N-player quantum games in an EPR setting

The N-player quantum games are analyzed that use an Einstein-Podolsky-Rosen (EPR) experiment, as the underlying physical setup. In this setup, a player's strategies are not unitary transformations as in alternate quantum game-theoretic frameworks, but a classical choice between two directions along which spin or polarization measurements are made. The players' strategies thus remain identical to their strategies in the mixed-strategy version of the classical game. In the EPR setting the quantum game reduces itself to the corresponding classical game when the shared quantum state reaches zero entanglement. We find the relations for the probability distribution for N-qubit GHZ and W-type states, subject to general measurement directions, from which the expressions for the players' payoffs and mixed Nash equilibrium are determined. Players' N x N payoff matrices are then defined using linear functions so that common two-player games can be easily extended to the N-player case and permit analytic expressions for the Nash equilibrium. As a specific example, we solve the Prisoners' Dilemma game for general N ≥ 2. We find a new property for the game that for an even number of players the payoffs at the Nash equilibrium are equal, whereas for an odd number of players the cooperating players receive higher payoffs. By dispensing with the standard unitary transformations on state vectors in Hilbert space and using instead rotors and multivectors, based on Clifford's geometric algebra (GA), it is shown how the N-player case becomes tractable. The new mathematical approach presented here has wide implications in the areas of quantum information and quantum complexity, as it opens up a powerful way to tractably analyze N-partite qubit interactions.     

Analyzing three-player quantum games in an EPR type setup

We use the formalism of Clifford Geometric Algebra (GA) to develop an analysis of quantum versions of three-player non-cooperative games. The quantum games we explore are played in an Einstein-Podolsky-Rosen (EPR) type setting. In this setting, the players' strategy sets remain identical to the ones in the mixed-strategy version of the classical game that is obtained as a proper subset of the corresponding quantum game. Using GA we investigate the outcome of a realization of the game by players sharing GHZ state, W state, and a mixture of GHZ and W states. As a specific example, we study the game of three-player Prisoners' Dilemma.     

Predicting the timing and duration of sleep in an operational setting using social factors

In recent years, there has been increasing interest in the use of bio-mathematical models to predict alertness, performance, and/or fatigue in operational settings. Current models use only biological factors to make their estimations, which can be limited in operational settings where social and geo-physical factors also dictate when sleep occurs. The interaction between social and biological factors that help determine the timing and duration of sleep during layover periods have been investigated in order to create and initially validate a mathematical model that may better predict sleep in the field. Participants were 32 male transmeridian airline pilots (17 captains, 10 first officers, and 5 second officers) flying the Sydney-Bangkok-London-Singapore-Sydney (SYD-LHR) pattern. Participants continued their regular schedule while wearing activity monitors and completing sleep and work diaries. The theoretical sleep timing model underpinning this analysis consists of separate formulations for short (<32 h) and long (>32 h) break periods. Longer break periods are split into three distinct phases-recovery (break start until first local night), personal (first local night until last local night), and preparation phases (last local night until break end)-in order to exploit potential differences specific to each. Furthermore, an iterative procedure combining prediction and retrodiction (i.e., using future duty timing information to predict current sleep timing) was developed to optimize predictive ability. Analysis found an interaction between the social and circadian sleep pressures that changed over the break period. Correlation analysis indicated a strong relationship between the actual sleep and new model's predictions (r = 0.7-0.9), a significant improvement when compared to existing models (r = 0.1-0.4). Social and circadian pressures play important roles in regulating sleep for international flight crews. An initial model has been developed in order to regulate sleep in these crews. The initial results have shown promise when applied to small sets of data; however, more rigorous validation must be carried out.     

Detailed methods for the quantification of nitric oxide in aqueous solutions using either an oxygen monitor or EPR

The interest in nitric oxide has grown with the discovery that it has many biological functions. This has heightened the need for methods to quantify nitric oxide. Here we report two separate methods for the quantification of aqueous stock solutions of nitric oxide. The first is a new method based on the reaction of nitric oxide with oxygen in liquid phase (*NO + O2 + 2H2O --> 4HNO2); an oxygen monitor is used to measure the consumption of oxygen by nitric oxide. This method offers the advantages of being both simple and direct. The presence of nitrite or nitrate, frequent contaminants in nitric oxide stock solutions, does not interfere with the quantification of nitric oxide. Measuring the disappearance of dissolved oxygen, a reactant, in the presence of known amounts of nitric oxide has provided verification of the 4:1 stoichiometry of the reaction. The second method uses electron paramagnetic resonance spectroscopy (EPR) and the nitric oxide trap [Fe2+-(MGD)2], (MGD = N-methyl-D-glucamine dithiocarbamate). The nitrosyl complex is stable and easily quantitated as a room temperature aqueous solution. These two methods are validated with Sievers 280 Nitric Oxide Analyzer and cross-checked with standards using UV-Vis spectroscopy. The practical lower limits for measuring the concentration of nitric oxide using the oxygen monitor approach and EPR are approximately 3 microM and 500 nM, respectively. Both methods provide straightforward approaches for the standardization of nitric oxide in solution.     

Characterization of heterogeneous immobilized enzyme subpopulations using EPR spectroscopy

Direct evidence was obtained for the existence of two distinct forms of active alpha-chymotrypsin immobilized on CNBr-activated Sepharose 4B. Electron paramagnetic resonance (EPR) spectra of five different spin-labeled immobilized enzyme formulations in the presence of indole were all resolved into the same two spectral components. Both subpopulation spectra were approximately identified experimentally, and the subpopulation exhibiting greatly restricted spin-label motion was shown also to be relatively inaccessible to solvent. Using overall specific activity data and subpopulation fractions from EPR spectral analysis, the specific activity of the more constricted immobilized enzyme active form was shown to be approximately 15 times smaller than that of the other class of immobilized enzyme molecules with an indole EPR spectrum similar to that of chymotrypsin in solution. Variations in overall specific activity of formulations with different loadings and different supports results entirely from changes in the proportions of the same two subpopulations of immobilized enzyme molecules.     

An institutional mechanism for assortment in an ecology of games

Recent research has revived Long's "ecology of games" model to analyze how social actors cooperate in the context of multiple political and social games. However, there is still a paucity of theoretical work that considers the mechanisms by which large-scale cooperation can be promoted in a dynamic institutional landscape, in which actors can join new games and leave old ones. This paper develops an agent-based model of an ecology of games where agents participate in multiple public goods games. In addition to contribution decisions, the agents can leave and join different games, and these processes are de-coupled. We show that the payoff for cooperation is greater than for defection when limits to the number of actors per game ("capacity constraints") structure the population in ways that allow cooperators to cluster, independent of any complex individual-level mechanisms such as reputation or punishment. Our model suggests that capacity constraints are one effective mechanism for producing positive assortment and increasing cooperation in an ecology of games. The results suggest an important trade-off between the inclusiveness of policy processes and cooperation: Fully inclusive policy processes reduce the chances of cooperation.     

Detection and characterisation of radicals in biological materials using EPR methodology

Background

Electron paramagnetic resonance (EPR) spectroscopy (also known as electron spin resonance, ESR, spectroscopy) is widely considered to be the “gold standard” for the detection and characterisation of radicals in biological systems.

Scope of review

The article reviews the major positive and negative aspects of EPR spectroscopy and discusses how this technique and associated methodologies can be used to maximise useful information, and minimise artefacts, when used in biological studies. Consideration is given to the direct detection of radicals (at both ambient and low temperature), the use of spin trapping and spin scavenging (e.g. reaction with hydroxylamines), the detection of nitric oxide and the detection and quantification of some transition metal ions (particularly iron and copper) and their environment.

Major conclusions

When used with care this technique can provide a wealth of valuable information on the presence of radicals and some transition metal ions in biological systems. It can provide definitive information on the identity of the species present and also information on their concentration, structure, mobility and interactions. It is however a technique that has major limitations and the user needs to understand the various pitfalls and shortcoming of the method to avoid making errors.

General significance

EPR remains the most definitive method of identifying radicals in complex systems and is also a valuable method of examining radical kinetics, concentrations and structure. This article is part of a Special Issue entitled Current methods to study reactive oxygen species — pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.     

Dispelling dog dogma: an investigation of heterochrony in dogs using 3D geometric morphometric analysis of skull shape

Heterochrony is an evolutionary mechanism that generates diversity via perturbations of the rate or timing of development that requires very little genetic innovation. As such, heterochrony is thought to be a common evolutionary mechanism in the generation of diversity. Previous research has suggested that dogs evolved via heterochrony and are paedomorphic wolves. This study uses three-dimensional landmark-based coordinate data to investigate heterochronic patterns within the skull morphology of the domestic dog. A total of 677 adult dogs representing 106 different breeds were measured and compared with an ontogenetic series of 401 wolves. Geometric morphometric analysis reveals that the cranial shape of none of the modern breeds of dogs resembles the cranial shapes of adult or juvenile wolves. In addition, investigations of regional heterochrony in the face and neurocranium also reject the hypothesis of heterochrony. Throughout wolf cranial development the position of the face and the neurocranium remain in the same plane. Dogs, however, have a de novo cranial flexion in which the palate is tilted dorsally in brachycephalic and mesaticephalic breeds or tilted ventrally in dolichocephalic and down-face breeds. Dogs have evolved very rapidly into an incredibly morphologically diverse species with very little genetic variation. However, the genetic alterations to dog cranial development that have produced this vast range of phylogenetically novel skull shapes do not coincide with the expectations of the heterochronic model. Dogs are not paedomorphic wolves.     

Secular changes in craniofacial morphology of the Portuguese using geometric morphometrics

This study examines patterns of secular change in cranial morphology in the New Lisbon collection, a documented skeletal collection from Lisbon, Portugal with birth years from 1806 to 1954. This period represents a time when Lisbon was undergoing increased urbanization and population growth, as well as changes in mortality and fertility patterns. Previous studies from the U.S., Europe, and Japan have reported significant secular changes in cranial morphology over the past 200 years. In the current study, secular changes were analyzed using three-dimensional geometric morphometrics methods. The results from this study demonstrate a significant change in cranial morphology over the roughly 150-year period. Allometry was rejected as a causal factor of this change because there was no association found between temporal change and size. The pattern of temporal change is similar to that observed in other populations in the U.S., Europe, and Japan, including decreased facial breadth and a more inferiorly placed cranial base. This study, along with previous research, suggests a similar pattern of change occurs in genetically and geographically diverse populations experiencing modern environmental conditions. We argue that because the secular changes are focused in the cranial base, a region of the skull that experiences a relatively early growth curve, changes related to declines in childhood morbidity and mortality are likely important factors related to the observed changes.     

Quantitative genetic variation in an ecological setting

The machinery was developed to investigate the behavior of quantitative genetic variation in an ecological model of a finite number of islands of finite size, with migration rate m and extinction rate e, for a quantitative genetic model general for numbers of alleles and loci and additive, dominance, and additive by additive epistatic effects. It was necessary to reckon with seven quadratic genetic components, whose coefficients in the genotypic variance components within demes, sigma Gw2, between demes within populations, sigma s2, and between replicate populations, sigma r2, are given by descent measures. The descent measures at any time are calculated with the use of transition equations which are determined by the parameters of the ecological model. Numerical results were obtained for the coefficients of the quadratic genetic components in each of the three genotypic variance components in the early phase of differentiation. The general effect of extinction is to speed up the time course leading to fixation, to increase sigma r2, and to decrease sigma s2 (with a few exceptions) in comparison with no extinction. The general effect of migration is to slow down the time course leading to fixation, to increase sigma Gw2, at least in the later generations, and to decrease sigma s2 (with a few exceptions) in comparison with no migration. Except for these, the effects of migration and extinction on the variance components are complex, depending on the genetic model, and sometimes involve interaction of migration and extinction. Sufficient details are given for an investigator to evaluate numerically the results for variations in the quantitative genetic and ecological models.     

The spread of Mycoplasma pneumoniae is polyclonal in both an endemic setting in France and in an epidemic setting in Israel

Mycoplasma pneumoniae infections occur both endemically and epidemically, and macrolide resistance has been spreading for 10 years worldwide. A substantial increased incidence of M. pneumoniae infections has been reported in several countries since 2010. Whether this increased incidence is attributed to different or to the same M. pneumoniae genotype is unknown. We have developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for the molecular typing of M. pneumoniae isolates. In this study, the MLVA typing method was modified and validated to be applicable directly to respiratory tract specimens without culture. This method was applied to 34 M. pneumoniae-positive specimens received at the Bordeaux Hospital, France, between 2007 and 2010 in an endemic setting, and to 63 M. pneumoniae-positive specimens collected during an epidemic surge of M. pneumoniae infections in 2010 in Jerusalem, Israel. The M. pneumoniae endemic spread was shown to be polyclonal in France, with 15 MLVA types identified. Strikingly, the Israeli epidemic surge was also a multi-clonal phenomenon, with 18 circulating MLVA types. The macrolide resistance-associated substitution, A2058G, was found in 22% of the Israeli patients. Macrolide-resistant M. pneumoniae belonged to four MLVA types, the MLVA type Z being the most frequent one. An association between the MLVA type Z and macrolide resistance might exist since macrolide resistance was present or generated during the course of illness in all patients infected with this MLVA type. In conclusion, the discriminatory power of the MLVA showed that the spread of M. pneumoniae strains in France in an endemic setting was polyclonal as well as the surge of M. pneumoniae infections in Israel in 2010.     

High photoluminescence quantum yield of TiO2 nanocrystals prepared using an alcohothermal method.

Highly dispersible TiO2 nanocrystals (approximately 6 nm) were prepared by an alcohothermal method. A strong and stable photoluminescence emission with a maximum at 450 nm was observed in the original TiO2 nanocrystals colloid. Compared with the emission from quinine sulphate in 0.05 mol/L sulphuric acid, the emission quantum yield of TiO2 nanocrystals was determined to be about 0.20, which was much higher than the values (0.002 and 0.001) reported in previous studies. The fluorescence micrograph of TiO2 nanocrystals encapsulated in lipsomes shows that TiO2 nanocrystals prepared in such a way have potential application as a fluorescence probe in biological imaging. Research on the luminescence mechanism indicates that the surface state and extent of crystallization of the TiO2 nanocrystals are crucial factors in the high photoluminescence quantum yield obtained in this study.     

In vivo measurement of tumor redox environment using EPR spectroscopy

Solid tumors are characterized by a number of physiological properties such as occurrence of significant hypoxia, large amounts of cellular reducing equivalents, compromised blood-flow and low pH, all of which are distinctly different from normal tissues. Tumor therapeutic regimens such as radiation or chemotherapy attempt to exploit these physiological differences between normal and malignant tissue. Thus, methods that can detect these subtle differences would greatly aid in devising appropriate treatment strategies. Low-frequency in vivo electron paramagnetic resonance (EPR) spectroscopy is capable of providing non-invasive measurements of these parameters in tumors. This requires the use of appropriate exogenously injected free radical reporter molecules (probes), such as nitroxides. In the present study we performed measurements of nitroxide metabolism in RIF-1 murine tumors, in vivo, and demonstrated that the rate of nitroxide decay correlated with the tumor redox environment. The results showed the existence of significantly higher reducing environment in the tumor tissue compared to normal tissue. The dependence of the tumor redox status on the intracellular GSH levels and tissue oxygenation was investigated. The measurement of redox status and its manipulation may have important implications in the understanding of tumor growth and therapy.     

In vivo measurement of tumor redox environment using EPR spectroscopy

Solid tumors are characterized by a number of physiological properties such as occurrence of significant hypoxia, large amounts of cellular reducing equivalents, compromised blood-flow and low pH, all of which are distinctly different from normal tissues. Tumor therapeutic regimens such as radiation or chemotherapy attempt to exploit these physiological differences between normal and malignant tissue. Thus, methods that can detect these subtle differences would greatly aid in devising appropriate treatment strategies. Low-frequency in vivo electron paramagnetic resonance (EPR) spectroscopy is capable of providing non-invasive measurements of these parameters in tumors. This requires the use of appropriate exogenously injected free radical reporter molecules (probes), such as nitroxides. In the present study we performed measurements of nitroxide metabolism in RIF-1 murine tumors, in vivo, and demonstrated that the rate of nitroxide decay correlated with the tumor redox environment. The results showed the existence of significantly higher reducing environment in the tumor tissue compared to normal tissue. The dependence of the tumor redox status on the intracellular GSH levels and tissue oxygenation was investigated. The measurement of redox status and its manipulation may have important implications in the understanding of tumor growth and therapy.     

EPR detection of cellular and mitochondrial superoxide using cyclic hydroxylamines

Superoxide (O???) has been implicated in the pathogenesis of many human diseases, but detection of the O(2)(?-) radicals in biological systems is limited due to inefficiency of O??? spin trapping and lack of site-specific information. This work studied production of extracellular, intracellular and mitochondrial O??? in neutrophils, cultured endothelial cells and isolated mitochondria using a new set of cationic, anionic and neutral hydroxylamine spin probes with various lipophilicity and cell permeability. Cyclic hydroxylamines rapidly react with O???, producing stable nitroxides and allowing site-specific cO??? detection in intracellular, extracellular and mitochondrial compartments. Negatively charged 1-hydroxy-4-phosphono-oxy-2,2,6,6-tetramethylpiperidine (PP-H) and positively charged 1-hydroxy-2,2,6,6-tetramethylpiperidin-4-yl-trimethylammonium (CAT1-H) detected only extramitochondrial O???. Inhibition of EPR signal by SOD2 over-expression showed that mitochondria targeted mitoTEMPO-H detected intramitochondrial O??? both in isolated mitochondria and intact cells. Both 1-hydroxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine (CP-H) and 1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine (CM-H) detected an increase in cytoplasm O??? stimulated by PMA, but only CM-H and mitoTEMPO-H showed an increase in rotenone-induced mitochondrial O???. These data show that a new set of hydroxylamine spin probes provide unique information about site-specific production of the O??? radical in extracellular or intracellular compartments, cytoplasm or mitochondria.     

Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching

A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three-dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub-graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all-against-all comparison of phosphate binding sites in a number of different nucleotide phosphate-binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding and Rossman-like fold] and FAD-binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods.