bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-eddy simulation of a curved open-channel flow over topography
Authors: van Balen W. , Uijttewaal W. S. J. , Blanckaert K.
Published: July 2010

Large-eddy simulation (LES) is performed of a curved open-channel flow over topography based on the laboratory experiment by Blanckaert [“Topographic steering, flow circulation, velocity redistribution and bed topography in sharp meander bends,” Water Resour. Res., doi:10.1029/2009WR008303 (in press)]. In the experiment, the large-scale bed topography had developed to a more or less stationary shape which was prescribed in the LES model as boundary conditions neglecting the small-scale dune forms by means of a straightforward immersed boundary scheme in combination with a simple wall-modeling approach. The small-scale dunes are accounted for in the numerical model by means of parametrization. Sensitivity of the flow to this roughness parametrization is examined by simulating the flow for three different roughness heights. It was found that, notwithstanding the coarse method of representing the dune forms, the qualitative agreement of the experimental results and the LES results is rather good. Comparison of the LES results with the Reynolds averaged numerical simulation results of Zeng et al. [“Flow and bathymetry in sharp open-channel bends: Experiments and predictions,” Water Resour. Res. 44, W09401, doi:10.1029/2007WR006303 (2008)] reveals surprisingly good agreement. This good agreement is explained by the minor importance of turbulence stress gradients in the contribution to the transverse and streamwise momentum balance. Moreover, it is found that in the bend the structure of the Reynolds stress tensor shows a tendency toward isotropy which enhances the performance of isotropic eddy viscosity closure models of turbulence. This observation is remarkable since highly anisotropic turbulence might well be expected considering the complex nature of the geometry. Furthermore, the LES results reveal a pronounced recirculation zone near the convex inner bank of the flume due to the shallowness of the flow and strong curvature of the flume. At the interface between the recirculation zone and the main flow, a curved mixing layer is identified as well as strong upwelling flow motion that is accompanied with large production of turbulent kinetic energy.
Partitioning networks into clusters and residuals with average association
Authors: Vejmelka Martin , Paluš Milan
Published: July 2010

We investigate the problem of detecting clusters exhibiting higher-than-average internal connectivity in networks of interacting systems. We show how the average association objective formulated in the context of spectral graph clustering leads naturally to a clustering strategy where each system is assigned to at most one cluster. A residual set is formed of the systems that are not members of any cluster. Maximization of the average association objective leads to a discrete optimization problem, which is difficult to solve, but a relaxed version can be solved using an eigendecomposition of the connectivity matrix. A simple approach to extracting clusters from a relaxed solution is described and developed by applying a variance maximizing solution to the relaxed solution, which leads to a method with increased accuracy and sensitivity. Numerical studies of theoretical connectivity models and of synchronization clusters in a lattice of coupled Lorenz oscillators are conducted to show the efficiency of the proposed approach. The method is applied to an experimentally obtained human resting state functional magnetic resonance imaging dataset and the results are discussed.
Two-dimensional dielectric spectroscopy: Implementation and validation of a scanning open-ended coaxial probe
Authors: Habibi Mohammad , Klemer David P. , Raicu Valerica
Published: July 2010

Dielectric spectroscopy is a powerful tool for characterizing and classifying materials based on their electrical properties. In order to perform dielectric measurements on a sample with spatially varying properties, the measuring probe typically is repositioned manually on the surface of the sample for each measurement. In this paper, we present a novel technique, based on a reconfigurable multielectrode array, which facilitates the recording of measurements at various different spatial locations without physically moving the measuring electrodes. By electronically selecting one of the electrodes as the inner line and connecting the remainder of the electrodes together to form the outer line, an open-ended coaxial probe is created, which can be repositioned by simply selecting different electrode combinations; hence the name of a “traveling” coaxial probe. The geometric factor, or the cell constant, of each coaxial probe in the array was estimated from measurements on saline solutions with known electrical characteristics. In order to validate the setup for measurement of dielectric properties of biological cells, the plasma membrane capacitance and cytoplasm conductivity of yeast cells suspended in aqueous solutions were measured and compared to results from published reports. Dielectric spectroscopy imaging was carried out on tissue phantoms made of an agar gel with inclusions consisting of concentrated yeast cell suspensions. Measurements were performed on the phantoms, and the dielectric data were spatially mapped with respect to electrode location. The spatial electrical data correlated precisely with locations of yeast cell inclusions within the phantoms.
Variations of trends of indicators describing complex systems: Change of scaling precursory to extreme events
Authors: Keilis-Borok V. I. , Soloviev A. A.
Published: July 2010

Socioeconomic and natural complex systems persistently generate extreme events also known as disasters, crises, or critical transitions. Here we analyze patterns of background activity preceding extreme events in four complex systems: economic recessions, surges in homicides in a megacity, magnetic storms, and strong earthquakes. We use as a starting point the indicators describing the system’s behavior and identify changes in an indicator’s trend. Those changes constitute our background events (BEs). We demonstrate a premonitory pattern common to all four systems considered: relatively large magnitude BEs become more frequent before extreme event. A premonitory change of scaling has been found in various models and observations. Here we demonstrate this change in scaling of uniformly defined BEs in four real complex systems, their enormous differences notwithstanding.
Microstructure and intergranular diffusion in exchange-coupled Sm–Co/Fe nanocomposites
Authors: Zhang Ying , Kramer M. J. , Rong Chuanbing , Liu J. Ping
Published: July 2010

We demonstrate homogenous distribution of bcc FeCo soft phase with grain size of 20–30 nm in the annealed Sm–Co/Fe bulk samples by energy filtered transmission electron microscopy (EFTEM). Quantitative Co/Fe interdiffusion measured using both energy dispersive spectroscopy (EDS) and parallel electron energy loss spectroscopy (PEELS) shows Fe60±5%Co40±5% for the magnetically soft bcc phase and Sm2(Co0.82Fe0.18)7 and Sm(Co0.80Fe0.20)5 respectively for the magnetically hard phases in these two alloy systems after optimal annealing. The graded interface develops in both samples due to the Co/Fe interchange between the hard and soft phases and the bcc soft phase was determined.
Anharmonicity in LiBH4–LiI induced by anion exchange and temperature
Authors: Borgschulte A. , Gremaud R. , Kato S. , Stadie N. P. , Remhof A. , Züttel A. , Matsuo M. , Orimo S.-I.
Published: July 2010

The feasibility of spatially resolved Raman spectroscopy probing diffusion multiples as a high-throughput method to study phase transformations in Li-ion conductors is demonstrated. The method is applied to the pseudobinary LiBH4–LiI system, which shows high Li-ion conductivity in the HT-phase of LiBH4. The vibrational properties measured as a function of composition and temperature corroborate the formation of a solid solution of Li(BH4)1−cIc over nearly the entire phase diagram (0<c≤0.8±0.2). The results shed light on anharmonic effects responsible for the structural phase transformation in this system.
Comprehensive modeling of resistive switching in the Al/TiOx/TiO2/Al heterostructure based on space-charge-limited conduction
Authors: Kim Sungho , Jeong Hu Young , Choi Sung-Yool , Choi Yang-Kyu
Published: July 2010

The reversible resistance switching (RS) effect of the Al/TiOx/TiO2/Al heterostructure is investigated in this study. This RS was attributed to space-charge-limited conduction (SCLC) as controlled by localized traps in the TiOx layer. The preexisting SCLC theory was extended to describe the abrupt resistance transition. An analytical model was developed with consideration of the ratio of free and trapped carrier density, which was extracted from the experimental data to show exponentially distributed traps in energy. The proposed model can be applicable to RS phenomena induced by interface-type traps in other material system.
Effects of piezopotential spatial distribution on local contact dictated transport property of ZnO micro/nanowires
Authors: Zhang Yan , Hu Youfan , Xiang Shu , Wang Zhong Lin
Published: July 2010

We present a study on the effect of deformation induced piezoelectric potential (piezopotential) in a ZnO micro/nanowire on its electrical transport properties by choosing different contacting locations on the wire to form a metal-ZnO contact. When a ZnO wire is under nonuniform deformation, the local piezopotential distribution at different positions shows significant effect on and distinct trend of variation in the charge carrier transport characteristic. This study has a broad impact on understanding the characteristics of piezotronic devices based on nanowires of wurtzite materials by controlling local contact position and contact size.
Continuous wave laser generation at 1064 nm in femtosecond laser inscribed Nd:YVO4 channel waveguides
Authors: Tan Yang , Chen Feng , Vázquez de Aldana J. R. , Torchia G. A. , Benayas A. , Jaque D.
Published: July 2010

We report on continuous wave 1064 nm laser generation from an ultrafast laser inscribed neodymium-doped yttrium orthovanadate channel waveguide with pumping at 808 nm. Single-mode stable laser operations have been observed with pump powers at threshold as low as 14 mW and with laser slope efficiencies as high as 38.7%.
Relation between glass and quasicrystal formation in the Zr–Nb–Cu–Ni–Al alloys upon solidification
Authors: Zhu Zhengwang , Zhang Wei , Xie Guoqiang , Inoue Akihisa
Published: July 2010

We reported the relationship among the icosahedral short-range order (ISRO), glass formation and quasicrystal formation in the Zr–Nb–Cu–Ni–Al alloys. The alloys with the Nb addition stabilized ISRO, making the alloys form the amorphous, quasicrystal and crystal with decreasing the cooling rate. Not only bulk glass but also bulk quasicrystal were found to form for these alloys. The structural evolution from the amorphous phase, to the quasicrystal and crystals with the variation in the Nb content or the cooling rate is present. These findings were related to the degree of ISRO, which are advantageous for understanding the glass formation phenomenon.
Negotiating the turbulent boundary: the challenges of building a science - management collaboration for landscape-scale monitoring of environmental flows
Authors: Webb J. Angus , Stewardson Michael J. , Chee Yung En , Schreiber E. Sabine G. , Sharpe Andrew K. , Jensz Michael C.
Published: July 2010

With drought and climate change leading to increased water scarcity at a time of increasing consumptive demand, the provision of environmental flows is a potentially divisive issue. Demonstrating the ecological effects of environmental flows is thus important for supporting policy and management decisions. We describe the development of a multi-basin monitoring and assessment program for environmental flows in Victoria, Australia. We examine the challenges associated with negotiating the turbulent boundary between water science and water management when building a partnership between multiple partners with differing priorities, expectations and responsibilities. We describe the mistakes made and corrective actions taken, and present a critical analysis of the lessons learned. Strong science–management collaboration will be aided by: explicit recognition of the importance of the engagement process, establishing the partnership at the outset, assessing and understanding the disparate needs of individual partners, frequent articulation of the shared vision that motivated the collaboration, and providing sufficient opportunities for information exchange among partners. Cullen first described the challenges to science-management collaboration twenty years ago, but to some extent, the same mistakes continue to be made. Our real-world example shows that it is possible to develop a strong partnership, even when such mistakes are made at the outset.
Metastability in a river subject to multiple disturbances may constrain restoration options
Authors: Robson B. J. , Mitchell B. D.
Published: July 2010

Metastability may arise in rivers subject to multiple disturbance processes because external constraints to ecosystem change sustain the metastable state; this has important implications for management, especially river restoration. The Glenelg River and its southern Australian landscape have been extensively studied by different researchers across many projects, and several restoration actions implemented across different reaches and spatial scales. Research involving diverse researchers and projects over extended periods shows strengths such as flexibility in pursuing emerging research questions, increased regional capacity by facilitating research training, and the generation of broader perspectives on river management. We conclude that metastability is a likely state for rivers with multiple interacting disturbances in regions with Mediterranean-type climates. In such rivers, disrupted relationships between the physical environment and ecological processes are likely, such that habitat restoration might have limited effectiveness. Restoration practices that constitute a disturbance might also risk disrupting metastability, or their impact may be limited because metastability confers resistance to further disturbance. Restoration may be more effectively targeted at less-disturbed reaches where ecosystems have a greater capacity to respond. Similarly, restoration in disturbed reaches might be more effectively directed at supporting metastability in the face of landscape change, than attempting to restore antecedent conditions.
Can a collaborative focus on solutions improve our capacity to achieve sustainable water management?
Authors: Gawne Ben , Crase Lin , Watson Alistair S.
Published: July 2010

Despite the influence of freshwater ecology on investment and management worldwide, many aquatic ecosystems remain severely degraded. By using the Murray–Darling Basin, Australia, as an example, we examined the relationship between freshwater ecological research and interventions implemented to achieve management objectives. We explored four related issues about why freshwater ecologists are rarely satisfied with management solutions and why some adopted remedies have not achieved sustainable management outcomes. We argue that, as a discipline, freshwater ecology does not focus enough on the development of solutions. Many proposed solutions create problems elsewhere and implementation of these solutions can prove unduly problematic. Although there is no simple panacea, changes to the training and career structure of freshwater ecologists could increase researchers’ focus on solutions and enhance their capacity for cross-disciplinary collaboration, especially with social scientists. Such cross-disciplinary outputs are more likely to be palatable because of their system focus. Professor Peter Cullen advocated the importance of undertaking collaborative research to generate predictive capacity. We extend that call by advocating greater cross-disciplinary collaboration and the need for research to focus on the development of solutions rather than problem delineation.
Integrated catchment management research: lessons for interdisciplinary science from the Motueka Catchment, New Zealand
Authors: Phillips Chris , Allen Will , Fenemor Andrew , Bowden Breck , Young Roger
Published: July 2010

Integrative research projects are becoming more common and inherently face challenges that single-discipline or multi-disciplinary projects seldom do. It is difficult to learn what makes a successful integrative research project as many of these challenges and solutions often go unreported. Using the New Zealand Integrated Catchment Management (ICM) for the Motueka River research program, we reflect on the demands confronting research programs attempting to operate in an integrative interdisciplinary manner. We highlight seven key lessons that may help others learn of the benefits and difficulties that confront scientists and stakeholders involved in undertaking similar research. These are (1) clarify the goal and work with key people; (2) manage expectations; (3) agree on integrative concepts and face the challenge of epistemology; (4) leadership; (5) communication in an atmosphere of mutual trust and respect; (6) acknowledge that different modes of learning mean that a wide range of knowledge products are needed; and (7) measure and celebrate success. The recognition that many environmental problems can only be solved through the creation of new knowledge and through social processes that engage the research and management domains has been a major benefit of the research program.
Managing the world's most international river: the Danube River Basin
Authors: Sommerwerk Nike , Bloesch Jürg , Paunović Momir , Baumgartner Christian , Venohr Markus , Schneider-Jacoby Martin , Hein Thomas , Tockner Klement
Published: July 2010

Transboundary river-basin management is a challenging task emerging from lack of on-site expert knowledge, high administrative and socioeconomic complexity, various stakeholder interests, and difficulties enforcing international and national law. Therefore, an efficient ‘science–policy interface’ is a crucial ingredient for the successful development and implementation of adequate management strategies. The Danube River Basin (DRB) drains areas of 19 countries with different cultural, political, and environmental legacies. The European Water Framework Directive (WFD) has provided the guiding legal instrument for DRB management since 2000, supported by several multilateral agreements. The International Commission for the Protection of the Danube River (ICPDR) is responsible for the implementation of the WFD in the DRB. It stimulates management-oriented research and coordinates the various activities of the contracting parties and observers, including those of many NGOs and stakeholders. The development of the first DRB Management Plan in 2009 constituted a milestone of cooperation among scientific, political, and public organisations. Key stressors and pressures have been identified, a new basin-wide monitoring network has been established, and numerous conservation and restoration sites have been designated. A major challenge in DRB management will be to establish synergies among the competing interests of navigation, hydropower production, flood protection and nature conservation. This paper examines the strengths and weaknesses of DRB science–policy interactions and outlines future strategies for sustainable development of the DRB as a template for transboundary river basin management.
Identification of a microRNA signature of renal ischemia reperfusion injury
Authors: Godwin Jonathan G. , Ge Xupeng , Stephan Kristin , Jurisch Anke , Tullius Stefan G. , Iacomini John
Published: July 2010

Renal ischemia reperfusion injury (IRI) is associated with significant morbidity and mortality. Given the importance of microRNAs (miRNAs) in regulating gene expression, we examined expression profiles of miRNAs following renal IRI. Global miRNA expression profiling on samples prepared from the kidneys of C57BL/6 mice that underwent unilateral warm ischemia revealed nine miRNAs (miR-21, miR-20a, miR-146a, miR-199a-3p, miR-214, miR-192, miR-187, miR-805, and miR-194) that are differentially expressed following IRI when compared with sham controls. These miRNAs were also differently expressed following IRI in immunodeficient RAG-2/common γ-chain double-knockout mice, suggesting that the changes in expression observed are not significantly influenced by lymphocyte infiltration and therefore define a lymphocyte-independent signature of renal IRI. In vitro studies revealed that miR-21 is expressed in proliferating tubular epithelial cells (TEC) and up-regulated by both cell-intrinsic and -extrinsic mechanisms resulting from ischemia and TGF-β signaling, respectively. In vitro, knockdown of miR-21 in TEC resulted in increased cell death, whereas overexpression prevented cell death. However, overexpression of miR-21 alone was not sufficient to prevent TEC death following ischemia. Our findings therefore define a molecular fingerprint of renal injury and suggest miR-21 may play a role in protecting TEC from death.
Greenhouse gas emissions from alternative futures of deforestation and agricultural management in the southern Amazon
Authors: Galford Gillian L. , Melillo Jerry M. , Kicklighter David W. , Cronin Timothy W. , Cerri Carlos E. P. , Mustard John F. , Cerri Carlos C.
Published: July 2010

The Brazilian Amazon is one of the most rapidly developing agricultural areas in the world and represents a potentially large future source of greenhouse gases from land clearing and subsequent agricultural management. In an integrated approach, we estimate the greenhouse gas dynamics of natural ecosystems and agricultural ecosystems after clearing in the context of a future climate. We examine scenarios of deforestation and postclearing land use to estimate the future (2006–2050) impacts on carbon dioxide (CO
2
), methane (CH
4
), and nitrous oxide (N
2
O) emissions from the agricultural frontier state of Mato Grosso, using a process-based biogeochemistry model, the Terrestrial Ecosystems Model (TEM). We estimate a net emission of greenhouse gases from Mato Grosso, ranging from 2.8 to 15.9 Pg CO
2
-equivalents (CO
2
-e) from 2006 to 2050. Deforestation is the largest source of greenhouse gas emissions over this period, but land uses following clearing account for a substantial portion (24–49%) of the net greenhouse gas budget. Due to land-cover and land-use change, there is a small foregone carbon sequestration of 0.2–0.4 Pg CO
2
-e by natural forests and cerrado between 2006 and 2050. Both deforestation and future land-use management play important roles in the net greenhouse gas emissions of this frontier, suggesting that both should be considered in emissions policies. We find that avoided deforestation remains the best strategy for minimizing future greenhouse gas emissions from Mato Grosso.
Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres
Authors: Lewis Peter W. , Elsaesser Simon J. , Noh Kyung-Min , Stadler Sonja C. , Allis C. David
Published: July 2010

The histone variant H3.3 is implicated in the formation and maintenance of specialized chromatin structure in metazoan cells. H3.3-containing nucleosomes are assembled in a replication-independent manner by means of dedicated chaperone proteins. We previously identified the death domain associated protein (Daxx) and the α-thalassemia X-linked mental retardation protein (ATRX) as H3.3-associated proteins. Here, we report that the highly conserved N terminus of Daxx interacts directly with variant-specific residues in the H3.3 core. Recombinant Daxx assembles H3.3/H4 tetramers on DNA templates, and the ATRX–Daxx complex catalyzes the deposition and remodeling of H3.3-containing nucleosomes. We find that the ATRX–Daxx complex is bound to telomeric chromatin, and that both components of this complex are required for H3.3 deposition at telomeres in murine embryonic stem cells (ESCs). These data demonstrate that Daxx functions as an H3.3-specific chaperone and facilitates the deposition of H3.3 at heterochromatin loci in the context of the ATRX–Daxx complex.
The fragility of visuals
Authors: Lundell Åsa Kroon
Published: July 2010

This study aims at understanding how politicians of both genders who are constantly in the media relate to, and manage, their mediated visibility. I assume that politicians who are constantly subject to visual exposure need to manage their experienced lack of control by developing various strategies in order to feel more empowered than perhaps is possible given the media’s power of framing their political personas. Six Swedish politicians in prominent positions were interviewed qualitatively using open-ended questions relating to their views on press photographers, the role of visuals and personal experiences of being visualised in the press. It was found that the politicians develop both manifest counter-strategies as well as more latent, reflexive ones which all imply an unwillingness to submit to the media’s visual framing power.
Remuneration discrepancies in the landlocked economies of Malaŵi and Uganda
Authors: Munthali Alister , Matagi Leon , Tumwebaze Callist
Published: July 2010

Although the original study of remuneration differences between local and expatriate development workers took place in the landlocked economy of Malaŵi, the study has never been replicated outside of one sector and organization (the National University), and took place prior to the 2000 Millennium Development Goals. Participating in the present studies were 458 aid and development professionals, working across a range of sectors in Malaŵi (n = 241, response rate = 50%) and Uganda (n = 217, response rate = 51%). The size of the gap between local and international workers, measured using the World Bank's purchasing power parity, was higher in Malaŵi (4.04:1) than in Uganda (1.97:1). The ratio was more clearly within tolerance levels in Uganda than in Malaŵi. Consistent with these differences, and controlling for organization, cultural, and demographic factors, locally remunerated workers reported more and expatriate workers less injustice and demotivation in Malaŵi than in Uganda. Although sample sizes for the internationally remunerated are small, the findings suggest that wider disparities may (1) hinder perspective‐taking and (2) decrease motivation. In‐country workshops with stakeholders and subject‐matter experts considered the findings, and potential solutions offered through the survey form. They recommended the implementation of performance‐based remuneration, including competency‐based job analysis and evaluation. Competencies in such functions can be provided by humanitarian work psychology.
Online counselling: An initial examination of the process in a synchronous chat environment
Authors: Mallen Michael J. , Jenkins Indria M. , Vogel David L. , Day Susan X.
Published: July 2010

Aims: The present study investigates the dynamics of an initial counselling session held in a synchronous chat environment between counsellors‐in‐training and a trained confederate posing as a client. Specifically, the study examines (a) the interventions used, (b) the therapeutic alliance, and (c) the ability of the counsellor to accurately diagnose the client. Methods: Transcripts from 54 online sessions were analysed to investigate counsellors’ responses and interventions in an online environment. Results: The use of counselling interventions were similar to those used in face‐to‐face sessions, but with some differences. Reassurance and open questions were used about twice as often, while interpretation and direct guidance were used less frequently. Most participants (86–90%) reached the correct diagnosis when the symptoms represented a single diagnosis but had more trouble when the symptoms were mixed (36%). Participants reported feeling some distance from the client but reported an increase in their ability to form a therapeutic alliance after conducting an online session.Conclusions: The present study clarifies some of the benefits and limitations of online counselling and provides some new insights into the issues that may need to be addressed for the training of counsellors to work in this area.
Cultural ruptures in short‐term therapy: Working alliance as a mediator between clients' perceptions of microaggressions and therapy outcomes
Authors: Owen Jesse , Imel Zac , Tao Karen W. , Wampold Bruce , Smith Amanda , Rodolfa Emil
Published: July 2010

Aim: To determine whether or not clients' perceptions of microaggressions varied based on their own and the therapist's race/ethnicity and whether or not they would be negatively related to the effectiveness of therapy and if the working alliance would mediate this effect. Method: The study utilised a cross‐sectional, retrospective, methodology. Clients were recruited from a large university counselling centre in the United States (N=232 clients and 29 therapists). Results: Neither clients' race/ethnicity, therapists’ race/ethnicity, nor client‐therapist ethnic matching predicted perceptions of microaggressions. Clients' ratings of microaggressions were negatively associated with their psychological wellbeing; however, this effect was mediated by clients' ratings of the working alliance. Implications: Therapists should take into account the cultural messages they may be conveying to both white and racial/ethnic minority clients. Therapists should develop strategies that are consistent with a general therapeutic approach that promotes discussions about culture with their clients and, most importantly, should attend to the therapeutic relationship.
RETRACTED: Doping of Tin-oxides pinning centers into YBCO films by MOD method
Authors: R Teranishi  , Y Miyanaga  , K Yamada  , N Mori  , M Mukaida  , M Inoue  , T Kiss  , M Miura  , M Yoshizumi  , T Izumi  , M Namba  , S Awaji  , K Watanabe
Published: July 2010

Tin-oxides were doped into YBCO films as pinning centers to improve Jc properties in a magnetic field. YBCO films were grown by a metal organic deposition process using tri-fluoroacetates starting solutions which contains tin compounds such as SnO2 particles or tin-acetylacetonate salts for pinning centers. J
c of the YBCO films were enhanced by introducing pinning centers both SnO2 and tin-acetylacetonates in the wide range of the magnetic angle. Especially, Jc of YBCO film grown by the solution with tin-acetylacetnates increased in all magnetic field angles. XRD analysis and TEM observation revealed the existence of BaSnO3 particles with the size of about 30 nm in the YBCO film grown by the solution with tin-acetylacetnates. The BaSnO3 nano particles were distributed randomly in the film and were considered to act as 3-dimentional pinning centers.
Prophossi: automating expert validation of phosphopeptide–spectrum matches from tandem mass spectrometry
Authors: Martin David M.A. , Nett Isabelle R.E. , Vandermoere Franck , Barber Jonathan D. , Morrice Nicholas A. , Ferguson Michael A.J.
Published: July 2010

Motivation: Complex patterns of protein phosphorylation mediate many cellular processes. Tandem mass spectrometry (MS/MS) is a powerful tool for identifying these post-translational modifications. In high-throughput experiments, mass spectrometry database search engines, such as MASCOT provide a ranked list of peptide identifications based on hundreds of thousands of MS/MS spectra obtained in a mass spectrometry experiment. These search results are not in themselves sufficient for confident assignment of phosphorylation sites as identification of characteristic mass differences requires time-consuming manual assessment of the spectra by an experienced analyst. The time required for manual assessment has previously rendered high-throughput confident assignment of phosphorylation sites challenging.

Results: We have developed a knowledge base of criteria, which replicate expert assessment, allowing more than half of cases to be automatically validated and site assignments verified with a high degree of confidence. This was assessed by comparing automated spectral interpretation with careful manual examination of the assignments for 501 peptides above the 1% false discovery rate (FDR) threshold corresponding to 259 putative phosphorylation sites in 74 proteins of the Trypanosoma brucei proteome. Despite this stringent approach, we are able to validate 80 of the 91 phosphorylation sites (88%) positively identified by manual examination of the spectra used for the MASCOT searches with a FDR < 15%.

Conclusions:High-throughput computational analysis can provide a viable second stage validation of primary mass spectrometry database search results. Such validation gives rapid access to a systems level overview of protein phosphorylation in the experiment under investigation.

Availability: A GPL licensed software implementation in Perl for analysis and spectrum annotation is available in the supplementary material and a web server can be assessed online at http://www.compbio.dundee.ac.uk/prophossi

Contact:  d.m.a.martin@dundee.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Direct Interaction Between the Rice yellow mottle virus (RYMV) VPg and the Central Domain of the Rice eIF(iso)4G1 Factor Correlates with Rice Susceptibility and RYMV Virulence
Authors: Hébrard Eugénie , Poulicard Nils , Gérard Clément , Traoré Oumar , Wu Hui-Chen , Albar Laurence , Fargette Denis , Bessin Yannick , Vignols Florence
Published: July 2010

The adaptation of Rice yellow mottle virus (RYMV) to recessive resistance mediated by the rymv1-2 allele has been reported as a model to study the emergence and evolution of virulent variants. The resistance and virulence factors have been identified as eukaryotic translation initiation factor eIF(iso)4G1 and viral genome–linked protein (VPg), respectively, but the molecular mechanisms involved in their interaction are still unknown. In this study, we demonstrated a direct interaction between RYMV VPg and the central domain of rice eIF(iso)4G1 both in vitro, using recombinant proteins, and in vivo, using a yeast two-hybrid assay. Insertion of the E309K mutation in eIF(iso)4G1, conferring resistance in planta, strongly diminished the interaction with avirulent VPg. The efficiency of the major virulence mutations at restoring the interaction with the resistance protein was assessed. Our results explain the prevalence of virulence mutations fixed during experimental evolution studies and are consistent with the respective viral RNA accumulation levels of avirulent and virulent isolates. Our results also explain the origin of the residual multiplication of wild-type isolates in rymv1-2–resistant plants and the role of genetic context in the poor adaptability of the S2/S3 strain. Finally, the strategies of RYMV and members of family Potyviridae to overcome recessive resistance were compared.
Understanding the Plant Immune System
Authors: Katagiri Fumiaki , Tsuda Kenichi
Published: July 2010

Plant immunity is controlled by a complex signaling network. Here, we discuss how the complexity of the network affects our views and approaches in studying the plant immune network. We propose that the mode of plant immunity is mainly determined by how the shared signaling network is used rather than by a signaling machinery specific to each mode, that balancing the robustness of immunity and the negative effect of immunity on plant fitness is a key driver in evolution of the immune network, that comparisons of plant mutant to wild-type phenotypes may not be very effective in elucidating the underlying signaling mechanisms, and that mechanistic understanding of the network can improve our ability to predict the performance of immunity.
Intracellular Transport of Viruses and Their Components: Utilizing the Cytoskeleton and Membrane Highways
Authors: Harries Phillip A. , Schoelz James E. , Nelson Richard S.
Published: July 2010

Plant viruses are obligate organisms that require host components for movement within and between cells. A mechanistic understanding of virus movement will allow the identification of new methods to control virus systemic spread and serve as a model system for understanding host macromolecule intra- and intercellular transport. Recent studies have moved beyond the identification of virus proteins involved in virus movement and their effect on plasmodesmal size exclusion limits to the analysis of their interactions with host components to allow movement within and between cells. It is clear that individual virus proteins and replication complexes associate with and, in some cases, traffic along the host cytoskeleton and membranes. Here, we review these recent findings, highlighting the diverse associations observed between these components and their trafficking capacity. Plant viruses operate individually, sometimes within virus species, to utilize unique interactions between their proteins or complexes and individual host cytoskeletal or membrane elements over time or space for their movement. However, there is not sufficient information for any plant virus to create a complete model of its intracellular movement; thus, more research is needed to achieve that goal.
Deletion of the Bacillus anthracis capB homologue in Francisella tularensis subspecies tularensis generates an attenuated strain that protects mice against virulent tularaemia
Authors: Michell Stephen L. , Dean Rachel E. , Eyles Jim E. , Hartley Margaret Gill , Waters Emma , Prior Joann L. , Titball Richard W. , Oyston Petra C. F.
Published: July 2010

As there is currently no licensed vaccine against Francisella tularensis, the causative agent of tularaemia, the bacterium is an agent of concern as a potential bioweapon. Although F. tularensis has a low infectious dose and high associated mortality, it possesses few classical virulence factors. An analysis of the F. tularensis subspecies tularensis genome sequence has revealed the presence of a region containing genes with low sequence homology to part of the capBCADE operon of Bacillus anthracis. We have generated an isogenic capB mutant of F. tularensis subspecies tularensis SchuS4 and shown it to be attenuated. Furthermore, using BALB/c mice, we have demonstrated that this capB strain affords protection against significant homologous challenge with the wild-type strain. These data have important implications for the development of a defined and efficacious tularaemia vaccine.
Identification of species of the Burkholderia cepacia complex by sequence analysis of the hisA gene
Authors: Papaleo Maria Cristiana , Perrin Elena , Maida Isabel , Fondi Marco , Fani Renato , Vandamme Peter
Published: July 2010

Bacteria of the Burkholderia cepacia complex (Bcc) are opportunistic human pathogens that can cause serious infections in the lungs of cystic fibrosis patients. The Bcc is a complex taxonomic group and comprises 17 closely related species of both biotechnological and clinical importance that have been discriminated by a polyphasic taxonomic approach. In this study we focused on the hisA gene, which encodes a 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase involved in histidine biosynthesis, as a new target gene to discriminate among the Bcc species. PCR primers were designed to amplify a hisA DNA fragment of 442 bp from 78 strains representative of all the 17 Bcc species known at the time of writing. The nucleotide sequences of the amplicons were determined and aligned with the 54 Bcc sequences available in databases. Then a phylogenetic tree was constructed on the basis of this alignment and this revealed that this hisA region allows discrimination of all Bcc species, suggesting that this gene fragment can be used for the identification of Bcc strains. In addition, an 11 nucleotide letter code for the rapid discrimination of Bcc species was identified.
Origins, evolution, and phenotypic impact of new genes
Authors: Kaessmann Henrik
Published: July 2010

Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms. The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations uncovered different evolutionary pathways that led to the emergence of novel functions from these newly minted sequences and, with respect to animals, attributed a potentially important role to one specific tissue—the testis—in the process of gene birth. Remarkably, these studies also demonstrated that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits. Consequently, it is now firmly established that new genes have indeed been major contributors to the origin of adaptive evolutionary novelties.
Effect of Carbohydrate on the Rheological Parameters of Paste Extrusion
Authors: Chen Ying , Burbidge Adam , Bridgwater John
Published: July 2010

Carbohydrates are often key components in the formulation of extrusion pastes, yet the reasons for selection are presently empirical. The influence on paste extrusion of various types of carbohydrates, such as starch, dextrin, lactose, and glucose, have been studied and related to their water retention capacities. The bulk yield stress and the surface shear stress both decrease as the moisture content increases; however, the way in which the water that is present interacts with the carbohydrate has an important influence. The behavior of some carbohydrates can be substantially accounted for by a consideration of packing effects; however, dextrin behaves differently. The carbohydrates function not only as a binder but also as a means of retaining the liquid phase.
Phase Equilibria near (Bi,Pb)‐2223, As a Function of Oxygen Partial Pressure
Authors: MacManus‐Driscoll Judith L. , Yi Zhuan
Published: July 2010

The phase equilibria near (Bi,Pb)2Sr2Ca2Cu3O10+delta ((Bi,Pb)‐2223) was studied in the temperature range of 750°‐820°C in air and in reducing atmospheres. In air, (Bi,Pb)‐2223 was in equilibrium with one or more of the following phases: (Bi,Pb)2Sr2CaCu2O8+delta ((Bi,Pb)‐2212), (Sr,Ca)14Cu24O41 (14:24), (Ca,Sr)2CuO3, (Bi,Pb)4(Sr,Ca)5‐CuOx (451), Ca2PbO4, and CuO. Ca2PbO4 and the 451 phase were not in equilibrium with (Bi,Pb)‐2223 at an oxygen partial pressure (pO2) of 10‐3 atm, which is indicative of higher lead solubility in (Bi,Pb)‐2223 under more‐reducing conditions. In a second set of experiments, the lead content in both (Bi,Pb)‐2212 single crystals and (Bi,Pb)‐2223 powders was investigated as a function of pO2 at a constant temperature of 750°C. Lead solubility in (Bi,Pb)‐2212 and (Bi,Pb)‐2223 increased as pO2 decreased.
Bioceramics
Authors: Hench Larry L.
Published: July 2010

Ceramics used for the repair and reconstruction of diseased or damaged parts of the musculo‐skeletal system, termed bioceramics, may be bioinert (e.g., alumina and zirconia), resorbable (e.g., tricalcium phosphate), bioactive (e.g., hydroxyapatite, bioactive glasses, and glass‐ceramics), or porous for tissue ingrowth (e.g., hydroxyapatite‐coated metals). Applications include replacements for hips, knees, teeth, tendons, and ligaments and repair for periodontal disease, maxillofacial reconstruction, augmentation and stabilization of the jaw bone, spinal fusion, and bone repair after tumor surgery. Pyrolytic carbon coatings are thromboresistant and are used for prosthetic heart valves. The mechanisms of tissue bonding to bioactive ceramics have resulted in the molecular design of bioceramics for interfacial bonding with hard and soft tissue. Bioactive composites are being developed with high toughness and elastic modulus that match with bone. Therapeutic treatment of cancer has been achieved by localized delivery of radioactive isotopes via glass beads. Clinical success of bioceramics has led to a remarkable advance in the quality of life for millions of people.
Dissolution of Iron in Silicate Melts
Authors: Dumm John Q. , Brown Paul W.
Published: July 2010

The oxidation and dissolution of metallic iron in silicate melts were investigated. The base composition consisted of Idaho soil with quartz and potassium feldspars as primary phases. Iron immersed in melts of unaltered soil and SiO2‐K2O underwent minimal oxidation at 1400°C. Melts consisting of soil, 10 wt% of added K2O, and 5‐20 wt% of added Fe2O3 were capable of dissolving Fe. Progressively greater Fe dissolution occurred with increasing Fe2O3 content. A melt containing 20 wt% Fe2O3 dissolved 10 wt% Fe within 3 h. Melts containing greater than 10 wt% Fe2O3 crystallized almost entirely as magnetite (Fe3O4) and augite (Ca(Mg,Fe(2+))(SiO3)2). The data obtained also suggest that added Fe2O3 contributed to an increased rate of oxygen diffusion in these melts.
Investigation of the Physical and Mechanical Properties of Hot‐Pressed Boron Nitride/Oxide Ceramic Composites
Authors: Trice Rodney W. , Halloran John W.
Published: July 2010

Billets of hexagonal boron nitride powders (h‐BN) were hot‐pressed, varying the alignment of the platelike particles and the amount of oxide additives. Increasing either alignment of individual grains or the amount of additives was shown to increase flexural strength, to approximately 120 MPa at ambient temperatures. h‐BN was shown to deflect cracks initially propagating normal to its basal planes.
Electrical and Optical Properties of Transparent Conducting Homologous Compounds in the Indium–Gallium–Zinc Oxide System
Authors: Moriga Toshihiro , Kammler Daniel R. , Mason Thomas O. , Palmer George B. , Poeppelmeier Kenneth R.
Published: July 2010

The homologous compounds In1−xGa1+xO3(ZnO)k (where k= 1, 2, or 3) were prepared at a temperature of 1400°C. The solubility limits (as determined via X‐ray diffractometry) were 0.47 < [In]/([In] + [Ga]) < 0.67 for the k= 1 member, 0.35 < [In]/([In]+[Ga]) < 0.77 for the k= 2 member, and 0.29 < [In]/([In]+[Ga]) < 1.00 for the k= 3 member. Four‐point‐conductivity and diffuse‐reflectance measurements were performed on as‐fired and reduced samples. The band gap that was determined from diffuse reflectance increased as the Ga3+ content increased and k decreased. The conductivity increased as k decreased and the In3+ content increased. A maximum conductivity of 250 S/cm was obtained for k= 3 and [In]/([In]+[Ga]) = 1 after reduction. The minimum absorption edge of 325 nm was obtained for k= 2 and [In]/([In]+[Ga]) = 0.35 prior to reduction. The potential for metastable phases in the In‐Ga‐Zn‐O system with enhanced transparent‐conducting properties has been discussed.