bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sparsity and normalization in word similarity systems
Authors: GAWRON JEAN MARK , STEPHENS KELLEN 
Published: August 2015

AbstractWe investigate the problem of improving performance in distributional word similarity systems trained on sparse data, focusing on a family of similarity functions we call Dice-family functions (Dice 1945Ecology26(3): 297–302), including the similarity function introduced in Lin (1998Proceedings of the 15th International Conference on Machine Learning, 296–304), and Curran (2004 PhD thesis, University of Edinburgh. College of Science and Engineering. School of Informatics), as well as a generalized version of Dice Coefficient used in data mining applications (Strehl 2000, 55). We propose a generalization of the Dice-family functions which uses a weight parameter α to make the similarity functions asymmetric. We show that this generalized family of functions (α systems) all belong to the class of asymmetric models first proposed in Tversky (1977Psychological Review84: 327–352), and in a multi-task evaluation of ten word similarity systems, we show that α systems have the best performance across word ranks. In particular, we show that α-parameterization substantially improves the correlations of all Dice-family functions with human judgements on three words sets, including the Miller–Charles/Rubenstein Goodenough word set (Miller and Charles 1991Language and Cognitive Processes6(1): 1–28; Rubenstein and Goodenough 1965Communications of the ACM8: 627–633).
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
Authors: Brum Jennifer R , Hurwitz Bonnie L , Schofield Oscar , Ducklow Hugh W , Sullivan Matthew B 
Published: August 2015

Abstract
Rapid warming in the highly productive western Antarctic Peninsula (WAP) region of the Southern Ocean has affected multiple trophic levels, yet viral influences on microbial processes and ecosystem function remain understudied in the Southern Ocean. Here we use cultivation-independent quantitative ecological and metagenomic assays, combined with new comparative bioinformatic techniques, to investigate double-stranded DNA viruses during the WAP spring–summer transition. This study demonstrates that (i) temperate viruses dominate this region, switching from lysogeny to lytic replication as bacterial production increases, and (ii) Southern Ocean viral assemblages are genetically distinct from lower-latitude assemblages, primarily driven by this temperate viral dominance. This new information suggests fundamentally different virus–host interactions in polar environments, where intense seasonal changes in bacterial production select for temperate viruses because of increased fitness imparted by the ability to switch replication strategies in response to resource availability. Further, temperate viral dominance may provide mechanisms (for example, bacterial mortality resulting from prophage induction) that help explain observed temporal delays between, and lower ratios of, bacterial and primary production in polar versus lower-latitude marine ecosystems. Together these results suggest that temperate virus–host interactions are critical to predicting changes in microbial dynamics brought on by warming in polar marine systems.
Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy
Authors: Zhu Xiaojie , Zhu Yun , Ye Sheng , Wang Qian , Xu Wei , Su Shan , Sun Zhiwu , Yu Fei , Liu Qi , Wang Chao , Zhang Tianhong , Zhang Zhenqing , Zhang Xiaoyan , Xu Jianqing , Du Lanying , Liu Keliang , Lu Lu , Zhang Rongguang , Jiang Shibo 
Published: August 2015

AbstractEnfuvirtide (T20), is the first HIV fusion inhibitor approved for treatment of HIV/AIDS patients who fail to respond to the current antiretroviral drugs. However, its clinical application is limited because of short half-life, drug resistance and cross-reactivity with the preexisting antibodies in HIV-infected patients. Using an artificial peptide strategy, we designed a peptide with non-native protein sequence, AP3, which exhibited potent antiviral activity against a broad spectrum of HIV-1 strains, including those resistant to T20 and had remarkably longer in vivo half-life than T20. While the preexisting antibodies in HIV-infected patients significantly suppressed T20’s antiviral activity, these antibodies neither recognized AP3, nor attenuated its anti-HIV-1 activity. Structurally different from T20, AP3 could fold into single-helix and interact with gp41 NHR. The two residues, Met and Thr, at the N-terminus of AP3 form a hook-like structure to stabilize interaction between AP3 and NHR helices. Therefore, AP3 has potential for further development as a new HIV fusion inhibitor with improved antiviral efficacy, resistance profile and pharmacological properties over enfuvirtide. Meanwhile, this study highlighted the advantages of artificially designed peptides and confirmed that this strategy could be used in developing artificial peptide-based viral fusion inhibitors against HIV and other enveloped viruses.
Peptidylarginine deiminase type 4 deficiency reduced arthritis severity in a glucose-6-phosphate isomerase-induced arthritis model
Authors: Seri Yu , Shoda Hirofumi , Suzuki Akari , Matsumoto Isao , Sumida Takayuki , Fujio Keishi , Yamamoto Kazuhiko 
Published: August 2015

AbstractPeptidyl arginine deiminase 4 (PAD4) is an enzyme that is involved in protein citrullination and is a target for anti-citrullinated peptide antibodies (ACPAs) in rheumatoid arthritis (RA). Genetic polymorphisms in the PADI4 gene encoding PAD4 are associated with RA susceptibility. We herein analyzed the roles of PADI4 in inflammatory arthritis using a glucose-6-phosphate isomerase (GPI)-induced arthritis (GIA) model in Padi4 knockout (KO) mice. Arthritis severity, serum anti-GPI antibody titers and IL-6 concentrations were significantly reduced in Padi4 KO mice. The frequency of Th17 cells was decreased in GPI-immunized Padi4 KO mice, whereas WT and Padi4-deficient naïve CD4+ T cells displayed the same efficiencies for Th17 cell differentiation in vitro. In addition, the numbers of myeloid lineage cells were reduced with the increased expression of pro-apoptotic genes in GPI-immunized Padi4 KO mice. Furthermore, the survival of Padi4-deficient neutrophils was impaired in vitro. Our results suggest that PADI4 exacerbates arthritis with diverse immunological modifications.
Sensory eye balance in surgically corrected intermittent exotropes with normal stereopsis
Authors: Feng Lixia , Zhou Jiawei , Chen Li , Hess Robert F. 
Published: August 2015

AbstractSurgery to align a deviated or strabismic eye is often done for both functional as well as cosmetic reasons. Although amblyopia is often an impediment to regaining full binocularity in strabismics in general, intermittent exotropes, because their deviation is intermittent, have no amblyopia and some degree of stereopsis. Binocular function, including a balanced ocular dominance, could be expected to be normal after surgical correction if normal levels of stereopsis and visual acuity are postsurgically achieved. Here we used a binocular phase combination paradigm to quantitatively assess the ocular dominance in a group of surgically corrected intermittent exotropes who have normal stereo and visual acuity as defined clinically. Interestingly, we found significant interocular imbalance (balance point < 0.9) in most of the surgically treated patients (8 out 10) but in none of the controls. We conclude that the two eyes may still have a residual sensory imbalance in surgically corrected strabismus even if stereopsis is within normal limits. Our study opens the possibility that a further treatment aimed at re-balancing the ocular dominance might be necessary in surgically treated intermittent exotropia to provide more efficient binocular processing in the long term.
Supersymmetry in quantum optics and in spin-orbit coupled systems
Authors: Tomka Michael , Pletyukhov Mikhail , Gritsev Vladimir 
Published: August 2015

AbstractLight-matter interaction is naturally described by coupled bosonic and fermionic subsystems. This suggests that a certain Bose-Fermi duality is naturally present in the fundamental quantum mechanical description of photons interacting with atoms. We reveal submanifolds in parameter space of a basic light-matter interacting system where this duality is promoted to a supersymmetry (SUSY) which remains unbroken. We show that SUSY is robust with respect to decoherence and dissipation. In particular, the stationary density matrix at the supersymmetric lines in parameter space has a degenerate subspace. The dimension of this subspace is given by the Witten index and thus is topologically protected. As a consequence, the dissipative dynamics is constrained by a robust additional conserved quantity which translates information about an initial state into the stationary state. In addition, we demonstrate that the same SUSY structures are present in condensed matter systems with spin-orbit couplings of Rashba and Dresselhaus types and therefore spin-orbit coupled systems at the SUSY lines should be robust with respect to various types of disorder. Our findings suggest that optical and condensed matter systems at the SUSY points can be used for quantum information technology and can open an avenue for quantum simulation of SUSY field theories.
Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains
Authors: Gtari Maher , Ghodhbane-Gtari Faten , Nouioui Imen , Ktari Amir , Hezbri Karima , Mimouni Wajdi , Sbissi Imed , Ayari Amani , Yamanaka Takashi , Normand Philippe , Tisa Louis S , Boudabous Abdellatif 
Published: August 2015

AbstractThe repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media and fulfilled Koch’s postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.
Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids
Authors: Yu Guanghui , Xiang Hai , Tian Jianhui , Yin Jingdong , Pinkert Carl A. , Li Qiuyan , Zhao Xingbo 
Published: August 2015

AbstractIn farm animals, mitochondrial DNA mutations exist widely across breeds and individuals. In order to identify differences among mtDNA haplotypes, two porcine transmitochondrial cybrids were generated by fusion of a Lantang pig cell line devoid of mitochondrial DNA with enucleated cytoplasm from either a Large White pig or a Xiang pig harboring potentially divergent mitochondrial haplotypes. These cybrid cells were subjected to mitochondrial genome sequencing, copy number detecting and analysis of biochemical traits including succinate dehydrogenase (SDH) activity, ATP content and susceptibility to reactive oxygen species (ROS). The Lantang and Xiang mitochondrial genomes were highly homologous with only 18 polymorphic sites and differed radically from the Large White with 201 and 198 mutations respectively. The Large White and Xiang cybrids exhibited similar mtDNA copy numbers and different values among biochemical traits, generated greater ROS production (P < 0.05) and less SDH activity (P < 0.05) and a lesser ATP content (P < 0.05). The results show that functional differences exist between cybrid cells which differ in mitochondrial genomic background. In conclusion, transmitochondrial cybrids provide the first direct evidence on pig biochemical traits linking different mitochondrial genome haplotypes.
Generation of entanglement in quantum parametric oscillators using phase control
Authors: Gonzalez-Henao J. C. , Pugliese E. , Euzzor S. , Abdalah S.F. , Meucci R. , Roversi J. A. 
Published: August 2015

AbstractThe control of quantum entanglement in systems in contact with environment plays an important role in information processing, cryptography and quantum computing. However, interactions with the environment, even when very weak, entail decoherence in the system with consequent loss of entanglement. Here we consider a system of two coupled oscillators in contact with a common heat bath and with a time dependent oscillation frequency. The possibility to control the entanglement of the oscillators by means of an external sinusoidal perturbation applied to the oscillation frequency has been theoretically explored. We demonstrate that the oscillators become entangled exactly in the region where the classical counterpart is unstable, otherwise when the classical system is stable, entanglement is not possible. Therefore, we can control the entanglement swapping from stable to unstable regions by adjusting amplitude and phase of our external controller. We also show that the entanglement rate is approximately proportional to the real part of the Floquet coefficient of the classical counterpart of the oscillators. Our results have the intriguing peculiarity of manipulating quantum information operating on a classical system.
Female heterogamety in Madagascar chameleons (Squamata: Chamaeleonidae: Furcifer): differentiation of sex and neo-sex chromosomes
Authors: Rovatsos Michail , Pokorná Martina Johnson , Altmanová Marie , Kratochvíl Lukáš 
Published: August 2015

AbstractAmniotes possess variability in sex determining mechanisms, however, this diversity is still only partially known throughout the clade and sex determining systems still remain unknown even in such a popular and distinctive lineage as chameleons (Squamata: Acrodonta: Chamaeleonidae). Here, we present evidence for female heterogamety in this group. The Malagasy giant chameleon (Furcifer oustaleti) (chromosome number 2n = 22) possesses heteromorphic Z and W sex chromosomes with heterochromatic W. The panther chameleon (Furcifer pardalis) (2n = 22 in males, 21 in females), the second most popular chameleon species in the world pet trade, exhibits a rather rare Z1Z1Z2Z2/Z1Z2W system of multiple sex chromosomes, which most likely evolved from W-autosome fusion. Notably, its neo-W chromosome is partially heterochromatic and its female-specific genetic content has expanded into the previously autosomal region. Showing clear evidence for genotypic sex determination in the panther chameleon, we resolve the long-standing question of whether or not environmental sex determination exists in this species. Together with recent findings in other reptile lineages, our work demonstrates that female heterogamety is widespread among amniotes, adding another important piece to the mosaic of knowledge on sex determination in amniotes needed to understand the evolution of this important trait.
Gap junctional protein Cx43 is involved in the communication between extracellular vesicles and mammalian cells
Authors: Soares Ana Rosa , Martins-Marques Tania , Ribeiro-Rodrigues Teresa , Ferreira Joao Vasco , Catarino Steve , Pinho Maria João , Zuzarte Monica , Isabel Anjo Sandra , Manadas Bruno , P.G. Sluijter Joost , Pereira Paulo , Girao Henrique 
Published: August 2015

AbstractIntercellular communication is vital to ensure tissue and organism homeostasis and can occur directly, between neighbour cells via gap junctions (GJ), or indirectly, at longer distances, through extracellular vesicles, including exosomes. Exosomes, as intercellular carriers of messenger molecules, mediate the transfer of biological information between donor and acceptor cells. Although the biological effects of exosomes in target cells have been intensively studied, the mechanisms that govern exosomal uptake are not fully understood. Here, we show that Connexin 43 (Cx43), the most widely expressed GJ protein, is present in exosomes in the form of hexameric channels and, more importantly, that exosomal Cx43 is able to modulate the interaction and transfer of information between exosomes and acceptor cells. This study envisions a new paradigm where Cx43-containing channels mediate the release of exosomal content into cells, which constitutes a novel and unanticipated mechanism to modulate intercellular communication.
Simple synthesis of highly catalytic carbon-free MnCo2O4@Ni as an oxygen electrode for rechargeable Li–O2 batteries with long-term stability
Authors: Kalubarme Ramchandra S. , Jadhav Harsharaj S. , Ngo Duc Tung , Park Ga-Eun , Fisher John G. , Choi Yun-Il , Ryu Won-Hee , Park Chan-Jin 
Published: August 2015

AbstractAn effective integrated design with a free standing and carbon-free architecture of spinel MnCo2O4 oxide prepared using facile and cost effective hydrothermal method as the oxygen electrode for the Li–O2 battery, is introduced to avoid the parasitic reactions of carbon and binder with discharge products and reaction intermediates, respectively. The highly porous structure of the electrode allows the electrolyte and oxygen to diffuse effectively into the catalytically active sites and hence improve the cell performance. The amorphous Li2O2 will then precipitate and decompose on the surface of free-standing catalyst nanorods. Electrochemical examination demonstrates that the free-standing electrode without carbon support gives the highest specific capacity and the minimum capacity fading among the rechargeable Li–O2 batteries tested. The Li-O2 cell has demonstrated a cyclability of 119 cycles while maintaining a moderate specific capacity of 1000 mAh g−1. Furthermore, the synergistic effect of the fast kinetics of electron transport provided by the free-standing structure and the high electro-catalytic activity of the spinel oxide enables excellent performance of the oxygen electrode for Li-O2 cells.
Taming of Modulation Instability by Spatio-Temporal Modulation of the Potential
Authors: Kumar S. , Herrero R. , Botey M. , Staliunas K. 
Published: August 2015

AbstractSpontaneous pattern formation in a variety of spatially extended nonlinear systems always occurs through a modulation instability, sometimes called Turing instability: the homogeneous state of the system becomes unstable with respect to growing modulation modes. Therefore, the manipulation of the modulation instability is of primary importance in controlling and manipulating the character of spatial patterns initiated by that instability. We show that a spatio-temporal periodic modulation of the potential of spatially extended systems results in a modification of its pattern forming instability. Depending on the modulation character the instability can be partially suppressed, can change its spectrum (for instance the long wave instability can transform into short wave instability), can split into two, or can be completely eliminated. The latter result is of special practical interest, as it can be used to stabilize the intrinsically unstable system. The result bears general character, as it is shown here on a universal model of the Complex Ginzburg-Landau equation in one and two spatial dimensions (and time). The physical mechanism of the instability suppression can be applied to a variety of intrinsically unstable dissipative systems, like self-focusing lasers, reaction-diffusion systems, as well as in unstable conservative systems, like attractive Bose Einstein condensates.
All-solid-state lithium-oxygen battery with high safety in wide ambient temperature range
Authors: Kitaura Hirokazu , Zhou Haoshen 
Published: August 2015

AbstractThere is need to develop high energy storage devices with high safety to satisfy the growing industrial demands. Here, we show the potential to realize such batteries by assembling a lithium-oxygen cell using an inorganic solid electrolyte without any flammable liquid or polymer materials. The lithium-oxygen battery using Li1.575Al0.5Ge1.5(PO4)3 solid electrolyte was examined in the pure oxygen atmosphere from room temperature to 120 °C. The cell works at room temperature and first full discharge capacity of 1420 mAh g−1 at 10 mA g−1 (based on the mass of carbon material in the air electrode) was obtained. The charge curve started from 3.0 V and that the majority of it lay below 4.2 V. The cell also safely works at high temperature over 80 °C with the improved battery performance. Furthermore, fundamental data of the electrochemical performance, such as cyclic voltammogram, cycle performance and rate performance was obtained and this work demonstrated the potential of the all-solid-state lithium-oxygen battery for wide temperature application as a first step.
Atomic View of Filament Growth in Electrochemical Memristive Elements
Authors: Lv Hangbing , Xu Xiaoxin , Sun Pengxiao , Liu Hongtao , Luo Qing , Liu Qi , Banerjee Writam , Sun Haitao , Long Shibing , Li Ling , Liu Ming 
Published: August 2015

AbstractMemristive devices, with a fusion of memory and logic functions, provide good opportunities for configuring new concepts computing. However, progress towards paradigm evolution has been delayed due to the limited understanding of the underlying operating mechanism. The stochastic nature and fast growth of localized conductive filament bring difficulties to capture the detailed information on its growth kinetics. In this work, refined programming scheme with real-time current regulation was proposed to study the detailed information on the filament growth. By such, discrete tunneling and quantized conduction were observed. The filament was found to grow with a unit length, matching with the hopping conduction of Cu ions between interstitial sites of HfO2 lattice. The physical nature of the formed filament was characterized by high resolution transmission electron microscopy. Copper rich conical filament with decreasing concentration from center to edge was identified. Based on these results, a clear picture of filament growth from atomic view could be drawn to account for the resistance modulation of oxide electrolyte based electrochemical memristive elements.