bluuebunny/crossref_metadata_2025 huggingface dataset:
Low temperature plasma processing of nc-Si/a-SiNx:H QD thin films with high carrier mobility and preferred (220) crystal orientation: a promising material for third generation solar cells
Authors: Sain Basudeb , Das Debajyoti
Published: August 2014

The nc-Si-QDs/a-SiNx:H (∼5.7–1.3 nm) thin-films grown by low-temperature Inductively-coupled plasma, possess high carrier-mobility, electrical-conductivity, photosensitivity and preferred (220) crystal orientation, suitable for third-generation solar cells.
Intramolecular OHO bonding in dibenzoylmethane: symmetry and spectral manifestations
Authors: Petković Milena , Etinski Mihajlo
Published: August 2014

Calculations reveal that both symmetric and asymmetric structures of dibenzoylmethane are present in the gas phase at room temperature.
The studies on bioactivity in vitro of ruthenium(ii) polypyridyl complexes towards human lung carcinoma A549 cells
Authors: Han Bing-Jie , Jiang Guang-Bin , Wang Ji , Li Wei , Huang Hong-Liang , Liu Yun-Jun
Published: August 2014

Three complexes were synthesized and characterized. The cytotoxicity, apoptosis, cellular uptake, reactive oxygen species, mitochondrial membrane potential, cell cycle arrest and western blot analysis were investigated.
Construction of micelles based on biocompatible pseudo-graft polymers via β-cyclodextrin/cholesterol interaction for protein delivery
Authors: Han Hui , Liu De-E , Lu Hongguang , Gu Wen-Xing , Gao Hui
Published: August 2014

A pseudo-graft copolymer micelle was constructed from the self-assembly of (6-(2-aminoethyl)-amino-6-deoxy)-cyclodextrin (β-CDen)-modified poly(aspartic acid) (PASP-CD) with cholesterol-modified poly(d,l-lactide) (PLA-Chol) using host–guest inclusion complexation in water.
Biological co-production of ethanol and biodiesel from wheat straw: a case of dilute acid pretreatment
Authors: Morikawa Yuichi , Zhao Xuebing , Liu Dehua
Published: August 2014

A process for co-production of ethanol and biodiesel from wheat straw was proposed.
Palladium-catalyzed intramolecular Cp–H bond functionalization/arylation: an enantioselective approach to planar chiral quinilinoferrocenes
Authors: Ma Xinna , Gu Zhenhua
Published: August 2014

A palladium-catalyzed intramolecular asymmetric Cp–H functionalization/cyclization reaction to construct planar chiral quinilinoferrocenes was reported.
Analysing the distribution of questions in the gas law chapters of secondary and introductory college chemistry textbooks from the United States
Authors: Gillette Gabriel , Sanger Michael J.
Published: August 2014

This study analysed the distribution of questions from the gas law chapters of four high school and four college chemistry textbooks based on six variables—Book Type (secondaryversusintroductory college), Cognitive Skill (lower-orderversushigher-order), Question Format (calculationversusmultiple-choiceversusshort-answer), Question Placement (in-chapterversusend-of-chapterversustest-bank), Question Type (qualitativeversusquantitative), and Representation (macroscopicversusparticulateversussymbolic). The questions in these chapters were homogeneously distributed for the Cognitive Skill and the Representation variables, but showed differences in question distribution based on the Book Type, Question Format, Question Placement, and Question Type variables. The loglinear analysis method used in this study provides one way to analyse the distribution of different types of questions appearing in chemistry textbooks, and these differences in question distribution can be helpful for textbook authors to evaluate the types of questions appearing in their textbooks and how they are presented, and can be helpful for chemistry instructors to determine how they need to adapt their instructional lessons to prepare students for course examinations or college/career placement examinations.
Highly selective CO2 separation membranes through tunable poly(4-vinylphenolate)–CO2 interactions
Authors: Hammann Markus , Castillo Dante , Anger Christian , Rieger Bernhard
Published: August 2014

Reactive transport enhancement of CO2 in poly(4-vinylphenolate)s.
Controlling fuel crossover and hydration in ultra-thin proton exchange membrane-based fuel cells using Pt-nanosheet catalysts
Authors: Wang Rujie , Zhang Wenjing , He Gaohong , Gao Ping
Published: August 2014

A fuel cell with a 9 μm thick proton exchange membrane bearing Pt-nanosheet catalysts delivered 200% more power density as compared with a fuel cell with commercial Nafion® 211 membrane.
Inhibition of glioma proliferation and migration by magnetic nanoparticle mediated JAM-2 silencing
Authors: Qi Lifeng , Liu Jing , Zhu Haiyan , Li Zhuoquan , Lu Kun , Li Tian , Shi Donglu
Published: August 2014

Brain invasion is a biological hallmark of glioma that leads to its aggressiveness and prognosis.
A high efficiency approach for a titanium surface antifouling modification: PEG-o-quinone linked with titanium via electron transfer process
Authors: Liu Songtao , Chen Lijuan , Tan Lin , Cao Fuhu , Bai Longchao , Wang Yanmei
Published: August 2014

The stability and long-term antifouling properties of the electro-assembly monolayers of PEG-o-quinone are better than that of the self-assembly monolayers of PEG-catechol.
Molecular mechanisms of asymmetric RAF dimer activation
Authors: Jambrina Pablo G. , Bohuszewicz Olga , Buchete Nicolae-Viorel , Kolch Walter , Rosta Edina
Published: August 2014

Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms.
Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies
Authors: Wilkes Edmund H. , Casado Pedro , Cutillas Pedro R.
Published: August 2014

The ability of cells in multicellular organisms to respond to signals in their environment is critical for their survival, development and differentiation. Once differentiated and occupying their functional niche, cells need to maintain phenotypic stability while responding to diverse extracellular perturbations and environmental signals (such as nutrients, temperature, cytokines and hormones) in a co-ordinated manner. To achieve these requirements, cells have evolved numerous intracellular signalling mechanisms that confer on them the ability to resist, respond and adapt to external changes. Although fundamental to normal biological processes, as is evident from their evolutionary conservation, such mechanisms also allow cancer cells to evade targeted therapies, a problem of immediate clinical importance. In the present article, we discuss the role of signalling plasticity in the context of the mechanisms underlying both intrinsic and acquired resistance to targeted cancer therapies. We then examine the emerging analytical techniques and theoretical paradigms that are contributing to a greater understanding of signalling on a global and untargeted scale. We conclude with a discussion on how integrative approaches to the study of cell signalling have been used, and could be used in the future, to advance our understanding of resistance mechanisms to therapies that target the kinase signalling network.
Resistance acquisition to MDM2 inhibitors
Authors: Cinatl Jindrich , Speidel Daniel , Hardcastle Ian , Michaelis Martin
Published: August 2014

Various experimental strategies aim to (re)activate p53 signalling in cancer cells. The most advanced clinically are small-molecule inhibitors of the autoregulatory interaction between p53 and MDM2 (murine double minute 2). Different MDM2 inhibitors are currently under investigation in clinical trials. As for other targeted anti-cancer therapy approaches, relatively rapid resistance acquisition may limit the clinical efficacy of MDM2 inhibitors. In particular, MDM2 inhibitors were shown to induce p53 mutations in experimental systems. In the present article, we summarize what is known about MDM2 inhibitors as anti-cancer drugs with a focus on the acquisition of resistance to these compounds.
Selection shaped the evolution of mouse androgen-binding protein (ABP) function and promoted the duplication ofAbpgenes
Authors: Karn Robert C. , Laukaitis Christina M.
Published: August 2014

In the present article, we summarize two aspects of our work on mouse ABP (androgen-binding protein): (i) the sexual selection function producing incipient reinforcement on the European house mouse hybrid zone, and (ii) the mechanism behind the dramatic expansion of the Abp gene region in the mouse genome. Selection unifies these two components, although the ways in which selection has acted differ. At the functional level, strong positive selection has acted on key sites on the surface of one face of the ABP dimer, possibly to influence binding to a receptor. A different kind of selection has apparently driven the recent and rapid expansion of the gene region, probably by increasing the amount of Abp transcript, in one or both of two ways. We have shown previously that groups of Abp genes behave as LCRs (low-copy repeats), duplicating as relatively large blocks of genes by NAHR (non-allelic homologous recombination). The second type of selection involves the close link between the accumulation of L1 elements and the expansion of the Abp gene family by NAHR. It is probably predicated on an initial selection for increased transcription of existing Abp genes and/or an increase in Abp gene number providing more transcriptional sites. Either or both could increase initial transcript production, a quantitative change similar to increasing the volume of a radio transmission. In closing, we also provide a note on Abp gene nomenclature.
A role for the pseudokinase HER3 in the acquired resistance against EGFR- and HER2-directed targeted therapy
Authors: Claus Jeroen , Patel Gargi , Ng Tony , Parker Peter J.
Published: August 2014

Specific inhibition of members of the EGFR (epidermal growth factor receptor) family, particularly EGFR and HER2 (human epidermal growth factor receptor 2), are an important therapeutic strategy in many human cancers. Compared with classical chemotherapy, these targeted therapeutics are very specific and initially effective, but acquired resistance against these targeted therapies is a recurring threat. A growing body of recent work has highlighted a pseudokinase in the EGFR family, HER3, and its ligand, NRG (neuregulin β1), to be of importance in models of resistant cancers, as well as in patients. In the present article, we describe some of the roles in which HER3 can mediate acquired resistance and discuss the current efforts to target HER3 itself in cancer.
RBFOX2 protein domains and cellular activities
Authors: Arya Anurada D. , Wilson David I. , Baralle Diana , Raponi Michaela
Published: August 2014

RBFOX2 (RNA-binding protein, Fox-1 homologue 2)/RBM9 (RNA-binding-motif protein 9)/RTA (repressor of tamoxifen action)/HNRBP2 (hexaribonucleotide-binding protein 2) encodes an RNA-binding protein involved in tissue specific alternative splicing regulation and steroid receptors transcriptional activity. Its ability to regulate specific splicing profiles depending on context has been related to different expression levels of the RBFOX2 protein itself and that of other splicing regulatory proteins involved in the shared modulation of specific genes splicing. However, this cannot be the sole explanation as to why RBFOX2 plays a widespread role in numerous cellular mechanisms from development to cell survival dependent on cell/tissue type. RBFOX2 isoforms with altered protein domains exist. In the present article, we describe the main RBFOX2 protein domains, their importance in the context of splicing and transcriptional regulation and we propose that RBFOX2 isoform distribution may play a fundamental role in RBFOX2-specific cellular effects.
Do you smell what I smell? Genetic variation in olfactory perception
Authors: Logan Darren W.
Published: August 2014

The sense of smell is mediated by the detection of chemical odours by ORs (olfactory receptors) in the nose. This initiates a neural percept of the odour in the brain, which may provoke an emotional or behavioural response. Analogous to colour-blindness in the visual system, some individuals report a very different percept of specific odours to others, in terms of intensity, valence or detection threshold. A significant proportion of variance in odour perception is heritable, and recent advances in genome sequencing and genotyping technologies have permitted studies into the genes that underpin these phenotypic differences. In the present article, I review the evidence that OR genes are extremely variable between individuals. I argue that this contributes to a unique receptor repertoire in our noses that provides us each with a personalized perception of our environment. I highlight specific examples where known OR variants influence odour detection and discuss the wider implications of this for both humans and other mammals that use chemical communication for social interaction.
Decoding RAS isoform and codon-specific signalling
Authors: Newlaczyl Anna U. , Hood Fiona E. , Coulson Judy M. , Prior Ian A.
Published: August 2014

RAS proteins are key signalling hubs that are oncogenically mutated in 30% of all cancer cases. Three genes encode almost identical isoforms that are ubiquitously expressed, but are not functionally redundant. The network responses associated with each isoform and individual oncogenic mutations remain to be fully characterized. In the present article, we review recent data defining the differences between the RAS isoforms and their most commonly mutated codons and discuss the underlying mechanisms.
eIF4E-binding proteins: new factors, new locations, new roles
Authors: Kamenska Anastasiia , Simpson Clare , Standart Nancy
Published: August 2014

The cap-binding translation initiation factor eIF4E (eukaryotic initiation factor 4E) is central to protein synthesis in eukaryotes. As an integral component of eIF4F, a complex also containing the large bridging factor eIF4G and eIF4A RNA helicase, eIF4E enables the recruitment of the small ribosomal subunit to the 5′ end of mRNAs. The interaction between eIF4E and eIF4G via a YXXXXLϕ motif is regulated by small eIF4E-binding proteins, 4E-BPs, which use the same sequence to competitively bind eIF4E thereby inhibiting cap-dependent translation. Additional eIF4E-binding proteins have been identified in the last 10–15 years, characterized by the YXXXXLϕ motif, and by interactions (many of which remain to be detailed) with RNA-binding proteins, or other factors in complexes that recognize the specific mRNAs. In the present article, we focus on the metazoan 4E-T (4E-transporter)/Cup family of eIF4E-binding proteins, and also discuss very recent examples in yeast, fruitflies and humans, some of which predictably inhibit translation, while others may result in mRNA decay or even enhance translation; altogether considerably expanding our understanding of the roles of eIF4E-binding proteins in gene expression regulation.
Emerging functions of alternative splicing coupled with nonsense-mediated decay
Authors: Hamid Fursham M. , Makeyev Eugene V.
Published: August 2014

Higher eukaryotes rely on AS (alternative splicing) of pre-mRNAs (mRNA precursors) to generate more than one protein product from a single gene and to regulate mRNA stability and translational activity. An important example of the latter function involves an interplay between AS and NMD (nonsense-mediated decay), a cytoplasmic quality control mechanism eliminating mRNAs containing PTCs (premature translation termination codons). Although originally identified as an error surveillance process, AS-NMD additionally provides an efficient strategy for deterministic regulation of gene expression outputs. In this review, we discuss recently published examples of AS–NMD and delineate functional contexts where recurrent use of this mechanism orchestrates expression of important genes.
Intracellular redistribution of acetyl-CoA, the pivotal point in differential susceptibility of cholinergic neurons and glial cells to neurodegenerative signals
Authors: Szutowicz Andrzej , Bielarczyk Hanna , Ronowska Anna , Gul-Hinc Sylwia , Klimaszewska-Łata Joanna , Dyś Aleksandra , Zyśk Marlena , Pawełczyk Tadeusz
Published: August 2014

Intramitochondrial decarboxylation of glucose-derived pyruvate by PDHC (pyruvate dehydrogenase complex) is a principal source of acetyl-CoA, for mitochondrial energy production and cytoplasmic synthetic pathways in all types of brain cells. The inhibition of PDHC, ACO (aconitase) and KDHC (ketoglutarate dehydrogenase complex) activities by neurodegenerative signals such as aluminium, zinc, amyloid β-peptide, excess nitric oxide (NO) or thiamine pyrophosphate deficits resulted in much deeper losses of viability, acetyl-CoA and ATP in differentiated cholinergic neuronal cells than in non-differentiated cholinergic, and cultured microglial or astroglial cell lines. In addition, in cholinergic cells, such conditions caused inhibition of ACh (acetylcholine) synthesis and its quantal release. Furthermore, cholinergic neuronal cells appeared to be resistant to high concentrations of LPS (lipopolysaccharide). In contrast, in microglial cells, low levels of LPS caused severalfold activation of NO, IL-6 (interleukin 6) and TNFα (tumour necrosis factor α) synthesis/release, accompanied by inhibition of PDHC, KDHC and ACO activities, and suppression of acetyl-CoA, but relatively small losses in their ATP contents and viability parameters. Compounds that protected these enzymes against inhibitory effects of neurotoxins alleviated acetyl-CoA and ATP deficits, thereby maintaining neuronal cell viability. These data indicate that preferential susceptibility of cholinergic neurons to neurodegenerative insults may result from competition for acetyl-CoA between mitochondrial energy-producing and cytoplasmic ACh-synthesizing pathways. Such a hypothesis is supported by the existence of highly significant correlations between mitochondrial/cytoplasmic acetyl-CoA levels and cell viability/transmitter functions respectively.
Mitochondria and redox homoeostasis as chemotherapeutic targets
Authors: Briehl Margaret M. , Tome Margaret E. , Wilkinson Sarah T. , Jaramillo Melba C. , Lee Kristy
Published: August 2014

Characteristics of cancer cells include a more oxidized redox environment, metabolic reprogramming and apoptosis resistance. Our studies with a lymphoma model have explored connections between the cellular redox environment and cancer cell phenotypes. Alterations seen in lymphoma cells made resistant to oxidative stress include: a more oxidized redox environment despite increased expression of antioxidant enzymes, enhanced net tumour growth, metabolic changes involving the mitochondria and resistance to the mitochondrial pathway to apoptosis. Of particular importance, the cells show cross-resistance to multiple chemotherapeutic agents used to treat aggressive lymphomas. Analyses of clinical and tumour data reveal the worst prognosis when patients’ lymphomas have gene expression patterns consistent with the most oxidized redox environment. Lymphomas from patients with the worst survival outcomes express increased levels of proteins involved in oxidative phosphorylation, including cytochrome c. This is consistent with these cells functioning as metabolic opportunists. Using lymphoma cell models and primary lymphoma cultures, we observed enhanced killing using genetic and drug approaches which further oxidize the cellular redox environment. These approaches include increased expression of SOD2 (superoxide dismutase 2), treatment with a manganoporphyrin that oxidizes the glutathione redox couple, or treatment with a copper chelator that inhibits SOD1 and leads to peroxynitrite-dependent cell death. The latter approach effectively kills lymphoma cells that overexpress the anti-apoptotic protein Bcl-2. Given the central role of mitochondria in redox homoeostasis, metabolism and the intrinsic pathway to apoptosis, our studies support the development of new anti-cancer drugs to target this organelle.
Physiological roles of the pantothenate kinases
Authors: Dansie Lorraine E. , Reeves Stacy , Miller Karen , Zano Stephen P. , Frank Matthew , Pate Caroline , Wang Jina , Jackowski Suzanne
Published: August 2014

CoA (coenzyme A) is an essential cofactor that is involved in many metabolic processes. CoA is derived from pantothenate in five biosynthetic reactions. The CoA biosynthetic pathway is regulated by PanKs (pantothenate kinases) and four active isoforms are expressed in mammals. The critical physiological functions of the PanKs are revealed by systematic deletion of the Pank genes in mice.
Reassessing cellular glutathione homoeostasis: novel insights revealed by genetically encoded redox probes
Authors: Morgan Bruce
Published: August 2014

Glutathione is the most abundant small molecule thiol in nearly all eukaryotes. Whole-cell levels of oxidized (GSSG) and reduced (GSH) glutathione are variable and responsive to genetic and chemical manipulations, which has led to their relative levels being widely used as a marker of the ‘cellular redox state’ and to indicate the level of ‘oxidative stress’ experienced by cells, tissues and organisms. However, the applicability of glutathione as a marker for a generalized ‘cellular redox state’ is questionable, especially in the light of recent observations in yeast cells. In yeast, whole-cell GSSG changes are almost completely dependent upon the activity of an ABC-C (ATP-binding cassette-C) transporter, Ycf1 (yeast cadmium factor 1), which mediates sequestration of GSSG to the vacuole. In the absence of Ycf1 whole-cell GSSG content is strongly decreased and extremely robust to perturbation. These observations are consistent with highly specific redox-sensitive GFP probe-based measurements of the cytosolic glutathione pool and indicate that cytosolic GSSG reductive systems are easily able to reduce nearly all GSSG formed, even following treatment with large concentrations of oxidant. In the present paper, I discuss the consequences of these new findings for our understanding of glutathione homoeostasis in the eukaryotic cell.
Regulation of gene expression through production of unstable mRNA isoforms
Authors: Sibley Christopher R.
Published: August 2014

Alternative splicing is universally accredited for expanding the information encoded within the transcriptome. In recent years, several tightly regulated alternative splicing events have been reported which do not lead to generation of protein products, but lead to unstable mRNA isoforms. Instead these transcripts are targets for NMD (nonsense-mediated decay) or retained in the nucleus and degraded. In the present review I discuss the regulation of these events, and how many have been implicated in control of gene expression that is instrumental to a number of developmental paradigms. I further discuss their relevance to disease settings and conclude by highlighting technologies that will aid identification of more candidate events in future.
Alteration of the coenzyme A biosynthetic pathway in neurodegeneration with brain iron accumulation syndromes
Authors: Venco Paola , Dusi Sabrina , Valletta Lorella , Tiranti Valeria
Published: August 2014

NBIA (neurodegeneration with brain iron accumulation) comprises a heterogeneous group of neurodegenerative diseases having as a common denominator, iron overload in specific brain areas, mainly basal ganglia and globus pallidus. In the past decade a bunch of disease genes have been identified, but NBIA pathomechanisms are still not completely clear. PKAN (pantothenate kinase-associated neurodegeneration), an autosomal recessive disorder with progressive impairment of movement, vision and cognition, is the most common form of NBIA. It is caused by mutations in the PANK2 (pantothenate kinase 2) gene, coding for a mitochondrial enzyme that phosphorylates vitamin B5 in the first reaction of the CoA (coenzyme A) biosynthetic pathway. A distinct form of NBIA, denominated CoPAN (CoA synthase protein-associated neurodegeneration), is caused by mutations in the CoASY (CoA synthase) gene coding for a bifunctional mitochondrial enzyme, which catalyses the final steps of CoA biosynthesis. These two inborn errors of CoA metabolism further support the concept that dysfunctions in CoA synthesis may play a crucial role in the pathogenesis of NBIA.
About the dangers, costs and benefits of living an aerobic lifestyle
Authors: Knoefler Daniela , Leichert Lars I.O. , Thamsen Maike , Cremers Claudia M. , Reichmann Dana , Gray Michael J. , Wholey Wei-Yun , Jakob Ursula
Published: August 2014

The era in which ROS (reactive oxygen species) were simply the ‘bad boys of biology’ is clearly over. High levels of ROS are still rightfully considered to be toxic to many cellular processes and, as such, contribute to disease conditions and cell death. However, the high toxicity of ROS is also extremely beneficial, particularly as it is used to kill invading micro-organisms during mammalian host defence. Moreover, a transient, often more localized, increase in ROS levels appears to play a major role in signal transduction processes and positively affects cell growth, development and differentiation. At the heart of all these processes are redox-regulated proteins, which use oxidation-sensitive cysteine residues to control their function and by extension the function of the pathways that they are part of. Our work has contributed to changing the view about ROS through: (i) our characterization of Hsp33 (heat-shock protein 33), one of the first redox-regulated proteins identified, whose function is specifically activated by ROS, (ii) the development of quantitative tools that reveal extensive redox-sensitive processes in bacteria and eukaryotes, and (iii) the discovery of a link between early exposure to oxidants and aging. Our future research programme aims to generate an integrated and system-wide view of the beneficial and deleterious effects of ROS with the central goal to develop more effective antioxidant strategies and more powerful antimicrobial agents.
Understanding life and death decisions in human leukaemias
Authors: MacEwan David J. , Barrera Lawrence N. , Keadsanti Sujitra , Rushworth Stuart A. , Shah Niraj M. , Yuan Tianma , Zaitseva Lyubov
Published: August 2014

Human leukaemia cells have an often unique ability to either undergo apoptotic cell death mechanisms or, at other times, undergo proliferative expansion, sometimes to the same stimulus such as the pluripotent cytokine TNFα (tumour necrosis factor α). This potential for life/death switching helps us to understand the molecular signalling machinery that underlies these cellular processes. Furthermore, looking at the involvement of these switching signalling pathways that may be aberrant in leukaemia informs us of their importance in cancer tumorigenesis and how they may be targeted pharmacologically to treat various types of human leukaemias. Furthermore, these important pathways may play a crucial role in acquired chemotherapy resistance and should be studied further to overcome in the clinic many drug-resistant forms of blood cancers. In the present article, we uncover the relationship that exists in human leukaemia life/death switching between the anti-apoptotic pro-inflammatory transcription factor NF-κB (nuclear factor κB) and the cytoprotective antioxidant-responsive transcription factor Nrf2 (nuclear factor-erythroid 2-related factor 2). We also discuss recent findings that reveal a major role for Btk (Bruton's tyrosine kinase) in both lymphocytic and myeloid forms of human leukaemias and lymphomas.
Vertebrate pheromones and other semiochemicals: the potential for accommodating complexity in signalling by volatile compounds for vertebrate management
Authors: Pickett John A. , Barasa Stephen , Birkett Michael A.
Published: August 2014

The interaction between volatile and non-volatile, e.g. proteinaceous, components of pheromone and other semiochemical-based signalling systems presents a daunting set of problems for exploitation in the management of vertebrates, good or bad. Aggravating this is the complexity of the mixtures involved with pheromones, not only by definition associated with each species, but also with individual members of that species and their positions within their immediate communities. Nonetheless, already in some contexts, particularly where signals are perceived at other trophic levels from those of the vertebrates, e.g. by arthropods, reductionist approaches can be applied whereby the integrity of complex volatile mixtures is maintained, but perturbed by augmentation with individual components. In the present article, this is illustrated for cattle husbandry, fish farming and human health. So far, crude formulations have been used to imitate volatile semiochemical interactions with non-volatile components, but new approaches must be developed to accommodate more sophisticated interactions and not least the activities of the non-volatile, particularly proteinaceous components, currently being deduced.
Protein acetylation as a means to regulate protein function in tune with metabolic state
Authors: Shi Lei , Tu Benjamin P.
Published: August 2014

Protein acetylation has emerged as a prominent post-translational modification that can occur on a wide variety of proteins. The metabolite acetyl-CoA is a key intermediate in energy metabolism that also serves as the acetyl group donor in protein acetylation modifications. Therefore such acetylation modifications might be coupled to the intracellular availability of acetyl-CoA. In the present article, we summarize recent evidence suggesting that the particular protein acetylation modifications enable the regulation of protein function in tune with acetyl-CoA availability and thus the metabolic state of the cell.
Regulation of miRNA strand selection: follow the leader?
Authors: Meijer Hedda A. , Smith Ewan M. , Bushell Martin
Published: August 2014

miRNA strand selection is the process that determines which of the two strands in a miRNA duplex becomes the active strand that is incorporated into the RISC (RNA-induced silencing complex) (named the guide strand, leading strand or miR) and which one gets degraded (the passenger strand or miR*). Thermodynamic features of the duplex appear to play an important role in this decision; the strand with the weakest binding at its 5′-end is more likely to become the guide strand. Other key characteristics of human miRNA guide strands are a U-bias at the 5′-end and an excess of purines, whereas the passenger strands have a C-bias at the 5′-end and an excess of pyrimidines. Several proteins are known to play a role in strand selection [Ago (Argonaute), DICER, TRBP (trans-activation response RNA-binding protein), PACT (protein activator of dsRNA-dependent protein kinase) and Xrn-1/2]; however, the mechanisms by which these proteins act are largely unknown. For several miRNAs the miR/miR* ratio varies dependent on cell type, developmental stage and in different disease states, suggesting that strand selection is a tightly controlled process. The present review discusses our current knowledge regarding the factors and processes involved in strand selection and the many questions that still remain.
Signalling functions of coenzyme A and its derivatives in mammalian cells
Authors: Davaapil Hongorzul , Tsuchiya Yugo , Gout Ivan
Published: August 2014

In all living organisms, CoA (coenzyme A) is synthesized in a highly conserved process that requires pantothenic acid (vitamin B5), cysteine and ATP. CoA is uniquely designed to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. The role of CoA and its thioester derivatives, including acetyl-CoA, malonyl-CoA and HMG-CoA (3-hydroxy-3-methylglutaryl-CoA), in the regulation of cellular metabolism has been extensively studied and documented. The main purpose of the present review is to summarize current knowledge on extracellular and intracellular signalling functions of CoA/CoA thioesters and to speculate on future developments in this area of research.
Conflict RNA modification, host–parasite co-evolution, and the origins of DNA and DNA-binding proteins
Authors: McLaughlin Paul J. , Keegan Liam P.
Published: August 2014

Nearly 150 different enzymatically modified forms of the four canonical residues in RNA have been identified. For instance, enzymes of the ADAR (adenosine deaminase acting on RNA) family convert adenosine residues into inosine in cellular dsRNAs. Recent findings show that DNA endonuclease V enzymes have undergone an evolutionary transition from cleaving 3′ to deoxyinosine in DNA and ssDNA to cleaving 3′ to inosine in dsRNA and ssRNA in humans. Recent work on dsRNA-binding domains of ADARs and other proteins also shows that a degree of sequence specificity is achieved by direct readout in the minor groove. However, the level of sequence specificity observed is much less than that of DNA major groove-binding helix–turn–helix proteins. We suggest that the evolution of DNA-binding proteins following the RNA to DNA genome transition represents the major advantage that DNA genomes have over RNA genomes. We propose that a hypothetical RNA modification, a RRAR (ribose reductase acting on genomic dsRNA) produced the first stretches of DNA in RNA genomes. We discuss why this is the most satisfactory explanation for the origin of DNA. The evolution of this RNA modification and later steps to DNA genomes are likely to have been driven by cellular genome co-evolution with viruses and intragenomic parasites. RNA modifications continue to be involved in host–virus conflicts; in vertebrates, edited cellular dsRNAs with inosine–uracil base pairs appear to be recognized as self RNA and to suppress activation of innate immune sensors that detect viral dsRNA.
Thioredoxin as a putative biomarker and candidate target in age-related immune decline
Authors: Griffiths Helen R. , Bennett Stuart J. , Olofsson Peter , Dunston Christopher R.
Published: August 2014

The oxidoreductase Trx-1 (thioredoxin 1) is highly conserved and found intra- and extra-cellularly in mammalian systems. There is increasing interest in its capacity to regulate immune function based on observations of altered distribution and expression during ageing and disease. We have investigated previously whether extracellular T-cell or peripheral blood mononuclear cell Trx-1 levels serve as a robust marker of ageing. In a preliminary study of healthy older adults compared with younger adults, we showed that there was a significant, but weak, relationship with age. Interestingly, patients with rheumatoid arthritis and cancer have been described by others to secrete or express greater surface Trx-1 than predicted. It is interesting to speculate whether a decline in Trx-1 during ageing protects against such conditions, but correspondingly increases risk of disease associated with Trx-1 depletion such as cardiovascular disease. These hypotheses are being explored in the MARK-AGE study, and preliminary findings confirm an inverse correlation of surface Trx-1 with age. We review recent concepts around the role of Trx-1 and its partners in T-cell function on the cell surface and as an extracellular regulator of redox state in a secreted form. Further studies on the redox state and binding partners of surface and secreted Trx-1 in larger patient datasets are needed to improve our understanding of why Trx-1 is important for lifespan and immune function.
The multifacet graphically contracted function method. I. Formulation and implementation
Authors: Shepard Ron , Gidofalvi Gergely , Brozell Scott R.
Published: August 2014

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that both the energy and the gradient computation scale as O(N2n4) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N2 dissociation, cubic H8 dissociation, the symmetric dissociation of H2O, and the insertion of Be into H2. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.
The multifacet graphically contracted function method. II. A general procedure for the parameterization of orthogonal matrices and its application to arc factors
Authors: Shepard Ron , Gidofalvi Gergely , Brozell Scott R.
Published: August 2014

Practical algorithms are presented for the parameterization of orthogonal matrices Q ∈ $\mathbb{R}$R m×n in terms of the minimal number of essential parameters {φ}. Both square n = m and rectangular n < m situations are examined. Two separate kinds of parameterizations are considered, one in which the individual columns of Q are distinct, and the other in which only Span(Q) is significant. The latter is relevant to chemical applications such as the representation of the arc factors in the multifacet graphically contracted function method and the representation of orbital coefficients in SCF and DFT methods. The parameterizations are represented formally using products of elementary Householder reflector matrices. Standard mathematical libraries, such as LAPACK, may be used to perform the basic low-level factorization, reduction, and other algebraic operations. Some care must be taken with the choice of phase factors in order to ensure stability and continuity. The transformation of gradient arrays between the Q and {φ} parameterizations is also considered. Operation counts for all factorizations and transformations are determined. Numerical results are presented which demonstrate the robustness, stability, and accuracy of these algorithms.
Comparison of double-quantum NMR normalization schemes to measure homonuclear dipole-dipole interactions
Authors: Saalwächter Kay
Published: August 2014

A recent implementation of a double-quantum (DQ) recoupling solid-state NMR experiment, dubbed DQ-DRENAR, provides a quantitative measure of homonuclear dipole-dipole coupling constants in multispin-1/2 systems. It was claimed to be more robust than another, previously known experiment relying on the recording of point-by-point normalized DQ build-up curves. Focusing on the POST-C7 and BaBa-xy16 DQ pulse sequences, I here present an in-depth comparison of both approaches based upon spin-dynamics simulations, stressing that they are based upon very similar principles and that they are largely equivalent when no imperfections are present. With imperfections, it is found that DQ-DRENAR/POST-C7 does not fully compensate for additional signal dephasing related to chemical shifts (CS) and their anisotropy (CSA), which over-compensates the intrinsic CS(A)-related efficiency loss of the DQ Hamiltonian and leads to an apparent cancellation effect. The simulations further show that the CS(A)-related dephasing in DQ-DRENAR can be removed by another phase cycle step or an improved super-cycled wideband version. Only the latter, or the normalized DQ build-up, are unaffected by CS(A)-related signal loss and yield clean pure dipolar-coupling information subject to unavoidable, pulse sequence specific performance reduction related to higher-order corrections of the dipolar DQ Hamiltonian. The intrinsically super-cycled BaBa-xy16 is shown to exhibit virtually no CS(A) related imperfection terms, but its dipolar performance is somewhat more challenged by CS(A) effects than POST-C7, which can however be compensated when applied at very fast MAS (>50 kHz). Practically, DQ-DRENAR uses a clever phase cycle separation to achieve a significantly shorter experimental time, which can also be beneficially employed in normalized DQ build-up experiments.
Fundamental measure theory for smectic phases: Scaling behavior and higher order terms
Authors: Wittmann René , Marechal Matthieu , Mecke Klaus
Published: August 2014

The recent extension of Rosenfeld's fundamental measure theory to anisotropic hard particles predicts nematic order of rod-like particles. Our analytic study of different aligned shapes provides new insights into the structure of this density functional, which is basically founded on experience with hard spheres. We combine scaling arguments with dimensional crossover and motivate a modified expression, which enables an appropriate description of smectic layering. We calculate the nematic–smectic-A transition of monodisperse hard spherocylinders with and without orientational degrees of freedom and present the equation of state and phase diagram including these two liquid crystalline phases in good agreement with simulations. We also find improved results related to the isotropic–nematic interface. We discuss the quality of empirical corrections and the convergence towards an exact second virial coefficient, including higher order terms.
Microelectromechanical magnetic field sensor based on ΔE effect
Authors: Jahns R. , Zabel S. , Marauska S. , Gojdka B. , Wagner B. , Knöchel R. , Adelung R. , Faupel F.
Published: August 2014

We present a fully integrated microelectromechanical magnetic field sensor based on the ΔE effect. The vacuum encapsulated sensor extends our previous approach [B. Gojdka et al., Appl. Phys. Lett. 99, 223502 (2011); Nature 480, 155 (2011)] and now involves an intermediate piezoelectric AlN layer between a SiO2 cantilever and a magnetostrictive FeCoBSi top layer. The AlN layer serves two functions: It drives the resonator, and it is used for electrical read out. The limit of detection was strongly enhanced to 12 nT/Hz at 10 Hz.
Note: Absolute detection efficiency of a tapered microchannel plate for Ne+ ions
Authors: Matoba S. , Ishikawa G. , Moriya S. , Takahashi K. , Koizumi T. , Shiromaru H.
Published: August 2014

The absolute detection efficiency of a tapered microchannel plate with an open-area ratio of 90% was measured for Ne+ with energies up to 5 keV, and comparison with the results for Xe+ was made. As in the case of Xe+, the maximum detection efficiency was 90%. The energy dependence of the efficiency curves normalized with respect to the open-area ratios was examined based on the scaling law proposed previously.
Rectification control points selection method of triangle mesh in optical pressure measurement of wind-tunnel test
Authors: Chen Yong , Chen Chang
Published: August 2014

In optical pressure measurement of wind-tunnel test, triangle mesh is usually built to rectify the images that are distorted in geometry. In this paper, a novel method of control points selection of triangle mesh is proposed by combining the artificial points and margin control points. For the problem that in the condition of wind the margin control point is difficult to extract due to model distortion and grey variation, an improved Smallest Univalue Segment Assimilating Nucleus algorithm based on region selection and adaptive threshold is designed. The connection method is employed to verify the availability of points, which avoids that the noisy points are mistakenly regarded as the angular points. The distorted images of aircraft model are rectified and the results are analyzed. Experiments demonstrate that the proposed method greatly improves the rectification effect.
Designing of the massive gas injection valve for the joint Texas experimental tokamak
Authors: Luo Y. H. , Chen Z. Y. , Tang Y. , Wang S. Y. , Ba W. G. , Wei Y. N. , Ma T. K. , Huang D. W. , Tong R. H. , Yan W. , Geng P. , Shao J. , Zhuang G.
Published: August 2014

In order to mitigate the negative effects of the plasma disruption a massive gas injection (MGI) valve is designed for the joint Texas experimental tokamak. The MGI valve is based on the eddy-current repulsion mechanism. It has a fueling volume of 30 ml. The piston of the MGI valve is made by non-ferromagnetic material, so it can be installed close to the vacuum vessel which has a strong toroidal magnetic field. A diode is use to prevent current oscillation in the discharge circuit. The drive coil of the valve is installed outside the gas chamber. The opening characteristics and the gas flow of the MGI valve have been tested by a 60 l vacuum chamber. Owing to the large electromagnetic force the reaction time of the valve is shorter than 0.3 ms. Duration for the opening of the MGI valve is in the order of 10 ms.
Ultrafast electrical control of a resonantly driven single photon source
Authors: Cao Y. , Bennett A. J. , Ellis D. J. P. , Farrer I. , Ritchie D. A. , Shields A. J.
Published: August 2014

We demonstrate generation of a pulsed stream of electrically triggered single photons in resonance fluorescence, by applying high frequency electrical pulses to a single quantum dot in a p-i-n diode under resonant laser excitation. Single photon emission was verified, with the probability of multiple photon emission reduced to 2.8%. We show that despite the presence of charge noise in the emission spectrum of the dot, resonant excitation acts as a “filter” to generate narrow bandwidth photons.
The effect of generalized uncertainty principle on square well, a case study
Authors: Ma Meng-Sen , Zhao Ren
Published: August 2014

According to a special case (β = 0) of the generalized uncertainty relation we derive the energy eigenvalues of the infinite potential well. It is shown that the obtained energy levels are different from the usual result with some correction terms. And the correction terms of the energy eigenvalues are independent of other parameters except α. But the eigenstates will depend on another two parameters besides α.
Large anomalous Hall effect in ferromagnetic insulator-topological insulator heterostructures
Authors: Alegria L. D. , Ji H. , Yao N. , Clarke J. J. , Cava R. J. , Petta J. R.
Published: August 2014

We demonstrate the van der Waals epitaxy of the topological insulator compound Bi2Te3 on the ferromagnetic insulator Cr2Ge2Te6. The layers are oriented with (001)Bi2Te3||(001)Cr2Ge2Te6 and (110)Bi2Te3||(100)Cr2Ge2Te6. Cross-sectional transmission electron microscopy indicates the formation of a sharp interface. At low temperatures, bilayers consisting of Bi2Te3 on Cr2Ge2Te6 exhibit a large anomalous Hall effect (AHE). Tilted field studies of the AHE indicate that the easy axis lies along the c-axis of the heterostructure, consistent with magnetization measurements in bulk Cr2Ge2Te6. The 61 K Curie temperature of Cr2Ge2Te6 and the use of near-stoichiometric materials may lead to the development of spintronic devices based on the AHE.