bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standards‐based metadata management for molecular simulations
Authors: Grunzke Richard , Breuers Sebastian , Gesing Sandra , Herres‐Pawlis Sonja , Kruse Martin , Blunk Dirk , de la Garza Luis , Packschies Lars , Schäfer Patrick , Schärfe Charlotta , Schlemmer Tobias , Steinke Thomas , Schuller Bernd , Müller‐Pfefferkorn Ralph , Jäkel René , Nagel Wolfgang E. , Atkinson Malcolm , Krüger Jens 
Published: September 2013

SUMMARYState‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright © 2013 John Wiley & Sons, Ltd.
Designing a fine‐grained parallel differential evolution with Pareto tournaments for solving an optical networking problem
Authors: Rubio‐Largo Álvaro , Vega‐Rodríguez Miguel A. , González‐Álvarez David L. 
Published: September 2013

SUMMARYThe future of designing optical networks focuses on the wavelength division multiplexing technology. This technology divides the huge bandwidth of an optical fiber into different wavelengths, providing different available channels per link of optical fiber. However, when it is required to establish a set of demands, a problem comes up. This problem is known as routing and wavelength assignment problem. In this work, we have tackled the static routing and wavelength assignment problem by using multiobjective evolutionary computing. The algorithm applied is the differential evolution but modified with the Pareto tournaments concept for being adapted to the multiobjective context. By using OpenMP, an application programming interface that supports multiplatform shared memory multiprocessing programming, we have demonstrated that this algorithm is highly suitable to be parallelized. We have performed several experiments in multicore systems with two, four, and eight cores, obtaining 97.57% of mean efficiency. To ensure that our heuristic obtains relevant results, we have compared it with a parallel version of the standard fast nondominated sorting genetic algorithm. Finally, in order to show the goodness and effectiveness of the differential evolution with Pareto tournaments algorithm when dealing with this problem, we present diverse multiobjective comparisons with the nondominated sorting genetic algorithm and other approaches published in the literature. Copyright © 2013 John Wiley & Sons, Ltd.
Childhood interparental conflict and HPA axis activity in young adulthood: Examining nonlinear relations
Authors: Hagan Melissa J. , Roubinov Danielle S. , Purdom Marreiro Catherine L. , Luecken Linda J. 
Published: September 2013

ABSTRACTRelations between early adversity and the neuroendocrine stress response are most often tested in a linear framework. Findings from studies of nonlinear relations between early stress and reactivity in childhood are suggestive, but curvilinear associations between childhood family stress and stress reactivity at later developmental stages remain unexplored. The current study examined curvilinear relations between childhood interparental conflict (IPC) and cortisol reactivity in young adulthood. Participants (n = 91; Mean age = 18.7, SD = .97; 59% White, 25% Hispanic) reported on the frequency and intensity of childhood exposure to IPC and salivary cortisol was sampled before and after a challenging interpersonal role‐play task. Significant curvilinear relations were found such that higher total cortisol and cortisol reactivity during the task was observed among youth reporting lower and higher frequency of IPC, suggesting that moderate IPC exposure may be associated with lower cortisol activity at a later developmental stage. © 2013 Wiley Periodicals, Inc. Dev Psychobiol 56: 871–880, 2014.
Interpreting the results of the Semmes‐Weinstein monofilament test: accounting for false‐positive answers in the international consensus on the diabetic foot protocol by a new model
Authors: Slater Robert A. , Koren Shlomit , Ramot Yoram , Buchs Andreas , Rapoport Micha J. 
Published: September 2013

AbstractAimsThe Semmes‐Weinstein monofilament is the most widely used test to diagnose the loss of protective sensation. The commonly used protocol of the International Consensus on the Diabetic Foot includes a ‘sham’ application that allows for false‐positive answers. We sought to study the heretofore unexamined significance of false‐positive answers.MethodsForty‐five patients with diabetes and a history of pedal ulceration (Group I) and 81 patients with diabetes but no history of ulceration (Group II) were studied. The three original sites of the International Consensus on the Diabetic Foot at the hallux, 1st metatarsal and 5th metatarsal areas were used. At each location, the test was performed three times: 2 actual and 1 “sham” applications. Scores were graded from 0 to 3 based upon correct responses. Determination of loss of protective sensation was performed with and without calculating a false‐positive answer as a minus 1 score.ResultsFalse‐positive responses were found in a significant percentage of patients with and without history of ulceration. Introducing false‐positive results as minus 1 into the test outcome significantly increased the number of patients diagnosed with loss of protective sensation in both groups.ConclusionsFalse‐positive answers can significantly affect Semmes‐Weinstein monofilament test results and the diagnosis of LOPS. A model that accounts for false‐positive answers is offered. Copyright © 2013 John Wiley & Sons, Ltd.
Iridium Complexes Containing a PNP Pincer Ligand: Syntheses, Structural Chemistry, and Bond Activations
Authors: Grüger Nora , Wadepohl Hubert , Gade Lutz H. 
Published: September 2013

AbstractThe coordination chemistry of the monoanionic PNP pincer ligand 3,6‐di‐tert‐butyl‐1,8‐bis[(diphenylphosphanyl)methyl]carbazole (Cbzdiphos) was investigated for different iridium(I) and iridium(III) complexes. Reaction of the protio ligand with [Ir(acac)(cod)] (acac = acetylacetonate; cod = 1,5‐cyclooctadienyl) gave [(Cbzdiphos)Ir(cod)] (1). Upon hydrogenation the dihydrido complex [(Cbzdiphos)IrH2] (2) was obtained, and its reactivity in different organometallic transformations was examined. Treating 2 with ammonia afforded [(Cbzdiphos)IrH2(NH3)] (3), whereas treatment with diphenylacetylene (dpa) yielded the IrI compound [(Cbzdiphos)Ir(dpa)] (4) and trans‐stilbene. Furthermore, the conversion with norbornene led to a reactive species, which activated C–H and C–Cl bonds. The reaction with THF gave a Fischer carbene [(Cbzdiphos)Ir{=C(OC3H6)}] (8) after double C–H bond activation, whereas treatment with benzene or chlorobenzene afforded the oxidative addition products [(Cbzdiphos)Ir(Ph)H] (5) and [(Cbzdiphos)Ir(Ph)Cl] (7).
Enrichment of pan‐frying refined oils with olive leaf phenolic‐rich extract to extend the usage life
Authors: Zribi Akram , Gargouri Boutheina , Jabeur Hazem , Rebaï Ahmed , Abdelhedi Ridha , Bouaziz Mohamed 
Published: September 2013

Refined olive and refined soybean oils (RSO) have been analyzed in order to evaluate their physicochemical behavior during potatoes pan‐frying. These refined oils exhibit significant variations in the physicochemical parameters when heated. A significant decrease (p<0.001) was practically observed in all analytical determination values except the induction time which showed a significant increase (p<0.001) with the enrichment with hydrolyzate olive leaf hydroxytyrosol‐rich extract at 500 ppm during pan‐frying. In fact, such enrichment has shown a remarkable resistance to oxidative deterioration, and the formation of trans‐fatty acids (TFA) was found to be lower in the enriched refined oil samples during pan‐frying. Such results have proven that not only is hydroxytyrosol‐rich extract excellent antioxidant enrichment for refined olive and RSOs during pan‐frying, but also it can be useful as substitute for synthetic ones. This study has shown that enriching refined oils with easily‐found and cheap natural plant extracts could extend their usage life.Practical applications: The results of this research study have shown that refined pan‐frying oils can successfully be enriched with hydrolyzate olive leaf hydroxytyrosol‐rich extract at 500 ppm in order to enhance thermo‐oxidative stability and reduce significantly the formation of trans‐fatty acids. The hydrolyzate extract was found to be very suitable for this purpose. These materials are common agro‐food by‐products and can be produced very easily at a low cost. Besides, this type of enrichment may enable consumers to get some beneficial phenolic compounds through fried food consumption. In addition, these types of applications may open another area for marketing the named extract of natural origin.
Oxazolone‐Based Photoswitches: Synthesis and Properties
Authors: Blanco‐Lomas Marina , Funes‐Ardoiz Ignacio , Campos Pedro J. , Sampedro Diego 
Published: September 2013

AbstractThe synthesis, photophysics and photochemistry of a family of molecular switches inspired by the green fluorescent protein (GFP) chromophore is presented. These compounds can be synthesized in one step and good yields, their photophysical properties may be tuned by the substituents, solvent and wavelength of irradiation, and they show very efficient and fast photoisomerization. Furthermore, their high thermal stability and limited photodecomposition could allow these switches to be used in a range of applications. Finally, oxazolone photoswitches may be activated by the use of light and deactivated by either heat or light of a different wavelength.
Synthesis of Four Stereoisomers of (S)‐2‐Methylpent‐3‐yl 3,13‐Dimethylpentadecanoate, a Sex Pheromone of the Bagworm Moth Clania variegate, Using Stereospecific Inversion of Secondary Sulfonates as a Key Step
Authors: Taguri Tomonori , Yamamoto Masanobu , Fujii Toru , Muraki Yuta , Ando Tetsu 
Published: September 2013

AbstractFemales of some lepidopteran species produce novel sex pheromones with a methyl‐branched structure, such as 2‐methylpent‐3‐yl 3,13‐dimethylpentadecanoate secreted by the bagworm moth Clania variegate. Recently, we have established a simple preparative method for the synthesis of methyl‐branched building blocks by utilizing an SN2 reaction of chiral secondary tosylates derived from (S)‐ and (R)‐propylene oxides. The usefulness of these building blocks was demonstrated by their application in the synthesis of all four stereoisomers of an acid moiety in the bagworm pheromone. The enantiomeric purities of all building blocks were confirmed by enantioselective HPLC analysis. We found that a secondary mesylate was superior to the corresponding tosylate because it avoided an elimination side reaction, and racemization in the SN2 reaction was not observed even at high temperature (150 °C). Finally, each optically active acid was esterified with (S)‐2‐methyl‐3‐pentanol, which was synthesized by a new route starting from (S)‐valine.
Variations in lethal and sublethal effects of cypermethrin among aquatic stages and species of anuran amphibians
Authors: Biga Lindsay M. , Blaustein Andrew R. 
Published: September 2013

Abstract

Despite the use of model species to predict the effects of chemicals in the environment, unpredicted variation in levels of risk to organisms from xenobiotics can be observed. Physiological and morphological differences between species and life stages may lead to differences in sensitivity, while seasonal and spatial variation in pesticide concentrations may affect the level of risk faced by organisms in the environment. Because anurans breed in aquatic habitats subject to contamination by runoff and spraying, they are particularly vulnerable to pesticides. In the present study, embryos, newly hatched larvae, and larvae with limb buds of 3 anuran amphibian species—Pseudacris regilla, Rana cascadae, and Rana aurora—were exposed for 48 h to either 0.5 µg/L or 5.0 µg/L cypermethrin under laboratory conditions. The authors monitored hatching success, larval survival, and measured growth. Additionally, they assayed avoidance behavior 2 wk after exposure or 2 wk after hatching for individuals exposed as embryos. Hatching and survival were not affected in animals of any species exposed as embryos. After exposure as embryos and as newly hatched larvae, however, P. regilla displayed behavioral abnormalities in response to prodding. Cypermethrin increased mortality in P. regilla exposed in both larval stages. Cypermethrin also increased mortality in larval R. cascadae when exposed at the early stage. These results indicate variation in sensitivity to environmentally relevant concentrations of cypermethrin among anuran species and life stages. Environ Toxicol Chem 2013;32:2855–2860. © 2013 SETAC
Previous exposure of predatory fish to a pesticide alters palatability of larval amphibian prey
Authors: Hanlon Shane M. , Parris Matthew J. 
Published: September 2013

Abstract

Habitat preferences of organisms are reliant on a variety of factors. For amphibians specifically, preferences can depend on factors such as food availability, water quality, and the presence of potential predators. Because some amphibians breed in permanent bodies of water (e.g., ponds), the threat of predation (e.g., from fish) is constant. Thus, some amphibians are unpalatable to many predators, allowing them to coexist in the same habitats. However, the addition of anthropogenic stressors (i.e., pesticides) may alter the perceived palatability of prey items to predators. The authors tested the hypothesis that bluegill fish (Lepomis macrochirus), previously exposed to the pesticide carbaryl, would consume more unpalatable prey (Fowler's toad [Anaxyrus fowleri] tadpoles) than unexposed predators. Carbaryl is a pesticide that attacks the nervous system and is linked to taste sense in organisms. Moreover, the authors conducted an identical test using palatable prey (gray treefrog [Hyla versicolor] tadpoles) and predicted that no change in preference would be observed. In support of the primary hypothesis, bluegill exposed to the highest concentration of carbaryl consumed more A. fowleri tadpoles compared with those exposed to carbaryl at the lowest concentration or water control. Moreover, an effect of carbaryl on predation success on H. versicolor tadpoles was not observed. The present study shows that an anthropogenic stressor (carbaryl) can alter the perceived palatability of noxious prey to fish predators, potentially altering predator–prey relationships in natural settings. Environ Toxicol Chem 2013;32:2861–2865. © 2013 SETAC
3G network traffic sources measurement and analysis
Authors: Goleva Rossitza , Atamian Dimitar , Mirtchev Seferin , Dimitrova Desislava , Grigorova Lyubina 
Published: September 2013

ABSTRACTIn this paper, we show statistical analyses of several types of traffic sources in a 3G network, namely voice, video and data sources. For each traffic source type, measurements were collected in order to, on the one hand, gain better understanding of the statistical characteristics of the sources and, on the other hand, enable forecasting traffic behaviour in the network. The latter can be used to estimate service times and quality of service parameters. The probability density function, mean, variance, mean square deviation, skewness and kurtosis of the interarrival times are estimated by Wolfram Mathematica and Crystal Ball statistical tools. Based on evaluation of packet interarrival times, we show how the gamma distribution can be used in network simulations and in evaluation of available capacity in opportunistic systems. As a result, from our analyses, shape and scale parameters of gamma distribution are generated. Data can be applied also in dynamic network configuration in order to avoid potential network congestions or overflows. Copyright © 2013 John Wiley & Sons, Ltd.
Intensive mixing along an island chain controls oceanic biogeochemical cycles
Authors: Nishioka Jun , Nakatsuka Takeshi , Watanabe Yutaka W. , Yasuda Ichiro , Kuma Kenshi , Ogawa Hiroshi , Ebuchi Naoto , Scherbinin Alexey , Volkov Yuri N. , Shiraiwa Takayuki , Wakatsuchi Masaaki 
Published: September 2013

AbstractThe subarctic Pacific is a high‐nutrient low‐chlorophyll (HNLC) region in which phytoplankton growth is broadly limited by iron (Fe) availability. However, even with Fe limitation, the western subarctic Pacific (WSP) has significant phytoplankton growth and greater seasonal variability in lower trophic levels than the eastern subarctic Pacific. Therefore, differences in Fe supply must explain the west‐to‐east decrease in seasonal phytoplankton growth. The Fe flux to the euphotic zone in the WSP occurs at a “moderate” value, in that it is significantly higher than its value on the eastern side, yet it is not sufficient enough to cause widespread macronutrient depletion, that is, HNLC status is maintained. Although we recognize several Fe supply processes in the WSP, the mechanisms that account for this moderate value of Fe supply have not previously been explained. Here we demonstrate the pivotal role of tidal mixing in the Kuril Islands chain (KIC) for determining the moderate value. A basin‐scale meridional Fe section shows that Fe derived from sediments in the Sea of Okhotsk is discharged through the KIC into the intermediate water masses (~ 800 m) of the western North Pacific. The redistribution of this Fe‐rich intermediate water by intensive mixing as it crosses the KIC is the predominant process determining the ratio of micronutrient (Fe) to macronutrients (e.g., nitrate) in subsurface waters. This ratio can quantitatively explain the differences in surface macronutrient consumption between the western and eastern subarctic, as well as the general formation and biogeochemistry of HNLC waters of the subarctic North Pacific.
Der Selbstfiltrationsindex als Suffosionskriterium für nichtbindige Erdstoffe
Authors: Witt Karl Josef 
Published: September 2013

AbstractSuffosionsempfindliche Böden sind durch eine Struktur aus einem tragenden Skelett der groben Kornfraktion und aus einer darin eingelagerten Feinfraktion gekennzeichnet. Bei der Durchströmung solcher Böden können Teile der Feinfraktion erodieren und ausgetragen werden, wenn das Skelett nicht in der Lage ist, die mobilen Körner an den Engstellen des Porenraums zurückzuhalten. Der Beitrag gibt einen kurzen Überblick über die gängigen Kriterien und beschreibt eine einfache Methode, mit der das Suffosionspotenzial eines nichtbindigen Bodens anhand der Steigung der Korngrößenverteilung im unteren Bereich bewertet wird. Suffosion wird als Filtration im dreidimensionalen Porensystem betrachtet. Der Nachweis der Stabilität wird damit auf die Filtration an einer Grenzschicht zurückgeführt. Der Selbstfiltrationsindex IFS drückt das Abstandsverhältnis der aufgetrennten Korngrößenverteilung des zu beurteilenden Bodens aus. Die innere Stabilität lässt sich anhand dieser Kenngröße quantifizieren. Die potenziell erodierbare Masse kann durch die Identifikation des relevanten Trenndurchmessers abgeschätzt werden.The Self‐Filtration‐Index as an internal stability criterion for granular soils. Soils susceptible to internal erosion are characterized by a structure consisting out of a load bearing skeleton formed by the coarser particles and embedded fine‐grained material. Due to seepage through such soils, fine particles can be eroded if the skeleton is unable to catch these moving grains at the constrictions of the pore network. This process of washing out fine particles is called suffusion. If suffusion cannot occur due to geometrical considerations, soils are called internally stable. The article describes a simple method to assess the internal stability of non‐cohesive soils based on the slope of the lower part of its grain size distribution. Suffusion is considered as spatial filtration, were the skeleton acts as filter to catch the embedded mobile particles. A Self‐Filtration‐Index ISF is introduced which expresses the geometric ratio of the separated grain‐size‐distribution into the skeleton and the mobile fines. Internal stability of a representative grain‐size‐distribution and the potential of suffusion can be quantified by ISF. The amount of eroded mass can be estimated.
Constructing the global distribution of chorus wave intensity using measurements of electrons by the POES satellites and waves by the Van Allen Probes
Authors: Li W. , Ni B. , Thorne R. M. , Bortnik J. , Green J. C. , Kletzing C. A. , Kurth W. S. , Hospodarsky G. B. 
Published: September 2013

AbstractWe adopt a physics‐based technique to infer chorus wave amplitudes from the low‐altitude electron population (30–100 keV) measured by multiple Polar Orbiting Environmental Satellites (POES), which provide extensive coverage over a broad region in L‐shell and magnetic local time (MLT). This technique is validated by analyzing conjunction events between the Van Allen Probes measuring chorus wave amplitudes near the equator and POES satellites measuring the 30–100 keV electron population at the conjugate low altitudes. We apply this technique to construct the chorus wave distributions during the 8–9 October storm in 2012 and demonstrate that the inferred chorus wave amplitudes agree reasonably well with conjugate measurements of chorus wave amplitudes from the Van Allen Probes. The evolution of the chorus wave intensity inferred from low‐altitude electron measurements can provide real‐time global estimates of the chorus wave intensity, which cannot be obtained from in situ chorus wave measurements by equatorial satellites alone, but is crucial in quantifying radiation belt electron dynamics.
Production of methanol, acetaldehyde, and acetone in the Atlantic Ocean
Authors: Dixon Joanna L. , Beale Rachael , Nightingale Philip D. 
Published: September 2013

AbstractThe biogeochemistry of oxygenated volatile organic compounds (OVOCs) like methanol, acetaldehyde, and acetone in marine waters is poorly understood. We report the first in situ gross production rates for methanol, acetaldehyde, and acetone of 49–103, 25–98, and 2–26 nmol L−1 d−1 over contrasting areas of marine productivity, including oligotrophic gyres and eutrophic upwellings. Photochemical production estimates are mostly negligible for methanol, up to 68% for acetaldehyde and up to 100% of gross production rates for acetone. Microbial surface OVOC oxidation to CO2 accounts for between 10–50% and 0.5–13% of the methanol and acetone losses, respectively, but largely control acetaldehyde concentrations (49–100%). Biological lifetimes in a coastal upwelling vary between ≤1 day for acetaldehyde, to approximately 7 days for methanol and up to ~80 days for acetone. In open oceanic environments, the lifetime of acetaldehyde ranges between 2 and 5 h, compared to 10–26 days for methanol and 5–55 days for acetone.