bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic variation contributes to bacterial host specificity
Authors: Yue Min , Han Xiangan , Masi Leon De , Zhu Chunhong , Ma Xun , Zhang Junjie , Wu Renwei , Schmieder Robert , Kaushik Radhey S. , Fraser George P. , Zhao Shaohua , McDermott Patrick F. , Weill François-Xavier , Mainil Jacques G. , Arze Cesar , Fricke W. Florian , Edwards Robert A. , Brisson Dustin , Zhang Nancy R. , Rankin Shelley C. , Schifferli Dieter M. 
Published: October 2015

AbstractUnderstanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.
Measurement of geometric dephasing using a superconducting qubit
Authors: Berger S. , Pechal M. , Kurpiers P. , Abdumalikov A. A. , Eichler C. , Mlynek J. A. , Shnirman A. , Gefen Yuval , Wallraff A. , Filipp S. 
Published: October 2015

AbstractA quantum system interacting with its environment is subject to dephasing, which ultimately destroys the information it holds. Here we use a superconducting qubit to experimentally show that this dephasing has both dynamic and geometric origins. It is found that geometric dephasing, which is present even in the adiabatic limit and when no geometric phase is acquired, can either reduce or restore coherence depending on the orientation of the path the qubit traces out in its projective Hilbert space. It accompanies the evolution of any system in Hilbert space subjected to noise.
Ultra-high modulation depth exceeding 2,400% in optically controlled topological surface plasmons
Authors: Sim Sangwan , Jang Houk , Koirala Nikesh , Brahlek Matthew , Moon Jisoo , Sung Ji Ho , Park Jun , Cha Soonyoung , Oh Seongshik , Jo Moon-Ho , Ahn Jong-Hyun , Choi Hyunyong 
Published: October 2015

AbstractModulating light via coherent charge oscillations in solids is the subject of intense research topics in opto-plasmonics. Although a variety of methods are proposed to increase such modulation efficiency, one central challenge is to achieve a high modulation depth (defined by a ratio of extinction with/without light) under small photon-flux injection, which becomes a fundamental trade-off issue both in metals and semiconductors. Here, by fabricating simple micro-ribbon arrays of topological insulator Bi2Se3, we report an unprecedentedly large modulation depth of 2,400% at 1.5 THz with very low optical fluence of 45 μJ cm−2. This was possible, first because the extinction spectrum is nearly zero due to the Fano-like plasmon–phonon-destructive interference, thereby contributing an extremely small denominator to the extinction ratio. Second, the numerator of the extinction ratio is markedly increased due to the photoinduced formation of massive two-dimensional electron gas below the topological surface states, which is another contributor to the ultra-high modulation depth.
Angiotensin II receptor blockade promotes repair of skeletal muscle through down-regulation of aging-promoting C1q expression
Authors: Yabumoto Chizuru , Akazawa Hiroshi , Yamamoto Rie , Yano Masamichi , Kudo-Sakamoto Yoko , Sumida Tomokazu , Kamo Takehiro , Yagi Hiroki , Shimizu Yu , Saga-Kamo Akiko , Naito Atsuhiko T. , Oka Toru , Lee Jong-Kook , Suzuki Jun-ichi , Sakata Yasushi , Uejima Etsuko , Komuro Issei 
Published: October 2015

AbstractDisruption of angiotensin II type 1 (AT1) receptor prolonged life span in mice. Since aging-related decline in skeletal muscle function was retarded in Atgr1a−/− mice, we examined the role of AT1 receptor in muscle regeneration after injury. Administration of AT1 receptor blocker irbesartan increased the size of regenerating myofibers, decreased fibrosis and enhanced functional muscle recovery after cryoinjury. We recently reported that complement C1q, secreted by macrophages, activated Wnt/β-catenin signaling and promoted aging-related decline in regenerative capacity of skeletal muscle. Notably, irbesartan induced M2 polarization of macrophages, but reduced C1q expression in cryoinjured muscles and in cultured macrophage cells. Irbesartan inhibited up-regulation of Axin2, a downstream gene of Wnt/β-catenin pathway, in cryoinjured muscles. In addition, topical administration of C1q reversed beneficial effects of irbesartan on skeletal muscle regeneration after injury. These results suggest that AT1 receptor blockade improves muscle repair and regeneration through down-regulation of the aging-promoting C1q-Wnt/β-catenin signaling pathway.
Fast synthesis of platinum nanopetals and nanospheres for highly-sensitive non-enzymatic detection of glucose and selective sensing of ions
Authors: Taurino Irene , Sanzó Gabriella , Mazzei Franco , Favero Gabriele , De Micheli Giovanni , Carrara Sandro 
Published: October 2015

AbstractNovel methods to obtain Pt nanostructured electrodes have raised particular interest due to their high performance in electrochemistry. Several nanostructuration methods proposed in the literature use costly and bulky equipment or are time-consuming due to the numerous steps they involve. Here, Pt nanostructures were produced for the first time by one-step template-free electrodeposition on Pt bare electrodes. The change in size and shape of the nanostructures is proven to be dependent on the deposition parameters and on the ratio between sulphuric acid and chloride-complexes (i.e., hexachloroplatinate or tetrachloroplatinate). To further improve the electrochemical properties of electrodes, depositions of Pt nanostructures on previously synthesised Pt nanostructures are also performed. The electroactive surface areas exhibit a two order of magnitude improvement when Pt nanostructures with the smallest size are used. All the biosensors based on Pt nanostructures and immobilised glucose oxidase display higher sensitivity as compared to bare Pt electrodes. Pt nanostructures retained an excellent electrocatalytic activity towards the direct oxidation of glucose. Finally, the nanodeposits were proven to be an excellent solid contact for ion measurements, significantly improving the time-stability of the potential. The use of these new nanostructured coatings in electrochemical sensors opens new perspectives for multipanel monitoring of human metabolism.
Social redistribution of pain and money
Authors: Story Giles W. , Vlaev Ivo , Metcalfe Robert D. , Crockett Molly J. , Kurth-Nelson Zeb , Darzi Ara , Dolan Raymond J. 
Published: October 2015

AbstractPeople show empathic responses to others’ pain, yet how they choose to apportion pain between themselves and others is not well understood. To address this question, we observed choices to reapportion social allocations of painful stimuli and, for comparison, also elicited equivalent choices with money. On average people sought to equalize allocations of both pain and money, in a manner which indicated that inequality carried an increasing marginal cost. Preferences for pain were more altruistic than for money, with several participants assigning more than half the pain to themselves. Our data indicate that, given concern for others, the fundamental principle of diminishing marginal utility motivates spreading costs across individuals. A model incorporating this assumption outperformed existing models of social utility in explaining the data. By implementing selected allocations for real, we also found that while inequality per se did not influence pain perception, altruistic behavior had an intrinsic analgesic effect for the recipient.
The quantum Ising model: finite sums and hyperbolic functions
Authors: Damski Bogdan 
Published: October 2015

AbstractWe derive exact closed-form expressions for several sums leading to hyperbolic functions and discuss their applicability for studies of finite-size Ising spin chains. We show how they immediately lead to closed-form expressions for both fidelity susceptibility characterizing the quantum critical point and the coefficients of the counterdiabatic Hamiltonian enabling arbitrarily quick adiabatic driving of the system. Our results generalize and extend the sums presented in the popular Gradshteyn and Ryzhik Table of Integrals, Series and Products.
Plant Species Rather Than Climate Greatly Alters the Temporal Pattern of Litter Chemical Composition During Long-Term Decomposition
Authors: Li Yongfu , Chen Na , Harmon Mark E. , Li Yuan , Cao Xiaoyan , Chappell Mark A. , Mao Jingdong 
Published: October 2015

AbstractA feedback between decomposition and litter chemical composition occurs with decomposition altering composition that in turn influences the decomposition rate. Elucidating the temporal pattern of chemical composition is vital to understand this feedback, but the effects of plant species and climate on chemical changes remain poorly understood, especially over multiple years. In a 10-year decomposition experiment with litter of four species (Acer saccharum, Drypetes glauca, Pinus resinosa and Thuja plicata) from four sites that range from the arctic to tropics, we determined the abundance of 11 litter chemical constituents that were grouped into waxes, carbohydrates, lignin/tannins and proteins/peptides using advanced 13C solid-state NMR techniques. Decomposition generally led to an enrichment of waxes and a depletion of carbohydrates, whereas the changes of other chemical constituents were inconsistent. Inconsistent convergence in chemical compositions during decomposition was observed among different litter species across a range of site conditions, whereas one litter species converged under different climate conditions. Our data clearly demonstrate that plant species rather than climate greatly alters the temporal pattern of litter chemical composition, suggesting the decomposition-chemistry feedback varies among different plant species.
An NMR Study of Biomimetic Fluorapatite – Gelatine Mesocrystals
Authors: Vyalikh Anastasia , Simon Paul , Rosseeva Elena , Buder Jana , Scheler Ulrich , Kniep Rüdiger 
Published: October 2015

AbstractThe mesocrystal system fluoroapatite—gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix impregnated by isolated phosphate groups, Ca3F motifs and water molecules. Our NMR data provide clear evidence for the existence of precursor complexes in the gelatine phase, which were not involved in the formation of apatite crystals, proving hence theoretical predictions on the structural pre-treatment of gelatine by ion impregnation. The interfacial interactions, which may be described as the glue holding the composite materials together, comprise hydrogen bond interactions with the apatite PO43− groups. The reported results are in a good agreement with molecular dynamics simulations, which address the mechanisms of a growth control by collagen fibers and with experimental observations of an amorphous cover layer in biominerals.
Griffiths phase behaviour in a frustrated antiferromagnetic intermetallic compound
Authors: Ghosh Krishanu , Mazumdar Chandan , Ranganathan R. , Mukherjee S. 
Published: October 2015

AbstractThe rare coexistence of a Griffiths phase (GP) and a geometrically frustrated antiferromagnetism in the non-stoichiometric intermetallic compound GdFe0.17Sn2 (the paramagnetic Weiss temperature θp ~ −59 K) is reported in this work. The compound forms in the Cmcm space group with large structural anisotropy (b/c ~ 4). Interestingly, all the atoms in the unit cell possess the same point group symmetry (Wycoff position 4c), which is rather rare. The frustration parameter, f = |θp|/TN has been established as 3.6, with the Néel temperature TN and Griffiths temperature TG being 16.5 and 32 K, respectively. The TG has been determined from the heat capacity measurement and also from the magnetocaloric effect (MCE). It is also shown that substantial difference in GP region may exist between zero field and field cooled measurements - a fact hitherto not emphasized so far.
Formation of charged ferroelectric domain walls with controlled periodicity
Authors: Bednyakov Petr S. , Sluka Tomas , Tagantsev Alexander K. , Damjanovic Dragan , Setter Nava 
Published: October 2015

AbstractCharged domain walls in proper ferroelectrics were shown recently to possess metallic-like conductivity. Unlike conventional heterointerfaces, these walls can be displaced inside a dielectric by an electric field, which is of interest for future electronic circuitry. In addition, theory predicts that charged domain walls may influence the electromechanical response of ferroelectrics, with strong enhancement upon increased charged domain wall density. The existence of charged domain walls in proper ferroelectrics is disfavoured by their high formation energy and methods of their preparation in predefined patterns are unknown. Here we develop the theoretical background for the formation of charged domain walls in proper ferroelectrics using energy considerations and outline favourable conditions for their engineering. We experimentally demonstrate, in BaTiO3 single crystals the controlled build-up of high density charged domain wall patterns, down to a spacing of 7 μm with a predominant mixed electronic and ionic screening scenario, hinting to a possible exploitation of charged domain walls in agile electronics and sensing devices.
Associations between occupation exposure to Formaldehyde and semen quality, a primary study
Authors: Wang Hai-xu , Li He-cheng , Lv Mo-qi , Zhou Dang-xia , Bai Li-zhi , Du Liang-zhi , Xue Xia , Lin Pu , Qiu Shu-dong 
Published: October 2015

AbstractFormaldehyde (FA), a ubiquitous environmental pollutant, has long been suspected of having male reproductive toxicity. However, FA male reproductive toxicity was inconclusive due to dearth of human studies. Therefore, we sought to investigate whether occupational exposure to FA affects semen quality. Semen quality including five conventional parameters and seven kinematics parameters were compared between 114 male workers occupationally exposed to FA and 76 referents. FA exposure index (FEI) was measured and calculated. Our results showed that sperm progressive motility, total sperm motility, VCL, VSL and VAP were statistically significant decreased in FA exposure workers compared with the referents. Moreover, FEI was significantly negative associated with sperm progressive motility (β = −0.19, P = 0.01) and total sperm motility (β = −0.23, P = 0.004). In addition, a significant elevated risk of abnormal sperm progressive motility were observed in both low- (OR = 2.58; 95% CI: 1.11–5.97) and high-FA-exposed group (OR = 3.41; 95% CI: 1.45–7.92) respectively. Furthermore, a significant increased risk was also estimated for abnormal total sperm motility in both low- (OR = 3.21; 95% CI: 1.24–8.28) and high-FA-exposed group (OR = 4.84; 95% CI: 1.83–12.81) respectively. In conclusion, our study revealed the adverse effects of FA occupation exposure on semen quality, especially on sperm motion parameters.
The C-terminal region of the non-structural protein 2B from Hepatitis A Virus demonstrates lipid-specific viroporin-like activity
Authors: Shukla Ashutosh , Dey Debajit , Banerjee Kamalika , Nain Anshu , Banerjee Manidipa 
Published: October 2015

AbstractViroporins are virally encoded, membrane-active proteins, which enhance viral replication and assist in egress of viruses from host cells. The 2B proteins in the picornaviridae family are known to have viroporin-like properties and play critical roles during virus replication. The 2B protein of Hepatitis A Virus (2B), an unusual picornavirus, is somewhat dissimilar from its analogues in several respects. HAV 2B is approximately 2.5 times the length of other 2B proteins and does not disrupt calcium homeostasis or glycoprotein trafficking. Additionally, its membrane penetrating properties are not yet clearly established. Here we show that the membrane interacting activity of HAV 2B is localized in its C-terminal region, which contains an alpha-helical hairpin motif. We show that this region is capable of forming small pores in membranes and demonstrates lipid specific activity, which partially rationalizes the intracellular localization of full-length 2B. Using a combination of biochemical assays and molecular dynamics simulation studies, we also show that HAV 2B demonstrates a marked propensity to dimerize in a crowded environment and probably interacts with membranes in a multimeric form, a hallmark of other picornavirus viroporins. In sum, our study clearly establishes HAV 2B as a bona fide viroporin in the picornaviridae family.
Polarization and Thickness Dependent Absorption Properties of Black Phosphorus: New Saturable Absorber for Ultrafast Pulse Generation
Authors: Li Diao , Jussila Henri , Karvonen Lasse , Ye Guojun , Lipsanen Harri , Chen Xianhui , Sun Zhipei 
Published: October 2015

AbstractBlack phosphorus (BP) has recently been rediscovered as a new and interesting two-dimensional material due to its unique electronic and optical properties. Here, we study the linear and nonlinear optical properties of BP flakes. We observe that both the linear and nonlinear optical properties are anisotropic and can be tuned by the film thickness in BP, completely different from other typical two-dimensional layered materials (e.g., graphene and the most studied transition metal dichalcogenides). We then use the nonlinear optical properties of BP for ultrafast (pulse duration down to ~786 fs in mode-locking) and large-energy (pulse energy up to >18 nJ in Q-switching) pulse generation in fiber lasers at the near-infrared telecommunication band ~1.5 μm. We observe that the output of our BP based pulsed lasers is linearly polarized (with a degree-of-polarization ~98% in mode-locking, >99% in Q-switching, respectively) due to the anisotropic optical property of BP. Our results underscore the relatively large optical nonlinearity of BP with unique polarization and thickness dependence and its potential for polarized optical pulse generation, paving the way to BP based nonlinear and ultrafast photonic applications (e.g., ultrafast all-optical polarization switches/modulators, frequency converters etc.).
Coexistence of Antiferromagnetism and Superconductivity in Heavy Fermion Cerium Compound Ce3PdIn11
Authors: Kratochvílová M. , Prokleška J. , Uhlířová K. , Tkáč V. , Dušek M. , Sechovský V. , Custers J. 
Published: October 2015

AbstractMany current research efforts in strongly correlated systems focus on the interplay between magnetism and superconductivity. Here we report on coexistence of both cooperative ordered states in recently discovered stoichiometric and fully inversion symmetric heavy fermion compound Ce3PdIn11 at ambient pressure. Thermodynamic and transport measurements reveal two successive magnetic transitions at T1 = 1.67 K and TN = 1.53 K into antiferromagnetic type of ordered states. Below Tc = 0.42 K the compound enters a superconducting state. The large initial slope of dBc2/dT ≈ – 8.6 T/K indicates that heavy quasiparticles form the Cooper pairs. The origin of the two magnetic transitions and the coexistence of magnetism and superconductivity is briefly discussed in the context of the coexistence of the two inequivalent Ce-sublattices in the unit cell of Ce3PdIn11 with different Kondo couplings to the conduction electrons.
Phonon and magnetic structure in δ-plutonium from density-functional theory
Authors: Söderlind Per , Zhou F. , Landa A. , Klepeis J. E. 
Published: October 2015

AbstractWe present phonon properties of plutonium metal obtained from a combination of density-functional-theory (DFT) electronic structure and the recently developed compressive sensing lattice dynamics (CSLD). The CSLD model is here trained on DFT total energies of several hundreds of quasi-random atomic configurations for best possible accuracy of the phonon properties. The calculated phonon dispersions compare better with experiment than earlier results obtained from dynamical mean-field theory. The density-functional model of the electronic structure consists of disordered magnetic moments with all relativistic effects and explicit orbital-orbital correlations. The magnetic disorder is approximated in two ways: (i) a special quasi-random structure and (ii) the disordered-local-moment method within the coherent potential approximation. Magnetism in plutonium has been debated intensely, but the present magnetic approach for plutonium is validated by the close agreement between the predicted magnetic form factor and that of recent neutron-scattering experiments.
Biochar, activated carbon and carbon nanotubes have different effects on fate of 14C-catechol and microbial community in soil
Authors: Shan Jun , Ji Rong , Yu Yongjie , Xie Zubin , Yan Xiaoyuan 
Published: October 2015

AbstractThis study investigated the effects of biochar, activated carbon (AC)- and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20 and 2,000 mg/kg dry soil) on the fate of 14C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of 14C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of 14C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of 14C-catechol and microbial community in soil.