bluuebunny/crossref_metadata_2025 huggingface dataset:
Terahertz quantum cascade lasers with large wall-plug efficiency
Authors: Vitiello Miriam S. , Scamarcio Gaetano , Spagnolo Vincenzo , Dhillon Sukhdeep S. , Sirtori Carlo
Published: May 2007

Improved optical power performance of bound-to-continuum quantum-cascade lasers operating at 2.83THz is reported. Peak optical powers of 100mW at 4K and power conversion-efficiencies as high as ηw=(5.5±0.4)% in continuous wave at 40K were measured. The ηw values were assessed via an experimental method based on the analysis of the local lattice temperature as extracted by microprobe photoluminescence versus electrical power. From the measured ηw values they extracted a slope efficiency value 0.41±0.11W∕A.
Ferroelectric and optical properties of single crystal BaZnF4
Authors: Víllora Encarnación G. , Shimamura Kiyoshi , Jing Fangli , Medvedev Andrey , Takekawa Shunji , Kitamura Kenji
Published: May 2007

Single crystalline BaZnF4 is grown by the Czochralski technique. Optical measurements indicate a wide transparency from the vacuum ultraviolet to the far infrared (0.145–10μm). The ferroelectric properties are determined for the first time by the polarization hysteresis. The spontaneous polarization Ps is found to be 9μC∕cm2, while the coercive field Ec varies between 9 and 75kV∕cm, depending on the field frequency. The material properties are compared with those of BaMgF4, which is another candidate for the realization of all-solid-state lasers emitting in the ultraviolet wavelength region.
Current transport in short channel top-contact pentacene field-effect transistors investigated with the selective molecular doping technique
Authors: Fujimori F. , Shigeto K. , Hamano T. , Minari T. , Miyadera T. , Tsukagoshi K. , Aoyagi Y.
Published: May 2007

The contact doping profile is controlled in the top-contact configuration to clarify a transistor operation based on a current injection process from the metal contact to the organic channel in a submicron channel pentacene field-effect transistor. The molecular doping in the pentacene film underneath the metal contact, in which a thin layer of iron (III) chloride was introduced, drastically changes transistor characteristics. The doping profile control directly revealed the resistive part for current injection. A model to explain the saturation behavior of the top-contact short channel organic transistor is presented.
Rolling up SiGe on insulator
Authors: Cavallo F. , Songmuang R. , Ulrich C. , Schmidt O. G.
Published: May 2007

SiGe on insulator films of 10–50nm thickness are fabricated by Ge condensation applying different oxidation times. The layers are released from the substrate by selectively etching the insulator film. Due to the varying Ge composition, the layers bend downward toward the substrate surface and roll up into microtubes. Depending on the Ge condensation, the strain distribution in the SiGe layers varies and allows a scaling of the tube diameters between 1 and 4μm. Assuming pseudomorphic SiGe layers, the tube diameters are smaller than expected from continuum mechanical theory. This suggests the occurrence of additional strain in the oxidized films.
Individual carbon nanotube soldering with gold nanoink deposition
Authors: Dockendorf Cedric P. R. , Steinlin Markus , Poulikakos Dimos , Choi Tae-Youl
Published: May 2007

A method for soldering carbon nanotubes lying on microfabricated metal pads is presented. By employing the fountain-pen principle, the authors deposited a gold nanoparticle suspension (nanoink) film on the area where the carbon nanotube contacts the metal pad. The nanoink was deposited by using a capillary tube that was pulled into a micropipette with the tip outer diameter of 2μm. Individual carbon nanotubes were aligned selectively across the electrodes dielectrophoretically. After annealing and sintering of the nanoink pattern the four-point-probe resistance of the carbon nanotubes was measured, resulting in a good Ohmic or near-Ohmic contact (2–15kΩ).
Lattice vibrational properties of ZnMgO grown by pulsed laser deposition
Authors: Belogorokhov A. I. , Polyakov A. Y. , Smirnov N. B. , Govorkov A. V. , Kozhukhova E. A. , Kim H. S. , Norton D. P. , Pearton S. J.
Published: May 2007

Vibrational modes were studied in n-type and p-type ZnMgO films doped with P (Mg composition of 7at.%) grown by pulsed laser deposition on sapphire. The characteristic phonon frequencies were deduced from the analysis of IR reflectance measured by Fourier-transform spectroscopy. From comparison with similarly grown ZnO (P) films, Mg incorporation reduced the frequency of TO phonons by 14.5cm−1 and introduced two Mg related modes near 530 and 969cm−1. The first is likely to belong to the local vibrational mode of substitutional Mg, and the second is tentatively attributed to strongly lattice relaxed off-center Mg atoms. In addition, it was found that Mg incorporation triggers the formation of two phonon bands with characteristic frequencies of 501 and 634cm−1 that most likely belong to lattice defects.
Elastic moduli and hardness of c-Zr2.86(N0.88O0.12)4 having Th3P4-type structure
Authors: Dzivenko Dmytro A. , Zerr Andreas , Schweitzer Elmar , Göken Mathias , Boehler Reinhard , Riedel Ralf
Published: May 2007

The equation of state of the recently discovered oxygen-bearing cubic zirconium (IV) nitride, c-Zr2.86(N0.88O0.12)4, was measured at room temperature in a diamond anvil cell using x-ray powder diffraction combined with synchrotron radiation. From these studies the bulk modulus B0=219(13)GPa and its first pressure derivative B0′=4.4(1.0) [or B0=223(5)GPa, for B0′ fixed at 4] were obtained. Applying nanoindentation techniques the reduced modulus Er≈220GPa and hardness H≈18GPa were measured for porous c-Zr2.86(N0.88O0.12)4. The shear modulus of c-Zr2.86(N0.88O0.12)4 was estimated to be at least G0=96(13)GPa using the experimental data of B0 and Er, exclusively.
Reduction of the contact resistance by doping in pentacene few monolayers thin film transistors and self-assembled nanocrystals
Authors: Vanoni Claudio , Tsujino Soichiro , Jung Thomas A.
Published: May 2007

The authors study the contact resistance of gold-pentacene interface by applying the transmission-line method to a few monolayers thick pentacene films in thin film transistor geometry. It was found that tetrafluorotetracyanoquinodimethane (F4TCNQ) doping reduces the contact resistance by more than a factor of 20. In addition, a significant improvement of the conductance of pentacene nanocrystals self-assembled on 10nm gap Au nanojunction devices by F4TCNQ doping is observed. The result demonstrates the importance of doping on the performance of organic electronic devices from 10nm scale up to 100μm scale.
Potential for algal blooms in tropical rivers of the Northern Territory, Australia
Authors: Ganf George G. , Rea Naomi
Published: May 2007

Rivers in the Northern Territory (NT) of Australia are under pressure from increasing vegetation clearance, land use and nutrient run-off. The literature on algal blooms clearly identifies the predisposing factors but in the NT, these factors are not well researched. We report on the potential for tropical rivers to experience problems related to algal growth. NT rivers were found to have a low nutrient status and a viable inoculum of blue-green, brown and green algal communities. The growth response of these algal groups to nutrient enrichment via bioassays and pulse-amplitude-modulation (PAM) fluorometry measurements varied among rivers and the addition of N, P or N&P. However, the overwhelming findings were that all rivers had the potential to experience algal blooms with enrichment. Back-calculations based on the chlorophyll concentrations recorded in bioassay experiments and stoichiometric ratios of chlorophyll:nutrients suggest there are pools of biologically available organic forms of N and P in addition to inorganic forms. The role of river length in the development of algal blooms was investigated: the longer the river reach, the slower the flow, and the greater the availability of nutrients, the higher potential for algal blooms. Given the strong indications that increased nutrient run-off to tropical rivers will result in algal blooms, prudent land-use and development with nutrient management strategies is essential.
Application of calorimetry on a chip to high-pressure materials
Authors: Navrotsky Alexandra , Dorogova Maria , Hellman Frances , Cooke David W. , Zink Barry L. , Lesher Charles E. , Boerio-Goates Juliana , Woodfield Brian F. , Lang Brian
Published: May 2007

Silicon micromachined calorimeters (“calorimeter on a chip”) are used to measure heat capacities and phase transition enthalpies for thin film, single crystal, and powder samples (5–500 μg). The technology is thus compatible with the small samples produced in multianvil and large diamond anvil cells. Techniques for handling small samples and attaching them to the calorimetric devices have been developed. Initial data illustrate application to CoO and to Fe
2
SiO
4
olivine and spinel, a quenched high pressure phase metastable at ambient conditions. The calorimetric entropy of the olivine - spinel transition in Fe
2
SiO
4
(−16 ± 5 J/mol·K) is in good agreement with that calculated from phase equilibrium data (−14 ± 3 J/mol·K). A magnetic transition in iron silicate spinel, detected previously by Mossbauer spectroscopy, is seen in the calorimetric signal.
Caspase-9 regulates apoptosis/proliferation balance during metamorphic brain remodeling in
Xenopus
Authors: Coen Laurent , Le Blay Karine , Rowe Isaline , Demeneix Barbara A.
Published: May 2007

During anuran metamorphosis, the tadpole brain is transformed producing the sensorial and motor systems required for the frog's predatory lifestyle. Nervous system remodeling simultaneously implicates apoptosis, cell division, and differentiation. The molecular mechanisms underlying this remodeling have yet to be characterized. Starting from the observation that active caspase-9 and the Bcl-X
L
homologue, XR11 are highly expressed in tadpole brain during metamorphosis, we determined their implication in regulating the balance of apoptosis and proliferation in the developing tadpole brain.
In situ
hybridization showed caspase-9 mRNA to be expressed mainly in the ventricular area, a site of neuroblast proliferation. To test the functional role of caspase-9 in equilibrating neuroblast production and elimination, we overexpressed a dominant-negative caspase-9 protein, DN9, in the tadpole brain using somatic gene transfer and germinal transgenesis. In both cases, abrogating caspase-9 activity significantly decreased brain apoptosis and increased numbers of actively proliferating cells in the ventricular zone. Moreover, overexpression of XR11 with or without DN9 was also effective in decreasing apoptosis and increasing cell division in the tadpole brain. We conclude that XR11 and caspase-9, two key members of the mitochondrial death pathway, are implicated in controlling the proliferative status of neuroblasts in the metamorphosing
Xenopus
brain. Modification of their expression during the critical period of metamorphosis alters the outcome of metamorphic neurogenesis, resulting in a modified brain phenotype in juvenile
Xenopus
.
Local viscosity of supercooled glycerol near
T
g
probed by rotational diffusion of ensembles and single dye molecules
Authors: Zondervan Rob , Kulzer Florian , Berkhout Gregorius C. G. , Orrit Michel
Published: May 2007

We probe the rotational diffusion of a perylene dye in supercooled glycerol, 5–25 K above the glass-transition temperature (
T
g
= 190 K) at the ensemble and the single-molecule level. The single-molecule results point to a broad distribution of local viscosities that vary by a factor of five or more for different individual fluorophores at a given temperature. By following the same single molecules at various temperatures, we find that the distribution of local viscosities itself broadens upon approaching
T
g
. This spatial heterogeneity is found to relax extremely slowly, persisting over hours or even days. These results convey a picture of heterogeneous liquid pockets separated by solid-like walls, which exist already well above the viscosimetric glass transition.
Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium
Authors: Hayouka Zvi , Rosenbluh Joseph , Levin Aviad , Loya Shoshana , Lebendiker Mario , Veprintsev Dmitry , Kotler Moshe , Hizi Amnon , Loyter Abraham , Friedler Assaf
Published: May 2007

Proteins are involved in various equilibria that play a major role in their activity or regulation. The design of molecules that shift such equilibria is of great therapeutic potential. This fact was demonstrated in the cases of allosteric inhibitors, which shift the equilibrium between active and inactive (R and T) states, and chemical chaperones, which shift folding equilibrium of proteins. Here, we expand these concepts and propose the shifting of oligomerization equilibrium of proteins as a general methodology for drug design. We present a strategy for inhibiting proteins by “shiftides”: ligands that specifically bind to an inactive oligomeric state of a disease-related protein and modulate its activity by shifting the oligomerization equilibrium of the protein toward it. We demonstrate the feasibility of our approach for the inhibition of the HIV-1 integrase (IN) protein by using peptides derived from its cellular-binding protein, LEDGF/p75, which specifically inhibit IN activity by a noncompetitive mechanism. The peptides inhibit the DNA-binding of IN by shifting the IN oligomerization equilibrium from the active dimer toward the inactive tetramer, which is unable to catalyze the first integration step of 3′ end processing. The LEDGF/p75-derived peptides inhibit the enzymatic activity of IN
in vitro
and consequently block HIV-1 replication in cells because of the lack of integration. These peptides are promising anti-HIV lead compounds that modulate oligomerization of IN via a previously uncharacterized mechanism, which bears advantages over the conventional interface dimerization inhibitors.
Surveillance mechanism linking Bub1 loss to the p53 pathway
Authors: Gjoerup Ole V. , Wu Jiaping , Chandler-Militello Devin , Williams Grace L. , Zhao Jean , Schaffhausen Brian , Jat Parmjit S. , Roberts Thomas M.
Published: May 2007

Bub1 is a kinase believed to function primarily in the mitotic spindle checkpoint. Mutation or aberrant Bub1 expression is associated with chromosomal instability, aneuploidy, and human cancer. We now find that targeting Bub1 by RNAi or simian virus 40 (SV40) large T antigen in normal human diploid fibroblasts results in premature senescence. Interestingly, cells undergoing replicative senescence were also low in Bub1 expression, although ectopic Bub1 expression in presenescent cells was insufficient to extend lifespan. Premature senescence caused by lower Bub1 levels depends on p53. Senescence induction was blocked by dominant negative p53 expression or depletion of p21
CIP1
, a p53 target. Importantly, cells with lower Bub1 levels and inactivated p53 became highly aneuploid. Taken together, our data highlight a role for p53 in monitoring Bub1 function, which may be part of a more general spindle checkpoint surveillance mechanism. Our data support the hypothesis that Bub1 compromise triggers p53-dependent senescence, which limits the production of aneuploid and potentially cancerous cells.
Persistent voids: a new structural metric for membrane fusion
Authors: Kasson Peter M. , Zomorodian Afra , Park Sanghyun , Singhal Nina , Guibas Leonidas J. , Pande Vijay S.
Published: May 2007

Motivation: Membrane fusion constitutes a key stage in cellular processes such as synaptic neurotransmission and infection by enveloped viruses. Current experimental assays for fusion have thus far been unable to resolve early fusion events in fine structural detail. We have previously used molecular dynamics simulations to develop mechanistic models of fusion by small lipid vesicles. Here, we introduce a novel structural measurement of vesicle topology and fusion geometry: persistent voids.

Results: Persistent voids calculations enable systematic measurement of structural changes in vesicle fusion by assessing fusion stalk widths. They also constitute a generally applicable technique for assessing lipid topological change. We use persistent voids to compute dynamic relationships between hemifusion neck widening and formation of a full fusion pore in our simulation data. We predict that a tightly coordinated process of hemifusion neck expansion and pore formation is responsible for the rapid vesicle fusion mechanism, while isolated enlargement of the hemifusion diaphragm leads to the formation of a metastable hemifused intermediate. These findings suggest that rapid fusion between small vesicles proceeds via a small hemifusion diaphragm rather than a fully expanded one.

Availability: Software available upon request pending public release.

Contact:  kasson@cmgm.stanford-edu or pande@stanford.edu

Supplementary information: Supplementary data are available on Bioinformatics online.
Seed-borne Fungi Detected in Sugar Beet Seeds Imported into India during Last Three Decades
Authors: Agarwal P. C. , Dev Usha , Rani Indra , Khetarpal R. K.
Published: May 2007

Quarantine processing of 1,111 samples of germplasm and inbred lines of sugar beet seed imported into India from 1976 to 2005 resulted in the interception of 10 pathogenic fungi including Uromyces beticola, the beet rust pathogen which is not yet reported from India. Other seed-borne fungi of high economic significance that were detected included Colletotrichum dematium, Fusarium solani, Pleospora betae, and Verticillium albo-atrum as well as other fungal pathogens for which sugar beet is a non-host crop, such as Drechslera halodes, D. rostrata, D. sorokiniana, Cephalosporium sp., and Pestalotia sp. Various fungi detected in sugar beet seed imported from different countries are presented and their economic significance is discussed. Seeds contaminated with U. beticola were disinfected by dipping them in concentrated sulphuric acid for 1 min while those infected with P. betae were disinfected by hot water treatment at 50°C for 30 min.

Accepted for publication 8 September 2006. Published 11 December 2006.
Penicillium expansum Invades Apples Through Stems during Controlled Atmosphere Storage
Authors: Rosenberger David A. , Engle Catherine A. , Meyer Frederick W. , Watkins Christopher B.
Published: May 2007

Empire apples were collected from six orchards in 1997 and 1998 and were then subjected to various inoculation and storage regimes to determine how non-wounded fruit become infected with Penicillium expansum and to determine if decay susceptibility varies with orchard source. Replicated samples of fruit were inoculated within 24 h of harvest either by placing a 10 μl droplet containing 500 conidia of P. expansum onto the end of the apple stems or by placing 500 μl containing 10,000 conidia into the stem basin. Fruit were stored for 7 to 9 months either in cold air (1.1°C) or in controlled-atmosphere (CA) storage (1.1°C, 1.6% oxygen and 2.2% carbon dioxide), and were then evaluated for decay. Twenty-seven to 47% of fruit that had been inoculated by placing spores on the ends of stems developed decay during CA storage whereas less than 1% of similarly inoculated fruit decayed during cold-air storage. Placing spore suspension into the stem basins also resulted in less than 1% decay. Orchard-to-orchard variation in incidence of decay that developed was positively correlated with boron concentrations in both apple leaves (R2 = 0.66) and apple fruit (R2 = 0.62). This is the first report of P. expansum causing commercial losses in apples due to invasion through stems and also the first

Accepted for publication 28 September 2006. Published 13 December 2006.
Evaluation of Pathogenicity of Bipolaris and Curvularia spp. on Dwarf and Ultradwarf Bermudagrasses in Florida
Authors: Brecht Matthew O. , Stiles Carol M. , Datnoff Lawrence E.
Published: May 2007

Isolates of Curvularia lunata, C. geniculata, Bipolaris hawaiiensis, and B. cynodontis were tested for pathogenicity on the hybrid bermudagrass cultivars Tifdwarf, TifEagle, and FloraDwarf at 20 and 30°C. Curvularia lunata, C. geniculata, and B. hawaiiensis produced some minor leaf tip necrosis at the cut ends of leaves 24 to 48 h after inoculation. Bipolaris cynodontis produced significant tip dieback and leaf spotting on all three cultivars at both 20 and 30°C, and disease severity was higher at 20°C than at 30°C. With C. lunata, C. geniculata, and B. hawaiiensis, occasional leaf-spotting occurred only on senescing, older leaves. Bipolaris cynodontis is considered pathogenic on bermudagrasses, while C. lunata, C. geniculata, and B. hawaiiensis are considered senectopathic, able to incite disease only in senescing plant tissue. Curvularia lunata and B. hawaiiensis resulted in higher disease severity at 30°C than at 20°C, indicating that these species are senectopathic at higher temperatures.

Accepted for publication 29 September 2006. Published 19 January 2007.
On-Farm Trial Assessing Efficacy of Three Insecticide Classes for Management of Stink Bug and Fruit Damage on Processing Tomatoes
Authors: Cullen Eileen M. , Zalom Frank G.
Published: May 2007

Five foliar insecticides representing a neonicotinoid (thiamethoxam), a pyrethroid (lambda-cyhalothrin), a neonicotinoid plus pyrethroid (thiamethoxam and lambda-cyhalothrin), and two organophosphates (dimethoate and methamidophos, respectively) were evaluated for relative efficacy in managing consperse stink bug (Euschistus conspersus Uhler) on California processing tomatoes. E. conspersus density and percentage fruit damage were measured at harvest in an on-farm experiment at two locations in 2002, and small plot experiments in 2002 and 2003. Results showed that thiamethoxam plus lambda-cyhalothrin, lambda-cyhalothrin, and methamidophos can provide equivalent control of E. conspersus on processing tomatoes. Relative efficacy of the same treatments was inconsistent when applied before completion of small nymph development as estimated by the E. conspersus phenology model. Results can be utilized by growers with canning contracts that limit total organophosphate active ingredient per season, or in cases where stink bug treatment thresholds are reached within the processor preharvest interval for organophosphates. Insecticide efficacy evaluation is discussed within the context of continued research to provide IPM-compatible insecticide options to growers facing low processor tolerance for stink bug damaged fruit, and organophosphate insecticide restrictions in tomato canning contracts.

Accepted for publication 22 November 2006. Published 23 March 2007.
Detection of Candidatus Liberibacter asiaticus from Wampee (Clausena lansium Skeels) by Nested PCR
Authors: Deng Xiaoling , Zhou Gen , Li Huaping , Chen Jianchi , Civerolo Edwin L.
Published: May 2007

Wampee (Clausena lansium Skeels) is native to southern China and Southeast Asia. Wampee trees are attractive, with grape-like fruits and a muscat taste and are popular in home gardens. Like other members of Rutaceae, wampee has long been suspected to have yellow shoot disease or Huanglongbing (HLB) and Diaphorina citri, the disease vector, was capable of a long-term survival on Wampee. The authors recommend that eradication of wampee trees surrounding citrus orchards should be part of the overall management of citrus HLB.

Accepted for publication 20 December 2007. Published 19 April 2007.
Increasing Outbreaks and Impact of Iris yellow spot virus in Bulb and Seed Onion Crops in the Imperial and Antelope Valleys of California
Authors: Poole Grant J. , Pappu Hanu R. , Davis Richard M. , Turini Thomas A.
Published: May 2007

Outbreaks of IYSV were first observed in May 2003 in two Imperial County onion seed fields. In August, 2005, symptomatic onion plants were widespread in four fields in the Antelope Valley, Los Angeles County, CA. IYSV infection was confirmed by ELISA and RT-PCR. This was the first known recording of IYSV in Antelope Valley. Increasing incidence and impact of IYSV in a major onion-growing area highlights the need for research into developing managing options for this important disease of onion.

Accepted for publication 22 January 2007. Published 8 May 2007.
Occurrence of Begomovirus Associated with Yellow Vein Mosaic Disease of Kenaf (Hibiscus cannabinus) in Northern India
Authors: Ghosh Raju , Paul Sujay , Roy Anirban , Mir Javid Iqbal , Ghosh S. K. , Srivastava R. K. , Yadav U. S.
Published: May 2007

The occurrence, distribution, and disease incidence of yellow vein mosaic (YVM) disease of kenaf (Hibiscus cannabinus) in northern India are reported. The disease was found in both commercial and experimental farms in the Bahraich district, Uttar Pradesh, India and caused significant reduction in plant height and crop yield. Southern hybridization with begomovirus-specific probe and PCR amplification with DNA β and coat protein primers confirmed the association of begomovirus with the disease.

Accepted for publication 25 January 2007. Published 8 May 2007.
Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes
Authors: Real Leslie A , Biek Roman
Published: May 2007

Explicit spatial analysis of infectious disease processes recognizes that host–pathogen interactions occur in specific locations at specific times and that often the nature, direction, intensity and outcome of these interactions depend upon the particular location and identity of both host and pathogen. Spatial context and geographical landscape contribute to the probability of initial disease establishment, direction and velocity of disease spread, the genetic organization of resistance and susceptibility, and the design of appropriate control and management strategies. In this paper, we review the manner in which the physical organization of the landscape has been shown to influence the population dynamics and spatial genetic structure of host–pathogen interactions, and how we might incorporate landscape architecture into spatially explicit population models of the infectious disease process to increase our ability to predict patterns of disease occurrence and optimally design vaccination and control policies.
Massive particles, Kerr–Minkowski fields and singularity removal in relativistic quantum mechanics
Authors: Bramson Brian
Published: May 2007

This paper concerns the spacetime locations of massive spinning particles in relativistic quantum mechanics. Using techniques from twistor theory and the unitary representations of the Lorentz group, it is shown that, for a particle of mass
m
and spin
j
, the radial distance from the particle to the observer is bounded below by

. If the particle is the source of a Kerr–Minkowski field, the analogue of a Kerr field in general relativity, it is further shown that quantization removes the ring singularity if
j
is Fermionic or zero.
Soybean Root Suberin: Anatomical Distribution, Chemical Composition, and Relationship to Partial Resistance to Phytophthora sojae
Authors: Thomas Raymond , Fang Xingxiao , Ranathunge Kosala , Anderson Terry R. , Peterson Carol A. , Bernards Mark A.
Published: May 2007

Soybean (Glycine max L. Merr.) is a versatile and important agronomic crop grown worldwide. Each year millions of dollars of potential yield revenues are lost due to a root rot disease caused by the oomycete Phytophthora sojae (Kaufmann & Gerdemann). Since the root is the primary site of infection by this organism, we undertook an examination of the physicochemical barriers in soybean root, namely, the suberized walls of the epidermis and endodermis, to establish whether or not preformed suberin (i.e. naturally present in noninfected plants) could have a role in partial resistance to P. sojae. Herein we describe the anatomical distribution and chemical composition of soybean root suberin as well as its relationship to partial resistance to P. sojae. Soybean roots contain a state I endodermis (Casparian bands only) within the first 80 mm of the root tip, and a state II endodermis (Casparian bands and some cells with suberin lamellae) in more proximal regions. A state III endodermis (with thick, cellulosic, tertiary walls) was not present within the 200-mm-long roots examined. An exodermis was also absent, but some walls of the epidermal and neighboring cortical cells were suberized. Chemically, soybean root suberin resembles a typical suberin, and consists of waxes, fatty acids, ω-hydroxy acids, α,ω-diacids, primary alcohols, and guaiacyl- and syringyl-substituted phenolics. Total suberin analysis of isolated soybean epidermis/outer cortex and endodermis tissues demonstrated (1) significantly higher amounts in the endodermis compared to the epidermis/outer cortex, (2) increased amounts in the endodermis as the root matured from state I to state II, (3) increased amounts in the epidermis/outer cortex along the axis of the root, and (4) significantly higher amounts in tissues isolated from a cultivar (‘Conrad’) with a high degree of partial resistance to P. sojae compared with a susceptible line (OX760-6). This latter correlation was extended by an analysis of nine independent and 32 recombinant inbred lines (derived from a ‘Conrad’ × OX760-6 cross) ranging in partial resistance to P. sojae: Strong negative correlations (−0.89 and −0.72, respectively) were observed between the amount of the aliphatic component of root suberin and plant mortality in P. sojae-infested fields.
The Roman fine wares of ed‐Dur (Umm al‐Qaiwain, U.A.E.) and their distribution in the Persian Gulf and the Indian Ocean
Authors: Rutten Katrien
Published: May 2007

Excavations and surveys at ed‐Dur have produced a small amount of Roman fine ware sherds of varied Mediterranean origin. This article aims to offer a full description and analysis of this material and to assess the distribution of these wares from their region of production to their final destination at ed‐Dur. These wares reveal a local Arabian exchange system of Mediterranean goods and provide evidence for a link between the two major sea routes through the Persian Gulf and the Indian Ocean.
An Iron Age II snake cult in the Oman peninsula: evidence from Bithnah (Emirate of Fujairah)
Authors: Benoist Anne
Published: May 2007

Excavations carried out by the French Archaeological Mission at Bithnah‐44/50 (Emirate of Fujairah) have provided new data about Iron Age II cultic practices in the Arabian Peninsula centred on the symbol of the snake. The site includes a public building, various types of shrines, and a central area of offerings where the remains of animal sacrifices were buried in pits. These remains are presented and a preliminary account of the evolution of the site is given on the base of the site's stratigraphy.
Nitrative and oxidative DNA damage in cervical intraepithelial neoplasia associated with human papilloma virus infection
Authors: Hiraku Yusuke , Tabata Tsutomu , Ma Ning , Murata Mariko , Ding Xiaohui , Kawanishi Shosuke
Published: May 2007

Recently, it was proposed that inflammation plays an integral role in the development of human papilloma virus (HPV)‐induced cervical cancer. The present study sought to examine if 8‐nitroguanine, a mutagenic nitrative DNA lesion formed during inflammation, contributes to cervical carcinogenesis. We obtained biopsy specimens from 30 patients with cervical intraepithelial neoplasia (CIN)1 (n = 9), CIN2 (n = 10), CIN3 (n = 6) and condyloma acuminatum (n = 5). We used immunohistochemistry to detect the formation of 8‐nitroguanine and 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanosine (8‐oxodG), an oxidative DNA lesion, and compared it with the expression of the cyclin‐dependent kinase inhibitor p16, which is considered to be a biomarker for cervical neoplasia. Double immunofluorescence labeling revealed that 8‐nitroguanine and 8‐oxodG were colocalized in cervical epithelial cells. Samples from CIN2–3 patients, most of whom were infected with high‐risk HPV subtypes, exhibited significantly more intense staining for 8‐nitroguanine than those with condyloma acuminatum. 8‐Nitroguanine and 8‐oxodG immunoreactivities correlated significantly with the CIN grade. We observed the expression of inducible nitric oxide synthase in epithelial and inflammatory cells from CIN lesions. Proliferating cell nuclear antigen was expressed specifically in dysplastic epithelial cells, but not in those of condyloma acuminatum. There were no statistically significant differences in p16 expression between CIN and condyloma acuminatum samples. These results suggest that high‐risk HPV types promote inducible nitric oxide synthase‐dependent DNA damage, which leads to dysplastic changes and carcinogenesis; in contrast, p16 appears to be merely a marker of HPV infection. Thus, 8‐nitroguanine is a more suitable and promising biomarker for evaluating the risk of inflammation‐mediated cervical carcinogenesis than p16. (Cancer Sci 2007; 98: 964–972)
Condensin mutations and abnormal chromosomal structures in pyothorax‐associated lymphoma
Authors: Ham Maria Francisca , Takakuwa Tetsuya , Rahadiani Nur , Tresnasari Kristianti , Nakajima Hiroo , Aozasa Katsuyuki
Published: May 2007

Transfer of genetic information during mitosis is accurately conducted by proper condensation and segregation of chromosomes, for which condensins play a central role. Both condensin I and II have common structural maintenance of chromosomes subunits, named hCAP‐C and hCAP‐E. Pyothorax‐associated lymphoma (PAL) is a non‐Hodgkin's lymphoma developing in the pleural cavity of patients with long‐standing pyothorax. Mutations of hCAP‐C and hCAP‐E were investigated in 24 leukemia–lymphoma cell lines including eight PAL cell lines, and their influences in chromosome morphology were evaluated. Heterozygous point mutations within hCAP‐C were found in two PAL cell lines and corresponding tumor samples (OPL‐3 and OPL‐7). Deletion of exon 24 within hCAP‐E and a point mutation at the donor splice site of intron 24 were detected in OPL‐5 and original tumor samples. OPL‐5 showed an extensive reduction in expression of not only hCAP‐E but also hCAP‐C proteins. OPL‐5 occasionally showed the chromosome bridge in anaphase and telophase, indicating that segregation is not accurate. OPL‐7 showed reduced hCAP‐C protein expression, abnormality in chromosome length and width, and abnormal aggregates of hCAP‐C protein. These findings indicated that condensin gene alteration might play a role in genome instability, which accelerates the accumulation of other gene alterations in PAL. (Cancer Sci 2007; 98: 1041–1047)
Identification of a novel NY‐ESO‐1 promiscuous helper epitope presented by multiple MHC class II molecules found frequently in the Japanese population
Authors: Ohkuri Takayuki , Sato Masayoshi , Abe Hiroyuki , Tsuji Keiko , Yamagishi Yuka , Ikeda Hiroaki , Matsubara Naoki , Kitamura Hidemitsu , Nishimura Takashi
Published: May 2007

NY‐ESO‐1 is a cancer‐testis antigen that elicits strong cellular and humoral immune responses against NY‐ESO‐1‐expressing tumors. Although CD4+ T cells play a critical role in inducing antitumor immunity, little is known about MHC class II‐restricted helper epitopes of the NY‐ESO‐1 antigen compared with MHC class I‐restricted epitopes. Here, we searched for new NY‐ESO‐1 helper epitopes presented by MHC class II molecules, especially those found frequently in the Japanese population. We established five NY‐ESO‐1‐specific helper T‐cell lines from healthy Japanese donors using NY‐ESO‐1 recombinant protein and peptide. Using MHC class II‐specific antibodies and a panel of Epstein–Barr virus‐transformed B‐cell lines, it was demonstrated that four out of the five T‐cell lines recognized a region within NY‐ESO‐1119–143 in the context of HLA‐DRB1*0802, DRB1*0901, DRB1*1502 or DRB1*0405/*0410. In addition, using a set of overlapping 15‐mer synthetic peptides, we found that NY‐ESO‐1122–138 was a promiscuous region that bound to four distinct HLA‐DR molecules found in the Japanese population. These findings expand the usefulness of NY‐ESO‐1 as a tool for tumor vaccine therapy in eliciting NY‐ESO‐1‐specific helper T‐cell responses, especially in Japanese cancer patients. (Cancer Sci 2007; 98: 1092–1098)
Immune tolerance induction with a high purity von Willebrand factor/VIII complex concentrate in haemophilia A patients with inhibitors at high risk of a poor response
Authors: GRINGERI A. , MUSSO R. , MAZZUCCONI M. G. , PISEDDU G. , SCHIAVONI M. , PIGNOLONI P. , MANNUCCI P. M. ,   FOR THE RITS‐FITNHES STUDY GROUP
Published: May 2007

Summary.  Immune tolerance induction (ITI) is effective in approximately 70% of haemophilia patients with inhibitors. Poor prognostic factors are age >6 years, ITI started >1 year from inhibitor development, inhibitor peaks >200 BU, inhibitor titre >10 BU when ITI is started and previously failed ITI. The objective of this study was to identify the effectiveness in ITI of a high purity von Willebrand factor/factor VIII (VWF/FVIII) complex concentrate in inhibitor patients at high risk of failure. Patients with severe or moderate haemophilia A and high responding inhibitors who had at least one poor prognostic factor for ITI failure were prospectively followed‐up. Success was defined by undetectable inhibitor, recovery and half life >66% of expected values. ITI dose regimens were chosen by each haemophilia centre. Seventeen haemophiliacs (16 severe, one moderate), aged 4–54 years (median 23) were followed‐up for 6–71 months. Poor prognostic factors were delayed‐onset ITI (n = 16), age >6 years (n = 16), previously failed ITI (n = 4), inhibitor peak >200 BU (n = 2) and inhibitor >10 BU when ITI was started (n = 4). Complete success was obtained in nine patients (53%) after 4–30 months of treatment (median 24), including two of four patients who had previously failed ITI. Seven patients achieved a partial success, with sustained low inhibitor titres (median 1.5 BU, range 1.1–2.8) but abnormal recovery and/or half‐life, while the remaining patient withdrew ITI after 12 months when the inhibitor titer was still 70 BU. These findings suggest that high purity VWF/FVIII complex concentrates are effective in ITI, even in patients at high risk of failure.
Dose‐dependent modulation of CD8 and functional avidity as a result of peptide encounter
Authors: Kroger Charles J. , Alexander‐Miller Martha A.
Published: May 2007

The generation of an optimal CD8+ cytotoxic T lymphocyte (CTL) response is critical for the clearance of many intracellular pathogens. Previous studies suggest that one contributor to an optimal immune response is the presence of CD8+ cells exhibiting high functional avidity. In this regard, CD8 expression has been shown to contribute to peptide sensitivity. Here, we investigated the ability of naive splenocytes to modulate CD8 expression according to the concentration of stimulatory peptide antigen. Our results showed that the level of CD8 expressed was inversely correlated with the amount of peptide used for the primary stimulation, with higher concentrations of antigen resulting in lower expression of both CD8α and CD8β. Importantly the ensuing CD8low and CD8high CTL populations were not the result of the selective outgrowth of naive CD8+ T‐cell subpopulations expressing distinct levels of CD8. Subsequent encounter with peptide antigen resulted in continued modulation of both the absolute level and the isoform of CD8 expressed and in the functional avidity of the responding cells. We propose that CD8 cell surface expression is not a static property, but can be modulated to ‘fine tune’ the sensitivity of responding CTL to a defined concentration of antigen.
Culture adaptation of embryonic stem cells echoes germ cell malignancy
Authors: Harrison Neil J , Baker Duncan , Andrews Peter W
Published: May 2007

Teratocarcinomas are a subset of tumours that result from the neoplastic transformation of primordial germ cells. Such germ cell tumours (GCT) are histologically heterogeneous, reflecting a capacity for differentiation (pluripotency) of their embryonal carcinoma (EC) stem cells. However, malignant evolution of these tumours may ultimately correlate with a decrease in pluripotency, because this would tend to increase the propensity of EC cells for self‐renewal. Human embryonic stem (ES) cells, derived from early blastocysts, closely resemble EC cells and, on prolonged culture in vitro, acquire progressive genetic changes that show striking similarity to those seen in GCT (e.g. gain of material from chromosome 12). In parallel, these abnormal ES cells show enhanced population growth rates and plating efficiencies, indicative of their adaptation to culture conditions. Understanding the mechanisms that drive such culture adaptation of ES cells may also provide insights into the development and progression of GCT.
Evolution of an invasive rodent on an archipelago as revealed by molar shape analysis: the house mouse in the Canary Islands
Authors: Michaux Jacques , Cucchi Thomas , Renaud Sabrina , Garcia‐Talavera Francisco , Hutterer Rainer
Published: May 2007

Aim The aim of this paper is to identify the patterns in the morphological differentiation in Canary Island mice, based on fossil and modern samples. In order to achieve this, the mouse species present on the archipelago were first compared with a set of continental mice. The differences between the continental and Canary Island samples, and among the Canary Island samples, provide insights into the processes of colonization and the subsequent insular evolution.

Location Canary archipelago.

Methods An outline analysis based on Fourier transformation was used to quantify shape differences between lower molars. Together with the fossil and modern Canary Island samples, a reference set of genotyped continental populations of the commensalMus musculusand the wildMus spretuswas used for comparison.

Results The morphometric analysis showed that all the mouse specimens from the Canary Islands and Cape Verde belonged toMus musculus domesticus.Lower molars of extant mice from La Gomera, El Hierro, Gran Canaria, Tenerife, and to a lesser degree from Lanzarote, were similar to those of genotypedM. m. domesticusfrom the continent, while teeth of extant mice from Fuerteventura were more divergent. Fossil mice from Fuerteventura were very similar to the extant representatives on this island, and similar to the fossil mice on the nearby islands of Lobos and La Graciosa.

Main conclusions The mouse present on the Canary archipelago has been identified as the house mouseM. m. domesticus. Based on the shape of the lower molar, the Canary Island mice are divergent from the continental ones, but the degree of divergence varies with the geography of the archipelago. Overall, populations from eastern islands are more divergent from the continental mice than populations from western ones. Fossil populations indicate that this situation was established several centuries ago. Two main factors may have contributed to this pattern: the appearance of different types of environment on the islands since the successful settlement of the mouse, and/or the number of subsequent introductions of continental individuals via shipping.
Gene structure of an antimicrobial peptide from mandarin fish, Siniperca chuatsi (Basilewsky), suggests that moronecidins and pleurocidins belong in one family: the piscidins
Authors: Sun B J , Xie H X , Song Y , Nie P
Published: May 2007

The gene of piscidin, an antimicrobial peptide, has been cloned from the mandarin fish, Siniperca chuatsi. From the first transcription initiation site, the mandarin fish piscidin gene extends 1693 nucleotides to the end of the 3′ untranslated region and contains four exons and three introns. A predicted 79‐residue prepropeptide consists of three domains: a signal peptide (22 aa), a mature peptide (22 aa) and a C‐terminal prodomain (35 aa). The shortage of XQQ motif in the prodomain of mandarin fish piscidin and the similar gene structure between moronecidins (piscidins) and pleurocidins may indicate that they are derived from the same ancestor gene. We thus suggest that piscidin should be used as a terminology for these antimicrobial peptides in the future. The mandarin fish piscidin mRNA was abundant in intestine, spleen, pronephros and kidney analysed by real‐time polymerase chain reaction. After stimulation with lipopoly saccharides (LPS), a marked increase in transcripts was observed in most tissues, indicating that piscidin is not only a constitutively expressed molecule, but also has an increased response to bacterial infection. The synthetic, amidated mandarin fish piscidin exhibited different antimicrobial activity against different fish bacterial pathogens, especially against species of Aeromonas, which may to certain extent reflect the pathogenicity of these bacteria.
Molecular typing by pulsed‐field gel electrophoresis of Flavobacterium psychrophilum isolates derived from Japanese fish
Authors: Arai H , Morita Y , Izumi S , Katagiri T , Kimura H
Published: May 2007

Sixty‐four isolates of Flavobacterium psychrophilum from ayu, Plecoglossus altivelis altivelis (Temminck & Schlegel), and other fish (n = 16) in Japan and the type strain (NCIMB 1947T) were typed using pulsed‐field gel electrophoresis (PFGE) with endonuclease BlnI and XhoI. These isolates were classified into 20 clusters and 42 genotypes by PFGE analysis. The most predominant cluster of isolates from ayu was cluster XII (n = 20), followed by clusters XVII, XVI, XX, XI, IX, X, XIII and XV; the remaining 17 isolates from other fish were divided into clusters I, II, III, IV, V, VI, VII, VIII, XIV, XVIII and XIX. The PFGE genotype of isolates from ayu clearly differed from those of other fish. The isolates from ayu in Gunma Prefecture belonged to clusters XII, XVI, XVII and XX, and the strains of three of these clusters (XII, XVII and XX) were isolated from ayu in 15 of 19 prefectures. PFGE typing enabled more accurate classification of isolates into clusters than previously achieved by analysing the restriction fragment length polymorphism of PCR products. These results suggest that F. psychrophilum isolated from ayu and other fish are genetically different and strains with several PFGE types have spread within Japan.
A potential bias in the temporal method for estimatingNein admixed populations under natural selection
Authors: ARAKI HITOSHI , WAPLES ROBIN S. , BLOUIN MICHAEL S.
Published: May 2007

Indirect genetic methods are frequently used to estimate the effective population size (Ne) or effective number of breeders (Nb) in natural populations. Although assumptions behind these methods are often violated, there have been few attempts to evaluate how accurate these estimates really are in practice. Here we investigate the influence of natural selection following a population admixture on the temporal method for estimatingNe. Our analytical and simulation results suggest thatNeis often underestimated in this method when subpopulations differ substantially in allele frequencies and in reproductive success. The underestimation is exacerbated when trueNeand the fraction of the low‐fitness group are large. As an empirical example, we comparedNbestimated in natural populations of steelhead trout (Oncorhynchus mykiss) using the temporal method (N̂b[temp]) with estimates based on direct demographic methods (N̂b[demo]) and the linkage disequilibrium method (N̂b[LD]). WhileN̂b[LD]was generally in close agreement withN̂b[demo],N̂b[temp]was much lower in sample sets that were dominated by nonlocal hatchery fish with low reproductive success, as predicted by the analytical results. This bias in the temporal method, which arises when genes associated with a particular group of parents are selected against in the offspring sample, has not been widely appreciated before. Such situations may be particularly common when artificial propagation or translocations are used for conservation. The linkage disequilibrium method, which requires data from only one sample, is robust to this type of bias, although it can be affected by other factors.