bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy loss of charged projectiles in a self-gravitating Lorentzian dusty plasma
Authors: Sarwar M. Adnan , Mirza Arshad M. , Malik Assad A.
Published: July 2006

The energy loss of a pair of test charge projectiles passing through a multicomponent, self-gravitating, dusty plasma with a generalized Lorentzian distribution is presented. Analytical and numerical results are obtained for the shielded potential and for the slowing down of a pair of test charge projectiles. The correlation and interference effects of two collinear and noncollinear projectiles on the shielded potential as well as on the energy loss are presented. An interference contribution of these projectiles to the potential and energy loss is observed that depends upon their orientation and separation distance. It is found that the energy loss of collinear projectiles decreases with the increase of the dust Jeans frequency for any separation distance. On the other hand, with small values of κ (the generalized Lorentzian distribution case), the test charge projectile gains energy instead of losing for projectile velocity greater than the thermal velocity of the dust, and this gain is increased as we increase the dust Jeans frequency. These results are helpful to understand the energy loss mechanism, which plays an important role in explaining the coagulation of dust particles in molecular clouds as well as in dust plasma crystal formation.
Magnetic moments of bare and benzene-capped cobalt clusters
Authors: Knickelbein Mark B.
Published: July 2006

Magnetic moments of bare cobalt clusters Con (n=7–32) and benzene-capped cobalt clusters Con(bz)m have been measured at temperatures ranging from 54to150K using a molecular beam deflection method. It was observed that Co12–32 produced at temperatures greater than ∼100K display high-field-seeking behavior at all temperatures in the range investigated, indicating that they are superparamagnetic species. At temperatures below ∼100K, the field-on beam profiles of Co7–11 and some larger clusters displayed substantial symmetric broadening, indicating that some fraction of the clusters in the beam were no longer superparamagnetic, but rather were in a blocked (locked-moment) state. In the superparamagnetic regime (T=150K) Con clusters in the n=7–32 size range were found to possess per-atom moments ranging from 1.96±0.04μb(Co24) to 2.53±0.04μb(Co16), significantly above the bulk value of 1.72μb. Locked-moment isomers were found to display moments of ∼1μb per atom. Cobalt clusters containing a layer of adsorbed benzene molecules were found to possess significantly lower moments per cobalt atom than the corresponding bare cobalt clusters.
Linear theory of the electron cyclotron maser based on TM circular waveguide mode
Authors: Jiao Chongqing , Luo Jirun
Published: July 2006

A linear theory of the electron cyclotron maser, which is applicable to any TM circular waveguide mode, is developed by using Laplace transforms. This theory can be used to analyze the linear behaviors of both the TM mode gyrotron traveling wave tube (gyro-TWT) and the TM mode gyrotron backward wave oscillator (gyro-BWO). Numerical results show that, although the TM mode is less effective than the TE mode for the gyro-TWT interaction, the TM mode may be as effective as the TE mode for the gyro-BWO interaction, even in the case of weak relativistic electron energy.
Core-shell particle model for optical transparency in glass ceramics
Authors: Edgar Andrew
Published: July 2006

The light scattering from particles in a glass ceramic is calculated for a particle model comprising a crystalline core and a surrounding shell, created by nucleation and diffusive processes from the original homogeneous glass, with diffusing atoms limited to the core-shell volume. The scatterings from core and shell are found to cancel in first order for small particles within the approximations of the Rayleigh-Debye theory. The residual scattering varies as the inverse eighth power of wavelength and is most pronounced in the backscatter geometry.
Photoluminescence imaging of silicon wafers
Authors: Trupke T. , Bardos R. A. , Schubert M. C. , Warta W.
Published: July 2006

Photoluminescence imaging is demonstrated to be an extremely fast spatially resolved characterization technique for large silicon wafers. The spatial variation of the effective minority carrier lifetime is measured without being affected by minority carrier trapping or by excess carriers in space charge regions, effects that lead to experimental artifacts in other techniques. Photoluminescence imaging is contactless and can therefore be used for process monitoring before and after individual processing stages, for example, in photovoltaics research. Photoluminescence imaging is also demonstrated to be fast enough to be used as an in-line tool for spatially resolved characterization in an industrial environment.
Low resistance nonalloyed Ni∕Au Ohmic contacts to p-GaN irradiated by KrF excimer laser
Authors: Oh Min-Suk , Hwang Dae-Kue , Lim Jae-Hong , Kang Chang-Goo , Park Seong-Ju
Published: July 2006

A specific contact resistance of 8.9×10−5Ωcm2 was obtained for a Ni∕Au Ohmic layer on the KrF laser-irradiated p-GaN. It was found that laser irradiation increases the hole concentration from 4.1×1017to9.7×1017cm−3 by removing hydrogen atoms from p-GaN layer. The native oxide was also removed as evidenced by the Ga 2p peak shift and the decrease in the intensity of O 1s peak in the x-ray photoelectron spectra. The formation of a low resistance is attributed to the increase in the hole concentration and the removal of native oxide from p-GaN by laser irradiation.
Room temperature SiO2∕SiO2 covalent bonding
Authors: Tong Q.-Y. , Fountain G. , Enquist P.
Published: July 2006

Room temperature covalent bonds between bonded silicon oxide layers can be realized by forming surface and subsurface absorption layers followed by terminating outmost bonding surfaces with desired bonding groups prior to bonding. For example, by introducing fluorine into bonding oxide layers and NH2 groups onto surfaces of bonding oxide layers before bonding, bonding energy equivalent to silicon fracture energy (2500mJ∕m2) has been realized at room temperature after storage in air. Fluorine incorporation causes Si–O–Si ring breaking leading to fluorinated oxide formation with lower density, thus facilitating a higher diffusion rate of polymerization by-products and enhanced moisture absorptivity. Results indicate that by-products of the polymerization reaction between NH2 groups on mating surfaces appear to be more easily diffused and dispersed away from the bonding interface by the low density fluorinated oxide than are polymerization by-products of OH groups. This enhanced by-product removal results in covalent bonding at room temperature.
Diffusion and activation of ultrashallow B implants in silicon on insulator: End-of-range defect dissolution and the buried Si∕SiO2 interface
Authors: Hamilton J. J. , Cowern N. E. B. , Sharp J. A. , Kirkby K. J. , Collart E. J. H. , Colombeau B. , Bersani M. , Giubertoni D. , Parisini A.
Published: July 2006

The fabrication of preamorphized p-type ultrashallow junctions in silicon-on-insulator (SOI) has been investigated. Electrical and structural measurements after annealing show that boron deactivation and transient enhanced diffusion are reduced in SOI compared to bulk wafers. The reduction is strongest when the end-of-range defects of the preamorphizing implant are located deep within the silicon overlayer of the SOI silicon substrate. Results reveal a very substantial increase in the dissolution rate of the end-of-range defect band. A key player in this effect is the buried Si∕SiO2 interface, which acts as an efficient sink for interstitials competing with the silicon surface.
Adaptive response of
Yersinia pestis
to extracellular effectors of innate immunity during bubonic plague
Authors: Sebbane Florent , Lemaître Nadine , Sturdevant Daniel E. , Rebeil Roberto , Virtaneva Kimmo , Porcella Stephen F. , Hinnebusch B. Joseph
Published: July 2006

Yersinia pestis
causes bubonic plague, characterized by an enlarged, painful lymph node, termed a bubo, that develops after bacterial dissemination from a fleabite site. In susceptible animals, the bacteria rapidly escape containment in the lymph node, spread systemically through the blood, and produce fatal sepsis. The fulminant progression of disease has been largely ascribed to the ability of
Y. pestis
to avoid phagocytosis and exposure to antimicrobial effectors of innate immunity.
In vivo
microarray analysis of
Y. pestis
gene expression, however, revealed an adaptive response to nitric oxide (NO)-derived reactive nitrogen species and to iron limitation in the extracellular environment of the bubo. Polymorphonuclear neutrophils recruited to the infected lymph node expressed abundant inducible NO synthase, and several
Y. pestis
homologs of genes involved in the protective response to reactive nitrogen species were up-regulated in the bubo. Mutation of one of these genes, which encodes the Hmp flavohemoglobin that detoxifies NO, attenuated virulence. Thus, the ability of
Y. pestis
to destroy immune cells and remain extracellular in the bubo appears to limit exposure to some but not all innate immune effectors. High NO levels induced during plague may also influence the developing adaptive immune response and contribute to septic shock.
Differential HIV-1 replication in neonatal and adult blood mononuclear cells is influenced at the level of HIV-1 gene expression
Authors: Sundaravaradan Vasudha , Saxena Shailendra K. , Ramakrishnan Rajesh , Yedavalli Venkat R. K. , Harris David T. , Ahmad Nafees
Published: July 2006

The majority of HIV-1-infected neonates and infants have a higher level of viremia and develop AIDS more rapidly than infected adults, including differences seen in clinical manifestations. To determine the mechanisms of HIV-1 infection in neonates vs. adults, we compared the replication kinetics of HIV-1 in neonatal (cord) and adult blood T lymphocytes and monocyte-derived macrophages (MDM) from seven different donors. We found that HIV-1 replicated 3-fold better in cord blood T lymphocytes compared with adult blood T lymphocytes and 9-fold better in cord MDM than adult MDM. We also show that this differential HIV-1 replication did not depend on differences in cell proliferative capabilities, cell surface expression of CD4, CXCR4, and CCR5, or in the amount of PCR products of reverse transcription, DNA synthesis, and translocation of preintegration complex into the nucleus in cord and adult T lymphocytes and MDM. Furthermore, using a single-cycle replication competent HIV-1-NL4–3-Env
−
luciferase amphotropic virus, which measures HIV-1 transcriptional activity independent of receptor and coreceptor expression, we found there was a 3-fold increase of HIV-1 LTR-driven luciferase expression in cord T lymphocytes compared with adult T lymphocytes and 10-fold in cord MDM than in adult MDM. The HIV-1 LTR-driven luciferase expression correlated with HIV-1 LTR transcription, as measured by ribonuclease protection assay. These data suggest that the increased replication of HIV-1 in cord blood compared with adult blood mononuclear cells is regulated at the level of HIV-1 gene expression, resulting in a higher level of viremia and faster disease progression in neonates than adults.
Ecological and immunological determinants of dengue epidemics
Authors: Wearing Helen J. , Rohani Pejman
Published: July 2006

The management of infectious diseases is an increasingly important public health issue, the effective implementation of which is often complicated by difficulties in teasing apart the relative roles of extrinsic and intrinsic factors influencing transmission. Dengue, a vector-borne strain polymorphic disease, is one such infection where transmission dynamics are affected by environmental variables as well as immune-mediated serotype interactions. To understand how alternative hypotheses concerning dengue infection and transmission may explain observed multiannual cycles in disease incidence, we adopt a theoretical approach that combines both ecological and immunological mechanisms. We demonstrate that, contrary to perceived wisdom, patterns generated solely by antibody-dependent enhancement or heterogeneity in virus virulence are not consistent with serotype-specific notification data in important ways. Furthermore, to generate epidemics with the characteristic signatures observed in data, we find that a combination of seasonal variation in vector demography and, crucially, a short-lived period of cross-immunity is sufficient. We then show how understanding the persistence and eradication of dengue serotypes critically depends on the alternative assumed mechanisms.
DRB1*0401-restricted human T cell clone specific for the major proinsulin73-90 epitope expresses a down-regulatory T helper 2 phenotype
Authors: Durinovic-Belló Ivana , Rosinger Silke , Olson Jennifer A. , Congia Mauro , Ahmad Regina C. , Rickert Mathias , Hampl Johannes , Kalbacher Hubert , Drijfhout Jan W. , Mellins Elizabeth D. , Al Dahouk Sascha , Kamradt Thomas , Maeurer Markus J. , Nhan Carol , Roep Bart O. , Boehm Bernhard O. , Polychronakos Constantin , Nepom Gerald T. , Karges Wolfram , McDevitt Hugh O. , Sønderstrup Grete
Published: July 2006

Recently, we have identified proinsulin (P-Ins)73-90as an immunodominant T cell epitope of HLA-DRB1*0401 (DR4) subjects with β-islet cell autoimmunity and of HLA-DR4/CD4 double-transgenic mice immunized with human P-Ins. We have compared the fine specificities of one human CD4 T cell clone and two mouse T cell hybridoma clones recognizing this epitope, and, although these three clones all recognized the same core region (LALEGSLQK), there were major differences in how they interacted with the peptide (p)/HLA complex, reflecting the fact that human P-Ins is a foreign antigen in the mouse and an autoantigen in the type 1 diabetes patient. The human T cell clone was forkhead transcription factor 3 (Foxp3)-positive, a marker for regulatory T cell lineages, and secreted predominantly IL-5, IL-10, and low levels of IFNγ in response to P-Ins73-90. This finding is compatible with the previously detected regulatory cytokine pattern in subjects with β-cell autoimmunity. However, added N- or C-terminal amino acids drastically changed HLA and tetramer binding capacity as well as T cell reactivity and the cytokine phenotype of the P-Ins73-90-specific human CD4 T cell clone, suggesting a potential for this P-Ins epitope as a target for therapeutic intervention in HLA-DR4-positive humans with β-islet cell autoimmunity or recent-onset type 1 diabetes.
Noninvasive localized delivery of Herceptin to the mouse brain by MRI-guided focused ultrasound-induced blood–brain barrier disruption
Authors: Kinoshita Manabu , McDannold Nathan , Jolesz Ferenc A. , Hynynen Kullervo
Published: July 2006

Antibody-based anticancer agents are promising chemotherapeutic agents. Among these agents, Herceptin (trastuzumab), a humanized anti-human epidermal growth factor receptor 2 (HER2/c-erbB2) monoclonal antibody, has been used successfully in patients with breast cancer. However, in patients with brain metastasis, the blood–brain barrier limits its use, and a different delivery method is needed to treat these patients. Here, we report that Herceptin can be delivered locally and noninvasively into the mouse central nervous system through the blood–brain barrier under image guidance by using an MRI-guided focused ultrasound blood–brain barrier disruption technique. The amount of Herceptin delivered to the target tissue was correlated with the extent of the MRI-monitored barrier opening, making it possible to estimate indirectly the amount of Herceptin delivered. Histological changes attributable to this procedure were minimal. This method may represent a powerful technique for the delivery of macromolecular agents such as antibodies to treat patients with diseases of the central nervous system.
An early role for Sonic hedgehog from foregut endoderm in jaw development: Ensuring neural crest cell survival
Authors: Brito José M. , Teillet Marie-Aimée , Le Douarin Nicole M.
Published: July 2006

We have investigated the role of Sonic hedgehog (Shh) in the development of facial structures by depriving chicken embryos of the most anterior sources of this morphogen, including the prechordal plate and the anterior ventral endoderm of the foregut, before the onset of neural crest cell (NCC) migration to the first branchial arch (BA1). The entire forehead, including the foregut endoderm, was removed at 5- to 10-somite stage (ss), which led to the absence of the lower jaw when the operation was performed before 7-ss. If the embryos were deprived of their forehead at 8- to 10-ss, they were later on endowed with a lower beak. In embryos that were operated on early, the NCCs migrated normally to BA1 but were subjected to massive apoptosis a few hours later. Cell death did not occur when forehead excision was performed at a later stage. In this case, onward expression of
Shh
in the ventral foregut endoderm extended caudally over the excision limit, and we hypothesized that absence of
Shh
production by the endoderm in embryos that were operated on early could be responsible for the NCC apoptosis and the failure of BA1 development. We thus provided exogenous Shh to the embryos that were operated on before 7-ss. In this case, the development of the lower jaw was rescued. Therefore, Shh derived from the ventral foregut endoderm ensures the survival of NCCs at a critical stage of BA1 development.
Targeting lentiviral vectors to specific cell types
in vivo
Authors: Yang Lili , Bailey Leslie , Baltimore David , Wang Pin
Published: July 2006

We have developed an efficient method to target lentivirus-mediated gene transduction to a desired cell type. It involves incorporation of antibody and fusogenic protein as two distinct molecules into the lentiviral surface. The fusogen is constructed by modifying viral envelope proteins, so that they lack the ability to bind to their cognate receptor but still retain the ability to trigger pH-dependent membrane fusion. Thus, the specificity of such a lentiviral vector is solely determined by the antibody, which is chosen to recognize a specific surface antigen of the desired cell type. This specific binding then induces endocytosis of the surface antigen, bringing the lentivirus into an endosome. There, the fusogen responds to the low pH environment and mediates membrane fusion, allowing the virus core to enter the cytosol. Using CD20 as a target antigen for human B cells, we have demonstrated that this targeting strategy is effective both
in vitro
and in intact animals. This methodology is flexible and can be extended to other forms of cell type-specific recognition to mediate targeting. The only requirement is that the antibody (or other binding protein) must be endocytosed after interaction with its cell surface-binding determinant.
The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer
Authors: Enkhmandakh Badam , Makeyev Alexandr V. , Bayarsaihan Dashzeveg
Published: July 2006

Lim1, Ssdp1, and Ldb1 proteins are components of the Ldb1-associated transcriptional complex, which is important in the head-organizing activity during early mouse development. Depletion of each individual protein alone causes a headless phenotype. To explore in more detail the modular architecture of the complex, we have generated two different gene-trapped mouse lines that express truncated forms of Ssdp1. Embryos derived from the gene-trapped line that encodes a truncated Ssdp1 lacking the proline-rich sequence exhibit a lethal abnormal head-development phenotype, resembling mouse embryos deficient for
Lim1
,
Ssdp1
, or
Otx2
genes. Embryos derived from the second gene-trapped line, in which most of the proline-rich domain of Ssdp1 is retained, did not show abnormalities in head development. Our data demonstrate that components of the Ldb1-dependent module can be subdivided further into discrete functional domains and that the proline-rich stretch of Ssdp1 is critical for embryonic head development. Furthermore, phylogenetic comparisons revealed that in
Caenorhabditis elegans
, a similar proline-rich sequence is absent in Ssdp but present in Ldb1. We conclude that although the overall architecture of the Ldb1-dependent module has been preserved, the genetic specification of its individual components has diversified during evolution, without compromising the function of the module.
Assembly of the cytokinetic contractile ring from a broad band of nodes in fission yeast
Authors: Wu Jian-Qiu , Sirotkin Vladimir , Kovar David R. , Lord Matthew , Beltzner Christopher C. , Kuhn Jeffrey R. , Pollard Thomas D.
Published: July 2006

We observed live fission yeast expressing pairs of functional fluorescent fusion proteins to test the popular model that the cytokinetic contractile ring assembles from a single myosin II progenitor or a Cdc12p-Cdc15p spot. Under our conditions, the anillin-like protein Mid1p establishes a broad band of small dots or nodes in the cortex near the nucleus. These nodes mature by the addition of conventional myosin II (Myo2p, Cdc4p, and Rlc1p), IQGAP (Rng2p), pombe Cdc15 homology protein (Cdc15p), and formin (Cdc12p). The nodes coalesce laterally into a compact ring when Cdc12p and profilin Cdc3p stimulate actin polymerization. We did not observe assembly of contractile rings by extension of a leading cable from a single spot or progenitor. Arp2/3 complex and its activators accumulate in patches near the contractile ring early in anaphase B, but are not concentrated in the contractile ring and are not required for assembly of the contractile ring. Their absence delays late steps in cytokinesis, including septum formation and cell separation.
Inhibition of nitrogen mineralization in young humic fractions by anaerobic decomposition of rice crop residues
Authors: Olk D. C. , Samson M. I. , Gapas P.
Published: July 2006

Field observations indicate a long‐term decrease in crop uptake of N derived from soil organic matter under continuous production of irrigated lowland rice (Oryza sativa L.). Decreased availability has been associated with an accumulation of phenolic lignin residues in soil organic matter, which can chemically bind N. To evaluate the hypothesis that the decrease in N availability results primarily from anaerobic decomposition of incorporated crop residues, 15N‐labelled fertilizer was applied three times during one growing season in a field study that compared anaerobic decomposition with aerobic decomposition for annual rotations of rice (Oryza sativa L.)–rice and rice–maize (Zea mays L.). Contents of 15N and total N during the growing season were measured in humic fractions and total soil organic matter. Results indicated an inhibition of N mineralization for the rice–rice rotation with anaerobic decomposition of crop residues, both for 15N that was immobilized after application and for total N. The inhibition was strongest for 15N that was applied at planting. It became more evident as the season progressed and reached significant levels during mid‐season stages of plant growth when crop demand for N peaks. These results were clearest for a young, phenolic‐rich humic fraction that was active in 15N immobilization and remineralization. Comparable but less significant trends were evident for a more recalcitrant humic fraction and for soil organic matter. Trends in crop‐N uptake associated the combination of rice–rice rotation and anaerobic decomposition with inhibited uptake of soil organic N but uninhibited uptake of fertilizer N. Increased aeration of rice soils through aerobic decomposition of crop residues or crop rotation is a promising management technique for improving soil N supply in lowland rice cropping.
Adsorption of phthalic acid and salicylic acid by two variable charge soils as influenced by sulphate and phosphate
Authors: Xu R. K. , Xiao S. C. , Zhang H. , Jiang J. , Ji G. L.
Published: July 2006

Low‐molecular‐weight (LMW) organic acids exist widely in soils, especially in the rhizosphere, and the adsorption of these acids may affect their reactions in soils. The adsorption behaviour of phthalic acid and salicylic acid by two variable charge soils (a Rhodic Ferralsol and a Haplic Acrisol) was investigated. Both soils exhibited great adsorption capacity for these organic acids, with a greater affinity for phthalic acid. The Rhodic Ferralsol adsorbed more organic acids of both kinds than the Haplic Acrisol, which was consistent with the content of iron and aluminum oxides in the two soils. The iron oxides in these soils played a significant role in adsorption of the organic acids, whilst the soil aluminosilicate minerals, such as kaolinite, showed a small adsorption capacity. The presence of phosphate and sulphate caused a decrease in the adsorption of both organic acids because of their competition with them for sorption sites. The phosphate showed a bigger inhibition on the adsorption than sulphate as a result of a greater amount of phosphate adsorbed by the soils. The adsorption of both organic acids was affected by pH only slightly at pH < 4.5. However, the adsorption decreased with the increase in pH at pH > 4.5. A similar trend was observed for the phosphate system, but the opposite was seen for the sulphate system. This suggests that the inhibition of sulphate on the adsorption of the organic acids decreased with the increase in pH, because the adsorption of sulphate decreased strongly with increasing pH.
Are serum adiponectin concentrations in a population sample of 64‐year‐old Caucasian women with varying glucose tolerance associated with ultrasound‐assessed atherosclerosis?
Authors: BEHRE C. J. , BROHALL G. , HULTHE J. , WIKSTRAND J. , FAGERBERG B.
Published: July 2006

Objective.  To examine whether serum adiponectin concentrations were associated with subclinical atherosclerosis assessed as intima media thickness (IMT) in the carotid arteries in Caucasian women with varying degrees of glucose tolerance.

Research design and methods.  From a population‐based cohort of 64‐year‐old Swedish women, 533 subjects with type 2 diabetes (DM2, n = 177), impaired glucose tolerance (IGT; n = 178) or normal glucose tolerance (NGT, n = 178) were recruited. Anthropometrics, usual cardiovascular risk factors were examined and ultrasound examination of the carotid arteries was performed.

Results.  Women with low adiponectin concentrations were characterized by thick IMT, higher prevalence of DM2, history of previous myocardial infarction, angina pectoris, anti‐hypertensive treatment and high body mass index (BMI), waist circumference, plasma insulin, serum triglycerides, fasting glucose, HbA1c, and low serum HDL cholesterol levels. Carotid IMT correlated with HbA1c (r = 0.24, P < 0.001), waist circumference (r = 0.22, P < 0.001), plasma insulin (r = 0.19, P < 0.001), BMI (r = 0.18, P < 0.001), DM2 (r = 0.16, P < 0.001), systolic blood pressure (r = 0.16, P < 0.001), blood glucose (r = 0.16, P < 0.001), triglycerides (r = 0.15, P < 0.001), and reversely to adiponectin (r = −0.11, P = 0.01), HDL cholesterol (r = −0.13, P = 0.004), and alcohol intake (r = −0.087, P < 0.05). A more detailed analysis of underlying associations was difficult due to a high co‐linearity between these variable.

Conclusions.  Low serum adiponectin concentrations were associated with increased carotid artery IMT, and several risk factors for cardiovascular diseases, mainly those constituting the metabolic syndrome.
Characterization of full‐length hepatitis C virus genotype 4 sequences
Authors: Timm J. , Neukamm M. , Kuntzen T. , Kim A. Y. , Chung R. T. , Brander C. , Lauer G. M. , Walker B. D. , Allen T. M.
Published: July 2006

Summary.  Over 85% of the world's nearly 170 million hepatitis C virus (HCV)‐infected subjects exist in regions of Africa, Southeast Asia and Middle Eastern countries where genotypes 4–6 are very common. In particular, HCV genotype 4 is highly prevalent in Egypt with more than 19% of the population infected and chronic HCV representing one of the top five leading causes of death, due in part to ineffective interferon alpha treatment against this genotype. Despite this, very little work has been carried out to characterize the sequence diversity of genotype 4, which will be critical to the development of effective vaccines and antiviral therapies against this genotype. As a result of the paucity of sequence data available for HCV genotype 4, for which only one full genome sequence is currently available, we were interested in characterizing additional genotype 4 sequences and to provide reagents for amplification of this genotype. Here we describe seven unique HCV genotype 4a full genomes, in addition to a single genotype 4d genome, and characterize their sequence diversity in relation to other more closely characterized HCV genotypes.
Conservation genetics and the resilience of reef‐building corals
Authors: VAN OPPEN MADELEINE J. H. , GATES RUTH D.
Published: July 2006

Coral reefs have suffered long‐term decline due to a range of anthropogenic disturbances and are now also under threat from climate change. For appropriate management of these vulnerable and valuable ecosystems it is important to understand the factors and processes that determine their resilience and that of the organisms inhabiting them, as well as those that have led to existing patterns of coral reef biodiversity. The scleractinian (stony) corals deposit the structural framework that supports and promotes the maintenance of biological diversity and complexity of coral reefs, and as such, are major components of these ecosystems. The success of reef‐building corals is related to their obligate symbiotic association with dinoflagellates of the genus Symbiodinium. These one‐celled algal symbionts (zooxanthellae) live in the endodermal tissues of their coral host, provide most of the host's energy budget and promote rapid calcification. Furthermore, zooxanthellae are the main primary producers on coral reefs due to the oligotrophic nature of the surrounding waters. In this review paper, we summarize and critically evaluate studies that have employed genetics and/or molecular biology in examining questions relating to the evolution and ecology of reef‐building corals and their algal endosymbionts, and that bear relevance to coral reef conservation. We discuss how these studies can focus future efforts, and examine how these approaches enhance our understanding of the resilience of reef‐building corals.
Spatial population genetic structure and limited dispersal in a Rocky Mountain alpine stream insect
Authors: FINN DEBRA S. , THEOBALD DAVID M. , BLACK WILLIAM C. , POFF N. LEROY
Published: July 2006

Using the mitochondrial cytochrome oxidase I (COI) gene, we assessed the phylogeographic structure ofProsimulium neomacropyga, a black fly (Simuliidae) whose distribution in the US Southern Rockies ecoregion is limited to alpine tundra streams. Given high habitat specificity, lack of hydrological connection between streams, and a terrestrial environment restrictive to insect flight, we hypothesized limited gene flow. A spatially nested sampling design showed that grouping populations according to high‐elevation ‘islands’ of alpine tundra (which typically include headwater streams of > 1 watershed) explained a significant proportion of genetic variation while grouping streams according to major watershed (across islands) did not. Nested clade analysis and isolation‐by‐distance (IBD) relationships further implicated limited ongoing gene flow within but not among the isolated alpine islands. IBD was strong among five streams within an individual island using each of four alternative models of pairwise landscape connectivity for flying insects. Results of all landscape models were positively correlated, suggesting that straight‐line distance is an acceptable surrogate for presumably more biologically meaningful connectivity measures in this system. IBD was significantly weaker across the entire study area, comprised of three separate islands. Overall, population structure was significant withFST = 0.38, suggesting limited dispersal across a small spatial extent.
Conservation value of degraded habitats for forest birds in southern Peninsular Malaysia
Authors: Peh Kelvin S.‐H. , Sodhi Navjot S. , De Jong Johnny , Sekercioglu Cagan H. , Yap Charlotte A.‐M. , Lim Susan L.‐H.
Published: July 2006

Clearance of tropical forest for agricultural purposes is generally assumed to seriously threaten the survival of forest species. In this study, we quantified the conservation value, for forest bird species, of three degraded habitat types in Peninsular Malaysia, namely rubber tree plantations, oil palm plantations, and open areas. We surveyed these degraded habitats using point counts to estimate their forest bird species richness and abundance. We assessed whether richness, abundance, and activities of different avian dietary groups (i.e. insectivores and frugivores) varied among the habitats. We identified the critical habitat elements that accounted for the distribution of forest avifauna in these degraded habitats. Our results showed that these habitats harboured a moderate fraction of forest avifauna (approximately 46–76 species) and their functions were complementary (i.e. rubber tree plantations for moving; open habitats for perching; shrubs in oil palm plantations for foraging). In terms of species richness and abundance, rubber tree plantations were more important than oil palm plantations and open habitats. The relatively high species richness of this agricultural landscape was partly due to the contiguity of our study areas with extensive forest areas. Forecasts of forest‐species presence under various canopy cover scenarios suggest that leaving isolated trees among non‐arboreal crops could greatly attract relatively tolerant species that require tree canopy. The conservation value of degraded habitats in agricultural landscapes seems to depend on factors such as the type of crops planted and distance to primary forest remnants.
Respiratory Q10 of marigold (Tagetes patula) in response to long‐term temperature differences and its relationship to growth and maintenance respiration
Authors: Van Iersel Marc W.
Published: July 2006

Acclimation of respiration to temperature is not well understood. To determine whether whole plant respiration responses to long‐term temperature treatments can be described using the Q10 concept, the CO2 exchange rate of marigolds (Tagetes patula L. ‘Queen Sophia’), grown at 20°C or 30°C, was measured for 62 days. When plants of the same age were compared, plants grown at 20°C consistently had a higher specific respiration (Rspc) than plants grown at 30°C (long‐term Q10= 0.71–0.97). This was due to a combination of greater dry mass at 30°C and a decrease in Rspc with increasing mass. When plants of the same dry mass were compared, the long‐term Q10 was 1.35–1.55; i.e. Rspc was higher at 30°C than at 20°C. Whole plant respiration could be accurately described by dividing respiration into growth and maintenance components. The maintenance respiration coefficient was higher at 30°C than at 20°C, while the growth respiration coefficient was lower at 30°C, partly because of temperature‐dependent changes in plant composition. These results suggest difficulties with interpreting temperature effects on whole plant respiration, because conclusions depend greatly on whether plants of the same age or mass are compared. These difficulties can be minimized by describing whole plant respiration on the basis of growth and maintenance components.
Field Cricket Species Differences in the Temporal Patterns of Long‐Distance Mate Attraction Signals
Authors: Bertram Susan M. , Bowen Mia
Published: July 2006

We quantify variation in the temporal components of long‐distance mate attraction signals produced by a North American field cricket, Gryllus rubens Scudder. Total signaling time, trilling bout duration, and hourly bout number exhibit high repeatability within individuals. Extensive variation exists across individuals: some males never signal while others signal for several hours each night; of the signalers, average trilling bout duration ranges from <1 min to well over an hour; some males produce only one trilling bout in an evening while others produce three bouts every 2 h. Body size, weight, wing morphology, and condition do not appear to explain the variation. We compare the temporal signaling components of G. rubens with its sister species, G. texensis. Although G. rubens produce slightly more trills per hour with slightly shorter trilling bout durations, the temporal components of these long‐distance mate attraction signals are surprisingly similar across species.
Age‐Related Changes in Signalling of Need by Nestling Tree Swallows (Tachycineta bicolor)
Authors: Leonard Marty L. , Horn Andrew G.
Published: July 2006

Despite a large literature on the ontogeny of behaviour, few studies have examined how the function of juvenile behaviour changes during development. One of the most widespread and important juvenile behaviours is begging, the display used by young animals to solicit food from their parents. Begging signals generally vary reliably with offspring need for food and have served as models for understanding the evolution of honest signalling. Little is known, however, about whether the relationship between begging and need varies over the period of rapid juvenile development. Here, we examine whether tree swallow,Tachycineta bicolor, begging calls consistently reflect hunger levels across the 20 d nestling period. We recorded begging calls at 5, 10 and 15 d post‐hatch, during an hour of food deprivation, and related call features to time without food (i.e. hunger) at each age. The overall correlation between call structure and hunger, as measured by canonical correlation, was consistent across ages. The particular features that correlated with hunger varied, however. Call rate and length increased with hunger at all ages, but call amplitude and frequency range increased with hunger at days 10 and 15 only. The results of our study suggest that begging calls consistently convey information about offspring hunger throughout the nestling period, with the number of call features encoding hunger increasing with nestling age. This change may enhance the ability of parents to assess offspring hunger levels by adding redundancy to the signal.
Social Dominance among Male Meadow Voles is Inversely Related to Reproductive Success
Authors: Spritzer Mark D. , Solomon Nancy G. , Meikle Douglas B.
Published: July 2006

Intrasexual selection can occur through direct aggressive interactions between males for access to females. We tested the relationship between social dominance and male reproductive success among meadow voles, Microtus pennsylvanicus. Dominance ranks of wild‐caught males were determined using neutral arena trials, with the winner of two of three trials considered dominant. These males were then released into field enclosures and allowed to visit females housed in nestboxes for 8 wk, and males’ home range sizes were determined using weekly grid trapping. Male reproductive success was determined using molecular paternity analysis (six microsatellite primers) for all pups born during the field experiment. Males with higher dominance ranks had larger home ranges. However, male dominance rank was not predictive of the number of total visits to females’ nestboxes or the number of visits to each male's most frequently visited nestbox. Males that made more visits to nestboxes sired more litters. Males that had higher dominance ranks sired fewer litters. These results suggest that there is a reproductive disadvantage to having higher dominance rank among male meadow voles.
Synthetic Prions
Authors: Eiden M. , Buschmann A. , Kupfer L. , Groschup M. H.
Published: July 2006

The prion theory postulates that prions are novel infectious agents that are composed largely, if not entirely, of abnormally folded host‐encoded prion proteins. However, the existence of different prion strains is enigma, if these novel infectious agents lack a genetic element, such as a nucleic acid. The best proof for this ‘protein‐only’ concept would be the in vitro generation of prions from synthetic sources. Indeed, a substantial body of evidence has meanwhile been accumulated in favour of this postulate. This mini review recapitulates all relevant studies and experimental data on the generation of synthetic prions.
Analysis of common transforming growth factor beta‐1 gene polymorphisms in gastric and duodenal ulcer disease: Pilot study
Authors: Polonikov Alexey V , Ivanov Vladimir P , Belugin Dmitry A , Khoroshaya Irina V , Kolchanova Inessa O , Solodilova Mariya A , Tutochkina Margarita P , Stepchenko Alexander A
Published: July 2006

Background and Aim:  Transforming growth factor‐β1 (TGF‐β1) has been shown to be an important cytokine that plays a role in cell proliferation, differentiation, tissue injury repair and ulcer healing. The purpose of this pilot study was to investigate if common polymorphisms Leu10Pro, Arg25Pro and C‐509T within the TGF‐β1 gene are associated with susceptibility to gastric and duodenal ulcer disease in Russians.

Method:  Blood samples from 377 unrelated patients with gastric and duodenal ulcer disease and 226 sex‐ and age‐matched healthy controls were used to determine TGF‐β1 gene polymorphisms by polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP).

Results:  Leu10Pro substitution in the signal peptide of TGF‐β1 has been found to be associated with susceptibility to gastric ulcer (odds ratio [OR] 1.76, 95% confidence interval [CI] 1.12–2.77). A genotype combination of 10Leu/Leu × 25Arg/Arg × −509C/C was also associated with susceptibility to gastric ulcer disease (OR 1.81, P = 0.01). In addition, the frequency of a combination of genotypes 10Pro/Pro × 25Arg/Pro × −509C/T was statistically lower in patients with duodenal ulcer than in controls (OR 0.42, P = 0.05). A significant difference (P = 0.04) in the distribution of rare haplotypes of the TGF‐β1 gene between patients with duodenal ulcer and healthy controls has been found. Polymorphism Leu10Pro was in positive linkage disequilibrium with C‐509T polymorphism (coefficient D = 0.191; P < 0.0001).

Conclusions:  These findings indicate that the Leu10Pro and C‐509T polymorphisms may be involved in the modulation of expression of the TGF‐β1 gene, and therefore a predisposition to peptic ulcer disease could be linked to particular alleles of this gene. In particular, a possible role of TGF‐β1 in the pathogenesis of gastric ulcer disease is discussed.
Restriction of dietary calories, fat and iron improves non‐alcoholic fatty liver disease
Authors: Yamamoto Mika , Iwasa Motoh , Iwata Kazuko , Kaito Masahiko , Sugimoto Ryosuke , Urawa Naohito , Mifuji Rumi , Konishi Masayoshi , Kobayashi Yoshinao , Adachi Yukihiko
Published: July 2006

Background:  The pathogenesis of non‐alcoholic steatohepatitis (NASH) is unclear. Recent studies suggested that oxidative stress plays an important role in the mechanism of NASH. Excessive accumulation of iron in the liver causes oxidative stress. The aim of the present study was to evaluate the grade of hepatic iron accumulation and the therapeutic response to restriction of calories, fat and iron in patients with non‐alcoholic fatty liver disease (NAFLD).

Methods:  Twenty‐seven NAFLD patients were enrolled. The patients were categorized into two groups: 17 patients with NASH and 10 with simple steatosis. Twelve NAFLD patients (NASH, n = 9; simple steatosis, n = 3) were given a dietary prescription including restriction of energy, fat and iron.

Results:  Positive iron staining was observed in 71% and 50% of patients with NASH and simple steatosis, respectively. The average energy intake, fat energy fraction and iron intake decreased significantly 6 months after the beginning of the diet in all patients. In addition, the levels of serum transaminase and ferritin were significantly decreased.

Conclusion:  Dietary restriction of calories, fat and iron improved NAFLD. Reduced serum ferritin levels appear to reduce oxidative stress in the liver.
Association of body mass index with heartburn, regurgitation and esophagitis: Results of the Progression of Gastroesophageal Reflux Disease study
Authors: Nocon Marc , Labenz Joachim , Jaspersen Daniel , Meyer‐Sabellek Wolfgang , Stolte Manfred , Lind Tore , Malfertheiner Peter , Willich Stefan N
Published: July 2006

Background:  Overweight and obesity are believed to be risk factors for gastroesophageal reflux disease (GERD). The aim of the present study was to analyze the impact of body mass index (BMI) on the severity and frequency of reflux symptoms and esophagitis in a large cohort of reflux patients.

Methods:  As part of the Progression of Gastroesophageal Reflux Disease (ProGERD) study, 6215 patients with clinically assessed GERD were included in the present investigation (53% male, 52 ± 14 years; 47% female, 56 ± 14 years). Heartburn and regurgitation symptoms were assessed using the validated Reflux Disease Questionnaire. Endoscopies were performed and patients were subsequently classified as having non‐erosive or erosive disease. To examine the association between BMI, GERD symptoms, and esophagitis, odds ratios (OR) and 95% confidence intervals (95%CI) were calculated using logistic regression models.

Results:  In patients with GERD, higher BMI was associated with more frequent and more severe heartburn and regurgitation, as well as with esophagitis. The effects were more pronounced for regurgitation than for heartburn. The strongest association was between obesity and severity of regurgitation symptoms (women: OR 2.11, 95%CI 1.60–2.77; men: OR 2.15, 95%CI 1.59–2.90). Obese women, but not men, had an increased risk of severe esophagitis compared to women with normal weight (OR 2.51, 95%CI 1.53–4.12).

Conclusions:  In patients with GERD, higher BMI was associated with more severe and more frequent reflux symptoms and esophagitis.
Transient hyperphosphatasemia after pediatric liver transplantation
Authors: ARIKAN CIGDEM , ARSLAN MEHMET TAYYIP , KILIC MURAT , AYDOGDU SEMA
Published: July 2006

Background: Transient hyperphosphatasemia of infancy and early childhood is characterized by transiently increased serum activity of alkaline phosphatase (ALP), predominantly its bone or liver isoform, in children under 5 years of age. There is little information on the rate of transient hyperphosphatasemia in pediatric liver transplant recipients.

Methods: Patients who underwent liver transplantation at Ege University Organ Transplantation and Research Center, Izmir, Tureky, between January 1998 and January 2005, were included in the study. A total of 70 paediatric liver recipients’ medical records were analyzed retrospectively.

Results: Transient isolated hyperphosphatasemia was observed in two of 70 patients and the rate of transient hyperphosphatasemia was estimated to be 2.8% in pediatric liver transplant recipient. Diarrheal episode was noted prior to the peak ALP activity in both cases. In one case the causative agent was not found, whereas in the other case Rotavirus was detected in a stool specimen. ALP activity normalized at 4 months and 18 days in the first and second cases, respectively. They continue follow up at the outpatient clinics with stable graft function.

Conclusion: It is important to know that very high ALP levels can be seen without underlying significant pathology and the benign nature of the condition to avoid unnecessary investigations.