bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasion genetics of vendace (Coregonus albula(L.)) in theInari‐Pasvik watercourse: revealing the origin and expansion pattern of a rapid colonization event
Authors: Præbel Kim , Gjelland Karl Øystein , Salonen Erno , Amundsen Per‐Arne 
Published: April 2013

AbstractSpecies invasions can have wide‐ranging biological and socio‐economic effects and are generally unwanted by legislation. Identification of the source population as well as the ecology and genetics of both the invader population and the receiving community is of crucial importance. The rapid invasion of a small coregonid fish vendace (Coregonus albula) in a major northernEuropean subarctic watercourse has resulted in a labile ecological situation in the receiving community. The ecological impact of the invasion has been thoroughly documented, but the genetics of the invasion remains to be explored. We analyzed the genetic diversity and divergence patterns among the two possible source populations from southern Finnish Lapland and three colonists populations within theInari‐Pasvik watercourse using ten microsatellite loci in order to (i) identify the most likely source of the invasion, (ii) reveal the dispersal pattern and genetic structure of the secondary expansion, and (iii) to investigate whether the initial introduction and the secondary expansion were associated with founder effects. We revealed that repeated translocation of vendace fromLakeSinettäjärvi into a tributary lake ofL.Inari in 1964–1966 is the most plausible source for the invasion. Both the initial introduction and the secondary expansion were found not to be associated with significant founder effects. The secondary expansion followed a stepping stone pattern and the source and colonist populations of this expansion have undergone rapid genetic divergence within a period of 15–35 years (ca. 8–17 generations). The rapid divergence may be contributed to lack of gene flow among the source and colonist populations due to the extensive hydroelectric damming in the watercourse. Multiple introductions and substantial genetic variation in combination with the boom‐and‐bust population development of the species thus likely counteracted the founder effects as well as fueled the rapid establishment and expansion of this species within theInari‐Pasvik watercourse.
Simulation of two‐phase flow–body interaction problems using direct forcing/fictitious domain–level set method
Authors: Yoon Hyun Sik , Jeon Chung Ho , Jung Jae Hwan , Koo Bonguk , Choi Changyoung , Shin Sung Chul 
Published: April 2013

SUMMARYIn the present paper, a direct forcing/fictitious domain (DF/FD)–level set method is proposed to simulate the twophase flow–body interaction. The DF/FD does not sacrifice accuracy and robustness by employing a discrete δ (Dirac delta) function to transfer quantities between the Eulerian nodes and Lagrangian points explicitly as the immersed boundary method. The advantages of this approach are the simple concept, the easy implementation and the utilization of original governing equation without modification. The main idea is to combine DF/FD method with the level set method in the Cartesian coordinates. We present the results of a number of test cases to illustrate the effectiveness of the proposed method for single‐phase flow–body interaction problem and the two‐phase flows with a stationary body. Eventually, the simulations of various water entry problems have been conducted to validate the capability and the accuracy of the present method on solving the twophase flow–body interaction. Consequently, the present results are found to be in good agreement with those of previous studies. Copyright © 2013 John Wiley & Sons, Ltd.
Computational Resources for MHC Ligand Identification
Authors: Koch Christian P. , Pillong Max , Hiss Jan A. , Schneider Gisbert 
Published: April 2013

AbstractAdvances in the high‐throughput determination of functional modulators of major histocompatibility complex (MHC) and improved computational predictions of MHC ligands have rendered the rational design of immunomodulatory peptides feasible. Proteome‐derived peptides and ‘reverse vaccinology’ by computational means will play a driving role in future vaccine design. Here we review the molecular mechanisms of the MHC mediated immune response, present the computational approaches that have emerged in this area of biotechnology, and provide an overview of publicly available computational resources for predicting and designing new peptidic MHC ligands.
Signal Amplification Strategy Based on TiO2‐Nanotube Layers and Nanobeads Carrying Quantum Dots for Electrochemiluminescent Immunosensors
Authors: Gao Zhi‐Da , Zhuang Qian‐Lan , Song Yan‐Yan , Lee Kiyoung , Schmuki Patrik 
Published: April 2013

AbstractSelf‐organized TiO2‐nanotube layers can be used for immunoassay‐type sensing in combination with amplifying CdTe labels in a direct and very sensitive electrochemiluminescent (ECL) configuration. Key properties for this method are the conductivity of the TiO2 nanotubes, and their transparency for light emitted from the CdTe labels at approximately 2.4 eV. To demonstrate the potential of this platform, we constructed a sandwich‐type immunoassay onto the TiO2‐nanotube wall with a layer of (3‐aminopropyl)triethoxysilane as the cross‐linker for antibody immobilization. For the counter part of the sandwich, we created an amplification system consisting of TiO2 nanobeads carrying the secondary antibody and multiple CdTe quantum dots (multiQD). For antigen (IgG) detection, we find that this combination of 3D transparent electrode with multiQD labels allows for an ECL detection limit of 0.05 pg mL−1 and a linearity of the signal in the range of 0.1–108 pg mL−1.
Automated identification of binding sites for phosphorylated ligands in protein structures
Authors: Ghersi Dario , Sanchez Roberto 
Published: April 2013

AbstractPhosphorylation is a crucial step in many cellular processes, ranging from metabolic reactions involved in energy transformation to signaling cascades. In many instances, protein domains specifically recognize the phosphogroup. Knowledge of the binding site provides insights into the interaction, and it can also be exploited for therapeutic purposes. Previous studies have shown that proteins interacting with phosphogroups are highly heterogeneous, and no single property can be used to reliably identify the binding site. Here we present an energy‐based computational procedure that exploits the protein three‐dimensional structure to identify binding sites involved in the recognition of phosphogroups. The procedure is validated on three datasets containing more than 200 proteins binding to ATP, phosphopeptides, and phosphosugars. A comparison against other three generic binding site identification approaches shows higher accuracy values for our method, with a correct identification rate in the 80–90% range for the top three predicted sites. Addition of conservation information further improves the performance. The method presented here can be used as a first step in functional annotation or to guide mutagenesis experiments and further studies such as molecular docking. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin
Authors: Zhang Jin , Yamazaki Yoshikazu , Hikake Masanori , Murakami Midori , Ihara Kunio , Kouyama Tsutomu 
Published: April 2013

AbstractThe lifetime of the O intermediate of bacteriorhodopsin (BR) is extended by a factor of ∼250 in the Leu93‐to‐Ala mutant (BR_L93A). To clarify the structural changes occurring in the last stage of the proton pumping cycle of BR, we crystallized BR_L93A into a hexagonal P622 crystal. Diffraction data from the unphotolyzed state showed that the deletion of three carbon atoms from Leu93 is compensated by the insertion of four water molecules in the cytoplasmic vicinity of retinal. This insertion of water is suggested to be responsible for the blue‐shifted λmax (540 nm) of the mutant. A long‐lived substate of O with a red‐shifted λmax (∼565 nm) was trapped when the crystal of BR_L93A was flash‐cooled after illumination with green light. This substate (Oslow) bears considerable similarity to the M intermediate of native BR; that is, it commonly shows deformation of helix C and the FG loop, downward orientation of the side chain of Arg82, and disruption of the Glu194/Glu204 pair. In Oslow, however, the main chain of Lys216 is less distorted and retinal takes on the 13‐cis/15‐syn configuration. Another significant difference is seen in the pH dependence of the structure of the proton release group, the pKa value of which is suggested to be much lower in Oslow than in M. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Pressure as a denaturing agent in studies of single‐point mutants of an amyloidogenic protein human cystatin c
Authors: Jankowska Elzbieta , Stefanowicz Piotr , Sosnowska Marta , Karpowicz Przemyslaw , Radziszewska Karolina , Szewczuk Zbigniew , Szymańska Aneta 
Published: April 2013

AbstractRecently, we presented a convenient method combining a deuterium‐hydrogen exchange and electrospray mass spectrometry for studying high‐pressure denaturation of proteins (Stefanowicz et al., Biosci Rep 2009; 30:91–99). Here, we present results of pressure‐induced denaturation studies of an amyloidogenic protein—the wild‐type human cystatin C (hCC) and its single‐point mutants, in which Val57 residue from the hinge region was substituted by Asn, Asp or Pro, respectively. The place of mutation and the substituting residues were chosen mainly on a basis of theoretical calculations. Observation of H/D isotopic exchange proceeding during pressure induced unfolding and subsequent refolding allowed us to detect differences in the proteins stability and folding dynamics. On the basis of the obtained results we can conclude that proline residue at the hinge region makes cystatin C structure more flexible and dynamic, what probably facilitates the dimerization process of this hCC variant. Polar asparagine does not influence stability of hCC conformation significantly, whereas charged aspartic acid in 57 position makes the protein structure slightly more prone to unfolding. Our experiments also point out pressure denaturation as a valuable supplementary method in denaturation studies of mutated proteins. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Mechanical and electronic properties of stoichiometric silicene and germanene oxides from first‐principles
Authors: Wang Yanli , Ding Yi 
Published: April 2013

AbstractUsing first‐principles calculations, we investigate the fully oxidized silicene and germanene with stoichiometric ratio Si:O/Ge:O = 1:1. For both compounds, the zigzag ether‐like conformation (z‐sSiO/z‐sGeO) is found to be the most energetically favorable structure. These z‐sSiO and z‐sGeO nanosheets have prominent elastic characteristics, which even exhibit an unconventional auxetic behavior with negative Poisson ratios. After oxidation, the semi‐metallic nanosheets are transformed into semiconductors with narrow direct band gaps. Due to the anisotropic mechanical and electronic properties, the z‐sSiO and z‐sGeO possess an axially high intrinsic charge mobility up to the order of 104 cm2/Vs, which is comparable to that of graphene nanoribbons. Our studies demonstrate that the silicene and germanene oxides have peculiar mechanical and electronic properties, which endow these nanostructures for potential applications in nanoelectronics and devices. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the concentration of the number of solutions of random satisfiability formulas
Authors: Abbe Emmanuel , Montanari Andrea 
Published: April 2013

ABSTRACTLet Z(F) be the number of solutions of a random k‐satisfiability formula F with n variables and clause density α. Assume that the probability that F is unsatisfiable is for some . We show that (possibly excluding a countable set of “exceptional” α's) the number of solutions concentrates, i.e., there exists a non‐random function such that, for any , we have with high probability. In particular, the assumption holds for all , which proves the above concentration claim in the whole satisfiability regime of random 2‐SAT. We also extend these results to a broad class of constraint satisfaction problems. © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 45, 362–382, 2014
A new species ofCuora(Testudines: Geoemydidae) from the Miocene of Thailand and its evolutionary significance
Authors: NAKSRI WILAILUCK , TONG HAIYAN , LAUPRASERT KOMSORN , SUTEETHORN VARAVUDH , CLAUDE JULIEN 
Published: April 2013

AbstractA new species ofCuora,Cuora chiangmuanensissp. nov., is described on the basis of a nearly complete shell with limb bones from the late Middle – early Late Miocene Chiang Muan Mine, Phayao Province (Northern Thailand).C. chiangmuanensisis distinguished from other fossil and livingCuoraspecies mainly on the basis of its plastral morphology. Among fossil and extantCuorataxa, the new species appears to be a missing link between the taxa from Southeast Asia and those from East Asia. It represents the earliest record of the genus and demonstrates that by 11–12 Ma, Asian box turtles were already present in Southeast Asia.
Geometric algebra in plasma electrodynamics
Authors: RESENDES D. P. 
Published: April 2013

AbstractGeometric algebra (GA) is a recent broad mathematical framework incorporating synthetic and coordinate geometry, complex variables, quarternions, vector analysis, matrix algebra, spinors, tensors, and differential forms. It has been claimed to be a unified language for physics. GA is presented in the context of the Maxwell-Plasma system. In this formalism the divergence and curl differential operators are united in a single vector derivative, which is invertible, in the form of a first-order Green function. The four Maxwell equations can be combined into a single equation (for homogeneous and constant media) or into two equations involving the invertible vector derivative for more complex media. GA is applied to simple examples to illustrate the compactness of the notation and coordinate-free computations.
Transforming consumer information
Authors: Ritchie A. , Corrigan J. , Graham S. , Hague A. , Higham A. , Holt J. , Mowbray P. , Robinson H. 
Published: April 2013

AbstractThe Consumer Information Working Party has published this paper which explores how we can better engage consumers with long-term savings and investments. The working party considered the current state of consumer information, which is a long way from ideal, including: consumer insights and touch points, the current consumer information model, relevant considerations from behavioural economics, examples of information failures and some successes from other fields. They then propose a way to deliver more effective information, including a possible framework and some ideas for its application. They finish with proposals for immediate next steps and urge the Actuarial Profession to take a lead in this area.
Highly efficient bulk heterojunction photovoltaic cells based on C70 and tetraphenyldibenzoperiflanthene
Authors: Zheng Yan-qiong , Potscavage William J. , Komino Takeshi , Hirade Masaya , Adachi Junji , Adachi Chihaya 
Published: April 2013

Highly efficient photovoltaic cells based on a bulk heterojunction configuration composed of C70 with various donor materials at 5 wt. % donor concentration were fabricated. The tetraphenyldibenzoperiflanthene (DBP) donor achieved the highest power conversion efficiency (ηPCE) of 6.4% for the optimized cell. The improved performance with DBP arises from a combination of a higher absorption coefficient than 1,1-bis-(4-bis(4-methyl-phenyl)-amino-phenyl)-cyclohexane and a symmetrical molecular structure. The high ηPCE with only 5 wt. % donor is attributed to a sufficient donor concentration for enhanced Frenkel exciton dissociation in C70, while efficiency and electron mobility decrease at higher donor concentrations.
Site preparation, soil management and planting.
Authors: Pritts M. , Hanson E. 
Published: April 2013

Abstract

The treatment and management of the site and soil before planting can impact the growth and productivity of raspberries for years to come. Many consider the year prior to planting to be the most important because of the substantial effects that soil factors have on plant growth. The soil physical, biological, and chemical properties, soil quality evaluation, site preparation, field layout, and planting are discussed.
Crop production.
Authors: Stanton M. 
Published: April 2013

Abstract

Raspberries are widely known and grown around the world. In general, raspberries prefer a temperate climate in which they receive winter chilling, and while dormant most cultivars are very tolerant of cold temperatures to -20°C (-4°F) or lower. Raspberries tolerate a wide range of soils, but prefer medium textured soils. Raspberries need regular precipitation and/or irrigation. The Assessing plant health, growth and fruiting of floricane-fruiting cultivars, growth and fruiting of primocane raspberries, expected berry quality, managing soil water, crop management (before cane emergence, early in the growing season, flowering and fruiting, and postharvest) are discussed.
The effect of variable winter severity on size-dependent overwinter mortality caused by acute thermal stress in juvenile red drum (Sciaenops ocellatus)
Authors: Anderson Deena A. , Scharf Frederick S. 
Published: April 2013

AbstractMortality during winter can impact the population dynamics of fish at temperate latitudes. The red drum (Sciaenops ocellatus) supports valuable coastal fisheries throughout its range in the southeastern United States. At the northern edge of its distribution, severe winters may cause considerable overwinter loss and size-selective mortality among juveniles. We conducted a series of laboratory experiments to quantify overwinter survivorship of age 0 fish. To determine thermal tolerance, fish were exposed to various minima (1, 3, or 5°C) for up to 14 d. The effect of winter severity on survivorship was then evaluated by exposing fish to simulated cold-front events of varying frequency and duration. Body size was incorporated as a factor into each set of experiments. Age 0 red drum were intolerant of even brief exposure to temperatures ≤3°C and experienced mortality after prolonged exposure to 5°C. Higher frequency of simulated cold-front events impacted survivorship more than longer-event duration, and recovery time between events improved survivorship. Size-dependent mortality was only evident for fish exposed to mild and moderate winter severity conditions, with larger fish surviving longer. For juvenile red drum, severe winters may cause high mortality independent of body size, whereas size-dependent year-class restructuring may occur during milder winters.
Community forest management: Can the green economy contribute to environmental justice?
Authors: Barkin David , Fuente Mario 
Published: April 2013

AbstractPolicymakers face a dilemma in highly diverse societies with many ecosystems: how to implement national policies that allow for serious consideration of these differences. In connection with the attempts to advance towards sustainability in forest systems, Mexico is confronting this problem with difficulty. Although it has committed to implementing policies consistent with REDD+, there are competing pressures for supporting commercial development of plantations on the one hand, and community based management systems that involve multiple objectives in complex proposals on the other. We trace the implications for environmental justice of the choices being made by indigenous communities in the highlands of Oaxaca for promoting sustainable programmes that assure adequate living standards and environmental protection. The analysis shows that this alternative approach offers an interesting set of outcomes that the standard paradigm of the green economy has difficulty achieving.
24‐Hour Performance of Albumin Dialysis Assessed by a New Two‐Compartment In Vitro Model
Authors: Stiffel Melanie , Dammeier Nele , Schmidt Stephanie , Szyszkowitz Tina , Sikole Magdalena , Sieveking Catharina , Stange Jan 
Published: April 2013

AbstractExtracorporeal albumin dialysis as a measure to remove water soluble and protein bound toxins simultaneously has been shown to improve complications of liver failure. However, recent research suggests that only treatments associated with a measurable improvement of patient's albumin binding function by effective removal of albumin bound toxins leads to better survival. The aim of the present work was to develop a test platform for upcoming devices to evaluate long term effectiveness on toxin removal and improvement of patients' albumin binding capacity. The classical one compartment model consisting of a closed pool of toxin spiked plasma was combined with continuous infusion of water soluble and protein bound toxins mimicking physiological rebound rates reflected in the literature. The model was used to demonstrate the effect of stabilizer contamination of dialysate albumin on toxin clearance and albumin binding function. In comparison to the classical one compartment model, the two compartment model allows for long term effectiveness tests of liver assist devices not only for strongly albumin‐bound, but also water‐soluble molecules. The limitations of commercial albumin overloaded with caprylate ligands (5:1 molar ratio) were demonstrated by presenting a significant improvement of albumin binding function using 80 g deligandized albumin compared to no significant improvement using the standard 120 g albumin as dialysate. The new two compartment model allows for pre‐clinical evaluation of new upcoming devices aiming for improvement of patients' albumin binding function as a measure for clinically meaningful extracorporeal detoxification of albumin‐bound toxins.
Primary immunodeficiencies of pattern recognition receptors
Authors: Netea M. G. , van de Veerdonk F. L. , van der Meer J. W. M. 
Published: April 2013

AbstractPrimary immunodeficiencies (PIDs) are severe defects in the capacity of the host to mount a proper immune response, and are characterized by an increased susceptibility to infections. Although classical immunodeficiencies have been characterized based on broad defects in cell populations (e.g. T/B cells or polymorphonuclear leukocytes) or humoral factors (e.g. antibodies or complement), specific immune defects based on well‐defined molecular targets have been described more recently. Among these, genetic defects in pattern recognition receptors (PRRs), leading to impaired recognition of invading pathogens by the innate immune system, play an important role in specific defects against human pathogens. Defects have been described in three of the major families of PRRs: the Toll‐like receptors, the C‐type lectin receptors and the nucleotide‐binding domain leucine‐rich repeat‐containing receptors. By contrast, no defects in the intracellular viral receptors of the RigI helicase family have been described to date. Defects in the PRRs show a broad variation in severity, have a narrow specificity for certain classes of pathogens, and often decrease in severity with age; these characteristics distinguish them from other forms of PIDs. Their discovery has led to important insights into the pathophysiology of infections, and may offer potential novel therapeutic targets for immunotherapy.