bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria
Authors: Pittera Justine , Partensky Frédéric , Six Christophe 
Published: July 2016

Abstract
Marine Synechococcus play a key role in global oceanic primary productivity. Their wide latitudinal distribution has been attributed to the occurrence of lineages adapted to distinct thermal niches, but the physiological and molecular bases of this ecotypic differentiation remain largely unknown. By comparing six strains isolated from different latitudes, we showed that the thermostability of their light-harvesting complexes, called phycobilisomes (PBS), varied according to the average sea surface temperature at strain isolation site. Comparative analyses of thermal unfolding curves of the three phycobiliproteins (PBP) constituting PBS rods suggested that the differences in thermostability observed on whole PBSs relied on the distinct molecular flexibility and stability of their individual components. Phycocyanin was the least thermostable of all rod PBP, constituting a fragility point of the PBS under heat stress. Amino-acid composition analyses and structural homology modeling notably revealed the occurrence of two amino-acid substitutions, which might have a role in the observed differential thermotolerance of this phycobiliprotein among temperature ecotypes. We hypothesize that marine Synechococcus ancestors occurred first in warm niches and that during the colonization of cold, high latitude thermal niches, their descendants have increased the molecular flexibility of PBP to maintain optimal light absorption capacities, this phenomenon likely resulting in a decreased stability of these proteins. This apparent thermoadaptability of marine Synechococcus has most probably contributed to the remarkable ubiquity of these picocyanobacteria in the ocean.
Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability
Authors:   UK10K, Riazuddin S , Hussain M , Razzaq A , Iqbal Z , Shahzad M , Polla D L , Song Y , van Beusekom E , Khan A A , Tomas-Roca L , Rashid M , Zahoor M Y , Wissink-Lindhout W M , Basra M A R , Ansar M , Agha Z , van Heeswijk K , Rasheed F , Van de Vorst M , Veltman J A , Gilissen C , Akram J , Kleefstra T , Assir M Z , Grozeva D , Carss K , Raymond F L , O'Connor T D , Riazuddin S A , Khan S N , Ahmed Z M , de Brouwer A P M , van Bokhoven H , Riazuddin S 
Published: July 2016

AbstractIntellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1–3% of the general population. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause autosomal recessive ID (ARID) has lagged behind, predominantly due to non-availability of sizeable families. Here we present the results of exome sequencing in 121 large consanguineous Pakistani ID families. In 60 families, we identified homozygous or compound heterozygous DNA variants in a single gene, 30 affecting reported ID genes and 30 affecting novel candidate ID genes. Potential pathogenicity of these alleles was supported by co-segregation with the phenotype, low frequency in control populations and the application of stringent bioinformatics analyses. In another eight families segregation of multiple pathogenic variants was observed, affecting 19 genes that were either known or are novel candidates for ID. Transcriptome profiles of normal human brain tissues showed that the novel candidate ID genes formed a network significantly enriched for transcriptional co-expression (P<0.0001) in the frontal cortex during fetal development and in the temporal–parietal and sub-cortex during infancy through adulthood. In addition, proteins encoded by 12 novel ID genes directly interact with previously reported ID proteins in six known pathways essential for cognitive function (P<0.0001). These results suggest that disruptions of temporal parietal and sub-cortical neurogenesis during infancy are critical to the pathophysiology of ID. These findings further expand the existing repertoire of genes involved in ARID, and provide new insights into the molecular mechanisms and the transcriptome map of ID.
Two functionally distinct kinetochore pools of BubR1 ensure accurate chromosome segregation
Authors: Zhang Gang , Mendez Blanca Lopez , Sedgwick Garry G. , Nilsson Jakob 
Published: July 2016

AbstractThe BubR1/Bub3 complex is an important regulator of chromosome segregation as it facilitates proper kinetochore–microtubule interactions and is also an essential component of the spindle assembly checkpoint (SAC). Whether BubR1/Bub3 localization to kinetochores in human cells stimulates SAC signalling or only contributes to kinetochore–microtubule interactions is debated. Here we show that two distinct pools of BubR1/Bub3 exist at kinetochores and we uncouple these with defined BubR1/Bub3 mutants to address their function. The major kinetochore pool of BubR1/Bub3 is dependent on direct Bub1/Bub3 binding and is required for chromosome alignment but not for the SAC. A distinct pool of BubR1/Bub3 localizes by directly binding to phosphorylated MELT repeats on the outer kinetochore protein KNL1. When we prevent the direct binding of BubR1/Bub3 to KNL1 the checkpoint is weakened because BubR1/Bub3 is not incorporated into checkpoint complexes efficiently. In conclusion, kinetochore localization supports both known functions of BubR1/Bub3.
Raman spectroscopic signature of fractionalized excitations in the harmonic-honeycomb iridates β- and γ-Li2IrO3
Authors: Glamazda A. , Lemmens P. , Do S. -H. , Choi Y. S. , Choi K. -Y. 
Published: July 2016

AbstractThe fractionalization of elementary excitations in quantum spin systems is a central theme in current condensed matter physics. The Kitaev honeycomb spin model provides a prominent example of exotic fractionalized quasiparticles, composed of itinerant Majorana fermions and gapped gauge fluxes. However, identification of the Majorana fermions in a three-dimensional honeycomb lattice remains elusive. Here we report spectroscopic signatures of fractional excitations in the harmonic-honeycomb iridates β- and γ-Li2IrO3. Using polarization-resolved Raman spectroscopy, we find that the dynamical Raman response of β- and γ-Li2IrO3 features a broad scattering continuum with distinct polarization and composition dependence. The temperature dependence of the Raman spectral weight is dominated by the thermal damping of fermionic excitations. These results suggest the emergence of Majorana fermions from spin fractionalization in a three-dimensional Kitaev–Heisenberg system.
Negative capacitance transistors with monolayer black phosphorus
Authors: Liu Fei , Zhou Yan , Wang Yijiao , Liu Xiaoyan , Wang Jian , Guo Hong 
Published: July 2016

AbstractQuantum transport properties of negative capacitance transistors (NC-FETs) with monolayer black phosphorus (ML-BP) are theoretically studied. Our calculations show that atomistic thin ML-BP can enhance the amplification effect of the ferroelectric layer, and subthreshold swing is effectively reduced to 27 mV per decade in ML-BP NC-FETs. Device performance can be further improved by increasing the thickness of ferroelectric layer and using thinner or high-k insulate layer. Due to the temperature dependence of ferroelectric layer ML-BP NC-FETs have higher on-state current at low temperature, which is different from that of MOSFETs. By considering the metal–ferroelectric interface layer, our calculations show that the device performance is degraded by the interface. Compared with the International Technology Roadmap (ITRS) 2013 requirements, ML-BP NC-FETs can fulfil the ITRS requirements for high-performance logic with a reduced supply voltage. The new device can achieve very low power delay product per device width at VD=0.3 V, which is just 44% of that in ML-BP FETs.
Antibacterial effect of copper-bearing titanium alloy (Ti-Cu) against Streptococcus mutans and Porphyromonas gingivalis
Authors: Liu Rui , Memarzadeh Kaveh , Chang Bei , Zhang Yumei , Ma Zheng , Allaker Robert P. , Ren Ling , Yang Ke 
Published: July 2016

AbstractFormation of bacterial biofilms on dental implant material surfaces (titanium) may lead to the development of peri-implant diseases influencing the long term success of dental implants. In this study, a novel Cu-bearing titanium alloy (Ti-Cu) was designed and fabricated in order to efficiently kill bacteria and discourage formation of biofilms and then inhibit bacterial infection and prevent implant failure, in comparison with pure Ti. Results from biofilm based gene expression studies, biofilm growth observation, bacterial viability measurements and morphological examination of bacteria, revealed antimicrobial/antibiofilm activities of Ti-Cu alloy against the oral specific bacterial species, Streptococcus mutans and Porphyromonas gingivalis. Proliferation and adhesion assays with mesenchymal stem cells and measurement of the mean daily amount of Cu ion release demonstrated Ti-Cu alloy to be biocompatible. In conclusion, Ti-Cu alloy is a promising dental implant material with antimicrobial/antibiofilm activities and acceptable biocompatibility.
Collective Influence Algorithm to find influencers via optimal percolation in massively large social media
Authors: Morone Flaviano , Min Byungjoon , Bo Lin , Mari Romain , Makse Hernán A. 
Published: July 2016

AbstractWe elaborate on a linear-time implementation of Collective-Influence (CI) algorithm introduced by Morone, Makse, Nature 524, 65 (2015) to find the minimal set of influencers in networks via optimal percolation. The computational complexity of CI is O(N log N) when removing nodes one-by-one, made possible through an appropriate data structure to process CI. We introduce two Belief-Propagation (BP) variants of CI that consider global optimization via message-passing: CI propagation (CIP) and Collective-Immunization-Belief-Propagation algorithm (CIBP) based on optimal immunization. Both identify a slightly smaller fraction of influencers than CI and, remarkably, reproduce the exact analytical optimal percolation threshold obtained in Random Struct. Alg. 21, 397 (2002) for cubic random regular graphs, leaving little room for improvement for random graphs. However, the small augmented performance comes at the expense of increasing running time to O(N2), rendering BP prohibitive for modern-day big-data. For instance, for big-data social networks of 200 million users (e.g., Twitter users sending 500 million tweets/day), CI finds influencers in 2.5 hours on a single CPU, while all BP algorithms (CIP, CIBP and BDP) would take more than 3,000 years to accomplish the same task.
Standardized Chinese Formula Xin-Ke-Shu inhibits the myocardium Ca2+ overloading and metabolic alternations in isoproterenol-induced myocardial infarction rats
Authors: Liu Yue-Tao , Zhou Chao , Jia Hong-Mei , Chang Xing , Zou Zhong-Mei 
Published: July 2016

AbstractXin-Ke-Shu (XKS) is a traditional Chinese patent medicine used for treatment of coronary heart diseases in China. However, its mechanism of action is still unclear. In this paper, the mediation of XKS on the isoproterenol (ISO)-induced myocardial infarction (MI) rat were evaluated based on a tissue-targeted metabonomics in vitro/vivo. The result indicated that twelve metabolic pathways were involved in the therapeutic effect of XKS in vivo, where seven pathways were associated with the Ca2+ overloading mechanism. In agreement with regulation on metabolic variations, XKS markedly reversed the over-expressions of three involved proteins including phospholipase A2 IIA (PLA2 IIA), calcium/calmodulin-dependent protein kinase II (CaMK II) and Pro-Caspase-3. The metabolic regulations of XKS on H9c2 cell also partially confirmed its metabolic effect. These metabolic characteristics in vitro/vivo and western blotting analysis suggested that XKS protected from MI metabolic perturbation major via inhibition of Ca2+ overloading mechanism. Furthermore, 11 active ingredients of XKS exerted steady affinity with the three proteins through the molecular docking study. Our findings indicate that the metabonomics in vitro/vivo combined with western blotting analysis offers the opportunity to gain insight into the comprehensive efficacy of TCMs on the whole metabolic network.
Quantum information tapping using a fiber optical parametric amplifier with noise figure improved by correlated inputs
Authors: Guo Xueshi , Li Xiaoying , Liu Nannan , Ou Z. Y. 
Published: July 2016

AbstractOne of the important functions in a communication network is the distribution of information. It is not a problem to accomplish this in a classical system since classical information can be copied at will. However, challenges arise in quantum system because extra quantum noise is often added when the information content of a quantum state is distributed to various users. Here, we experimentally demonstrate a quantum information tap by using a fiber optical parametric amplifier (FOPA) with correlated inputs, whose noise is reduced by the destructive quantum interference through quantum entanglement between the signal and the idler input fields. By measuring the noise figure of the FOPA and comparing with a regular FOPA, we observe an improvement of 0.7 ± 0.1 dB and 0.84 ± 0.09 dB from the signal and idler outputs, respectively. When the low noise FOPA functions as an information splitter, the device has a total information transfer coefficient of Ts+Ti = 1.5 ± 0.2, which is greater than the classical limit of 1. Moreover, this fiber based device works at the 1550 nm telecom band, so it is compatible with the current fiber-optical network for quantum information distribution.
Vitamin D Deficiency Promotes Liver Tumor Growth in Transforming Growth Factor-β/Smad3-Deficient Mice Through Wnt and Toll-like Receptor 7 Pathway Modulation
Authors: Chen Jian , Katz Lior H. , Muñoz Nina M. , Gu Shoujun , Shin Ji-hyun , Jogunoori Wilma S. , Lee Mi-Hye , Belkin Mitchell D. , Kim Sang-Bae , White Jon C. , Andricovich Jaclyn , Tzatsos Alexandros , Li Shulin , Kim Sang Soo , Shetty Kirti , Mishra Bibhuti , Rashid Asif , Lee Ju-Seog , Mishra Lopa 
Published: July 2016

AbstractDisruption of the TGF-β pathway is associated with liver fibrosis and suppression of liver tumorigenesis, conditions associated with low Vitamin D (VD) levels. However, potential contributions of VD to liver tumor progression in the context of TGF-β signaling remain unexplored. Our analyses of VD deprivation (VDD) in in vivo models of liver tumor formation revealed striking three-fold increases in tumor burden in Smad3+/− mice, with a three-fold increase in TLR7 expression compared to controls. ChIP and transcriptional assays confirm Smad3 binding at two TLR7 promoter SBE sites. Molecular interactions between TGF-β pathway and VDD were validated clinically, where an absence of VD supplementation was associated with low TGF-β pathway member expression levels and β-catenin activation in fibrotic/cirrhotic human liver tissues. Subsequent supplementing VD led to restoration of TGF-β member expression with lower β-catenin levels. Bioinformatics analysis provides positive supportive correlation between somatic mutations for VD-related genes and the TGF-β pathway. We conclude that VDD promotes tumor growth in the context of Smad3 disruption, potentially through regulation of TLR7 expression and β-catenin activation. VD could therefore be a strong candidate for liver cancer prevention in the context of aberrant Smad3 signaling.
Gibberellin-Regulation and Genetic Variations in Leaf Elongation for Tall Fescue in Association with Differential Gene Expression Controlling Cell Expansion
Authors: Xu Qian , Krishnan Sanalkumar , Merewitz Emily , Xu Jichen , Huang Bingru 
Published: July 2016

AbstractLeaf elongation rate (LER) is an important factor controlling plant growth and productivity. The objective of this study was to determine whether genetic variation in LER for a fast-growing (‘K-31’), and a dwarf cultivar (‘Bonsai’) of tall fescue (Festuca arundinacea) and gibberellic acid (GA) regulation of LER were associated with differential expression of cell-expansion genes. Plants were treated with GA3, trinexapac-ethyl (TE) (GA inhibitor), or water (untreated control) in a hydroponic system. LER of ‘K-31’ was 63% greater than that of ‘Bonsai’, which corresponded with 32% higher endogenous GA4content in leaf and greater cell elongation and production rates under the untreated control condition. Exogenous application of GA3significantly enhanced LER while TE treatment inhibited leaf elongation due to GA3-stimulation or TE-inhibition of cell elongation and production rate in leaves for both cultivars. Real-time quantitative polymerase chain reaction analysis revealed that three α-expansins, one β-expansin, and three xyloglucan endotransglycosylase (XET) genes were associated with GA-stimulation of leaf elongation, of which, the differential expression ofEXPA4andEXPA7was related to the genotypic variation in LER of two cultivars. Those differentially-expressed expansin and XET genes could play major roles in genetic variation and GA-regulated leaf elongation in tall fescue.
Electrophysiological fingerprints of OFF bipolar cells in rat retina
Authors: Vielma Alex H. , Schmachtenberg Oliver 
Published: July 2016

AbstractRetinal bipolar cells (BCs) divide photoreceptor output into different channels for the parallel extraction of temporal and chromatic stimulus properties. In rodents, five types of OFF BCs have been differentiated, based on morphological and functional criteria, but their electrophysiological characterization remains incomplete. This study analyzed OFF BCs with the patch clamp technique in acute slices of rat retina. Their specific voltage-dependent currents and glutamate responses are shown to represent individual fingerprints which define the signal processing and filtering properties of each cell type and allow their unequivocal identification. Two additions to the rat BC repertoire are presented: OFF BC-2′, a variation of BC-2 with wider axonal arbours and prominent Na+currents, is described for the first time in rodents and OFF BC-3b, previously identified in mouse, is electrophysiologically characterized in rat. Moreover, the glutamate responses of rat OFF BCs are shown to be differentially sensitive to AMPA- and kainate-receptor blockers and to modulation by nitric oxide (NO) through a cGMP-dependent mechanism. These results contribute to our understanding of the diversity and function of bipolar cells in mammals.
Ligand binding to an Allergenic Lipid Transfer Protein Enhances Conformational Flexibility resulting in an Increase in Susceptibility to Gastroduodenal Proteolysis
Authors: Abdullah Syed Umer , Alexeev Yuri , Johnson Philip E. , Rigby Neil M. , Mackie Alan R. , Dhaliwal Balvinder , Mills E. N. Clare 
Published: July 2016

AbstractNon-specific lipid transfer proteins (LTPs) are a family of lipid-binding molecules that are widely distributed across flowering plant species, many of which have been identified as allergens. They are highly resistant to simulated gastroduodenal proteolysis, a property that may play a role in determining their allergenicity and it has been suggested that lipid binding may further increase stability to proteolysis. It is demonstrated that LTPs from wheat and peach bind a range of lipids in a variety of conditions, including those found in the gastroduodenal tract. Both LTPs are initially cleaved during gastroduodenal proteolysis at three major sites between residues 39–40, 56–57 and 79–80, with wheat LTP being more resistant to cleavage than its peach ortholog. The susceptibility of wheat LTP to proteolyic cleavage increases significantly upon lipid binding. This enhanced digestibility is likely to be due to the displacement of Tyr79 and surrounding residues from the internal hydrophobic cavity upon ligand binding to the solvent exposed exterior of the LTP, facilitating proteolysis. Such knowledge contributes to our understanding as to how resistance to digestion can be used in allergenicity risk assessment of novel food proteins, including GMOs.
Self-assembly Controls Self-cleavage of HHR from ASBVd (−): a Combined SANS and Modeling Study
Authors: Leclerc Fabrice , Zaccai Giuseppe , Vergne Jacques , Řìhovà Martina , Martel Anne , Maurel Marie-Christine 
Published: July 2016

AbstractIn the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (−) RNAs thus generated are processed by cleavage to unit-length where ASBVd (−) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (−) and its derived 79-nt HHR (−). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (−) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (−) though with a remoter region from an extension of the HI domain.
Quantum phase estimation using path-symmetric entangled states
Authors: Lee Su-Yong , Lee Chang-Woo , Lee Jaehak , Nha Hyunchul 
Published: July 2016

AbstractWe study the sensitivity of phase estimation using a generic class of path-symmetric entangled states |φ〉|0〉 + |0〉|φ〉, where an arbitrary state |φ〉 occupies one of two modes in quantum superposition. With this generalization, we identify the fundamental limit of phase estimation under energy constraint that is characterized by the photon statistics of the component state |φ〉. We show that quantum Cramer-Rao bound (QCRB) can be indefinitely lowered with super-Poissonianity of the state |φ〉. For possible measurement schemes, we demonstrate that a full photon-counting employing the path-symmetric entangled states achieves the QCRB over the entire range [0, 2π] of unknown phase shift ϕ whereas a parity measurement does so in a certain confined range of ϕ. By introducing a component state of the form "Equation missing", we particularly show that an arbitrarily small QCRB can be achieved even with a finite energy in an ideal situation. This component state also provides the most robust resource against photon loss among considered entangled states over the range of the average input energy Nav > 1. Finally we propose experimental schemes to generate these path-symmetric entangled states for phase estimation.