bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-dimensional distributed-phase-reference protocol for quantum key distribution
Authors: Bacco Davide , Christensen Jesper Bjerge , Castaneda Mario A. Usuga , Ding Yunhong , Forchhammer Søren , Rottwitt Karsten , Oxenløwe Leif Katsuo 
Published: December 2016

AbstractQuantum key distribution (QKD) and quantum communication enable the secure exchange of information between remote parties. Currently, the distributed-phase-reference (DPR) protocols, which are based on weak coherent pulses, are among the most practical solutions for long-range QKD. During the last 10 years, long-distance fiber-based DPR systems have been successfully demonstrated, although fundamental obstacles such as intrinsic channel losses limit their performance. Here, we introduce the first two-dimensional DPR-QKD protocol in which information is encoded in the time and phase of weak coherent pulses. The ability of extracting two bits of information per detection event, enables a higher secret key rate in specific realistic network scenarios. Moreover, despite the use of more dimensions, the proposed protocol remains simple, practical, and fully integrable.
Rapid stability of ferroelectric polarization in the Ca, Ce hybrid doped BaTiO3 ceramics
Authors: Liu Shujuan , Zhang Lixue , Wang Jiping , Shi Xiujing , Zhao Yingying , Zhang Dawei 
Published: December 2016

AbstractIn this work, we report a rapid stability phenomenon of ferroelectric polarization in the Ca, Ce hybrid doped BaTiO3 ceramics (BCaxT+BTCe8) (x = 10, 20, 24, 30 mol%) prepared by separate doping Ca2+ and Ce4+ ions. Double hysteresis loops are identified in the aged BCaxT+BTCe8 samples; meanwhile, the polarization of these loops present a rapid decrease within very short aging time (about 1 h), and then the polarization remains almost unchanged over the followed ~1000 h. This phenomenon is not reported in previous researches. Raman scattering spectrum indicates that oxygen vacancies are generated because of Ca2+ ions entering into Ti sites partly in the BCaxT+BTCe8 samples, and then the oxygen vacancies are quantitatively characterized by half of the Ce3+ content through the XPS test. The emergence of the aging phenomenon is explained through the "Equation missing" defect dipole reorientation mechanism. The larger radius of Ca2+ ions is further discussed as a possible reason for the rapid stability phenomenon of ferroelectric polarization. It may provide an effective design method from the viewpoint of the ionic radius to accelerate polarization stability, and thus to facilitate the possible practical applications of the aging effect.
Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection
Authors: Al-Wathiqui Nooria , Fallon Timothy R. , South Adam , Weng Jing-Ke , Lewis Sara M. 
Published: December 2016

AbstractPostcopulatory sexual selection is recognized as a key driver of reproductive trait evolution, including the machinery required to produce endogenous nuptial gifts. Despite the importance of such gifts, the molecular composition of the non-gametic components of male ejaculates and their interactions with female reproductive tracts remain poorly understood. During mating, male Photinus fireflies transfer to females a spermatophore gift manufactured by multiple reproductive glands. Here we combined transcriptomics of both male and female reproductive glands with proteomics and metabolomics to better understand the synthesis, composition and fate of the spermatophore in the common Eastern firefly, Photinus pyralis. Our transcriptome of male glands revealed up-regulation of proteases that may enhance male fertilization success and activate female immune response. Using bottom-up proteomics we identified 208 functionally annotated proteins that males transfer to the female in their spermatophore. Targeted metabolomic analysis also provided the first evidence that Photinus nuptial gifts contain lucibufagin, a firefly defensive toxin. The reproductive tracts of female fireflies showed increased gene expression for several proteases that may be involved in egg production. This study offers new insights into the molecular composition of male spermatophores, and extends our understanding of how nuptial gifts may mediate postcopulatory interactions between the sexes.
Investigating the Neuroprotective Effects of Turmeric Extract: Structural Interactions of β-Amyloid Peptide with Single Curcuminoids
Authors: Randino Rosario , Grimaldi Manuela , Persico Marco , De Santis Augusta , Cini Elena , Cabri Walter , Riva Antonella , D’Errico Gerardino , Fattorusso Caterina , D’Ursi Anna Maria , Rodriquez Manuela 
Published: December 2016

AbstractA broad biophysical analysis was performed to investigate the molecular basis of the neuroprotective action of Curcuma longa extracts in Alzheimer’s disease. By combining circular dichroism and electron paramagnetic resonance experiments with molecular modeling calculations, the minor components of Curcuma longa extracts, such as demethoxycurcumin (2, DMC), bisdemethoxycurcumin (3, BDMC) and cyclocurcumin (4, CYC), were analyzed in a membrane environment mimicking the phospholipid bilayer. Our study provides the first evidence on the relative role of single curcuminoids interacting with Aβ-peptide. When the CYC and curcumin metabolite tetrahydrocurcumin (5, THC) were inserted into an anionic lipid solution, a significant modification of the Aβ CD curves was detected. These data were implemented by EPR experiments, demonstrating that CYC reaches the inner part of the bilayer, while the other curcuminoids are localized close to the membrane interface. Computational studies provided a model for the curcuminoid-Aβ interaction, highlighting the importance of a constrained “semi-folded” conformation to interact with Aβ analogously to the pattern observed in α-helical coiled-coil peptide structures. This combined approach led to a better understanding of the intriguing in vitro and in vivo activity of curcuminoids as anti-Alzheimer agents, paving a new path for the rational design of optimized druggable analogues.
Molecular typing and virulence analysis of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from Egyptian hospitals
Authors: Wasfi Reham , Elkhatib Walid F. , Ashour Hossam M. 
Published: December 2016

AbstractKlebsiella pneumonia infection rates have increased dramatically. Molecular typing and virulence analysis are powerful tools that can shed light on Klebsiella pneumonia infections. Whereas 77.7% (28/36) of clinical isolates indicated multidrug resistant (MDR) patterns, 50% (18/36) indicated carpabenem resistance. Gene prevalence for the AcrAB efflux pump (82.14%) was more than that of the mdtK efflux pump (32.14%) in the MDR isolates. FimH-1 and mrkD genes were prevalent in wound and blood isolates. FimH-1 gene was prevalent in sputum while mrkD gene was prevalent in urine. Serum resistance associated with outer membrane protein coding gene (traT) was found in all blood isolates. IucC, entB, and Irp-1 were detected in 32.14%, 78.5% and 10.7% of MDR isolates, respectively. We used two Polymerase Chain Reaction (PCR) analyses: Enterobacterial Repetitive Intergenic Consensus (ERIC) and Random Amplified Polymorphic DNA (RAPD). ERIC-PCR revealed 21 and RAPD-PCR revealed 18 distinct patterns of isolates with similarity ≥80%. ERIC genotyping significantly correlated with resistance patterns and virulence determinants. RAPD genotyping significantly correlated with resistance patterns but not with virulence determinants. Both RAPD and ERIC genotyping methods had no correlation with the capsule types. These findings can help up better predict MDR Klebsiella pneumoniae outbreaks associated with specific genotyping patterns.
3-D Microwell Array System for Culturing Virus Infected Tumor Cells
Authors: El Assal Rami , Gurkan Umut A. , Chen Pu , Juillard Franceline , Tocchio Alessandro , Chinnasamy Thiruppathiraja , Beauchemin Chantal , Unluisler Sebnem , Canikyan Serli , Holman Alyssa , Srivatsa Srikar , Kaye Kenneth M. , Demirci Utkan 
Published: December 2016

AbstractCancer cells have been increasingly grown in pharmaceutical research to understand tumorigenesis and develop new therapeutic drugs. Currently, cells are typically grown using two-dimensional (2-D) cell culture approaches, where the native tumor microenvironment is difficult to recapitulate. Thus, one of the main obstacles in oncology is the lack of proper infection models that recount main features present in tumors. In recent years, microtechnology-based platforms have been employed to generate three-dimensional (3-D) models that better mimic the native microenvironment in cell culture. Here, we present an innovative approach to culture Kaposi’s sarcoma-associated herpesvirus (KSHV) infected human B cells in 3-D using a microwell array system. The results demonstrate that the KSHV-infected B cells can be grown up to 15 days in a 3-D culture. Compared with 2-D, cells grown in 3-D had increased numbers of KSHV latency-associated nuclear antigen (LANA) dots, as detected by immunofluorescence microscopy, indicating a higher viral genome copy number. Cells in 3-D also demonstrated a higher rate of lytic reactivation. The 3-D microwell array system has the potential to improve 3-D cell oncology models and allow for better-controlled studies for drug discovery.
Fixation Probabilities for Any Configuration of Two Strategies on Regular Graphs
Authors: Chen Yu-Ting , McAvoy Alex , Nowak Martin A. 
Published: December 2016

AbstractPopulation structure and spatial heterogeneity are integral components of evolutionary dynamics, in general, and of evolution of cooperation, in particular. Structure can promote the emergence of cooperation in some populations and suppress it in others. Here, we provide results for weak selection to favor cooperation on regular graphs for any configuration, meaning any arrangement of cooperators and defectors. Our results extend previous work on fixation probabilities of rare mutants. We find that for any configuration cooperation is never favored for birth-death (BD) updating. In contrast, for death-birth (DB) updating, we derive a simple, computationally tractable formula for weak selection to favor cooperation when starting from any configuration containing any number of cooperators. This formula elucidates two important features: (i) the takeover of cooperation can be enhanced by the strategic placement of cooperators and (ii) adding more cooperators to a configuration can sometimes suppress the evolution of cooperation. These findings give a formal account for how selection acts on all transient states that appear in evolutionary trajectories. They also inform the strategic design of initial states in social networks to maximally promote cooperation. We also derive general results that characterize the interaction of any two strategies, not only cooperation and defection.
Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster
Authors: Phillips Mark A. , Long Anthony D. , Greenspan Zachary S. , Greer Lee F. , Burke Molly K. , Villeponteau Bryant , Matsagas Kennedy C. , Rizza Cristina L. , Mueller Laurence D. , Rose Michael R. 
Published: December 2016

AbstractExperimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.
Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV
Authors: Ragupathy Raja , Ravichandran Sridhar , Mahdi Md. Safiur Rahman , Huang Douglas , Reimer Elsa , Domaratzki Michael , Cloutier Sylvie 
Published: December 2016

AbstractUnderstanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiation, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory gene-based marker assisted selection depends on accurate identification of stress induced miRNAs.
A new formulation of Bacillus thuringiensis: UV protection and sustained release mosquito larvae studies
Authors: Zhang Lingling , Zhang Xiaojuan , Zhang Yi , Wu Songqin , Gelbič Ivan , Xu Lei , Guan Xiong 
Published: December 2016

AbstractPersistence of Bacillus thuringiensis is an important factor in determining the success of this product as a pest control agent. In this report we present the development of a highly active mosquitocidal formulation with high resistance to UV. LLP29-M19 strain of Bt, selected by repeated exposure to UV was found to be highly resistant to UV. The product was optimized and the methods used were statistically analyzed. Using single-factor experiments it was determined that the optimal concentration of sodium alginate, CaCl2 and hollow glass beads in the formulation were 1.0%, 2.0% and 3.5%, respectively. Plackett-Burman design was used to screen the interaction of the three factors, CaCl2, sodium alginate and hollow glass beads in the sustained-release formulation. The best combined concentration and mutual effects of the three factors were optimized by response surface methodology. The results showed that the most favorable composition was sodium alginate 0.78%, CaCl2 4.52%, hollow glass bead 3.12%, bacterial powder 3.0%, melanin 0.015%, sodium benzoate 0.2%, and mouse feed 0.5%, resulting in the immobilization time of 4.5 h, at which time the corrected sustained-release virulence rose 2391.67 fold, which was 6.07-fold higher than the basic formulation and deviated only 5.0% from the value predicted by RSM.
Tyrosine Hydroxylase Binding to Phospholipid Membranes Prompts Its Amyloid Aggregation and Compromises Bilayer Integrity
Authors: Baumann Anne , Jorge-Finnigan Ana , Jung-KC Kunwar , Sauter Alexander , Horvath Istvan , Morozova-Roche Ludmilla A. , Martinez Aurora 
Published: December 2016

AbstractTyrosine hydroxylase (TH), a rate-limiting enzyme in the synthesis of catecholamine neurotransmitters and hormones, binds to negatively charged phospholipid membranes. Binding to both large and giant unilamellar vesicles causes membrane permeabilization, as observed by efflux and influx of fluorescence dyes. Whereas the initial protein-membrane interaction involves the N-terminal tail that constitutes an extension of the regulatory ACT-domain, prolonged membrane binding induces misfolding and self-oligomerization of TH over time as shown by circular dichroism and Thioflavin T fluorescence. The gradual amyloid-like aggregation likely occurs through cross-β interactions involving aggregation-prone motives in the catalytic domains, consistent with the formation of chain and ring-like protofilaments observed by atomic force microscopy in monolayer-bound TH. PC12 cells treated with the neurotoxin 6-hydroxydopamine displayed increased TH levels in the mitochondrial fraction, while incubation of isolated mitochondria with TH led to a decrease in the mitochondrial membrane potential. Furthermore, cell-substrate impedance and viability assays showed that supplementing the culture media with TH compromises cell viability over time. Our results revealed that the disruptive effect of TH on cell membranes may be a cytotoxic and pathogenic factor if the regulation and intracellular stability of TH is compromised.
Composition of the Hemagglutinin Polybasic Proteolytic Cleavage Motif Mediates Variable Virulence of H7N7 Avian Influenza Viruses
Authors: Abdelwhab E. M. , Veits Jutta , Ulrich Reiner , Kasbohm Elisa , Teifke Jens P. , Mettenleiter Thomas C. 
Published: December 2016

AbstractAcquisition of a polybasic cleavage site (pCS) in the hemagglutinin (HA) is a prerequisite for the shift of low pathogenic (LP) avian influenza virus (AIV) to the highly pathogenic (HP) form in chickens. Whereas presence of a pCS is required for high pathogenicity, less is known about the effect of composition of pCS on virulence of AIV particularly H7N7. Here, we investigated the virulence of four avian H7N7 viruses after insertion of different naturally occurring pCS from two HPAIV H7N7 (designated pCSGE and pCSUK) or from H7N1 (pCSIT). In vitro, the different pCS motifs modulated viral replication and the HA cleavability independent on the HA background. However, in vivo, the level of virulence conferred by the different pCS varied significantly. Within the respective viral backgrounds viruses with pCSIT and pCSGE were more virulent than those coding for pCSUK. The latter showed also the most restricted spread in inoculated birds. Besides the pCS, other gene segments modulated virulence of these H7N7 viruses. Together, the specific composition of the pCS significantly influences virulence of H7N7 viruses. Eurasian LPAIV H7N7 may shift to high pathogenicity after acquisition of “specific” pCS motifs and/or other gene segments from HPAIV.
STAT3 Undergoes Acetylation-dependent Mitochondrial Translocation to Regulate Pyruvate Metabolism
Authors: Xu Yan S. , Liang Jinyuan J. , Wang Yumei , Zhao Xiang-zhong J. , Xu Li , Xu Ye-yang , Zou Quanli C. , Zhang Junxun M. , Tu Cheng-e , Cui Yan-ge , Sun Wei-hong , Huang Chao , Yang Jing-hua , Chin Y. Eugene 
Published: December 2016

AbstractCytoplasmic STAT3, after activation by growth factors, translocates to different subcellular compartments, including nuclei and mitochondria, where it carries out different biological functions. However, the precise mechanism by which STAT3 undergoes mitochondrial translocation and subsequently regulates the tricarboxylic acid (TCA) cycle-electron transport chain (ETC) remains poorly understood. Here, we clarify this process by visualizing STAT3 acetylation in starved cells after serum reintroduction or insulin stimulation. CBP-acetylated STAT3 undergoes mitochondrial translocation in response to serum introduction or insulin stimulation. In mitochondria, STAT3 associates with the pyruvate dehydrogenase complex E1 (PDC-E1) and subsequently accelerates the conversion of pyruvate to acetyl-CoA, elevates the mitochondrial membrane potential, and promotes ATP synthesis. SIRT5 deacetylates STAT3, thereby inhibiting its function in mitochondrial pyruvate metabolism. In the A549 lung cancer cell line, constitutively acetylated STAT3 localizes to mitochondria, where it maintains the mitochondrial membrane potential and ATP synthesis in an active state.
Olaparib significantly delays photoreceptor loss in a model for hereditary retinal degeneration
Authors: Sahaboglu Ayse , Barth Melanie , Secer Enver , Amo Eva M. del , Urtti Arto , Arsenijevic Yvan , Zrenner Eberhart , Paquet-Durand François 
Published: December 2016

AbstractThe enzyme poly-ADP-ribose-polymerase (PARP) mediates DNA-repair and rearrangements of the nuclear chromatin. Generally, PARP activity is thought to promote cell survival and in recent years a number of PARP inhibitors have been clinically developed for cancer treatment. Paradoxically, PARP activity is also connected to many diseases including the untreatable blinding disease Retinitis Pigmentosa (RP), where PARP activity appears to drive the pathogenesis of photoreceptor loss. We tested the efficacy of three different PARP inhibitors to prevent photoreceptor loss in the rd1 mouse model for RP. In retinal explant cultures in vitro, olaparib had strong and long-lasting photoreceptor neuroprotective capacities. We demonstrated target engagement by showing that olaparib reduced photoreceptor accumulation of poly-ADP-ribosylated proteins. Remarkably, olaparib also reduced accumulation of cyclic-guanosine-monophosphate (cGMP), a characteristic marker for photoreceptor degeneration. Moreover, intravitreal injection of olaparib in rd1 animals diminished PARP activity and increased photoreceptor survival, confirming in vivo neuroprotection. This study affirms the role of PARP in inherited retinal degeneration and for the first time shows that a clinically approved PARP inhibitor can prevent photoreceptor degeneration in an RP model. The wealth of human clinical data available for olaparib highlights its strong potential for a rapid clinical translation into a novel RP treatment.
Tunable Spin dependent beam shift by simultaneously tailoring geometric and dynamical phases of light in inhomogeneous anisotropic medium
Authors: Pal Mandira , Banerjee Chitram , Chandel Shubham , Bag Ankan , Majumder Shovan K. , Ghosh Nirmalya 
Published: December 2016

AbstractSpin orbit interaction and the resulting Spin Hall effect of light are under recent intensive investigations because of their fundamental nature and potential applications. Here, we report an interesting manifestation of spin Hall effect of light and demonstrate its tunability in an inhomogeneous anisotropic medium exhibiting spatially varying retardance level. In our system, the beam shift occurs only for one circular polarization mode keeping the other orthogonal mode unaffected, which is shown to arise due to the combined spatial gradients of the geometric phase and the dynamical phase of light. The constituent two orthogonal circular polarization modes of an input linearly polarized light evolve in different trajectories, eventually manifesting as a large and tunable spin separation. The spin dependent beam shift and the demonstrated principle of simultaneously tailoring space-varying geometric and dynamical phase of light for achieving its tunability (of both magnitude and direction), may provide an attractive route towards development of spin-optical devices.