bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles
Authors: Omelyan Igor P. , Kovalenko Andriy 
Published: December 2011

We have developed several multiple time stepping techniques to overcome the limitations on efficiency of molecular dynamics simulations of complex fluids. They include the modified canonical and isokinetic schemes, as well as the extended isokinetic Nosé-Hoover chain approach. The latter generalizes the method of Minary, Tuckerman, and Martyna for translational motion [Phys. Rev. Lett. 93, 150201 (2004)]10.1103/PhysRevLett.93.150201 to systems with both translational and orientational degrees of freedom. Although the microcanonical integrators are restricted to relatively small outer time steps of order of 16 fs, we show on the basis of molecular dynamics simulations of ambient water that in the canonical and isokinetic thermostats the size of these steps can be increased to 50 and 75 fs, respectively (at the same inner time step of 4 fs). Within the generalized isokinetic Nosé-Hoover chain algorithm we have derived, huge outer time steps of order of 500 fs can be used without losing numerical stability and affecting equilibrium properties
Optimal Multiwavelength Source Detection: Experience Gained from the WISE Mission
Authors: Marsh K. A. , Jarrett T. H. 
Published: December 2011

AbstractWe discuss the optimal detection of point sources from multiwavelength imaging data using an approach, referred to as MDET, which requires no prior knowledge of the source spectrum. MDET may be regarded as a somewhat more general version of the so-called ‘chi-squared’ technique. We describe the theoretical basis of the technique, and show examples of its performance with four-channel infrared broadband imaging data from the WISE mission. We also discuss the potential benefits of applying it to the multifrequency data cubes of the ASKAP surveys, and suggest that it could increase the detection sensitivity of searches for neutral hydrogen emission at moderately high redshifts.
Impacts of Adfluvial Fish on the Ecology of Two Great Lakes Tributaries
Authors: Ivan Lori N. , Rutherford Edward S. , Johengen Thomas H. 
Published: December 2011

AbstractAnadromous and adfluvial fish can transport high concentrations of nutrients and energy into streams during spawning runs. While the ecological effects of their spawning migrations are variable, in some instances these fish contribute to increased nutrient concentrations, primary productivity, invertebrate biomass, and resident fish growth and survival in the nutrient‐poor streams of the Pacific Northwest. In tributaries of the Great Lakes, the effects of introduced salmonid and native adfluvial fish are poorly documented. We conducted field experiments to determine the effects of a semelparous fall fish, Chinook salmon Oncorhynchus tshawytscha, and an iteroparous spring fish, steelhead O. mykiss, on the ecology and productivity of two tributaries to the Muskegon River, Michigan, a Lake Michigan tributary. We sampled stream biota and water chemistry before and after the introduction of Chinook salmon carcasses and eggs in the fall and steelhead eggs in the spring in a tributary stream with natural spawning runs and in another tributary stream without runs but with carcass and egg additions. There was no response in terms of invertebrate density or water chemistry to spawning migrations or salmon carcass introductions in either tributary. The density of resident brown trout Salmo trutta increased in both stream types after the introduction of salmon carcasses in the fall, and energy consumption increased after the addition of salmon eggs in the fall and spring in the manipulated stream. Based on stomach content analysis, fish that had eggs in their stomachs also consumed more energy than fish that did not consume eggs. The results suggest that adfluvial fish may affect some tributaries of the Great Lakes by providing high‐energy food sources to resident stream fish, but the potential effect of this egg consumption on resident fish growth and survival requires more research.
Concentration of Infectious Aquatic Rhabdoviruses from Freshwater and Seawater Using Ultrafiltration
Authors: Grant Amelia A. M. , Jakob Eva , Richard Jon , Garver Kyle A. 
Published: December 2011

Abstract
Infectious hematopoietic necrosis virus (IHNV), viral hemorrhagic septicemia virus, and spring viremia of carp virus were concentrated and detected from freshwater and seawater samples by using hollow-fiber ultrafiltration. Within 60 min, virus in a 50-L freshwater or saltwater sample was concentrated more than 70-fold, and virus retention efficiencies were consistently greater than 88%. Retention efficiency was highly dependent upon concentrations of column blocking and sample stabilization solutions. A large column with a surface area of 1.15 m2 and a filtration capacity of 5–200 L exhibited optimal viral retention when blocked with 2% fetal bovine serum (FBS) and when the samples were supplemented with 0.1% FBS. Conversely, a small column with 100-fold less surface area and a filtering capacity of 0.5–2.0 L was optimized when blocked with 1% FBS and when the samples were supplemented with 0.1% FBS. The optimized ultrafiltration procedure was further validated with water from a tank that contained IHNV-exposed juvenile sockeye salmon Oncorhynchus nerka, resulting in an average virus retention efficiency of 91.6 ± 4.1% (mean ± SE). Virus quantification of concentrated samples demonstrated that IHNV shedding in sockeye salmon preceded mortality; shedding of the virus was observed to increase significantly as early as 7 d postchallenge and peaked at day 14, when virus levels reached 4.87 × 103 plaque-forming units/mL. We conclude that ultrafiltration is a reliable and effective method for concentrating viable aquatic rhabdoviruses from large volumes of water and has application for the analysis of environmental water samples.
Received April 22, 2011; accepted August 4, 2011
Stimulus velocity effect in a complex interceptive task in right‐ and left‐handers
Authors: Rodrigues Paula C. , Barbosa Ricardo , Carita Ana Isabel , Barreiros João , Vasconcelos Olga 
Published: December 2011

AbstractThis study investigated stimulus velocity effect on manual asymmetry during planning and execution of a complex coincidence‐anticipation task. Left‐ and right‐handers were required to press six buttons sequentially in conjunction with visual stimulus provided by a coincidence‐anticipation device. Results showed that (1) stimulus velocity affected timing response and timing accuracy only for right‐handers, who responded faster but less accurately in the fast stimulus velocity, (2) manual asymmetries for both handedness groups revealed a left‐hand advantage for initiating the movement, and a preferred‐hand advantage for movement time. The preferred‐hand advantage in timing accuracy was only observed in the fast stimulus velocity. These findings are discussed in the framework of the hemispheric functional lateralisation.
Combustion synthesis and characterization of Er3+-doped and Er3+, Yb3+-codoped YVO4 nanophosphors oriented for luminescent biolabeling applications
Authors: Nguyen Vu , Chi Tran Thi Kim , Nguyen Duc Van 
Published: December 2011

Abstract

YVO
4:Er
3+ and YVO
4:Er
3+, Yb
3+ nanomaterials were prepared via combustion synthesis using urea as fuel and metal nitrates as precursor. The morphology and the structure of the prepared samples were characterized by x-ray diffraction, scanning electron microscopy and transmission electron microscopy. The average size of the prepared materials ranged from 20 to 30 nm in diameter. The effects of Er
3+ and Yb
3+ doping concentrations on structure and optical properties have been investigated. Optical properties of YVO
4:Er
3+ and YVO
4:Er
3+, Yb
3+ nanoparticles were measured by photoluminescent excitation and emission spectroscopies. For the YVO
4:Er
3+ and YVO
4:Er
3+, Yb
3+ samples, two strong green emissions centered at 524 and 552 nm are found, corresponding to the 2
H
11/2—4
I
15/2 and 4
S
11/2—4
I
15/2 transitions of Er
3+ ions, respectively. Upconversion emission in the green region of the YVO
4:Er
3+ nanoparticles under 980 nm excitation was also investigated. Strong emission from these materials is promising for luminescent biolabeling applications.
Combined use of high‐sensitivity ST2 and NTproBNP to improve the prediction of death in heart failure
Authors: Bayes‐Genis Antoni , de Antonio Marta , Galán Amparo , Sanz Héctor , Urrutia Agustin , Cabanes Roser , Cano Lucía , González Beatriz , Díez Cristanto , Pascual Teresa , Elosúa Roberto , Lupón Josep 
Published: December 2011

AimsTo address the incremental usefulness of biomarkers from different disease pathways for predicting risk of death in heart failure (HF).Methods and resultsWe used data from consecutive patients treated at a structured multidisciplinary HF unit to investigate whether a combination of biomarkers reflecting ventricular fibrosis, remodelling, and stretch [ST2 and N‐terminal pro brain natriuretic peptide (NTproBNP)] improved the risk stratification of a HF patient beyond an assessment based on established mortality risk factors (age, sex, ischaemic aetiology, left ventricular ejection fraction, New York Heart Association functional class, diabetes, glomerular filtration rate, sodium, haemoglobin, and beta‐blocker and angiotensin‐converting enzyme inhibitor/angiotensin II receptor blocker treatments). ST2 was measured with a novel high‐sensitivity immunoassay. During a median follow‐up time of 33.4 months, 244 of the 891 participants in the study (mean age 70.2 years at baseline) died. In the multivariable Cox proportional hazards model, both ST2 and NTproBNP significantly predicted the risk of death. The individual inclusion of ST2 and NTproBNP in the model with established mortality risk factors significantly improved the C statistic for predicting death [0.79 (0.76–0.81); P < 0.001]. The net improvement in reclassification after the separate addition of ST2 to the model with established risk factors and NTproBNP was estimated at 9.90% [95% confidence interval (CI) 4.34–15.46; P < 0.001] and the integrated discrimination improvement at 1.54 (95% CI 0.29–2.78); P = 0.015).ConclusionsOur data suggest that in a real‐life cohort of HF patients, the addition of ST2 and NTproBNP substantially improves the risk stratification for death beyond that of a model that is based only on established mortality risk factors.
The European CRT Survey: 1 year (9–15 months) follow‐up results
Authors: Bogale Nigussie , Priori Silvia , Cleland John G.F. , Brugada Josep , Linde Cecilia , Auricchio Angelo , van Veldhuisen Dirk J. , Limbourg Tobias , Gitt Anselm , Gras Daniel , Stellbrink Christoph , Gasparini Maurizio , Metra Marco , Derumeaux Geneviève , Gadler Fredrik , Buga Laszlo , Dickstein Kenneth ,   on behalf of the Scientific Committee, National Coordinators, and Investigators
Published: December 2011

AimsThe European CRT Survey is a joint initiative of the Heart Failure Association (HFA) and the European Heart Rhythm Association (EHRA) of the European Society of Cardiology evaluating the contemporary implantation practice of cardiac resynchronization therapy (CRT) in Europe.Methods and resultsPatients who had a successful CRT implantation were enrolled from 141 centres in 13 countries between November 2008 and June 2009. Baseline demographics, clinical and implantation data were collected, with a follow‐up of ∼1 year (9–15 months). The current report describes clinical outcomes including symptom severity, cardiovascular (CV) hospitalization, and survival. A total of 2438 patients were enrolled, and follow‐up data were acquired from 2111 patients (87%). The population included important groups of patients poorly represented in randomized controlled trials, including very elderly patients and those with prior device implantation, atrial fibrillation, and/or QRS duration <120 ms. Investigators reported substantial improvement in New York Heart Association (NYHA) functional class at follow‐up. Patient self‐assessment indicated that 81% of the patients felt improved, 16% reported no change, and 4% reported deterioration. During follow‐up, 207 (10%) patients died, 346 (16%) had a CV hospitalization, and 501 (24%) died or had CV hospitalization. Worse NYHA functional class, atrial fibrillation, ischaemic aetiology, and device type (CRT‐P, i.e. CRT alone) were associated with poorer survival. Women had a better outcome, as did patients who had a CRT‐D (with an implantable cardioverter defibrillator function) device.ConclusionsOutcomes including death and hospitalization in this European CRT survey were consistent with results from clinical trials of CRT. At 1 year follow‐up, most patients who received a CRT device considered their symptoms improved compared with their pre‐implant assessment. Although prospective, this is an observational study of successful CRT implantations, and outcomes in subgroup analyses must be interpreted with appropriate conservatism.Clinical study no: NCT 01185392
Clathrin‐mediated endocytosis regulates occludin, and not focal adhesion, distribution during epithelial wound healing
Authors: Fletcher Sarah J. , Poulter Natalie S. , Haining Elizabeth J. , Rappoport Joshua Z. 
Published: December 2011

AbstractBackground informationVesicle trafficking has long been suggested to play mechanistic roles in regulating directed cell migration. Recent evidence demonstrates that specific cell types and modes of migration involve transport of particular cargo through particular pathways. Epithelial wound healing is essential in tissue repair. However, investigations into the mechanisms regulating cell migration have mainly focused upon other models such as fibroblast‐derived cells. Roles for vesicle trafficking pathways in regulating directed cell migration have been identified in recent studies, but mechanisms through which endocytosis might be involved in epithelial wound healing have not been as well studied. Therefore, we analysed potential regulatory roles for endocytosis pathways during epithelial cell motility, with a particular focus on cell adhesion.ResultsSpecifically, and in contrast to studies in fibroblasts, we find no evidence for a link between endocytosis and the distribution of focal adhesions. However, the localisation of occludin, an essential component of tight junctions, is regulated through endocytosis. We identified epithelial monolayer wounding as a stimulus for endocytosis of occludin and have shown that internalisation of occludin from the wound edge occurs through clathrin‐mediated endocytosis (CME) into a rab5‐positive compartment.ConclusionsThus, these studies have evaluated mechanistic roles for dynamin‐dependant, CME and caveolar endocytosis during epithelial wound healing and have provided contrasting observations between analyses of cell motility in fibroblast models and epithelial cells. In conclusion, these studies have identified a novel mechanism for regulation of occludin during wound healing.
Multi‐colour direct STORM with red emitting carbocyanines
Authors: Lampe André , Haucke Volker , Sigrist Stephan J. , Heilemann Mike , Schmoranzer Jan 
Published: December 2011

AbstractBackground informationSingle molecule‐based super‐resolution methods have become important tools to study nanoscale structures in cell biology. However, the complexity of multi‐colour applications has prevented them from being widely used amongst biologists. Direct stochastic optical reconstruction microscopy (dSTORM) offers a simple way to perform single molecule super‐resolution imaging without the need for an activator fluorophore and compatible with many conventionally used fluorophores. The search for the ideal dye pairs suitable for dual‐colour dSTORM has been compromised by the fact that fluorophores spectrally apt for dual‐colour imaging differ with respect to the optimal buffer conditions required for photoswitching and the generation of prolonged non‐fluorescent (OFF) states.ResultsWe present a novel variant of dSTORM that combines advantages of spectral demixing with the buffer compatible blinking properties of red emitting carbocyanine dyes, spectral demixing dSTORM (SD‐dSTORM). In contrast to previously published work, SD‐dSTORM requires reduced laser power and fewer imaging frames for the faithful reconstruction of super‐resolved biological nanostructures. In addition, SD‐dSTORM allows the use of commercially available rather than custom‐made probes and does not rely on potentially error‐prone cross‐talk correction, thus allowing reliable co‐localisation.ConclusionsSD‐dSTORM presents a significant advance towards user‐friendly single molecule localisation‐based super‐resolution microscopy combining advantages of state‐of‐the‐art methodologies to perform fast, reliable and efficient multi‐colour dSTORM.
Long‐term maintenance treatment with omeprazole in children with healed erosive oesophagitis: a prospective study
Authors: Hassall E. , Shepherd R. , Koletzko S. , Radke M. , Henderson C. , Lundborg P. 
Published: December 2011

SummaryBackground  Short‐term studies show that PPIs heal erosive esophagitis in children. There are no prospective studies that examine long‐term maintenance therapy of erosive esophagitis in children with and without underlying GERD‐predisposing disorders.Aim  To determine prospectively the dose of omeprazole needed to maintain remission of erosive oesophagitis and reflux symptoms in children.Methods  Patients aged 1–16 years with healed erosive reflux oesophagitis after omeprazole treatment (0.7–3.5 mg/kg/day) entered a 21‐month maintenance phase where they initially received half the dose of omeprazole required to heal. Endoscopy was performed after 3, 12 and 21 months. The omeprazole dose was increased if erosive oesophagitis or reflux symptoms recurred.Results  A total of 46 patients entered the study and 32 completed it. Of these, 17 (53%) remained on the maintenance dose, 12 (38%) returned to their healing dose and 3 (9%) ended the study on a dose higher than their healing dose. Three‐quarters of the completers (24/32) had no erosive oesophagitis relapse. Four patients (13%) had relapse of only erosive oesophagitis, 4 (13%) had relapse of erosive oesophagitis and symptoms, and 10 (31%) had only symptomatic relapse. Of the 46 patients, 48% had GERD‐predisposing disorders (neurological impairment or oesophageal atresia). Overall, 62.5% (5/8) of patients who had an erosive oesophagitis relapse had a GERD‐predisposing disorder versus 33.3% (8/24) of those who did not.Conclusions  Remission of erosive oesophagitis is maintained with omeprazole treatment for at least 21 months in most children aged 1–16 years, and the drug is well tolerated. To maintain remission, some 60% of patients require more than half the dose required for healing. In children with GERD‐predisposing conditions, GERD is often chronic and relapsing, and requires long‐term management.
Geological habitat template overrides late Quaternary climate change as a determinant of range dynamics and phylogeography in some habitat‐specialist water beetles
Authors: Abellán Pedro , Arribas Paula , Svenning Jens‐Christian 
Published: December 2011

AbstractAim We investigated the roles of lithology and climate in constraining the ranges of four co‐distributed species of Iberian saline‐habitat specialist water beetles (Ochthebius glaber,Ochthebius notabilis,Enochrus falcariusandNebrioporus baeticus) across the late Quaternary and in shaping their geographical genetic structure. The aim was to improve our understanding of the effects of past climate changes on the biota of arid Mediterranean environments and of the relative importance of history and landscape on phylogeographical patterns.Location Iberian Peninsula, Mediterranean.Methods We combined species distribution modelling (SDM) and comparative phylogeography. We used a multi‐model inference and model‐averaging approach both for assessment of range determinants (climate and lithology) and for provision of spatially explicit estimates of the species current and Last Glacial Maximum (LGM) potential ranges. Potential LGM distributions were then contrasted with the phylogeographical and population expansion patterns as assessed using mitochondrial DNA sequence data. We also evaluated the relative importance of geographical distance, habitat resistance and historical isolation for genetic structure in a causal modelling framework.Results Lithology poses a strong constraint on the distribution of Iberian saline‐habitat specialist water beetles, with a variable, but generally moderate, additional influence by climate. The degree to which potential LGM distributions were reduced and fragmented decreased with increasing importance of lithology. These SDM‐based suitability predictions were mostly congruent with phylogeographical and population genetic patterns across the study species, with stronger geographical structure in the genetic diversity of the more temperature‐sensitive species (O. glaberandE. falcarius). Furthermore, while historical isolation was the only factor explaining genetic structure in the more temperature‐sensitive species, lithology‐controlled landscape configuration also played an important role for those species with more lithology‐determined ranges (O. notabilisandN. baeticus).Main conclusions Our data show that lithology is an important constraint on the distribution and range dynamics of endemic Iberian saline‐habitat water beetles, in interaction with climate and long‐term climate change, and overrides the latter in importance for some species. Hence, geological landscape structure and long‐term history may codetermine the overall range and the distribution of genetic lineages in endemic species with specialized edaphic requirements.
Plant‐derived auxin plays an accessory role in symptom development upon Rhodococcus fascians infection
Authors: Stes Elisabeth , Prinsen Els , Holsters Marcelle , Vereecke Danny 
Published: December 2011

SummaryThe biotrophic phytopathogen Rhodococcus fascians has a profound impact on plant development, mainly through its principal virulence factors, a mix of synergistically acting cytokinins that induce shoot formation. Expression profiling of marker genes for several auxin biosynthesis routes and mutant analysis demonstrated that the bacterial cytokinins stimulate the auxin biosynthesis of plants via specific targeting of the indole‐3‐pyruvic acid (IPA) pathway, resulting in enhanced auxin signaling in infected tissues. The double mutant tryptophan aminotransferase 1‐1 tryptophan aminotransferase related 2‐1 (taa1‐1 tar2‐1) of Arabidopsis (Arabidopsis thaliana), in which the IPA pathway is defective, displayed a decreased responsiveness towards R. fascians infection, although bacterial colonization and virulence gene expression were not impaired. These observations implied that plant‐derived auxin was employed to reinforce symptom formation. Furthermore, the increased auxin production and, possibly, the accumulating bacterial cytokinins in infected plants modified the polar auxin transport so that new auxin maxima were repetitively established and distributed, a process that is imperative for symptom onset and maintenance. Based on these findings, we extend our model of the mode of action of bacterial and plant signals during the interaction between R. fascians and Arabidopsis.