bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of para substituents in controlling photophysical behavior and different non-covalent weak interactions in zinc complexes of a phenol based “end-off” compartmental ligand
Authors: Chakraborty Prateeti , Adhikary Jaydeep , Samanta Sugata , Majumder Ishani , Massera Chiara , Escudero Daniel , Ghosh Sanjib , Bauza Antonio , Frontera Antonio , Das Debasis
Published: October 2015

The role of para substituents of three dinuclear zinc(ii) complexes on the structure, photophysical properties and their different weak interactions is investigated.
pH-Dependent solution dynamics of a manganese(ii) polyoxometalate, [Mn4(H2O)2(P2W15O56)2]16−, and [Mn(H2O)6]2+
Authors: Sharma Rupali , Zhang Jie , André Ohlin C.
Published: October 2015

The NMR-determined pH-dependent water–ligand exchange rate of a Mn(ii)-polyoxometalate varies by more than an order of magnitude, in contrast with those of a hexa-aqua ion.
Photocatalytic reduction of CO2 with H2O to CH4 over ultrathin SnNb2O6 2D nanosheets under visible light irradiation
Authors: Zhu Shuying , Liang Shijing , Bi Jinhong , Liu Minghua , Zhou Limin , Wu Ling , Wang Xuxu
Published: October 2015

Ultrathin SnNb2O6 2D nanosheets could be used as an efficient photocatalyst for the reduction of CO2 to methane and exhibit much higher photocatalytic activity than that of the bulk counterpart due to the unique structural features.
Synthesis and photophysics of selective functionalized π-conjugated, blue light emitting, highly fluorescent C7-imidazo indolizine derivatives
Authors: Sarkar Rajib , Chaudhuri Tandrima , Karmakar Animesh , Mukhopadhyay Chhanda
Published: October 2015

Synthesis and photophysics of selective functionalized π-conjugated, blue light emitting highly fluorescent C7-imidazo indolizine derivatives.
Correction: Nickel-catalyzed reductive coupling of alkyl halides with other electrophiles: concept and mechanistic considerations
Authors: Gu Jun , Wang Xuan , Xue Weichao , Gong Hegui
Published: October 2015

Correction for ‘Nickel-catalyzed reductive coupling of alkyl halides with other electrophiles: concept and mechanistic considerations’ by Jun Gu et al., Org. Chem. Front., 2015, 2, 1411–1421.
The interaction of (7-chloroquinolin-4-yl)-(2,5-dimethoxyphenyl)-amine hydrochloride dihydrate with serum albumin proteins, inputs from spectroscopic, molecular docking and X-ray diffraction studies
Authors: Singh Shailja , Sharma Kumkum , Awasthi Satish K.
Published: October 2015

The interaction of (7-chloroquinolin-4-yl)-(2,5-dimethoxyphenyl)-amine hydrochloride dihydrate (CQDPA), a combination partner in antimalarial therapy, with serum albumin proteins (BSA and HSA) was assessed using spectroscopic techniques.
Keratin–polyethylene oxide bio-nanocomposites reinforced with ultrasonically functionalized graphene
Authors: Grkovic M. , Stojanovic D. B. , Kojovic A. , Strnad S. , Kreze T. , Aleksic R. , Uskokovic P. S.
Published: October 2015

Polyethylene oxide (PEO) functionalized graphene (f-G) was prepared by ultrasonication of pristine graphene in PEO aqueous solution.
Benzoquinone–imidazole hybrids as selective colorimetric sensors for cyanide in aqueous, solid and gas phases
Authors: Manivannan Ramalingam , Ciattini Samuele , Chelazzi Laura , Elango Kuppanagounder P.
Published: October 2015

One of the five new receptors developed, which works via the formation of H-bonds, exhibited a striking visible colour change selectively with cyanide ion in solid, aqueous and gas phases.
Simultaneous extraction and preconcentration of some metal ions using eucalyptus-wood based activated carbon modified with silver hydroxide nanoparticles and a chelating agent: optimization by an experimental design
Authors: Rajabi Maryam , Rezaie Alireza , Ghaedi Mehrorang
Published: October 2015

In the present work, the solid phase extraction (SPE) of Cr(iii), Cu(ii), Pb(ii), Ni(ii), Cd(ii), and Co(ii) metal ions was carried out using a new adsorbent, activated carbon modified with silver hydroxide nanoparticles and a chelating agent.
Synthesis of fluorinated SnO2 3D hierarchical structures assembled from nanosheets and their enhanced photocatalytic activity
Authors: Wang Youzhi , Cheng Guoe , Zhang Yu , Ke Hanzhong , Zhu Chunling
Published: October 2015

Fluorinated 3D SnO2 hierarchical structures assembled from nanosheets were synthesized via a hydrothermal treatment and present excellent photocatalytic degradation of RhB.
Magnetic silica nanoparticle–Taq polymerase hybrids for multiple uses in polymerase chain reaction
Authors: Ozalp V. Cengiz , Bayramoglu G. , Arica M. Yakup
Published: October 2015

Magnetic-silica core–shell nanoparticles were proposed as a fast purification strategy for recombinant enzymes and their subsequent usability in catalysis reactions. A proof-of-concept study with Taq polymerase hybrids was demonstrated.
Two step and one step preparation of porous nanocomposite cellulose membranes doped with TiO2
Authors: Wittmar Alexandra , Vorat Dimitri , Ulbricht Mathias
Published: October 2015

A facile and easily up-scalable method for the preparation of catalytically active TiO2doped cellulose membranes has been developed.
Electronic structure and optical properties of Zn(OH)2: LDA+U calculations and intense yellow luminescence
Authors: Wang Mingsong , Jiang Lingxia , Kim Eui Jung , Hahn Sung Hong
Published: October 2015

Assigned U values in the LDA+U calculations should assure an appropriate overlap of the p−d states.
Enhanced electrochemical performances of MoO2 nanoparticles composited with carbon nanotubes for lithium-ion battery anodes
Authors: Qiu Song , Lu Guixia , Liu Jiurong , Lyu Hailong , Hu Chenxi , Li Bo , Yan Xingru , Guo Jiang , Guo Zhanhu
Published: October 2015

Lab-made CNT nanocomposites decorated with MoO2 nanoparticles (MoO2/CNTs) demonstrated superior cycling and rate performances as LIB anode materials.
Pressure evolution of the potential barriers for transformations of layered BN to dense structures
Authors: Fan Xiaofeng , Zheng W. T. , Jiang Qing , Singh David J.
Published: October 2015

The energy barrier and stacking way from layered BN to dense phase under pressure.
Overview of catalyst application in petroleum refinery for biomass catalytic pyrolysis and bio-oil upgrading
Authors: Ma Zhongyi , Wei Lin , Zhou Wei , Jia Litao , Hou Bo , Li Debao , Zhao Yongxiang
Published: October 2015

Because there are some similarities in the reaction pathway and feedstock, the success and lessons of catalyst applications in petroleum refinery may help to make a breakthrough in biomass conversion.
Redox-promoted associative assembly of metal–organic materials
Authors: Glavinović Martin , Qi Feng , Katsenis Athanassios D. , Friščić Tomislav , Lumb Jean-Philip
Published: October 2015

We develop an associative synthesis of metal–organic materials that combines solid-state metal oxidation and coordination-driven self-assembly into a one-step, waste-free transformation.
Using the hydrogen and oxygen in water directly for hydrogenation reactions and glucose oxidation by photocatalysis
Authors: Zhou Baowen , Song Jinliang , Zhou Huacong , Wu Tianbin , Han Buxing
Published: October 2015

This work reports the utilization of hydrogen in water for the hydrogenation of organic compounds and the oxygen for the oxidation of glucose simultaneously by photocatalysis.
Particle jumps in structural glasses
Authors: Ciamarra Massimo Pica , Pastore Raffaele , Coniglio Antonio
Published: October 2015

We review recent results on the cage-jump motion of supercooled liquids.
Toughening rubbers with a hybrid filler network of graphene and carbon nanotubes
Authors: Li Hengyi , Yang Lei , Weng Gengsheng , Xing Wang , Wu Jinrong , Huang Guangsu
Published: October 2015

The hybrid filler network of GE/CNTs dissipates energy upon deformation and this leads to remarkable toughening and reinforcing effects on rubbers.
Poly(vinylpyrrolidone)–wrapped carbon nanotube-based fuel cell electrocatalyst shows high durability and performance under non-humidified operation
Authors: Yang Zehui , Nakashima Naotoshi
Published: October 2015

Low durability and performance have limited the wide commercialization of high-temperature polymer electrolyte fuel cells (HT-PEFCs).
Modulation of the osteoconductive property and immune response of poly(ether ether ketone) by modification with calcium ions
Authors: Toita R. , Sunarso Sunarso , Rashid A. N. , Tsuru K. , Ishikawa K.
Published: October 2015

A Ca-modified PEEK facilitates osteoblastic cell proliferation and differentiation and shifts macrophage phenotype towards anti-inflammatory/wound healing type.
Strong correlation between the crystal structure and the thermoelectric properties of pavonite homologue Cux+yBi5−yCh8(Ch = S or Se) compounds
Authors: Hwang Jae-Yeol , Oh Min-Wook , Lee Kyu Hyoung , Kim Sung Wng
Published: October 2015

Strong correlation between interstitial sites and thermoelectric properties of pavonite homologue Cux+yBi5−yCh8(Ch = S or Se) compounds.
miR-381 suppresses C/EBPα-dependent Cx43 expression in breast cancer cells
Authors: Ming Jia , Zhou Yan , Du Junze , Fan Shenghao , Pan Beibei , Wang Yinhuan , Fan Lingjun , Jiang Jun
Published: October 2015

Cx43 (connexin43) is an enhancer of the metastasis of breast cancer cells. Our previous study identified miR-381 as an indirect suppressor of Cx43 gene expression, with the precise mechanism being not understood. In the present study, using a reporter gene assay, we found that miR-381 suppressed Cx43 gene expression via the promoter region −500/−250. With site-directed gene mutation, we demonstrated that miR-381 could directly bind with the sequences CACUUGUAU in the 3′-UTR so as to inhibit C/EBPα (CCAAT/enhancer-binding protein α) expression. C/EBPα was further identified as a novel transcription factor by binding to a canonic element (AATTGTC) locating at −459/−453 in the promoter region of the Cx43 gene. Functionally, we demonstrated that miR-381 suppressed C/EBPα- and Cx43-dependent migration and invasion of breast cancer cells. Finally, we revealed that decreased levels of miR-381 as well as increased expression of C/EBPα and Cx43 in the metastatic breast cancer cells and tissues. Therefore we are the first to identify that miR-381 suppresses C/EBPα-dependent Cx43 expression in breast cancer cells. The miR-381–C/EBPα–Cx43 axis might be a useful diagnostic and therapeutic target of metastatic breast cancer.
Biochemical studies on Francisella tularensis RelA in (p)ppGpp biosynthesis
Authors: Wilkinson Rachael C. , Batten Laura E. , Wells Neil J. , Oyston Petra C.F. , Roach Peter L.
Published: October 2015

The bacterial stringent response is induced by nutrient deprivation and is mediated by enzymes of the RSH (RelA/SpoT homologue; RelA, (p)ppGpp synthetase I; SpoT, (p)ppGpp synthetase II) superfamily that control concentrations of the ‘alarmones’ (p)ppGpp (guanosine penta- or tetra-phosphate). This regulatory pathway is present in the vast majority of pathogens and has been proposed as a potential anti-bacterial target. Current understanding of RelA-mediated responses is based on biochemical studies using Escherichia coli as a model. In comparison, the Francisella tularensis RelA sequence contains a truncated regulatory C-terminal region and an unusual synthetase motif (EXSD). Biochemical analysis of F. tularensis RelA showed the similarities and differences of this enzyme compared with the model RelA from Escherichia coli. Purification of the enzyme yielded a stable dimer capable of reaching concentrations of 10 mg/ml. In contrast with other enzymes from the RelA/SpoT homologue superfamily, activity assays with F. tularensis RelA demonstrate a high degree of specificity for GTP as a pyrophosphate acceptor, with no measurable turnover for GDP. Steady state kinetic analysis of F. tularensis RelA gave saturation activity curves that best fitted a sigmoidal function. This kinetic profile can result from allosteric regulation and further measurements with potential allosteric regulators demonstrated activation by ppGpp (5′,3′-dibisphosphate guanosine) with an EC50 of 60±1.9 μM. Activation of F. tularensis RelA by stalled ribosomal complexes formed with ribosomes purified from E. coli MRE600 was observed, but interestingly, significantly weaker activation with ribosomes isolated from Francisella philomiragia.
Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange–MS (HDX–MS)
Authors: Vadas Oscar , Burke John E.
Published: October 2015

Many cellular signalling events are controlled by the selective recruitment of protein complexes to membranes. Determining the molecular basis for how lipid signalling complexes are recruited, assembled and regulated on specific membrane compartments has remained challenging due to the difficulty of working in conditions mimicking native biological membrane environments. Enzyme recruitment to membranes is controlled by a variety of regulatory mechanisms, including binding to specific lipid species, protein–protein interactions, membrane curvature, as well as post-translational modifications. A powerful tool to study the regulation of membrane signalling enzymes and complexes is hydrogen deuterium exchange–MS (HDX–MS), a technique that allows for the interrogation of protein dynamics upon membrane binding and recruitment. This review will highlight the theory and development of HDX–MS and its application to examine the molecular basis of lipid signalling enzymes, specifically the regulation and activation of phosphoinositide 3-kinases (PI3Ks).
The role of chordin fragments generated by partial tolloid cleavage in regulating BMP activity
Authors: Troilo Helen , Barrett Anne L. , Wohl Alexander P. , Jowitt Thomas A. , Collins Richard F. , Bayley Christopher P. , Zuk Alexandra V. , Sengle Gerhard , Baldock Clair
Published: October 2015

Chordin-mediated regulation of bone morphogenetic protein (BMP) family growth factors is essential in early embryogenesis and adult homoeostasis. Chordin binds to BMPs through cysteine-rich von Willebrand factor type C (vWC) homology domains and blocks them from interacting with their cell surface receptors. These domains also self-associate and enable chordin to target related proteins to fine-tune BMP regulation. The chordin–BMP inhibitory complex is strengthened by the secreted glycoprotein twisted gastrulation (Tsg); however, inhibition is relieved by cleavage of chordin at two specific sites by tolloid family metalloproteases. As Tsg enhances this cleavage process, it serves a dual role as both promoter and inhibitor of BMP signalling. Recent developments in chordin research suggest that rather than simply being by-products, the cleavage fragments of chordin continue to play a role in BMP regulation. In particular, chordin cleavage at the C-terminus potentiates its anti-BMP activity in a type-specific manner.
The αRep artificial repeat protein scaffold: a new tool for crystallization and live cell applications
Authors: Valerio-Lepiniec Marie , Urvoas Agathe , Chevrel Anne , Guellouz Asma , Ferrandez Yann , Mesneau Agnès , de la Sierra-Gallay Ines Li , Aumont-Nicaise Magali , Desmadril Michel , van Tilbeurgh Herman , Minard Philippe
Published: October 2015

We have designed a new family of artificial proteins, named αRep, based on HEAT (acronym for Huntingtin, elongation factor 3 (EF3), protein pphosphatase 2A (PP2A), yeast kinase Tor1) repeat proteins containing an α-helical repeated motif. The sequence of the repeated motifs, first identified in a thermostable archae protein was optimized using a consensus design strategy and used for the construction of a library of artificial proteins. All proteins from this library share the same general fold but differ both in the number of repeats and in five highly randomized amino acid positions within each repeat. The randomized side chains altogether provide a hypervariable surface on αRep variants. Sequences from this library are efficiently expressed as soluble, folded and very stable proteins. αRep binders with high affinity for various protein targets were selected by phage display. Low micromolar to nanomolar dissociation constants between partners were measured and the structures of several complexes (specific αRep/protein target) were solved by X-ray crystallography. Using GFP as a model target, it was demonstrated that αReps can be used as bait in pull-down experiments. αReps can be expressed in eukaryotic cells and specifically interact with their target addressed to different cell compartments.
Biomolecular templating of functional hybrid nanostructures using repeat protein scaffolds
Authors: Romera David , Couleaud Pierre , Mejias Sara H. , Aires Antonio , Cortajarena Aitziber L.
Published: October 2015

The precise synthesis of materials and devices with tailored complex structures and properties is a requisite for the development of the next generation of products based on nanotechnology. Nowadays, the technology for the generation of this type of devices lacks the precision to determine their properties and is accomplished mostly by ‘trial and error’ experimental approaches. The use of bottom-up approaches that rely on highly specific biomolecular interactions of small and simple components is an attractive approach for the templating of nanoscale elements. In nature, protein assemblies define complex structures and functions. Engineering novel bio-inspired assemblies by exploiting the same rules and interactions that encode the natural diversity is an emerging field that opens the door to create nanostructures with numerous potential applications in synthetic biology and nanotechnology. Self-assembly of biological molecules into defined functional structures has a tremendous potential in nano-patterning and the design of novel materials and functional devices. Molecular self-assembly is a process by which complex 3D structures with specified functions are constructed from simple molecular building blocks. Here we discuss the basis of biomolecular templating, the great potential of repeat proteins as building blocks for biomolecular templating and nano-patterning. In particular, we focus on the designed consensus tetratricopeptide repeats (CTPRs), the control on the assembly of these proteins into higher order structures and their potential as building blocks in order to generate functional nanostructures and materials.
Conservation of gene and tissue networks regulating insulin signalling in flies and vertebrates
Authors: Das Rahul , Dobens Leonard L.
Published: October 2015

Fruit flies have emerged as a powerful tool to investigate metabolism. Not only are gene structures and gene networks that control metabolism conserved through evolution, but the interactions among organs to store and process metabolites have strong similarities between flies and humans. Accordingly, the Drosophila system has the potential to address human disorders associated with metabolic dysfunction including obesity, type 2 diabetes and lipotoxicity.
Tribbles in inflammation
Authors: Johnston Jessica , Basatvat Shaghayegh , Ilyas Zabran , Francis Sheila , Kiss-Toth Endre
Published: October 2015

Inflammation is part of the physiological innate immune response to invading pathogens and tissue injury. However, unresolved inflammation leads to human disease. The tribbles (TRIB) family of pseudokinase proteins has been shown to modulate key inflammatory signalling pathways, including the MAPK (mitogen-activated protein kinase) and PI3K (phosphoinositide 3-kinase) networks. This review summarizes our current knowledge on TRIBs in the context of inflammation, both at the level of molecular mechanisms and in disease development.
TRIB2 and the ubiquitin proteasome system in cancer
Authors: Salomè Mara , Campos Joana , Keeshan Karen
Published: October 2015

Tribbles family of pseudokinase proteins are known to mediate the degradation of target proteins in Drosophila and mammalian systems. The main protein proteolysis pathway in eukaryotic cells is the ubiquitin proteasome system (UPS). The tribbles homolog 2 (TRIB2) mammalian family member has been well characterized for its role in murine and human leukaemia, lung and liver cancer. One of the most characterized substrates for TRIB2-mediated degradation is the myeloid transcription factor CCAAT enhancer binding protein α (C/EBPα). However, across a number of cancers, the molecular interactions that take place between TRIB2 and factors involved in the UPS are varied and have differential downstream effects. This review summarizes our current knowledge of these interactions and how this information is important for our understanding of TRIB2 in cancer.
Understanding the function of ABCA7 in Alzheimer's disease
Authors: Li Hongyun , Karl Tim , Garner Brett
Published: October 2015

ATP-binding cassette transporter A7 (ABCA7) is highly expressed in the brain. Recent genome-wide association studies (GWAS) identify ABCA7 single nt polymorphisms (SNPs) that increase Alzheimer's disease (AD) risk. It is now important to understand the true function of ABCA7 in the AD context. We have begun to address this using in vitro and in vivo AD models. Our initial studies showed that transient overexpression of ABCA7 in Chinese hamster ovary cells stably expressing human amyloid precursor protein (APP) resulted in an approximate 50% inhibition in the production of the AD-related amyloid-β (Aβ) peptide as compared with mock-transfected cells. This increased ABCA7 expression was also associated with alterations in other markers of APP processing and an accumulation of cellular APP. To probe for a function of ABCA7 in vivo, we crossed Abca7−/− mice with J20 mice, an amyloidogenic transgenic AD mouse model [B6.Cg-Tg(PDGFB-APPSwInd)20Lms/J] expressing a mutant form of human APP bearing both the Swedish (K670N/M671L) and Indiana (V717F) familial AD mutations. We found that ABCA7 loss doubled insoluble Aβ levels and amyloid plaques in the brain. This did not appear to be related to changes in APP processing (C-terminal fragment analysis), which led us to assess other mechanism by which ABCA7 may modulate Aβ homoeostasis. As we have shown that microglia express high levels of ABCA7, we examined a role for ABCA7 in the phagocytic clearance of Aβ. Our data indicated that the capacity for bone marrow-derived macrophages derived from Abca7−/− mice to phagocytose Aβ was reduced by 51% compared with wild-type (WT) mice. This suggests ABCA7 plays a role in the regulation of Aβ homoeostasis in the brain and that this may be related to Aβ clearance by microglia.
Plant ABC transporters: time for biochemistry?
Authors: Lefèvre François , Baijot Amandine , Boutry Marc
Published: October 2015

ATP-binding cassette (ABC) proteins form a large and ubiquitous family, most members of which are membrane-associated primary transporters. Plant genomes code for a particularly large number of these ABC proteins, with more than 120 genes present in both Arabidopsis thaliana and Oryza sativa (rice). Although plant ABC transporters were initially identified as detoxifiers, sequestering xenobitotics into the vacuole, they were later found to be involved in a wide range of essential physiological processes. Currently, the exact substrates transported by most of these transporters are still unknown and we therefore cannot exclude that a single substrate (e.g. a hormone) is responsible for the diversity of physiological roles. This gap in our knowledge is mainly due to the fact that only a few studies have used direct methods to identify the substrates of these membrane transporters. To address this issue, transport assays involving isolated cells, vesicular membranes or reconstituted liposomes are essential. In this review, we will highlight the importance of the direct biochemical characterization of plant ABC transporters and give some insights into the current status of the homologous and heterologous expression of such proteins.
Tribbles pseudokinases: novel targets for chemical biology and drug discovery?
Authors: Foulkes Daniel M. , Byrne Dominic P. , Bailey Fiona P. , Eyers Patrick A.
Published: October 2015

Tribbles (TRIB) proteins are pseudokinase mediators of eukaryotic signalling that have evolved important roles in lipoprotein metabolism, immune function and cellular differentiation and proliferation. In addition, an evolutionary-conserved modulation of PI3K/AKT signalling pathways highlights them as novel and rather unusual pharmaceutical targets. The three human TRIB family members are uniquely defined by an acidic pseudokinase domain containing a ‘broken’ α C-helix and a MEK (MAPK/ERK)-binding site at the end of the putative C-lobe and a distinct C-terminal peptide motif that interacts directly with a small subset of cellular E3 ubiquitin ligases. This latter interaction drives proteasomal-dependent degradation of networks of transcription factors, whose rate of turnover determines the biological attributes of individual TRIB family members. Defining the function of individual Tribs has been made possible through evaluation of individual TRIB knockout mice, siRNA/overexpression approaches and genetic screening in flies, where the single TRIB gene was originally described 15 years ago. The rapidly maturing TRIB field is primed to exploit chemical biology approaches to evaluate endogenous TRIB signalling events in intact cells. This will help define how TRIB-driven protein–protein interactions and the atypical TRIB ATP-binding site, fit into cellular signalling modules in experimental scenarios where TRIB-signalling complexes remain unperturbed. In this mini-review, we discuss how small molecules can reveal rate-limiting signalling outputs and functions of Tribs in cells and intact organisms, perhaps serving as guides for the development of new drugs. We predict that appropriate small molecule TRIB ligands will further accelerate the transition of TRIB pseudokinase analysis into the mainstream of cell signalling.
Tribbles role in reproduction
Authors: Basatvat Shaghayegh , Carter Deborah Angela Louise , Kiss-Toth Endre , Fazeli Alireza
Published: October 2015

Tribbles (TRIB) proteins, a family of evolutionary conserved psuedokinase proteins, modulate various signalling pathways within the cell. The regulatory roles of TRIB make them an important part of a number of biological processes ranging from cell proliferation to metabolism, immunity, inflammation and carcinogenesis. Innate immune system plays a pivotal role during the regulation of reproductive processes that allows successful creation of an offspring. Its involvement initiates from fertilization of the oocyte by spermatozoon and lasts throughout early embryonic development, pregnancy and labour. Therefore, there is a close cooperation between the reproductive system and the innate immune system. Evidence from our lab has demonstrated that improper activation of the innate immune system can reduce embryo implantation, thus leading to infertility. Therefore, control mechanisms regulating the innate immune system function can be critical for successful reproductive events.
Oncosuppressive functions of tribbles pseudokinase 3
Authors: Salazar María , Lorente Mar , Orea-Soufi Alba , Dávila David , Erazo Tatiana , Lizcano José , Carracedo Arkaitz , Kiss-Toth Endre , Velasco Guillermo
Published: October 2015

Tribbles pseudokinase 3 (TRIB3) belongs to the tribbles family of pseudokinases. In this article, we summarize several observation obtained by our laboratories supporting that TRIB3 plays a crucial role in the anti-cancer activity of cannabinoids (a novel family of potential anti-cancer agents derived from marijuana) and that TRIB3 genetic inactivation enhances cancer generation and progression.
Exploiting species differences to understand the CFTR Cl− channel
Authors: Bose Samuel J. , Scott-Ward Toby S. , Cai Zhiwei , Sheppard David N.
Published: October 2015

The anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is a unique ATP-binding cassette (ABC) transporter. CFTR plays a pivotal role in transepithelial ion transport as its dysfunction in the genetic disease cystic fibrosis (CF) dramatically demonstrates. Phylogenetic analysis suggests that CFTR first appeared in aquatic vertebrates fulfilling important roles in osmosensing and organ development. Here, we review selectively, knowledge of CFTR structure, function and pharmacology, gleaned from cross-species comparative studies of recombinant CFTR proteins, including CFTR chimeras. The data argue that subtle changes in CFTR structure can affect strongly channel function and the action of CF mutations.
The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity
Authors: Maqbool Abbas , Horler Richard S.P. , Muller Axel , Wilkinson Anthony J. , Wilson Keith S. , Thomas Gavin H.
Published: October 2015

ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms. Most prokaryotes have many SBP-dependent ABC transporters that recognize a broad range of ligands from metal ions to amino acids, sugars and peptides. Herein, we review the structure and function of a number of more unusual SBPs, including an ABC transporter involved in the transport of rare furanose forms of sugars and an SBP that has evolved to specifically recognize the bacterial cell wall-derived murein tripeptide (Mtp). Both these examples illustrate that subtle changes in binding-site architecture, including changes in side chains not directly involved in ligand co-ordination, can result in significant alteration of substrate range in novel and unpredictable ways.
Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications
Authors: Stockner Thomas , Mullen Anna , MacMillan Fraser
Published: October 2015

ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented.
Context aware image enhancement for online fish behaviour monitoring
Authors: Ye Linning , Hou Zujun , Eng How‐Lung
Published: October 2015

Image enhancement is an essential step in developing a robust computer vision system. This study presents an image contrast enhancement method for an online fish behaviour monitoring system. The method executes in three steps. First, the critical information on the context of the image is derived from different responses of two edge detectors: one with high threshold and the other with low threshold, which differentiate the image structure into the good contrast part and the poor contrast part. Then, statistics of the gradient field in the former part are used to modify the gradient field in the latter part. Finally, in the modified region, the image contents are reconstructed through solving a Poisson equation with the Dirichlet boundary condition. Comparison with state‐of‐the‐art methods has been made both qualitatively and quantitatively using realistic images and advantages of the proposed method have been demonstrated.
Improved grid voltage sensorless control strategy for railway power conditioners
Authors: Bozorgi Amir Masoud , Sanatkar Chayjani Majid , Mohammad Nejad Reza , Monfared Mohammad
Published: October 2015

Rapid development of high‐speed trains confronts the power grid with serious power quality problems. In this study, to compensate power quality, an improved grid voltage sensorless control method for the railway power conditioner (RPC) is proposed. The proposed control strategy utilises a moving average filter to better detect the compensating currents and a proportional‐resonant controller to control the compensating currents. Moreover, a sensorless virtual flux method based on second order low‐pass filters is presented to replace the AC voltage sensors. Using the proposed strategy, the dynamic and steady‐state characteristic of the RPC is significantly enhanced. Through simulation tests, the effectiveness of the proposed methods is confirmed.
A study of internal energy relaxation in shocks using molecular dynamics based models
Authors: Li Zheng , Parsons Neal , Levin Deborah A.
Published: October 2015

Recent potential energy surfaces (PESs) for the N2 + N and N2 + N2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N2 + N2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.
A minimal model of self-sustaining turbulence
Authors: Thomas Vaughan L. , Farrell Brian F. , Ioannou Petros J. , Gayme Dennice F.
Published: October 2015

In this work, we examine the turbulence maintained in a Restricted Nonlinear (RNL) model of plane Couette flow. This model is a computationally efficient approximation of the second order statistical state dynamics obtained by partitioning the flow into a streamwise averaged mean flow and perturbations about that mean, a closure referred to herein as the RNL∞ model. The RNL model investigated here employs a single member of the infinite ensemble that comprises the covariance of the RNL∞ dynamics. The RNL system has previously been shown to support self-sustaining turbulence with a mean flow and structural features that are consistent with direct numerical simulations (DNS). Regardless of the number of streamwise Fourier components used in the simulation, the RNL system’s self-sustaining turbulent state is supported by a small number of streamwise varying modes. Remarkably, further truncation of the RNL system’s support to as few as one streamwise varying mode can suffice to sustain the turbulent state. The close correspondence between RNL simulations and DNS that has been previously demonstrated along with the results presented here suggest that the fundamental mechanisms underlying wall-turbulence can be analyzed using these highly simplified RNL systems.
The electron forewake: Shadowing and drift-energization as flowing magnetized plasma encounters an obstacle
Authors: Haakonsen Christian Bernt , Hutchinson Ian H.
Published: October 2015

Flow of magnetized plasma past an obstacle creates a traditional wake, but also a forewake region arising from shadowing of electrons. The electron forewakes resulting from supersonic flows past insulating and floating-potential obstacles are explored with 2D electrostatic particle-in-cell simulations, using a physical ion to electron mass ratio. Drift-energization is discovered to give rise to modifications to the electron velocity-distribution, including a slope-reversal, providing a novel drive of forewake instability. The slope-reversal is present at certain locations in all the simulations, and appears to be quite robustly generated. Wings of enhanced electron density are observed in some of the simulations, also associated with drift-energization. In the simulations with a floating-potential obstacle, the specific potential structure behind that obstacle allows fast electrons to cross the wake, giving rise to a more traditional shadowing-driven two-stream instability. Fluctuations associated with such instability are observed in the simulations, but this instability-mechanism is expected to be more sensitive to the plasma parameters than that associated with the slope-reversal.
Transport theory in the collisional boundary layer regime for finite aspect ratio tokamaks with broken symmetry
Authors: Shaing K. C.
Published: October 2015

Transport theory in the collisional boundary layer regime for tokamaks with broken symmetry is extended to include the effects of the finite aspect ratio and finite plasma β. Here, β is the ratio of the plasma thermal pressure to the magnetic field pressure. Transport fluxes are calculated on the perturbed magnetic surface where plasma pressure is constant. The extension of the theory to finite aspect ratio tokamaks is made possible because the perturbed particle distribution that contributes to the transport fluxes in the collisional boundary layer regime is localized in the pitch angle space. Invoking the flux-force relation, the transport fluxes can be used for modeling toroidal plasma flow in tokamaks.
Frequency-domain deviational Monte Carlo method for linear oscillatory gas flows
Authors: Ladiges Daniel R. , Sader John E.
Published: October 2015

Oscillatory non-continuum low Mach number gas flows are often generated by nanomechanical devices in ambient conditions. These flows can be simulated using a range of particle based Monte Carlo techniques, which in their original form operate exclusively in the time-domain. Recently, a frequency-domain weight-based Monte Carlo method was proposed [D. R. Ladiges and J. E. Sader, “Frequency-domain Monte Carlo method for linear oscillatory gas flows,” J. Comput. Phys. 284, 351–366 (2015)] that exhibits superior statistical convergence when simulating oscillatory flows. This previous method used the Bhatnagar-Gross-Krook (BGK) kinetic model and contains a “virtual-time” variable to maintain the inherent time-marching nature of existing Monte Carlo algorithms. Here, we propose an alternative frequency-domain deviational Monte Carlo method that facilitates the use of a wider range of molecular models and more efficient collision/relaxation operators. We demonstrate this method with oscillatory Couette flow and the flow generated by an oscillating sphere, utilizing both the BGK kinetic model and hard sphere particles. We also discuss how oscillatory motion of arbitrary time-dependence can be simulated using computationally efficient parallelization. As in the weight-based method, this deviational frequency-domain Monte Carlo method is shown to offer improved computational speed compared to the equivalent time-domain technique.
Beam imaging in the injection line of the INFN-LNS superconducting cyclotron
Authors: Nicolosi Dario , Cosentino Luigi , Mascali David , Pappalardo Alfio , Castro Maurizio , Celona Luigi , Marchetta Carmelo , Marletta Salvatore , Maugeri Antonio , Rifuggiato Danilo , Seminara Angelo , Gammino Santo
Published: October 2015

A cheap and efficient diagnostic system for beam monitoring has been recently developed at INFN-LNS in Catania. It consists of a high sensitivity CCD camera detecting the light produced by an ion beam hitting the surface of a scintillating screen and a frame grabber for image acquisition. A scintillating screen, developed at INFN-LNS and consisting of a 2 μm BaF2 layer evaporated on an aluminium plate, has been tested by using 20Ne and 40Ar beams in the keV energy range. The CAESAR ECR ion source has been used for investigating the influence of the frequency and magnetic field tuning effects, the impact of the microwave injected power, and of the focusing solenoids along the low energy beam transport on the beam shape and current. These tests will allow to better understand the interplay between the plasma and beam dynamics and, moreover, to improve the transport efficiency along the low energy beam line and the matching with the superconducting cyclotron, particularly relevant in view of the expected upgrade of the machine.
Metal-to-metal charge transfer between dopant and host ions: Photoconductivity of Yb-doped CaF2 and SrF2 crystals
Authors: Barandiarán Zoila , Seijo Luis
Published: October 2015

Dopant-to-host electron transfer is calculated using ab initio wavefunction-based embedded cluster methods for Yb/Ca pairs in CaF2 and Yb/Sr pairs in SrF2 crystals to investigate the mechanism of photoconductivity. The results show that, in these crystals, dopant-to-host electron transfer is a two-photon process mediated by the 4fN−15d excited states of Y b2+: these are reached by the first photon excitation; then, they absorb the second photon, which provokes the Y b2+ + Ca2+ (Sr2+) → Y b3+ + Ca+ (Sr+) electron phototransfer. This mechanism applies to all the observed Y b2+ 4f–5d absorption bands with the exception of the first one: Electron transfer cannot occur at the first band wavelengths in CaF2:Y b2+ because the Y b3+–Ca+ states are not reached by the two-photon absorption. In contrast, Yb-to-host electron transfer is possible in SrF2:Y b2+ at the wavelengths of the first 4f–5d absorption band, but the mechanism is different from that described above: first, the two-photon excitation process occurs within the Y b2+ active center, then, non-radiative Yb-to-Sr electron transfer can occur. All of these features allow to interpret consistently available photoconductivity experiments in these materials, including the modulation of the photoconductivity by the absorption spectrum, the differences in photoconductivity thresholds observed in both hosts, and the peculiar photosensitivity observed in the SrF2 host, associated with the lowest 4f–5d band.
Approximate singly excited states from a two-component Hartree-Fock reference
Authors: Goings Joshua J. , Ding Feizhi , Davidson Ernest R. , Li Xiaosong
Published: October 2015

For many molecules, relaxing the spin symmetry constraint on the wave function results in the lowest energy mean-field solution. The two-component Hartree-Fock (2cHF) method relaxes all spin symmetry constraints, and the wave function is no longer an eigenfunction of the total spin, spin projection, or time-reversal symmetry operators. For ground state energies, 2cHF is a superior mean-field method for describing spin-frustrated molecules. For excited states, the utility of 2cHF is uncertain. Here, we implement the 2cHF extensions of two single-reference excited state methods, the two-component configuration interaction singles and time-dependent Hartree-Fock. We compare the results to the analogous methods based off of the unrestricted Hartree-Fock approximation, as well as the full configuration interaction for three small molecules with distinct 2cHF solutions, and discuss the nature of the 2cHF excited state solutions.
Solid-state dewetting of magnetic binary multilayer thin films
Authors: Esterina Ria , Liu X. M. , Adeyeye A. O. , Ross C. A. , Choi W. K.
Published: October 2015

We examined solid-state dewetting behavior of magnetic multilayer thin film in both miscible (CoPd) and immiscible (CoAu) systems and found that CoPd and CoAu dewetting stages follow that of elemental materials. We established that CoPd alloy morphology and dewetting rate lie in between that of the elemental materials. Johnson-Mehl-Avrami analysis was utilized to extract the dewetting activation energy of CoPd. For CoAu, Au-rich particles and Co-rich particles are distinguishable and we are able to predict the interparticle spacings and particle densities for the particles that agree well with the experimental results. We also characterized the magnetic properties of CoPd and CoAu nanoparticles.
Binding energies from diffusion Monte Carlo for the MB-pol H2O and D2O dimer: A comparison to experimental values
Authors: Mallory Joel D. , Mandelshtam Vladimir A.
Published: October 2015

The diffusion Monte Carlo (DMC) method is applied to compute the ground state energies of the water monomer and dimer and their D2O isotopomers using MB-pol; the most recent and most accurate ab inito-based potential energy surface (PES). MB-pol has already demonstrated excellent agreement with high level electronic structure data, as well as agreement with some experimental, spectroscopic, and thermodynamic data. Here, the DMC binding energies of (H2O)2 and (D2O)2 agree with the corresponding values obtained from velocity map imaging within, respectively, 0.01 and 0.02 kcal/mol. This work adds two more valuable data points that highlight the accuracy of the MB-pol PES.
Silicon nitride anti-reflection coating on the glass and transparent conductive oxide interface for thin film solar cells and modules
Authors: Iwahashi T. , Morishima M. , Fujibayashi T. , Yang R. , Lin J. , Matsunaga D.
Published: October 2015

Anti-reflection coating (ARC) is well known as an important technique to enhance solar cell performance. Typical ARC has been applied on the glass surface to reduce light reflection loss at the air/glass interface. However, reflection loss occurs not only at glass surface but also at other interfaces such as glass/transparent conductive oxide (TCO) interface. The refractive index of SiNx is tunable from 1.6 to 2.7, and the range from 1.7 to 2.0 is suitable for ARC at glass/TCO interface. In this study, we examined the AR effect of silicon nitride (SiNx) deposited by plasma enhanced chemical vapor deposition at the glass/TCO interface with thin film silicon solar cell and module. Reflectivity reduction of 1.6% for glass/ZnO substrate has been obtained with optimal SiNx layer, which contribute 2.0% gain in cell efficiency. Besides, we also confirmed the relative efficiency gain of around 2% for large-sized solar module, leading to a world-record large area stabilized module conversion efficiency of 12.34%.