bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluxon-based gate controls of capacitively coupled flux-based-phase qubits
Authors: Matsuo Shigemasa , Furuta Kanoko , Fujii Toshiyuki , Nagai Katsuhiko , Hatakenaka Noriyuki
Published: August 2007

The authors propose a scheme for controlling the gate operation for qubit-qubit interactions in superconducting flux-based phase qubits using a moving fluxon. The basic unit is composed of three capacitively coupled flux-based phase qubits. One of the qubits acts as a switch connecting the other two (two logical qubits) with an identical energy separation. The fluxon controls the energy separation of the switch qubit via its inductive coupling, leading to the resonance among qubits appropriately adjusting the fluxon velocity. As a result, the resonance is capable of performing a gate operation between two logical qubits.
Homogeneous strain-relaxation effects in La0.67Ca0.33MnO3 films grown on NdGaO3
Authors: Seiro S. , Koller E. , Fasano Y. , Fischer Ø.
Published: August 2007

X-ray diffraction and transport measurements on a series of La0.67Ca0.33MnO3 films grown on (110)-cut NdGaO3 substrates are presented. Contrary to widespread belief assuming strain-free growth, this work shows the presence of strain in a 42nm film. On increasing thickness structural relaxation occurs, reaching a bulklike state for 500nm. No evidence of coexistence of strained and relaxed regions is found. The evolution of lattice parameters toward bulk values is accompanied by an increase of the metal-to-insulator transition temperature and a decrease of the polaron activation energy. Therefore, strain effects cannot always be neglected in La0.67Ca0.33MnO3 films grown on small-mismatch NdGaO3.
White light generation by frequency upconversion in Tm3+∕Ho3+∕Yb3+-codoped fluorolead germanate glass
Authors: Gouveia-Neto A. S. , Bueno L. A. , do Nascimento R. F. , da Silva E. A. , da Costa E. B. , do Nascimento V. B.
Published: August 2007

White light was produced exploiting an additive synthesis of red, green, and blue fluorescence through frequency upconversion in fluorolead-germanate glass codoped with Ho3+, Tm3+, and Yb3+. The 475, 540, and 650nm signals were, respectively, assigned to thulium (G41-H63) and holmium (S25;F45)→I85 and F55→I85, excited via energy tranfer from ytterbium. The dopant concentrations were adjusted, yielding the emission of a wide color gamut in the visible spectrum and the production of white light using excitation at 975nm. The spectral positions and purity (blue, 97%; green, 100%; red, 95%) of the three colors produced CIE-X=0.3438 and CIE-Y=0.3639 coordinates.
Er
2
O
3
as a high-K dielectric candidate
Authors: Losurdo Maria , Giangregorio Maria M , Bruno Giovanni , Yang Dongxing , Irene Eugene A. , Suvorova Alexandra A. , Saunders M.
Published: August 2007

Erbium oxide (Er2O3) films have been deposited by metal organic chemical vapor deposition on Si(001) using tris(isopropylcyclopentadienyl)erbium. The impact of Si surface passivation by the metal organic prior growth initiation was investigated. The correlation between the Er2O3 films structure, the optical response, the static dielectric constant (K), and density of interface traps is discussed. An Er-silicate interfacial layer with a thickness of 1.5nm, a static dielectric constant of 10–12.4, and a density of interface traps of 4.2×1010cm2eV−1 measured for a film with a physical thickness of 8.2nm (with an equivalent oxide thickness of 2.7nm) render Er2O3 an interesting candidate as a high-K dielectric.
Dopant position in Ti-doped high-temperature phase Ta2O5: First principles study
Authors: Zhang R. Z. , Wang C. L. , Li J. C. , Zhang J. L. , Yang K. , Zhang C. , Chen H. M.
Published: August 2007

The ab initio calculation and bond valence model (BVM) are employed to investigate dopant occupancy in the Ti-doped high-temperature phase Ta2O5. In this structure, there are two types of Ta atoms, which the authors denote as Ta1 locating inside oxygen octahedral and Ta2 locating inside oxygen decahedral. The 5d state electron configuration of Ta1 and Ta2 is different, the hybridization between Ta1 5d state and O 2p state is stronger than that between Ta2 and O. The chemical bonding between Ta and oxygen ions is mainly covalent. However, there is an increase of the covalent character in going from Ta1–O bond to Ta2–O bond. Both total energy method and BVM indicate that Ti substituting Ta1 is energy favorable, and this maybe due to different electronic structures of Ta1 and Ta2.
Initial stages of chain formation in a single layer of (In,Ga)As quantum dots grown on GaAs (100)
Authors: Schmidbauer M. , Wang Zh. M. , Mazur Yu. I. , Lytvyn P. M. , Salamo G. J. , Grigoriev D. , Schäfer P. , Köhler R. , Hanke M.
Published: August 2007

The self-organized formation of In0.40Ga0.60As quantum dot chains was investigated using x-ray scattering. Two samples were compared grown on GaAs(100) by molecular beam epitaxy. The first sample with a single layer of In0.40Ga0.60As dots shows weak quantum dot alignment and a corresponding elongated shape along [01¯1], while the top layer of a multilayered In0.40Ga0.60As∕GaAs sample exhibits extended and highly regular quantum dot chains oriented along [01¯1]. Numerical calculations of the three-dimensional strain fields are used to explain the initial stages of chain formation by anisotropic strain relaxation induced by the elongated dot shape.
Enhanced electromagnetic wave absorption properties of Fe nanowires in gigaherz range
Authors: Liu Jiu-rong , Itoh Masahiro , Terada Masao , Horikawa Takashi , Machida Ken-ichi
Published: August 2007

Fe nanowires with 70–200nm in diameter and 20–50μm in length were synthesized by a chemical vapor deposition method for electromagnetic wave absorption application. The frequency dependences of relative permittivity (εr) and permeability (μr) were strongly dependent on the diameter of Fe wires. Compared with micrometer wires or flakelike samples, nanowires exhibited a magnetic resonance (μr″) peak in the range of 1–18GHz, suggesting that nanowires have significant effect for reducing the eddy current loss, therefore, the resin compacts of 29vol% Fe nanowires with thicknesses of 1.3–4.0mm provided good electromagnetic wave absorption performances in the range of 5.6–18GHz.
Localized, low-voltage electro-osmotic pumping across nanoporous membranes
Authors: Gupta A. , Denver H. , Hirsa A. H. , Stenken J. A. , Borca-Tasciuc D.-A.
Published: August 2007

This work demonstrates the principle of localized, low-voltage, continuous current electro-osmotic pumping across thin membranes. Localization of the pumping effect is obtained by employing ring electrodes, microfabricated on each side of nanoporous alumina membranes. Low voltage actuation is achieved by having the separation of the two electrodes in the microscale range—the thickness of the membrane. The measured electro-osmotic velocity increases linearly from 40μm∕s at 5V to 200μm∕s at 20V. Experimental results compare well with predictions of an electro-osmotic flow model considering the nonuniform distribution of the electric field between the electrodes.
Thermal gate SiO2 for Ge metal-oxide-semiconductor capacitors fabricated on Si substrate
Authors: Wu Yung-Hsien , Wu Jia-Rong , Wu Min-Lin
Published: August 2007

With the Si substrate, a process to fabricate Ge metal-oxide-semiconductor (MOS) capacitors with thermally grown SiO2 as the gate dielectric has been presented. The good crystallinity of the epitaxial Ge, the thermal oxide with tiny Ge content, and the smooth interface between oxide and Ge layer demonstrate the eligibility for device operation. From the electrical characterization of the MOS capacitors, enhanced dielectric constant of the gate oxide without deteriorating the leakage current and hysteresis can be achieved by proper NH3 nitridation and subsequent N2O treatment which shows the high potential to be employed in the fabrication of high performance Ge metal-oxide-semiconductor field-effect transist.
Joining patch-clamp and atomic force microscopy techniques for studying black lipid bilayers
Authors: Ovalle-García Erasmo , Ortega-Blake Iván
Published: August 2007

An experimental protocol that enables the direct characterization of freestanding lipid bilayers through a combination of atomic force microscopy and single channel recording is presented. The method consists of producing a 15μm diameter pore in a 3μm thick Mylar film that delimits two vessels. The micropore was done by a glass microneedle. L-α-phosphatidylcholine bilayers were routinely painted on the pore, observed by atomic force microscopy, and tested with gramicidin D ion channels.
Role of defect states on Auger processes in resonantly pumped CdSe nanorods
Authors: Cretí Arianna , Anni Marco , Zavelani Rossi Margherita , Lanzani Guglielmo , Manna Liberato , Lomascolo Mauro
Published: August 2007

The authors investigated, by femtosecond pump-probe measurements, the effects on Auger and trapping processes of excitation resonant (R) to the 1S absorption in CdSe nanorods. They demonstrate that R pumping allows one to avoid exciton trapping in high energy defect states and that the presence of empty defect states leads to an enhancement of the Auger relaxation, with respect to the pumping at energies high above the band gap. Moreover, they show that, despite the Auger enhancement, R pumping increases the stimulated emission lifetime demonstrating that it is not limited by Auger scattering, as widely believed, but by photoabsorption processes, involving defect states.
Neoliberalising Nature: Processes, Effects, and Evaluations
Authors: Castree Noel
Published: August 2007

This and a previous paper review systematically a new and fast-growing geographical research literature about ‘neoliberalising nature’. This literature, authored by critical geographers for the most part, is largely case study based and focuses on a range of biophysical phenomena in different parts of the contemporary world. In an attempt to take stock of what has been learnt and what is left to do, the two papers survey the literature theoretically and empirically, cognitively and normatively. Specifically, they aim to parse the critical literature on nature's neoliberalisation with a view to answering four key questions: (1) what are the reasons why all manner of qualitatively different nonhuman phenomena in different parts of the world are being ‘neoliberalised’? (2) what are the principal ways in which nature is neoliberalised in practice? (3) what are the effects of nature's neoliberalisation? and (4) how should these effects be evaluated? Without such an effort of synthesis, this literature could remain a collection of substantively disparate, theoretically informed case studies unified only in name (by virtue of their common focus on ‘neoliberal’ policies). This paper addresses questions 2, 3, and 4, while the previous paper concentrated on the first. It is argued that some unresolved issues in the published literature make it very difficult for readers and future researchers in this area to draw ‘wider’ lessons about process, effects, and evaluations. This is not so much a ‘failing’ of the literature as a reflection of its newness and the way its constituent parts have evolved. It is argued that these issues require careful attention in future so that the ‘general’ lessons of the literature published to date on nature's neoliberalisation can be made clear. Where the previous paper detected some ‘signals in the noise’ viz question 1, this paper suggests that more work needs to be done viz questions 2 to 4 for any signals to be detected.
Rethinking Sustainable Urban Regeneration: Ambiguity, Creativity, and the Shared Territory
Authors: Evans James , Jones Phil
Published: August 2007

Despite its broad definition, the concept of sustainability has become central to regeneration policy in the UK. A growing body of research, however, suggests that the policy goals of urban regeneration and sustainable development are not being integrated in practice. Ambiguity surrounding what ‘sustainability’ actually means is often cited as the reason why projects fail to achieve policy goals. We seek to make an innovative contribution to this debate, arguing that sustainability does make a positive difference in practice, and that it is necessary to develop approaches that capture these ‘actually existing sustainabilities’. Using a detailed case study of a multistakeholder regeneration project, we develop a more positive analysis of the role which ambiguity plays in the development process. We advance a dialogic conception of sustainability based upon Michel Bakhtin's sociolinguistic theory of the word as a ‘shared territory’. We suggest that the notion of sustainability acts as a shared territory for meaning around which diverse stakeholder groups coalesce, and show how the ambiguity inherent in this shared conception can generate more creative (and sustainable) outcomes to developmental challenges. Viewing sustainability as a shared territory makes ambiguity not only intelligible, but also desirable to the development process, and it is argued that there is a need to avoid the reduction of sustainability to the assessment of predetermined benchmarks or policy goals, both within the regeneration literature and across studies of planning policy and practice more generally.
Expertise and Scientific Uncertainty: Understanding Trust Amongst Professional Stakeholders in Environment and Health
Authors: Dunn Christine E , Crowley Philip , Bush Judith , Pless-Mulloli Tanja , McKinney Patricia A
Published: August 2007

There is a substantial literature on notions of public trust in relation to risks from environmental and technological hazards. Rather less work has sought to explore trust in terms of professional interstakeholder relations in this context. Drawing on a case study for northern England, we consider dimensions of trust amongst those with a ‘professional’ involvement in the arena of environmental hazards and public health. We explore specifically the interrelated themes of scientific uncertainty and expertise, which were central to the shaping of trust relations. Against a background of indeterminacy in the scientific search for causality in environment–health relationships, the empirical work on which the paper is based is also set in a context of change and insecurity in organisational terms. The notion of ‘independence’ was brought into question through aspects of role demarcation while concerns about levels of expertise were superimposed with a sense of exclusion of community groups from ‘official’ environment–health debates. We argue that a simple deficit approach was being adopted on the part of salaried professionals towards community involvement in such debates.
Technology Incubators and Knowledge Networks: A Rough Set Approach in Comparative Project Analysis
Authors: Soetanot Danny P , van Geenhuizen Marina
Published: August 2007

Technology incubators have emerged in many places as a tool in facilitating the establishment and survival of high-technology firms. Some incubators develop quickly and produce a fast-increasing number of new ventures, while others remain stable in size. Despite a growing public investment in technology incubators, systematic studies of the factors determining their growth are scarce, meaning that policy decisions are taken without sufficient practical insights into critical conditions for growth. In response to that situation, we explore several factors in determining differences in growth patterns. We use a quantitative approach derived from the field of artificial intelligence that matches with meta-analysis and qualitative (and sometimes fuzzy) data—that is, rough set analysis. Benefits and challenges of rough set analysis are discussed, including experience with a stepwise procedure with various accuracy checks. The findings suggest that a strong performance of incubators mainly rests on diversity in stakeholder involvement and a location in nonmetropolitan areas. Rough set analysis turns out to be a helpful tool in comparative project analysis, but there is still a need for standardization of measures used in the interpretation of the results.
Perceived Health Contributes to the Attractiveness of Facial Symmetry, Averageness, and Sexual Dimorphism
Authors: Rhodes Gillian , Yoshikawa Sakiko , Palermo Romina , Simmons Leigh W , Peters Marianne , Lee Kieran , Halberstadt Jamin , Crawford John R
Published: August 2007

Symmetry, averageness, and sexual dimorphism (femininity in female faces, masculinity in male faces) are attractive in faces. Many have suggested that preferences for these traits may be adaptations for identifying healthy mates. If they are, then the traits should be honest indicators of health and their attractiveness should result from their healthy appearance. Much research has focused on whether these traits honestly signal health. Here we focused on whether the appeal of these traits results from their healthy appearance. Specifically, we tested whether the attractiveness of symmetry, averageness, and sexual dimorphism is reduced or eliminated when perceived health is controlled, in two large samples of Western faces and a large sample of Japanese faces. The appeal of symmetric faces was largely due to their healthy appearance, with most associations between symmetry and attractiveness eliminated when perceived health was controlled. A healthy appearance also contributed to the appeal of averageness and femininity in female faces and masculinity in male faces, although it did not fully explain their appeal. These results show that perceptions of attractiveness are sensitive to a healthy appearance, and are consistent with the hypothesis that preferences may be adaptations for mate choice.
Spatial regulation of Raf kinase signaling by RKTG
Authors: Feng Lin , Xie Xiaoduo , Ding Qiurong , Luo Xiaolin , He Jing , Fan Fengjuan , Liu Weizhong , Wang Zhenzhen , Chen Yan
Published: August 2007

Subcellular compartmentalization has become an important theme in cell signaling such as spatial regulation of Ras by RasGRP1 and MEK/ERK by Sef. Here, we report spatial regulation of Raf kinase by RKTG (Raf kinase trapping to Golgi). RKTG is a seven-transmembrane protein localized at the Golgi apparatus. RKTG expression inhibits EGF-stimulated ERK and RSK phosphorylation, blocks NGF-mediated PC12 cell differentiation, and antagonizes Ras- and Raf-1-stimulated Elk-1 transactivation. Through interaction with Raf-1, RKTG changes the localization of Raf-1 from cytoplasm to the Golgi apparatus, blocks EGF-stimulated Raf-1 membrane translocation, and reduces the interaction of Raf-1 with Ras and MEK1. In RKTG-null mice, the basal ERK phosphorylation level is increased in the brain and liver. In RKTG-deleted mouse embryonic fibroblasts, EGF-induced ERK phosphorylation is enhanced. Collectively, our results reveal a paradigm of spatial regulation of Raf kinase by RKTG via sequestrating Raf-1 to the Golgi apparatus and thereby inhibiting the ERK signaling pathway.
Dichotomy and perceptual distortions in absolute pitch ability
Authors: Athos E. Alexandra , Levinson Barbara , Kistler Amy , Zemansky Jason , Bostrom Alan , Freimer Nelson , Gitschier Jane
Published: August 2007

Absolute pitch (AP) is the rare ability to identify the pitch of a tone without the aid of a reference tone. Understanding both the nature and genesis of AP can provide insights into neuroplasticity in the auditory system. We explored factors that may influence the accuracy of pitch perception in AP subjects both during the development of the trait and in later age. We used a Web-based survey and a pitch-labeling test to collect perceptual data from 2,213 individuals, 981 (44%) of whom proved to have extraordinary pitch-naming ability. The bimodal distribution in pitch-naming ability signifies AP as a distinct perceptual trait, with possible implications for its genetic basis. The wealth of these data has allowed us to uncover unsuspected note-naming irregularities suggestive of a “perceptual magnet” centered at the note “A.” In addition, we document a gradual decline in pitch-naming accuracy with age, characterized by a perceptual shift in the “sharp” direction. These findings speak both to the process of acquisition of AP and to its stability.
Risky prey behavior evolves in risky habitats
Authors: Urban Mark C.
Published: August 2007

Longstanding theory in behavioral ecology predicts that prey should evolve decreased foraging rates under high predation threat. However, an alternative perspective suggests that growth into a size refuge from gape-limited predation and the future benefits of large size can outweigh the initial survival costs of intense foraging. Here, I evaluate the relative contributions of selection from a gape-limited predator (
Ambystoma opacum
) and spatial location to explanations of variation in foraging, growth, and survival in 10 populations of salamander larvae (
Ambystoma maculatum
). Salamander larvae from populations naturally exposed to intense
A. opacum
predation risk foraged more actively under common garden conditions. Higher foraging rates were associated with low survival in populations exposed to free-ranging
A. opacum
larvae. Results demonstrate that risky foraging activity can evolve in high predation-risk habitats when the dominant predators are gape-limited. This finding invites the further exploration of diverse patterns of prey foraging behavior that depends on natural variation in predator size-selectivity. In particular, prey should adopt riskier behaviors under predation threat than expected under existing risk allocation models if foraging effort directly reduces the duration of risk by growth into a size refuge. Moreover, evidence from this study suggests that foraging has evolved over microgeographic scales despite substantial modification by regional gene flow. This interaction between local selection and spatial location suggests a joint role for adaptation and maladaptation in shaping species interactions across natural landscapes, which is a finding with implications for dynamics at the population, community, and metacommunity levels.
The synthesis and
in vitro
testing of a zinc-activated MRI contrast agent
Authors: Major Jody L. , Parigi Giacomo , Luchinat Claudio , Meade Thomas J.
Published: August 2007

Zinc(II) plays a vital role in normal cellular function as an essential component of numerous enzymes, transcription factors, and synaptic vesicles. While zinc can be linked to a variety of physiological processes, the mechanisms of its cellular actions are less discernible. Here, we have synthesized and tested a Zn(II)-activated magnetic resonance imaging (MRI) contrast agent in which the coordination geometry of the complex rearranges upon binding of Zn(II). In the absence of Zn(II) water is restricted from binding to a chelated Gd(III) ion by coordinating acetate arms resulting in a low relaxivity of 2.33 mM
−1
·s
−1
at 60 MHz. Upon addition of Zn(II) the relaxivity of the Gd(III)–Zn(II) complex increases to 5.07 mM
−1
·s
−1
and is consistent with one water molecule bound to Gd(III). These results were confirmed by nuclear magnetic relaxation dispersion analysis. There was no observed change in relaxivity of the Gd(III) complex when physiologically competing cations Ca(II) and Mg(II) were added. A competitive binding assay gave a dissociation constant of 2.38 × 10
−4
M for the Gd(III)–Zn(II) complex.
In vitro
magnetic resonance images confirm that Zn(II) concentrations as low as 100 μM can be detected by using this contrast agent.
An extracellular region of the erythropoietin receptor of the subterranean blind mole rat
Spalax
enhances receptor maturation
Authors: Ravid Orly , Shams Imad , Ben Califa Nathalie , Nevo Eviatar , Avivi Aaron , Neumann Drorit
Published: August 2007

Erythropoietic functions of erythropoietin (EPO) are mediated by its receptor (EPO-R), which is present on the cell surface of erythroid progenitors and induced by hypoxia. We focused on EPO-R from
Spalax galili
(sEPO-R), one of the four Israeli species of the subterranean blind mole rat,
Spalax ehrenbergi
superspecies, as a special natural animal model of high tolerance to hypoxia. Led by the intriguing observation that most of the mouse EPO-R (mEPO-R) is retained in the endoplasmic reticulum (ER), we hypothesized that sEPO-R is expressed at higher levels on the cell surface, thus maximizing the response to elevated EPO, which has been reported in this species. Indeed, we found increased cell-surface levels of sEPO-R as compared with mEPO-R by using flow cytometry analysis of BOSC cells transiently expressing HA-tagged EPO-Rs (full length or truncated). We then postulated that unique extracellular sEPO-R sequence features contribute to its processing and cell-surface expression. To map these domains of the sEPO-R that augment receptor maturation, we generated EPO-R derivatives in which parts of the extracellular region of mEPO-R were replaced with the corresponding fragments of sEPO-R. We found that an extracellular portion of sEPO-R, harboring the N-glycosylation site, conferred enhanced maturation and increased transport to the cell surface of the respective chimeric receptor. Taken together, we demonstrate higher surface expression of sEPO-R, attributed at least in part to increased ER exit, mediated by an extracellular region of this receptor. We speculate that these sEPO-R sequence features play a role in the adaptation of
Spalax
to extreme hypoxia.
Blood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockade
Authors: Allantaz Florence , Chaussabel Damien , Stichweh Dorothee , Bennett Lynda , Allman Windy , Mejias Asuncion , Ardura Monica , Chung Wendy , Smith Elisabeth , Wise Carol , Palucka Karolina , Ramilo Octavio , Punaro Marilynn , Banchereau Jacques , Pascual Virginia
Published: August 2007

Systemic onset juvenile idiopathic arthritis (SoJIA) represents up to 20% of juvenile idiopathic arthritis. We recently reported that interleukin (IL) 1 is an important mediator of this disease and that IL-1 blockade induces clinical remission. However, lack of specificity of the initial systemic manifestations leads to delays in diagnosis and initiation of therapy. To develop a specific diagnostic test, we analyzed leukocyte gene expression profiles of 44 pediatric SoJIA patients, 94 pediatric patients with acute viral and bacterial infections, 38 pediatric patients with systemic lupus erythematosus (SLE), 6 patients with PAPA syndrome, and 39 healthy children. Statistical group comparison and class prediction identified genes differentially expressed in SoJIA patients compared with healthy children. These genes, however, were also changed in patients with acute infections and SLE. An analysis of significance across all diagnostic groups identified 88 SoJIA-specific genes, 12 of which accurately classified an independent set of SoJIA patients with systemic disease. Transcripts that changed significantly in patients undergoing IL-1 blockade were also identified. Thus, leukocyte transcriptional signatures can be used to distinguish SoJIA from other febrile illnesses and to assess response to therapy. Availability of early diagnostic markers may allow prompt initiation of therapy and prevention of disabilities.
TMpro web server and web service: transmembrane helix prediction through amino acid property analysis
Authors: Ganapathiraju Madhavi , Jursa Christopher Jon , Karimi Hassan A. , Klein-Seetharaman Judith
Published: August 2007

Summary: TMpro is a transmembrane (TM) helix prediction algorithm that uses language processing methodology for TM segment identification. It is primarily based on the analysis of statistical distributions of properties of amino acids in transmembrane segments. This article describes the availability of TMpro on the internet via a web interface. The key features of the interface are: (i) output is generated in multiple formats including a user-interactive graphical chart which allows comparison of TMpro predicted segment locations with other labeled segments input by the user, such as predictions from other methods. (ii) Up to 5000 sequences can be submitted at a time for prediction. (iii) TMpro is available as a web server and is published as a web service so that the method can be accessed by users as well as other services depending on the need for data integration.

Availability:  http://linzer.blm.cs.cmu.edu/tmpro/ (web server and help), http://blm.sis.pitt.edu:8080/axis/services/TMProFetcherService (web service)

Contact:  judithks@cs.cmu.edu or jks33@pitt.edu
Identification of compositionally distinct regions in genomes using the centroid method
Authors: Rajan Issaac , Aravamuthan Sarang , Mande Sharmila S.
Published: August 2007

Motivation: It is known that most genomic regions of special interest, e.g. horizontally acquired sequences, genomic islands, etc. have distinct word (m-mer) compositions. Most of the earlier work along this direction, addressed di- and tri-nucleotide compositions. We present an approach that can be applied to analyze compositions of any given word size. The method, called the centroid approach, can reveal compositionally distinct regions in genomic sequences for any given word size.

Results: We applied our method to 50 bacterial genomes and demonstrated its ability to identify embedded sequences of varying lengths from distantly related organisms. We also investigated the genetic makeup of the regions identified as compositionally distinct by our method, for four organisms from our dataset. Pathogenicity island (PAI) components and genes encoding strain-specific proteins are all frequently seen to be constituents of these regions.

Availability: Program is available on request from the authors.

Contact:  sharmila@atc.tcs.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Fourth Joint Task Force of the European Society of Cardiology and other Societies on Cardiovascular Disease Prevention in Clinical Practice (constituted by representatives of nine societies and by invited experts)
Authors: Graham Ian , Atar Dan , Borch-Johnsen Knut , Boysen Gudrun , Burell Gunilla , Cifkova Renata , Dallongeville Jean , Backer Guy De , Ebrahim Shah , Gjelsvik Bjørn , Herrmann-Lingen Christoph , Hoes Arno , Humphries Steve , Knapton Mike , Perk Joep , Priori Silvia G. , Pyorala Kalevi , Reiner Zeljko , Ruilope Luis , Sans-Menendez Susana , Op Reimer Wilma Scholte , Weissberg Peter , Wood David , Yarnell John , Jose Luis Zamorano
Published: August 2007

Other experts who contributed to parts of the guidelines: Edmond Walma, Tony Fitzgerald, Marie Therese Cooney, Alexandra Dudina

European Society of Cardiology (ESC) Committee for Practice Guidelines (CPG): Alec Vahanian (Chairperson), John Camm, Raffaele De Caterina, Veronica Dean, Kenneth Dickstein, Christian Funck-Brentano, Gerasimos Filippatos, Irene Hellemans, Steen Dalby Kristensen, Keith McGregor, Udo Sechtem, Sigmund Silber, Michal Tendera, Petr Widimsky, Jose Luis Zamorano

Document reviewers: Irene Hellemans (CPG Review Co-ordinator), Attila Altiner, Enzo Bonora, Paul N. Durrington, Robert Fagard, Simona Giampaoli, Harry Hemingway, Jan Hakansson, Sverre Erik Kjeldsen, Mogens Lytken Larsen, Giuseppe Mancia, Athanasios J. Manolis, Kristina Orth-Gomer, Terje Pedersen, Mike Rayner, Lars Ryden, Mario Sammut, Neil Schneiderman, Anton F. Stalenhoef, Lale Tokgözoglu, Olov Wiklund, Antonis Zampelas
The role of conservation agriculture in sustainable agriculture
Authors: Hobbs Peter R , Sayre Ken , Gupta Raj
Published: August 2007

The paper focuses on conservation agriculture (CA), defined as minimal soil disturbance (no-till, NT) and permanent soil cover (mulch) combined with rotations, as a more sustainable cultivation system for the future. Cultivation and tillage play an important role in agriculture. The benefits of tillage in agriculture are explored before introducing conservation tillage (CT), a practice that was borne out of the American dust bowl of the 1930s. The paper then describes the benefits of CA, a suggested improvement on CT, where NT, mulch and rotations significantly improve soil properties and other biotic factors. The paper concludes that CA is a more sustainable and environmentally friendly management system for cultivating crops. Case studies from the rice–wheat areas of the Indo-Gangetic Plains of South Asia and the irrigated maize–wheat systems of Northwest Mexico are used to describe how CA practices have been used in these two environments to raise production sustainably and profitably. Benefits in terms of greenhouse gas emissions and their effect on global warming are also discussed. The paper concludes that agriculture in the next decade will have to sustainably produce more food from less land through more efficient use of natural resources and with minimal impact on the environment in order to meet growing population demands. Promoting and adopting CA management systems can help meet this goal.
Marker-assisted selection: an approach for precision plant breeding in the twenty-first century
Authors: Collard Bertrand C.Y , Mackill David J
Published: August 2007

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker–trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.
The legacy of harvest and fire on ecosystem carbon storage in a north temperate forest
Authors: GOUGH CHRISTOPHER M. , VOGEL CHRISTOPH S. , HARROLD KATHERINE H. , GEORGE KRISTEN , CURTIS PETER S.
Published: August 2007

Forest harvesting and wildfire were widespread in the upper Great Lakes region of North America during the early 20th century. We examined how long this legacy of disturbance constrains forest carbon (C) storage rates by quantifying C pools and fluxes after harvest and fire in a mixed deciduous forest chronosequence in northern lower Michigan, USA. Study plots ranged in age from 6 to 68 years and were created following experimental clear‐cut harvesting and fire disturbance. Annual C storage was estimated biometrically from measurements of wood, leaf, fine root, and woody debris mass, mass losses to herbivory, soil C content, and soil respiration. Maximum annual C storage in stands that were disturbed by harvest and fire twice was 26% less than a reference stand receiving the same disturbance only once. The mechanism for this reduction in annual C storage was a long‐lasting decrease in site quality that endured over the 62‐year timeframe examined. However, during regrowth the harvested and burned forest rapidly became a net C sink, storing 0.53 Mg C ha−1 yr−1after 6 years. Maximum net ecosystem production (1.35 Mg C ha−1 yr−1) and annual C increment (0.95 Mg C ha−1 yr−1) were recorded in the 24‐ and 50‐year‐old stands, respectively. Net primary production averaged 5.19 Mg C ha−1 yr−1in experimental stands, increasing by < 10% from 6 to 50 years. Soil heterotrophic respiration was more variable across stand ages, ranging from 3.85 Mg C ha−1 yr−1in the 6‐year‐old stand to 4.56 Mg C ha−1 yr−1in the 68‐year‐old stand. These results suggest that harvesting and fire disturbances broadly distributed across the region decades ago caused changes in site quality and successional status that continue to limit forest C storage rates.
Age‐related histopathological lesions in the Mongolian gerbil ventral prostate as a good model for studies of spontaneous hormone‐related disorders
Authors: Campos Silvana Gisele Pegorin , Zanetoni Cristiani , Scarano Wellerson Rodrigo , Vilamaior Patrícia Simone Leite , Taboga Sebastião Roberto
Published: August 2007

The Meriones unguiculatus (Mongolian) gerbil has demonstrated significant prostatic responses to hormonal treatments, and to drugs against human prostatic hyperplasia Spontaneous neoplasia develops in the older animals. Thirty gerbils (age 18 months) were divided into non‐affected and prostatic lesion bearers and the prostate lesions were evaluated morphologically, immunohistochemically and quantitatively. The most frequent changes were in epithelial sites and, namely prostatic intraepithelial neoplasias, microinvasive carcinomas and adenocarcinomas. In the stromal compartment, cellular hyperplasia, when verified, was always associated with the sites of anomalous epithelium. Additionally, larger deposition of collagen fibrils, generating stromal fibrosis, was found in all the old gerbils analysed. The quantitative analysis showed that prostatic tissue proportions differed in altered areas, being specific for each lesion type. Isolated nuclear and nucleolar parameters were not effective in diagnosing the malign potential of lesions. However, the cellular proliferation and death indexes indicated larger cellular turnover in invasive lesions such as carcinomas. With these analyses, it could be verified that old gerbils present high propensity to develop spontaneous prostate changes and this may aid in a better understanding of the biological behaviour of human prostate cancer.
Protein metabolism in slow‐ and fast‐twitch skeletal muscle during turpentine‐induced inflammation
Authors: Muthny Tomas , Kovarik Miroslav , Sispera Ludek , Tilser Ivan , Holecek Milan
Published: August 2007

The aim of our study was to evaluate the differences in protein and amino acid metabolism after subcutaneous turpentine administration in the soleus muscle (SOL), predominantly composed of red fibres, and the extensor digitorum longus muscle (EDL) composed of white fibres. Young rats (40–60 g) were injected subcutaneously with 0.2 ml of turpentine oil/100 g body weight (inflammation) or with the same volume of saline solution (control). Twenty‐four hours later SOL and EDL were dissected and incubated in modified Krebs–Heinseleit buffer to estimate total and myofibrillar proteolysis, chymotrypsin‐like activity of proteasome (CHTLA), leucine oxidation, protein synthesis and amino acid release into the medium. The data obtained demonstrate that in intact rats, all parameters measured except protein synthesis are significantly higher in SOL than in EDL. In turpentine treated animals, CHTLA increased and protein synthesis decreased significantly more in EDL. Release of leucine was inhibited significantly more in SOL. We conclude that turpentine‐induced inflammation affects more CHTLA, protein synthesis and leucine release in EDL compared to SOL.
TECHNICAL ADVANCE: Free‐flow electrophoresis for purification of plant mitochondria by surface charge
Authors: Eubel Holger , Lee Chun Pong , Kuo John , Meyer Etienne H. , Taylor Nicolas L. , Millar A. Harvey
Published: August 2007

Sample purity is the key for a successful in‐depth analysis of any given subcellular proteome. The suitability of free‐flow electrophoresis to assist conventional, centrifugation‐based techniques in the preparation of plant mitochondria from green and non‐green tissue was assessed by various means, including functional assays, immunoblots, electron microscopy and differential gel electrophoresis. Results indicated a significant increase in purity of the mitochondrial samples, highlighted specific contaminants previously reported as mitochondrial proteins, and also pointed to new means for separating plastids and peroxisomes from mitochondria in plant organellar extracts by exploiting differences in surface charge. This approach has the potential to allow a deeper and more comprehensive investigation of the Arabidopsis organellar proteomes, by providing a second dimension of separation based on surface charge in addition to conventional centrifugation purification protocols relying on size and density.
Dihydrodipicolinate reductase‐like protein, CRR1, is essential for chloroplast NAD(P)H dehydrogenase in Arabidopsis
Authors: Shimizu Hideyuki , Shikanai Toshiharu
Published: August 2007

Chloroplast NAD(P)H dehydrogenase (NDH) is a homolog of the bacterial NADH dehydrogenase NDH‐1 and is involved in cyclic electron transport around photosystem I. In higher plants, 14 subunits of the NDH complex have been identified. The subunit that contains the electron donor‐binding site or an electron donor to NDH has not been determined. Arabidopsis crr1 (chlororespiratory reduction 1) mutants were isolated by chlorophyll fluorescence imaging on the basis of their lack of NDH activity. CRR1 is homologous to dihydrodipicolinate reductase (DHPR), which functions in a lysine biosynthesis pathway. However, the dihydrodipicolinate‐binding motif was not conserved in CRR1, and the crr1 defect was specific to accumulation of the NDH complex, implying that CRR1 is not involved in lysine biosynthesis in Arabidopsis. Similarly to other nuclear‐encoded genes for NDH subunits, CRR1 was expressed only in photosynthetic tissue. CRR1 contained a NAD(P)H‐binding motif and was a candidate electron donor‐binding subunit of the NDH complex. However, CRR1 was detected in the stroma but not in the thylakoid membranes, where the NDH complex is localized. Furthermore, CRR1 was stable in crr2‐2 lacking the NDH complex. These results suggest that CRR1 is involved in biogenesis or stabilization of the NDH complex, possibly via the reduction of an unknown substrate.
Treatment of inherited protein C deficiency by replacement therapy with the French purified plasma‐derived protein C concentrate (PROTEXEL®)
Authors: Dreyfus M. , Ladouzi A. , Chambost H. , Gruel Y. , Tardy B. , Ffrench P. , Bridey F. , Tellier Z. ,   the PROTEXEL® study group
Published: August 2007

Background/Objectives  A multicentre retrospective study was performed to assess the efficacy/safety of a French purified plasma‐derived protein C (PC) concentrate in inherited PC deficiency.

Materials and Methods  Nine patients were enrolled, five children aged < 5 weeks, among whom four with a severe deficiency were homozygous, and four patients < 37 years with PC levels ranging 14–25%, including one compound heterozygous.

Results  Thirty replacement therapy courses were recorded with mean PC dosages ranging between 24–90 IU/kg/day for prophylactic courses and 51–209 IU/kg/day for treatment courses. Recoveries varied between 0·8 and 1·12% IU/kg in preventive situations and between 1·09 and 1·91% IU/kg for treatment courses; 23 treatment courses were performed in patients aged 1 day to 18 years, 19 out of 23 treatments resulted in complete recovery with no sequelae. Treatment efficacy was difficult to assess in four out of 23 cases because the thrombotic event was not confirmed in one case and due to late treatment initiation in the three other cases. Seven prophylactic treatments were used either in association of vitamin K antagonists or to prevent thrombotic events due to vitamin K antagonist introduction or withdrawal. The safety assessed during 914 infusions was excellent. No abnormal bleeding was reported, including with high doses, during surgery, with heparin therapy.

Conclusions  Replacement therapy with this French PC concentrate is safe and effective in patients with inherited PC deficiency.
Prevalence of and risk factors for gallbladder polyps detected by ultrasonography among healthy Chinese: Analysis of 34 669 cases
Authors: Lin Wey‐Ran , Lin Deng‐Yn , Tai Dar‐In , Hsieh Sen‐Yung , Lin Chun‐Yen , Sheen I‐Shyan , Chiu Cheng‐Tang
Published: August 2007

Background and Aim:  Gallbladder (GB) polyps are tumor or tumor‐like projections arising from GB mucosa. Although most polyps are benign, some early GB carcinomas present as polypoid lesions. The diagnosis of GB polyps is relatively easy by ultrasonography. Although numerous studies have investigated GB polyps, few studies have addressed the prevalence of and factors associated with GB polyps for specific ethnic populations. This study analyzes the prevalence and factors associated with GB polyps in a Chinese population who can afford a paid general checkup.

Methods:  The prevalence of and risk factors for GB polyps diagnosed by ultrasonography were retrospectively investigated in 34 669 Chinese patients who underwent a general checkup at Chang Gung Memorial Hospital (Taipei, Taiwan) between 2000 and 2003. Demographic, hemogram, serum biochemistry, hepatitis B surface antigen, hepatitis C antibody, and ultrasonography study data was available for all the patients. The correlations between the prevalence of GB polyps and age, sex, body height, body weight, body mass index, hemogram, serum biochemistry, and viral markers were examined for all the patients.

Results:  Excluding the patients who underwent cholecystectomy, the overall prevalence of GB polyps was 9.5% and highest for middle‐aged males. The analyzed risk factors with increased odds ratios (OR) for the development of GB polyps were male sex (OR 0.646, P < 0.0005) and hepatitis B virus surface antigen positivity (OR 1.113, P < 0.0005). Other demographic characteristics and biochemical parameters, including body height, body weight, body mass index, lipid profile, chronic hepatitis C virus infection, and liver function did not correlate with the presence of GB polyps.

Conclusion:  The prevalence of GB polyps among the Chinese in this study is higher than that reported for other populations. Chinese males and other patients with chronic hepatitis B viral infections have a high risk for developing GB polyps.
Functional hepatic recovery after xenotransplantation of cryopreserved fetal liver cells or soluble cell‐factor administration in a cirrhotic rat model: Are viable cells necessary?
Authors: Ochenashko Olga V , Nikitchenko Yurii V , Volkova Nataliya A , Mazur Svetlana P , Somov Alexander Y , Fuller Barry J , Petrenko Alexander Y
Published: August 2007

Background and Aim:  Chronic liver failure results in the decrease of the number of functioning hepatocytes. It dictates the necessity of using exogenous viable cells or/and agents that can stimulate hepatic regenerative processes. Fetal liver contains both hepatic and hematopoietic stem cells with high proliferative potential, which may replace damaged cells. Also, immature cells produce fetal‐specific factors which may support the injured liver. Our aim was to test the ability of human fetal liver cells and cell‐free fetal‐specific factors of non‐hepatic origin to stimulate recovery processes in an experimental model of carbon tetrachloride–induced cirrhosis in rats.

Methods:  Cirrhotic rats were intrasplenically injected with fetal liver cells (1 × 107 cells/0.3 mL medium) or cell‐free fetal‐specific factors (0.3 mL/1 mg protein). Control groups received medium alone. Serum indexes, hepatic functions, and morphology were evaluated for 15 days.

Result:  Human fetal liver cell transplantation was shown to abrogate the mortality of cirrhotic animals, to improve serum markers, and to restore liver mitochondrial function and detoxification. Morphological patterns of liver recovery were observed by histology. In comparison, an injection of fetal‐specific factors produced similar functional recovery, whilst a more limited liver regeneration was observed by histology.

Conclusions:  The positive effects of fetal liver cell and cell‐free fetal‐specific factors in experimental cirrhosis may result from the presence of stage‐specific factors activating hepatocellular repair.