 2008

Alzheimer's disease (AD) is characterized by neuronal atrophy caused by soluble amyloid β protein (Aβ) peptide “oligomers” and a microglial-mediated inflammatory response elicited by extensive amyloid deposition in the brain. We show that CNI-1493, a tetravalent guanylhydrazone with established antiinflammatory properties, interferes with Aβ assembly and protects neuronal cells from the toxic effect of soluble Aβ oligomers. Administration of CNI-1493 to TgCRND8 mice overexpressing human amyloid precursor protein (APP) for a treatment period of 8 wk significantly reduced Aβ deposition. CNI-1493 treatment resulted in 70% reduction of amyloid plaque area in the cortex and 87% reduction in the hippocampus of these animals. Administration of CNI-1493 significantly improved memory performance in a cognition task compared with vehicle-treated mice. In vitro analysis of CNI-1493 on APP processing in an APP-overexpressing cell line revealed a significant dose-dependent decrease of total Aβ accumulation. This study indicates that the antiinflammatory agent CNI-1493 can ameliorate the pathophysiology and cognitive defects in a murine model of AD.
FIRMA: a method for detection of alternative splicing from exon array data
Authors: Purdom E. , Simpson K. M. , Robinson M. D. , Conboy J. G. , Lapuk A. V. , Speed T.P.
Published: June 2008

Motivation: Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent of exon and tiling microarrays means that researchers now have the capacity to experimentally measure alternative splicing on a genome wide level. New methods are needed to analyze the data from these arrays.

Results: We present a method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle be extended to other exon arrays, tiling arrays or splice junction arrays. We have evaluated the method using simulated data, and have also applied it to two datasets: a panel of 11 human tissues and a set of 10 pairs of matched normal and tumor colon tissue. FIRMA is able to detect exons in several genes confirmed by reverse transcriptase PCR.

Availability: R code implementing our methods is contributed to the package aroma.affymetrix.

Contact:  epurdom@stat.berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
On correcting the overestimation of the permutation-based false discovery rate estimator
Authors: Jiao Shuo , Zhang Shunpu
Published: June 2008

Motivation: Recent attempts to account for multiple testing in the analysis of microarray data have focused on controlling the false discovery rate (FDR), which is defined as the expected percentage of the number of false positive genes among the claimed significant genes. As a consequence, the accuracy of the FDR estimators will be important for correctly controlling FDR. Xie et al. found that the standard permutation method of estimating FDR is biased and proposed to delete the predicted differentially expressed (DE) genes in the estimation of FDR for one-sample comparison. However, we notice that the formula of the FDR used in their paper is incorrect. This makes the comparison results reported in their paper unconvincing. Other problems with their method include the biased estimation of FDR caused by over- or under-deletion of DE genes in the estimation of FDR and by the implicit use of an unreasonable estimator of the true proportion of equivalently expressed (EE) genes. Due to the great importance of accurate FDR estimation in microarray data analysis, it is necessary to point out such problems and propose improved methods.

Results: Our results confirm that the standard permutation method overestimates the FDR. With the correct FDR formula, we show the method of Xie et al. always gives biased estimation of FDR: it overestimates when the number of claimed significant genes is small, and underestimates when the number of claimed significant genes is large. To overcome these problems, we propose two modifications. The simulation results show that our estimator gives more accurate estimation.

Contact:  szhang3@unl.edu
Database indexing for production MegaBLAST searches
Authors: Morgulis Aleksandr , Coulouris George , Raytselis Yan , Madden Thomas L. , Agarwala Richa , Schäffer Alejandro A.
Published: June 2008

Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar.

Results: We developed a new version of the MegaBLAST module of BLAST that does the initial phase of finding short seeds for matches by searching a database index. We also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. We show that the new ‘indexed MegaBLAST’ is faster than the ‘non-indexed’ version for most practical uses. We show that indexed MegaBLAST is faster than miBLAST, another implementation of BLAST nucleotide searching with a preprocessed database, for most of the 200 queries we tested. To deploy indexed MegaBLAST as part of NCBI'sWeb BLAST service, the storage of databases and the queueing mechanism were modified, so that some machines are now dedicated to serving queries for a specific database. The response time for such Web queries is now faster than it was when each computer handled queries for multiple databases.

Availability: The code for indexed MegaBLAST is part of the blastn program in the NCBI C++ toolkit. The preprocessor program makembindex is also in the toolkit. Indexed MegaBLAST has been used in production on NCBI's Web BLAST service to search one version of the human and mouse genomes since October 2007. The Linux command-line executables for blastn and makembindex, documentation, and some query sets used to carry out the tests described below are available in the directory: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast

Contact:  schaffer@helix.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Building for the Shah: Market Entry, Political Reality and Risks on the Iranian Market, 1933–1939
Authors: Andersen Steen
Published: June 2008

Unlike other Western European companies operating in Iran between the first and second world wars, the Danish construction firm Kampsax pursued a forestalling strategy in dealing with the political imperative of Reza Shah. The British Bank of the Middle East and the Anglo-Persian Oil Company, by contrast, pursued an absorption strategy. That is, they actively tried to “Iranize” their operations by appointing native Iranians to important managerial positions. Kampsax, however, made no attempt at “Iranization,” depending entirely on contractual relations with local builders and labor forces. This no doubt contributed to the firm's exposure as a totally foreign enterprise and lessened their chances of gaining favor with the Shah's advisors, who pursued an overtly nationalistic set of policies. The history of Kampsax in Iran therefore offers a useful case to use the concept of the political risks in relation to multinationals working in dictatorial settings. This paper undertakes such a study and concludes that the absorption strategy that was already being pursued by British firms offers a better way of managing such risks.
“The Biggest Small-Town Store in America”: Independent Retailers and the Rise of Consumer Culture
Authors: Howard Vicki
Published: June 2008

The case study of Bresee's Department Store in Oneonta, New York, suggests that small-town department stores were not necessarily fully “modern” by the early twentieth century. This article demonstrates how modern, big-store, business methods came later and documents how earlier modes of trade, such as credit and bartering, persisted into the early twentieth century, even in non-rural, northern contexts. Preliminary findings suggest that eliminating the urban bias in much historiography by including small-town retailing practices may lead to a later periodization of American consumer society.
Biodiversity of North Sea fish: why do the politicians care but marine scientists appear oblivious to this issue?
Authors: Greenstreet Simon P. R.
Published: June 2008

Greenstreet, S. P. R. 2008. Biodiversity of North Sea fish: why do the politicians care but marine scientists appear oblivious to this issue? – ICES Journal of Marine Science, 65: 1515–1519. Political drivers underpinning the development of an Ecosystem Approach to Marine Management (EAMM) focus on conserving and restoring biodiversity. However, the Element of Ecological Quality for Fish Communities that emerged from the 2002 Bergen North Sea Ministerial Conference relates to “Changes in the proportion of large fish and hence the average weight and average maximum length of the fish community”. How did this apparent change in direction arise? Responding to advice requests from OSPAR, ICES established seven criteria for identifying “state” indicators capable of supporting indicator-based management. Application of these criteria underlined the merits of indicators of fish size, whereas diversity indices performed poorly against four of the criteria. These difficulties are examined here. Far from being oblivious to the issue of biodiversity, marine scientists recognized that they were not in a position to recommend Ecological Quality Objectives (EcoQOs) for fish biodiversity that would have relied on the use of biodiversity indicators. The use of indicators of size structure, for which the theoretical foundation was better developed, allowed the continued development of an EAMM in the short term. However, if the issue of biodiversity is to be addressed in the longer term, then shortcomings associated with the use of biodiversity indicators need to be addressed.
Changes in spawning-stock structure and recruitment pattern of red mullet, Mullus barbatus, after a trawl ban in the Gulf of Castellammare (central Mediterranean Sea)
Authors: Fiorentino F. , Badalamenti F. , D’Anna G. , Garofalo G. , Gianguzza P. , Gristina M. , Pipitone C. , Rizzo P. , Fortibuoni T.
Published: June 2008

Fiorentino, F., Badalamenti, F., D’Anna, G., Garofalo, G., Gianguzza, P., Gristina, M., Pipitone, C., Rizzo, P., and Fortibuoni, T. 2008. Changes in spawning-stock structure and recruitment pattern of red mullet, Mullus barbatus, after a trawl ban in the Gulf of Castellammare (central Mediterranean Sea). – ICES Journal of Marine Science, 65: 1175–1183. The increase in biomass of red mullet, Mullus barbatus, in the Gulf of Castellammare (northwestern Sicily, central Mediterranean) after a 14-year trawl ban, prompted us to compare the spawning-stock structure and the recruitment pattern before and after the closure. Datasets obtained from three experimental trawl surveys were available before the ban (April and September 1985; April–May 1986) and four post-ban (September and November 2004; March and May 2005). Spawning-stock biomass increased significantly after the ban. Moreover, females at depths >50 m in the post-ban period were larger than those collected before the ban at the same depth. The recruitment pattern of the population also changed. Notably, recruit numbers increased and recruitment occurs over a broader period. The increase in biomass after the trawl ban seems to be the result of a combination of different processes, mainly associated with the lowering of fishing mortality. A positive trend in sea surface temperature in the area may have played a role too.
An efficient approach to converting three-dimensional image data into highly accurate computational models
Authors: Young P.G , Beresford-West T.B.H , Coward S.R.L , Notarberardino B , Walker B , Abdul-Aziz A
Published: June 2008

Image-based meshing is opening up exciting new possibilities for the application of computational continuum mechanics methods (finite-element and computational fluid dynamics) to a wide range of biomechanical and biomedical problems that were previously intractable owing to the difficulty in obtaining suitably realistic models. Innovative surface and volume mesh generation techniques have recently been developed, which convert three-dimensional imaging data, as obtained from magnetic resonance imaging, computed tomography, micro-CT and ultrasound, for example, directly into meshes suitable for use in physics-based simulations. These techniques have several key advantages, including the ability to robustly generate meshes for topologies of arbitrary complexity (such as bioscaffolds or composite micro-architectures) and with any number of constituent materials (multi-part modelling), providing meshes in which the geometric accuracy of mesh domains is only dependent on the image accuracy (image-based accuracy) and the ability for certain problems to model material inhomogeneity by assigning the properties based on image signal strength. Commonly used mesh generation techniques will be compared with the proposed enhanced volumetric marching cubes (EVoMaCs) approach and some issues specific to simulations based on three-dimensional image data will be discussed. A number of case studies will be presented to illustrate how these techniques can be used effectively across a wide range of problems from characterization of micro-scaffolds through to head impact modelling.
Patient-specific simulation as a basis for clinical decision-making
Authors: Sadiq S. Kashif , Mazzeo Marco D , Zasada Stefan J , Manos Steven , Stoica Ileana , Gale Catherine V , Watson Simon J , Kellam Paul , Brew Stefan , Coveney Peter V
Published: June 2008

Patient-specific medical simulation holds the promise of determining tailored medical treatment based on the characteristics of an individual patient (for example, using a genotypic assay of a sequence of DNA). Decision-support systems based on patient-specific simulation can potentially revolutionize the way that clinicians plan courses of treatment for various conditions, ranging from viral infections to arterial abnormalities. Basing medical decisions on the results of simulations that use models derived from data specific to the patient in question means that the effectiveness of a range of potential treatments can be assessed before they are actually administered, preventing the patient from experiencing unnecessary or ineffective treatments. We illustrate the potential for patient-specific simulation by first discussing the scale of the evolving international grid infrastructure that is now available to underpin such applications. We then consider two case studies, one concerned with the treatment of patients with HIV/AIDS and the other addressing neuropathologies associated with the intracranial vasculature. Such patient-specific medical simulations require access to both appropriate patient data and the computational resources on which to perform potentially very large simulations. Computational infrastructure providers need to furnish access to a wide range of different types of resource, typically made available through heterogeneous computational grids, and to institute policies that facilitate the performance of patient-specific simulations on those resources. To support these kinds of simulations, where life and death decisions are being made, computational resource providers must give urgent priority to such jobs, for example by allowing them to pre-empt the queue on a machine and run straight away. We describe systems that enable such priority computing.