bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale insights into doping behavior, particle size and surface effects in trivalent metal doped SnO2
Authors: Cojocaru Bogdan , Avram Daniel , Kessler Vadim , Parvulescu Vasile , Seisenbaeva Gulaim , Tiseanu Carmen 
Published: August 2017

AbstractDespite considerable research, the location of an aliovalent dopant into SnO2 nanoparticles is far to be clarified. The aim of the present study on trivalent lanthanide doped SnO2 is to differentiate between substitutional versus interstitial and surface versus bulk doping, delineate the bulk and surface defects induced by doping and establish an intrinsic dopant distribution. We evidence for the first time a complex distribution of intrinsic nature composed of substitutional isolated, substitutional associates with defects as well as surface centers. Such multi-modal distribution is revealed for Eu and Sm, while Pr, Tb and Dy appear to be distributed mostly on the SnO2 surface. Like the previously reported case of Eu, Sm displays a long-lived luminescence decaying in the hundreds of ms scale which is likely related to a selective interaction between the traps and the substitutional isolated center. Analyzing the time-gated luminescence, we conclude that the local lattice environment of the lattice Sn is not affected by the particle size, being remarkably similar in the ~2 and 20 nm particles. The photocatalytic measurements employed as a probe tool confirm the conclusions from the luminescence measurements concerning the nature of defects and the temperature induced migration of lanthanide dopants.
A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns
Authors: Zhang Yue , Cheung Yiu-ming , Su Weifeng 
Published: August 2017

AbstractVariations in DNA copy number carry important information on genome evolution and regulation of DNA replication in cancer cells. The rapid development of single-cell sequencing technology enables exploration of gene-expression heterogeneity among single cells, providing important information on cell evolution. Evolutionary relationships in accumulated sequence data can be visualized by adjacent positioning of similar cells so that similar copy-number profiles are shown by block patterns. However, single-cell DNA sequencing data usually have low amount of starting genome, which requires an extra step of amplification to accumulate sufficient samples, introducing noise and making regular pattern-finding challenging. In this paper, we will propose to tackle this issue of recovering the hidden blocks within single-cell DNA-sequencing data through continuous sample permutations such that similar samples are positioned adjacently. The permutation is guided by the total variational norm of the recovered copy number profiles, and is continued until the total variational norm is minimized when similar samples are stacked together to reveal block patterns. An efficient numerical scheme for finding this permutation is designed, tailored from the alternating direction method of multipliers. Application of this method to both simulated and real data demonstrates its ability to recover the hidden structures of single-cell DNA sequences.
A rumor spreading model based on information entropy
Authors: Wang Chao , Tan Zong Xuan , Ye Ye , Wang Lu , Cheong Kang Hao , Xie Neng-gang 
Published: August 2017

AbstractRumor spreading can have a significant impact on people’s lives, distorting scientific facts and influencing political opinions. With technologies that have democratized the production and reproduction of information, the rate at which misinformation can spread has increased significantly, leading many to describe contemporary times as a ‘post-truth era’. Research into rumor spreading has primarily been based on either model of social and biological contagion, or upon models of opinion dynamics. Here we present a comprehensive model that is based on information entropy, which allows for the incorporation of considerations like the role of memory, conformity effects, differences in the subjective propensity to produce distortions, and variations in the degree of trust that people place in each other. Variations in the degree of trust are controlled by a confidence factor β, while the propensity to produce distortions is controlled by a conservation factor K. Simulations were performed using a Barabási–Albert (BA) scale-free network seeded with a single piece of information. The influence of β and K upon the temporal evolution of the system was subsequently analyzed regarding average information entropy, opinion fragmentation, and the range of rumor spread. These results can aid in decision-making to limit the spread of rumors.
Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection
Authors: Pickering Harry , Teng Andy , Faal Nkoyo , Joof Hassan , Makalo Pateh , Cassama Eunice , Nabicassa Meno , Last Anna R. , Burr Sarah E. , Rowland-Jones Sarah L. , Thomson Nicholas R. , Roberts Chrissy h. , Mabey David C. W. , Bailey Robin L. , Hayward Richard D. , de la Maza Luis M. , Holland Martin J. 
Published: August 2017

AbstractThe frequency and duration ofChlamydia trachomatis(Ct) ocular infections decrease with age, suggesting development of partial immunity. However, there is a lack of clear correlates of immunity to Ct infection in humans. We screened sera from a cohort of Gambian children followed for six-months against a Ct-proteome microarray. At genome sequence level, we detected signatures of selection from a population of ocular Ct isolates from Guinea-Bissau. Together these approaches allowed us to highlight the focus of humoral responses and hypothesise new modes of pathogen immune evasion. Children who were susceptible to frequent and/or prolonged Ct infection had a less focussed antibody response, including preferential recognition of forty-two antigens. There was evidence of positive and purifying selection across the genome, but little balancing selection. In contrast, most antigens that were associated with susceptibility were under neutral selection. These data suggest an evasion strategy in which Ct presents a large panel of irrelevant antigens to the immune system to block or misdirect protective responses. Development of a focused immune response, possibly induced through vaccination, may be an effective strategy to promote protection to Ct infection.
Salt tolerance response revealed by RNA-Seq in a diploid halophytic wild relative of sweet potato
Authors: Luo Yan , Reid Robert , Freese Daniella , Li Changbao , Watkins Jonathan , Shi Huazhong , Zhang Hengyou , Loraine Ann , Song Bao-Hua 
Published: August 2017

AbstractCrop wild relatives harbor exotic and novel genetic resources, which hold great potential for crop improvement. Ipomoea imperati is a wild diploid relative of sweet potato with the capability of high salinity tolerance. We compared the transcriptomes of I. imperati under salt stress vs. control to identify candidate genes and pathways involved in salt response. De novo assembly produced 67,911 transcripts with a high depth of coverage. A total of 39,902 putative genes were assigned annotations, and 936 and 220 genes involved in salt response in roots and leaves, respectively. Functional analysis indicated a whole system response during salt stress in I. imperati, which included four metabolic processes: sensory initiation, transcriptional reprogramming, cellular protein component change, and cellular homeostasis regulation. We identified a number of candidate genes involved in the ABA signaling pathway, as well as transcription factors, transporters, antioxidant enzymes, and enzymes associated with metabolism of synthesis and catalysis. Furthermore, two membrane transporter genes, including vacuole cation/proton exchanger and inositol transporter, were considered to play important roles in salt tolerance. This study provided valuable information not only for understanding the genetic basis of ecological adaptation but also for future application in sweet potato and other crop improvements.
Aspergillus flavus infection triggered immune responses and host-pathogen cross-talks in groundnut during in-vitro seed colonization
Authors: Nayak Spurthi N , Agarwal Gaurav , Pandey Manish K , Sudini Hari K , Jayale Ashwin S , Purohit Shilp , Desai Aarthi , Wan Liyun , Guo Baozhu , Liao Boshou , Varshney Rajeev K 
Published: August 2017

AbstractAflatoxin contamination, caused by fungal pathogen Aspergillus flavus, is a major quality and health problem delimiting the trade and consumption of groundnut (Arachis hypogaea L.) worldwide. RNA-seq approach was deployed to understand the host-pathogen interaction by identifying differentially expressed genes (DEGs) for resistance to in-vitro seed colonization (IVSC) at four critical stages after inoculation in J 11 (resistant) and JL 24 (susceptible) genotypes of groundnut. About 1,344.04 million sequencing reads have been generated from sixteen libraries representing four stages in control and infected conditions. About 64% and 67% of quality filtered reads (1,148.09 million) were mapped onto A (A. duranensis) and B (A. ipaёnsis) subgenomes of groundnut respectively. About 101 million unaligned reads each from J 11 and JL 24 were used to map onto A. flavus genome. As a result, 4,445 DEGs including defense-related genes like senescence-associated proteins, resveratrol synthase, 9s-lipoxygenase, pathogenesis-related proteins were identified. In A. flavus, about 578 DEGs coding for growth and development of fungus, aflatoxin biosynthesis, binding, transport, and signaling were identified in compatible interaction. Besides identifying candidate genes for IVSC resistance in groundnut, the study identified the genes involved in host-pathogen cross-talks and markers that can be used in breeding resistant varieties.
In-situ observation of ultrafast 90° domain switching under application of an electric field in (100)/(001)-oriented tetragonal epitaxial Pb(Zr0.4Ti0.6)O3 thin films
Authors: Ehara Yoshitaka , Yasui Shintaro , Oikawa Takahiro , Shiraishi Takahisa , Shimizu Takao , Tanaka Hiroki , Kanenko Noriyuki , Maran Ronald , Yamada Tomoaki , Imai Yasuhiko , Sakata Osami , Valanoor Nagarajan , Funakubo Hiroshi 
Published: August 2017

AbstractFerroelastic domain switching significantly affects piezoelectric properties in ferroelectric materials. The ferroelastic domain switching and the lattice deformation of both a-domains and c-domains under an applied electric field were investigated using in-situ synchrotron X-ray diffraction in conjunction with a high-speed pulse generator set up for epitaxial (100)/(001)-oriented tetragonal Pb(Zr0.4Ti0.6)O3 (PZT) films grown on (100)
c
SrRuO3//(100)KTaO3 substrates. The 004 peak (c-domain) position shifts to a lower 2θ angle, which demonstrates the elongation of the c-axis lattice parameter of the c-domain under an applied electric field. In contrast, the 400 peak (a-domain) shifts in the opposite direction (higher angle), thus indicating a decrease in the a-axis lattice parameter of the a-domain. 90° domain switching from (100) to (001) orientations (from a-domain to c-domain) was observed by a change in the intensities of the 400 and 004 diffraction peaks by applying a high-speed pulsed electric field 200 ns in width. This change also accompanied a tilt in the angles of each domain from the substrate surface normal direction. This behaviour proved that the 90° domain switched within 40 ns under a high-speed pulsed electric field. Direct observation of such high-speed switching opens the way to design piezo-MEMS devices for high-frequency operation.
Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter
Authors: Woodcock Dan J. , Krusche Peter , Strachan Norval J. C. , Forbes Ken J. , Cohan Frederick M. , Méric Guillaume , Sheppard Samuel K. 
Published: August 2017

AbstractHorizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of host segregating alleles, distributed as predicted for niche specifying genes, and the opportunity for host transition could interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of homologous recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.
Embodiment in a Child-Like Talking Virtual Body Influences Object Size Perception, Self-Identification, and Subsequent Real Speaking
Authors: Tajadura-Jiménez Ana , Banakou Domna , Bianchi-Berthouze Nadia , Slater Mel 
Published: August 2017

AbstractPeople’s mental representations of their own body are malleable and continuously updated through sensory cues. Altering one’s body-representation can lead to changes in object perception and implicit attitudes. Virtual reality has been used to embody adults in the body of a 4-year-old child or a scaled-down adult body. Child embodiment was found to cause an overestimation of object sizes, approximately double that during adult embodiment, and identification of the self with child-like attributes. Here we tested the contribution of auditory cues related to one’s own voice to these visually-driven effects. In a 2 × 2 factorial design, visual and auditory feedback on one’s own body were varied across conditions, which included embodiment in a child or scaled-down adult body, and real (undistorted) or child-like voice feedback. The results replicated, in an older population, previous findings regarding size estimations and implicit attitudes. Further, although auditory cues were not found to enhance these effects, we show that the strength of the embodiment illusion depends on the child-like voice feedback being congruent or incongruent with the age of the virtual body. Results also showed the positive emotional impact of the illusion of owning a child’s body, opening up possibilities for health applications.
Hypertension Susceptibility Loci are Associated with Anthracycline-related Cardiotoxicity in Long-term Childhood Cancer Survivors
Authors: Hildebrandt Michelle A. T. , Reyes Monica , Wu Xifeng , Pu Xia , Thompson Kara A. , Ma Jianzhong , Landstrom Andrew P. , Morrison Alanna C. , Ater Joann L. 
Published: August 2017

AbstractAnthracycline-based chemotherapy is associated with dose-dependent, irreversible damage to the heart. Childhood cancer survivors with hypertension after anthracycline exposure are at increased risk of cardiotoxicity, leading to the hypothesis that genetic susceptibility loci for hypertension may serve as predictors for development of late cardiotoxicity. Therefore, we determined the association between 12 GWAS-identified hypertension-susceptibility loci and cardiotoxicity in a cohort of long-term childhood cancer survivors (N = 108) who received anthracyclines and were screened for cardiac function via echocardiograms. Hypertension-susceptibility alleles of PLCE1:rs9327264 and ATP2B1:rs17249754 were significantly associated with cardiotoxicity risk conferring a protective effect with a 64% (95% CI: 0.18–0.76, P = 0.0068) and 74% (95% CI: 0.07–0.96, P = 0.040) reduction in risk, respectively. In RNAseq experiments of human induced pluripotent stem cell (iPSC) derived cardiomyocytes treated with doxorubicin, both PLCE1 and ATP2B1 displayed anthracycline-dependent gene expression profiles. In silico functional assessment further supported this relationship - rs9327264 in PLCE1 (P = 0.0080) and ATP2B1 expression (P = 0.0079) were both significantly associated with daunorubicin IC50 values in a panel of lymphoblastoid cell lines. Our findings demonstrate that the hypertension-susceptibility variants in PLCE1 and ATP2B1 confer a protective effect on risk of developing anthracycline-related cardiotoxicity, and functional analyses suggest that these genes are influenced by exposure to anthracyclines.
Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization
Authors: Alexandrov Ludmil B. , Rasmussen Kim Ø. , Bishop Alan R. , Alexandrov Boian S. 
Published: August 2017

AbstractThe innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. Here, we develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Further, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.
One-reactor plasma assisted fabrication of ZnO@TiO
2
multishell nanotubes: assessing the impact of a full coverage on the photovoltaic performance
Authors: Filippin Alejandro Nicolas , Macias-Montero Manuel , Saghi Zineb , Idígoras Jesús , Burdet Pierre , Sanchez-Valencia Juan R. , Barranco Angel , Migdley Paul A. , Anta Juan A. , Borras Ana 
Published: August 2017

AbstractThis paper addresses the fabrication of vertically aligned ZnO@TiO2 multishell nanotubes by a combined full vacuum-plasma approach at mild temperatures. The growth is carried out within the premises of a one-reactor approach, i.e. minimizing the number of vacuum chambers and sample transferences. In this way, the interface between ZnO and TiO2 is fully preserved from humidity thus increasing ZnO durability and stability. These nanostructures are studied by scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM) and energy dispersive X-ray spectroscopy in STEM (EDX-STEM). High density one-dimensional arrays of these nanotubes formed on FTO substrates are applied as photoanode in a dye-sensitized solar cell (DSC). The evolution of the dye adsorption capacity and solar cells parameters are explored as a function of the crystallinity and thickness of the TiO2 shell. The results show the critical effect of a full coverage by TiO2 of ZnO core to explain the mixed results found in the literature.
A heart-coronary arteries structure of carbon nanofibers/graphene/silicon composite anode for high performance lithium ion batteries
Authors: Ma Xiaoxin , Hou Guangmei , Ai Qing , Zhang Lin , Si Pengchao , Feng Jinkui , Ci Lijie 
Published: August 2017

AbstractIn an animal body, coronary arteries cover around the whole heart and supply the necessary oxygen and nutrition so that the heart muscle can survive as well as can pump blood in and out very efficiently. Inspired by this, we have designed a novel heart-coronary arteries structured electrode by electrospinning carbon nanofibers to cover active anode graphene/silicon particles. Electrospun high conductive nanofibers serve as veins and arteries to enhance the electron transportation and improve the electrochemical properties of the active “heart” particles. This flexible binder free carbon nanofibers/graphene/silicon electrode consists of millions of heart-coronary arteries cells. Besides, in the graphene/silicon “hearts”, graphene network improves the electrical conductivity of silicon nanopaticles, buffers the volume change of silicon, and prevents them from directly contacting with electrolyte. As expected, this novel composite electrode demonstrates excellent lithium storage performance with a 86.5% capacity retention after 200 cycles, along with a high rate performance with a 543 mAh g−1 capacity at the rate of 1000 mA g−1.
A new route to enhance the ferromagnetic transition temperature in diluted magnetic semiconductors
Authors: Pradhan Kalpataru , Das Subrat K. 
Published: August 2017

AbstractWe investigate the magnetic and the transport properties of diluted magnetic semiconductors using a spin-fermion Monte-Carlo method on a simple cubic lattice in the intermediate coupling regime. The ferromagnetic transition temperature Tc shows an optimization behavior with respect to the absolute carrier density pabs and the magnetic impurity concentration x as seen in the experiments. Our calculations also show an insulator-metal-insulator transition across the optimum pabs where the Tc is maximum. Remarkably, the optimum pabs values lie in a narrow range around 0.11 (holes/site) for all x values and the ferromagnetic Tc increases with x. We explain our results using the polaron percolation mechanism and outline a new route to enhance the ferromagnetic transition temperature in experiments.
Anosmia impairs homing orientation but not foraging behaviour in free-ranging shearwaters
Authors: Padget O. , Dell’Ariccia G. , Gagliardo A. , González-Solís J. , Guilford T. 
Published: August 2017

AbstractShearwaters deprived of their olfactory sense before being displaced to distant sites have impaired homing ability but it is unknown what the role of olfaction is when birds navigate freely without their sense of smell. Furthermore, treatments used to induce anosmia and to disrupt magneto-reception in displacement experiments might influence non-specific factors not directly related to navigation and, as a consequence, the results of displacement experiments can have multiple interpretations. To address this, we GPS-tracked the free-ranging foraging trips of incubating Scopoli’s shearwaters within the Mediterranean Sea. As in previous experiments, shearwaters were either made anosmic with 4% zinc sulphate solution, magnetically impaired by attachment of a strong neodymium magnet or were controls. We found that birds from all three treatments embarked on foraging trips, had indistinguishable at-sea schedules of behaviour and returned to the colony having gained mass. However, we found that in the pelagic return stage of their foraging trips, anosmic birds were not oriented towards the colony though coastal navigation was unaffected. These results support the case for zinc sulphate having a specific effect on the navigational ability of shearwaters and thus the view that seabirds consult an olfactory map to guide them across seascapes.