bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent Technologies Usher in New Era of Coastal Geomorphology Research
Authors: Hanes Daniel M.
Published: July 2009

Research in the field of coastal geomorphology has been energized by the development of two new complementary high‐spatial‐resolution technologies: swath bathymetry sonar systems (SBSSs), and process‐based numerical models (PBNMs) of hydrodynamics, sediment transport, and morphodynamics.

The combination and integration of the two should lead to rapid expansion of scientific understanding of the genesis and evolution of morphology in coastal regions, the accretion and erosion of coastlines, and the effects of climate change on fluvial systems, estuaries, and coasts. For example, dredging shipping channels and harbors, protecting coastal property from erosion, evaluating risks due to coastal flooding, and other chronic and enduring societal problems can now be approached with new optimism due to the high spatial resolution of SBSSs and PBNMs.
The Unexpected Awakening of Chaitén Volcano, Chile
Authors: Carn Simon A. , Pallister John S. , Lara Luis , Ewert John W. , Watt Sebastian , Prata Alfred J. , Thomas Ronald J. , Villarosa Gustavo
Published: July 2009

On 2 May 2008, a large eruption began unexpectedly at the inconspicuous Chaitén volcano in Chile's southern volcanic zone. Ash columns abruptly jetted from the volcano into the stratosphere, followed by lava dome effusion and continuous low‐altitude ash plumes [Lara, 2009]. Apocalyptic photographs of eruption plumes suffused with lightning were circulated globally.

Effects of the eruption were extensive. Floods and lahars inundated the town of Chaitén, and its 4625 residents were evacuated. Widespread ashfall and drifting ash clouds closed regional airports and cancelled hundreds of domestic flights in Argentina and Chile and numerous international flights [Guffanti et al., 2008]. Ash heavily affected the aquaculture industry in the nearby Gulf of Corcovado, curtailed ecotourism, and closed regional nature preserves. To better prepare for future eruptions, the Chilean government has boosted support for monitoring and hazard mitigation at Chaitén and at 42 other highly hazardous, active volcanoes in Chile.
Initiative to Improve Process Representation in Chemistry‐Climate Models
Authors: Doherty Sarah J. , Rasch Philip J. , Ravishankara A. R.
Published: July 2009

Chemically active species in the atmosphere (e.g., aerosols, ozone, methane) play important roles in climate and air quality. Atmospheric concentrations of these species respond relatively rapidly to changes in emissions, providing opportunities for rapid response mitigation options. Because of the large spatial and temporal variability of these species, their global distributions must be calculated with a model, as must their influence on climate. Models are also needed for future projections of these species and their interaction with climate. Understanding what controls the distribution of these species, their role in climate change, how they will change with climate, and the coupling between climate and air quality is therefore critical.
New Study Finds Increasing Gender Equity at U.S. Research Institutions
Authors: Showstack Randy
Published: July 2009

Women and men faculty in science, engineering, and mathematics for the most part have comparable opportunities within major U.S. research universities, according to a report released 2 June by the U.S. National Research Council (NRC). The report found that gender does not appear to have been a factor in a number of important career transitions and outcomes, including hiring for tenure track and tenure positions and promotions.

“That is probably going to be surprising to many people. It was surprising to our own panel. And it may not have been the case if we had done the study in 1985 instead of 2005,” said Claude Canizares, co‐chair of the NRC committee that prepared the report, entitled Gender Differences at Critical Transitions in the Careers of Science, Engineering and Mathematics Faculty.
On the origins of temporal power‐law behavior in the global atmospheric circulation
Authors: Vyushin Dmitry I. , Kushner Paul J. , Mayer Josh
Published: July 2009

Climate variations on timescales longer than a year are often characterized by temporal scaling (“power‐law”) behavior for which spectral power builds up at low frequencies, in contrast to red‐noise behavior for which spectral power saturates at low frequencies. Checks on the ability of climate prediction models to simulate temporal scaling behavior represent stringent performance tests on the models. We here estimate temporal power‐law exponents (“Hurst exponents”) for the global atmospheric circulation of the stratosphere and troposphere during the 20th century. We show that current generation climate models generally simulate the spatial distribution of the Hurst exponents well. We then use simulations with different climate forcings to explain the Hurst exponent distribution and to account for discrepancies in scaling behavior between different observational products. We conclude that characterization of temporal power‐law behavior provides a valuable tool for cross‐validating low‐frequency variability in various datasets, for elucidating the physical mechanisms underlying this variability, and for statistical testing of trends and periodicities in climate time series.
Radar simulation and physical modeling of time diversity satellite systems
Authors: Capsoni Carlo , D'Amico Michele , Nebuloni Roberto
Published: July 2009

Satellite telecommunication systems that make use of frequencies higher than 10 GHz can experience strong attenuation due to rain. One of the countermeasures that can be adopted is time diversity. In this paper the performance of the time diversity technique is investigated through both radar simulation and modeling. We first exploit an extensive database of radar maps of precipitation collected in northern Italy to generate synthetic time series of attenuation; the performance of the time diversity technique is evaluated for different frequencies and elevation angles. The same analysis is then performed using the ExCell attenuation prediction model, whose input parameters are elevation, frequency and polarization of the Earth terminal, and the “effective” rainfall rate. The model‐predicted diversity gain is found to agree well with that obtained through radar simulation, demonstrating that the performance of the time diversity technique can be evaluated from the time series of rain rate, acquired by a rain gauge.
HAT–HDAC interplay modulates global histone H3K14 acetylation in gene‐coding regions during stress
Authors: Johnsson Anna , Durand‐Dubief Mickaël , Xue‐Franzén Yongtao , Rönnerblad Michelle , Ekwall Karl , Wright Anthony
Published: July 2009

Histone acetylation and deacetylation are important for gene regulation. The histone acetyltransferase, Gcn5, is an activator of transcriptional initiation that is recruited to gene promoters. Here, we map genome‐wide Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes, where it collaborates antagonistically with the class‐II histone deacetylase, Clr3, to modulate H3K14ac levels and transcriptional elongation. An interplay between Gcn5 and Clr3 is crucial for the regulation of many stress‐response genes. Our findings suggest a new role for Gcn5 during transcriptional elongation, in addition to its known role in transcriptional initiation.
The Eukaryote Genome Annotation Platform at Genoscope
Authors: Porcel Betina , Aniere Franck , Bonneval Sylvain , Noel Benjamin , Aury Jean-Marc , Da Silva Corinne , Jaillon Olivier , Denoeud France , Scarpelli Claude , Weissenbach Jean , Wincker Patrick , Artiguenave François
Published: July 2009

The Genoscope annotation workflow for eukaryote genomes relies on evidence from ab initio gene models predictions combined with homology searches, using collections of expressed sequences - full length cDNAs, ESTs or massive-scale mRNA sequences from the same or closely related organisms – proteins or other genomic sequences. Global analysis of these drafts or complete sequences are then combining both approaches in the form of gene prediction data integration using GAZE, capable to identify a majority of the existing gene features. Although of very good quality, gene-modelling remains still tentative at the end of the process. Even though computational predictors are useful on large scale annotation for global genomics analysis, there is no complete genome for which all gene structures, in terms of exons, introns and coding regions, have been experimentally confirmed.Finished genomes can provide exciting insights into the genome organization and evolution. Additional experimental data generated by genome sequencing projects give assistance to genome annotation aiming to a better understanding of the biology of the organism. Therefore, gene models and annotation can be improved by human curation to find errors or to resolve incongruous evidence on the automatic annotation of the genome. We now provide to collaborators carrying sequencing projects with a distributed annotation platform allowing expert evaluation of the annotation, in addition to our automated gene prediction pipeline.To ensure at most the participation of the scientific community, an annotation tool for revising annotations has been set up using components of the Generic Model Organism Database toolkit, which provides tools for managing organism databases. A CHADO database, linked to an Apollo graphical interface, permit users to correct gene structures and store them in a dedicated organism database, as we will show on a few examples. Such a tool would facilitate connecting and comparing predicted annotations with existing biological data, becoming the repository of complete annotated finished genome sequence.
Pyruvate dehydrogenase kinase isoenzyme 4 (PDHK4) deficiency attenuates the long-term negative effects of a high-saturated fat diet
Authors: Hwang Byounghoon , Jeoung Nam Ho , Harris Robert A.
Published: July 2009

The hypothesis that PDHK4 (pyruvate dehydrogenase kinase isoenzyme 4) has potential as a target for the treatment of type 2 diabetes was tested by feeding wild-type and PDHK4 knockout mice a high saturated fat diet that induces hyperglycemia, hyperinsulinaemia, glucose intolerance, hepatic steatosis and obesity. Previous studies have shown that PDHK4 deficiency lowers blood glucose by limiting the supply of three carbon gluconeogenic substrates to the liver. There is concern, however, that the increase in glucose oxidation caused by less inhibition of the pyruvate dehydrogenase complex by phosphorylation will inhibit fatty acid oxidation, promote ectopic fat accumulation and worsen insulin sensitivity. This was examined by feeding wild-type and PDHK4 knockout mice a high saturated fat diet for 8 months. Fasting blood glucose levels increased gradually in both groups but remained significantly lower in the PDHK4 knockout mice. Hyperinsulinaemia developed in both groups, but glucose tolerance was better and body weight was lower in the PDHK4 knockout mice. At termination, less fat was present in the liver and skeletal muscle of the PDHK4 knockout mice. Higher amounts of PGC-1α [PPARγ (peroxisome proliferator-activated receptor γ) coactivator 1α] and PPARα and lower amounts of fatty acid synthase and acetyl-CoA carboxylase isoenzyme 1 were present in the liver of the PDHK4 knockout mice. These findings suggest PDHK4 deficiency creates conditions that alter upstream signalling components involved in the regulation of lipid metabolism. The findings support the hypothesis that PDHK4 is a viable target for the treatment of type 2 diabetes.
Exact-exchange kernel of time-dependent density functional theory: Frequency dependence and photoabsorption spectra of atoms
Authors: Hellgren Maria , von Barth Ulf
Published: July 2009

In this work we have calculated excitation energies and photoionization cross sections of Be and Ne in the exact-exchange (EXX) approximation of time-dependent density functional theory (TDDFT). The main focus has been on the frequency dependence of the EXX kernel and on how it affects the spectrum as compared to the corresponding adiabatic approximation. We show that for some discrete excitation energies the frequency dependence is essential to reproduce the results of time-dependent Hartree-Fock theory. Unfortunately, we have found that the EXX approximation breaks down completely at higher energies, producing a response function with the wrong analytic structure and making inner-shell excitations disappear from the calculated spectra. We have traced this failure to the existence of vanishing eigenvalues of the Kohn-Sham non-interacting response function. Based on the adiabatic TDDFT formalism we propose a new way of deriving the Fano parameters of autoionizing resonances.
Vibrational branching ratios in the (b2u)−1 photoionization of C6F6
Authors: Lucchese Robert R. , Bozek John D. , Das Aloke , Poliakoff E. D.
Published: July 2009

The vibrational branching ratios in the photoionization of C6F6 leading to the C B22u state of C6F6+ are considered. Computational and experimental data are compared for the excitation of two totally symmetric modes. Resonant features at photon energies near 19 and 21 eV are found. A detailed analysis of the computed results shows that the two resonance states have different responses to changes in the C–C and C–F bond lengths. We find that the energies of both of the resonant states decrease with increasing bond lengths. In contrast to the energy positions, however, the resonant widths and the integrated oscillator strength of the resonances can either increase or decrease with increasing bond length depending on the nature and location of the resonant state and the location of the bond under consideration. With increasing C–F bond length, we find that the energy of the antibonding σ resonance localized on the ring has a decreasing resonance energy and also a decreasing lifetime. This behavior is in contrast to the usual behavior of shape resonance energies where increasing a bond length leads to decreasing resonance energies and increasing resonance lifetimes. Finally, for the first time, we examine the effect of simultaneously occurring multiple vibrations on the resonance profile for valence photoionization, and we find that the inclusion of more than a single vibrational mode substantially attenuates the strength of resonance.
Thickness-dependent dielectric and tunable properties of barium stannate titanate thin films
Authors: Song Sannian , Zhai Jiwei , Gao Lina , Yao Xi , Lu Shengbo , Xu Zhengkui
Published: July 2009

Barium stannate titanate Ba(Sn0.15Ti0.85)O3 (BTS) thin films with different thicknesses were grown by sol-gel process on single crystal LaAlO3 (LAO) and Pt/Ti/SiO2/Si substrates, respectively. Coplanar capacitance and parallel plate capacitance structure configurations were formed by preparing interdigital electrodes and parallel plate electrodes on BTS thin films. Both of the films exhibited an enhanced dielectric constant and tunability as the film thickness increases but these two cases are actually based on different mechanisms. The thickness dependent dielectric properties of the films deposited on Pt/Ti/SiO2/Si substrates were mainly attributed to the “dead layer” effect while those of the films grown on LAO substrates were due to strain and grain size of the films.
Abrupt transition to complete congestion on complex networks and control
Authors: Wang Wen-Xu , Wu Zhi-Xi , Jiang Rui , Chen Guanrong , Lai Ying-Cheng
Published: July 2009

Previous works on traffic-flow dynamics on complex networks have mostly focused on continuous phase transition from a free-flow state to a locally congested state as a parameter, such as the packet-generating rate, is increased through a critical value. Above the transition point congestion occurs on a small subset of nodes. Utilizing a conventional traffic-flow model based on the packet birth-death process and more importantly, taking into account the fact that in realistic networks nodes have only finite buffers, we find an abrupt transition from free flow to complete congestion. Slightly below the transition point, the network can support the maximum amount of traffic for some optimal value of the routing parameter. We develop a mean-field theory to explain the surprising transition phenomenon and provide numerical support. Furthermore, we propose a control strategy based on the idea of random packet dropping to prevent/break complete congestion. Our finding provides insights into realistic communication networks where complete congestion can occur directly from a free-flow state without any apparent precursor, and our control strategy can be effective to restore traffic flow once complete congestion has occurred.
Observation of space-separated multiexciton generation in photocurrent of Au/por-Si/p-Si structure
Authors: Sreseli O. M. , El’tsina O. S. , Belyakov L. V. , Goryachev D. N.
Published: July 2009

Photocurrent efficiency (ratio of the number of photogenerated carriers to the number of absorbed photons) of Au/por-Si/p-Si structure in a wide spectral range was investigated. The low-energy edge of nanoporous silicon (por-Si) sensibility was determined, and the enhancement in por-Si photocurrent efficiency was observed for incident photon energies above 3.5 eV. This threshold was demonstrated to exceed twice a bandgap of most nanocrystals in por-Si. Carrier tunneling among nanocrystals through thin oxide layers was shown as well. Efficiency enhancement is explained by space-separated double-exciton generation, when a high-energy photon absorbed in a nanocrystal results in two excitons in adjacent nanocrystals.
Temperature dependence, spatial scale, and tree species diversity in eastern Asia and North America
Authors: Wang Zhiheng , Brown James H. , Tang Zhiyao , Fang Jingyun
Published: July 2009

The increase of biodiversity from poles to equator is one of the most pervasive features of nature. For 2 centuries since von Humboldt, Wallace, and Darwin, biogeographers and ecologists have investigated the environmental and historical factors that determine the latitudinal gradient of species diversity, but the underlying mechanisms remain poorly understood. The recently proposed metabolic theory of ecology (MTE) aims to explain ecological patterns and processes, including geographical patterns of species richness, in terms of the effects of temperature and body size on the metabolism of organisms. Here we use 2 comparable databases of tree distributions in eastern Asia and North America to investigate the roles of environmental temperature and spatial scale in shaping geographical patterns of species diversity. We find that number of species increases exponentially with environmental temperature as predicted by the MTE, and so does the rate of spatial turnover in species composition (slope of the species-area relationship). The magnitude of temperature dependence of species richness increases with spatial scale. Moreover, the relationship between species richness and temperature is much steeper in eastern Asia than in North America: in cold climates at high latitudes there are more tree species in North America, but the reverse is true in warmer climates at lower latitudes. These patterns provide evidence that the kinetics of ecological and evolutionary processes play a major role in the latitudinal pattern of biodiversity.
High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis
Authors: Chen Jianbo , Nikolaitchik Olga , Singh Jatinder , Wright Andrew , Bencsics Craig E. , Coffin John M. , Ni Na , Lockett Stephen , Pathak Vinay K. , Hu Wei-Shau
Published: July 2009

A long-standing question in retrovirus biology is how RNA genomes are distributed among virions. In the studies presented in this report, we addressed this issue by directly examining HIV-1 RNAs in virions using a modified HIV-1 genome that contained recognition sites for BglG, an antitermination protein in the
Escherichia coli
bgl
operon, which was coexpressed with a fragment of BglG RNA binding protein fused to a fluorescent protein. Our results demonstrate that the majority of virions (>90%) contain viral RNAs. We also coexpressed HIV-1 genomes containing binding sites for BglG or the bacteriophage MS2 coat protein along with 2 fluorescent protein-tagged RNA binding proteins. This method allows simultaneously labeling and discrimination of 2 different RNAs at single-RNA-detection sensitivity. Using this strategy, we obtained physical evidence that virions contain RNAs derived from different parental viruses (heterozygous virion) at ratios expected from a random distribution, and we found that this ratio can be altered by changing the dimerization sequences. Our studies of heterozygous virions also support a generally accepted but unproven assumption that most particles contain 1 dimer. This study provides answers to long-standing questions in HIV-1 biology and illustrates the power and sensitivity of the 2-RNA labeling method, which can also be adapted to analyze various issues of RNA biogenesis including the detection of different RNAs in live cell imaging.
Systematic Review of Preventive Interventions for Children's Mental Health: What Would Work in Australian Contexts?
Authors: Bayer Jordana , Hiscock Harriet , Scalzo Katherine , Mathers Megan , McDonald Myfanwy , Morris Alison , Birdseye Joanna , Wake Melissa
Published: July 2009

In childhood, mental health problems primarily consist of behaviour and emotional problems. These affect one in every seven children (i.e. 200 000 in Australia). Left untreated, up to 50% of preschool problems continue through the childhood years. Because of their high prevalence, population-based approaches will be needed to reduce their associated burden. The aim of the present study was therefore to identify evidence-based preventive interventions for behavioural and emotional problems of children aged 0–8 years. Randomized controlled trials of preventive interventions for behavioural and emotional problems were located by searching standard clinical databases and systematic reviews. The authors determined which programmes were effective and ineffective, dividing the effective programmes into those with high or low risk of trial bias. Among effective programmes, the most promising for delivery in Australian contexts were identified, selected for their strength of evidence, sample comparability to Australia's population, and programme compatibility with Australia's service system. Around 50 preventive interventions have been evaluated in randomized controlled trials. Most targeted children's behavioural problems, and a few targeted emotional problems. Three US programmes have the best balance of evidence: in infancy, the individual Nurse Home Visitation Programme; at preschool age, the individual Family Check Up; at school age, the Good Behaviour Game class programme. Three parenting programmes in England and Australia are also worthy of highlight: the Incredible Years group format, Triple P individual format, and Parent Education Programme group format. Effective preventive interventions exist primarily for behaviour and, to a lesser extent, emotional problems, and could be disseminated from research to mainstream in Australia, ensuring fidelity to original programmes. Future research should develop programmes targeting emotional problems, and replicate effective programmes for behaviour problems in quality population translation trials. Randomized trial methods in staged roll-outs can determine population cost–benefits for children's mental health without delaying dissemination.
Community Outcomes of Mentally Disordered Homicide Offenders in Victoria
Authors: Ong Kevin , Carroll Andrew , Reid Shannon , Deacon Adam
Published: July 2009

Objective: The aim of the present study was to describe characteristics and post-release outcomes of Victorian homicide offenders under the Crimes (Mental Impairment and Unfitness to be Tried) Act 1997 (and/or its forerunner legislation) released from forensic inpatient psychiatric care since the development of specialist forensic services.

Method: A legal database identified subjects meeting inclusion criteria: hospitalized in forensic psychiatric care due to finding of mental impairment or unfitness to stand trial for homicide in Victoria; released into the community; and released between 1 January 1991 and 30 April 2002. Using clinical records, demographics, index offence, progress in hospital, diagnosis, psychosocial and criminological data were obtained. Outcomes (offending or readmission into secure care) were obtained from the clinical records.

Results: Of the 25 subjects, 19 (76%) were male. Primary diagnoses on admission to forensic hospital care were schizophrenia, n = 16 (64%); other psychotic disorder, n = 5 (20%); depression, n = 3 (12%); and personality disorder, n = 1 (4%). Mean time in custodial supervision was 11 years and 2 months, less for those whose offence occurred after the development of forensic rehabilitation services. In the first 3 years after release, there was a single episode of criminal recidivism, representing a recidivism rate of 1 in 25 (4%) over 3 years. Twelve subjects (48%) were readmitted at some point in the 3 year follow up.

Conclusion: There was a very low rate of recidivism after discharge, but readmissions to hospital were common. Lengths of custodial care were reduced after the introduction of forensic rehabilitation facilities. Recidivism is low when there are well-designed and implemented forensic community treatment programmes, consistent with other data suggesting a reciprocal relationship between safe community care and a low threshold for readmission to hospital, lessening re-offending at times of crisis. Further research should be directed at timing of release decisions, based on reducing identified risk factors to acceptable levels.
Abnormal Hippocampal Distribution of TDP-43 in Patients With-Late Onset Psychosis
Authors: Velakoulis Dennis , Walterfang Mark , Mocellin Ramon , Pantelis Christos , Dean Brian , McLean Catriona
Published: July 2009

Objective: Young patients with frontotemporal dementia (FTD) may present with schizophrenia-like psychosis. Few studies have investigated whether FTD-like neuropathological changes are present in schizophrenia. The purpose of the present study was therefore to determine whether FTD-like abnormalities in TARDNA binding protein (TDP-43) and ubiquitin are detectable in hippocampal dentate gyrus of patients with schizophrenia and bipolar disorder. A secondary objective was to identify clinicopathological relationships of any such abnormalities.

Methods: Hippocampal sections from 12 patients (nine with schizophrenia and three with bipolar disorder) and 11 control subjects Facility from the National Neural Tissue Resource Centre, Melbourne were blindly rated for the presence or absence of normal TDP-43 staining or ubiquitin-positive neuronal inclusions within the dentate gyrus. The clinical files of all subjects were reviewed for demographic and clinical information.

Results: In three patients the normal expression of nuclear TDP-43 staining was not detected. Significantly, all three subjects presented after the age of 50 and had an adult child diagnosed with the same psychiatric disorder.

Conclusion: Abnormalities in TDP-43 nuclear expression were identified in patients with late-onset psychosis and a positive family history.
Bolus compared with continuous infusion of microbubble contrast agent using real-time contrast harmonic imaging ultrasound in breast tumors
Authors: Saracco A. , Aspelin P. , Leifland K. , Themudo R. , Wilczek B. , Axelsson R.
Published: July 2009

Background: Contrast-enhanced ultrasound (CEUS) has gained interest because of its ability to gather vascular information in various organs. There is still a matter of debate concerning its value in breast lesions. The method of choice on how to administer the contrast agent varies depending on the organ to be studied. Infusion of microbubbles is used in echocardiography, while bolus administration is the preferred technique for abdominal organs.

Purpose: To compare—in equal doses—bolus versus continuous infusion of microbubbles, using real-time contrast harmonic imaging in breast tumors.

Material and Methods: A total of 29 female patients (mean age 54 years) with either clear malignant or benign findings in the breast or axilla were included. Contrast harmonic imaging (CHI US) was performed with a Philips iU22 using an L9-3 MHz linear probe, especially designed for this purpose. A low mechanical index (0.06–0.07) was used to avoid massive destruction of the microbubbles. A dose of 2.4 ml of Sono Vue was first infused intravenously over 1 min with an infusion pump. After 10 min, the same dose was injected as a bolus over 2 s, followed by a flush of 10 ml of saline solution. Contrast uptakes by the tumors were recorded 2 min from the moment of injection, with both methods for each patient.

Results: Bolus administration of contrast agent provided a sharply demarcated enhancement and wash-out pattern for all lesions. The continuous infusion of the same contrast agent failed to show any wash-in/wash-out or time-to-peak/peak intensity phenomena in all cases.

Conclusion: CEUS using real-time harmonic imaging in order to evaluate breast tumors should be performed with bolus administration of contrast agent in order to achieve better intensity/time curve outcomes.
ARMin III – Arm Therapy Exoskeleton with an Ergonomic Shoulder Actuation
Authors: Nef Tobias , Guidali Marco , Riener Robert
Published: July 2009

Rehabilitation robots have become important tools in stroke rehabilitation. Compared to manual arm training, robot‐supported training can be more intensive, of longer duration and more repetitive. Therefore, robots have the potential to improve the rehabilitation process in stroke patients. Whereas a majority of previous work in upper limb rehabilitation robotics has focused on end‐effector‐based robots, a shift towards exoskeleton robots is taking place because they offer a better guidance of the human arm, especially for movements with a large range of motion. However, the implementation of an exoskeleton device introduces the challenge of reproducing the motion of the human shoulder, which is one of the most complex joints of the body. Thus, this paper starts with describing a simplified model of the human shoulder. On the basis of that model, a new ergonomic shoulder actuation principle that provides motion of the humerus head is proposed, and its implementation in the ARMin III arm therapy robot is described. The focus lies on the mechanics and actuation principle. The ARMin III robot provides three actuated degrees of freedom for the shoulder and one for the elbow joint. An additional module provides actuated lower arm pro/supination and wrist flexion/extension. Five ARMin III devices have been manufactured and they are currently undergoing clinical evaluation in hospitals in Switzerland and in the United States.
Editorial
Authors: Pons José L. , Barrios Luis J. , Azorín José M.
Published: July 2009

Erratum to “Corrigendum”dx.doi.org/10.1080/11762320903287693
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential
Authors: Levy-Moonshine Ami , Amir El-ad David , Keasar Chen
Published: July 2009

Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models.

Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns.

Availability: The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/∼meshi.

Contact:  chen.keasar@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
PathBuilder—open source software for annotating and developing pathway resources
Authors: Kandasamy Kumaran , Keerthikumar Shivakumar , Raju Rajesh , Keshava Prasad T. S. , Ramachandra Y. L. , Mohan Sujatha , Pandey Akhilesh
Published: July 2009

Summary: We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein–protein interactions, enzyme–substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets.

Availability: PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms.

Contact:  pandey@jhmi.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis
Authors: Armisen Javier , Gilchrist Michael J. , Wilczynska Anna , Standart Nancy , Miska Eric A.
Published: July 2009

Small regulatory RNAs have recently emerged as key regulators of eukaryotic gene expression. Here we used high-throughput sequencing to determine small RNA populations in the germline and soma of the African clawed frog Xenopus tropicalis. We identified a number of miRNAs that were expressed in the female germline. miRNA expression profiling revealed that miR-202-5p is an oocyte-enriched miRNA. We identified two novel miRNAs that were expressed in the soma. In addition, we sequenced large numbers of Piwi-associated RNAs (piRNAs) and other endogenous small RNAs, likely representing endogenous siRNAs (endo-siRNAs). Of these, only piRNAs were restricted to the germline, suggesting that endo-siRNAs are an abundant class of small RNAs in the vertebrate soma. In the germline, both endogenous small RNAs and piRNAs mapped to many high copy number loci. Furthermore, endogenous small RNAs mapped to the same specific subsets of repetitive elements in both the soma and the germline, suggesting that these RNAs might act to silence repetitive elements in both compartments. Data presented here suggest a conserved role for miRNAs in the vertebrate germline. Furthermore, this study provides a basis for the functional analysis of small regulatory RNAs in an important vertebrate model system.
The price of advice
Authors: Eső Péter , Szentes Balázs
Published: July 2009

We develop a model of consulting (advising) where the role of the consultant is to reveal signals to her client that refine the client's original private estimate of the profitability of a project. Although the client can perfectly observe and evaluate these signals, the consultant may only be able to do the same imperfectly, or not at all. This captures the idea that the expert may not fully understand the impact of her advice on the client. We characterize the optimal contract between the consultant and her client. It is a menu consisting of pairs of transfers specifying payments between the two parties in case the project is undertaken by the client and in case it is not. The main result of the article is that in the optimal mechanism, the consultant obtains the same profit as though she could perfectly observe and evaluate the impact of the signals whose release she controls on the client's profit estimate.
The rules of standard‐setting organizations: an empirical analysis
Authors: Chiao Benjamin , Lerner Josh , Tirole Jean
Published: July 2009

This article empirically explores standard‐setting organizations' policy choices. Consistent with our earlier theoretical work, we find (i) a negative relationship between the extent to which an SSO is oriented to technology sponsors and the concession level required of sponsors and (ii) a positive correlation between the sponsor friendliness of the selected SSO and the quality of the standard. We also develop and test two extensions of the earlier model: the presence of provisions mandating royalty‐free licensing is negatively associated with disclosure requirements, and the relationship between concessions and user friendliness is weaker when there is only a limited number of SSOs.
Semiparametric estimation of multinomial discrete‐choice models using a subset of choices
Authors: Fox Jeremy T.
Published: July 2009

Nonlogit maximum‐likelihood estimators are inconsistent when using data on a subset of the choices available to agents. I show that the semiparametric, multinomial maximum‐score estimator is consistent when using data on a subset of choices. No information is required for choices outside of the subset. The required conditions about the error terms are the same conditions as for using all the choices. Estimation can proceed under additional restrictions if agents have unobserved, random consideration sets. A solution exists for instrumenting endogenous continuous variables. Monte Carlo experiments show the estimator performs well using small subsets of choices.
Do enhancements to loyalty programs affect demand? The impact of international frequent flyer partnerships on domestic airline demand
Authors: Lederman Mara
Published: July 2009

Frequent flyer programs (FFPs) may allow airlines to exercise market power on routes that depart from airports at which they are dominant. Prior research, however, has not disentangled the effects of FFPs from other advantages that dominant airlines may possess. I exploit variation in the extent and scope of U.S. airlines' FFP partnerships with international carriers to evaluate the economic impact of enhancements to FFPs. The results indicate that enhancements to an airline's FFP are associated with increases in its demand on specifically those routes that depart from airports at which it is dominant.
The effect of social environment during ontogeny on life history expression in the guppy Poecilia reticulata
Authors: Magellan K. , Magurran A.E.
Published: July 2009

The effects of the social environment during development on life‐history decisions and adult behaviour were assessed using male guppies Poecilia reticulata. Males raised with adults developed secondary sexual characteristics later than males raised either singly or with four of their siblings indicating social inhibition of maturation was evident in P. reticulata. There was no effect, however, of rearing environment on male behaviour. The results reveal that social environment during development can influence life‐history decisions but is less important than immediate social context in determining male behavioural phenotype in P. reticulata.
Colour morph of a probable queen angelfish Holacanthus ciliaris from Dry Tortugas, Florida
Authors: Feeley M. W. , Luiz jr O. J. , Zurcher N.
Published: July 2009

An unusual colour morph of a probable Holacanthus ciliaris was observed in Dry Tortugas, Florida, which can possibly be explained by recessive homozygosity, however, further testing is necessary. This variation of H. ciliaris has previously only been described at St Paul's Rocks, Mid‐Atlantic Ridge.
Promoter‐wide analysis of Smad4 binding sites in human epithelial cells
Authors: Koinuma Daizo , Tsutsumi Shuichi , Kamimura Naoko , Imamura Takeshi , Aburatani Hiroyuki , Miyazono Kohei
Published: July 2009

Smad4, the common partner Smad, is a key molecule in transforming growth factor‐β (TGF‐β) family signaling. Loss of Smad4 expression is found in several types of cancer, including pancreatic cancer and colon cancer, and is related to carcinogenesis. Here we identified Smad4 binding sites in the promoter regions of over 25 500 known genes by chromatin immunoprecipitation on a microarray (ChIP‐chip) in HaCaT human keratinocytes. We identified 925 significant Smad4 binding sites. Approximately half of the identified sites overlapped the binding regions of Smad2 and Smad3 (Smad2/3, receptor‐regulated Smads in TGF‐β signaling), while the rest of the regions appeared dominantly occupied by Smad4 even when a different identification threshold for Smad2/3 binding regions was used. Distribution analysis showed that Smad4 was found in the regions relatively distant from the transcription start sites, while Smad2/3 binding regions were more often present near the transcription start sites. Motif analysis also revealed that activator protein 1 (AP‐1) sites were especially enriched in the sites common to Smad2/3 and Smad4 binding regions. In contrast, GC‐rich motifs were enriched in Smad4‐dominant binding regions. We further determined putative target genes of Smad4 whose expression was regulated by TGF‐β. Our findings revealed some general characteristics of Smad4 binding regions, and provide resources for examining the role of Smad4 in epithelial cells and cancer pathogenesis. (Cancer Sci 2009)
High WT1 gene expression before haematopoietic stem cell transplant in children with acute myeloid leukaemia predicts poor event‐free survival
Authors: Jacobsohn David A. , Tse William T. , Chaleff Stanley , Rademaker Alfred , Duerst Reggie , Olszewski Marie , Huang Wei , Chou Pauline M. , Kletzel Morris
Published: July 2009

WT1 gene expression has been proposed as a useful marker of minimal residual disease in leukaemia. Its utility in paediatric haematopoietic stem cell transplantation (HSCT) has not been studied. We studied the prognostic value of WT1 expression in peripheral blood prior to HSCT in 36 children with acute myeloid leukaemia (AML). Samples were obtained 2 weeks pre‐transplant to determine the level of WT1 expression. WT1 expression was normalized using K562 cells as a control and a relative value of 0·5 was chosen as the cut‐off point between high and low WT1 expression. The median level of pre‐transplant WT1 expression in the 36 patients was 0·09 (range 0·0001–11·0), with 11patients having WT1 ≥ 0·5 and 25, WT1 < 0·5. After HSCT, 76% of patients with high pre‐transplant WT1 expression relapsed, in contrast to 0% of the patients with low WT1 expression. Those with high WT1 expression had significantly lower 5‐year event‐free survival (EFS) (18%, 95% CI 0–40%) as compared to those with low WT1 expression (68%, 95% CI 50–86%, P = 0·007). Multivariate analysis showed that pre‐transplant WT1 level is the only significant prognostic factor for the difference in EFS. Our finding suggests that elevated WT1 gene expression before HSCT in paediatric AML predicts relapse and poor long‐term EFS. A larger prospective study is warranted to compare the value of high WT1 expression and other markers of minimal residue disease in predicting clinical outcomes after HSCT.
Anti‐oxidized LDL antibody levels are reduced in women with hypertension
Authors: Garrido‐Sánchez L. , García‐Fuentes E. , Cardona F. , Rojo‐Martínez G. , Soriguer F. , Tinahones F. J.
Published: July 2009

Background  Previous studies have suggested that hypertension may be associated with increased oxidized low‐density lipoprotein (LDL). Increased in vitro oxidizability of LDL or elevated titers of anti‐oxidized LDL antibodies have been shown in subjects with essential hypertension. However, the relationship between oxidized LDL and hypertension is equivocal. We examined the association between hypertension and levels of IgG anti‐oxidized LDL antibodies in a group of women from the general population.

Materials and methods  The study included 619 women classified according to their blood pressure values. IgG anti‐oxidized LDL antibodies were measured by enzyme‐linked immunosorbent assay and the women were classified as being above or below the 50th percentile.

Results  Hypertension was present in 54·3% of the women. These women had significantly lower levels of IgG anti‐oxidized LDL antibodies than the normotensive women (0·280 ± 0·117 vs. 0·336 ± 0·125, P < 0·001). Both systolic and the diastolic blood pressures showed a significant negative correlation with the levels of IgG anti‐oxidized LDL antibodies (r = −0·204, P < 0·001; r = −0·225, P < 0·001, respectively). Women with IgG anti‐oxidized LDL antibody levels above the 50th percentile had a lower prevalence of hypertension than those with IgG anti‐oxidized LDL antibody levels below the 50th percentile (40·2% vs. 59·8%) (P < 0·001).

Conclusions  Women with hypertension had lower levels of IgG anti‐oxidized LDL antibodies than normotensive women.
User involvement in developing mobile and temporarily interconnected systems
Authors: Henfridsson Ola , Lindgren Rikard
Published: July 2009

Information systems (IS) research on user involvement has primarily theorized relationships between developers, managers and users in systems development. However, so far, marginal attention has been paid to differences in user involvement practices between information systems. This paper explores user involvement in developing mobile and temporarily interconnected systems (MTIS). We refer to MTIS as heterogeneous systems that rely on network technologies for increasing the ubiquity of information services for users on the move. Such systems are becoming increasingly important in leveraging, e.g. car infotainment, supply chain management and wireless e‐commerce. With particular emphasis on the nature of MTIS and its implications for user involvement, the paper analyses the systems development process of an action research project. The findings suggest that user involvement practices need to be adapted to accommodate features of this class of systems. Being an early attempt to trace the implications of technology features such as use context switches and temporary system relationships, the paper contributes to the development of an updated theory of the user role in an era of increased system complexity and stakeholder ambiguity.
Who are the users? Who are the developers? Webs of users and developers in the development process of a technical standard
Authors: Millerand Florence , Baker Karen S.
Published: July 2009

The paper presents an empirical study of user involvement in developing a technical standard for a scientific community's information system project. The case illustrates how multiple perspectives are involved when considering the user role in practice. The case presents a situation where both developers and users were pre‐defined in the design and development phases of the standard as homogeneous groups of actors. Groups of actors changed to become more heterogeneous and ‘fluid’ in the deployment and implementation phases, thus forming ‘webs of developers’ and ‘webs of users’. Detailed analysis of the process in its entirety shows the blurredness of boundaries between ‘developer’ and ‘user’ categories and roles, and reveals challenges at social and organizational levels. Three models pertaining to the system development process are presented in order to illuminate differing perspectives on the user and on the development process itself. The paper draws theoretically from information systems, social informatics, and science and technology studies. The research contributes to a deeper, interdisciplinary understanding of ‘the’ user, of multiple roles in systems development, and of dynamic sets of user–developer relations.