bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing highly complex distributed systems: a software engineering perspective
Authors: Autili Marco , Inverardi Paola , Pelliccione Patrizio , Tivoli Massimo 
Published: November 2011

Abstract
What is a highly complex distributed system in the future era? What are the needs that may drive the development of such systems? And what is their life cycle? Is there any new challenge for Software Engineering (SE)? In this paper, we try to provide a partial answer to the above questions by characterizing few application domains that we consider of raising interest in the next years. Our thesis is that there is a need to rethink the whole software process for such systems. The traditional boundaries between static and dynamic activities disappear and development support mingles with run time support thus invading the middleware territory.
Assessing fetal response to maternal speech using a noninvasive functional brain imaging technique
Authors: Jardri Renaud , Houfflin‐Debarge Véronique , Delion Pierre , Pruvo Jean‐Pierre , Thomas Pierre , Pins Delphine 
Published: November 2011

AbstractEvidence for cortical sensory activation in the human fetus at the beginning of the third trimester of pregnancy was provided in a recent imaging study. Although hearing is functional before birth, it is not clear whether recognition of the mother's voice is learned in utero or rapidly following delivery. We developed an original fMRI procedure that allows for the specific exploration of fetal brain response to auditory stimuli. This procedure provides the first in vivo evidence for the development of maternal voice recognition in utero between 33 and 34 weeks of gestation. This methodology could have crucial implications in the study of fetal cognition.
Boundary-layer-separation-driven vortex shedding beneath internal solitary waves of depression
Authors: Aghsaee Payam , Boegman Leon , Diamessis Peter J. , Lamb Kevin G. 
Published: November 2011

AbstractWe investigate global instability and vortex shedding in the separated laminar boundary layer beneath internal solitary waves (ISWs) of depression in a two-layer stratified fluid by performing high-resolution two-dimensional direct numerical simulations. The simulations were conducted with waves propagating over a flat bottom and shoaling over relatively mild $(S= 0. 05)$ and steep $(S= 0. 1)$ slopes. Over a flat bottom, the potential for vortex shedding is shown to be directly dependent on wave amplitude, for a particular stratification, owing to increase of the adverse pressure gradient ($\mathrm{d} P/ \mathrm{d} x\gt 0$ for leftward propagating waves) beneath the trailing edge of larger amplitude waves. The generated eddies can ascend from the bottom boundary to as high as 33 % of the total depth in two-dimensional simulations. Over sloping boundaries, global instability occurs beneath all waves as they steepen. For the slopes considered, vortex shedding begins before wave breaking and the vortices, shed from the bottom boundary, can reach the pycnocline, modifying the wave breaking mechanism. Combining the results over flat and sloping boundaries, a unified criterion for vortex shedding in arbitrary two-layer continuous stratifications is proposed, which depends on the momentum-thickness Reynolds number and the non-dimensionalized ISW-induced pressure gradient at the point of separation. The criterion is generalized to a form that may be readily computed from field data and compared to published laboratory experiments and field observations. During vortex shedding events, the bed shear stress, vertical velocity and near-bed Reynolds stress were elevated, in agreement with laboratory observations during re-suspension events, indicating that boundary layer instability is an important mechanism leading to sediment re-suspension.
The UK great bustard Otis tarda reintroduction trial: a 5-year progress report
Authors: Burnside Robert J. , Carter Ian , Dawes Alasdair , Waters David , Lock Leigh , Goriup Paul , Székely Tamás 
Published: November 2011

AbstractThe great bustard Otis tarda became extinct in the UK during the 19th century due to a combination of factors, including hunting, egg collection and changes in agriculture. In 2003 a 10-year licence was granted to begin a trial to reintroduce the species back to the UK. Here we report on the first 5 years of the trial and assess the progress made towards establishing a founder population. From April 2004 to September 2009 a total of 102 great bustard chicks were imported from Russia and 86 released on Salisbury Plain. Monitoring showed that post-release survival was 18% in the first year following release, and that mortality of released bustards was mainly attributable to predation and collisions. Estimated adult survival was 74%, although the sample size was small. All known surviving great bustards are faithful to the surroundings of the release site, returning throughout the year. A lek has been established where males have been observed displaying to females. The first nesting attempt was in 2007, and in 2009 two females aged 3 and 4 years successfully nested, fledging one chick each. Models incorporating the new demographic estimates suggest that at the end of the 10-year trial period the project can expect to have 8–26 adults as a founder population.
Modelling the impact of extended vaccination strategies on the epidemiology of pertussis
Authors: ROZENBAUM M. H. , De VRIES R. , LE H. H. , POSTMA M. J. 
Published: November 2011

SUMMARYThe aim of this study was to investigate the optimal pertussis booster vaccination strategy for The Netherlands. A realistic age-structured deterministic model was designed. Assuming a steady-state situation and correcting for underreporting, the model was calibrated using notification data from the period 1996–2000. Several sensitivity analyses were performed to explore the impact of different assumptions for parameters surrounded by uncertainty (e.g. duration of protection after natural infection, underreporting factors, and transmission probabilities). The optimal age of an additional booster dose is in the range of 10–15 years, and implementation of this booster dose will reduce both symptomatic and asymptomatic infections, although the incidence of symptomatic infections in older age groups will increase. The impact of the different assumptions used in the model was in general limited. We conclude that over a wide range of assumptions, an additional booster dose can reduce the incidence of pertussis in the population.
Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter
Authors: Oakley Brian B , Carbonero Franck , Dowd Scot E , Hawkins Robert J , Purdy Kevin J 
Published: November 2011

Abstract
Understanding the ecological principles underlying the structure and function of microbial communities remains an important goal for microbial ecology. We examined two biogeochemically important taxa, the sulfate-reducing bacterial genus, Desulfobulbus, and the methanogenic archaeal genus, Methanosaeta, to compare and contrast niche partitioning by these two taxa that are ecologically linked as anaerobic terminal oxidizers of organic material. An observational approach utilizing functional gene pyrosequencing was combined with a community-based reciprocal incubation experiment and characterization of a novel Desulfobulbus isolate. To analyze the pyrosequencing data, we constructed a data analysis pipeline, which we validated with several control data sets. For both taxa, particular genotypes were clearly associated with certain portions of an estuarine gradient, consistent with habitat or niche partitioning. Methanosaeta genotypes were generally divided between those found almost exclusively in the marine habitat (∼30% of operational taxonomic units (OTUs)), and those which were ubiquitously distributed across all or most of the estuary (∼70% of OTUs). In contrast to this relatively monotonic distribution, for Desulfobulbus, there were many more genotypes, and their distributions represented a wide range of inferred niche widths from specialist genotypes found only at a single site, to ubiquitous or generalist genotypes found in all 10 sites examined along the full estuarine gradient. Incubation experiments clearly showed that, for both taxa, communities from opposite ends of the estuary did not come to resemble one another, regardless of the chemical environment. Growth of a Desulfobulbus isolated into pure culture indicated that the potential niche of this organism is significantly larger than the realized niche. We concluded that niche partitioning can be an important force structuring microbial populations, with biotic and abiotic components having very different effects depending on the physiology and ecology of each taxon.
Bidirectional transport of organelles: unity and struggle of opposing motors
Authors: Bryantseva Sofiya A. , Zhapparova Olga N. 
Published: November 2011

AbstractBidirectional transport along microtubules is ensured by opposing motor proteins: cytoplasmic dynein that drives cargo to the minus‐ends and various kinesins that generally move to the plus‐ends of microtubules. Regulation of motor proteins that are simultaneously bound to the same organelle is required to maintain directional transport and prevent pausing of cargo pulled away by motors of opposite polarity. Debates of the recent decade have been focused on two possible mechanisms of such regulation: (i) coordination, which implies that only one type of motors is active at a given time, and (ii) tug‐of‐war, which assumes that both motors are active at the same time and that direction of transport depends on the outcome of motor's confrontation. The initial idea of coordination has been challenged by observations of simultaneous activity of plus‐ and minus‐end‐directed motors applied to the same cargo. Analysis of the available data indicates that coordination and tug‐of‐war theories rather complement than contradict each other: cargo interacts with two teams of active motors, the resulting direction and the winner team are determined by coordination complexes, but the activity of the loser team is never completely inhibited and remains at some background level. Such persisting activity might enhance the overall efficiency of transport by increasing processivity or helping to overcome the obstacles on microtubule track.
Laser-assisted surface patterning of magnesium with silver nanoparticles: synthesis, characterization and modelling
Authors: Foroozmehr Ehsan , Alemohammad Hamidreza , Wang Xiang , Toyserkani Ehsan , Esmaeili Shahrzad 
Published: November 2011

Abstract
Surface patterning of biocompatible materials may improve cell adhesion, infiltration and proliferation. Magnesium is a biocompatible metal which has bioresorption capability, as well as a low elastic modulus. This unique combination of properties has attracted researchers to develop biodegradable magnesium devices. In this work, the patterning of magnesium with silver nanoparticles printed by the laser-assisted maskless microdeposition (LAMM) process was studied. The geometry and microstructure of the printed silver patterns and the diffusion zone at the Mg/Ag interface were studied using profilometry, scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDS) and transmission electron microscopy (TEM). The TEM analysis suggested that some intermetallic particles may form at the interface during laser sintering. The penetration curve of the Ag–Mg diffusion couple was obtained using EDS analysis. A finite element model is developed to simulate the LAMM process of silver nanoparticles on magnesium substrates. The model included a thermal analysis for determining the temperature history throughout the process, coupled with a diffusion model for evaluating compositional profiles across the interface. A comparison of the predicted profiles with the EDS results showed that the modelling and the experimental results qualitatively match. The analysis of SEM micrographs of the sintered nanoparticles, in light of the thermal modelling results, suggested that a minimum laser heat input was required for effective sintering of the nanoparticles.
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation
Authors: Gatto Laurent , Lilley Kathryn S. 
Published: November 2011

Abstract
Summary: MSnbase is an R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. It provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation. MSnbase allows direct integration of quantitative proteomics data with additional facilities for statistical analysis provided by the Bioconductor project.
Availability: MSnbase is implemented in R (version ≥2.13.0) and available at the Bioconductor web site (http://www.bioconductor.org/). Vignettes outlining typical workflows, input/output capabilities and detailing underlying infrastructure are included in the package.
Contact: lg390@cam.ac.uk
Supplementary information: Supplementary data are available from Bioinformatics online.
Assembly of the Light-Harvesting Chlorophyll Antenna in the Green Alga Chlamydomonas reinhardtii Requires Expression of the TLA2-CpFTSY Gene
Authors: Kirst Henning , García-Cerdán Jose Gines , Zurbriggen Andreas , Melis Anastasios 
Published: November 2011

Abstract
The truncated light-harvesting antenna2 (tla2) mutant of Chlamydomonas reinhardtii showed a lighter-green phenotype, had a lower chlorophyll (Chl) per-cell content, and higher Chl a/b ratio than corresponding wild-type strains. Physiological analyses revealed a higher intensity for the saturation of photosynthesis and greater P max values in the tla2 mutant than in the wild type. Biochemical analyses showed that the tla2 strain was deficient in the Chl a-b light-harvesting complex, and had a Chl antenna size of the photosystems that was only about 65% of that in the wild type. Molecular and genetic analyses showed a single plasmid insertion in the tla2 strain, causing a chromosomal DNA rearrangement and deletion/disruption of five nuclear genes. The TLA2 gene, causing the tla2 phenotype, was cloned by mapping the insertion site and upon complementation with each of the genes that were deleted. Successful complementation was achieved with the C. reinhardtii TLA2-CpFTSY gene, whose occurrence and function in green microalgae has not hitherto been investigated. Functional analysis showed that the nuclear-encoded and chloroplast-localized CrCpFTSY protein specifically operates in the assembly of the peripheral components of the Chl a-b light-harvesting antenna. In higher plants, a cpftsy null mutation inhibits assembly of both the light-harvesting complex and photosystem complexes, thus resulting in a seedling-lethal phenotype. The work shows that cpftsy deletion in green algae, but not in higher plants, can be employed to generate tla mutants. The latter exhibit improved solar energy conversion efficiency and photosynthetic productivity under mass culture and bright sunlight conditions.
RNA‐Seq reveals infection‐related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew
Authors: KUNJETI SRIDHARA G. , EVANS THOMAS A. , MARSH ADAM G. , GREGORY NANCY F. , KUNJETI SARITHA , MEYERS BLAKE C. , KALAVACHARLA VENUGOPAL S. , DONOFRIO NICOLE M. 
Published: November 2011

SUMMARYLima bean is an important vegetable processing crop to the mid‐Atlantic USA and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew. Genetic resistance and fungicides are used to manage P. phaseoli and often fail. Currently, the molecular basis of the interaction between this host and pathogen is unknown. To begin to rectify this situation, we used Illumina RNA‐Seq to perform a global transcriptome analysis comparing P. phaseoli growing in culture with P. phaseoli infecting its host. Sequence reads from a total of six libraries mapped to gene models from the closely related late blight pathogen, Phytophthora infestans, resulting in 10 427 P. phaseoli genes with homology to P. infestans and expression in at least one library. Of these, 318 P. phaseoli homologues matched known or putative virulence genes in P. infestans. Two well‐studied classes, RxLRs and elicitins, were up‐regulated in planta, whereas the reverse was true for another class, called crinklers. These results are discussed with respect to the differences and similarities in the pathogenicity mechanisms of P. phaseoli and P. infestans.
The long‐term outcome of patients with polycystic liver disease treated with lanreotide
Authors: Chrispijn M. , Nevens F. , Gevers T. J. G. , Vanslembrouck R. , van Oijen M. G. H. , Coudyzer W. , Hoffmann A. L. , Dekker H. M. , de Man R. A. , van Keimpema L. , Drenth J. P. H. 
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 266–274SummaryBackground  Polycystic liver disease (PLD) is a phenotypical expression of autosomal dominant polycystic kidney disease and isolated polycystic liver disease. Somatostatin analogues, such as lanreotide, reduce polycystic liver volume.Aim  To establish long‐term outcome and safety of lanreotide.Methods  This was an open‐label, observational extension study of a 6‐month, randomised, placebo‐controlled trial with lanreotide (120 mg/month) in PLD. The length of total treatment was 12 months. Primary endpoint was relative change in liver volume, as determined by CT‐volumetry after 12 months of treatment. We offered patients a CT scan 6 months after stopping lanreotide.Results  A total of 41/54 (76%) patients participated in the extension study. Liver volume decreased by 4% (IQR −8% to −1%) after 12 months of treatment. The greatest effect was observed during the first 6 months of treatment (decrease of 4% (IQR −6% to −1%)). Liver volume remained unchanged during the following 6 months. We found that liver volume increased by 4% (IQR 0–6%) 6 months after end of treatment (n = 22).Conclusions  Lanreotide reduces liver volume within the first 6 months of treatment and the beneficial effect is maintained in the following 6 months. Stopping results in recurrence of polycystic liver growth. This suggests that continuous use of lanreotide is needed to maintain its effect.
Efficacy and tolerability of methotrexate therapy for refractory Crohn’s disease: a large single‐centre experience
Authors: Suares N. C. , Hamlin P. J. , Greer D. P. , Warren L. , Clark T. , Ford A. C. 
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 284–291SummaryBackground  Randomised controlled trials demonstrate that methotrexate is effective in inducing remission and preventing relapse of Crohn’s disease (CD) as a first‐line immunosuppressant, but efficacy data after failure with, or intolerance to, thiopurines are limited.Aims  To report efficacy of methotrexate in a cohort of refractory CD patients, most of whom had not responded to, or were intolerant of, thiopurines.Methods  Data were collected for patients receiving methotrexate for active CD. Response to methotrexate induction therapy at 4 months, and sustained clinical benefit at last point of follow‐up with maintenance therapy, were assessed via physician’s global assessment. Demographic and disease factors predicting response, or sustained clinical benefit, were examined by univariate and multivariate analysis.Results  Sixty‐six [38 (54%) female patients, mean age at diagnosis 29.4 years] patients received methotrexate between 2001 and 2010, 61 (92%) of whom received the drug parenterally. Sixty patients had failed, or were intolerant of, thiopurines. Response to therapy at 4 months occurred in 54 (82%) patients. However, sustained clinical benefit occurred in only 19 (29%) patients at last point of follow‐up, including six patients who discontinued the drug for family planning reasons. No predictors of response or sustained clinical benefit were identified. Adverse events occurred in 20 (30%) patients.Conclusions  These data suggest that methotrexate is effective in terms of initial response in Crohn’s disease patients who have failed, or are intolerant of, thiopurines. However, efficacy is not sustained in the long term.
Meta‐analysis: the relative efficacy of oral bowel preparations for colonoscopy 1985–2010
Authors: Belsey J. , Crosta C. , Epstein O. , Fischbach W. , Layer P. , Parente F. , Halphen M. 
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 222–237SummaryBackground  Previous reviews of bowel preparation for colonoscopy have given contradictory answers.Aim  To provide a definitive insight, using PRISMA‐compliant methodology.Methods  A comprehensive literature review identified randomised controlled trials comparing bowel preparation regimens. Data for quality of bowel preparation were pooled in multiple meta‐analyses exploring a range of inclusion criteria.Results  A total of 104 qualifying studies were identified, the majority of which involved comparisons of sodium phosphate (NaP) or polyethylene glycol (PEG). There was no significant difference demonstrated between NaP and PEG overall (OR = 0.82; 95% CI = 0.56–1.21; P = 0.36). Cumulative meta‐analysis demonstrated that this conclusion has been qualitatively similar since the mid 1990s, with little quantitative change for the past 10 years. Amongst studies with previous day dosing in both study arms there was a significant advantage in favour of PEG (OR = 1.78; 95% CI = 1.13–2.81; P = 0.006). Studies focussing on results in the proximal colon also favoured PEG (OR = 2.36; 95% CI = 1.16–4.77; P = 0.012). PEG was also significantly more effective than non‐NaP bowel preparation regimens (OR = 2.02; 95% CI = 1.08–3.78; P = 0.03). Other comparisons showed no significant difference between regimens.Conclusions  Although there is no compelling evidence favouring either of the two most commonly used bowel preparation regimens, this may reflect shortcomings in study design. Where studies have ensured comparable dosage, or the clinically relevant outcome of proximal bowel clearance is considered, PEG‐based regimens offer the most effective option.