bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses
Authors: Edwards Taylor , Tollis Marc , Hsieh PingHsun , Gutenkunst Ryan N. , Liu Zhen , Kusumi Kenro , Culver Melanie , Murphy Robert W. 
Published: January 2016

AbstractEvolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).
Arsenic uptake and distribution in Cucumis melo and Citrullus lanatus plants
Authors: Pineda‐Chacón Gabriela , Alarcón‐Herrera María Teresa 
Published: January 2016

The use of groundwater with high arsenic (As) content in agricultural irrigation is a regular practice in many regions of the world, which results in the accumulation of As in soils to levels that can alter their physicochemical properties, decrease fertility, and reduce crop yield. Plants absorb many elements from soil and irrigation water. Some of these elements have a biological function but others can be toxic to the plants such as As. The presence of As in plants pose a risk due to the possible bioaccumulation of this metalloid through the trophic chains. The uptake, biotransformation, and bioaccumulation mechanisms of As occurring in plants is substantially affected by plant species and genotypes. The effects and distribution of As in melon (Cucumis melo) and watermelon plants (Citrullus lanatus) irrigated with As in a soil mesocosm were evaluated. The accumulation of As for Cucumis melo and Citrullus lanatus is presented according to the following: root > leaf > stem. In a period of 35 weeks with 1.4 mg L−1 of As concentration in irrigation water, adverse effects on the development of both genotypes were observed. For these As concentrations, Citrullus lanatus showed a clear reduction of root growth. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 750–757, 2016
Development of a hybrid particle‐mesh method for two‐phase flow simulations
Authors: Liu X. , Guo L. , Morita K. , Zhang S. 
Published: January 2016

SUMMARYA hybrid particle‐mesh method was developed for efficient and accurate simulations of two‐phase flows. In this method, the main component of the flow is solved using the constrained interpolated profile/multi‐moment finite volumemethod; the two‐phase interface is rendered using the finite volume particle (FVP) method. The effect of surface tension is evaluated using the continuum surface force model. Numerical particles in the FVP method are distributed only on the surface of the liquid in simulating the interface between liquid and gas; these particles are used to determine the density of each mesh grid. An artificial term was also introduced to mitigate particle clustering in the direction of maximum compression and sparse discretization errors in the stretched direction. This enables accurate interface tracking without diminishing numerical efficiency. Two benchmark simulations are used to demonstrate the validity of the method developed and its numerical stability. Copyright © 2016 John Wiley & Sons, Ltd.
High orientation of long chain branched poly (lactic acid) with enhanced blood compatibility and bionic structure
Authors: Li Zhengqiu , Ye Lin , Zhao Xiaowen , Coates Phil , Caton‐Rose Fin , Martyn Michasel 
Published: January 2016

AbstractHighly oriented poly (lactic acid) (PLA) with bionic microgrooves was fabricated through solid hot drawing technology for further improving the mechanical properties and blood biocompatibility of PLA. In order to enhance the melt strength and thus obtain high orientation degree, long chain branched PLA was prepared at first through a two‐step ring‐opening reaction during processing. Linear viscoelasticity combined with branch‐on‐branch model was used to predict probable compositions and chain topologies of the products, and it was found that the molecular weight of PLA increased and topological structures with star like chain with three arms and tree‐like chain with two generations formed during reactive processing, and consequently draw ratio as high as1200% can be achieved during the subsequent hot stretching. With the increase of draw ratio, the tensile strength and orientation degree of PLA increased dramatically. Long chain branching and orientation could significantly enhance the blood compatibility of PLA by prolonging clotting time and decreasing platelet activation. Microgrooves can be observed on the surface of the oriented PLA which were similar to the intimal layer of blood vessel, and such bionic structure resulted from the formation of the oriented shish kebab‐like crystals along the draw direction. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1082–1089, 2016.
Investigating the optical NOR gate using plasmonic nanorods
Authors: Kaboli Milad , Akhlaghi Majid , Shahmirzaee Hossein 
Published: January 2016

SummaryIn this paper, a coherent perfect absorption‐type NOR gate based on plasmonic nano particles is proposed. It consists of two plasmonic nanorod arrays on top of two serial arms with quartz substrate. The operation principle is based on the absorbable formation of a conductive path in the dielectric layer of a plasmonic nanoparticle waveguide. Because the coherent perfect absorption efficiency depends strongly on the number of plasmonic nanorods and the locations of nanorods, an efficient binary optimization method based the Particle Swarm Optimization algorithm is used to design an optimized array of the plasmonic nanorods in order to achieve the maximum absorption coefficient in the ‘off’ state and the minimum absorption coefficient in the ‘on’ state. In Binary Particle Swarm Optimization, a group of birds consists a matrix with binary entries, control the presence (‘1’) or the absence (‘0’) of nanorods in the array. Copyright © 2016 John Wiley & Sons, Ltd.
Interband optical transitions of Zn
Authors: Karpus V. , Tumėnas S. , Eikevičius A. , Arwin H. 
Published: January 2016

AbstractExperimental results of an optical study of single‐crystal zinc are presented. Components of the Zn dielectric function tensor were measured by spectroscopic ellipsometry in the 0.1–5 eV spectral range. In the NIR–VIS range, the dielectric function spectra show two clearly resolved, polarization‐dependent optical features located at about 1 and 1.7 eV. The optical features were analyzed in a framework of parallel‐band optical transitions. The performed theoretical calculations of the optical conductivity spectra well reproduce the experimental data with respect to positions, intensities, and polarization dependencies of the observed interband absorption peaks.
How does code obfuscation impact energy usage?
Authors: Sahin Cagri , Wan Mian , Tornquist Philip , McKenna Ryan , Pearson Zachary , Halfond William G. J. , Clause James 
Published: January 2016

AbstractSoftware piracy is an important concern for application developers. Such concerns are especially relevant in mobile application development, where piracy rates can be greater than 90%. The most common approach used by mobile developers to prevent piracy is code obfuscation. However, the decision to apply such transformations is currently made without regard to the impacts of obfuscations on another area of increasing concern for mobile application developers, energy usage. Because both software piracy and battery life are important concerns, mobile application developers must strike a balance between protecting their applications and preserving the battery lives of their users' devices. To help them make such choices, we conducted an empirical study of the effects of 18 code obfuscations on the amount of energy consumed by executing a total of 21 usage scenarios spread across 11 Android applications on four different mobile phone platforms. The results of the study indicate that, while obfuscations can have a statistically significant impact on energy usage and are more likely to increase energy usage than to decrease energy usage, the magnitudes of such impacts are unlikely to be meaningful to mobile application users. Copyright © 2016 John Wiley & Sons, Ltd.
Efficient Encapsulation of a Water‐Soluble Molecule into Lipid Vesicles Using W/O/W Multiple Emulsions via Solvent Evaporation
Authors: Kuroiwa Takashi , Horikoshi Kaname , Suzuki Akihiko , Neves Marcos A. , Kobayashi Isao , Uemura Kunihiko , Nakajima Mitsutoshi , Kanazawa Akihiko , Ichikawa Sosaku 
Published: January 2016

AbstractWe developed a novel method for preparing lipid vesicles with high entrapment efficiency and controlled size using water‐in‐oil‐in‐water (W/O/W) multiple emulsions as vesicle templates. Preparation consists of three steps. First, a water‐in‐oil (W/O) emulsion containing to‐be‐entrapped hydrophilic molecules in the water phase and vesicle‐forming lipids in the oil phase was formulated by sonication. Second, this W/O emulsion was introduced into a microchannel emulsification device to prepare a W/O/W multiple emulsion. In this step, sodium caseinate was used as the external emulsifier. Finally, organic solvent in the oil phase was removed by simple evaporation under ambient conditions to afford lipid vesicles. The diameter of the prepared vesicles reflected the water droplet size of the primary W/O emulsions, indicating that vesicle size could be controlled by the primary W/O emulsification process. Furthermore, high entrapment yields for hydrophilic molecules (exceeding 80 % for calcein) were obtained. The resulting vesicles had a multilamellar vesicular structure, as confirmed by transmission electron microscopy.
Enhanced efficacy of combined HDAC and PARP targeting in glioblastoma
Authors: Rasmussen Rikke D. , Gajjar Madhavsai K. , Jensen Kamilla E. , Hamerlik Petra 
Published: January 2016

Recent clinical trials have demonstrated that targeting chromatin remodeling factors is as a promising strategy for the treatment of glioblastoma (GBM). We and others have shown constitutive activation of DNA damage response (DDR) pathways in gliomas and suggested that targeting the DDR may improve the currently grim prognosis for patients. Based on our previous findings that inhibition of poly(ADP‐ribose) polymerase (PARP) increases radio‐sensitivity of the notoriously radio‐resistant GBM cells, we hypothesized that epigenetic down‐regulation of the DDR responses and induction of oxidative stress via HDAC inhibition would contribute to more efficient targeting of this deadly disease. Our data show that SAHA, an HDAC class I + II inhibitor, in combination with olaparib (PARP inhibitor): i) enhanced inhibition of GBM cell survival, ii) induced apoptosis, and iii) impaired cell cycle progression. These results provide a pre‐clinical rationale for combined administration of SAHA and olaparib, which are already individually in clinical trials.
Nationalism and authoritarianism in Russia: Introduction to the special issue
Authors: Kuzio Taras 
Published: January 2016

This article discusses different aspects of the political evolution of Russian President and former Prime Minister Vladimir Putin and the impact of his evolution upon the type of regime that has evolved from soft authoritarianism to a ‘militocracy‘ and ‘consolidated authoritarian regime.’ The article discusses eight contributions to this special issue by placing them within the broader context of how the West misread two areas pertaining to Russia. The first is how the West by wrongly believing that Russia, being a member of G8, the NATO-Russia Council and other Western structures, continued to be interested in becoming a Western political and economic system. The second is the tradition, stretching back to Sovietology, of ignoring and downplaying the issue of how the nationalities question and different nationalisms interact with democratic revolutions, transitions and, specifically, with Russian politics.The introductory article next discusses the eight contributions within the context of: Russian messianism, the Russkii Mir (Russian World), how and when nationalists and fascists became mainstream in Russian politics, Putin’s great power nationalism, Ukrainophobia and Russian chauvinism, historical myths and re-Stalinization of Putin’s political system. The final section compares Russia’s invasions of Georgia and Ukraine in 2008 and 2014 respectively and the growing xenophobia in Russian foreign policy.
Effort-Reward Imbalance and Post-Traumatic Stress After a Workplace Terror Attack
Authors: Hem Camilla , Nielsen Morten Birkeland , Hansen Marianne Bang , Heir Trond 
Published: January 2016

AbstractObjectiveFollowing adverse work conditions, health consequences can be explained by an imbalance between the effort made and the reward received. We investigated the association between extra effort, perceived reward, and post-traumatic stress disorder (PTSD). The Effort-Reward Imbalance Model was used to examine whether extra effort at work in the aftermath of a workplace-related terrorist attack affected the risk of PTSD and the effects of reward for extra effort from a leader or colleagues.MethodsCross-sectional data were collected 10 months after a terrorist attack in Norway in 2011. Out of 3520 Ministry employees invited, 1927 agreed to participate. Employees reported any extra effort performed as a result of the bomb explosion and any reward received from a leader or colleagues. PTSD was assessed with the PTSD Checklist.ResultsEmployees who reported extra effort displayed increased risk for PTSD (odds ratio [OR]=1.71, 95% confidence interval [CI]: 1.15-2.55, P=0.008). Perceived reward for extra effort from a leader was associated with lower risk for PTSD (OR=0.39, 95% CI: 0.23-0.64, P<0.001) but not perceived reward from colleagues.ConclusionsExtra effort may increase the risk of PTSD, but reward from a leader may mitigate this effect. The Effort-Reward Imbalance Model appears to be an appropriate approach that may contribute to understanding of the etiology of work-related PTSD. (Disaster Med Public Health Preparedness. 2016;10:219–224)
Injury Patterns After the Landslide Disaster in Oshima, Tokyo, Japan on October 16, 2013
Authors: Homma Yasuhiro , Watari Taiji , Baba Tomonori , Suzuki Misako , Shimizu Tadanori , Fujii Yuji , Takazawa Yuji , Maruyama Yuichiro , Kaneko Kazuo 
Published: January 2016

AbstractIntroductionLandslides represent a frequent and threatening natural disaster. The aim of this study was to investigate the injury patterns observed after a landslide and to discuss how to minimize the damage caused by a landslide disaster.MethodsA landslide occurred on Oshima Island, Japan, on October 16, 2013. A total of 49 victims with landslide-related injuries were identified and analyzed.ResultsThe patients ranged in age from 5 to 89 years with an average age of 61.0±19.3 years. Of all patients, 69.4% were triaged as black. Of 15 patients who were treated in the nearest hospital (the only hospital on the island), 8 were triaged as red and yellow with severe chest or pelvic injury and a high Injury Severity Score (average score, 25.6; range, 4–45). Of these, 75% had chest injury and 75% had pelvic injury. The percentage of chest and/or pelvic injury was 100% in patients triaged as red or yellow. Traumatic asphyxia was diagnosed in 62.5% of these patients.ConclusionsCompression of the trunk was the main injury in patients triaged as red or yellow after this landslide disaster. Evacuation in advance, the rapid launch of emergency medical support, and knowledge of this specific injury pattern are essential to minimize the potential damage resulting from landslide disasters. (Disaster Med Public Health Preparedness. 2016;10:248–252)
Vitamin D3 and 25-hydroxyvitamin D3 in pork and their relationship to vitamin D status in pigs
Authors: Burild Anders , Lauridsen Charlotte , Faqir Nasrin , Sommer Helle M. , Jakobsen Jette 
Published: January 2016

AbstractThe content of vitamin D in pork produced in conventional systems depends on the vitamin D concentration in the pig feed. Both vitamin D3 and 25-hydroxyvitamin D3 (25(OH)D3) are essential sources of dietary vitamin D; however, bioavailability assessed by serum 25(OH)D3 concentration is reported to be different between the two sources. Furthermore, the relationship between serum 25(OH)D3 level and the tissue content of vitamin D3 and 25(OH)D3 is unknown. The objective of this study was to investigate the potential of increasing the content of vitamin D in different pig tissues by increasing the levels of vitamin D3 and 25(OH)D3 in the pig feed for 49 d before slaughter. Concurrently, the 25(OH)D3 level in serum was investigated as a biomarker to assess the content of vitamin D3 and 25(OH)D3 in pig tissues. Adipose tissue, white and red muscle, the liver and serum were sampled from pigs fed feed containing either vitamin D3 or 25(OH)D3 at 5, 20, 35 or 50 µg/kg feed for 7 weeks before slaughter. The tissue 25(OH)D3 level was significantly higher in the pigs fed 25(OH)D3 compared with those fed vitamin D3, while the tissue vitamin D3 level was higher in the pigs fed vitamin D3 compared with those fed 25(OH)D3. The content of 25(OH)D3 in the different tissues fully correlated with the serum 25(OH)D3 level, whereas the correlation between the tissue content of vitamin D3 and serum 25(OH)D3 was dependent on the source of the ingested vitamin D3.
On Geodesics in Asymptotic Universal Teichmüller Space
Authors: Zemin Zhou , Jixiu Chen 
Published: January 2016

AbstractLet AT(Δ) be the asymptotic universal Teichmüller space, viewed as the space of all asymptotic Teichmüller equivalence classes [[μ]]. We show that ifμis asymptotically extremal in AT(Δ) andhp([[μ]]) <h([[μ]]) for some boundary pointpofΔ, then there are infinitely many geodesics joining [[0]] and [[μ]] in AT(Δ). As a corollary, a necessary condition for a complex dilatation to be uniquely extremal in AT(Δ) is given.
Examining cellular immune responses to inform development of a blood-stage malaria vaccine
Authors: STANISIC DANIELLE I. , GOOD MICHAEL F. 
Published: January 2016

SUMMARYNaturally acquired immunity to the blood-stage of the malaria parasite develops slowly in areas of high endemicity, but is not sterilizing. It manifests as a reduction in parasite density and clinical symptoms. Immunity as a result of blood-stage vaccination has not yet been achieved in humans, although there are many animal models where vaccination has been successful. The development of a blood-stage vaccine has been complicated by a number of factors including limited knowledge of human-parasite interactions and which antigens and immune responses are critical for protection. Opinion is divided as to whether this vaccine should aim to accelerate the acquisition of responses acquired following natural exposure, or whether it should induce a different response. Animal and experimental human models suggest that cell-mediated immune responses can control parasite growth, but these responses can also contribute to significant immunopathology if unregulated. They are largely ignored in most blood-stage malaria vaccine development strategies. Here, we discuss key observations relating to cell-mediated immune responses in the context of experimental human systems and field studies involving naturally exposed individuals and how this may inform the development of a blood-stage malaria vaccine.
Naturally acquired immunity to sexual stageP. falciparumparasites
Authors: STONE WILL J. R. , DANTZLER KATHLEEN W. , NILSSON SANDRA K. , DRAKELEY CHRIS J. , MARTI MATTHIAS , BOUSEMA TEUN , RIJPMA SANNA R. 
Published: January 2016

SUMMARYGametocytes are the specialized form ofPlasmodiumparasites that are responsible for human-to-mosquito transmission of malaria. Transmission of gametocytes is highly effective, but represents a biomass bottleneck for the parasite that has stimulated interest in strategies targeting the transmission stages separately from those responsible for clinical disease. Studying targets of naturally acquired immunity against transmission-stage parasites may reveal opportunities for novel transmission reducing interventions, particularly the development of a transmission blocking vaccine (TBV). In this review, we summarize the current knowledge on immunity against the transmission stages ofPlasmodium. This includes immune responses against epitopes on the gametocyte-infected erythrocyte surface during gametocyte development, as well as epitopes present upon gametocyte activation in the mosquito midgut. We present an analysis of historical data on transmission reducing immunity (TRI), as analysed in mosquito feeding assays, and its correlation with natural recognition of sexual stage specific proteins Pfs48/45 and Pfs230. Although high antibody titres towards either one of these proteins is associated with TRI, the presence of additional, novel targets is anticipated. In conclusion, the identification of novel gametocyte-specific targets of naturally acquired immunity against different gametocyte stages could aid in the development of potential TBV targets and ultimately an effective transmission blocking approach.
Immunological processes underlying the slow acquisition of humoral immunity to malaria
Authors: RYG-CORNEJO VICTORIA , LY ANN , HANSEN DIANA S. 
Published: January 2016

SUMMARYMalaria is one of the most serious infectious diseases with ~250 million clinical cases annually. Most cases of severe disease are caused byPlasmodium falciparum. The blood stage ofPlasmodiumparasite is entirely responsible for malaria-associated pathology. Disease syndromes range from fever to more severe complications, including respiratory distress, metabolic acidosis, renal failure, pulmonary oedema and cerebral malaria. The most susceptible population to severe malaria is children under the age of 5, with low levels of immunity. It is only after many years of repeated exposure, that individuals living in endemic areas develop clinical immunity. This form of protection does not result in sterilizing immunity but prevents clinical episodes by substantially reducing parasite burden. Naturally acquired immunity predominantly targets blood-stage parasites and it is known to require antibody responses. A large body of epidemiological evidence suggests that antibodies toPlasmodiumantigens are inefficiently generated and rapidly lost in the absence of ongoing exposure, which suggests a defect in the development of B cell immunological memory. This review summarizes the main findings to date contributing to our understanding on cellular processes underlying the slow acquisition of humoral immunity to malaria. Some of the key outstanding questions in the field are discussed.