Human emotion in the brain and the body: Why language matters. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Herbert, Cornelia

2015-06-01

What is an Emotion? This question has fascinated scientific research since William James. Despite the fact that a consensus has been reached about the biological origin of emotions, uniquely human aspects of emotions are still poorly understood. One of these blind spots concerns the relationship between emotion and human language. Historically, many theories imply a duality between emotions on the one hand and cognitive functions such as language on the other hand. Especially for symbolic forms of written language and word processing, it has been assumed that semantic information would bear no relation to bodily, affective, or sensorimotor processing (for an overview see Ref. [1]). The Quartet Theory proposed by Koelsch and colleagues [2] could provide a solution to this problem. It offers a novel, integrative neurofunctional model of human emotions which considers language and emotion as closely related. Crucially, language - be it spoken or written - is assumed to "regulate, modulate, and partly initiate" activity in core affective brain systems in accord with physical needs and individual concerns [cf. page 34, line 995]. In this regard, the Quartet Theory combines assumptions from earlier bioinformational theories of emotions [3], contemporary theories of embodied cognition [4], and appraisal theories such as the Component Process Model [5] into one framework, thereby providing a holistic model for the neuroscientific investigation of human emotion processing at the interface of emotion and cognition, mind and body.

The quartet theory: Implications for autism spectrum disorder. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Pehrs, Corinna; Samson, Andrea C.; Gross, James J.

2015-06-01

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by social and communication deficits as well as restricted and repetitive behaviors [1]. Specific deficits include failure to initiate reciprocal social interactions, verbal and non-verbal communication difficulties, decreased sensitivity to social and emotional cues, and limited perspective-taking abilities. Social withdrawal, avoidance or indifference to affection or physical contact, lack of eye contact, and decreased joint attention and facial responsiveness are also common [2]. In addition to these core features, there is a growing body of literature that describes problematic patterns of emotional reactivity (increased negative and decreased positive emotions) and emotion regulation (increased use of maladaptive and decreased use of adaptive emotion regulation strategies) [3-5]. The present comment seeks to link difficulties in socio-emotional domains to the Quartet Theory of Human Emotions by mapping characteristic ASD social deficits and emotion dysregulation onto two of the affect systems described in this theory: the hippocampal and orbitofrontal-centered systems.

The Origin of Floral Organ Identity Quartets

PubMed Central

van Mourik, Hilda; Kaufmann, Kerstin

2017-01-01

The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive, and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting of phylogenetically related MADS domain proteins. Using ancestral MADS domain protein reconstruction, we trace the evolution of organ identity quartets along the stem lineage of crown angiosperms. We provide evidence that current floral quartets specifying male organ identity, which consist of four types of subunits, evolved from ancestral complexes of two types of subunits through gene duplication and integration of SEPALLATA proteins just before the origin of flowering plants. Our results suggest that protein interaction changes underlying this compositional shift were the result of a gradual and reversible evolutionary trajectory. Modeling shows that such compositional changes may have facilitated the evolution of the perfect, bisexual flower. PMID:28100708

The Origin of Floral Organ Identity Quartets.

PubMed

Ruelens, Philip; Zhang, Zhicheng; van Mourik, Hilda; Maere, Steven; Kaufmann, Kerstin; Geuten, Koen

2017-02-01

The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive, and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting of phylogenetically related MADS domain proteins. Using ancestral MADS domain protein reconstruction, we trace the evolution of organ identity quartets along the stem lineage of crown angiosperms. We provide evidence that current floral quartets specifying male organ identity, which consist of four types of subunits, evolved from ancestral complexes of two types of subunits through gene duplication and integration of SEPALLATA proteins just before the origin of flowering plants. Our results suggest that protein interaction changes underlying this compositional shift were the result of a gradual and reversible evolutionary trajectory. Modeling shows that such compositional changes may have facilitated the evolution of the perfect, bisexual flower. © 2017 American Society of Plant Biologists. All rights reserved.

Musical rhythm and affect. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Witek, Maria A. G.; Kringelbach, Morten L.; Vuust, Peter

2015-06-01

The Quartet Theory of Human Emotion (QT) proposed by Koelsch et al. [1] adds to existing affective models, e.g. by directing more attention to emotional contagion, attachment-related and non-goal-directed emotions. Such an approach seems particularly appropriate to modelling musical emotions, and music is indeed a recurring example in the text, used to illustrate the distinct characteristics of the affect systems that are at the centre of the theory. Yet, it would seem important for any theory of emotion to account for basic functions such as prediction and anticipation, which are only briefly mentioned. Here we propose that QT, specifically its focus on emotional contagion, attachment-related and non-goal directed emotions, might help generate new ideas about a largely neglected source of emotion - rhythm - a musical property that relies fundamentally on the mechanism of prediction.

Additional electrodes on the Quartet™ LV lead provide more programmable pacing options than bipolar and tripolar equivalents.

PubMed

O'Donnell, David; Sperzel, Johannes; Thibault, Bernard; Rinaldi, Christopher A; Pappone, Carlo; Gutleben, Klaus-Jürgen; Leclercq, Christopher; Razavi, Hedi; Ryu, Kyungmoo; Mcspadden, Luke C; Fischer, Avi; Tomassoni, Gery

2017-04-01

The aim of this study was to evaluate any benefits to the number of viable pacing vectors and maximal spatial coverage with quadripolar left ventricular (LV) leads when compared with tripolar and bipolar equivalents in patients receiving cardiac resynchronization therapy (CRT). A meta-analysis of five previously published clinical trials involving the Quartet™ LV lead (St Jude Medical, St Paul, MN, USA) was performed to evaluate the number of viable pacing vectors defined as capture thresholds ≤2.5 V and no phrenic nerve stimulation and maximal spatial coverage of viable vectors in CRT patients at pre-discharge (n = 370) and first follow-up (n = 355). Bipolar and tripolar lead configurations were modelled by systematic elimination of two and one electrode(s), respectively, from the Quartet lead. The Quartet lead with its four pacing electrodes exhibited the greatest number of pacing vectors per patient when compared with the best bipolar and the best tripolar modelled equivalents. Similarly, the Quartet lead provided the highest spatial coverage in terms of the distance between two furthest viable pacing cathodes when compared with the best bipolar and the best tripolar configurations (P < 0.05). Among the three modelled bipolar configurations, the lead configuration with the two most distal electrodes resulted in the highest number of viable pacing vectors. Among the four modelled tripolar configurations, elimination of the second proximal electrode (M3) resulted in the highest number of viable pacing options per patient. There were no significant differences observed between pre-discharge and first follow-up analyses. The Quartet lead with its four electrodes and the capability to pace from four anatomical locations provided the highest number of viable pacing vectors at pre-discharge and first follow-up visits, providing more flexibility in device programming and enabling continuation of CRT in more patients when compared with bipolar and tripolar equivalents. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

Misleading Betas: An Educational Example

ERIC Educational Resources Information Center

Chong, James; Halcoussis, Dennis; Phillips, G. Michael

2012-01-01

The dual-beta model is a generalization of the CAPM model. In the dual-beta model, separate beta estimates are provided for up-market and down-market days. This paper uses the historical "Anscombe quartet" results which illustrated how very different datasets can produce the same regression coefficients to motivate a discussion of the…

Evolutionary considerations on complex emotions and music-induced emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Gingras, Bruno; Marin, Manuela M.

2015-06-01

Recent efforts to uncover the neural underpinnings of emotional experiences have provided a foundation for novel neurophysiological theories of emotions, adding to the existing body of psychophysiological, motivational, and evolutionary theories. Besides explicitly modeling human-specific emotions and considering the interactions between emotions and language, Koelsch et al.'s original contribution to this challenging endeavor is to identify four brain areas as distinct "affect systems" which differ in terms of emotional qualia and evolutionary pathways [1]. Here, we comment on some features of this promising Quartet Theory of Emotions, focusing particularly on evolutionary and biological aspects related to the four affect systems and their relation to prevailing emotion theories, as well as on the role of music-induced emotions.

Exchange and Inelastic OH(+) + H Collisions on the Doublet and Quartet Electronic States.

PubMed

Bulut, Niyazi; Lique, François; Roncero, Octavio

2015-12-17

The exchange and inelastic state-to-state cross sections for the OH(+) + H collisions are computed from wave packet calculations using the doublet and quartet ground electronic potential energy surface (PES) correlating to the open shell reactants, for collision energies in the range of 1 meV to 0.7 eV. The doublet PES presents a deep insertion well, of ≈6 eV, but the exchange reaction has a rather low probability, showing that the mechanism is not statistical. This well is also responsible of a rather high rotational energy transfer, which makes the rigid-rotor approach overestimate the cross section for low Δj transitions and for high collisonal energies. The quartet PES, with a much shallower well, also presents a low exchange reaction cross section, but the inelastic state-to-state cross sections are very well reproduced by rigid-rotor calculations. When the electronic partition is used to obtain the total state-to-state cross section, the contribution of the doublet state becomes small, and the resulting total cross sections become close to those obtained for the quartet state. Thus, the total (quartet and doublet) cross sections for this open shell system can be reproduced rather satisfactorily by those obtained with the rigid-rotor approximation on the quartet state. Finally, we compare the new OH(+)-H cross sections with OH(+)-He ones recently computed. We found significant differences, especially for transitions with large Δj showing that specific OH(+)-H calculations had to be performed to accurately analyze the OH(+) emission from interstellar molecular clouds.

X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

DOE PAGES

Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan; ...

2016-06-02

We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG 3 (TTAG 3) 3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

The multi-instrumentalist hippocampus. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Strange, Bryan A.; Yebra, Mar

2015-06-01

Characterizing the neural circuitry of emotion is important not only from a basic science perspective, but also for understanding how these circuits may malfunction in psychiatric disease. A fundamental question for affective neuroscience is whether there are specialised neuroanatomical areas, or "modules", dedicated to the processing of emotional stimuli. In their review, Koelsch and colleagues [1] argue for the existence of a quartet of neuroanatomically distinct cerebral systems involved in the generation of a specific class of affects. Intriguingly, all four systems (brainstem-, diencephalon-, hippocampus-, and orbitofrontal-centred) comprise brain areas whose role in emotional processing is in addition to mediating other specific aspects of cognition. One member of the quartet in which this is particularly apparent is the hippocampus, a structure known to be critical for episodic memory and navigation. If areas involved in emotion also mediate other brain functions, this raises an issue of whether these multiple functions are executed by segregated circuits within each structure - i.e., a "module" for emotion residing in a sub-division of a brain structure - or whether these circuits are superimposed.

X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yasar, Selcuk; Schimelman, Jacob B.; Aksoyoglu, M. Alphan

We report that observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystallinemore » phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG 3 (TTAG 3) 3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG(4)T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.« less

Compositions and methods for the expression of selenoproteins in eukaryotic cells

DOEpatents

Gladyshev, Vadim [Lincoln, NE; Novoselov, Sergey [Puschino, RU

2012-09-25

Recombinant nucleic acid constructs for the efficient expression of eukaryotic selenoproteins and related methods for production of recombinant selenoproteins are provided. The nucleic acid constructs comprise novel selenocysteine insertion sequence (SECIS) elements. Certain novel SECIS elements of the invention contain non-canonical quartet sequences. Other novel SECIS elements provided by the invention are chimeric SECIS elements comprising a canonical SECIS element that contains a non-canonical quartet sequence and chimeric SECIS elements comprising a non-canonical SECIS element that contains a canonical quartet sequence. The novel SECIS elements of the invention facilitate the insertion of selenocysteine residues into recombinant polypeptides.

Ultrafast intersystem crossings in Fe-Co Prussian blue analogues

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Veenendaal, Michel

Ultrafast spincrossover is studied in Fe-Co Prussian blue analogues using a dissipative quantum-mechanical model of a cobalt ion coupled to a breathing mode. All electronic interactions are treated on an equal footing. It is theoretically demonstrated that the divalent cobalt ion reaches 90% of the S = 3/2 value within 20 fs after photoexciting a low-spin Co 3+ ion by an iron-to-cobalt charge transfer. The doublet-to-quartet spin crossover is significantly faster than the oscillation period of the breathing mode. The system relaxes to the lowest manifold of divalent cobalt ( 4T 1) in 150-200 fs. In conclusion, strong oscillations inmore » spin-orbit coupling and the involvement of higher-lying quartets are found.« less

Ultrafast intersystem crossings in Fe-Co Prussian blue analogues

DOE PAGES

van Veenendaal, Michel

2017-07-27

Ultrafast spincrossover is studied in Fe-Co Prussian blue analogues using a dissipative quantum-mechanical model of a cobalt ion coupled to a breathing mode. All electronic interactions are treated on an equal footing. It is theoretically demonstrated that the divalent cobalt ion reaches 90% of the S = 3/2 value within 20 fs after photoexciting a low-spin Co 3+ ion by an iron-to-cobalt charge transfer. The doublet-to-quartet spin crossover is significantly faster than the oscillation period of the breathing mode. The system relaxes to the lowest manifold of divalent cobalt ( 4T 1) in 150-200 fs. In conclusion, strong oscillations inmore » spin-orbit coupling and the involvement of higher-lying quartets are found.« less

Mixed-up trees: the structure of phylogenetic mixtures.

PubMed

Matsen, Frederick A; Mossel, Elchanan; Steel, Mike

2008-05-01

In this paper, we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture distributions forms a convex polytope and we calculate its dimension; corollaries include a simple criterion for when a mixture of branch lengths on the star tree can mimic the site pattern frequency vector of a resolved quartet tree. Furthermore, by computing volumes of polytopes we can clarify how "common" non-identifiable mixtures are under the CFN model. We also present a new combinatorial result which extends any identifiability result for a specific pair of trees of size six to arbitrary pairs of trees. Next we present a positive result showing identifiability of rates-across-sites models. Finally, we answer a question raised in a previous paper concerning "mixed branch repulsion" on trees larger than quartet trees under the CFN model.

Evolutionary perspectives on emotions and their link to intentions, dispositions and behavior. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Wildgruber, Dirk; Kreifelts, Benjamin

2015-06-01

Koelsch and coworkers present a sophisticated neuroanatomical model of emotions comprising four affect-systems and four output-systems, each bound to a specific brain area [1]. Moreover, they suggest the emergence of distinct components of subjective feelings or "emotion percepts" due to integration of the activation across these subsystems. Incorporating numerous neurobiological, psychological and philosophical findings on human emotions, the model reflects an extensive interdisciplinary approach. Considering an evolutionary perspective, however, we would like to address some issues concerning emotions and their link to intentions, dispositions and behavior that are not fully covered by the Quartet Model. Charles Darwin pointed out that individuals that are better adapted to their environment have increased chances of survival and reproduction. Therefore, natural selection leads to a rising prevalence of properties offering a survival benefit across generations [2]. To better understand the biological functions of emotions we propose to ask the question: How do emotions provide a benefit for survival and reproduction?

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2016-11-11

Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.

String Quartets as Self-Managed Teams: An Interdisciplinary Perspective

ERIC Educational Resources Information Center

Gilboa, Avi; Tal-Shmotkin, Malka

2012-01-01

This article examines empirically and systematically whether a string quartet (SQ) ensemble is perceived as a self-managed team (SMT). SMTs, which were initially employed in the industrial world, are groups of employees that have a total responsibility for a defined project. The hypothesis that the SQ would exhibit more typical SMT characteristics…

The Pulsar Quartet: Listening to a Galactic Symphony

NASA Astrophysics Data System (ADS)

Kiziltan, Bülent

2014-06-01

Pulsars are exotic dead stars that emit very regular radio pulses. These pulses are attributed to their regular rotation. Some pulsars are spinning fast enough that the audio equivalent waveform of their pulses fall within our hearing range. If human ears were tuned to radio waves it would have been possible to ‘hear’ these very compact stars. We produced the audio waveform of these pulsar signals and mapped them onto a frequency chart to find the corresponding musical notes. We use these ‘audible' pulsars like musical instruments in a symphony orchestra to play a full quartet. At the same time, an accompanying visual interface shows the realistic distribution of all pulsars in our own Galaxy. Pulsars shine as they play each note in the quartet with realistic brightening and subsequent dimming proportional to their rotational energies. This can serve as an educational tool at all levels to demonstrate many interesting aspects of stellar evolution and articulate an aesthetic connection of us with the cosmos. Interested in watching the light show while the Milky Way Pulsar Orchestra plays a quartet?

The naked and the dead: the ABCs of gymnosperm reproduction and the origin of the angiosperm flower.

PubMed

Melzer, Rainer; Wang, Yong-Qiang; Theissen, Günter

2010-02-01

20 years after establishment of the ABC model many of the molecular mechanisms underlying development of the angiosperm flower are relatively well understood. Central players in the gene regulatory network controlling flower development are SQUA-like, DEF/GLO-like, AG-like and AGL6/SEP1-like MIKC-type MADS-domain transcription factors. These provide class A, class B, class C and the more recently defined class E floral homeotic functions, respectively. There is evidence that the floral homeotic proteins recognize the DNA of target genes in an organ-specific way as multimeric protein complexes, thus constituting 'floral quartets'. In contrast to the detailed insights into flower development, how the flower originated during evolution has remained enigmatic. However, while orthologues of all classes of floral homeotic genes appear to be absent from all non-seed plants, DEF/GLO-like, AG-like, and AGL6-like genes have been found in diverse extant gymnosperms, the closest relatives of the angiosperms. While SQUA-like and SEP1-like MADS-box genes appear to be absent from extant gymnosperms, reconstruction of MADS-box gene phylogeny surprisingly suggests that the most recent common ancestor of gymnosperms and angiosperms possessed representatives of both genes, but that these have been lost in the lineage that led to extant gymnosperms. Expression studies and genetic complementation experiments indicate that both angiosperm and gymnosperm AG-like and DEF/GLO-like genes have conserved functions in the specification of reproductive organs and in distinguishing male from female organs, respectively. Based on these findings novel models about the molecular basis of flower origin, involving changes in the expression patterns of DEF/GLO-like or AGL6/SEP1/SQUA-like genes in reproductive structures, were developed. While in angiosperms SEP1-like proteins play an important role in floral quartet formation, preliminary evidence suggests that gymnosperm DEF/GLO-like and AG-like proteins alone can already form floral quartet-like complexes, further corroborating the view that the formation of floral quartet-like complexes predated flower origin during evolution. Copyright 2009 Elsevier Ltd. All rights reserved.

The Effect of Body Movement on Listeners' Perceptions of Musicality in Trombone Quartet Performance

ERIC Educational Resources Information Center

Silveira, Jason M.

2014-01-01

The purpose of this study was to determine what effect body movement would have on listeners' (N = 90) perceptions of a professional chamber ensemble performance. Specifically, an audio/video recording of a trombone quartet performance was used for the music stimulus. Listeners were asked to rate each performance on the basis of perceived…

Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'.

PubMed

Wang, Yong-Qiang; Melzer, Rainer; Theissen, Günter

2010-10-01

Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

The "New Deadly Quartet" for cardiovascular disease in the 21st century: obesity, metabolic syndrome, inflammation and climate change: how does statin therapy fit into this equation?

PubMed

Clearfield, Michael; Pearce, Melissa; Nibbe, Yasmin; Crotty, David; Wagner, Alesia

2014-01-01

Despite population-based improvements in cardiovascular risk factors, such as blood pressure, cholesterol and smoking, cardiovascular disease still remains the number-one cause of mortality in the United States. In 1989, Kaplan coined the term "Deadly Quartet" to represent a combination of risk factors that included upper body obesity, glucose intolerance, hypertriglyceridemia and hypertension [Kaplan in Arch Int Med 7:1514-1520, 1989]. In 2002, the third report of the National Cholesterol Education Program Adult Treatment Panel (NCEP-ATP III) essentially added low HDL-C criteria and renamed this the "metabolic syndrome." [The National Cholesterol Education Program (NCEP) in JAMA 285:2486-2497, 2001] However, often forgotten was that a pro-inflammatory state and pro-thrombotic state were also considered components of the syndrome, albeit the panel did not find enough evidence at the time to recommend routine screening for these risk factors [The National Cholesterol Education Program (NCEP) in JAMA 285:2486-2497, 2001]. Now over a decade later, it may be time to reconsider this deadly quartet by reevaluating the roles of obesity and subclinical inflammation as they relate to the metabolic syndrome. To complete this new quartet, the addition of increased exposure to elevated levels of particulate matter in the atmosphere may help elucidate why this cardiovascular pandemic continues, despite our concerted efforts. In this article, we will summarize the evidence, focusing on how statin therapy may further impact this new version of the "deadly quartet".

A "Knowledge Quartet" Used to Identify a Second-Year Pre-Service Teacher's Primary Mathematical Content Knowledge

ERIC Educational Resources Information Center

Livy, Sharyn

2010-01-01

This paper draws on observation of a primary mathematics lesson prepared and taught by a second-year pre-service teacher who lacked mathematical content knowledge. A "knowledge quartet" (Rowland, Turner, Thwaites, & Huckstep, 2009) was used to investigate when and how a pre-service teacher drew on their knowledge of mathematics during primary…

Investigation of guanosine-quartet assemblies by vibrational and electronic circular dichroism spectroscopy, a novel approach for studying supramolecular entities.

PubMed

Setnicka, Vladimír; Urbanová, Marie; Volka, Karel; Nampally, Sreenivasachary; Lehn, Jean-Marie

2006-11-24

The self-assembly of guanosine-5'-hydrazide G-1 in D(2)O, in the presence and absence of sodium cations, has been investigated by chiroptical techniques: electronic (ECD) and the newly introduced vibrational (VCD) circular dichroism spectroscopy. Using a combination of ECD and VCD with other methods such as IR, electron microscopy, and electrospray ionization mass spectrometry (ESI-MS) it was found that G-1 produces long-range chiral aggregates consisting of G-quartets, (G-1)(4), subsequently stacked into columns, [(G-1)(4)](n), induced by binding of metal cations between the (G-1)(4) species. This process, accompanied by gelation of the sample, is highly efficient in the presence of an excess of sodium cations, leading to aggregates with strong quartet-quartet interaction. Thermally induced conformational changes and conformational stability of guanosine-5'-hydrazide assemblies were studied by chiroptical techniques and the melting temperature of the hydrogels formed was obtained. The temperature-dependent experiments indicate that the long-range supramolecular aggregates are dissociated by increasing temperature into less ordered species, monomers, or other intermediates in equilibrium, as indicated by MS experiments.

Aesthetic emotions goals. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid

2015-06-01

Review by Koelsch et al. [10] presents an interdisciplinary theory of emotions, including a neurobiological emotion theory originating in four core emotional systems. The Quartet Theory (QT) includes specifically human emotions and considers the role of language for emotions. This comment considers questions about how the QT can address aesthetic emotions, what class of emotions they are, and what their function in cognition is. Can QT help defining aesthetic emotions neurally and functionally? Such a definition of aesthetic emotions would be necessary for their scientific exploration, because as widely used today there is no definition, aesthetics is defined through art, and art through aesthetics. Since contents of many art museums are not accepted as art by many artists and admirers of art, it is not clear what should be the subject of aesthetic emotions research.

Using the "Knowledge Quartet" to Quantify Mathematical Knowledge in Teaching: The Development of a Protocol for Initial Teacher Education

ERIC Educational Resources Information Center

Weston, Tracy L.

2013-01-01

This study examined trainee teachers' mathematical knowledge in teaching (MKiT) over their final year in a US Initial Teacher Education (ITE) programme. This paper reports on an exploratory methodological approach taken to use the "Knowledge Quartet" to quantify MKiT through the development of a new protocol to code trainees' teaching of…

Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro.

PubMed

Jing, N; Marchand, C; Liu, J; Mitra, R; Hogan, M E; Pommier, Y

2000-07-14

The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.

Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

PubMed

Zeil, Catharina; Widmann, Michael; Fademrecht, Silvia; Vogel, Constantin; Pleiss, Jürgen

2016-05-01

The Lactamase Engineering Database (www.LacED.uni-stuttgart.de) was developed to facilitate the classification and analysis of TEM β-lactamases. The current version contains 474 TEM variants. Two hundred fifty-nine variants form a large scale-free network of highly connected point mutants. The network was divided into three subnetworks which were enriched by single phenotypes: one network with predominantly 2be and two networks with 2br phenotypes. Fifteen positions were found to be highly variable, contributing to the majority of the observed variants. Since it is expected that a considerable fraction of the theoretical sequence space is functional, the currently sequenced 474 variants represent only the tip of the iceberg of functional TEM β-lactamase variants which form a huge natural reservoir of highly interconnected variants. Almost 50% of the variants are part of a quartet. Thus, two single mutations that result in functional enzymes can be combined into a functional protein. Most of these quartets consist of the same phenotype, or the mutations are additive with respect to the phenotype. By predicting quartets from triplets, 3,916 unknown variants were constructed. Eighty-seven variants complement multiple quartets and therefore have a high probability of being functional. The construction of a TEM β-lactamase network and subsequent analyses by clustering and quartet prediction are valuable tools to gain new insights into the viable sequence space of TEM β-lactamases and to predict their phenotype. The highly connected sequence space of TEM β-lactamases is ideally suited to network analysis and demonstrates the strengths of network analysis over tree reconstruction methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation

PubMed Central

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-01-01

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events. PMID:15840720

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation.

PubMed

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-04-26

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events.

The movements made by performers in a skilled quartet: a distinctive pattern, and the function that it serves

PubMed Central

Glowinski, Donald; Mancini, Maurizio; Cowie, Roddy; Camurri, Antonio; Chiorri, Carlo; Doherty, Cian

2013-01-01

When people perform a task as part of a joint action, their behavior is not the same as it would be if they were performing the same task alone, since it has to be adapted to facilitate shared understanding (or sometimes to prevent it). Joint performance of music offers a test bed for ecologically valid investigations of the way non-verbal behavior facilitates joint action. Here we compare the expressive movement of violinists when playing in solo and ensemble conditions. The first violinists of two string quartets (SQs), professional and student, were asked to play the same musical fragments in a solo condition and with the quartet. Synchronized multimodal recordings were created from the performances, using a specially developed software platform. Different patterns of head movement were observed. By quantifying them using an appropriate measure of entropy, we showed that head movements are more predictable in the quartet scenario. Rater evaluations showed that the change does not, as might be assumed, entail markedly reduced expression. They showed some ability to discriminate between solo and ensemble performances, but did not distinguish them in terms of emotional content or expressiveness. The data raise provocative questions about joint action in realistically complex scenarios. PMID:24312065

Control of social monogamy through aggression in a hermaphroditic shrimp

PubMed Central

2011-01-01

Introduction Sex allocation theory predicts that in small mating groups simultaneous hermaphroditism is the optimal form of gender expression. Under these conditions, male allocation is predicted to be very low and overall per-capita reproductive output maximal. This is particularly true for individuals that live in pairs, but monogamy is highly susceptible to cheating by both partners. However, certain conditions favour social monogamy in hermaphrodites. This study addresses the influence of group size on group stability and moulting cycles in singles, pairs, triplets and quartets of the socially monogamous shrimp Lysmata amboinensis, a protandric simultaneous hermaphrodite. Results The effect of group size was very strong: Exactly one individual in each triplet and exactly two individuals in each quartet were killed in aggressive interactions, resulting in group sizes of two individuals. All killed individuals had just moulted. No mortality occurred in single and pair treatments. The number of moults in the surviving shrimp increased significantly after changing from triplets and quartets to pairs. Conclusion Social monogamy in L. amboinensis is reinforced by aggressive expulsion of supernumerous individuals. We suggest that the high risk of mortality in triplets and quartets results in suppression of moulting in groups larger than two individuals and that the feeding ecology of L. amboinensis favours social monogamy. PMID:22078746

Control of social monogamy through aggression in a hermaphroditic shrimp.

PubMed

Wong, Janine Wy; Michiels, Nico K

2011-11-11

Sex allocation theory predicts that in small mating groups simultaneous hermaphroditism is the optimal form of gender expression. Under these conditions, male allocation is predicted to be very low and overall per-capita reproductive output maximal. This is particularly true for individuals that live in pairs, but monogamy is highly susceptible to cheating by both partners. However, certain conditions favour social monogamy in hermaphrodites. This study addresses the influence of group size on group stability and moulting cycles in singles, pairs, triplets and quartets of the socially monogamous shrimp Lysmata amboinensis, a protandric simultaneous hermaphrodite. The effect of group size was very strong: Exactly one individual in each triplet and exactly two individuals in each quartet were killed in aggressive interactions, resulting in group sizes of two individuals. All killed individuals had just moulted. No mortality occurred in single and pair treatments. The number of moults in the surviving shrimp increased significantly after changing from triplets and quartets to pairs. Social monogamy in L. amboinensis is reinforced by aggressive expulsion of supernumerous individuals. We suggest that the high risk of mortality in triplets and quartets results in suppression of moulting in groups larger than two individuals and that the feeding ecology of L. amboinensis favours social monogamy.

Understanding Motherhood as Maturation: Maternity Scripts in Lois Lowry's "Son"

ERIC Educational Resources Information Center

Deszcz-Tryhubczak, Justyna; Marecki, Mateusz

2015-01-01

When put together with the other parts of The Giver Quartet, "Son" (2012), Lowry's recently published concluding book, emerges as an odd exception to the focus on young adult protagonists since it foregrounds the mother's perspective and addresses the issue of motherhood. It presents the reader with at least three conceptual models of…

Statistical modeling of the reactions Fe(+) + N2O → FeO(+) + N2 and FeO(+) + CO → Fe(+) + CO2.

PubMed

Ushakov, Vladimir G; Troe, Jürgen; Johnson, Ryan S; Guo, Hua; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A

2015-08-14

The rates of the reactions Fe(+) + N2O → FeO(+) + N2 and FeO(+) + CO → Fe(+) + CO2 are modeled by statistical rate theory accounting for energy- and angular momentum-specific rate constants for formation of the primary and secondary cationic adducts and their backward and forward reactions. The reactions are both suggested to proceed on sextet and quartet potential energy surfaces with efficient, but probably not complete, equilibration by spin-inversion of the populations of the sextet and quartet adducts. The influence of spin-inversion on the overall reaction rate is investigated. The differences of the two reaction rates mostly are due to different numbers of entrance states (atom + linear rotor or linear rotor + linear rotor, respectively). The reaction Fe(+) + N2O was studied either with (6)Fe(+) or with (4)Fe(+) reactants. Differences in the rate constants of (6)Fe(+) and (4)Fe(+) reacting with N2O are attributed to different contributions from electronically excited potential energy surfaces, such as they originate from the open-electronic shell reactants.

Pathgroups, a dynamic data structure for genome reconstruction problems.

PubMed

Zheng, Chunfang

2010-07-01

Ancestral gene order reconstruction problems, including the median problem, quartet construction, small phylogeny, guided genome halving and genome aliquoting, are NP hard. Available heuristics dedicated to each of these problems are computationally costly for even small instances. We present a data structure enabling rapid heuristic solution to all these ancestral genome reconstruction problems. A generic greedy algorithm with look-ahead based on an automatically generated priority system suffices for all the problems using this data structure. The efficiency of the algorithm is due to fast updating of the structure during run time and to the simplicity of the priority scheme. We illustrate with the first rapid algorithm for quartet construction and apply this to a set of yeast genomes to corroborate a recent gene sequence-based phylogeny. http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html chunfang313@gmail.com Supplementary data are available at Bioinformatics online.

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

Music Regulators in Two String Quartets: A Comparison of Communicative Behaviors between Low- and High-Stress Performance Conditions.

PubMed

Biasutti, Michele; Concina, Eleonora; Wasley, David; Williamon, Aaron

2016-01-01

In ensemble performances, group members use particular bodily behaviors as a sort of "language" to supplement the lack of verbal communication. This article focuses on music regulators, which are defined as signs to other group members for coordinating performance. The following two music regulators are considered: body gestures for articulating attacks (a set of movements externally directed that are used to signal entrances in performance) and eye contact. These regulators are recurring observable behaviors that play an important role in non-verbal communication among ensemble members. To understand how they are used by chamber musicians, video recordings of two string quartet performances (Quartet A performing Bartók and Quartet B performing Haydn) were analyzed under two conditions: a low stress performance (LSP), undertaken in a rehearsal setting, and a high stress performance (HSP) during a public recital. The results provide evidence for more emphasis in gestures for articulating attacks (i.e., the perceived strength of a performed attack-type body gesture) during HSP than LSP. Conversely, no significant differences were found for the frequency of eye contact between HSP and LSP. Moreover, there was variability in eye contact during HSP and LSP, showing that these behaviors are less standardized and may change according to idiosyncratic performance conditions. Educational implications are discussed for improving interpersonal communication skills during ensemble performance.

Music Regulators in Two String Quartets: A Comparison of Communicative Behaviors between Low- and High-Stress Performance Conditions

PubMed Central

Biasutti, Michele; Concina, Eleonora; Wasley, David; Williamon, Aaron

2016-01-01

In ensemble performances, group members use particular bodily behaviors as a sort of “language” to supplement the lack of verbal communication. This article focuses on music regulators, which are defined as signs to other group members for coordinating performance. The following two music regulators are considered: body gestures for articulating attacks (a set of movements externally directed that are used to signal entrances in performance) and eye contact. These regulators are recurring observable behaviors that play an important role in non-verbal communication among ensemble members. To understand how they are used by chamber musicians, video recordings of two string quartet performances (Quartet A performing Bartók and Quartet B performing Haydn) were analyzed under two conditions: a low stress performance (LSP), undertaken in a rehearsal setting, and a high stress performance (HSP) during a public recital. The results provide evidence for more emphasis in gestures for articulating attacks (i.e., the perceived strength of a performed attack-type body gesture) during HSP than LSP. Conversely, no significant differences were found for the frequency of eye contact between HSP and LSP. Moreover, there was variability in eye contact during HSP and LSP, showing that these behaviors are less standardized and may change according to idiosyncratic performance conditions. Educational implications are discussed for improving interpersonal communication skills during ensemble performance. PMID:27610089

Design and Applications of Noncanonical DNA Base Pairs.

PubMed

Jissy, A K; Datta, Ayan

2014-01-02

While the Watson-Crick base pairs are known to stabilize the DNA double helix and play a vital role in storage/replication of genetic information, their replacement with non-Watson-Crick base pairs has recently been shown to have interesting practical applications. Nowadays, theoretical calculations are routinely performed on very complex systems to gain a better understanding of how molecules interact with each other. We not only bring together some of the basic concepts of how mispaired or unnatural nucleobases interact with each other but also look at how such an understanding influences the prediction of novel properties and development of new materials. We highlight the recent developments in this field of research. In this Perspective, we discuss the success of DFT methods, particularly, dispersion-corrected DFT, for applications such as pH-controlled molecular switching, electric-field-induced stacking of disk-like molecules with guanine quartets, and optical birefringence of alkali-metal-coordinated guanine quartets. The synergy between theoretical models and real applications is highlighted.

Solving general gauge theories on inner product spaces

NASA Astrophysics Data System (ADS)

Batalin, Igor; Marnelius, Robert

1995-02-01

By means of a generalized quartet mechanism we show in a model independent way that a BRST quantization on an inner product space leads to physical states of the form ph> = exp [ Q, ψ]ph> 0 where Q is the nilpotent BRST operator, ψ a hermitian fermionic gauge-fixing operator, and ph> o BRST invariant states determined by a hermitian set of BRST doublets in involution. ph> 0 does not belong to an inner product space although ph> does. Since the BRST quartets are split into two sets of hermitian BRST doublets there are two choices for ph> 0 and the corresponding ψ. When applied to general, both irreducible and reducible, gauge theories of arbitrary rank within the BFV formulation we find that ph> 0 are trivial BRST invariant states which only depend on the matter variables for one set of solutions, and for the other set ph> 0 are solutions of a Dirac quantization. This generalizes previous Lie group solutions obtained by means of a bigrading.

Photoelectron Spectroscopy Study of Quinonimides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hossain, Ekram; Deng, Shihu M.; Gozem, Samer

Structures and energetics of o-, m- and p-quinonimide anions (OC6H4N) and quinoniminyl radicals have been investigated by using negative ion photoelectron spectroscopy. Modeling of the photoelectron spectrum of the ortho isomer shows that the ground state of the anion is a triplet, while the quinoniminyl radical has a doublet ground state with a doublet-quartet splitting of 35.5 kcal/mol. The para radical has doublet ground state, but a band for a quartet state is missing from the photoelectron spectrum indicating that the anion has a singlet ground state, in contrast to previously reported calculations. The theoretical modeling is revisited here, andmore » it is shown that accurate predictions for the electronic structure of the para quinonimide anion require both an accurate account of electron correlation and a sufficiently diffuse basis set. Electron affinities of o- and p-quinoniminyl radicals are measured to be 1.715 ± 0.010 and 1.675 ± 0.010 eV, respectively. The photoelectron spectrum of the m-quinonimide anion shows that the ion undergoes several different rearrangements, including a rearrangement to the energetically favorable para isomer. Such rearrangements preclude a meaningful analysis of the experimental spectrum.« less

Investigation of thermal and optical properties of some quartet mixed hydrogen-bonded liquid crystals

NASA Astrophysics Data System (ADS)

Okumuş, Mustafa

2017-11-01

In this study, the thermal and optical properties of quartet mixtures formed at different weight ratios (1:1:1:1 and 1.5:1:1:1) from liquid crystals 4-octyloxy-4‧-cyanobiphenyl (8OCB), 4-hexylbenzoic acid, 4-(octyloxy)benzoic acid and 4-(decyloxy)benzoic acid were investigated by differential scanning calorimeter (DSC) and polarized optic microscopy (POM). The phase transition temperatures of the novel quartet mixtures measured in the DSC experiments are in line with the POM experiments. The experimental results clearly show that the novel liquid crystal mixtures have displayed pure liquid crystalline properties. According to the phase diagram drawn from DSC results, the nematic range of the novel mixture at the eutectic point is larger than the nematic ranges of the components. The mesomorphic structures of produced homolog complex mixtures are found to be smectic and nematic phases. But the smectic phase cannot be observed in the novel complex 1.5:1:1:1 mixture during continuous cooling. The nematic range of the novel complex 1.5:1:1:1 mixture is bigger than the nematic range of the novel complex 1:1:1:1 mixture with increasing 8OCB. Also, the nematic-to-isotropic phase transition temperature decreases with increasing the weight ratio of 8OCB in the complex quartet mixture. Another interesting result is that the produced mixtures are to be like a medical cream at room temperatures. Furthermore, order parameter and thermal stability factor of the transitions are also calculated.

Pairing versus quarteting coherence length

NASA Astrophysics Data System (ADS)

Delion, D. S.; Baran, V. V.

2015-02-01

We systematically analyze the coherence length in even-even nuclei. The pairing coherence length in the spin-singlet channel for the effective density-dependent delta (DDD) and Gaussian interaction is estimated. We consider in our calculations bound states as well as narrow resonances. It turns out that the pairing gaps given by the DDD interaction are similar to those of the Gaussian potential if one renormalizes the radial width to the nuclear radius. The correlations induced by the pairing interaction have, in all considered cases, a long-range character inside the nucleus and a decrease towards the surface. The mean coherence length is larger than the geometrical radius for light nuclei and approaches this value for heavy nuclei. The effect of the temperature and states in the continuum is investigated. Strong shell effects are put in evidence, especially for protons. We generalize this concept to quartets by considering similar relations, but between proton and neutron pairs. The quartet coherence length has a similar shape, but with larger values on the nuclear surface. We provide evidence of the important role of proton-neutron correlations by estimating the so-called alpha coherence length, which takes into account the overlap with the proton-neutron part of the α -particle wave function. It turns out that it does not depend on the nuclear size and has a value comparable to the free α -particle radius. We have shown that pairing correlations are mainly concentrated inside the nucleus, while quarteting correlations are connected to the nuclear surface.

Four-Stranded Dna Formed by Isoguanine Quartets: Complex Stoichiometry, Thermal Stability and Resistance Against Exonucleases

NASA Astrophysics Data System (ADS)

Seela, Frank; Wei, Changfu; Melenewski, Alexander

1997-12-01

Single stranded DNA-fragments containing short runs of isoguanine such as d(T_4iG_4T_4) (5) or d(iG_4T_4) (6) form quartet structures by self-assembly of the isoguanine residues. The stoichiometry of the complexes is deduced from mixed aggregates formed between d(T_4iG_4T_4) and d(iG_4T_4). The iG_d-tetrads are more stable with regard to their thermal denaturation and to their resistance against enzymatic phosphodiester hydrolysis than those formed by dG.

The performative pleasure of imprecision: a diachronic study of entrainment in music performance.

PubMed

Geeves, Andrew; McIlwain, Doris J; Sutton, John

2014-01-01

This study focuses in on a moment of live performance in which the entrainment amongst a musical quartet is threatened. Entrainment is asymmetric in so far as there is an ensemble leader who improvises and expands the structure of a last chorus of a piece of music beyond the limits tacitly negotiated during prior rehearsals and performances. Despite the risk of entrainment being disturbed and performance interrupted, the other three musicians in the quartet follow the leading performer and smoothly transition into unprecedented performance territory. We use this moment of live performance to work back through the fieldwork data, building a diachronic study of the development and bases of entrainment in live music performance. We introduce the concept of entrainment and profile previous theory and research relevant to entrainment in music performance. After outlining our methodology, we trace the evolution of the structure of the piece of music from first rehearsal to final performance. Using video clip analysis, interviews and field notes we consider how entrainment shaped and was shaped by the moment of performance in focus. The sense of trust between quartet musicians is established through entrainment processes, is consolidated via smooth adaptation to the threats of disruption. Non-verbal communicative exchanges, via eye contact, gesture, and spatial proximity, sustain entrainment through phase shifts occurring swiftly and on the fly in performance contexts. These exchanges permit smooth adaptation promoting trust. This frees the quartet members to play with the potential disturbance of equilibrium inherent in entrained relationships and to play with this tension in an improvisatory way that enhances audience engagement and the live quality of performance.

The performative pleasure of imprecision: a diachronic study of entrainment in music performance

PubMed Central

Geeves, Andrew; McIlwain, Doris J.; Sutton, John

2014-01-01

This study focuses in on a moment of live performance in which the entrainment amongst a musical quartet is threatened. Entrainment is asymmetric in so far as there is an ensemble leader who improvises and expands the structure of a last chorus of a piece of music beyond the limits tacitly negotiated during prior rehearsals and performances. Despite the risk of entrainment being disturbed and performance interrupted, the other three musicians in the quartet follow the leading performer and smoothly transition into unprecedented performance territory. We use this moment of live performance to work back through the fieldwork data, building a diachronic study of the development and bases of entrainment in live music performance. We introduce the concept of entrainment and profile previous theory and research relevant to entrainment in music performance. After outlining our methodology, we trace the evolution of the structure of the piece of music from first rehearsal to final performance. Using video clip analysis, interviews and field notes we consider how entrainment shaped and was shaped by the moment of performance in focus. The sense of trust between quartet musicians is established through entrainment processes, is consolidated via smooth adaptation to the threats of disruption. Non-verbal communicative exchanges, via eye contact, gesture, and spatial proximity, sustain entrainment through phase shifts occurring swiftly and on the fly in performance contexts. These exchanges permit smooth adaptation promoting trust. This frees the quartet members to play with the potential disturbance of equilibrium inherent in entrained relationships and to play with this tension in an improvisatory way that enhances audience engagement and the live quality of performance. PMID:25400567

Aesthetic emotions to art - What they are and what makes them special. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Leder, Helmut; Markey, Patrick S.; Pelowski, Matthew

2015-06-01

Establishing a functional understanding of emotional processes is crucial for profound insight into human cognition and behavior [6]. The study of human interactions with art provides an excellent window into the complex emotional reactions that can be had with the environment. Recent advances in the empirical study of art reception have given rise to new models [8,9], and a growing interest in aesthetic affect and emotion.

Dissociative excitation of the manganese atom quartet levels by collisions e-MnBr2

NASA Astrophysics Data System (ADS)

Smirnov, Yu M.

2017-04-01

Dissociative excitation of quartet levels of the manganese atom was studied in collisions of electrons with manganese dibromide molecules. Eighty-two cross-sections for transitions originating at odd levels and eleven cross-sections for transitions originating at even levels have been measured at an incident electron energy of 100 eV. An optical excitation function has been recorded in the electron energy range of 0-100 eV for transitions originating from 3d 64p z 4 F° levels. For the majority of transitions, a comparison of the resulting cross-section values to cross-sections produced by direct excitation is provided.

The evolution of the zodiac in the context of ancient oriental history

NASA Astrophysics Data System (ADS)

Gurshtein, Alex A.

The dates for the second (ca. 2700 B.C. to within 250 years) and the third ecliptical quartets (ca. 1200 B.C. to within 400 years) evaluated earlier are considered in the context of ancient Egyptian history. The origin of the second quartet coincides with the Great Pyramids and the initiation of the Egyptian solar, or so-called "civil" calendar, the first of such a type in the world. The third quartet is concurrent with the solar conversion of Amenhotep IV (Akhenaton) and takes place at the finale of the great Sothic period of 1461 years after the initiation of the solar calendar. It is argued that the Great Pyramids seem to be monuments to the Sun-god built in honor of the Egyptians having reached an understanding of the Sun's track upon the starry background, Akhenaton's conversion being in a direct connection with the original Pyramids' ideology. This paper is the third part of a single investigation. The first two parts "On the Origin of the Zodiacal Constellations" and "Prehistory of Zodiac Dating: Three Strata of Upper Paleolithic Constellations" were published in Vistas in Astronomy in 1993 and 1995.

Molecular mechanisms underlying origin and diversification of the angiosperm flower.

PubMed

Theissen, Guenter; Melzer, Rainer

2007-09-01

Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the 'ABC model' and the 'floral quartet model'. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. We intend to explain how the 'ABC model' and the 'floral quartet model' are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better 'developmental switches' originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the 'classical' ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target genes.

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

PubMed

Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

2011-11-28

DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

Cantico Delle Creature: A microtonal original composition for soprano and string quartet to a text by St. Francis of Assisi, including analytical commentary

NASA Astrophysics Data System (ADS)

Sabol, Jason A.

Cantico delle Creature is an original piece of music for soprano and string quartet composed in 72 tone per octave equal temperament, dividing each semitone into six equal parts called twelfth-tones. This system of tuning makes it possible to combine just intonation and spectral principles based on the harmonic series with real imitation, modulation, and polyphony. Supplemental text discusses several aspects of microtonal structure and pedagogy, including the representation of the first 64 partials of the harmonic series in 72 tone equal temperament, performance of natural string harmonics, the relationship between interval size and vibration ratio, pitch to frequency conversion, and analysis of several passages in the musical score.

Sequences with high propensity to form G-quartet structures in kinetoplast DNA from Phytomonas serpens.

PubMed

Sá-Carvalho, D; Traub-Cseko, Y M

1995-06-01

Naturally occurring sequences containing repetitive guanine motifs have the potential to form tetraplex DNA. Phytomonas serpens minicircle DNA shows some regions where one strand is composed mainly of G and T (GT regions). These regions contain several stretches of contiguous guanines. An oligonucleotide was constructed with the sequence corresponding to one of these regions (Phyto-GT). It was demonstrated by native gel electrophoresis and methylation protection that Phyto-GT forms tetramolecular (G4), bimolecular (G'2) and unimolecular (G4') structures stabilized through G-quartets. Tetraplex DNA formation by this sequence could have biological relevance as it can be formed in physiological conditions and GT regions comprise approximately one-third of P. serpens and Crithidia oncopelti minicircles.

The music of earthquakes and Earthquake Quartet #1

USGS Publications Warehouse

Michael, Andrew J.

2013-01-01

Earthquake Quartet #1, my composition for voice, trombone, cello, and seismograms, is the intersection of listening to earthquakes as a seismologist and performing music as a trombonist. Along the way, I realized there is a close relationship between what I do as a scientist and what I do as a musician. A musician controls the source of the sound and the path it travels through their instrument in order to make sound waves that we hear as music. An earthquake is the source of waves that travel along a path through the earth until reaching us as shaking. It is almost as if the earth is a musician and people, including seismologists, are metaphorically listening and trying to understand what the music means.

DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC).

PubMed

Sato, Yoshiteru; Mitomi, Kenta; Sunami, Tomoko; Kondo, Jiro; Takénaka, Akio

2006-12-01

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

The low-lying quartet electronic states of group 14 diatomic borides XB (X = C, Si, Ge, Sn, Pb)

NASA Astrophysics Data System (ADS)

Pontes, Marcelo A. P.; de Oliveira, Marcos H.; Fernandes, Gabriel F. S.; Da Motta Neto, Joaquim D.; Ferrão, Luiz F. A.; Machado, Francisco B. C.

2018-04-01

The present work focuses in the characterization of the low-lying quartet electronic and spin-orbit states of diatomic borides XB, in which X is an element of group 14 (C, Si, Ge, Sn, PB). The wavefunction was obtained at the CASSCF/MRCI level with a quintuple-ζ quality basis set. Scalar relativistic effects were also taken into account. A systematic and comparative analysis of the spectroscopic properties for the title molecular series was carried out, showing that the (1)4Π→X4Σ- transition band is expected to be measurable by emission spectroscopy to the GeB, SnB and PbB molecules, as already observed for the lighter CB and SiB species.

Topical application of a G-Quartet aptamer targeting nucleolin attenuates choroidal neovascularization in a model of age-related macular degeneration.

PubMed

Leaderer, Derek; Cashman, Siobhan M; Kumar-Singh, Rajendra

2015-11-01

Choroidal neovascularization (CNV) associated with the 'wet' form of age related macular degeneration (AMD) is one of the most common causes of central vision loss among the elderly. The 'wet' form of AMD is currently treated by intravitreal delivery of anti-VEGF agents. However, intravitreal injections are associated with complications and long-term inhibition of VEGF leads to macular atrophy. Thus, there is currently an unmet need for the development of therapies for CNV that target molecules other than VEGF. Here, we describe nucleolin as a novel target for the 'wet' form of AMD. Nucleolin was found on the surface of endothelial cells that migrate from the choroid into the subretinal space in the laser-induced model of 'wet' AMD. AS1411 is a previously described G-quartet oligonucleotide that has been shown to bind nucleolin. We found that AS1411 inhibited the formation of tubes by human umbilical vein endothelial cells (HUVECs) by approximately 27.4% in vitro. AS1411 co-localized with the site of laser induced CNV in vivo. Intravitreally injected AS1411 inhibited laser-induced CNV by 37.6% and attenuated infiltration of macrophages by 40.3%. Finally, topical application of AS1411 led to a 43.4% reduction in CNV. Our observations have potential implications for the development of therapies for CNV and specifically for the 'wet' form of AMD. Copyright © 2015 Elsevier Ltd. All rights reserved.

Spin Uncoupling in Chemisorbed OCCO and CO 2: Two High-Energy Intermediates in Catalytic CO 2 Reduction

DOE PAGES

Hedstrom, Svante; dos Santos, Egon Campos; Liu, Chang; ...

2018-05-08

Here, the production of useful compounds via the electrochemical carbon dioxide reduction reaction (CO2RR) is a matter of intense research. Although the thermodynamics and kinetic barriers of CO2RR are reported in previous computational studies, the electronic structure details are often overlooked. We study two important CO2RR intermediates: ethylenedione (OCCO) and CO 2 covalently bound to cluster and slab models of the Cu(100) surface. Both molecules exhibit a near-unity negative charge as chemisorbed, but otherwise they behave quite differently, as explained by a spin-uncoupling perspective. OCCO adopts a high-spin, quartetlike geometry, allowing two covalent bonds to the surface with an averagemore » gross interaction energy of –1.82 eV/bond. The energy cost for electronically exciting OCCO– to the quartet state is 1.5 eV which is readily repaid via the formation of its two surface bonds. CO 2, conversely, retains a low-spin, doubletlike structure upon chemisorption, and its single unpaired electron forms a single covalent surface bond of –2.07 eV. The 5.0 eV excitation energy to the CO 2 – quartet state is prohibitively costly and cannot be compensated for by an additional surface bond.« less

The Sommerfeld enhancement in the scotogenic model with large electroweak scalar multiplets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chowdhury, Talal Ahmed; Nasri, Salah, E-mail: talal@du.ac.bd, E-mail: snasri@uaeu.ac.ae

2017-01-01

We investigate the Sommerfeld enhancement (SE) in the generalized scotogenic model with large electroweak multiplets. We focus on scalar dark matter (DM) candidate of the model and compare DM annihilation cross sections to WW , ZZ , γγ and γ Z at present day in the galactic halo for scalar doublet and its immediate generalization, the quartet in their respective viable regions of parameter space. We find that larger multiplet has sizable Sommerfeld enhanced annihilation cross section compared to the doublet and because of that it is more likely to be constrained by the current H.E.S.S. results and future CTAmore » sensitivity limits.« less

Arabidopsis SEPALLATA proteins differ in cooperative DNA-binding during the formation of floral quartet-like complexes

PubMed Central

Jetha, Khushboo; Theißen, Günter; Melzer, Rainer

2014-01-01

The SEPALLATA (SEP) genes of Arabidopsis thaliana encode MADS-domain transcription factors that specify the identity of all floral organs. The four Arabidopsis SEP genes function in a largely yet not completely redundant manner. Here, we analysed interactions of the SEP proteins with DNA. All of the proteins were capable of forming tetrameric quartet-like complexes on DNA fragments carrying two sequence elements termed CArG-boxes. Distances between the CArG-boxes for strong cooperative DNA-binding were in the range of 4–6 helical turns. However, SEP1 also bound strongly to CArG-box pairs separated by smaller or larger distances, whereas SEP2 preferred large and SEP4 preferred small inter-site distances for binding. Cooperative binding of SEP3 was comparatively weak for most of the inter-site distances tested. All SEP proteins constituted floral quartet-like complexes together with the floral homeotic proteins APETALA3 (AP3) and PISTILLATA (PI) on the target genes AP3 and SEP3. Our results suggest an important part of an explanation for why the different SEP proteins have largely, but not completely redundant functions in determining floral organ identity: they may bind to largely overlapping, but not identical sets of target genes that differ in the arrangement and spacing of the CArG-boxes in their cis-regulatory regions. PMID:25183521

H6+ in irradiated solid para-hydrogen and its decay dynamics: reinvestigation of quartet electron paramagnetic resonance lines assigned to H2-.

PubMed

Kumada, Takayuki; Tachikawa, Hiroto; Takayanagi, Toshiyuki

2005-03-07

The quartet electron paramagnetic resonance (EPR) lines observed in gamma- and X-ray irradiated solid para-H2, which have previously been assigned to H2-, are reinvestigated. We have reassigned the quartet lines to H6 rather than H2- mainly due to comparison of experimentally obtained EPR parameters to theoretical results. Based on the new assignment, trapping site, rotation, ortho-para conversion, quantum diffusion and isotope effect of H+ have been reinterpreted by the precise reanalysis as follows. The H6+ ion is composed of the collinearly aligned H2+ core at the center and two H2 rotors at both ends, occupies a single substitutional site, and has a precession motion around a crystalline axis with the angle of approximately 57 degrees. The ortho-para conversion of H2+ core of H6+ is completed within the time-scale of hours, whereas ortho-H2 molecules near H6+ convert much faster. H6+ diffuses quantum mechanically by the repetition of H6+ + H2 --> H2 + H6+ reaction. The diffusion terminates by the reaction, H6(+) + HD --> H5D(+) + H2, with a HD impurity contained in the para-H2 sample at natural abundance. Finally, we will propose a possible reason why H6+ is produced instead of H3+ in the irradiated solid H2.

Energy, fine structure, hyperfine structure, and radiative transition rates of the high-lying multi-excited states for B-like neon

NASA Astrophysics Data System (ADS)

Zhang, Chun Mei; Chen, Chao; Sun, Yan; Gou, Bing Cong; Shao, Bin

2015-04-01

The Rayleigh-Ritz variational method with multiconfiguration interaction wave functions is used to obtain the energies of high-lying multi-excited quartet states 1 s 22 s2 pnl and 1 s 22 p 2 nl 4Pe,o ( n ≥ 2) in B-like neon, including the mass polarization and relativistic corrections. The fine structure and hyperfine structure of the excited quartet states for this system are investigated. Configuration structures of the high-lying multi-excited series are further identified by relativistic corrections and fine structure splittings. The transition rates and wavelengths are also calculated. Calculated wavelengths include the quantum electrodynamic effects. The results are compared with other theoretical and experimental data in the literature.

Identifying guanosine self assembly at natural isotopic abundance by high-resolution 1H and 13C solid-state NMR spectroscopy.

PubMed

Webber, Amy L; Masiero, Stefano; Pieraccini, Silvia; Burley, Jonathan C; Tatton, Andrew S; Iuga, Dinu; Pham, Tran N; Spada, Gian Piero; Brown, Steven P

2011-12-14

By means of the (1)H chemical shifts and the proton-proton proximities as identified in (1)H double-quantum (DQ) combined rotation and multiple-pulse spectroscopy (CRAMPS) solid-state NMR correlation spectra, ribbon-like and quartet-like self-assembly can be identified for guanosine derivatives without isotopic labeling for which it was not possible to obtain single crystals suitable for diffraction. Specifically, characteristic spectral fingerprints are observed for dG(C10)(2) and dG(C3)(2) derivatives, for which quartet-like and ribbon-like self-assembly has been unambiguously identified by (15)N refocused INADEQUATE spectra in a previous study of (15)N-labeled derivatives (Pham, T. N.; et al. J. Am. Chem. Soc.2005, 127, 16018). The NH (1)H chemical shift is observed to be higher (13-15 ppm) for ribbon-like self-assembly as compared to 10-11 ppm for a quartet-like arrangement, corresponding to a change from NH···N to NH···O intermolecular hydrogen bonding. The order of the two NH(2)(1)H chemical shifts is also inverted, with the NH(2) proton closest in space to the NH proton having a higher or lower (1)H chemical shift than that of the other NH(2) proton for ribbon-like as opposed to quartet-like self-assembly. For the dG(C3)(2) derivative for which a single-crystal diffraction structure is available, the distinct resonances and DQ peaks are assigned by means of gauge-including projector-augmented wave (GIPAW) chemical shift calculations. In addition, (14)N-(1)H correlation spectra obtained at 850 MHz under fast (60 kHz) magic-angle spinning (MAS) confirm the assignment of the NH and NH(2) chemical shifts for the dG(C3)(2) derivative and allow longer range through-space N···H proximities to be identified, notably to the N7 nitrogens on the opposite hydrogen-bonding face. © 2011 American Chemical Society

The voltage-sensor quartet

PubMed Central

Bankston, J. R.; Kass, R. S.

2009-01-01

Decoding the workings of voltage-gated sodium channels is crucial because their mutation leads to severe disease and their activity is modulated by toxins and drugs. An innovative approach now allows such investigations. PMID:19005542

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

PubMed Central

Li, Mingkun; Rothwell, Rebecca; Vermaat, Martijn; Wachsmuth, Manja; Schröder, Roland; Laros, Jeroen F.J.; van Oven, Mannis; de Bakker, Paul I.W.; Bovenberg, Jasper A.; van Duijn, Cornelia M.; van Ommen, Gert-Jan B.; Slagboom, P. Eline; Swertz, Morris A.; Wijmenga, Cisca; Kayser, Manfred; Boomsma, Dorret I.; Zöllner, Sebastian; de Knijff, Peter; Stoneking, Mark

2016-01-01

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies. PMID:26916109

Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.

PubMed

Guédin, Aurore; Lin, Linda Yingqi; Armane, Samir; Lacroix, Laurent; Mergny, Jean-Louis; Thore, Stéphane; Yatsunyk, Liliya A

2018-06-01

Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

Predictive coding links perception, action, and learning to emotions in music. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Gebauer, L.; Kringelbach, M. L.; Vuust, P.

2015-06-01

The review by Koelsch and colleagues [1] offers a timely, comprehensive, and anatomically detailed framework for understanding the neural correlates of human emotions. The authors describe emotion in a framework of four affect systems, which are linked to effector systems, and higher order cognitive functions. This is elegantly demonstrated through the example of music; a realm for exploring emotions in a domain, that can be independent of language but still highly relevant for understanding human emotions [2].

Electric dipole moments and chemical bonding of diatomic alkali-alkaline earth molecules.

PubMed

Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2016-02-17

We investigate the properties of alkali-alkaline earth diatomic molecules in the lowest Σ(+) states of the doublet and quartet multiplicity by ab initio calculations. In all sixteen cases studied, the permanent electric dipole moment points in opposite directions for the two spin states. This peculiarity can be explained by molecular orbital theory. We further discuss dissociation energies and bond distances. We analyze trends and provide an empirically motivated model for the prediction of the permanent electric dipole moment for combinations of alkali and alkaline earth atoms not studied in this work.

What is reconfigured?. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Engelen, Eva-Maria

2015-06-01

The research group around Koelsch presents a neurobiological emotion theory that is supposed to have the following plus factors: (1) Interdisciplinary approach towards understanding human emotions and their neural correlates, (2) concentration on human emotions, (3) interaction between language and emotion, (4) allows research on short-term emotional phenomena and takes long-term emotional phenomena into account, as well as the differences of the neural correlates underlying short-term and long-term emotions [5]. This is a very ambitious program. My comment will focus on (3) and (4).

Big physics quartet win government backing

NASA Astrophysics Data System (ADS)

Banks, Michael

2014-09-01

Four major physics-based projects are among 10 to have been selected by Japan’s Ministry of Education, Culture, Sports, Science and Technology for funding in the coming decade as part of its “roadmap” of big-science projects.

A state interaction spin-orbit coupling density matrix renormalization group method

NASA Astrophysics Data System (ADS)

Sayfutyarova, Elvira R.; Chan, Garnet Kin-Lic

2016-06-01

We describe a state interaction spin-orbit (SISO) coupling method using density matrix renormalization group (DMRG) wavefunctions and the spin-orbit mean-field (SOMF) operator. We implement our DMRG-SISO scheme using a spin-adapted algorithm that computes transition density matrices between arbitrary matrix product states. To demonstrate the potential of the DMRG-SISO scheme we present accurate benchmark calculations for the zero-field splitting of the copper and gold atoms, comparing to earlier complete active space self-consistent-field and second-order complete active space perturbation theory results in the same basis. We also compute the effects of spin-orbit coupling on the spin-ladder of the iron-sulfur dimer complex [Fe2S2(SCH3)4]3-, determining the splitting of the lowest quartet and sextet states. We find that the magnitude of the zero-field splitting for the higher quartet and sextet states approaches a significant fraction of the Heisenberg exchange parameter.

3,4,5,6-Tetrafluorophenylnitren-2-yl: a ground-state quartet triradical.

PubMed

Grote, Dirk; Finke, Christopher; Kossmann, Simone; Neese, Frank; Sander, Wolfram

2010-04-19

The photochemistry of 2-iodo-3,4,5,6-tetrafluorophenyl azide (7 d) has been investigated in argon and neon matrices at 4 K, and the products characterized by IR and EPR spectroscopy. The primary photochemical step is loss of a nitrogen molecule and formation of phenyl nitrene 1 d. Further irradiation with UV or visible light results in mixtures of 1 d with azirine 5 d', ketenimine 6 d', nitreno radical 2 d, and azirinyl radical 9. The relative amounts of these products strongly depend on the matrix and on the irradiation conditions. Nitreno radical 2 d with a quartet ground state was characterized by EPR spectroscopy. Electronic structure calculations in combination with the experimental results allow for a detailed understanding of the properties of this unusual new type of organic high-spin molecules. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measuring ensemble interdependence in a string quartet through analysis of multidimensional performance data

PubMed Central

Papiotis, Panos; Marchini, Marco; Perez-Carrillo, Alfonso; Maestre, Esteban

2014-01-01

In a musical ensemble such as a string quartet, the musicians interact and influence each other's actions in several aspects of the performance simultaneously in order to achieve a common aesthetic goal. In this article, we present and evaluate a computational approach for measuring the degree to which these interactions exist in a given performance. We recorded a number of string quartet exercises under two experimental conditions (solo and ensemble), acquiring both audio and bowing motion data. Numerical features in the form of time series were extracted from the data as performance descriptors representative of four distinct dimensions of the performance: Intonation, Dynamics, Timbre, and Tempo. Four different interdependence estimation methods (two linear and two nonlinear) were applied to the extracted features in order to assess the overall level of interdependence between the four musicians. The obtained results suggest that it is possible to correctly discriminate between the two experimental conditions by quantifying interdependence between the musicians in each of the studied performance dimensions; the nonlinear methods appear to perform best for most of the numerical features tested. Moreover, by using the solo recordings as a reference to which the ensemble recordings are contrasted, it is feasible to compare the amount of interdependence that is established between the musicians in a given performance dimension across all exercises, and relate the results to the underlying goal of the exercise. We discuss our findings in the context of ensemble performance research, the current limitations of our approach, and the ways in which it can be expanded and consolidated. PMID:25228894

Helium cluster isolation spectroscopy

NASA Astrophysics Data System (ADS)

Higgins, John Paul

Clusters of helium, each containing ~103- 104 atoms, are produced in a molecular beam and are doped with alkali metal atoms (Li, Na, and K) and large organic molecules. Electronic spectroscopy in the visible and UV regions of the spectrum is carried out on the dopant species. Since large helium clusters are liquid and attain an equilibrium internal temperature of 0.4 K, they interact weakly with atoms or molecules absorbed on their surface or resident inside the cluster. The spectra that are obtained are characterized by small frequency shifts from the positions of the gas phase transitions, narrow lines, and cold vibrational temperatures. Alkali atoms aggregate on the helium cluster surface to form dimers and trimers. The spectra of singlet alkali dimers exhibit the presence of elementary excitations in the superfluid helium cluster matrix. It is found that preparation of the alkali molecules on the surface of helium clusters leads to the preferential formation of high-spin, van der Waals bound, triplet dimers and quartet trimers. Four bound-bound and two bound-free transitions are observed in the triplet manifold of the alkali dimers. The quartet trimers serve as an ideal system for the study of a simple unimolecular reaction in the cold helium cluster environment. Analysis of the lowest quartet state provides valuable insight into three-body forces in a van der Waals trimer. The wide range of atomic and molecular systems studied in this thesis constitutes a preliminary step in the development of helium cluster isolation spectroscopy, a hybrid technique combining the advantages of high resolution spectroscopy with the synthetic, low temperature environment of matrices.

Analysis of a DNA simulation model through hairpin melting experiments.

PubMed

Linak, Margaret C; Dorfman, Kevin D

2010-09-28

We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models.

Molecular Mechanisms Underlying Origin and Diversification of the Angiosperm Flower

PubMed Central

Theissen, Guenter; Melzer, Rainer

2007-01-01

Background Understanding the mode and mechanisms of the evolution of the angiosperm flower is a long-standing and central problem of evolutionary biology and botany. It has essentially remained unsolved, however. In contrast, considerable progress has recently been made in our understanding of the genetic basis of flower development in some extant model species. The knowledge that accumulated this way has been pulled together in two major hypotheses, termed the ‘ABC model’ and the ‘floral quartet model’. These models explain how the identity of the different types of floral organs is specified during flower development by homeotic selector genes encoding transcription factors. Scope We intend to explain how the ‘ABC model’ and the ‘floral quartet model’ are now guiding investigations that help to understand the origin and diversification of the angiosperm flower. Conclusions Investigation of orthologues of class B and class C floral homeotic genes in gymnosperms suggest that bisexuality was one of the first innovations during the origin of the flower. The transition from dimer to tetramer formation of floral homeotic proteins after establishment of class E proteins may have increased cooperativity of DNA binding of the transcription factors controlling reproductive growth. That way, we hypothesize, better ‘developmental switches’ originated that facilitated the early evolution of the flower. Expression studies of ABC genes in basally diverging angiosperm lineages, monocots and basal eudicots suggest that the ‘classical’ ABC system known from core eudicots originated from a more fuzzy system with fading borders of gene expression and gradual transitions in organ identity, by sharpening of ABC gene expression domains and organ borders. Shifting boundaries of ABC gene expression may have contributed to the diversification of the angiosperm flower many times independently, as may have changes in interactions between ABC genes and their target genes. PMID:17670752

Density-induced suppression of the {alpha}-particle condensate in nuclear matter and the structure of {alpha}-cluster states in nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Funaki, Y.; Horiuchi, H.; International Institute for Advanced Studies, Kizugawa 619-0225

2008-06-15

At low densities, with decreasing temperatures, in symmetric nuclear matter {alpha} particles are formed, which eventually give raise to a quantum condensate with four-nucleon {alpha}-like correlations (quartetting). Starting with a model of {alpha} matter, where undistorted {alpha} particles interact via an effective interaction such as the Ali-Bodmer potential, the suppression of the condensate fraction at zero temperature with increasing density is considered. Using a Jastrow-Feenberg approach, it is found that the condensate fraction vanishes near saturation density. Additionally, the modification of the internal state of the {alpha} particle due to medium effects will further reduce the condensate. In finite systems,more » an enhancement of the S-state wave function of the center-of-mass orbital of {alpha}-particle motion is considered as the correspondence to the condensate. Wave functions have been constructed for self-conjugate 4n nuclei that describe the condensate state but are fully antisymmetrized on the nucleonic level. These condensate-like cluster wave functions have been successfully applied to describe properties of low-density states near the n{alpha} threshold. Comparison with orthogonality condition model calculations in {sup 12}C and {sup 16}O shows strong enhancement of the occupation of the S-state center-of-mass orbital of the {alpha} particles. This enhancement is decreasing if the baryon density increases, similar to the density-induced suppression of the condensate fraction in {alpha} matter. The ground states of {sup 12}C and {sup 16}O show no enhancement at all, thus a quartetting condensate cannot be formed at saturation densities.« less

Creating A Choral Sound.

ERIC Educational Resources Information Center

Leenman, Tracy E.

1996-01-01

Covers a variety of strategies for creating a unique and identifiable choral sound. Provides specific instructions for developing singing in unison and recommends a standing arrangement of soprano, alto, tenor, and bass quartets. Provides other tips for instrumentation, sight reading, and quality rehearsal time. (MJP)

Levels of analysis in neuroscientific studies of emotion: Comment on "The quartet theory of human emotions: an integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Kuiken, Don; Douglas, Shawn

2015-06-01

In the conduct of neuroscience research, methodological choices and theoretical claims often reveal underlying metamethodological and ontological commitments. Koelsch et al. [1] accentuate such commitments in their description of four "neuroanatomically distinct systems," each the substrate of "a specific class of affects" (p. 1). Explication of those classes of affect require theoretical integration across methodologically diverse disciplines, including "psychology, neurobiology, sociology, anthropology, and psycholinguistics" (p. 3). (Philosophy is noticeably missing from this list, but several aspects of the authors' stance indicate that it is not ignored.)

Genetics Home Reference: anauxetic dysplasia

MedlinePlus

... one gene that provides instructions for making a protein component of the RNase MRP enzyme complex can also cause anauxetic ... A, Donskoi M, Kenna TJ, Thomas GP, Clark GR, Duncan EL, Brown MA. Whole-exome re-sequencing in a family quartet identifies POP1 mutations as ...

Ammonium Ion Binding to DNA G-Quadruplexes: Do Electrospray Mass Spectra Faithfully Reflect the Solution-Phase Species?

NASA Astrophysics Data System (ADS)

Balthasart, Françoise; Plavec, Janez; Gabelica, Valérie

2013-01-01

G-quadruplex nucleic acids can bind ammonium ions in solution, and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG4T4G4)2, (dG4T3G4)2, and (dG3T4G4)2, and the intramolecular G-quadruplexes dG4(T4G4)3 and dG2T2G2TGTG2T2G2 (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure traveling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets, can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments, therefore, help assign the number of inner ammonium ions in the solution phase structure.[Figure not available: see fulltext.

Microspore Separation in the quartet 3 Mutants of Arabidopsis Is Impaired by a Defect in a Developmentally Regulated Polygalacturonase Required for Pollen Mother Cell Wall Degradation1

PubMed Central

Rhee, Seung Y.; Osborne, Erin; Poindexter, Patricia D.; Somerville, Chris R.

2003-01-01

Mutations in the QUARTET loci in Arabidopsis result in failure of microspore separation during pollen development due to a defect in degradation of the pollen mother cell wall during late stages of pollen development. Mutations in a new locus required for microspore separation, QRT3, were isolated, and the corresponding gene was cloned by T-DNA tagging. QRT3 encodes a protein that is approximately 30% similar to an endopolygalacturonase from peach (Prunus persica). The QRT3 protein was expressed in yeast (Saccharomyces cerevisiae) and found to exhibit polygalacturonase activity. In situ hybridization experiments showed that QRT3 is specifically and transiently expressed in the tapetum during the phase when microspores separate from their meiotic siblings. Immunohistochemical localization of QRT3 indicated that the protein is secreted from tapetal cells during the early microspore stage. Thus, QRT3 plays a direct role in degrading the pollen mother cell wall during microspore development. PMID:14551328

Stability of soliton families in nonlinear Schrödinger equations with non-parity-time-symmetric complex potentials

NASA Astrophysics Data System (ADS)

Yang, Jianke; Nixon, Sean

2016-11-01

Stability of soliton families in one-dimensional nonlinear Schrödinger equations with non-parity-time (PT)-symmetric complex potentials is investigated numerically. It is shown that these solitons can be linearly stable in a wide range of parameter values both below and above phase transition. In addition, a pseudo-Hamiltonian-Hopf bifurcation is revealed, where pairs of purely-imaginary eigenvalues in the linear-stability spectra of solitons collide and bifurcate off the imaginary axis, creating oscillatory instability, which resembles Hamiltonian-Hopf bifurcations of solitons in Hamiltonian systems even though the present system is dissipative and non-Hamiltonian. The most important numerical finding is that, eigenvalues of linear-stability operators of these solitons appear in quartets (λ , - λ ,λ* , -λ*), similar to conservative systems and PT-symmetric systems. This quartet eigenvalue symmetry is very surprising for non- PT-symmetric systems, and it has far-reaching consequences on the stability behaviors of solitons.

A state interaction spin-orbit coupling density matrix renormalization group method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayfutyarova, Elvira R.; Chan, Garnet Kin-Lic

We describe a state interaction spin-orbit (SISO) coupling method using density matrix renormalization group (DMRG) wavefunctions and the spin-orbit mean-field (SOMF) operator. We implement our DMRG-SISO scheme using a spin-adapted algorithm that computes transition density matrices between arbitrary matrix product states. To demonstrate the potential of the DMRG-SISO scheme we present accurate benchmark calculations for the zero-field splitting of the copper and gold atoms, comparing to earlier complete active space self-consistent-field and second-order complete active space perturbation theory results in the same basis. We also compute the effects of spin-orbit coupling on the spin-ladder of the iron-sulfur dimer complex [Fe{submore » 2}S{sub 2}(SCH{sub 3}){sub 4}]{sup 3−}, determining the splitting of the lowest quartet and sextet states. We find that the magnitude of the zero-field splitting for the higher quartet and sextet states approaches a significant fraction of the Heisenberg exchange parameter.« less

The quartet theory of human emotions: An integrative and neurofunctional model

NASA Astrophysics Data System (ADS)

Koelsch, Stefan; Jacobs, Arthur M.; Menninghaus, Winfried; Liebal, Katja; Klann-Delius, Gisela; von Scheve, Christian; Gebauer, Gunter

2015-06-01

Despite an explosion of research in the affective sciences during the last few decades, interdisciplinary theories of human emotions are lacking. Here we present a neurobiological theory of emotions that includes emotions which are uniquely human (such as complex moral emotions), considers the role of language for emotions, advances the understanding of neural correlates of attachment-related emotions, and integrates emotion theories from different disciplines. We propose that four classes of emotions originate from four neuroanatomically distinct cerebral systems. These emotional core systems constitute a quartet of affect systems: the brainstem-, diencephalon-, hippocampus-, and orbitofrontal-centred affect systems. The affect systems were increasingly differentiated during the course of evolution, and each of these systems generates a specific class of affects (e.g., ascending activation, pain/pleasure, attachment-related affects, and moral affects). The affect systems interact with each other, and activity of the affect systems has effects on - and interacts with - biological systems denoted here as emotional effector systems. These effector systems include motor systems (which produce actions, action tendencies, and motoric expression of emotion), peripheral physiological arousal, as well as attentional and memory systems. Activity of affect systems and effector systems is synthesized into an emotion percept (pre-verbal subjective feeling), which can be transformed (or reconfigured) into a symbolic code such as language. Moreover, conscious cognitive appraisal (involving rational thought, logic, and usually language) can regulate, modulate, and partly initiate, activity of affect systems and effector systems. Our emotion theory integrates psychological, neurobiological, sociological, anthropological, and psycholinguistic perspectives on emotions in an interdisciplinary manner, aiming to advance the understanding of human emotions and their neural correlates.

Reimer through Confucian Lenses: Resonances with Classical Chinese Aesthetics

ERIC Educational Resources Information Center

Tan, Leonard

2015-01-01

In this paper, I compare all three editions of Bennett Reimer's "A Philosophy of Music Education" with early Chinese philosophy, in particular, classical Chinese aesthetics. I structure my analysis around a quartet of interrelated themes: aesthetic education, education of feeling, aesthetic experience, and ethics and aesthetics. This…

Perspectives on Pre-Service Teacher Knowledge for Teaching Early Algebra

ERIC Educational Resources Information Center

McAuliffe, Sharon; Lubben, Fred

2013-01-01

This paper examines a pre-service teacher's content knowledge for teaching early algebra from two perspectives, i.e. using "Rowland's Knowledge Quartet" theory and "Ball's framework for Mathematical Knowledge for Testing" (MKfT). The study intends to examine the differences between the influences using each framework and to…

Brief Report: Altered Horizontal Binding of Single Dots to Coherent Motion in Autism

ERIC Educational Resources Information Center

David, Nicole; Rose, Michael; Schneider, Till R.; Vogeley, Kai; Engel, Andreas K.

2010-01-01

Individuals with autism often show a fragmented way of perceiving their environment, suggesting a disorder of information integration, possibly due to disrupted communication between brain areas. We investigated thirteen individuals with high-functioning autism (HFA) and thirteen healthy controls using the metastable motion quartet, a stimulus…

A Quartet of Change Guides.

ERIC Educational Resources Information Center

Gates, Alan

Since spring 1979 numerous changes in Humanities offerings and operations have been discussed, agreed upon, and implemented at Clark College to revitalize enrollments and increase faculty energy levels. The process of change was based upon four principles: (1) the faculty perceived the need to change, wanted to explore the potential benefits of…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Wonjung; Kovacic, Gregor; Cai, David

Using the (1+1)D Majda-McLaughlin-Tabak model as an example, we present an extension of the wave turbulence (WT) theory to systems with strong nonlinearities. We demonstrate that nonlinear wave interactions renormalize the dynamics, leading to (i) a possible destruction of scaling structures in the bare wave systems and a drastic deformation of the resonant manifold even at weak nonlinearities, and (ii) creation of nonlinear resonance quartets in wave systems for which there would be no resonances as predicted by the linear dispersion relation. Finally, we derive an effective WT kinetic equation and show that our prediction of the renormalized Rayleigh-Jeans distributionmore » is in excellent agreement with the simulation of the full wave system in equilibrium.« less

A three-decade-long journey at the College of Optical Sciences

NASA Astrophysics Data System (ADS)

Sarid, Dror

2014-09-01

In 1980, Peter Franken, the second director of the Optical Sciences Center, recruited an international quartet of faculty members from the US, Canada, England and Israel (DS). Peter shaped the Center as a clockwork operation, nailing down every aspect of its administration, business model and academic vision. I found myself from day one in a highly competitive environment with extreme peer pressure to make good science and generate a lot of funds. This paper describes the academic journey through my three decades at the Optical Sciences Center that became the College of Optical Sciences (Optical Sciences, in short) until my retirement in 2010, by highlighting selected areas of my group's research.

Targeting Stat3 With G-Quartet Oligonucleotides in Metastatic Prostate Cancer

DTIC Science & Technology

2005-04-01

Wegenka UM, Lutticken C, Buschmann J, et al. The interleukin-6-activated acute- 34. Mazurmder A, Neamati N, Ojwang JO, Sunder S, Rando RF, Pommier Y...Chem 1995; 270: 1754-60. antisense directed against telomerase RNA. Oncogene 1998; 16: [8] Mazumder A, Neamati N, Ojwang JO, Sunder S, Rando RF, 3323

High-level ab initio studies of NO(X2Π)-O2(X3Σg -) van der Waals complexes in quartet states

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2018-05-01

Geometry optimisations were performed on nine different structures of NO(X2Π)-O2(X3Σg-) van der Waals complexes in their quartet states, using the explicitly correlated RCCSD(T)-F12b method with basis sets up to the cc-pVQZ-F12 level. For the most stable configurations, counterpoise-corrected optimisations as well as extrapolations to the complete basis set (CBS) were performed. The X structure in the 4A‧ state was found to be most stable, with a CBS binding energy of -157 cm-1. The slipped tilted structures with N closer to O2 (Slipt-N), as well as the slipped parallel structure with O of NO closer to O2 (Slipp-O) in 4A″ states have binding energies of about -130 cm-1. C2v and linear complexes are less stable. According to calculated harmonic frequencies, the X isomer is bound. Isotropic hyperfine coupling constants of the complex are compared with those of the monomers.

Thrombin-Binding Aptamer Quadruplex Formation: AFM and Voltammetric Characterization

PubMed Central

Diculescu, Victor Constantin; Chiorcea-Paquim, Ana-Maria; Eritja, Ramon; Oliveira-Brett, Ana Maria

2010-01-01

The adsorption and the redox behaviour of thrombin-binding aptamer (TBA) and extended TBA (eTBA) were studied using atomic force microscopy and voltammetry at highly oriented pyrolytic graphite and glassy carbon. The different adsorption patterns and degree of surface coverage were correlated with the sequence base composition, presence/absence of K+, and voltammetric behaviour of TBA and eTBA. In the presence of K+, only a few single-stranded sequences present adsorption, while the majority of the molecules forms stable and rigid quadruplexes with no adsorption. Both TBA and eTBA are oxidized and the only anodic peak corresponds to guanine oxidation. Upon addition of K+ ions, TBA and eTBA fold into a quadruplex, causing the decrease of guanine oxidation peak and occurrence of a new peak at a higher potential due to the oxidation of G-quartets. The higher oxidation potential of G-quartets is due to the greater difficulty of electron transfer from the inside of the quadruplex to the electrode surface than electron transfer from the more flexible single strands. PMID:20798847

Memory, mental time travel and The Moustachio Quartet.

PubMed

Clayton, Nicola; Wilkins, Clive

2017-06-06

Mental time travel allows us to revisit our memories and imagine future scenarios, and this is why memories are not only about the past, but they are also prospective. These episodic memories are not a fixed store of what happened, however, they are reassessed each time they are revisited and depend on the sequence in which events unfold. In this paper, we shall explore the complex relationships between memory and human experience, including through a series of novels 'The Moustachio Quartet' that can be read in any order. To do so, we shall integrate evidences from science and the arts to explore the subjective nature of memory and mental time travel, and argue that it has evolved primarily for prospection as opposed to retrospection. Furthermore, we shall question the notion that mental time travel is a uniquely human construct, and argue that some of the best evidence for the evolution of mental time travel comes from our distantly related cousins, the corvids, that cache food for the future and rely on long-lasting and highly accurate memories of what, where and when they stored their stashes of food.

Toxic genes present a unique phylogenetic signature.

PubMed

Avni, Eliran; Snir, Sagi

2017-11-01

Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution. Copyright © 2017 Elsevier Inc. All rights reserved.

High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation.

PubMed

Kerkour, Abdelaziz; Marquevielle, Julien; Ivashchenko, Stefaniia; Yatsunyk, Liliya A; Mergny, Jean-Louis; Salgado, Gilmar F

2017-05-12

Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Scale-free brain quartet: artistic filtering of multi-channel brainwave music.

PubMed

Wu, Dan; Li, Chaoyi; Yao, Dezhong

2013-01-01

To listen to the brain activities as a piece of music, we proposed the scale-free brainwave music (SFBM) technology, which translated scalp EEGs into music notes according to the power law of both EEG and music. In the present study, the methodology was extended for deriving a quartet from multi-channel EEGs with artistic beat and tonality filtering. EEG data from multiple electrodes were first translated into MIDI sequences by SFBM, respectively. Then, these sequences were processed by a beat filter which adjusted the duration of notes in terms of the characteristic frequency. And the sequences were further filtered from atonal to tonal according to a key defined by the analysis of the original music pieces. Resting EEGs with eyes closed and open of 40 subjects were utilized for music generation. The results revealed that the scale-free exponents of the music before and after filtering were different: the filtered music showed larger variety between the eyes-closed (EC) and eyes-open (EO) conditions, and the pitch scale exponents of the filtered music were closer to 1 and thus it was more approximate to the classical music. Furthermore, the tempo of the filtered music with eyes closed was significantly slower than that with eyes open. With the original materials obtained from multi-channel EEGs, and a little creative filtering following the composition process of a potential artist, the resulted brainwave quartet opened a new window to look into the brain in an audible musical way. In fact, as the artistic beat and tonal filters were derived from the brainwaves, the filtered music maintained the essential properties of the brain activities in a more musical style. It might harmonically distinguish the different states of the brain activities, and therefore it provided a method to analyze EEGs from a relaxed audio perspective.

Scale-Free Brain Quartet: Artistic Filtering of Multi-Channel Brainwave Music

PubMed Central

Wu, Dan; Li, Chaoyi; Yao, Dezhong

2013-01-01

To listen to the brain activities as a piece of music, we proposed the scale-free brainwave music (SFBM) technology, which translated scalp EEGs into music notes according to the power law of both EEG and music. In the present study, the methodology was extended for deriving a quartet from multi-channel EEGs with artistic beat and tonality filtering. EEG data from multiple electrodes were first translated into MIDI sequences by SFBM, respectively. Then, these sequences were processed by a beat filter which adjusted the duration of notes in terms of the characteristic frequency. And the sequences were further filtered from atonal to tonal according to a key defined by the analysis of the original music pieces. Resting EEGs with eyes closed and open of 40 subjects were utilized for music generation. The results revealed that the scale-free exponents of the music before and after filtering were different: the filtered music showed larger variety between the eyes-closed (EC) and eyes-open (EO) conditions, and the pitch scale exponents of the filtered music were closer to 1 and thus it was more approximate to the classical music. Furthermore, the tempo of the filtered music with eyes closed was significantly slower than that with eyes open. With the original materials obtained from multi-channel EEGs, and a little creative filtering following the composition process of a potential artist, the resulted brainwave quartet opened a new window to look into the brain in an audible musical way. In fact, as the artistic beat and tonal filters were derived from the brainwaves, the filtered music maintained the essential properties of the brain activities in a more musical style. It might harmonically distinguish the different states of the brain activities, and therefore it provided a method to analyze EEGs from a relaxed audio perspective. PMID:23717527

The quartet theory of human emotions: An integrative and neurofunctional model.

PubMed

Koelsch, Stefan; Jacobs, Arthur M; Menninghaus, Winfried; Liebal, Katja; Klann-Delius, Gisela; von Scheve, Christian; Gebauer, Gunter

2015-06-01

Despite an explosion of research in the affective sciences during the last few decades, interdisciplinary theories of human emotions are lacking. Here we present a neurobiological theory of emotions that includes emotions which are uniquely human (such as complex moral emotions), considers the role of language for emotions, advances the understanding of neural correlates of attachment-related emotions, and integrates emotion theories from different disciplines. We propose that four classes of emotions originate from four neuroanatomically distinct cerebral systems. These emotional core systems constitute a quartet of affect systems: the brainstem-, diencephalon-, hippocampus-, and orbitofrontal-centred affect systems. The affect systems were increasingly differentiated during the course of evolution, and each of these systems generates a specific class of affects (e.g., ascending activation, pain/pleasure, attachment-related affects, and moral affects). The affect systems interact with each other, and activity of the affect systems has effects on - and interacts with - biological systems denoted here as emotional effector systems. These effector systems include motor systems (which produce actions, action tendencies, and motoric expression of emotion), peripheral physiological arousal, as well as attentional and memory systems. Activity of affect systems and effector systems is synthesized into an emotion percept (pre-verbal subjective feeling), which can be transformed (or reconfigured) into a symbolic code such as language. Moreover, conscious cognitive appraisal (involving rational thought, logic, and usually language) can regulate, modulate, and partly initiate, activity of affect systems and effector systems. Our emotion theory integrates psychological, neurobiological, sociological, anthropological, and psycholinguistic perspectives on emotions in an interdisciplinary manner, aiming to advance the understanding of human emotions and their neural correlates. Copyright © 2015 Elsevier B.V. All rights reserved.

QuartetS-DB: A Large-Scale Orthology Database for Prokaryotes and Eukaryotes Inferred by Evolutionary Evidence

DTIC Science & Technology

2012-01-01

particular functions and identify species that contain these proteins. For example, if users select two species, Homo sapiens and Mus musculus, and...Kerr AR, McCormack TJ, Riley M: Evolution by leaps: gene duplication in bacteria. Biol Direct 2009, 4:46. 12. Remm M, Storm CE, Sonnhammer EL

A Case Study of Pedagogy of Mathematics Support Tutors without a Background in Mathematics Education

ERIC Educational Resources Information Center

Walsh, Richard

2017-01-01

This study investigates the pedagogical skills and knowledge of three tertiary-level mathematics support tutors in a large group classroom setting. This is achieved through the use of video analysis and a theoretical framework comprising Rowland's Knowledge Quartet and general pedagogical knowledge. The study reports on the findings in relation to…

The Fragile X Mental Retardation Protein, FMRP, Recognizes G-Quartets

ERIC Educational Resources Information Center

Darnell, Jennifer C.; Warren, Stephen T.; Darnell, Robert B.

2004-01-01

Fragile X mental retardation is a disease caused by the loss of function of a single RNA-binding protein, FMRP. Identifying the RNA targets recognized by FMRP is likely to reveal much about its functions in controlling some aspects of memory and behavior. Recent evidence suggests that one of the predominant RNA motifs recognized by the FMRP…

A Coin-Flipping Analogy and Web App for Teaching Spin-Spin Splitting in [superscript 1]H NMR Spectroscopy

ERIC Educational Resources Information Center

Azman, Adam M.; Esteb, John J.

2016-01-01

A coin-flipping analogy and free corresponding web app have been developed to facilitate student understanding of the origins of spin-spin splitting. First-order splitting patterns can easily be derived and understood. "Complex" splitting patterns (e.g., doublet of quartets), are easily incorporated into the analogy. A study of the…

Interaction of metallo- and free base meso-tetrakis(N-methylpyridium-4-yl)porphyrin with a G-quadruplex: effect of the central metal ions.

PubMed

Kim, Yun-Hwa; Lee, Changyun; Kim, Seog K; Jeoung, Sae Chae

2014-06-01

The effects of the central metal ion on complex formation between meso-tetrakis(N-methylpyridium-4-yl)porphyrin (TMPyP) and the thrombin-binding aptamer G-quadruplex, 5'G2T2G2TGTG2T2G2, were examined in this study. The central metal ions were vanadium and zinc. At a [porphyrin]/[G-quadruplex] ratio of less than one, the absorption and CD spectra were unaffected by the mixing ratio for all three porphyrins, suggesting that the binding mode is homogeneous. Relatively small changes in the absorption spectrum when forming the complexes with the G-quadruplex, the positive CD signal, and the large accessibility of the I(-) quencher, suggested that all these porphyrins are not intercalated between the G-quartet. Stabilization of the G-quadruplex by ZnTMPyP was most effective. The effect of VOTMPyP on G-quadruplex stabilization was moderate, whereas TMPyP slightly destabilized G-quadruplex. From this observation, the involvement of the ligation of one G-quartet component to the central metal ion in G-quadruplex stabilization by metallo-TMPyP is suggested. Copyright © 2014 Elsevier B.V. All rights reserved.

Quintessential quartic quasi-topological quartet

NASA Astrophysics Data System (ADS)

Ahmed, Jamil; Hennigar, Robie A.; Mann, Robert B.; Mir, Mozhgan

2017-05-01

We construct the quartic version of generalized quasi-topological gravity, which was recently constructed to cubic order in arXiv:1703.01631. This class of theories includes Lovelock gravity and a known form of quartic quasi-topological gravity as special cases and possess a number of remarkable properties: (i) In vacuum, or in the presence of suitable matter, there is a single independent field equation which is a total derivative. (ii) At the linearized level, the equations of motion on a maximally symmetric background are second order, coinciding with the linearized Einstein equations up to a redefinition of Newton's constant. Therefore, these theories propagate only the massless, transverse graviton on a maximally symmetric background. (iii) While the Lovelock and quasi-topological terms are trivial in four dimensions, there exist four new generalized quasi-topological terms (the quartet) that are nontrivial, leading to interesting higher curvature theories in d ≥ 4 dimensions that appear well suited for holographic study. We construct four dimensional black hole solutions to the theory and study their properties. A study of black brane solutions in arbitrary dimensions reveals that these solutions are modified from the `universal' properties they possess in other higher curvature theories, which may lead to interesting consequences for the dual CFTs.

On the possible origin and evolution of the genetic code

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1974-01-01

The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.

"Anything is good that stimulates thought" in the hippocampus. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Hofmann, Markus J.; Kuchinke, Lars

2015-06-01

While the emotional trias of brainstem, diencephalon, and orbitofrontal cortex is generally accepted to hold an affective function at its core, fewer researchers would agree that the least common denominator function of the hippocampus is affective [1]. There is a greater consensus on complementary learning systems theory proposing that in contrast to the outer cerebral cortex hosting more stable memories, synaptic associations in the hippocampus create novel knowledge in the context of episodic memories [2]. We chose Oscar Wilde's quote [3, p. 108] as title because we think that the novel hippocampal conjunction of for the most part familiar (long-term) knowledge patterns elicits the positive affect of appreciation [4,5].

The problem with emotion. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Bowling, Daniel L.

2015-06-01

In everyday use, emotion typically refers to conscious feelings. It feels like something to be happy or sad, afraid or angry. These emotions have qualia. That qualia are so central to what we mean by emotion makes emotion research both exciting and frustrating. Exciting because understanding how the brain gives rise to qualia is a fundamental goal of neuroscience, and frustrating because despite centuries of inquiry, qualia continue to defy a mechanistic explanation. But this obstacle has not completely blocked progress because there are other aspects of emotion - behavioral and physiological - that are more accessible to research, and the study of these has produced considerable advances in our understanding of how emotions work [13].

Toward Model Building for Visual Aesthetic Perception

PubMed Central

Lughofer, Edwin; Zeng, Xianyi

2017-01-01

Several models of visual aesthetic perception have been proposed in recent years. Such models have drawn on investigations into the neural underpinnings of visual aesthetics, utilizing neurophysiological techniques and brain imaging techniques including functional magnetic resonance imaging, magnetoencephalography, and electroencephalography. The neural mechanisms underlying the aesthetic perception of the visual arts have been explained from the perspectives of neuropsychology, brain and cognitive science, informatics, and statistics. Although corresponding models have been constructed, the majority of these models contain elements that are difficult to be simulated or quantified using simple mathematical functions. In this review, we discuss the hypotheses, conceptions, and structures of six typical models for human aesthetic appreciation in the visual domain: the neuropsychological, information processing, mirror, quartet, and two hierarchical feed-forward layered models. Additionally, the neural foundation of aesthetic perception, appreciation, or judgement for each model is summarized. The development of a unified framework for the neurobiological mechanisms underlying the aesthetic perception of visual art and the validation of this framework via mathematical simulation is an interesting challenge in neuroaesthetics research. This review aims to provide information regarding the most promising proposals for bridging the gap between visual information processing and brain activity involved in aesthetic appreciation. PMID:29270194

The Mother-Child Playgroup as Socialisation Context: A Short-Term Longitudinal Study of Mother-Child-Peer Relationship Dynamics

ERIC Educational Resources Information Center

Mize, Jacquelyn; Pettit, Gregory S.

2010-01-01

This study employed mother-child playgroups as a context for examining mothers' supervision of child-peer interactions and children's adaptation to a new peer-group setting. Six playgroups, consisting of quartets of mothers and their 24- to 54-month-old children (n = 23), were observed in ten 90-minute sessions. All mothers attended the first two…

Bruce's Magnificent Quartet: Inquiry, Community, Technology and Literacy--Implications for Renewing Qualitative Research in the Twenty-First Century

ERIC Educational Resources Information Center

Davidson, Judith

2014-01-01

Bruce and Bishop's community informatics work brings forward four critical concepts: inquiry, community, technology, and literacy. These four terms serve as the basis for a discussion of qualitative research in the twenty-first century--what is lacking and what is needed. The author suggests that to resolve the tensions or challenges…

Actual and Potential Effects of Medical Resident Coverage on Reimbursement for Inpatient Visits by Attending Physicians

PubMed Central

Shine, Daniel; Jessen, Laurie; Bajaj, Jasmeet; Pencak, Dorothy; Panush, Richard

2002-01-01

CONTEXT The impact of residents on hospital finance has been studied; there are no data describing the economic effect of residents on attending physicians. OBJECTIVE In a community teaching hospital, we compared allowable inpatient visit codes and payments (based on documentation in the daily progress notes) between a general medicine teaching unit and nonteaching general medicine units. DESIGN Retrospective chart review, matched cohort study. SETTING Six hundred fifty–bed community teaching hospital. PATIENTS Patients were discharged July 1998 through February 1999 from Saint Barnabas Medical Center. We randomly selected 200 patients in quartets. Each quartet consisted of a pair of patients cared for by residents and a pair cared for only by an attending physician. In each pair, 1 of the patients was under the care of an attending physician who usually admitted to the teaching service, and 1 was under the care of a usually nonteaching attending. Within each quartet, patients were matched for diagnosis-related group, length of stay, and discharge date. MAIN OUTCOME MEASURES We assigned the highest daily visit code justifiable by resident and attending chart documentation, determining relative value units (RVUs) and reimbursements allowed by each patient's insurance company. RESULTS Although more seriously ill, teaching-unit patients generated a mean 1.75 RVUs daily, compared with 1.84 among patients discharged from nonteaching units (P = .3). Median reimbursement, daily and per hospitalization, was similar on teaching and nonteaching units. Nonteaching attendings documented higher mean daily RVUs than teaching attendings (1.83 vs 1.76, P = .2). Median allowable reimbursements were $267 per case ($53 daily) among teaching attendings compared with $294 per case ($58 daily) among nonteaching attendings (Z = 1.54, P = .1). When only the resident note was considered, mean daily RVUs increased 39% and median allowable dollars per day 27% (Z = 4.21, P < .001). CONCLUSIONS Nonteaching attendings appear to document their visits more carefully from a billing perspective than do teaching attendings. Properly counter-documented, resident notes could substantially increase payments to attending physicians. PMID:12133156

Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.

PubMed

Sumner, Jeremy G; Taylor, Amelia; Holland, Barbara R; Jarvis, Peter D

2017-12-01

Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site patterns that, in expectation value, either vanish for particular evolutionary trees (in the case of phylogenetic invariants) or have well understood transformation properties (in the case of Markov invariants). While both approaches have been valued for their intrinsic mathematical interest, it is not clear how they relate to each other, and to what extent they can be used as practical tools for inference of phylogenetic trees. In this paper, by focusing on the special case of binary sequence data and quartets of taxa, we are able to view these two different polynomial-based approaches within a common framework. To motivate the discussion, we present three desirable statistical properties that we argue any invariant-based phylogenetic method should satisfy: (1) sensible behaviour under reordering of input sequences; (2) stability as the taxa evolve independently according to a Markov process; and (3) explicit dependence on the assumption of a continuous-time process. Motivated by these statistical properties, we develop and explore several new phylogenetic inference methods. In particular, we develop a statistically bias-corrected version of the Markov invariants approach which satisfies all three properties. We also extend previous work by showing that the phylogenetic invariants can be implemented in such a way as to satisfy property (3). A simulation study shows that, in comparison to other methods, our new proposed approach based on bias-corrected Markov invariants is extremely powerful for phylogenetic inference. The binary case is of particular theoretical interest as-in this case only-the Markov invariants can be expressed as linear combinations of the phylogenetic invariants. A wider implication of this is that, for models with more than two states-for example DNA sequence alignments with four-state models-we find that methods which rely on phylogenetic invariants are incapable of satisfying all three of the stated statistical properties. This is because in these cases the relevant Markov invariants belong to a class of polynomials independent from the phylogenetic invariants.

Properties of the Excited States of Molecular Ions.

DTIC Science & Technology

1981-04-13

FIg. 1). techniques have beest applied to the study of quartet states of Oi. The four potential curves most relevant Guyon et al., using a synchrotron...8217 a’ a a C ’U ~ ~ ~ ~ ~ ~ ~ 2 2,~ C a ’I C~- C ’ 𔃺 𔃺 𔃺 ’ ’ C- ~ C-E-38- ’- u A() A09a 265 SRI INTERNATIONAL 14FNLO PARK CA MOLECULAR PHYSICS LAB F

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

PubMed Central

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

2015-01-01

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

Empirical mass formula with proton-neutron interaction

NASA Astrophysics Data System (ADS)

Tachibana, Takahiro; Uno, Masahiro; Yamada, So; Yamada, Masami

1987-12-01

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A1/3 and ‖N-Z‖/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z=N odd-odd nuclei suggested by a quartet model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.

The difference between emotion and affect. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Cochrane, Tom

2015-06-01

Koelsch and colleagues have produced a fascinating model that convincingly argues for the existence of four neuroanatomically distinct systems involved in our emotions. As I understood it, the claim was that these systems build upon each other, each one introducing a new sophistication that allows a distinct class of emotional states to emerge. For instance, the hippocampus enables the generation of emotions related to long-term attachment as opposed to simple reward and punishment [1, Section 2.3.2]. However, it was uncertain why we should stop at four affect systems. Many different brain structures contribute an additional sophistication to emotional function; could there not be a class of emotions associated with each of these sophistications? How distinctive does the new function, or the new class of emotions have to be to qualify? Should we be on the lookout for neural structures associated with meta-emotions [2] or epistemic emotions [3] as well?

Mixed adenine/guanine quartets with three trans-a2 Pt(II) (a=NH(3) or MeNH(2)) cross-links: linkage and rotational isomerism, base pairing, and loss of NH(3).

PubMed

Albertí, Francisca M; Rodríguez-Santiago, Luis; Sodupe, Mariona; Mirats, Andrea; Kaitsiotou, Helena; Sanz Miguel, Pablo J; Lippert, Bernhard

2014-03-17

Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross-linked by three linear metal moieties such as trans-a2 Pt(II) (with a=NH3 or MeNH2 ) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)}2 ][(ClO4 )6 ]⋅3H2 O (1) (with 9-EtA=9-ethyladenine and 9-MeGH=9-methylguanine) was crystallized from water and found to adopt a flat Z-shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9-MeGH, a meander-like construct, trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)2 }][(ClO4 )6 ]⋅[(9-MeGH)2 ]⋅7 H2 O (2) is formed, in which the two extra 9-MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1. Compound 1, and likewise the analogous complex 1 a (with NH3 ligands only), undergo loss of an ammonia ligand and formation of NH4 (+) when dissolved in [D6 ]DMSO. From the analogy between the behavior of 1 and 1 a it is concluded that a NH3 ligand from the central Pt atom is lost. Addition of 1-methylcytosine (1-MeC) to such a DMSO solution reveals coordination of 1-MeC to the central Pt. In an analogous manner, 9-MeGH can coordinate to the central Pt in [D6 ]DMSO. It is proposed that the proton responsible for formation of NH4 (+) is from one of the exocyclic amino groups of the two adenine bases, and furthermore, that this process is accompanied by a conformational change of the cation from Z-form to U-form. DFT calculations confirm the proposed mechanism and shed light on possible pathways of this process. Calculations show that rotational isomerism is not kinetically hindered and that it would preferably occur previous to the displacement of NH3 by DMSO. This displacement is the most energetically costly step, but it is compensated by the proton transfer to NH3 and formation of U(-H(+) ) species, which exhibits an intramolecular hydrogen bond between the deprotonated N6H(-) of one adenine and the N6H2 group of the other adenine. Finally the question is examined, how metal cross-linking patterns in closed metallacyclic quartets containing two adenine and two guanine nucleobases influence the overall shape (square, rectangle, trapezoid) and the planarity of a metalated purine quartet. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yan; Lin, Hai

2009-05-01

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Model of ultrafast demagnetization driven by spin-orbit coupling in a photoexcited antiferromagnetic insulator Cr2O3

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Na; Jin, Wei; Chang, Jun

2017-06-01

We theoretically study the dynamic time evolution following laser pulse pumping in an antiferromagnetic insulator Cr2O3. From the photoexcited high-spin quartet states to the long-lived low-spin doublet states, the ultrafast demagnetization processes are investigated by solving the dissipative Schrödinger equation. We find that the demagnetization times are of the order of hundreds of femtoseconds, in good agreement with recent experiments. The switching times could be strongly reduced by properly tuning the energy gaps between the multiplet energy levels of Cr3+. Furthermore, the relaxation times also depend on the hybridization of atomic orbitals in the first photoexcited state. Our results suggest that the selective manipulation of the electronic structure by engineering stress-strain or chemical substitution allows effective control of the magnetic state switching in photoexcited insulating transition-metal oxides.

Time-dependent nonequilibrium soft x-ray response during a spin crossover

NASA Astrophysics Data System (ADS)

van Veenendaal, Michel

2018-03-01

A theoretical framework is developed for better understanding the time-dependent soft-x-ray response of dissipative quantum many-body systems. It is shown how x-ray absorption and resonant inelastic x-ray scattering (RIXS) at transition-metal L edges can provide insight into ultrafast intersystem crossings of importance for energy conversion, ultrafast magnetism, and catalysis. The photoinduced doublet-to-quartet spin crossover on cobalt in Fe-Co Prussian blue analogs is used as a model system to demonstrate how the x-ray response is affected by the nonequilibrium dynamics on a femtosecond time scale. Changes in local spin and symmetry and the underlying mechanism are reflected in strong broadenings, a collapse of clear selection rules during the intersystem crossing, fluctuations in the isotropic branching ratio in x-ray absorption, crystal-field collapse and/or oscillations, and time-dependent anti-Stokes processes in RIXS.

Second Topical Meeting on Laser Techniques in the Extreme Ultraviolet.

DTIC Science & Technology

1985-01-10

Dressed Resonances, Lasw for Product Detlection, John W. Hepburn, N. Slvakumnar,* J. H. Eberly and D. Agassi, Department of Physics and and Paul L...inversion production in a laser plasma allows us to - between core-excited quartet states of Na I. The classifica- test a possible laser cavity. tions are...used to increase radiation losses. Enhancement of hydrogen-like CVI 182R line intensity and population inversion in Li-like ions (CIV, OVI, FVII , and

Charge line quad pulser

DOEpatents

Booth, R.

1996-10-08

A quartet of parallel coupled planar triodes is removably mounted in a quadrahedron shaped PCB structure. Releasable brackets and flexible means attached to each triode socket make triode cathode and grid contact with respective conductive coatings on the PCB and a detachable cylindrical conductive element enclosing and contacting the triode anodes jointly permit quick and easy replacement of faulty triodes. By such orientation, the quad pulser can convert a relatively low and broad pulse into a very high and narrow pulse. 16 figs.

Charge line quad pulser

DOEpatents

Booth, Rex

1996-01-01

A quartet of parallel coupled planar triodes is removably mounted in a quadrahedron shaped PCB structure. Releasable brackets and flexible means attached to each triode socket make triode cathode and grid contact with respective conductive coatings on the PCB and a detachable cylindrical conductive element enclosing and contacting the triode anodes jointly permit quick and easy replacement of faulty triodes. By such orientation, the quad pulser can convert a relatively low and broad pulse into a very high and narrow pulse.

EPR and Bell's theorem: A critical review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stapp, H.P.

1991-01-01

The argument of Einstein, Podolsky, and Rosen is reviewed with attention to logical structure and character of assumptions. Bohr's reply is discussed. Bell's contribution is formulated without use of hidden variables, and efforts to equate hidden variables to realism are critically examined. An alternative derivation of nonlocality that makes no use of hidden variables, microrealism, counterfactual definiteness, or any other assumption alien to orthodox quantum thinking is described in detail, with particular attention to the quartet or broken-square question.

Separable Ernst-Shakin-Thaler expansions of local potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bund, G.W.

The boundary condition Ernst-Shakin-Thaler method, introduced previously to generate separable expansions of local potentials of finite range, is applied to the study of the triplet s-wave Malfliet-Tjon potential. The effect of varying the radius where the boundary condition is applied on the T matrix is analyzed. Further, we compare the convergence of the n-d scattering cross sections in the quartet state below the breakup threshold for expansions corresponding to two different boundaries.

GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE

PubMed Central

Puigbò, Pere; Wolf, Yuri I.; Koonin, Eugene V.

2013-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a ‘species tree’. PMID:22399455

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

PubMed

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-Ichi; Sugimoto, Naoki

2015-12-02

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers.

PubMed

Medina, Cintia Débora; Avila, Luciano Javier; Sites, Jack Walter; Santos, Juan; Morando, Mariana

2018-03-01

We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods. Copyright © 2017 Elsevier Inc. All rights reserved.

Mesodermal and axial determinants contribute to mesoderm regionalization in Bufo arenarum embryos.

PubMed

Manes, Mario E; Campos Casal, Fernando H

2002-09-01

The existence of mesodermal determinants in the equator of Bufo arenarum embryos has been previously demonstrated. In this work, their role in dorso-ventral regionalization of mesoderm was studied by transferring the determinants to animal blastomeres. The transfer was performed by cleavage reorientation and cytoplasmic microinjection. Forced inclination during early cleavage caused deviation of the third cleavage plane and annexation of equatorial cytoplasm into animal quartets. Animal blastomeres from embryos oriented with the dorsal side up, incorporated ventro-equatorial cytoplasm and formed blood cells, mesenchyme, and coelomic epithelium. In contrast, animal blastomeres from embryos oriented with the ventral side up, acquired dorso-equatorial cytoplasm and developed notochord, somites, mesenchyme, coelomic epithelium and nervous tissue. In order to investigate if this dorso-ventral differentiation pattern responds to an interaction of mesodermal and axial factors, isolated 8-cell-stage animal quartets were microinjected with subcortical cytoplasm from: (a) the ventro-equatorial region of synchronous embryos; (b) the vegetal pole of uncleaved eggs; (c) a combination of both cytoplasms. As expected, the implanted ventro-equatorial cytoplasm promoted ventral mesoderm differentiation. Conversely, the joint transfer of ventro-equatorial cytoplasm and vegetal pole cytoplasm behaved as the dorso-equatorial cytoplasm, promoting dorso-lateral mesoderm and neural formation. Thus, mesoderm regionalization in B. arenarum embryos seems to be caused by a concurrent action of both mesodermal and axial determinants.

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

PubMed

Puigbò, Pere; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

PubMed

Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

1991-05-11

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process.

Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

PubMed Central

Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

1991-01-01

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process. Images PMID:1645868

Can modular psychological concepts like affect and emotion be assigned to a distinct subset of regional neural circuits?. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Fehr, Thorsten; Herrmann, Manfred

2015-06-01

The proposed Quartet Theory of Human Emotions by Koelsch and co-workers [11] adumbrates evidence from various scientific sources to integrate and assign the psychological concepts of 'affect' and 'emotion' to four brain circuits or to four neuronal core systems for affect-processing in the brain. The authors differentiate between affect and emotion and assign several facultative, or to say modular, psychological domains and principles of information processing, such as learning and memory, antecedents of affective activity, emotion satiation, cognitive complexity, subjective quality feelings, degree of conscious appraisal, to different affect systems. Furthermore, they relate orbito-frontal brain structures to moral affects as uniquely human, and the hippocampus to attachment-related affects. An additional feature of the theory describes 'emotional effector-systems' for motor-related processes (e.g., emotion-related actions), physiological arousal, attention and memory that are assumed to be cross-linked with the four proposed affect systems. Thus, higher principles of emotional information processing, but also modular affect-related issues, such as moral and attachment related affects, are thought to be handled by these four different physiological sub-systems that are on the other side assumed to be highly interwoven at both physiological and functional levels. The authors also state that the proposed sub-systems have many features in common, such as the selection and modulation of biological processes related to behaviour, perception, attention and memory. The latter aspect challenges an ongoing discussion about the mind-body problem: To which degree do the proposed sub-systems 'sufficiently' cover the processing of complex modular or facultative emotional/affective and/or cognitive phenomena? There are current models and scientific positions that almost completely reject the idea that modular psychological phenomena are handled by a distinct selection of regional brain systems or neural modules, but rather suggest highly complex and cross-linked neural networks individually shaped by livelong learning and experience [e.g., 6,7,10,13]. This holds in particular true for complex emotional phenomena such as aggression or empathy in social interaction [8,13]. It thus remains questionable, whether - beyond primary sensory and motor-processing - a small number of modular sub-systems sufficiently cover the organisation of specific phenomenological and social features of perception and behaviour [7,10].

Constraining Galactic cosmic-ray parameters with Z ≤ 2 nuclei

NASA Astrophysics Data System (ADS)

Coste, B.; Derome, L.; Maurin, D.; Putze, A.

2012-03-01

Context. The secondary-to-primary B/C ratio is widely used for studying Galactic cosmic-ray propagation processes. The 2H/4He and 3He/4He ratios probe a different Z/A regime, which provides a test for the "universality" of propagation. Aims: We revisit the constraints on diffusion-model parameters set by the quartet (1H, 2H, 3He, 4He), using the most recent data as well as updated formulae for the inelastic and production cross-sections. Methods: Our analysis relies on the USINE propagation package and a Markov Chain Monte Carlo technique to estimate the probability density functions of the parameters. Simulated data were also used to validate analysis strategies. Results: The fragmentation of CNO cosmic rays (resp. NeMgSiFe) on the interstellar medium during their propagation contributes to 20% (resp. 20%) of the 2H and 15% (resp. 10%) of the 3He flux at high energy. The C to Fe elements are also responsible for up to 10% of the 4He flux measured at 1 GeV/n. The analysis of 3He/4He (and to a lesser extent 2H/4He) data shows that the transport parameters are consistent with those from the B/C analysis: the diffusion model with δ ~ 0.7 (diffusion slope), Vc ~ 20 km s-1 (galactic wind), Va ~ 40 km s-1 (reacceleration) is favoured, but the combination δ ~ 0.2, Vc ~ 0, and Va ~ 80 km s-1 is a close second. The confidence intervals on the parameters show that the constraints set by the quartet data can compete with those derived from the B/C data. These constraints are tighter when adding the 3He (or 2H) flux measurements, and the tightest when the He flux is added as well. For the latter, the analysis of simulated and real data shows an increased sensitivity to biases. Using the secondary-to-primary ratio along with a loose prior on the source parameters is recommended to obtain the most robust constraints on the transport parameters. Conclusions: Light nuclei should be systematically considered in the analysis of transport parameters. They provide independent constraints that can compete with those obtained from the B/C analysis.

Adinkras from ordered quartets of BC4 Coxeter group elements and regarding 1,358,954,496 matrix elements of the Gadget

NASA Astrophysics Data System (ADS)

Gates, S. James; Guyton, Forrest; Harmalkar, Siddhartha; Kessler, David S.; Korotkikh, Vadim; Meszaros, Victor A.

2017-06-01

We examine values of the Adinkra Holoraumy-induced Gadget representation space metric over all possible four-color, four-open node, and four-closed node adinkras. Of the 1,358,954,496 gadget matrix elements, only 226,492,416 are non-vanishing and take on one of three values: -1/3, 1/3, or 1 and thus a subspace isomorphic to a description of a body-centered tetrahedral molecule emerges.

U.S. and NATO Naval Engagement with Russia in the Black Sea: Historical Patterns and Current Prospects

DTIC Science & Technology

2016-09-01

European Ballistic Missile Defense Quartet,” U.S. Naval Institute News, September 25, 2015, http://news.usni.org/2015/09/25/ destroyer-uss-carney...cps/en/natohq/official_texts_133169.htm. 9David S. Yost, NATO’s Balancing Act (Washington, DC: United States Institute of Peace, 2014): 31. 10Sharyl...Ukrainian Research Institute , has written that “[Russia’s] southern flank has been one of the most unstable ones during the past two decades, [and

Regulating with imagery and the complexity of basic emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Meyer, Marcel; Kuchinke, Lars

2015-06-01

Literature, music and the arts have long attested to the complexity of human emotions. Hitherto, psychological and biological theories of emotions have largely neglected this rich heritage. In their review Koelsch and colleagues [1] have embarked upon the pioneering endeavour of integrating the diverse perspectives in emotion research. Noting that the focus of prior neurobiological theories relies mainly on animal studies, the authors sought to complement this body of research with a model of complex ("moral") emotions in humans (henceforth: complex emotions). According to this novel framework, there are four main interacting affective centres in the brain. Each centre is associated with a dominant affective function, such as ascending activation (brainstem), pain/pleasure (diencephalon), attachment-related affects (hippocampus) or moral emotions and unconscious cognitive appraisal (orbitofrontal cortex). Furthermore, language is ascribed a key role in (a) the communication of subjective feeling (reconfiguration) and (b) in the conscious regulation of emotions (by means of logic and rational thought).

In vivo dynamic turnover of cerebral 13C isotopomers from [U- 13C]glucose

NASA Astrophysics Data System (ADS)

Xu, Su; Shen, Jun

2006-10-01

An INEPT-based 13C MRS method and a cost-effective and widely available 11.7 Tesla 89-mm bore vertical magnet were used to detect dynamic 13C isotopomer turnover from intravenously infused [U- 13C]glucose in a 211 μL voxel located in the adult rat brain. The INEPT-based 1H → 13C polarization transfer method is mostly adiabatic and therefore minimizes signal loss due to B 1 inhomogeneity of the surface coils used. High quality and reproducible data were acquired as a result of combined use of outer volume suppression, ISIS, and the single-shot three-dimensional localization scheme built in the INEPT pulse sequence. Isotopomer patterns of both glutamate C4 at 34.00 ppm and glutamine C4 at 31.38 ppm are dominated first by a doublet originated from labeling at C4 and C5 but not at C3 (with 1JC4C5 = 51 Hz) and then by a quartet originated from labeling at C3, C4, and C5 (with 1JC3C4 = 35 Hz). A lag in the transition of glutamine C4 pattern from doublet-dominance to quartet dominance as compared to glutamate C4 was observed, which provides an independent verification of the precursor-product relationship between neuronal glutamate and glial glutamine and a significant intercompartmental cerebral glutamate-glutamine cycle between neurons and glial cells.

A tutorial on the principles of harmonic intonation for trombonists

NASA Astrophysics Data System (ADS)

Keener, Michael Kenneth

A Tutorial on the Principles of Harmonic Intonation for Trombonists includes a manual containing background information, explanations of the principles of harmonic intonation, and printed musical examples for use in learning and practicing the concepts of harmonic intonation. An audio compact disk containing music files corresponding to the printed music completes the set. This tutorial is designed to allow performing musicians and students to practice intonation skills with the pitch-controlled music on the compact disc. The music on the CD was recorded in movable-comma just intonation, replicating performance parameters of wind, string, and vocal ensembles. The compact disc includes sixty tracks of ear-training exercises and interval studies with which to practice intonation perception and adjustment. Tuning notes and examples of equal-tempered intervals and just intervals are included on the CD. The intonation exercises consist of musical major scales, duets, trios, and quartet phrases to be referenced while playing the printed music. The CD tracks allow the performer to play scales in unison (or practice other harmonic intervals) or the missing part of the corresponding duet, trio, or quartet exercise. Instructions in the manual guide the user through a process that can help prepare musicians for more accurate musical ensemble performance. The contextual essay that accompanies the tutorial includes a description of the tutorial, a review of related literature, methodology of construction of the tutorial, evaluations and outcomes, conclusions and recommendations for further research, and a selected bibliography.

ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 Are Polygalacturonases Required for Cell Separation during Reproductive Development in Arabidopsis[W

PubMed Central

Ogawa, Mikihiro; Kay, Pippa; Wilson, Sarah; Swain, Stephen M.

2009-01-01

Cell separation is thought to involve degradation of pectin by several hydrolytic enzymes, particularly polygalacturonase (PG). Here, we characterize an activation tagging line with reduced growth and male sterility caused by increased expression of a PG encoded by QUARTET2 (QRT2). QRT2 is essential for pollen grain separation and is part of a small family of three closely related endo-PGs in the Arabidopsis thaliana proteome, including ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1) and ADPG2. Functional assays and complementation experiments confirm that ADPG1, ADPG2, and QRT2 are PGs. Genetic analysis demonstrates that ADPG1 and ADPG2 are essential for silique dehiscence. In addition, ADPG2 and QRT2 contribute to floral organ abscission, while all three genes contribute to anther dehiscence. Expression analysis is consistent with the observed mutant phenotypes. INDEHISCENT (IND) encodes a putative basic helix-loop-helix required for silique dehiscence, and we demonstrate that the closely related HECATE3 (HEC3) gene is required for normal seed abscission and show that IND and HEC3 are required for normal expression of ADPG1 in the silique dehiscence zone and seed abscission zone, respectively. We also show that jasmonic acid and ethylene act together with abscisic acid to regulate floral organ abscission, in part by promoting QRT2 expression. These results demonstrate that multiple cell separation events, including both abscission and dehiscence, require closely related PG genes. PMID:19168715

Deciding what to see: the role of intention and attention in the perception of apparent motion.

PubMed

Kohler, Axel; Haddad, Leila; Singer, Wolf; Muckli, Lars

2008-03-01

Apparent motion is an illusory perception of movement that can be induced by alternating presentations of static objects. Already in Wertheimer's early investigation of the phenomenon [Wertheimer, M. (1912). Experimentelle Studien über das Sehen von Bewegung. Zeitschrift fur Psychologie, 61, 161-265], he mentions that voluntary attention can influence the way in which an ambiguous apparent motion display is perceived. But until now, few studies have investigated how strong the modulation of apparent motion through attention can be under different stimulus and task conditions. We used bistable motion quartets of two different sizes, where the perception of vertical and horizontal motion is equally likely. Eleven observers participated in two experiments. In Experiment 1, participants were instructed to either (a) hold the current movement direction as long as possible, (b) passively view the stimulus, or (c) switch the movement directions as quickly as possible. With the respective instructions, observers could almost double phase durations in (a) and more than halve durations in (c) relative to the passive condition. This modulation effect was stronger for the large quartets. In Experiment 2, observers' attention was diverted from the stimulus by a detection task at fixation while they still had to report their conscious perception. This manipulation prolonged dominance durations for up to 100%. The experiments reveal a high susceptibility of ambiguous apparent motion to attentional modulation. We discuss how feature- and space-based attention mechanisms might contribute to those effects.

Temperature and Pressure Dependences of the Reactions of Fe+ with Methyl Halides CH3X (X = Cl, Br, I): Experiments and Kinetic Modeling Results.

PubMed

Ard, Shaun G; Shuman, Nicholas S; Martinez, Oscar; Keyes, Nicholas R; Viggiano, Albert A; Guo, Hua; Troe, Jürgen

2017-06-01

The pressure and temperature dependences of the reactions of Fe + with methyl halides CH 3 X (X = Cl, Br, I) in He were measured in a selected ion flow tube over the ranges 0.4 to 1.2 Torr and 300-600 K. FeX + was observed for all three halides and FeCH 3 + was observed for the CH 3 I reaction. FeCH 3 X + adducts (for all X) were detected in all reactions. The results were interpreted assuming two-state reactivity with spin-inversions between sextet and quartet potentials. Kinetic modeling allowed for a quantitative representation of the experiments and for extrapolation to conditions outside the experimentally accessible range. The modeling required quantum-chemical calculations of molecular parameters and detailed accounting of angular momentum effects. The results show that the FeX + products come via an insertion mechanism, while the FeCH 3 + can be produced from either insertion or S N 2 mechanisms, but the latter we conclude is unlikely at thermal energies. A statistical modeling cannot reproduce the competition between the bimolecular pathways in the CH 3 I reaction, indicating that some more direct process must be important.

Earth, air, fire and water: A targetry quartet

NASA Astrophysics Data System (ADS)

Valdovinos, Hector F.; Graves, Stephen; Ellison, Paul; Barnhart, Todd; Nickles, Robert J.

2017-05-01

Cyclotron targets have made steady progress in terms of current capabilities, automated handling and application to isotopically-enriched material. These advances have followed a distinct trajectory at the University of Wisconsin, with the emphasis on maximizing the yield of the desired radionuclide within the strict constraints of heat transfer of beam power and the ultimate recycling of precious target stock. This approach leads to four target families, each employed in the production of the positron-emitting transition metals of the 3d- and 4d-subshells, with importance now arising as targeted molecular imaging agents.

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE PAGES

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus; ...

2018-02-20

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2018-02-28

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest.

Simulation of gas flow in micro-porous media with the regularized lattice Boltzmann method

DOE PAGES

Wang, Junjian; Kang, Qinjun; Wang, Yuzhu; ...

2017-06-01

One primary challenge for prediction of gas flow in the unconventional gas reservoir at the pore-scale such as shale and tight gas reservoirs is the geometric complexity of the micro-porous media. In this paper, a regularized multiple-relaxation-time (MRT) lattice Boltzmann (LB) model is applied to analyze gas flow in 2-dimensional micro-porous medium reconstructed by quartet structure generation set (QSGS) on pore-scale. In this paper, the velocity distribution inside the porous structure is presented and analyzed, and the effects of the porosity and specific surface area on the rarefied gas flow and apparent permeability are examined and investigated. The simulation resultsmore » indicate that the gas exhibits different flow behaviours at various pressure conditions and the gas permeability is strongly related to the pressure. Finally, the increased porosity or the decreased specific surface area leads to the increase of the gas apparent permeability, and the gas flow is more sensitive to the pore morphological properties at low-pressure conditions.« less

Design of activated serine-containing catalytic triads with atomic level accuracy

PubMed Central

Rajagopalan, Sridharan; Wang, Chu; Yu, Kai; Kuzin, Alexandre P.; Richter, Florian; Lew, Scott; Miklos, Aleksandr E.; Matthews, Megan L.; Seetharaman, Jayaraman; Su, Min; Hunt, John. F.; Cravatt, Benjamin F.; Baker, David

2014-01-01

A challenge in the computational design of enzymes is that multiple properties must be simultaneously optimized -- substrate-binding, transition state stabilization, and product release -- and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads, and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate-reactivity. Following optimization by yeast-display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest the designs could provide the basis for a new class of organophosphate captures agents. PMID:24705591

Simulation of gas flow in micro-porous media with the regularized lattice Boltzmann method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Junjian; Kang, Qinjun; Wang, Yuzhu

One primary challenge for prediction of gas flow in the unconventional gas reservoir at the pore-scale such as shale and tight gas reservoirs is the geometric complexity of the micro-porous media. In this paper, a regularized multiple-relaxation-time (MRT) lattice Boltzmann (LB) model is applied to analyze gas flow in 2-dimensional micro-porous medium reconstructed by quartet structure generation set (QSGS) on pore-scale. In this paper, the velocity distribution inside the porous structure is presented and analyzed, and the effects of the porosity and specific surface area on the rarefied gas flow and apparent permeability are examined and investigated. The simulation resultsmore » indicate that the gas exhibits different flow behaviours at various pressure conditions and the gas permeability is strongly related to the pressure. Finally, the increased porosity or the decreased specific surface area leads to the increase of the gas apparent permeability, and the gas flow is more sensitive to the pore morphological properties at low-pressure conditions.« less

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

PubMed Central

Sayyari, Erfan

2018-01-01

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. PMID:29495636

Diagnostic articulation tables

NASA Astrophysics Data System (ADS)

Mikhailov, V. G.

2002-09-01

In recent years, considerable progress has been made in the development of instrumental methods for general speech quality and intelligibility evaluation on the basis of modeling the auditory perception of speech and measuring the signal-to-noise ratio. Despite certain advantages (fast measurement procedures with a low labor consumption), these methods are not universal and, in essence, secondary, because they rely on the calibration based on subjective-statistical measurements. At the same time, some specific problems of speech quality evaluation, such as the diagnostics of the factors responsible for the deviation of the speech quality from standard (e.g., accent features of a speaker or individual voice distortions), can be solved by psycholinguistic methods. This paper considers different kinds of diagnostic articulation tables: tables of minimal pairs of monosyllabic words (DRT) based on the Jacobson differential features, tables consisting of multisyllabic quartets of Russian words (the choice method), and tables of incomplete monosyllables of the _VC/CV_ type (the supplementary note method). Comparative estimates of the tables are presented along with the recommendations concerning their application.

The Plausibility of a String Quartet Performance in Virtual Reality.

PubMed

Bergstrom, Ilias; Azevedo, Sergio; Papiotis, Panos; Saldanha, Nuno; Slater, Mel

2017-04-01

We describe an experiment that explores the contribution of auditory and other features to the illusion of plausibility in a virtual environment that depicts the performance of a string quartet. 'Plausibility' refers to the component of presence that is the illusion that the perceived events in the virtual environment are really happening. The features studied were: Gaze (the musicians ignored the participant, the musicians sometimes looked towards and followed the participant's movements), Sound Spatialization (Mono, Stereo, Spatial), Auralization (no sound reflections, reflections corresponding to a room larger than the one perceived, reflections that exactly matched the virtual room), and Environment (no sound from outside of the room, birdsong and wind corresponding to the outside scene). We adopted the methodology based on color matching theory, where 20 participants were first able to assess their feeling of plausibility in the environment with each of the four features at their highest setting. Then five times participants started from a low setting on all features and were able to make transitions from one system configuration to another until they matched their original feeling of plausibility. From these transitions a Markov transition matrix was constructed, and also probabilities of a match conditional on feature configuration. The results show that Environment and Gaze were individually the most important factors influencing the level of plausibility. The highest probability transitions were to improve Environment and Gaze, and then Auralization and Spatialization. We present this work as both a contribution to the methodology of assessing presence without questionnaires, and showing how various aspects of a musical performance can influence plausibility.

[Medicine, music, friendship and prejudices: Billroth I and Billroth II, the string quartets Opus 51, N° 1 and N° 2 by Johannes Brahms].

PubMed

Cabello, Felipe C

2012-06-01

The great German surgeon Theodor Billroth and the imaginative and creative composer Johannes Brahms had a very close friendship centered on musical activities, that lasted for more than thirty years while they lived and worked in Zurich and Vienna, during the second half of the Nineteenth Century. Billroth, besides his all-consuming medical activities, had time to be a musical enthusiast who directed orchestras, played the violin in chamber music groups, and wrote musical criticism for newspapers. The common affection between these two creative giants is documented by their abundant and effusive correspondence, by the constant requests by Brahms of Billroth's opinions regarding his compositions, and by the positive and stimulating answers that Billroth gave to these requests. Billroth opened his house for musical evenings to play Brahms chamber compositions for the first time, and Brahms dedicated his two Opus 51 string quartets Nos. 1 and 2, known in the musical milieu as Billroth I and II, to his physician friend. Unfortunately, the close bonds between these two geniuses weakened towards the end of their lives as a result of Billroth's becoming intolerant to the lack of social refinements and gruff behavior of the composer. This baffling intolerance of Billroth to his friend Brahms can be better understood after reading Billroth's writings in his book The Medical Sciences in the German Universities. A Study in the History of Civilization. There Billroth expresses strong prejudices against potential medical students of humble social origins, such as those of Brahms, coupled to a primitive anti-Semitism.

Blend in Singing Ensemble Performance: Vibrato Production in a Vocal Quartet.

PubMed

Daffern, Helena

2017-05-01

"Blend" is a defining characteristic of good vocal ensemble performance. To achieve this, directors often consider vibrato as a feature to be controlled and consequently restrict its use. Analysis of individual voices in ensemble situations presents several challenges, including the isolation of voices for analysis from recordings. This study considers vibrato production as a feature that contributes to blend through an ecological study of a vocal quartet. A vocal ensemble was recorded using head-worn microphones and electrolaryngograph electrodes to enable fundamental frequency analysis of the individual voices. The same four-part material was recorded over several weeks of rehearsal to allow analysis of conscious and subconscious changes to vibrato production over time. Alongside the recording of their rehearsal discussions, singers were also asked for opinions on vibrato production in connection with blend. The results indicate that vibrato is adjusted to some extent by individual singers to improve blend, with some instances of synchrony between voice parts. Some conscious alterations to vibrato were made to improve blend; however, these are not always evident in the data, suggesting that singers' own perceptions of their performance may be influenced by other factors. These findings indicate a need for further studies of vibrato as a feature of blend, particularly in terms of the synergies between expectation and actual production, and potential synchronicity between singers; increased understanding of vibrato in an ensemble setting will lead to more efficient rehearsal techniques and vocal training, and could prevent vocal misuse leading to pathology in the future. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmgren, D.E.; Walker, D.J.; Harris, S.E.

Certain quartet levels in alkali-like systems retain metastability against autoionization while acquiring large radiative yields. This quasi-metastability occurs through selective coupling to non-autoionizing doublet levels by the spin-orbit interaction. An example of such a level is the 5p/sup 5/5d6s /sup 4/P/sub 5/2/ level of neutral Cs, which has a calculated branching ratio for radiation at 1091 A of 43%. Experimentally, we find that this line has an emission intensity equal to 1/6 of that of the strongest ion line of Cs/sup +/, and is a promising candidate for an extreme ultraviolet laser.

Instrumentation development for the EUVE. [Extreme Ultraviolet Explorer Satellite

NASA Technical Reports Server (NTRS)

Finley, D.

1980-01-01

The prototype mirror was successfully replated with a thick layer of nickel and diamond turned again. Optimization of the sensitivity of the instruments was studied with emphasis on the filter material, and on the available telemetry. The JHU Preliminary Project Definition Document was critically analyzed. Further studies of the electron cloud distribution produced by a channel plate were performed, and a wedge and strip anode with 17 quartets per inch was shown to image with better than 0.5% linearity. Half the microchannel plates being used in the lifetest completed initial processing and are in the lifetest vacuum chamber.

In VivoLactate Editing with Simultaneous Detection of Choline, Creatine, NAA, and Lipid Singlets at 1.5 T Using PRESS Excitation with Applications to the Study of Brain and Head and Neck Tumors

NASA Astrophysics Data System (ADS)

Star-Lack, Josh; Spielman, Daniel; Adalsteinsson, Elfar; Kurhanewicz, John; Terris, David J.; Vigneron, Daniel B.

1998-08-01

Two T2-independentJ-difference lactate editing schemes for the PRESS magnetic resonance spectroscopy localization sequence are introduced. The techniques, which allow for simultaneous acquisition of the lactate doublet (1.3 ppm) and edited singlets upfield of and including choline (3.2 ppm), exploit the dependence of the in-phase intensity of the methyl doublet upon the time interval separating two inversion (BASING) pulses applied to its coupling partner after initial excitation. Editing method 1, which allows for echo times TE =n/J(n= 1, 2, 3, …), alters the BASING carrier frequency for each of two cycles so that, for one cycle, the quartet is inverted, whereas, for the other cycle, the quartet is unaffected. Method 2, which also provides water suppression, allows for editing for TE > 1/Jby alternating, between cycles, the time interval separating the inversion pulses. Experimental results were obtained at 1.5 T using a Shinnar Le-Roux-designed maximum phase inversion pulse with a filter transition bandwidth of 55 Hz. Spectra were acquired from phantoms andin vivofrom the human brain and neck. In a neck muscle study, the lipid suppression factor, achieved partly through the use of a novel phase regularization algorithm, was measured to be over 103. Spectra acquired from a primary brain and a metastatic neck tumor demonstrated the presence of lactate and choline signals consistent with abnormal spectral patterns. The advantages and limitations of the methods are analyzed theoretically and experimentally, and significance of the results is discussed.

Propargyl + O 2 Reaction in Helium Droplets: Entrance Channel Barrier or Not?

DOE PAGES

Moradi, Christopher P.; Morrison, Alexander M.; Klippenstein, Stephen J.; ...

2013-09-09

A combination of liquid He droplet experiments and multireference electronic structure calculations is used to probe the potential energy surface for the reaction between the propargyl radical and O 2. Infrared laser spectroscopy is used to probe the outcome of the low temperature, liquid He-mediated reaction. Bands in the spectrum are assigned to the acetylenic CH stretch (ν 1), the symmetric CH 2 stretch (ν 2), and the antisymmetric CH 2 stretch (ν 13) of the trans-acetylenic propargyl peroxy radical (•OO—CH 2—C≡CH). The observed band origins are in excellent agreement with previously reported anharmonic frequency computations for this species. Themore » Stark spectrum of the ν 1 band provides further evidence that the reaction leads only to the trans-acetylenic species. There are no other bands in the CH 2 stretching region that can be attributed to any of the other three propargyl peroxy isomers/conformers that are predicted to be minimum energy structures ( gauche-acetylenic, cis-allenic, and trans-allenic). There is also no evidence for the kinetic stabilization of a van der Waals complex between propargyl and O 2. A combination of multireference and coupled-cluster electronic structure calculations is used to probe the potential energy surface in the neighborhood of the transition state connecting reactants with the acetylenic adduct. The multireference based evaluation of the doublet-quartet splitting added to the coupled-cluster calculated quartet state energies yields what are likely the most accurate predictions for the doublet potential curve. As a result, this calculation suggests that there is no saddle point for the addition process, in agreement with the experimental observations. Other calculations suggest the possible presence of a small submerged barrier.« less

G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA)

PubMed Central

Peng, Chang Geng; Damha, Masad J.

2007-01-01

The impact of 2′-deoxy-2′-fluoroarabinonucleotide residues (2′F-araN) on different G-quadruplexes derived from a thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), an anti-HIV phosphorothioate aptamer PS-d(T2G4T2) and a DNA telomeric sequence d(G4T4G4) via UV thermal melting (Tm) and circular dichroism (CD) experiments has been investigated. Generally, replacement of deoxyguanosines that adopt the anti conformation (anti-guanines) with 2′F-araG can stabilize G-quartets and maintain the quadruplex conformation, while replacement of syn-guanines with 2′F-araG is not favored and results in a dramatic switch to an alternative quadruplex conformation. It was found that incorporation of 2′F-araG or T residues into a thrombin-binding DNA G-quadruplex stabilizes the complex (ΔTm up to ∼+3°C/2′F-araN modification); 2′F-araN units also increased the half-life in 10% fetal bovine serum (FBS) up to 48-fold. Two modified thrombin-binding aptamers (PG13 and PG14) show an approximately 4-fold increase in binding affinity to thrombin, as assessed via a nitrocellulose filter binding assay, both with increased thermal stability (∼1°C/2′F-ANA modification increase in Tm) and nuclease resistance (4–7-fold) as well. Therefore, the 2′-deoxy-2′-fluoro-d-arabinonucleic acid (2′F-ANA) modification is well suited to tune (and improve) the physicochemical and biological properties of naturally occurring DNA G-quartets. PMID:17636049

He2+ molecular ion and the He- atomic ion in strong magnetic fields

NASA Astrophysics Data System (ADS)

Vieyra, J. C. Lopez; Turbiner, A. V.

2017-08-01

We study the question of existence, i.e., stability with respect to dissociation of the spin-quartet permutation- and reflection-symmetric 4(-3) +g (Sz=-3 /2 ,M =-3 ) state of the (α α e e e ) Coulomb system: the He2 + molecular ion, placed in a magnetic field 0 ≤B ≤10 000 a.u. We assume that the α particles are infinitely massive (Born-Oppenheimer approximation of zero order) and adopt the parallel configuration, when the molecular axis and the magnetic field direction coincide, as the optimal configuration. The study of the stability is performed variationally with a physically adequate trial function. To achieve this goal, we explore several helium-containing compounds in strong magnetic fields, in particular; we study the spin-quartet ground state of the He- ion and the ground (spin-triplet) state of the helium atom, both for a magnetic field in 100 ≤B ≤10 000 a.u. The main result is that the He2 + molecular ion in the state 4(-3) +g is stable towards all possible decay modes for magnetic fields B ≳120 a .u . and with the magnetic field increase the ion becomes more tightly bound and compact with a cigar-type form of electronic cloud. At B =1000 a .u . , the dissociation energy of He2 + into He-+α is ˜702 eV and the dissociation energy for the decay channel to He +α +e is ˜729 eV , and both energies are in the energy window for one of the observed absorption features of the isolated neutron star 1E1207.4-5209.

The fourfold way of the genetic code.

PubMed

Jiménez-Montaño, Miguel Angel

2009-11-01

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a "least grammar" for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V(T)=(C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the KxK group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2' or 3' aminoacylation of tRNAs. J. Theor. Biol. 247, 391-394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161-169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341-355], respectively.

The electronic structure of vanadium monochloride cation (VCl+): Tackling the complexities of transition metal species

NASA Astrophysics Data System (ADS)

DeYonker, Nathan J.; Halfen, DeWayne T.; Allen, Wesley D.; Ziurys, Lucy M.

2014-11-01

Six electronic states (X 4Σ-, A 4Π, B 4Δ, 2Φ, 2Δ, 2Σ+) of the vanadium monochloride cation (VCl+) are described using large basis set coupled cluster theory. For the two lowest quartet states (X 4Σ- and A 4Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T0) and spectroscopic constants (re, r0, Be, B0, bar De, He, ωe, v0, αe, ωexe) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X 4Σ-), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state (2Γ) has a Te of ˜11 200 cm-1. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.

Self-organisation of an oligodeoxynucleotide containing the G- and C-rich stretches of the direct repeats of the human mitochondrial DNA.

PubMed

Nonin-Lecomte, Sylvie; Dardel, Frédéric; Lestienne, Patrick

2005-08-01

Stretches of cytosines and guanosines have been shown in vitro to adopt non-canonical structures known as i-motifs and G-quartets, respectively. When combined, such sequences are expected to either retain their structure or form duplexes or triple helices. All these structures may occur in vivo whenever the sequence criteria are met. Such stretches are present in the circular genome of human mitochondria, as two 10 nucleotide-long perfect tandem direct repeats (DR1 and DR2). The DR1 and DR2 repeats are G-rich on the heavy strand and C-rich on the light strand. Previous results suggested that during replication, transient formation of a parallel GGC triple helix between the neo-synthesised G-rich DR1 and the double-stranded homologous DR2 could be involved in a rearrangement process leading to genome instability. In order to get structural insights into the interaction between the two repeats, we have studied by nuclear magnetic resonance (NMR) the assembly properties of a 24-mer oligodeoxyribonucleotide in which the C- and G-rich segments of the DRs are covalently tethered by a TTTT linker. We show here that this 24-mer self-associates into a triplex-containing symmetrical tetramer. The core of the structure is composed of anti-parallel Watson-Crick (WC) base pairs. Two additional strands are hydrogen-bonded to the Hoogsteen side of the Gs, thus forming CGC(+) triple helices, with G-rich ends folding into G-quartets. These results suggest that such structures could occur when the two DRs are put to close proximity in a biological context.

Crowdsourced direct-to-consumer genomic analysis of a family quartet.

PubMed

Corpas, Manuel; Valdivia-Granda, Willy; Torres, Nazareth; Greshake, Bastian; Coletta, Alain; Knaus, Alexej; Harrison, Andrew P; Cariaso, Mike; Moran, Federico; Nielsen, Fiona; Swan, Daniel; Weiss Solís, David Y; Krawitz, Peter; Schacherer, Frank; Schols, Peter; Yang, Huangming; Borry, Pascal; Glusman, Gustavo; Robinson, Peter N

2015-11-07

We describe the pioneering experience of a Spanish family pursuing the goal of understanding their own personal genetic data to the fullest possible extent using Direct to Consumer (DTC) tests. With full informed consent from the Corpas family, all genotype, exome and metagenome data from members of this family, are publicly available under a public domain Creative Commons 0 (CC0) license waiver. All scientists or companies analysing these data ("the Corpasome") were invited to return results to the family. We released 5 genotypes, 4 exomes, 1 metagenome from the Corpas family via a blog and figshare under a public domain license, inviting scientists to join the crowdsourcing efforts to analyse the genomes in return for coauthorship or acknowldgement in derived papers. Resulting analysis data were compiled via social media and direct email. Here we present the results of our investigations, combining the crowdsourced contributions and our own efforts. Four companies offering annotations for genomic variants were applied to four family exomes: BIOBASE, Ingenuity, Diploid, and GeneTalk. Starting from a common VCF file and after selecting for significant results from company reports, we find no overlap among described annotations. We additionally report on a gut microbiome analysis of a member of the Corpas family. This study presents an analysis of a diverse set of tools and methods offered by four DTC companies. The striking discordance of the results mirrors previous findings with respect to DTC analysis of SNP chip data, and highlights the difficulties of using DTC data for preventive medical care. To our knowledge, the data and analysis results from our crowdsourced study represent the most comprehensive exome and analysis for a family quartet using solely DTC data generation to date.

Hypothesis: A Role for Fragile X Mental Retardation Protein in Mediating and Relieving MicroRNA-Guided Translational Repression?

PubMed Central

Plante, Isabelle; Provost, Patrick

2006-01-01

MicroRNA (miRNA)-guided messenger RNA (mRNA) translational repression is believed to be mediated by effector miRNA-containing ribonucleoprotein (miRNP) complexes harboring fragile X mental retardation protein (FMRP). Recent studies documented the nucleic acid chaperone properties of FMRP and characterized its role and importance in RNA silencing in mammalian cells. We propose a model in which FMRP could facilitate miRNA assembly on target mRNAs in a process involving recognition of G quartet structures. Functioning within a duplex miRNP, FMRP may also mediate mRNA targeting through a strand exchange mechanism, in which the miRNA* of the duplex is swapped for the mRNA. Furthermore, FMRP may contribute to the relief of miRNA-guided mRNA repression through a reverse strand exchange reaction, possibly initiated by a specific cellular signal, that would liberate the mRNA for translation. Suboptimal utilization of miRNAs may thus account for some of the molecular defects in patients with the fragile X syndrome. PMID:17057359

Fourier transform inequalities for phylogenetic trees.

PubMed

Matsen, Frederick A

2009-01-01

Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

Intramolecular H-transfer reactions in Si 2H n (for n=3-5)

NASA Astrophysics Data System (ADS)

Ernst, M. C.; Sax, A. F.; Kalcher, J.

1993-12-01

Intramolecular rearrangement reactions for doublet Si 2H 5 and Si 2H 3, quartet Si 2H 3, and singlet Si 2H 4 have been studied. aim of the study was to characterize a series of intramolecular H-transfer reactions in silicon hydrides with vrying degrees of saturation. The transition states belonging to the reactions presented in this work possess a monobridged Si 2H moiety. Structural features of the transition states and relative barrier heights have been examined; the geometry optimizations were performed with the use of CAS-SCF wavefunctions and the barrier height estimates were obtained with single-point CI calculations.

Natural radium and radon tracers to quantify water exchange and movement in reservoirs

USGS Publications Warehouse

Smith, Christopher G.; Baskaran, Mark

2011-01-01

Radon and radium isotopes are routinely used to quantify exchange rates between different hydrologic reservoirs. Since their recognition as oceanic tracers in the 1960s, both radon and radium have been used to examine processes such as air-sea exchange, deep oceanic mixing, benthic inputs, and many others. Recently, the application of radon-222 and the radium-quartet (223,224,226,228Ra) as coastal tracers has seen a revelation with the growing interest in coastal groundwater dynamics. The enrichment of these isotopes in benthic fluids including groundwater makes both radium and radon ideal tracers of coastal benthic processes (e.g. submarine groundwater discharge). In this chapter we review traditional and recent advances in the application of radon and radium isotopes to understand mixing and exchange between various hydrologic reservoirs, specifically: (1) atmosphere and ocean, (2) deep and shallow oceanic water masses, (3) coastal groundwater/benthic pore waters and surface ocean, and (4) aquifer-lakes. While the isotopes themselves and their distribution in the environment provide qualitative information about the exchange processes, it is mixing/exchange and transport models for these isotopes that provide specific quantitative information about these processes. Brief introductions of these models and mixing parameters are provided for both historical and more recent studies.

Quantum Chromodynamics and Color Confinement (confinement 2000) - Proceedings of the International Symposium

NASA Astrophysics Data System (ADS)

Suganuma, H.; Fukushima, M.; Toki, H.

The Table of Contents for the book is as follows: * Preface * Opening Address * Monopole Condensation and Quark Confinement * Dual QCD, Effective String Theory, and Regge Trajectories * Abelian Dominance and Monopole Condensation * Non-Abelian Stokes Theorem and Quark Confinement in QCD * Infrared Region of QCD and Confining Configurations * BRS Quartet Mechanism for Color Confinement * Color Confinement and Quartet Mechanism * Numerical Tests of the Kugo-Ojima Color Confinement Criterion * Monopoles and Confinement in Lattice QCD * SU(2) Lattice Gauge Theory at T > 0 in a Finite Box with Fixed Holonomy * Confining and Dirac Strings in Gluodynamics * Cooling, Monopoles, and Vortices in SU(2) Lattice Gauge Theory * Quark Confinement Physics from Lattice QCD * An (Almost) Perfect Lattice Action for SU(2) and SU(3) Gluodynamics * Vortices and Confinement in Lattice QCD * P-Vortices, Nexuses and Effects of Gribov Copies in the Center Gauges * Laplacian Center Vortices * Center Vortices at Strong Couplings and All Couplings * Simulations in SO(3) × Z(2) Lattice Gauge Theory * Exciting a Vortex - the Cost of Confinement * Instantons in QCD * Deformation of Instanton in External Color Fields * Field Strength Correlators in the Instanton Liquid * Instanton and Meron Physics in Lattice QCD * The Dual Ginzburg-Landau Theory for Confinement and the Role of Instantons * Lattice QCD for Quarks, Gluons and Hadrons * Hadronic Spectral Functions in QCD * Universality and Chaos in Quantum Field Theories * Lattice QCD Study of Three Quark Potential * Probing the QCD Vacuum with Flavour Singlet Objects : η' on the Lattice * Lattice Studies of Quarks and Gluons * Quarks and Hadrons in QCD * Supersymmetric Nonlinear Sigma Models * Chiral Transition and Baryon-number Susceptibility * Light Quark Masses in QCD * Chiral Symmetry of Baryons and Baryon Resonances * Confinement and Bound States in QCD * Parallel Session * Off-diagonal Gluon Mass Generation and Strong Randomness of Off-diagonal Gluon Phase in the Maximally Abelian Gauge * On the Colour Confinement and the Minimal Surface * Glueball Mass and String Tension of SU(2) Gluodynamics from Abelian Monopoles and Strings * Application of the Non-Perturbative Renormalization Group to the Nambu-Jona-Lasinio Model at Finite Temperature and Density * Confining Flux-Tube and Hadrons in QCD * Gauge Symmetry Breakdown due to Dynamical Higgs Scalar * Spatial Structure of Quark Cooper Pairs * New Approach to Axial Coupling Constants in the QCD Sum Rule and Instanton Effects * String Breaking on a Lattice * Bethe-Salpeter Approach for Mesons within the Dual Ginzburg-Landau Theory * Gauge Dependence and Matching Procedure of a Nonrelativistic QCD Boundstate Formalism * A Mathematical Approach to the SU(2)-Quark Confinement * Simulations of Odd Flavors QCD by Hybrid Monte Carlo * Non-Perturbative Renormalization Group Analysis of Dynamical Chiral Symmetry Breaking with Beyond Ladder Contributions * Charmonium Physics in Finite Temperature Lattice QCD * From Meson-Nucleon Scattering to Vector Mesons in Nuclear Matter * Symposium Program * List of Participants

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Photoluminescence dynamics of Co-doped Zn 1- xCd xSe and ZnS xSe 1- xcrystals

NASA Astrophysics Data System (ADS)

Born, H.; Thurian, P.; Surkova, T.; Hoffmann, A.; Busse, W.; Gumlich, H.-E.; Broser, I.; Giriat, W.

1998-02-01

Intra-shell d-d relaxation processes of Co 2+ centres are investigated by means of time-integrated and time-resolved photoluminescence spectroscopy. The composition dependence of the luminescence and the decay of the Co L-line in ZnCdSe and ZnSSe alloys is presented for the first time. Additionally, new Co-related infrared luminescence lines were observed near 1.6 eV. Taking into account the energy position of the L-line and the relaxation dynamics of the green and the infrared luminescence, the L-line is explained as an internal doublet-quartet d-d transition of the Co-centres.

KSC-2012-4261

NASA Image and Video Library

2012-08-03

CAPE CANAVERAL, Fla. – A string quartet from the Brevard Symphony Orchestra performed for graduates and guests at the closing ceremonies for the International Space University at the Kennedy Space center Visitor Complex on Aug. 3, 2012. The International Space University is a nine-week intensive course designed for post-graduate university students and professionals during the summer. The program is hosted by a different country each year, providing a unique educational experience for participants from around the world. NASA Kennedy Space Center and the Florida Institute of Technology co-hosted this year's event which ran from June 4 to Aug. 3. There were about 125 participants representing 31 countries. For more information, visit http://www.isunet.edu Photo credit: NASA/Kim Shiflett

Adinkras from ordered quartets of BC4 Coxeter group elements and regarding another Gadget’s 1,358,954,496 matrix elements

NASA Astrophysics Data System (ADS)

Gates, S. James; Kang, Lucas; Kessler, David S.; Korotkikh, Vadim

2018-04-01

A Gadget, more precisely a scalar Gadget, is defined as a mathematical calculation acting over a domain of one or more adinkra graphs and whose range is a real number. A 2010 work on the subject of automorphisms of adinkra graphs, implied the existence of multiple numbers of Gadgets depending on the number of colors under consideration. For four colors, this number is two. In this work, we verify the existence of a second such Gadget and calculate (both analytically and via explicit computer-enabled algorithms) its 1,358,954,496 matrix elements over 36,864 minimal valise adinkras related to the Coxeter Group BC4.

Rooting phylogenetic trees under the coalescent model using site pattern probabilities.

PubMed

Tian, Yuan; Kubatko, Laura

2017-12-19

Phylogenetic tree inference is a fundamental tool to estimate ancestor-descendant relationships among different species. In phylogenetic studies, identification of the root - the most recent common ancestor of all sampled organisms - is essential for complete understanding of the evolutionary relationships. Rooted trees benefit most downstream application of phylogenies such as species classification or study of adaptation. Often, trees can be rooted by using outgroups, which are species that are known to be more distantly related to the sampled organisms than any other species in the phylogeny. However, outgroups are not always available in evolutionary research. In this study, we develop a new method for rooting species tree under the coalescent model, by developing a series of hypothesis tests for rooting quartet phylogenies using site pattern probabilities. The power of this method is examined by simulation studies and by application to an empirical North American rattlesnake data set. The method shows high accuracy across the simulation conditions considered, and performs well for the rattlesnake data. Thus, it provides a computationally efficient way to accurately root species-level phylogenies that incorporates the coalescent process. The method is robust to variation in substitution model, but is sensitive to the assumption of a molecular clock. Our study establishes a computationally practical method for rooting species trees that is more efficient than traditional methods. The method will benefit numerous evolutionary studies that require rooting a phylogenetic tree without having to specify outgroups.

Lattice Boltzmann simulation of the gas-solid adsorption process in reconstructed random porous media.

PubMed

Zhou, L; Qu, Z G; Ding, T; Miao, J Y

2016-04-01

The gas-solid adsorption process in reconstructed random porous media is numerically studied with the lattice Boltzmann (LB) method at the pore scale with consideration of interparticle, interfacial, and intraparticle mass transfer performances. Adsorbent structures are reconstructed in two dimensions by employing the quartet structure generation set approach. To implement boundary conditions accurately, all the porous interfacial nodes are recognized and classified into 14 types using a proposed universal program called the boundary recognition and classification program. The multiple-relaxation-time LB model and single-relaxation-time LB model are adopted to simulate flow and mass transport, respectively. The interparticle, interfacial, and intraparticle mass transfer capacities are evaluated with the permeability factor and interparticle transfer coefficient, Langmuir adsorption kinetics, and the solid diffusion model, respectively. Adsorption processes are performed in two groups of adsorbent media with different porosities and particle sizes. External and internal mass transfer resistances govern the adsorption system. A large porosity leads to an early time for adsorption equilibrium because of the controlling factor of external resistance. External and internal resistances are dominant at small and large particle sizes, respectively. Particle size, under which the total resistance is minimum, ranges from 3 to 7 μm with the preset parameters. Pore-scale simulation clearly explains the effect of both external and internal mass transfer resistances. The present paper provides both theoretical and practical guidance for the design and optimization of adsorption systems.

Lattice Boltzmann simulation of the gas-solid adsorption process in reconstructed random porous media

NASA Astrophysics Data System (ADS)

Zhou, L.; Qu, Z. G.; Ding, T.; Miao, J. Y.

2016-04-01

The gas-solid adsorption process in reconstructed random porous media is numerically studied with the lattice Boltzmann (LB) method at the pore scale with consideration of interparticle, interfacial, and intraparticle mass transfer performances. Adsorbent structures are reconstructed in two dimensions by employing the quartet structure generation set approach. To implement boundary conditions accurately, all the porous interfacial nodes are recognized and classified into 14 types using a proposed universal program called the boundary recognition and classification program. The multiple-relaxation-time LB model and single-relaxation-time LB model are adopted to simulate flow and mass transport, respectively. The interparticle, interfacial, and intraparticle mass transfer capacities are evaluated with the permeability factor and interparticle transfer coefficient, Langmuir adsorption kinetics, and the solid diffusion model, respectively. Adsorption processes are performed in two groups of adsorbent media with different porosities and particle sizes. External and internal mass transfer resistances govern the adsorption system. A large porosity leads to an early time for adsorption equilibrium because of the controlling factor of external resistance. External and internal resistances are dominant at small and large particle sizes, respectively. Particle size, under which the total resistance is minimum, ranges from 3 to 7 μm with the preset parameters. Pore-scale simulation clearly explains the effect of both external and internal mass transfer resistances. The present paper provides both theoretical and practical guidance for the design and optimization of adsorption systems.

Evaluation of polar organic micropollutants as indicators for wastewater-related coastal water quality impairment.

PubMed

Nödler, Karsten; Tsakiri, Maria; Aloupi, Maria; Gatidou, Georgia; Stasinakis, Athanasios S; Licha, Tobias

2016-04-01

Results from coastal water pollution monitoring (Lesvos Island, Greece) are presented. In total, 53 samples were analyzed for 58 polar organic micropollutants such as selected herbicides, biocides, corrosion inhibitors, stimulants, artificial sweeteners, and pharmaceuticals. Main focus is the application of a proposed wastewater indicator quartet (acesulfame, caffeine, valsartan, and valsartan acid) to detect point sources and contamination hot-spots with untreated and treated wastewater. The derived conclusions are compared with the state of knowledge regarding local land use and infrastructure. The artificial sweetener acesulfame and the stimulant caffeine were used as indicators for treated and untreated wastewater, respectively. In case of a contamination with untreated wastewater the concentration ratio of the antihypertensive valsartan and its transformation product valsartan acid was used to further refine the estimation of the residence time of the contamination. The median/maximum concentrations of acesulfame and caffeine were 5.3/178 ng L(-1) and 6.1/522 ng L(-1), respectively. Their detection frequency was 100%. Highest concentrations were detected within the urban area of the capital of the island (Mytilene). The indicator quartet in the gulfs of Gera and Kalloni (two semi-enclosed embayments on the island) demonstrated different concentration patterns. A comparatively higher proportion of untreated wastewater was detected in the gulf of Gera, which is in agreement with data on the wastewater infrastructure. The indicator quality of the micropollutants to detect wastewater was compared with electrical conductivity (EC) data. Due to their anthropogenic nature and low detection limits, the micropollutants are superior to EC regarding both sensitivity and selectivity. The concentrations of atrazine, diuron, and isoproturon did not exceed the annual average of their environmental quality standards (EQS) defined by the European Commission. At two sampling locations irgarol 1051 exceeded its annual average EQS value but not the maximum allowable concentration of 16 ng L(-1). Copyright © 2016 Elsevier Ltd. All rights reserved.

Infrared spectroscopy of matrix-isolated neutral polycyclic aromatic nitrogen heterocycles: The acridine series

NASA Astrophysics Data System (ADS)

Mattioda, A. L.; Bauschlicher, C. W.; Ricca, A.; Bregman, J.; Hudgins, D. M.; Allamandola, L. J.

2017-06-01

The matrix-isolated, mid-infrared spectra of seven acridine-based polycyclic aromatic nitrogen heterocycles (PANHs) have been measured and compared to their non-nitrogen containing parent molecule. The acridine species investigated include acridine, benz[a]acridine, benz[c]acridine, dibenz[a,j]acridine, dibenz[c,h]acridine, dibenz[a,h]acridine and dibenz[a,c]acridine. The previously reported results for 1 and 2-azabenz[a]anthracenes are included for comparison. The experimentally determined band frequencies and intensities are compared with their B3LYP/6-31G(d) values. The overall agreement between experimental and theoretical values is good and in line with our previous investigations. Shifts, typically to the blue, are noted for the C-H out-of-plane (CHoop) motions upon insertion of a nitrogen atom. The formation of a bay region upon addition of additional benzene rings to the anthracene/acridine structure splits the solo hydrogen motions into a bay region solo and an external solo hydrogen, with the bay region solo hydrogen coupling to the quartet hydrogen motions and the external solo hydrogen coupling with the duo hydrogen motions resulting in an extreme decrease in intensity for the CHoop solo hydrogen band when the external hydrogen is replaced by a nitrogen atom. The C-C and C-H in-plane region of this acridine series exhibits the characteristic two fold increase in intensity, noted previously for PANHs. The strong ≈1400 cm-1 band, which was identified in the previous PANH study, is noted in several molecular species as well as another strong PANH feature between 1480 and 1515 cm-1 for several molecules. The presence of these strong bands appear to be primarily responsible for the two-fold increase in the C-H in-plane region's (1100-1600 cm-1) intensity. The C-H stretching region can be characterized by contributions from the solo (bay or external), duo and quartet hydrogens, similar to what was observed in the dibenzopolyacene compounds.

Radium isotope quartet in groundwater as a proxy for identification of aquifer rocks and mechanisms of water-rock interactions: examples from the Negev, Israel

NASA Astrophysics Data System (ADS)

Vengosh, A.; Pery, N.; Paytan, A.; Haquin, G.; Elhanani, S.; Pankratov, I.

2006-05-01

Many aquifer systems are composed of multiple rock types. Previous attempts to evaluate the specific aquifer rocks that control the groundwater chemistry and possible flow paths within these multiple lithological systems have used major ion chemistry and isotopic tracers (e.g., strontium isotopes). Here we propose an additional isotopic proxy that is based on the distribution of radium isotopes in groundwater. Radium has four radioactive isotopes that are part of the decay chains of uranium-238, thorium-232, and uranium-235. The abundance of radium isotope quartet (226Ra-half life 1600 y; 228Ra-5.6 y; 224Ra-3.6 d; 223Ra-11.4 d) in groundwater reflects the Th/U ratios in the rocks. Investigation of groundwater from the Negev, Israel, enabled us to discriminate between groundwaters flowing in the Lower Cretaceous Nubian Sandstone and the Upper Cretaceous Judea Group carbonate aquifers. Groundwater flowing in the sandstone aquifer has distinguishably high 228Ra/226Ra and 224Ra/223Ra ratios due to the high Th/U ratio in sandstone. In contrast, the predominance of uranium in carbonate rocks results in low 228Ra/226Ra and 224Ra/223Ra ratios in the associated groundwater. We show that the radium activity in groundwater in the two-aquifer systems is correlated with temperature, dissolved oxygen, and salinity. The increase of radium activity is also associated with changes in the isotopic ratios; 228Ra/226Ra ratios increase and decrease in the sandstone and carbonate aquifers, respectively. Given that the dissolution of radium isotopes depends on their decay constants, the use of the four radium isotopes with different decay constants enabled us to distinguish between dissolution (higher abundance of the long-lived isotopes) and recoil (predominance of the short-lived isotopes) processes. In spite of these isotopic fractionations, the radium isotopic discrimination between carbonate and sandstone aquifers is significant.

The electronic structure of vanadium monochloride cation (VCl{sup +}): Tackling the complexities of transition metal species

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeYonker, Nathan J., E-mail: ndyonker@memphis.edu; Halfen, DeWayne T.; Ziurys, Lucy M.

Six electronic states (X {sup 4}Σ{sup −}, A {sup 4}Π, B {sup 4}Δ, {sup 2}Φ, {sup 2}Δ, {sup 2}Σ{sup +}) of the vanadium monochloride cation (VCl{sup +}) are described using large basis set coupled cluster theory. For the two lowest quartet states (X {sup 4}Σ{sup −} and A {sup 4}Π), a focal point analysis (FPA) approach was used that conjoined a correlation-consistent family of basis sets up to aug-cc-pwCV5Z-DK with high-order coupled cluster theory through pentuple (CCSDTQP) excitations. FPA adiabatic excitation energies (T{sub 0}) and spectroscopic constants (r{sub e}, r{sub 0}, B{sub e}, B{sub 0}, D{sup ¯}{sub e}, H{sub e},more » ω{sub e}, v{sub 0}, α{sub e}, ω{sub e}x{sub e}) were extrapolated to the valence complete basis set Douglas-Kroll (DK) aug-cc-pV∞Z-DK CCSDT level of theory, and additional treatments accounted for higher-order valence electron correlation, core correlation, and spin-orbit coupling. Due to the delicate interplay between dynamical and static electronic correlation, single reference coupled cluster theory is able to provide the correct ground electronic state (X {sup 4}Σ{sup −}), while multireference configuration interaction theory cannot. Perturbations from the first- and second-order spin orbit coupling of low-lying states with quartet spin multiplicity reveal an immensely complex rotational spectrum relative to the isovalent species VO, VS, and TiCl. Computational data on the doublet manifold suggest that the lowest-lying doublet state ({sup 2}Γ) has a T{sub e} of ∼11 200 cm{sup −1}. Overall, this study shows that laboratory and theoretical rotational spectroscopists must work more closely in tandem to better understand the bonding and structure of molecules containing transition metals.« less

Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates.

PubMed

Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

2017-03-14

The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

More on the Best Evolutionary Rate for Phylogenetic Analysis

PubMed Central

Massingham, Tim; Goldman, Nick

2017-01-01

Abstract The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes. Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations. We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets. This finding encourages the use of methods that rely on a single optimal rate to predict a gene’s utility. Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0.45 substitutions from root to tip in average Yule trees and about 0.2 in difficult trees with short basal and long-apical branches, but all rates leading to divergence levels between about 0.1 and 0.5 perform reasonably well. Testing the performance of six methods that can be used to predict a gene’s utility against our simulation results, we find that the probability of resolution, signal-noise analysis, and Fisher information are good predictors of phylogenetic informativeness, but they require specification of at least part of a model tree. Likelihood quartet mapping also shows very good performance but only requires sequence alignments and is thus applicable without making assumptions about the phylogeny. Despite them being the most commonly used methods for experimental design, geometric quartet mapping and the integration of phylogenetic informativeness curves perform rather poorly in our comparison. Instead of derived predictors of phylogenetic informativeness, we suggest that the number of sites in a gene that evolve at near-optimal rates (as inferred here) could be used directly to prioritize genes for phylogenetic inference. In combination with measures of model fit, especially with respect to compositional biases and among-site and among-lineage rate variation, such an approach has the potential to greatly improve marker choice and should be tested on empirical data. PMID:28595363

Measuring social interaction in music ensembles

PubMed Central

D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-01-01

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. PMID:27069054

Measuring social interaction in music ensembles.

PubMed

Volpe, Gualtiero; D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-05-05

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. © 2016 The Author(s).

Brief report: altered horizontal binding of single dots to coherent motion in autism.

PubMed

David, Nicole; Rose, Michael; Schneider, Till R; Vogeley, Kai; Engel, Andreas K

2010-12-01

Individuals with autism often show a fragmented way of perceiving their environment, suggesting a disorder of information integration, possibly due to disrupted communication between brain areas. We investigated thirteen individuals with high-functioning autism (HFA) and thirteen healthy controls using the metastable motion quartet, a stimulus consisting of two dots alternately presented at four locations of a hypothetical square, thereby inducing an apparent motion percept. This percept is vertical or horizontal, the latter requiring binding of motion signals across cerebral hemispheres. Decreasing the horizontal distance between dots could facilitate horizontal percepts. We found evidence for altered horizontal binding in HFA: Individuals with HFA needed stronger facilitation to experience horizontal motion. These data are interpreted in light of reduced cross-hemispheric communication.

Synthesis of C13- and N15-Labeled DNAN

DTIC Science & Technology

2014-07-24

Multiplicities are described as singlet (s), doublet (d), triplet (t), quartet (q), doublet of doublets (dd), doublet of doublet of doublets ( ddd ), multiplet...dd, 4.8Hz, 2.6Hz, 1H), 8.40 ( ddd , 8.8Hz, 2.6Hz, 1.8Hz, 1H), and 7.81 (d, 8.8Hz, 1H) ppm. 13C NMR (CDCl3): δ 147.8 (dd, 18Hz, 3Hz), 146.3 (dd, 17Hz...Dinitroanisole mp: 86-88 °C 1H NMR (CDCl3): δ 8.77 (m, 4.8Hz, 2.6Hz, 1H), 8.46 ( ddd , 9.2Hz, 2.6Hz, 1.8Hz, 1H), 7.23 (d, 9.2Hz, 1H), and 4.10 (s, 3H

OMEGA{sup -}, XI*{sup -}, SIGMA*{sup -}, and DELTA{sup -} decuplet baryon magnetic moments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaughter, Milton Dean

The properties of the ground-state U spin =(3/2) baryon decuplet magnetic moments DELTA{sup -}, XI*{sup -}, SIGMA*{sup -}, and OMEGA{sup -} and their ground-state spin-(1/2) cousins p, n, LAMBDA, SIGMA{sup +}, SIGMA{sup 0}, SIGMA{sup -}, XI{sup +}, and XI{sup -} have been studied for many years with a modicum of success. The magnetic moments of many are yet to be determined. Of the decuplet baryons, only the magnetic moment of the OMEGA{sup -} has been accurately determined. We calculate the magnetic moments of the physical decuplet U spin =(3/2) quartet members without ascribing any specific form to their quark structuremore » or intraquark interactions.« less

Trochanteric area pain, the result of a quartet of bursal inflammation.

PubMed

Rothschild, Bruce

2013-07-18

Bursitis is quite responsive to therapeutic intervention, once the afflicted area is accurately identified. This is especially notable for some hip complaints. Patients' use of the term "hip" can relate to anything from the low back to groin to lateral thigh pain. Trochanteric area surface localization of "hip" pain may afford an opportunity for immediate cure. Effectiveness of therapeutic intervention is predicated upon injection of not one or two, but all four peri-trochanteric bursa with a depot (minimally water-soluble) corticosteroid. The term trochanteric bursitis suggests that the inflammation is more focal than what is clinically observed. While easier to express, perhaps it is time to refer to inflammation in this area, naming all four affected bursae.

Trochanteric area pain, the result of a quartet of bursal inflammation

PubMed Central

Rothschild, Bruce

2013-01-01

Bursitis is quite responsive to therapeutic intervention, once the afflicted area is accurately identified. This is especially notable for some hip complaints. Patients’ use of the term “hip” can relate to anything from the low back to groin to lateral thigh pain. Trochanteric area surface localization of “hip” pain may afford an opportunity for immediate cure. Effectiveness of therapeutic intervention is predicated upon injection of not one or two, but all four peri-trochanteric bursa with a depot (minimally water-soluble) corticosteroid. The term trochanteric bursitis suggests that the inflammation is more focal than what is clinically observed. While easier to express, perhaps it is time to refer to inflammation in this area, naming all four affected bursae. PMID:23878774

Index theorem and universality properties of the low-lying eigenvalues of improved staggered quarks.

PubMed

Follana, E; Hart, A; Davies, C T H

2004-12-10

We study various improved staggered quark Dirac operators on quenched gluon backgrounds in lattice QCD generated using a Symanzik-improved gluon action. We find a clear separation of the spectrum into would-be zero modes and others. The number of would-be zero modes depends on the topological charge as expected from the index theorem, and their chirality expectation value is large ( approximately 0.7). The remaining modes have low chirality and show clear signs of clustering into quartets and approaching the random matrix theory predictions for all topological charge sectors. We conclude that improvement of the fermionic and gauge actions moves the staggered quarks closer to the continuum limit where they respond correctly to QCD topology.

Observation of excited state absorption in the V-Cr Prussian blue analogue

NASA Astrophysics Data System (ADS)

Hedley, Luke; Horbury, Michael D.; Liedy, Florian; Johansson, J. Olof

2017-11-01

We present femtosecond transient transmission measurements of thin films of the VII/III-CrIII Prussian blue analogue (V-Cr PBA) in the spectral range 330-675 nm after exciting the ligand-to-metal charge-transfer transition (LMCT) at 400 nm. A global analysis including three decay-times of τ1 = 230 fs, τ2 = 1.38 ps and τ3 ≫ 2 ns could satisfactory describe the data. We observed an excited state absorption (ESA) at 345 nm, which was attributed to a charge-transfer transition from the 2E state on the Cr ions after fast intersystem crossing from the quartet manifold. An additional weak and short-lived ESA at 455 nm was also observed and was tentatively attributed to the initially populated 4LMCT state.

Horizontal vectorization of electron repulsion integrals.

PubMed

Pritchard, Benjamin P; Chow, Edmond

2016-10-30

We present an efficient implementation of the Obara-Saika algorithm for the computation of electron repulsion integrals that utilizes vector intrinsics to calculate several primitive integrals concurrently in a SIMD vector. Initial benchmarks display a 2-4 times speedup with AVX instructions over comparable scalar code, depending on the basis set. Speedup over scalar code is found to be sensitive to the level of contraction of the basis set, and is best for (lAlB|lClD) quartets when lD  = 0 or lB=lD=0, which makes such a vectorization scheme particularly suitable for density fitting. The basic Obara-Saika algorithm, how it is vectorized, and the performance bottlenecks are analyzed and discussed. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

Chiral alkylated-aniline as a noninvasive fluorescence sensor: Spectroscopic and molecular modeling studies

NASA Astrophysics Data System (ADS)

Sengupta, Bidisha; Mukherjee, Chirantan Sen; Chakraborty, Sandipan; Muhammad, Maria Jones; Gladney, William; Armstrong, George

2017-12-01

Aniline, heterocyclic aromatic amines, and arylamines are known carcinogens. Recently aniline mustard has come into prominence as a novel anticancer agent. In this project, microwave irradiation has been used to synthesize an optically active alkylated aniline namely 2,6-dimethyl-4-(1-(p-tolyl)ethyl)aniline (abbreviated DMPA). The presence of quartet and doublet peaks in NMR and a single chromatogram in HPLC verified that the final product DMPA, prepared from the synthesis reactions, had no major impurities. By using a Lux chiral column in HPLC, two peaks have been detected in the chromatogram, which correspond to two enantiomers of the chiral aniline derivative. Fluorescence spectroscopic measurements on DMPA indicated conspicuous dependence of its emission behavior on the polarity (in terms of the empirical polarity parameter ET(30)) of the homogeneous solvents used, a property important for an optical sensor. The nature of the emission profiles, along with the relevant parameter namely wavelength at emission maximum (λemmax) is used to infer the distribution, binding and microenvironment of the DMPA molecules in human serum albumin protein (HSA). DMPA is weakly fluorescent in aqueous buffer medium, with a dramatic enhancement in the fluorescence emission in the presence of HSA. Molecular modeling studies have been carried out on the two enantiomers (R and S) of DMPA with HSA. The implications of these findings are examined in relation to the potentialities of DMPA as a novel fluorescence sensor for biological systems.

SEP-class genes in Prunus mume and their likely role in floral organ development.

PubMed

Zhou, Yuzhen; Xu, Zongda; Yong, Xue; Ahmad, Sagheer; Yang, Weiru; Cheng, Tangren; Wang, Jia; Zhang, Qixiang

2017-01-13

Flower phylogenetics and genetically controlled development have been revolutionised during the last two decades. However, some of these evolutionary aspects are still debatable. MADS-box genes are known to play essential role in specifying the floral organogenesis and differentiation in numerous model plants like Petunia hybrida, Arabidopsis thaliana and Antirrhinum majus. SEPALLATA (SEP) genes, belonging to the MADS-box gene family, are members of the ABCDE and quartet models of floral organ development and play a vital role in flower development. However, few studies of the genes in Prunus mume have yet been conducted. In this study, we cloned four PmSEPs and investigated their phylogenetic relationship with other species. Expression pattern analyses and yeast two-hybrid assays of these four genes indicated their involvement in the floral organogenesis with PmSEP4 specifically related to specification of the prolificated flowers in P. mume. It was observed that the flower meristem was specified by PmSEP1 and PmSEP4, the sepal by PmSEP1 and PmSEP4, petals by PmSEP2 and PmSEP3, stamens by PmSEP2 and PmSEP3 and pistils by PmSEP2 and PmSEP3. With the above in mind, flower development in P. mume might be due to an expression of SEP genes. Our findings can provide a foundation for further investigations of the transcriptional factors governing flower development, their molecular mechanisms and genetic basis.

Chiral alkylated-aniline as a noninvasive fluorescence sensor: Spectroscopic and molecular modeling studies.

PubMed

Sengupta, Bidisha; Mukherjee, Chirantan Sen; Chakraborty, Sandipan; Muhammad, Maria Jones; Gladney, William; Armstrong, George

2017-12-05

Aniline, heterocyclic aromatic amines, and arylamines are known carcinogens. Recently aniline mustard has come into prominence as a novel anticancer agent. In this project, microwave irradiation has been used to synthesize an optically active alkylated aniline namely 2,6-dimethyl-4-(1-(p-tolyl)ethyl)aniline (abbreviated DMPA). The presence of quartet and doublet peaks in NMR and a single chromatogram in HPLC verified that the final product DMPA, prepared from the synthesis reactions, had no major impurities. By using a Lux chiral column in HPLC, two peaks have been detected in the chromatogram, which correspond to two enantiomers of the chiral aniline derivative. Fluorescence spectroscopic measurements on DMPA indicated conspicuous dependence of its emission behavior on the polarity (in terms of the empirical polarity parameter E T (30)) of the homogeneous solvents used, a property important for an optical sensor. The nature of the emission profiles, along with the relevant parameter namely wavelength at emission maximum (λ em max ) is used to infer the distribution, binding and microenvironment of the DMPA molecules in human serum albumin protein (HSA). DMPA is weakly fluorescent in aqueous buffer medium, with a dramatic enhancement in the fluorescence emission in the presence of HSA. Molecular modeling studies have been carried out on the two enantiomers (R and S) of DMPA with HSA. The implications of these findings are examined in relation to the potentialities of DMPA as a novel fluorescence sensor for biological systems. Copyright © 2017 Elsevier B.V. All rights reserved.

[From "deadly quartet" to "metabolic syndrome". An analysis of its clinical relevance].

PubMed

Vancheri, Federico; Burgio, Antonio; Dovico, Rossana

2007-03-01

The metabolic syndrome denotes a clustering of specific risk factors for both cardiovascular disease and type 2 diabetes, whose underlying pathophysiology is believed to include insulin resistance. It has been widely reported that the syndrome is a simple clinical tool to identify people at high long term risk of cardiovascular disease and diabetes. However, its clinical importance is under debate. There are substantial uncertainties about the clinical definition of the syndrome, as to whether the risk factors clustering indicates a single unifying disorder, whether the risk conferred by the condition as a whole is higher risk than its individual components, and whether its predictive value of future cardiovascular events or diabetes is greater than established predicting models such as the Framingham Risk Score and the Diabetes Risk Score. We undertook an extensive review of the literature. Our analysis indicates that current definitions of the syndrome are incomplete or ambiguous, more than one pathophysiological process underlies the syndrome, although the combination of insulin resistance and hyperinsulinemia are related to most cases; the risk associated with the syndrome is no greater than that explained by the presence of its components, and the syndrome is less effective in predicting the future development of cardiovascular events and diabetes than established predicting models. Although the syndrome has some importance in understanding the pathophysiology of cardiovascular and diabetes risk factors clustering, its use as a clinical syndrome is not justified by current data.

Exotic colored scalars at the LHC

NASA Astrophysics Data System (ADS)

Blum, Kfir; Efrati, Aielet; Frugiuele, Claudia; Nir, Yosef

2017-02-01

We study the phenomenology of exotic color-triplet scalar particles X with charge | Q| = 2 /3 , 4 /3 , 5 /3 , 7 /3 , 8 /3 and 10 /3. If X is an SU(2) W -non-singlet, mass splitting within the multiplet allows for cascade decays of the members into the lightest state. We study examples where the lightest state, in turn, decays into a three-body W ± jj final state, and show that in such case the entire multiplet is compatible with indirect precision tests and with direct collider searches for continuum pair production of X down to m X ˜ 250 GeV. However, bound states S, made of XX † pairs at m S ≈ 2 m X , form under rather generic conditions and their decay to diphoton can be the first discovery channel of the model. Furthermore, for SU(2) W -non-singlets, the mode S → W + W - may be observable and the width of S → γγ and S → jj may appear large as a consequence of mass splittings within the X-multiplet. As an example we study in detail the case of an SU(2) W -quartet, finding that m X ≃ 450 GeV is allowed by all current searches.

Submarine groundwater discharge and nutrient loadings in Tolo Harbor, Hong Kong using multiple geotracer-based models, and their implications of red tide outbreaks.

PubMed

Luo, Xin; Jiao, Jiu Jimmy

2016-10-01

Multiple tracers, including radium quartet, (222)Rn and silica are used to quantify submarine groundwater discharge (SGD) into Tolo Harbor, Hong Kong in 2005 and 2011. Five geotracer models based on the end member model of (228)Ra and salinity and mass balance models of (226)Ra, (228)Ra, (222)Rn, and silica were established and all the models lead to an estimate of the SGD rate of the same order of magnitude. In 2005 and 2011, respectively, the averaged SGD based on these models is estimated to be ≈ 5.42 cm d(-1) and ≈2.66 cm d(-1), the SGD derived DIN loadings to be 3.5 × 10(5) mol d(-1) and 1.5 × 10(5) mol d(-1), and DIP loadings to be 6.2 × 10(3) mol d(-1) and 1.1 × 10(3) mol d(-1). Groundwater borne nutrients are 1-2 orders of magnitude larger than other nutrient sources and the interannual variation of nutrient concentration in the embayment is more influenced by the SGD derived loadings. Annual DIP concentrations in the harbor water is positively correlated with the precipitation and annual mean tidal range, and negatively correlated with evapotranspiration from 2000 to 2013. Climatologically driven SGD variability alters the SGD derived DIP loadings in this phosphate limited environment and may be the causative factor of interannual variability of red tide outbreaks from 2000 to 2013. Finally, a conceptual model is proposed to characterize the response of red tide outbreaks to climatological factors linked by SGD. The findings from this study shed light on the prediction of red tide outbreaks and coastal management of Tolo Harbor and similar coastal embayments elsewhere. Copyright © 2016 Elsevier Ltd. All rights reserved.

Infrared spectroscopy of matrix-isolated neutral polycyclic aromatic nitrogen heterocycles: The acridine series.

PubMed

Mattioda, A L; Bauschlicher, C W; Ricca, A; Bregman, J; Hudgins, D M; Allamandola, L J

2017-06-15

The matrix-isolated, mid-infrared spectra of seven acridine-based polycyclic aromatic nitrogen heterocycles (PANHs) have been measured and compared to their non-nitrogen containing parent molecule. The acridine species investigated include acridine, benz[a]acridine, benz[c]acridine, dibenz[a,j]acridine, dibenz[c,h]acridine, dibenz[a,h]acridine and dibenz[a,c]acridine. The previously reported results for 1 and 2-azabenz[a]anthracenes are included for comparison. The experimentally determined band frequencies and intensities are compared with their B3LYP/6-31G(d) values. The overall agreement between experimental and theoretical values is good and in line with our previous investigations. Shifts, typically to the blue, are noted for the C-H out-of-plane (CH oop ) motions upon insertion of a nitrogen atom. The formation of a bay region upon addition of additional benzene rings to the anthracene/acridine structure splits the solo hydrogen motions into a bay region solo and an external solo hydrogen, with the bay region solo hydrogen coupling to the quartet hydrogen motions and the external solo hydrogen coupling with the duo hydrogen motions resulting in an extreme decrease in intensity for the CH oop solo hydrogen band when the external hydrogen is replaced by a nitrogen atom. The C-C and C-H in-plane region of this acridine series exhibits the characteristic two fold increase in intensity, noted previously for PANHs. The strong ≈1400cm -1 band, which was identified in the previous PANH study, is noted in several molecular species as well as another strong PANH feature between 1480 and 1515cm -1 for several molecules. The presence of these strong bands appear to be primarily responsible for the two-fold increase in the C-H in-plane region's (1100-1600cm -1 ) intensity. The C-H stretching region can be characterized by contributions from the solo (bay or external), duo and quartet hydrogens, similar to what was observed in the dibenzopolyacene compounds. Published by Elsevier B.V.

Pitch and Harmony in Gyorgy Ligeti's "Hamburg Concerto" and "Syzygy" for String Quartet

NASA Astrophysics Data System (ADS)

Corey, Charles

The analysis component of this dissertation focuses on intricate and complex pitch relationships in Gyorgy Ligeti's last work, the Hamburg Concerto. This piece uses two distinct tuning systems---twelve tone equal temperament and just intonation---throughout its seven movements. Often, these two systems are used simultaneously, creating complex harmonic relationships. This combination allows Ligeti to exploit the unique features of each system and explore their relationships to each other. Ligeti's just intonation in the Hamburg Concerto comes mainly from the five French horns, who are instructed to keep their hands out of the bell to allow the instrument to sound its exact harmonics. The horns themselves, however, are tuned to varying different fundamentals, creating a constantly changing series of just-intoned pitches anchored above an equal-tempered bass. This method of generating just-intoned intervals adds a second layer to the relationship between equal temperament and just intonation. This paper focuses on creating ways to understand this relationship, and describing the ramifications of these tunings as they unfold throughout the piece. Ligeti very carefully crafts this work in a way that creates a balance between the systems. Research done at the Paul Sacher Stiftung has uncovered a significant collection of errors in the published score. Clearing up these discrepancies allows for a much more accurate and more informed analysis. Throughout this dissertation, mistakes are corrected, and several aspects of the score are clarified. The tuning systems are described, and a likely tuning scheme for the horns is posited. (The analytical component of the dissertation delves into the many varying intervals which all fit into one interval class---a feature that is best explored when two distinct tuning systems are juxtaposed.) A language is created herein to better understand these pitch relationships that fit neither into equal temperament nor just intonation. The analysis clearly shows that very simple musical intervals turn out to be cornerstones of this piece, traceable throughout the entire Hamburg Concerto. The composition, Syzygy for string quartet, is written in just intonation. Through four movements, the relationships evoked by the titles (always groups of homonyms) are examined and illuminated.

Synthesis, characterization, structure and properties of heterobimetallic complexes [CuNi(μ-OAc) (μ-OH) (μ-OH2) (bpy)2] (BF4)2 and [CuNi(bz)3(bpy)2] ClO4 from 2,2‧ bipyridine

NASA Astrophysics Data System (ADS)

Kurbah, Sunshine D.; Kumar, A.; Syiemlieh, I.; Dey, A. K.; Lal, R. A.

2018-02-01

Heterobimetallic complexes of the composition [CuNi(bpy)2 (μ-OAc) (μ-OH) (μ-OH2)](BF4)2 (1) and [CuNi(bz)3 (bpy)2]ClO4 (2) were synthesized in moderate yield through solid state reaction and have been characterized by elemental analyses, molar conductance, mass spectra, magnetic moment, EPR, UV-Vis, IR spectroscopies and cyclic voltammetry. The ground state in complex (1) is doublet while that in complex (2), the ground state is a mixture of doublet and quartet, respectively. The structure of the complexes has been established by X-ray crystallography. The electron transfer reactions of the complexes have been investigated by cyclic voltammetry.

Some remarks on the genesis of scalar-tensor theories

NASA Astrophysics Data System (ADS)

Goenner, Hubert

2012-08-01

Between 1941 and 1962, scalar-tensor theories of gravitation were suggested four times by different scientists in four different countries. The earliest originator, the Swiss mathematician W. Scherrer, was virtually unknown until now whereas the chronologically latest pair gave their names to a multitude of publications on Brans-Dicke theory. P. Jordan, one of the pioneers of quantum mechanics and quantum field theory, and Y. Thiry, known by his book on celestial mechanics, a student of the mathematician Lichnerowicz, complete the quartet. Diverse motivations for and conceptual interpretations of their theories will be discussed as well as relations among them. Also, external factors like language, citation habits, or closeness to the mainstream are considered. It will become clear why Brans-Dicke theory, although structurally a déjà-vu, superseded all the other approaches.

Quartetting in Nuclear Matter and α Particle Condensation in Nuclear Systems

NASA Astrophysics Data System (ADS)

Röpke, G.; Schuck, P.; Horiuchi, H.; Tohsaki, A.; Funaki, Y.; Yamada, T.

2008-02-01

Alternatively to pairing, four-particle correlations may become of importance for the formation of quantum condensates in nuclear matter. With increasing density, four-particle correlations are suppressed because of Pauli blocking. Signatures of α-like clusters are expected to occur in low-density nuclear systems. The famous Hoyle state (02+ at 7.654 MeV in 12C) is identified as being an almost ideal condensate of three α-particles, hold together only by the Coulomb barrier. It, therefore, has a 8Be-α structure of low density. Transition probability and inelastic form factor together with position and other physical quantities are correctly reproduced without any adjustable parameter from our two parameter wave function of α-particle condensate type. The possibility of the existence of α-particle condensed states in heavier nα nuclei is also discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernards, C.; Heinze, S.; Jolie, J.

We present the results of a {gamma}{gamma} angular correlation experiment investigating the nucleus {sup 196}Hg and compare these with a theoretical description of {sup 196}Hg within the U{sub {nu}}(6/12) x U{sub {pi}}(6/4) extended supersymmetry. To populate excited {sup 196}Hg states, we used the Cologne FN Tandem accelerator inducing the reaction {sup 194}Pt({alpha},2n){sup 196}Hg and analyzed the {gamma} decays of levels up to an excitation energy of 2.4 MeV with the HORUS cube spectrometer. The new results on this mercury isotope allow a comparison between the experimental data and the supersymmetrical predictions and show good agreement. This way we can addmore » {sup 196}Hg as a fifth supermultiplet member to the so-called magical quartet consisting of {sup 194,195}Pt and {sup 195,196}Au.« less

G-quadruplexes as sensing probes.

PubMed

Ruttkay-Nedecky, Branislav; Kudr, Jiri; Nejdl, Lukas; Maskova, Darina; Kizek, Rene; Adam, Vojtech

2013-11-28

Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K+, Ca2+, Ag+, Hg2+, Cu2+, Pb2+, Sr2+, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.

Recent patents on self-quenching DNA probes.

PubMed

Knemeyer, Jens-Peter; Marmé, Nicole

2007-01-01

In this review, we report on patents concerning self-quenching DNA probes for assaying DNA during or after amplification as well as for direct assaying DNA or RNA, for example in living cells. Usually the probes consist of fluorescently labeled oligonucleotides whose fluorescence is quenched in the absence of the matching target DNA. Thereby the fluorescence quenching is based on fluorescence resonance energy transfer (FRET), photoinduced electron transfer (PET), or electronically interactions between dye and quencher. However, upon hybridization to the target or after the degradation during a PCR, the fluorescence of the dye is restored. Although the presented probes were originally developed for use in homogeneous assay formats, most of them are also appropriate to improve surface-based assay methods. In particular we describe patents for self-quenching primers, self-quenching probes for TaqMan assays, probes based on G-quartets, Molecular Beacons, Smart Probes, and Pleiades Probes.

Isoguanine quartets formed by d(T4isoG4T4): tetraplex identification and stability.

PubMed Central

Seela, F; Wei, C; Melenewski, A

1996-01-01

The self-aggregation of the oligonucleotide d(T4isoG4T4) (1) is investigated. Based on ion exchange HPLC experiments and CD spectroscopy, a tetrameric structure is identified. This structure was formed in the presence of sodium ions and shows almost the same chromatographic mobility on ion exchange HPLC as d(T4G4T4) (2). The ratio of aggregate versus monomer is temperature dependent and the tetraplex of [d(T4isoG4T4)]4 is more stable than that of [d(T4G4T4)]4. A mixture of d(T4isoG4T4) and d(T4G4T4) forms mixed tetraplexes containing strands of d(T4isoG4T4) and d(T4G4T4). PMID:9016664

On the structural stability of guanosine-based supramolecular hydrogels.

PubMed

Carducci, Federica; Yoneda, Juliana S; Itri, Rosangela; Mariani, Paolo

2018-04-18

Supramolecular hydrogels formed from the self-assembly of low molecular weight derivatives are very attractive systems, because of their potential applications in nano- and bio-technology. In this paper, the stable and transparent hydrogels observed in binary mixtures of guanosine derivatives (G), namely guanosine 5'-monophosphate (GMP) and guanosine (Gua), dissolved in water (at volume fractions larger than 0.95), were investigated by microscopy techniques and Small Angle X-ray Scattering (SAXS). The results confirm the presence of G-quadruplexes, chiral cylindrical rods obtained by the regular stacking of self-assembled planar cyclic guanosine quartets. However, the addition of Gua determines the formation of very stable hydrogels able to trap large amounts of water (up to a volume fraction of 0.99) and characterised by an unusual anisotropic order. A modified lateral helix-to-helix interaction pattern, tuned by Gua, is suggested to be responsible for the supramolecular gelation and the stability of the hydrogels during swelling.

Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

PubMed Central

Phan, Anh Tuân; Mergny, Jean-Louis

2002-01-01

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

Resonance magnetoplasticity in ultralow magnetic fields

NASA Astrophysics Data System (ADS)

Alshits, V. I.; Darinskaya, E. V.; Koldaeva, M. V.; Petrzhik, E. A.

2016-09-01

Resonance relaxation displacements of dislocations in NaCl crystals placed in crossed static and alternating ultralow magnetic fields in the electron paramagnetic resonance scheme are discussed. The Earth's magnetic field B Earth ≈ 50μT and other fields in the range of 26-261 μT are used as the static field. New strongly anisotropic properties of the effect have been revealed. Frequency spectra including numerous peaks of paths at low pump frequencies beginning with 10 kHz, as well as the quartet of equidistant peaks at high frequencies ( 1.4 MHz at B= B Earth), have been measured. The effect is also observed in the pulsed pump field with a resonance duration of 0.5 μs. Resonance changes have been detected in the microhardness of ZnO, triglycine sulfate, and potassium hydrogen phthalate crystals after their exposure in the Earth's magnetic field in the same electron paramagnetic resonance scheme.

TreeCmp: Comparison of Trees in Polynomial Time

PubMed Central

Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

2012-01-01

When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees.

Priming with real motion biases visual cortical response to bistable apparent motion

PubMed Central

Zhang, Qing-fang; Wen, Yunqing; Zhang, Deng; She, Liang; Wu, Jian-young; Dan, Yang; Poo, Mu-ming

2012-01-01

Apparent motion quartet is an ambiguous stimulus that elicits bistable perception, with the perceived motion alternating between two orthogonal paths. In human psychophysical experiments, the probability of perceiving motion in each path is greatly enhanced by a brief exposure to real motion along that path. To examine the neural mechanism underlying this priming effect, we used voltage-sensitive dye (VSD) imaging to measure the spatiotemporal activity in the primary visual cortex (V1) of awake mice. We found that a brief real motion stimulus transiently biased the cortical response to subsequent apparent motion toward the spatiotemporal pattern representing the real motion. Furthermore, intracellular recording from V1 neurons in anesthetized mice showed a similar increase in subthreshold depolarization in the neurons representing the path of real motion. Such short-term plasticity in early visual circuits may contribute to the priming effect in bistable visual perception. PMID:23188797

Neurological problems of famous musicians: the classical genre.

PubMed

Newmark, Jonathan

2009-08-01

Neurological histories of great musicians allow for a unique perspective on music physiology. Bedrich Smetana's autobiographical string quartet ends with the musical equivalent of tinnitus in the fourth movement, rendering the youthful and passionate themes of earlier movements moot as the piece ends depicting his ultimately fatal disease, neurosyphilis. Dmitri Shostakovich survived the censorship of Joseph Stalin's apparatchiks but suffered a prolonged form of paralysis attributable to slowly progressive motor neuron disease, although the viola sonata he wrote on his deathbed has become standard repertoire. Glenn Gould was a hypochondriacal pianist with obsessive-compulsive disorder and suspected Asperger syndrome. Vissarion Shebalin and (Ira) Randall Thompson had strokes followed by aphasia without amusia. Domenico Scarlatti provides an example of how even great composers must alter their technical expectations depending upon the skills and body habitus of their chief patrons. The focal dystonia afflicting Leon Fleisher and Gary Graffman catalyzed the discipline of performing arts medicine.

Bonding of Alkali-Alkaline Earth Molecules in the Lowest Σ^+ States of Doublet and Quartet Multiplicity

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Hauser, Andreas W.; Ernst, Wolfgang E.

2016-06-01

n the present study the ground state as well as the lowest ^4Σ^+ state were determined for 16 AK-AKE molecules. Multireference configuration interaction calculations were carried out in order to understand the bonding of diatomic alkali-alkaline earth (AK-AKE) molecules. The correlations between molecular properties (disociation energy, bond distances, electric dipole moment) and atomic properties (electronegativity, polarizability) will be discussed. A correlation between the dissociation energy and the dipole moment of the lowest ^4Σ^+ state was observed, while the dipole moment of the lowest ^2Σ^+ state does not show such a simple dependency. In this case an empirical relation could be established. The class of AK-AKE molecules was selected for this investigation due to their possible applications in ultracold molecular physics. J. V. Pototschnig, A. W. Hauser and W. E. Ernst, Phys. Chem. Chem. Phys., 2016,18, 5964-5973

Tetrahelical monomolecular architecture of DNA: a new building block for nanotechnology.

PubMed

Kankia, Besik

2014-06-12

DNA nanotechnology typically relies on Watson-Crick base pairing as both a recognition and structural element. This limits structural versatility and introduces errors during self-assembly of DNA. Guanine (G) quartet motifs show promise as an alternative to DNA duplexes, but the synthesis of long, precisely defined molecules is a significant challenge. Here we demonstrate a continuous tetrahelical DNA architecture capable of programmed self-assembly. We report that the homopolymer consisting of (G3T)3G3 monomeric units has the capability to fold into a monomolecular DNA tetrahelix with unprecedented speed and stability. For instance, in the presence of 1 mM K(+) ions the dimer, (G3T)2, folds readily and melts above 100 °C. These findings have the potential to revolutionize DNA nanotechnology by introducing fast and error-free self-assembly of long and extraordinarily stable molecules.

Hidden correlations entailed by q-non additivity render the q-monoatomic gas highly non trivial

NASA Astrophysics Data System (ADS)

Plastino, A.; Rocca, M. C.

2018-01-01

It ts known that Tsallis' q-non-additivity entails hidden correlations. It has also been shown that even for a monoatomic gas, both the q-partition function Z and the mean energy 〈 U 〉 diverge and, in particular, exhibit poles for certain values of the Tsallis non additivity parameter q. This happens because Z and 〈 U 〉 both depend on a Γ-function. This Γ, in turn, depends upon the spatial dimension ν. We encounter three different regimes according to the argument A of the Γ-function. (1) A > 0, (2) A < 0 and Γ > 0 outside the poles. (3) A displays poles and the physics is obtained via dimensional regularization. In cases (2) and (3) one discovers gravitational effects and quartets of particles. Moreover, bound states and gravitational effects emerge as a consequence of the hidden q-correlations.

Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

PubMed

Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

2017-11-01

Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele content might be an additional option. As this depends on sampling across species being reasonably even and a random distribution of non-informative instances of missing data, however, further exploration of this approach is needed. Properly chosen data summary approaches to inferring species trees from SNP data may represent a potential alternative to currently available individual-level coalescent analyses especially for quick data exploration and when dealing with computationally demanding or patchy datasets. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

Rh2(II,III) Catalysts with Chelating Carboxylate and Carboxamidate Supports: Electronic Structure and Nitrene Transfer Reactivity.

PubMed

Varela-Álvarez, Adrián; Yang, Tzuhsiung; Jennings, Heather; Kornecki, Katherine P; Macmillan, Samantha N; Lancaster, Kyle M; Mack, James B C; Du Bois, J; Berry, John F; Musaev, Djamaladdin G

2016-02-24

Dirhodium-catalyzed C-H amination is hypothesized to proceed via Rh2-nitrene intermediates in either the Rh2(II,II) or Rh2(II,III) redox state. Herein, we report joint theoretical and experimental studies of the ground electronic state (GES), redox potentials, and C-H amination of [Rh2(II,III)(O2CCH3)4(L)n](+) (1_L) (L = none, Cl(-), and H2O), [Rh2(esp)2](+) (2), and Rh2(espn)2Cl (3) (esp = α,α,α',α'-tetramethyl-1,3-benzenedipropanoate and espn = α,α,α',α'-tetramethyl-1,3-benzenedipropanamidate). CASSCF calculations on 1_L yield a wave function with two closely weighted configurations, (δ*)(2)(π1*)(2)(π2*)(1) and (δ*)(2)(π1*)(1)(π2*)(2), consistent with reported EPR g values [Chem. Phys. Lett. 1986, 130, 20-23]. In contrast, EPR spectra of 2 show g values consistent with the DFT-computed (π*)(4)(δ*)(1) GES. EPR spectra and Cl K-edge XAS for 3 are consistent with a (π*)(4)(δ*)(1) GES, as supported by DFT. Nitrene intermediates 2N_L and 3N_L are also examined by DFT (the nitrene is an NSO3R species). DFT calculations suggest a doublet GES for 2N_L and a quartet GES for 3N_L. CASSCF calculations describe the GES of 2N as Rh2(II,II) with a coordinated nitrene radical cation, (π*)(4)(δ*)(2)(π(nitrene,1))(1)(π(nitrene,2))(0). Conversely, the GES of 3N is Rh2(II,III) with a coordinated triplet nitrene, (π*)(4)(δ*)(1)(π(nitrene,1))(1)(π(nitrene,2))(1). Quartet transition states ((4)TSs) are found to react via a stepwise radical mechanism, whereas (2)TSs are found to react via a concerted mechanism that is lower in energy compared to (4)TSs for both 2N_L and 3N_L. The experimental (determined by intramolecular competition) and (2)TS-calculated kinetic isotopic effect (KIE) shows a KIE ∼ 3 for both 2N and 3N, which is consistent with a concerted mechanism.

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination.

PubMed

Dokmanić, Ivan; Sikić, Mile; Tomić, Sanja

2008-03-01

Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution <1.5 A and the set of nonredundant protein structures from the PDB. The former was used to determine the distances between each metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals.

Variability and situatedness of human emotions. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Nadal, Marcos; Rosselló, Jaume

2015-06-01

We commend Koelsch and colleagues [14] for developing a broad and integrative explanation of the neurobiological foundations of emotions. We especially welcome this framework's emphasis on the interaction between language and emotion, and its focus on the characteristically human moral emotions. Emotions elicited by art and aesthetics also seem to be distinctively human, but comparatively little research has been devoted to understanding these. This is probably because they are usually viewed as atypical in several respects. William James [12], for instance, regarded emotional responses to artworks and aesthetic qualities as subtler emotions, because they lacked the strong bodily changes and adaptive value characteristic of coarser emotions, such as joy, anger, or fear. This view is still predominant today, and aesthetic emotions are often distinguished from everyday emotions [13]. However, the notion of a class of aesthetic emotions, separate from everyday emotions, rests on the questionable assumption that artistic and aesthetic experiences and activities are different in essence from everyday experiences and activities. The discontinuity between "aesthetic experience [and] normal processes of living" [9, p. 10], however, is the product of social and cultural developments in Europe during the 18th century [7,15,20]. Distinctions that oppose art to craft, or aesthetic to practical, in reference to objects, behaviors, experiences, and emotions, make little sense in a broader historic and geographic context [1,7,20], and hinder empirical research [7].

Body sway reflects leadership in joint music performance.

PubMed

Chang, Andrew; Livingstone, Steven R; Bosnyak, Dan J; Trainor, Laurel J

2017-05-23

The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers' ratings of the "goodness" of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships.

Increased burden of deleterious variants in essential genes in autism spectrum disorder.

PubMed

Ji, Xiao; Kember, Rachel L; Brown, Christopher D; Bućan, Maja

2016-12-27

Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication, and repetitive behavior. It is estimated that hundreds of genes contribute to ASD. We asked if genes with a strong effect on survival and fitness contribute to ASD risk. Human orthologs of genes with an essential role in pre- and postnatal development in the mouse [essential genes (EGs)] are enriched for disease genes and under strong purifying selection relative to human orthologs of mouse genes with a known nonlethal phenotype [nonessential genes (NEGs)]. This intolerance to deleterious mutations, commonly observed haploinsufficiency, and the importance of EGs in development suggest a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. With a comprehensive catalog of 3,915 mammalian EGs, we provide compelling evidence for a stronger contribution of EGs to ASD risk compared with NEGs. By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, we show a significantly higher burden of damaging mutations in EGs in ASD probands compared with their non-ASD siblings. The analysis of EGs in the developing brain identified clusters of coexpressed EGs implicated in ASD. Finally, we suggest a high-priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Overall, we show that large-scale studies of gene function in model organisms provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of human disease.

Body sway reflects leadership in joint music performance

PubMed Central

Livingstone, Steven R.; Bosnyak, Dan J.; Trainor, Laurel J.

2017-01-01

The cultural and technological achievements of the human species depend on complex social interactions. Nonverbal interpersonal coordination, or joint action, is a crucial element of social interaction, but the dynamics of nonverbal information flow among people are not well understood. We used joint music making in string quartets, a complex, naturalistic nonverbal behavior, as a model system. Using motion capture, we recorded body sway simultaneously in four musicians, which reflected real-time interpersonal information sharing. We used Granger causality to analyze predictive relationships among the motion time series of the players to determine the magnitude and direction of information flow among the players. We experimentally manipulated which musician was the leader (followers were not informed who was leading) and whether they could see each other, to investigate how these variables affect information flow. We found that assigned leaders exerted significantly greater influence on others and were less influenced by others compared with followers. This effect was present, whether or not they could see each other, but was enhanced with visual information, indicating that visual as well as auditory information is used in musical coordination. Importantly, performers’ ratings of the “goodness” of their performances were positively correlated with the overall degree of body sway coupling, indicating that communication through body sway reflects perceived performance success. These results confirm that information sharing in a nonverbal joint action task occurs through both auditory and visual cues and that the dynamics of information flow are affected by changing group relationships. PMID:28484007

Increased burden of deleterious variants in essential genes in autism spectrum disorder

PubMed Central

Kember, Rachel L.; Brown, Christopher D.; Bućan, Maja

2016-01-01

Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication, and repetitive behavior. It is estimated that hundreds of genes contribute to ASD. We asked if genes with a strong effect on survival and fitness contribute to ASD risk. Human orthologs of genes with an essential role in pre- and postnatal development in the mouse [essential genes (EGs)] are enriched for disease genes and under strong purifying selection relative to human orthologs of mouse genes with a known nonlethal phenotype [nonessential genes (NEGs)]. This intolerance to deleterious mutations, commonly observed haploinsufficiency, and the importance of EGs in development suggest a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. With a comprehensive catalog of 3,915 mammalian EGs, we provide compelling evidence for a stronger contribution of EGs to ASD risk compared with NEGs. By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, we show a significantly higher burden of damaging mutations in EGs in ASD probands compared with their non-ASD siblings. The analysis of EGs in the developing brain identified clusters of coexpressed EGs implicated in ASD. Finally, we suggest a high-priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Overall, we show that large-scale studies of gene function in model organisms provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of human disease. PMID:27956632

Iron cation catalyzed reduction of N2O by CO: gas-phase temperature dependent kinetics.

PubMed

Melko, Joshua J; Ard, Shaun G; Fournier, Joseph A; Li, Jun; Shuman, Nicholas S; Guo, Hua; Troe, Jürgen; Viggiano, Albert A

2013-07-21

The ion-molecule reactions Fe(+) + N2O → FeO(+) + N2 and FeO(+) + CO → Fe(+) + CO2, which catalyze the reaction CO + N2O → CO2 + N2, have been studied over the temperature range 120-700 K using a variable temperature selected ion flow tube apparatus. Values of the rate constants for the former two reactions were experimentally derived as k2 (10(-11) cm(3) s(-1)) = 2.0(±0.3) (T/300)(-1.5(±0.2)) + 6.3(±0.9) exp(-515(±77)/T) and k3 (10(-10) cm(3) s(-1)) = 3.1(±0.1) (T/300)(-0.9(±0.1)). Characterizing the energy parameters of the reactions by density functional theory at the B3LYP/TZVP level, the rate constants are modeled, accounting for the intermediate formation of complexes. The reactions are characterized by nonstatistical intrinsic dynamics and rotation-dependent competition between forward and backward fluxes. For Fe(+) + N2O, sextet-quartet switching of the potential energy surfaces is quantified. The rate constant for the clustering reaction FeO(+) + N2O + He → FeO(N2O)(+) + He was also measured, being k4 (10(-27) cm(6) s(-1)) = 1.1(±0.1) (T/300)(-2.5(±0.1)) in the low pressure limit, and analyzed in terms of unimolecular rate theory.

A quartet of black holes and a missing duo: probing the low end of the MBH-σ relation with the adaptive optics assisted integral-field spectroscopy

NASA Astrophysics Data System (ADS)

Krajnović, Davor; Cappellari, Michele; McDermid, Richard M.; Thater, Sabine; Nyland, Kristina; de Zeeuw, P. T.; Falcón-Barroso, Jesús; Khochfar, Sadegh; Kuntschner, Harald; Sarzi, Marc; Young, Lisa M.

2018-07-01

We present mass estimates of supermassive black holes in six nearby fast rotating early-type galaxies (NGC 4339, NGC 4434, NGC 4474, NGC 4551, NGC 4578, and NGC 4762) with effective stellar velocity dispersion around 100 km s-1. We use near-infrared laser-guide adaptive optics observations with the GEMINI/NIFS to derive stellar kinematics in the galactic nuclei, and SAURON observations from the ATLAS3D Survey for large-scale kinematics. We build axisymmetric Jeans anisotropic models and axisymmetric Schwarzschild dynamical models. Both modelling approaches recover consistent orbital anisotropies and black hole masses within 1σ-2σ confidence level, except for one galaxy for which the difference is just above the 3σ level. Two black holes (NGC 4339 and NGC 4434) are amongst the largest outliers from the current black hole mass-velocity dispersion relation, with masses of (4.3^{+4.8}_{-2.3})× 10^7 and (7.0^{+2.0}_{-2.8})× 10^7 M⊙, respectively (3σ confidence level). The black holes in NGC 4578 and NGC 4762 lie on the scaling relation with masses of (1.9^{+0.6}_{-1.4})× 10^7 and (2.3^{+0.9}_{-0.6})× 10^7 M⊙, respectively (3σ confidence level). For two galaxies (NGC 4474 and NGC 4551), we are able to place upper limits on their black holes masses (<7 × 106 and <5 × 106 M⊙, respectively, 3σ confidence level). The kinematics for these galaxies clearly indicate central velocity dispersion drops within a radius of 35 and 80 pc, respectively. These drops cannot be associated with cold stellar structures and our data do not have the resolution to exclude black holes with masses an order of magnitude smaller than the predictions. Parametrizing the orbital distribution in spherical coordinates, the vicinity of the black holes is characterized by isotropic or mildly tangential anisotropy.

Determination of the hydrogen-bond network and the ferrimagnetic structure of a rockbridgeite-type compound, [Formula: see text].

PubMed

Röska, B; Park, S-H; Behal, D; Hess, K-U; Günther, A; Benka, G; Pfleiderer, C; Hoelzel, M; Kimura, T

2018-06-13

Applying neutron powder diffraction, four unique hydrogen positions were determined in a rockbridgeite-type compound, [Formula: see text] [Formula: see text]. Its honeycomb-like H-bond network running without interruption along the crystallographic [Formula: see text] axis resembles those in alkali sulphatic and arsenatic oxyhydroxides. They provide the so-called dynamically disordered H-bond network over which protons are superconducting in a vehicle mechanism. This is indicated by dramatic increases of dielectric constant and loss factor at room temperature. The relevance of static and dynamic disorder of OH and HOH groups are explained in terms of a high number of structural defects at octahedral chains alternatingly half-occupied by [Formula: see text] cations. The structure is built up by unusual octahedral doublet, triplet, and quartet clusters of aliovalent 3d transition metal cations, predicting complicate magnetic ordering and interaction. The ferrimagnetic structure below the Curie temperature [Formula: see text]-83 K could be determined from the structure analysis with neutron diffraction data at 25 K.

Non-monotonicity of Trace Distance Under Tensor Products

NASA Astrophysics Data System (ADS)

Maziero, Jonas

2015-10-01

The trace distance (TD) possesses several of the good properties required for a faithful distance measure in the quantum state space. Despite its importance and ubiquitous use in quantum information science, one of its questionable features, its possible non-monotonicity under taking tensor products of its arguments (NMuTP), has been hitherto unexplored. In this article, we advance analytical and numerical investigations of this issue considering different classes of states living in a discrete and finite dimensional Hilbert space. Our results reveal that although this property of TD does not show up for pure states and for some particular classes of mixed states, it is present in a non-negligible fraction of the regarded density operators. Hence, even though the percentage of quartets of states leading to the NMuTP drawback of TD and its strength decrease as the system's dimension grows, this property of TD must be taken into account before using it as a figure of merit for distinguishing mixed quantum states.

Reynolds-number-dependent dynamical transitions on hydrodynamic synchronization modes of externally driven colloids

NASA Astrophysics Data System (ADS)

Oyama, Norihiro; Teshigawara, Kosuke; Molina, John Jairo; Yamamoto, Ryoichi; Taniguchi, Takashi

2018-03-01

The collective dynamics of externally driven Np-colloidal systems (1 ≤Np≤4 ) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number as determined by the strength of the external driving force and the confining wall distance. For a system with Np=3 , we found that at a critical Reynolds number a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally. The dynamical mode transition was analyzed in detail from the following two viewpoints: (1) spectrum analysis of the time evolution of a tagged particle velocity and (2) the relative acceleration of the doublet cluster with respect to the singlet particle. For a system with Np=4 , we found similar dynamical mode transitions from the doublet-singlet-singlet mode to the triplet-singlet mode and further to the quartet mode.

Dioxygen activation by non-adiabatic oxidative addition to a single metal center [O 2 activation by non-adiabatic oxidative addition to a single metal center

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akturk, Eser S.; Yap, Glenn P. A.; Theopold, Klaus H.

2015-10-16

A chromium(I) dinitrogen complex reacts rapidly with O 2 to form the mononuclear dioxo complex [Tp tBu,MeCr V(O) 2] (Tp tBu,Me=hydrotris(3- tert-butyl-5-methylpyrazolyl)borate), whereas the analogous reaction with sulfur stops at the persulfido complex [Tp tBu,MeCr III(S 2)]. The transformation of the putative peroxo intermediate [Tp tBu,MeCr III(O 2)] (S= 3/ 2) into [Tp tBu,MeCr V(O) 2] (S= 1/ 2) is spin-forbidden. The minimum-energy crossing point for the two potential energy surfaces has been identified. Finally, although the dinuclear complex [(Tp tBu,MeCr) 2(μ-O) 2] exists, mechanistic experiments suggest that O 2 activation occurs on a single metal center, by an oxidativemore » addition on the quartet surface followed by crossover to the doublet surface.« less

Computational study on the functionalization of BNNC with pyrrole molecule

NASA Astrophysics Data System (ADS)

Payvand, Akram; Tavangar, Zahra

2018-05-01

The functionalization of the boron nitride nanocone (BNNC) by pyrrole molecule was studied using B3LYP/6-311+G(d) level of theory. The reaction was studied in three methods in different layers of the nanocone: Diels-Alder cycloaddition, quartet cycloaddition and the reaction of the nitrogen atom of the pyrrole molecule with the boron or nitrogen atom of the BNNC. Thermodynamic quantities, Chemical hardness and potential and electrophilicity index of the functionalized BNNC were studied. The results show that the tip of nanocone has a higher tendency for participation in the reaction and the most favorable product of the reaction between BNNC and pyrrole molecule is produced from the reaction of N atom of pyrrole with the B atom of BNNC. The reaction decreases the energy gap value which leads to increasing the reactivity and conductivity of functionalized nanocone. The calculated NICS values confirm the aromaticity in the pristine nanocone as well as in the functionalized nanocone.

Reynolds-number-dependent dynamical transitions on hydrodynamic synchronization modes of externally driven colloids.

PubMed

Oyama, Norihiro; Teshigawara, Kosuke; Molina, John Jairo; Yamamoto, Ryoichi; Taniguchi, Takashi

2018-03-01

The collective dynamics of externally driven N_{p}-colloidal systems (1≤N_{p}≤4) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number as determined by the strength of the external driving force and the confining wall distance. For a system with N_{p}=3, we found that at a critical Reynolds number a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally. The dynamical mode transition was analyzed in detail from the following two viewpoints: (1) spectrum analysis of the time evolution of a tagged particle velocity and (2) the relative acceleration of the doublet cluster with respect to the singlet particle. For a system with N_{p}=4, we found similar dynamical mode transitions from the doublet-singlet-singlet mode to the triplet-singlet mode and further to the quartet mode.

Galaxy evolution. Quasar quartet embedded in giant nebula reveals rare massive structure in distant universe.

PubMed

Hennawi, Joseph F; Prochaska, J Xavier; Cantalupo, Sebastiano; Arrigoni-Battaia, Fabrizio

2015-05-15

All galaxies once passed through a hyperluminous quasar phase powered by accretion onto a supermassive black hole. But because these episodes are brief, quasars are rare objects typically separated by cosmological distances. In a survey for Lyman-α emission at redshift z ≈ 2, we discovered a physical association of four quasars embedded in a giant nebula. Located within a substantial overdensity of galaxies, this system is probably the progenitor of a massive galaxy cluster. The chance probability of finding a quadruple quasar is estimated to be ∼10(-7), implying a physical connection between Lyman-α nebulae and the locations of rare protoclusters. Our findings imply that the most massive structures in the distant universe have a tremendous supply (≃10(11) solar masses) of cool dense (volume density ≃ 1 cm(-3)) gas, which is in conflict with current cosmological simulations. Copyright © 2015, American Association for the Advancement of Science.

A light-up probe targeting for Bcl-2 2345 G-quadruplex DNA with carbazole TO

NASA Astrophysics Data System (ADS)

Gu, Yingchun; Lin, Dayong; Tang, Yalin; Fei, Xuening; Wang, Cuihong; Zhang, Baolian; Zhou, Jianguo

2018-02-01

As its significant role, the selective recognition of G-quadruplex with specific structures and functions is important in biological and medicinal chemistry. Carbazole derivatives have been reported as a kind of fluorescent probe with many excellent optical properties. In the present study, the fluorescence of the dye (carbazole TO) increased almost 70 fold in the presence of bcl-2 2345 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10-30 fold than those in the presence of other DNAs. The binding study results by activity inhibition of G4/Hemin peroxidase experiment, NMR titration and molecular docking simulation showed the high affinity and selectivity to bcl-2 2345 G4 arises from its end-stacking interaction with G-quartet. It is said that a facile approach with excellent sensitive, good selectivity and quick response for bcl-2 2345 G-quadruplex was developed and may be used for antitumor recognition or antitumor agents.

The Sounds of Space

NASA Astrophysics Data System (ADS)

Gurnett, Donald

2009-11-01

The popular concept of space is that it is a vacuum, with nothing of interest between the stars, planets, moons and other astronomical objects. In fact most of space is permeated by plasma, sometimes quite dense, as in the solar corona and planetary ionospheres, and sometimes quite tenuous, as is in planetary radiation belts. Even less well known is that these space plasmas support and produce an astonishing large variety of waves, the ``sounds of space.'' In this talk I will give you a tour of these space sounds, starting with the very early discovery of ``whistlers'' nearly a century ago, and proceeding through my nearly fifty years of research on space plasma waves using spacecraft-borne instrumentation. In addition to being of scientific interest, some of these sounds can even be described as ``musical,'' and have served as the basis for various musical compositions, including a production called ``Sun Rings,'' written by the well-known composer Terry Riley, that has been performed by the Kronos Quartet to audiences all around the world.

Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

NASA Technical Reports Server (NTRS)

Stallcop, James R.; Partridge, Harry; Levin, Eugene

1996-01-01

Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions

NASA Astrophysics Data System (ADS)

Kocman, Vojč; Plavec, Janez

2017-05-01

Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5'-AGCGA-3' tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5'-AGCGA-3' and 5'-GGG-3' repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development.

Structural basis of efficient contagion: measles variations on a theme by parainfluenza viruses.

PubMed

Mateo, Mathieu; Navaratnarajah, Chanakha K; Cattaneo, Roberto

2014-04-01

A quartet of attachment proteins and a trio of fusion protein subunits play the cell entry concert of parainfluenza viruses. While many of these viruses bind sialic acid to enter cells, wild type measles binds exclusively two tissue-specific proteins, the lymphatic receptor signaling lymphocytic activation molecule (SLAM), and the epithelial receptor nectin-4. SLAM binds near the stalk-head junction of the hemagglutinin. Nectin-4 binds a hydrophobic groove located between blades 4 and 5 of the hemagglutinin β-propeller head. The mutated vaccine strain hemagglutinin binds in addition the ubiquitous protein CD46, which explains attenuation. The measles virus entry concert has four movements. Andante misterioso: the virus takes over the immune system. Allegro con brio: it rapidly spreads in the upper airway's epithelia. 'Targeting' fugue: the versatile orchestra takes off. Presto furioso: the virus exits the host with thunder. Be careful: music is contagious. Copyright © 2014 Elsevier B.V. All rights reserved.

Evidence for an exotic S= -2, Q= -2 baryon resonance in proton-proton collisions at the CERN SPS.

PubMed

Alt, C; Anticic, T; Baatar, B; Barna, D; Bartke, J; Betev, L; Białkowska, H; Billmeier, A; Blume, C; Boimska, B; Botje, M; Bracinik, J; Bramm, R; Brun, R; Buncić, P; Cerny, V; Christakoglou, P; Chvala, O; Cramer, J G; Csató, P; Darmenov, N; Dimitrov, A; Dinkelaker, P; Eckardt, V; Farantatos, G; Filip, P; Flierl, D; Fodor, Z; Foka, P; Freund, P; Friese, V; Gál, J; Gaździcki, M; Georgopoulos, G; Gładysz, E; Hegyi, S; Höhne, C; Kadija, K; Karev, A; Kniege, S; Kolesnikov, V I; Kollegger, T; Korus, R; Kowalski, M; Kraus, I; Kreps, M; van Leeuwen, M; Lévai, P; Litov, L; Makariev, M; Malakhov, A I; Markert, C; Mateev, M; Mayes, B W; Melkumov, G L; Meurer, C; Mischke, A; Mitrovski, M; Molnár, J; Mrówczyński, St; Pálla, G; Panagiotou, A D; Panayotov, D; Perl, K; Petridis, A; Pikna, M; Pinsky, L; Pühlhofer, F; Reid, J G; Renfordt, R; Retyk, W; Roland, C; Roland, G; Rybczyński, M; Rybicki, A; Sandoval, A; Sann, H; Schmitz, N; Seyboth, P; Siklér, F; Sitar, B; Skrzypczak, E; Stefanek, G; Stock, R; Ströbele, H; Susa, T; Szentpétery, I; Sziklai, J; Trainor, T A; Varga, D; Vassiliou, M; Veres, G I; Vesztergombi, G; Vranić, D; Wetzler, A; Włodarczyk, Z; Yoo, I K; Zaranek, J; Zimányi, J

2004-01-30

Results of resonance searches in the Xi(-)pi(-), Xi(-)pi(+), Xi;(+)pi(-), and Xi;(+)pi(+) invariant mass spectra in proton-proton collisions at sqrt[s]=17.2 GeV are presented. Evidence is shown for the existence of a narrow Xi(-)pi(-) baryon resonance with mass of 1.862+/-0.002 GeV/c(2) and width below the detector resolution of about 0.018 GeV/c(2). The significance is estimated to be above 4.2sigma. This state is a candidate for the hypothetical exotic Xi(--)(3/2) baryon with S=-2, I=3 / 2, and a quark content of (dsdsū). At the same mass, a peak is observed in the Xi(-)pi(+) spectrum which is a candidate for the Xi(0)(3/2) member of this isospin quartet with a quark content of (dsus[-]d). The corresponding antibaryon spectra also show enhancements at the same invariant mass.

Leishmania replication protein A-1 binds in vivo single-stranded telomeric DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neto, J.L. Siqueira; Instituto de Biologia, UNICAMP, Campinas, SP; Lira, C.B.B.

Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in different events of DNA metabolism. In yeast, subunits 1 (RPA-1) and 2 (RPA-2) work also as telomerase recruiters and, in humans, the complex unfolds G-quartet structures formed by the 3' G-rich telomeric strand. In most eukaryotes, RPA-1 and RPA-2 bind DNA using multiple OB fold domains. In trypanosomatids, including Leishmania, RPA-1 has a canonical OB fold and a truncated RFA-1 structural domain. In Leishmania amazonensis, RPA-1 alone can form a complex in vitro with the telomeric G-rich strand. In this work, we show that LaRPA-1 ismore » a nuclear protein that associates in vivo with Leishmania telomeres. We mapped the boundaries of the OB fold DNA-binding domain using deletion mutants. Since Leishmania and other trypanosomatids lack homologues of known telomere end binding proteins, our results raise questions about the function of RPA-1 in parasite telomeres.« less

LAMMPS framework for dynamic bonding and an application modeling DNA

NASA Astrophysics Data System (ADS)

Svaneborg, Carsten

2012-08-01

We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

A novel transition pathway of ligand-induced topological conversion from hybrid forms to parallel forms of human telomeric G-quadruplexes

PubMed Central

Wang, Zi-Fu; Li, Ming-Hao; Chen, Wei-Wen; Hsu, Shang-Te Danny; Chang, Ta-Chau

2016-01-01

The folding topology of DNA G-quadruplexes (G4s) depends not only on their nucleotide sequences but also on environmental factors and/or ligand binding. Here, a G4 ligand, 3,6-bis(1-methyl-4-vinylpyridium iodide)-9-(1-(1-methyl-piperidinium iodide)-3,6,9-trioxaundecane) carbazole (BMVC-8C3O), can induce topological conversion of non-parallel to parallel forms in human telomeric DNA G4s. Nuclear magnetic resonance (NMR) spectroscopy with hydrogen-deuterium exchange (HDX) reveals the presence of persistent imino proton signals corresponding to the central G-quartet during topological conversion of Tel23 and Tel25 G4s from hybrid to parallel forms, implying that the transition pathway mainly involves local rearrangements. In contrast, rapid HDX was observed during the transition of 22-CTA G4 from an anti-parallel form to a parallel form, resulting in complete disappearance of all the imino proton signals, suggesting the involvement of substantial unfolding events associated with the topological transition. Site-specific imino proton NMR assignments of Tel23 G4 enable determination of the interconversion rates of individual guanine bases and detection of the presence of intermediate states. Since the rate of ligand binding is much higher than the rate of ligand-induced topological conversion, a three-state kinetic model was evoked to establish the associated energy diagram for the topological conversion of Tel23 G4 induced by BMVC-8C3O. PMID:26975658

Appearance of the octupole ordered phase IV in CexLa1 -x B6

NASA Astrophysics Data System (ADS)

Sera, M.; Kunimori, K.; Matsumura, T.; Kondo, A.; Tanida, H.; Tou, H.; Iga, F.

2018-05-01

We investigated the physical properties of CexLa1 -xB6 at x ˜0.8 , below which the Tβ-type antiferro-octupole (AFO) ordered phase IV appears as a result of the larger suppression rate of TQ than TN by La doping. The most important result is that while the peak of the specific heat at TQ is rapidly suppressed and broadened by La doping, that at TIV is sharp and large. This indicates that although the Tβ-AFO order in the phase IV is robust against the local lattice distortion induced by La doping, the Ox y-type antiferroquadrupole (AFQ) ordered phase II is very weak. The Tx y z-AFO interaction is robust against La doping from the observation of the pronounced enhancement of TQ even in a small x region. Based on these La-doping effect of the multipole interactions, we carried out the mean-field calculation for the four-sublattice model to reproduce the magnetic phase diagrams of CexLa1 -xB6 . Based on the calculated results, we propose that the small splitting of the quartet is induced by La doping in phase I to explain the magnetic phase diagram for x <0.65 . We could obtain the calculated results roughly consistent with the experimental results, although there appear new problems. We classified the mechanisms of the four different types of the competition among the four interactions with roughly the same magnitude, which induce the interesting and complicated properties in CexLa1 -xB6 .

Far infrared VRT spectroscopy of two water trimer isotopomers vibrationally averaged structures and rearrangement dynamics

NASA Astrophysics Data System (ADS)

Liu, K.; Brown, M. G.; Viant, M. R.; Cruzan, J. D.; Saykally, R. J.

We report the measurement of far infrared vibration rotation tunnelling parallel bands of two partially deuterated water trimer isotopomers D O DOH and H O DOH at 97 2607 cm and 86 cm respectively The hydrogen bond rearrangement dynamics of the two mixed trimers can be described by the simplified molecular symmetry G which accounts for both the flipping and bifurcation tunnelling motions previously established for H O and D O The observed donor tunnelling quartet rather than triplet splitting indicates that the two homogeneous monomers D O or H O in each mixed trimer experience slightly different environments Vibrationally averaged structures of H O D O and D O DOH were examined in a Monte Carlo simulation of the out of plane flipping motions of the free atoms The simulation addresses both the symmetric top behaviour and the negative zero point inertial defect for H O and D O which were insufficiently counted in all previous structure models The average ground state O O separations which are correlated to other angular coordinates were determined to be 2 84 0 01 A for all three species The simulated difference in hydrogen bond nonlinearity also supports the inequivalency of the two homogeneous mono mers The structural simulation shows that the unique H in D O DOH is free while a torsional analysis suggests the unique D in H O DOH is bound within the cyclic ring Both bands can be assigned to the pseudorotational transitions which correlate to those found in the pure trimers

Lift Off for first pair of Cluster II spacecraft

NASA Astrophysics Data System (ADS)

2000-07-01

At 14.39 CEST, a Soyuz-Fregat launch vehicle provided by the French-Russian Starsem consortium lifted off with FM 6 and FM 7, the first pair of Cluster II satellites. Approximately 90 minutes into the mission, the rocket's Fregat fourth stage fired for a second time to insert the spacecraft into a 240 km - 18,000 km parking orbit. A few minutes later, the ground station in Kiruna, Sweden, acquired the two spacecraft and started to receive telemetry, confirming that the satellites had sucessfully separated from the Fregat and that they were now flying independently. "This has been an excellent start and we look forward to the second launch next month," said Professor Roger-Maurice Bonnet, ESA Director of Science. "Cluster is one of the key Cornerstone missions in our Horizons 2000 long-term scientific programme and it will provide unique insights that will revolutionise our understanding of near-Earth space." ESA's Cluster II project manager, Dr John Ellwood, paid tribute to the hundreds of scientists and engineers in many countries who have worked so hard to rebuild the four Cluster satellites since the tragic loss of the first group in 1996. "Without the dedication and teamwork of these people, today's success would not have been possible," he said. "Only three years after we began the Cluster II programme, we are already starting to see the fruits of all our efforts." Cluster II deputy project manager, Alberto Gianolio, also expressed his full satisfaction for the successful launch. "This launch marks a milestone in the cooperation between the European Space Agency and our Russian partners. We are looking forward to the continuation of this fruitful joint effort in the years to come". UK Winner For Cluster Competition - Rumba, Salsa, Samba, Tango into space! The winner of ESA's "Name The Cluster Quartet" competition was announced today, during a special launch event for the media at the European Space Operations Centre (ESOC) in Darmstadt, Germany. After an exhaustive examination of more than 5,000 entries from all 15 ESA member states, Professor Bonnet selected the winning entry from a shortlist recommended by the international jury. The lucky winner is Raymond Cotton of Bristol, who suggested the names of four dances - RUMBA, SALSA, SAMBA and TANGO - for the individual satellites of the Cluster quartet. "We thought of these because my wife and I both like ballroom dancing, and they seemed to fit with the movement of the satellites through space," he said. "The names are also international and will be recognised in any country." "It was an extremely hard decision," commented Professor Bonnet, "There were some excellent suggestions, but I considered the shortlisted entry from the UK to be the best because it is catchy, easy to remember, and reflects the way the four satellites will dance in formation around the heavens during their mission." The spacecraft will now be named as follows: FM 5 - Rumba FM 6 - Salsa FM 7 - Samba FM 8 - Tango Future Operations. Over the next week, the FM 6 (Salsa) and FM 7 (Samba) spacecraft will use their own onboard propulsion systems to reach their operational orbits, 19,000km - 119,000 km above the Earth. At their furthest point (apogee) from the Earth, the Cluster satellites will be almost one third of the distance to the Moon. Six engine firings will be required to enlarge the current orbits and change their inclination so that the spacecraft will eventually pass over the Earth's polar regions. These major manoeuvres are only possible because of the large amount of fuel they carry, which accounts for more than half the launch mass of each Cluster satellite. The second pair of Cluster spacecraft is scheduled for launch on 9 August. After they rendezvous with the spacecraft that were launched today, the quartet will undergo three months of instrument calibration and systems checkouts before beginning their scientific programme. They will then spend the next two years investigating the interaction between the Sun and our planet in unprecedented detail.

A First Experimental Limit on the Relative Rates of Muon Capture on Deuterium from the Quartet and Doublet Hyperfine Spin States of the mud Atom

NASA Astrophysics Data System (ADS)

Neely, Ray Kreswell

The Rosette nebula is a large, ring-shaped emission nebula with a distinctive central cavity excavated by its central cluster of OB stars. Toward understanding the three dimensional structure and fundamental physical processes of this object, we have acquired ux-calibrated, 4-degree field, deep exposures of the Rosette region through 3 nm bandwidth Halpha (656.3 nm) as well as Hbeta (486.1nm), [OIII] (500.7 nm) and [SII] (671.6 nm) filters with 4.5 nm bandwidth. The 4 arcsec/pixel images are supplemented with 4 degree field slit spectra and combined with archival data from the Galactic Evolution Explorer satellite (GALEX), Akari, the Infrared Astronomical Satellite (IRAS), the Midcourse Space Experiment (MSX), the Wide-field Infrared Survey Explorer (WISE), the Wilkinson Microwave Anisotropy Probe (WMAP) and the Planck mission, along with published single dish radio data of the hydrogen continuum at 1410, 2700, and 4750 MHz. These disparate sources have been converted to the same flux and spatial scale as our own wide field data to create a multispectral data cube which allows comparative analysis across the electromagnetic spectrum. Using ratios of data cube slices, spatial maps of extinction and ionization have been constructed to explore the spatial variation of these parameters across the nebula. Comparison of emission in different wavelengths across the data cube allows generation of a spectral energy distribution (SED) to probe dust temperature and geometry. A radial profile analysis of emission from the Rosette in each band supports a spherical shell model of three dimensional structure, and visual representations of this model have been generated in both Python and Javascript/GLSL. An investigation of anomalous dust emission in the center of the nebula via supplemental spectroscopy, conducted on the Anglo-Australian Telescope, is also presented.

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

NASA Astrophysics Data System (ADS)

Wolfe, Andrew L.; Singh, Kamini; Zhong, Yi; Drewe, Philipp; Rajasekhar, Vinagolu K.; Sanghvi, Viraj R.; Mavrakis, Konstantinos J.; Jiang, Man; Roderick, Justine E.; van der Meulen, Joni; Schatz, Jonathan H.; Rodrigo, Christina M.; Zhao, Chunying; Rondou, Pieter; de Stanchina, Elisa; Teruya-Feldstein, Julie; Kelliher, Michelle A.; Speleman, Frank; Porco, John A.; Pelletier, Jerry; Rätsch, Gunnar; Wendel, Hans-Guido

2014-09-01

The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For example, eIF4A promotes T-cell acute lymphoblastic leukaemia development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with silvestrol has powerful therapeutic effects against murine and human leukaemic cells in vitro and in vivo. We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependent transcripts. These include 5' untranslated region (UTR) sequences such as the 12-nucleotide guanine quartet (CGG)4 motif that can form RNA G-quadruplex structures. Notably, among the most eIF4A-dependent and silvestrol-sensitive transcripts are a number of oncogenes, superenhancer-associated transcription factors, and epigenetic regulators. Hence, the 5' UTRs of select cancer genes harbour a targetable requirement for the eIF4A RNA helicase.

'Deal with It. Name It': the diagnostic moment in film.

PubMed

Jutel, Thierry; Jutel, Annemarie

2017-09-01

The moment a serious diagnosis is announced creates an important crisis for a patient, as it shifts their sense of self and of their future potential. This essay discusses the creative representation and use of this diagnostic moment in film narratives. Using Still Alice , A Late Quartet , Wit and Cléo from 5 to 7 as examples, we describe how each of these uses the diagnostic moment in relation to narrative construction and characterisation in recognisable ways. We associate the diagnostic moment with certain narrative and visual devices that are frequently implemented in films as means for character development, and for managing the audience's empathy. This is the case whether or not the diagnosis is contested or accepted, and whether the diagnostic moment is the frame for the narrative, or a closing device. By analysing its representation in film, we emphasise the cultural significance of diagnosis as a life-transforming event. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Time-dependent nonequilibrium soft x-ray response during a spin crossover

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Veenendaal, Michel

The rapid development of high-brilliance pulsed X-ray sources with femtosecond time resolution has created a need for a better theoretical understanding of the time-dependent soft-X-ray response of dissipative many-body quantum systems. It is demonstrated how soft-X-ray spectroscopies, such as X-ray absorption and resonant inelastic X-ray scattering at transition-metal L-edges, can provide insight into intersystem crossings, such as a spin crossover. The photoinduced doublet-to-quartet spin crossover on cobalt in Fe-Co Prussian blue analogues is used as an example to demonstrate how the X-ray response is affected by the dissipative nonequilibrium dynamics. The time-dependent soft-X-ray spectra provide a wealth of information thatmore » reflect the changes in the nonequilibrium initial state via continuously changing spectral lineshapes that cannot be decomposed into initial photoexcited and final metastable spectra, strong broadenings, a collapse of clear selection rules during the intersystem crossing, strong fluctuations in the isotropic branching ratio in X-ray absorption, and crystal-field collapse/oscillations and strongly time-dependent anti-Stokes processes in RIXS.« less

Memory, mental time travel and The Moustachio Quartet

PubMed Central

Wilkins, Clive

2017-01-01

Mental time travel allows us to revisit our memories and imagine future scenarios, and this is why memories are not only about the past, but they are also prospective. These episodic memories are not a fixed store of what happened, however, they are reassessed each time they are revisited and depend on the sequence in which events unfold. In this paper, we shall explore the complex relationships between memory and human experience, including through a series of novels ‘The Moustachio Quartet’ that can be read in any order. To do so, we shall integrate evidences from science and the arts to explore the subjective nature of memory and mental time travel, and argue that it has evolved primarily for prospection as opposed to retrospection. Furthermore, we shall question the notion that mental time travel is a uniquely human construct, and argue that some of the best evidence for the evolution of mental time travel comes from our distantly related cousins, the corvids, that cache food for the future and rely on long-lasting and highly accurate memories of what, where and when they stored their stashes of food. PMID:28479980

The enigmatic Otway odd-clawed spider (Progradungula otwayensis Milledge, 1997, Gradungulidae, Araneae): Natural history, first description of the female and micro-computed tomography of the male palpal organ

PubMed Central

Michalik, Peter; Piacentini, Luis; Lipke, Elisabeth; Ramírez, Martin J.

2013-01-01

Abstract The recently described cribellate gradungulid Progradungula otwayensis Milledge, 1997 is endemic to the Great Otway National Park (Victoria, Australia) and known from only one male and a few juvenile specimens. In a recent survey we recorded 47 specimens at several localities across the western part of the Great Otway National park. Our field data suggest that this species is dependant on the microclimate in the hollows of old myrtle beech trees since other hollow trees were very much less inhabited. Furthermore, we describe the female for the first time and study the male palpal organ by using X-ray microtomography. The female genitalia are characterized by eight spermathecae which are grouped in two quartets. The spermophor resembles the general organization of gradungulids, but is similar to Kaiya Gray, 1987 by a convoluted appearance within the embolus. The muscle 30 is located in the cymbium and resembles the organization of other non-entelegyne Araneomorphae. PMID:24146568

Diet, Microbiota, Obesity, and NAFLD: A Dangerous Quartet

PubMed Central

Machado, Mariana Verdelho; Cortez-Pinto, Helena

2016-01-01

Recently, the importance of the gut-liver-adipose tissue axis has become evident. Nonalcoholic fatty liver disease (NAFLD) is the hepatic disease of a systemic metabolic disorder that radiates from energy-surplus induced adiposopathy. The gut microbiota has tremendous influences in our whole-body metabolism, and is crucial for our well-being and health. Microorganisms precede humans in more than 400 million years and our guest flora evolved with us in order to help us face aggressor microorganisms, to help us maximize the energy that can be extracted from nutrients, and to produce essential nutrients/vitamins that we are not equipped to produce. However, our gut microbiota can be disturbed, dysbiota, and become itself a source of stress and injury. Dysbiota may adversely impact metabolism and immune responses favoring obesity and obesity-related disorders such as insulin resistance/diabetes mellitus and NAFLD. In this review, we will summarize the latest evidence of the role of microbiota/dysbiota in diet-induced obesity and NAFLD, as well as the potential therapeutic role of targeting the microbiota in this set. PMID:27043550

Lejaren A. Hiller, Jr.: A Memorial Tribute to a Chemist-Composer

NASA Astrophysics Data System (ADS)

Wamser, Christian A.; Wamser, Carl C.

1996-07-01

Lejaren Hiller (1924-1994) was trained in chemistry but maintained a lifelong love of music. Like Alexander Borodin, the Russian chemist-composer, but eventually dedicated his career solely to music. His early work on the chemistry of polymers with Fred Wall at the University of Illinois introduced him to the Illiac computer, with which he did Monte Carlo calculations of polymer conformations. He promptly collaborated with Leonard Isaacson, a graduate student also associated with the Wall group, to teach the Illiac to compose music. Using a modified Monte Carlo technique to select the notes and other aspects of the music, they applied increasingly complex rules to define what constituted acceptable music. The result was their String Quartet #4, produced in 1957, often called the Illiac Suite. It is generally acknowledged as the first piece of music composed by a computer. Hiller remained a pioneer in the field of copmuter composition during his distinguished career at the University of Illinois and the State University of New York at Buffalo. This paper traces Hiller's careers in chemistry and music and examines the connections between the two.

Dr. Franjo (Franz) Kresnik (1869-1943): a physician and a violin maker.

PubMed

Skrobonja, Ante; Muzur, Amir

2007-01-01

Dr. Franjo (Franz) Kresnik (born Wien 1869 - died Rijeka 1943) was an excellent physician and a Central European intellectual, a bohemian mind whose two loves in life made him very special. His passions were medicine and violin making. Most of his life was spent in Susak (now a part of Rijeka, Croatia), where he worked, played music and studied the art of making stringed instruments. He visited Cremona on several occasions and studied a number of violins, drawings and tools made and used by old masters. For his profound knowledge of Cremonese violin making the Italians dubbed him "Uomo che legge violini" (The Man Who Can Read Violins). In his workshop he made fifty-two violins, two violas, two cellos and a string quartet. Some of these instruments are still played in Europe and America. The remaining violins and possessions (tools, manuscripts, drawings, literature and countless diplomas and certificates) have been kept in a memorial room at the Maritime and History Museum of the Croatian Littoral in Rijeka. In addition, a street near the Faculty of Medicine in Rijeka is named after Franjo Kresnik.

Microstructural effect on radiative scattering coefficient and asymmetry factor of anisotropic thermal barrier coatings

NASA Astrophysics Data System (ADS)

Chen, X. W.; Zhao, C. Y.; Wang, B. X.

2018-05-01

Thermal barrier coatings are common porous materials coated on the surface of devices operating under high temperatures and designed for heat insulation. This study presents a comprehensive investigation on the microstructural effect on radiative scattering coefficient and asymmetry factor of anisotropic thermal barrier coatings. Based on the quartet structure generation set algorithm, the finite-difference-time-domain method is applied to calculate angular scattering intensity distribution of complicated random microstructure, which takes wave nature into account. Combining Monte Carlo method with Particle Swarm Optimization, asymmetry factor, scattering coefficient and absorption coefficient are retrieved simultaneously. The retrieved radiative properties are identified with the angular scattering intensity distribution under different pore shapes, which takes dependent scattering and anisotropic pore shape into account implicitly. It has been found that microstructure significantly affects the radiative properties in thermal barrier coatings. Compared with spherical shape, irregular anisotropic pore shape reduces the forward scattering peak. The method used in this paper can also be applied to other porous media, which designs a frame work for further quantitative study on porous media.

India Allele Finder: a web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin.

PubMed

Zhang, Jimmy F; James, Francis; Shukla, Anju; Girisha, Katta M; Paciorkowski, Alex R

2017-06-27

We built India Allele Finder, an online searchable database and command line tool, that gives researchers access to variant frequencies of Indian Telugu individuals, using publicly available fastq data from the 1000 Genomes Project. Access to appropriate population-based genomic variant annotation can accelerate the interpretation of genomic sequencing data. In particular, exome analysis of individuals of Indian descent will identify population variants not reflected in European exomes, complicating genomic analysis for such individuals. India Allele Finder offers improved ease-of-use to investigators seeking to identify and annotate sequencing data from Indian populations. We describe the use of India Allele Finder to identify common population variants in a disease quartet whole exome dataset, reducing the number of candidate single nucleotide variants from 84 to 7. India Allele Finder is freely available to investigators to annotate genomic sequencing data from Indian populations. Use of India Allele Finder allows efficient identification of population variants in genomic sequencing data, and is an example of a population-specific annotation tool that simplifies analysis and encourages international collaboration in genomics research.

Transfer reactions induced by lithium ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogloblin, A.A.

The review deals with nuclear reactions induced by /sup 6/Li and /sup 7/ Li io ns having energies between 10 and 30 MeV. Due to the cluster structure of / sup 6/Li (/sup 6/Li= alpha +d) and /sup 7/Li (/sup 7/Li= alpha +t) and the low bindi ng energy of these nuclei, one of the clustcr is directly transferred in (/ sup 6/Li, d), (/sup 7/Li, t) (/sup 6/Li alpha ) and (/sup 7/Li, alpha ) reactions, i.e., the alpha p article, the deuteron, or the triton is directly transferred. Particular attention is paid to the (/sup 6/Li, d) andmore » (/sup 7/Li, t) reactions, in which the cluster-transfe r mechanism (alpha-particle transfer) appear in ita purest fomn. These reactions can be used to study the alpha- particle or quartet states of light nuclei, which are difficult or impossible to excite in any other way. The present state of the theory of multinucleon transfcr reactions is considered and the application of the theory to thc analysis of reactions induced by lithium atoms is discussed. (auth)« less

Determination of the hydrogen-bond network and the ferrimagnetic structure of a rockbridgeite-type compound, {Fe^{2+Fe^{3+}_{3.2}(Mn^{2+}, Zn)_{0.8}(PO_{4})_{3}(OH)_{4.2}(HOH)_{0.8}}}

NASA Astrophysics Data System (ADS)

Röska, B.; Park, S.-H.; Behal, D.; Hess, K.-U.; Günther, A.; Benka, G.; Pfleiderer, C.; Hoelzel, M.; Kimura, T.

2018-06-01

Applying neutron powder diffraction, four unique hydrogen positions were determined in a rockbridgeite-type compound, . Its honeycomb-like H-bond network running without interruption along the crystallographic axis resembles those in alkali sulphatic and arsenatic oxyhydroxides. They provide the so-called dynamically disordered H-bond network over which protons are superconducting in a vehicle mechanism. This is indicated by dramatic increases of dielectric constant and loss factor at room temperature. The relevance of static and dynamic disorder of OH and HOH groups are explained in terms of a high number of structural defects at octahedral chains alternatingly half-occupied by cations. The structure is built up by unusual octahedral doublet, triplet, and quartet clusters of aliovalent 3d transition metal cations, predicting complicate magnetic ordering and interaction. The ferrimagnetic structure below the Curie temperature –83 K could be determined from the structure analysis with neutron diffraction data at 25 K.

A case study of pedagogy of mathematics support tutors without a background in mathematics education

NASA Astrophysics Data System (ADS)

Walsh, Richard

2017-01-01

This study investigates the pedagogical skills and knowledge of three tertiary-level mathematics support tutors in a large group classroom setting. This is achieved through the use of video analysis and a theoretical framework comprising Rowland's Knowledge Quartet and general pedagogical knowledge. The study reports on the findings in relation to these tutors' provision of mathematics support to first and second year undergraduate engineering students and second year undergraduate science students. It was found that tutors are lacking in various pedagogical skills which are needed for high-quality learning amongst service mathematics students (e.g. engineering/science/technology students), a demographic which have low levels of mathematics upon entering university. Tutors teach their support classes in a very fast didactic way with minimal opportunities for students to ask questions or to attempt problems. It was also found that this teaching method is even more so exaggerated in mandatory departmental mathematics tutorials that students take as part of their mathematics studies at tertiary level. The implications of the findings on mathematics tutor training at tertiary level are also discussed.

Prevalence of multimorbidity in the Brazilian adult population according to socioeconomic and demographic characteristics

PubMed Central

Roncalli, Ângelo Giuseppe; Cancela, Marianna de Camargo; de Souza, Dyego Leandro Bezerra

2017-01-01

Knowledge on the occurrence of multimorbidity is important from the viewpoint of public policies, as this condition increases the consumption of medicines as well as the utilization and expenses of health services, affecting life quality of the population. The objective of this study was to estimate prevalence of self-reported multimorbidity in Brazilian adults (≥18 years old) according to socioeconomic and demographic characteristics. A descriptive study is presented herein, based on data from the National Health Survey, which was a household-based survey carried out in Brazil in 2013. Data on 60,202 adult participants over the age of 18 were included. Prevalences and its respective confidence intervals (95%) were estimated according to sex, age, education level, marital status, self-reported skin color, area of residence, occupation and federative units (states). Poisson regression models univariate and multivariate were used to evaluate the association between socioeconomic and demographic variables with multimorbidity. To observe the combinations of chronic conditions the most common groups in pairs, trios, quartets and quintets of chronic diseases were observed. The prevalence of multimorbidity was 23.6% and was higher among women, in individuals over 60 years of age, people with low educational levels, people living with partner, in urban areas and among unemployed persons. The states of the South and Southeast regions presented higher prevalence. The most common groups of chronic diseases were metabolic and musculoskeletal diseases. The results demonstrated high prevalence of multimorbidity in Brazil. The study also revealed that a considerable share of the economically active population presented two or more chronic diseases. Data of this research indicated that socioeconomic and demographic aspects must be considered during the planning of health services and development of prevention and treatment strategies for chronic diseases, and consequently, multimorbidity. PMID:28384178

Long repeating (TTAGGG)n single stranded DNA self-condenses into compact beaded filaments stabilized by G-quadruplex formation.

PubMed

Kar, Anirban; Jones, Nathan; Arat, N Özlem; Fishel, Richard; Griffith, Jack

2018-04-19

Conformations adopted by long stretches of single stranded DNA (ssDNA) are of central interest in understanding the architecture of replication forks, R loops, and other structures generated during DNA metabolism in vivo. This is particularly so if the ssDNA consists of short nucleotide repeats. Such studies have been hampered by the lack of defined substrates greater than ~150 nt, and the absence of high-resolution biophysical approaches. Here we describe the generation of very long ssDNA consisting of the mammalian telomeric repeat (5'-TTAGGG-3')n as well as the interrogation of its structure by electron microscopy (EM) and single molecule magnetic tweezers (smMT). This repeat is of particular interest as it contains a run of 3 contiguous guanine residues capable of forming G quartets as ssDNA. Fluorescent-dye exclusion assays confirmed that this G-strand ssDNA forms ubiquitous G-quadruplex folds. EM revealed thick bead-like filaments that condensed the DNA ~12 fold. The bead-like structures were 5 nm and 8 nm in diameter and linked by thin filaments. The G-strand ssDNA displayed initial stability to smMT force extension that ultimately released in steps that were multiples ~28 nm at forces between 6-12 pN; well below the >20 pN required to unravel G-quadruplexes. Most smMT steps were consistent with the disruption of the beads seen by EM. Binding by RAD51 distinctively altered the force extension properties of the G-strand ssDNA, suggesting a stochastic G-quadruplex-dependent condensation model that is discussed. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR.

PubMed

McAninch, Damian S; Heinaman, Ashley M; Lang, Cara N; Moss, Kathryn R; Bassell, Gary J; Rita Mihailescu, Mihaela; Evans, Timothy L

2017-07-25

G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited. Among the mRNAs predicted to form a G quadruplex structure within the 5'-UTR is the survival motor neuron domain containing 1 (SMNDC1) mRNA, encoding a protein that is critical to the spliceosome. Additionally, this mRNA has been identified as a potential target of the fragile X mental retardation protein (FMRP), whose loss of expression leads to fragile X syndrome. FMRP is an RNA binding protein involved in translation regulation that has been shown to bind mRNA targets that form G quadruplex structures. In this study we have used biophysical methods to investigate G quadruplex formation in the 5'-UTR of SMNDC1 mRNA and analyzed its interactions with FMRP. Our results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates. These findings suggest a model by which FMRP might regulate the translation of a subset of its mRNA targets by recognizing the G quadruplex structure present in their 5'-UTR, and affecting their accessibility by the protein synthesis machinery.

Differential lead component pulling as a possible mechanism of inside-out abrasion and conductor cable externalization.

PubMed

Lau, Ernest W

2013-09-01

Conductor cable externalization with protrusion (CCE*) is highly prevalent among the Riata 8F and ST 7F defibrillation (DF) leads and infrequently present in the QuickSite and the QuickFlex coronary sinus (CS) leads (St. Jude Medical, Sylmar, CA, USA). A model for CCE* based on differential lead component pulling and conjugate extension with reciprocal compression-bending was developed. Extension of a proximal lead body segment by pectoral or cardiac movements causes reciprocal compression-bending of a distal lead body segment mediated by inextensible conductor cables running down a lead body fixed at various points by fibrous adhesions. The "sawing" action of these cables under tension causes inside-out abrasion of insulation leading to CCE*. DF leads from different manufacturers and the QuickFlex and QuickFlex μ CS leads were subjected to simulated differential pulling. Restitution from differential pulling followed three patterns: complete, partial without escalation, and incomplete with escalation. Only the last pattern (only shown by the Riata 8F and ST 7F leads) was associated with an increased risk to CCE*. For CS leads, deformation concentrated on the more flexible segment when the lead body did not have a uniform construction. The Durata, Riata ST Optim, QuickFlex μ, and Quartet leads should be relatively immune to CCE*. The Durata leads are extremely resistant to longitudinal deformation and probably cause mediastinal displacement rather than differential pulling in response to pectoral movements in vivo. Implantation techniques and lead designs can be used to minimize the risk of CCE*. A bench test for CCE* can be constructed. ©2013, The Author. Journal compilation ©2013 Wiley Periodicals, Inc.

Probing ‘Spin-Forbidden’ Oxygen Atom Transfer: Gas-Phase Reactions of Chromium-Porphyrin Complexes

PubMed Central

Fornarini, Simonetta; Lanucara, Francesco; Warren, Jeffrey J.

2010-01-01

Oxygen-atom transfer reactions of metalloporphyrin species play an important role in biochemical and synthetic oxidation reactions. An emerging theme in this chemistry is that spin-state changes can play important roles, and a ‘two-state’ reactivity model has been extensively applied especially in iron-porphyrin systems. Herein we explore the gas phase oxygen-atom transfer chemistry of meso-tetrakis(pentafluorophenyl)porphyrin (TPFPP) chromium complexes, as well as some other tetradentate macrocyclic ligands. Electrospray ionization in concert with Fourier transform ion cyclotron resonance (FT-ICR) spectrometry has been used to characterize and observe reactivity of the ionic species [(TPFPP)CrIII]+ (1) and [(TPFPP)CrVO]+ (2). These are an attractive system to examine the effects of spin state change on oxygen atom transfer because the d1 CrV species are doublets while the CrIII complexes have quartet ground states with high-lying doublet excited states. In the gas phase, [(TPFPP)CrIII]+ forms adducts with a variety of neutral donors but O-atom transfer is only observed for NO2. Pyridine N-oxide adducts of 1 do yield 2 upon collision induced dissociation (CID), but the ethylene oxide, DMSO, and TEMPO analogs do not. [(TPFPP)CrVO]+ is shown by its reactivity and by CID experiments to be a terminal metal-oxo with a single vacant coordination site. It also displays limited reaction chemistry, being deoxygenated only by the very potent reductant P(OMe)3. In general, [(TPFPP)CrVO]+ species are much less reactive than the Fe and Mn analogs. Thermochemical analysis of the reactions points towards the involvement of spin issues in the lower observed reactivity of the chromium complexes. PMID:20218631

Multiple-region directed functional connectivity based on phase delays.

PubMed

Goelman, Gadi; Dan, Rotem

2017-03-01

Network analysis is increasingly advancing the field of neuroimaging. Neural networks are generally constructed from pairwise interactions with an assumption of linear relations between them. Here, a high-order statistical framework to calculate directed functional connectivity among multiple regions, using wavelet analysis and spectral coherence has been presented. The mathematical expression for 4 regions was derived and used to characterize a quartet of regions as a linear, combined (nonlinear), or disconnected network. Phase delays between regions were used to obtain network's temporal hierarchy and directionality. The validity of the mathematical derivation along with the effects of coupling strength and noise on its outcomes were studied by computer simulations of the Kuramoto model. The simulations demonstrated correct directionality for a large range of coupling strength and low sensitivity to Gaussian noise compared with pairwise coherences. The analysis was applied to resting-state fMRI data of 40 healthy young subjects to characterize the ventral visual system, motor system and default mode network (DMN). It was shown that the ventral visual system was predominantly composed of linear networks while the motor system and the DMN were composed of combined (nonlinear) networks. The ventral visual system exhibits its known temporal hierarchy, the motor system exhibits center ↔ out hierarchy and the DMN has dorsal ↔ ventral and anterior ↔ posterior organizations. The analysis can be applied in different disciplines such as seismology, or economy and in a variety of brain data including stimulus-driven fMRI, electrophysiology, EEG, and MEG, thus open new horizons in brain research. Hum Brain Mapp 38:1374-1386, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A black hole quartet: New solutions and applications to string theory

NASA Astrophysics Data System (ADS)

Padi, Megha

In this thesis, we study a zoo of black hole solutions which help us connect string theory to the universe we live in. The intuition for how to attack fundamental problems can often be found in a toy model. In Chapter 2, we show that three-dimensional topologically massive gravity with a negative cosmological constant -ℓ -2 and coupling constant has "warped AdS3" solutions with SL(2, R ) x U(1) isometry. For muℓ > 3, we show that certain discrete quotients of warped AdS3 lead to black holes. Their thermodynamics is consistent with the existence of a holographic dual CFT with central charges cR = 15mℓ 2+81Gmm ℓ2+27 and cL = 12mℓ 2Gmm ℓ2+27 . The entropy of many supersymmetric black holes have been accounted for, but more realistic non-supersymmetric black holes have been largely overlooked. In Chapter 3, we derive new single-centered and multi-centered non-BPS black hole solutions for several four dimensional models which, after Kaluza-Klein reduction, admit a description in terms of a sigma model with symmetric target space. In particular, we provide the exact solution with generic charges and asymptotic moduli in N=2 supergravity coupled to one vector multiplet. As it stands, the current formulation of string theory allows for an extremely large number of possible solutions (or vacua). We first analyze this landscape by looking for universal characteristics. In Chapter 4, we provide evidence for the conjecture that gravity is always the weakest force in any string compactification. We show that, in several examples arising in string theory, higher-derivative corrections always make extremal non-supersymmetric black holes lighter than the classical bound M/Q = 1. In Chapter 5, we construct novel black hole bound states, called orientiholes, that are T-dual to IIB orientifold compactifications. The gravitational entropy of such orientiholes provides an "experimental" estimate of the number of vacua in various sectors of the IIB landscape. Furthermore, basic physical properties of orientiholes map to (sometimes subtle) microscopic features, thus providing a useful alternative viewpoint on a number of issues arising in D-brane model building. We also suggest a relation to the topological string analogous to the OSV conjecture.

RNA synthesis is modulated by G-quadruplex formation in Hepatitis C virus negative RNA strand.

PubMed

Chloé, Jaubert; Amina, Bedrat; Laura, Bartolucci; Carmelo, Di Primo; Michel, Ventura; Jean-Louis, Mergny; Samir, Amrane; Marie-Line, Andreola

2018-05-25

DNA and RNA guanine-rich oligonucleotides can form non-canonical structures called G-quadruplexes or "G4" that are based on the stacking of G-quartets. The role of DNA and RNA G4 is documented in eukaryotic cells and in pathogens such as viruses. Yet, G4 have been identified only in a few RNA viruses, including the Flaviviridae family. In this study, we analysed the last 157 nucleotides at the 3'end of the HCV (-) strand. This sequence is known to be the minimal sequence required for an efficient RNA replication. Using bioinformatics and biophysics, we identified a highly conserved G4-prone sequence located in the stem-loop IIy' of the negative strand. We also showed that the formation of this G-quadruplex inhibits the in vitro RNA synthesis by the RdRp. Furthermore, Phen-DC3, a specific G-quadruplex binder, is able to inhibit HCV viral replication in cells in conditions where no cytotoxicity was measured. Considering that this domain of the negative RNA strand is well conserved among HCV genotypes, G4 ligands could be of interest for new antiviral therapies.

Rogue taxa phenomenon: a biological companion to simulation analysis

PubMed Central

Westover, Kristi M.; Rusinko, Joseph P.; Hoin, Jon; Neal, Matthew

2013-01-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. PMID:23707704

Rogue taxa phenomenon: a biological companion to simulation analysis.

PubMed

Westover, Kristi M; Rusinko, Joseph P; Hoin, Jon; Neal, Matthew

2013-10-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. Copyright © 2013 Elsevier Inc. All rights reserved.

NEQAIR96,Nonequilibrium and Equilibrium Radiative Transport and Spectra Program: User's Manual

NASA Technical Reports Server (NTRS)

Whiting, Ellis E.; Park, Chul; Liu, Yen; Arnold, James O.; Paterson, John A.

1996-01-01

This document is the User's Manual for a new version of the NEQAIR computer program, NEQAIR96. The program is a line-by-line and a line-of-sight code. It calculates the emission and absorption spectra for atomic and diatomic molecules and the transport of radiation through a nonuniform gas mixture to a surface. The program has been rewritten to make it easy to use, run faster, and include many run-time options that tailor a calculation to the user's requirements. The accuracy and capability have also been improved by including the rotational Hamiltonian matrix formalism for calculating rotational energy levels and Hoenl-London factors for dipole and spin-allowed singlet, doublet, triplet, and quartet transitions. Three sample cases are also included to help the user become familiar with the steps taken to produce a spectrum. A new user interface is included that uses check location, to select run-time options and to enter selected run data, making NEQAIR96 easier to use than the older versions of the code. The ease of its use and the speed of its algorithms make NEQAIR96 a valuable educational code as well as a practical spectroscopic prediction and diagnostic code.

Fourier transformation microwave spectroscopy of the methyl glycolate-H2O complex

NASA Astrophysics Data System (ADS)

Fujitake, Masaharu; Tanaka, Toshihiro; Ohashi, Nobukimi

2018-01-01

The rotational spectrum of one conformer of the methyl glycolate-H2O complex has been measured by means of the pulsed jet Fourier transform microwave spectrometer. The observed a- and b-type transitions exhibit doublet splittings due to the internal rotation of the methyl group. On the other hand, most of the c-type transitions exhibit quartet splittings arising from the methyl internal rotation and the inversion motion between two equivalent conformations. The spectrum was analyzed using parameterized expressions of the Hamiltonian matrix elements derived by applying the tunneling matrix formalism. Based on the results obtained from ab initio calculation, the observed complex of methyl glycolate-H2O was assigned to the most stable conformer of the insertion complex, in which a non-planer seven membered-ring structure is formed by the intermolecular hydrogen bonds between methyl glycolate and H2O subunits. The inversion motion observed in the c-type transitions is therefore a kind of ring-inversion motion between two equivalent conformations. Conformational flexibility, which corresponds to the ring-inversion between two equivalent conformations and to the isomerization between two possible conformers of the insertion complex, was investigated with the help of the ab initio calculation.

Multireference - Møller-Plesset Perturbation Theory Results on Levels and Transition Rates in Al-like Ions of Iron Group Elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santana, J A; Ishikawa, Y; Tr�abert, E

2009-02-26

Ground configuration and low-lying levels of Al-like ions contribute to a variety of laboratory and solar spectra, but the available information in databases are neither complete not necessarily correct. We have performed multireference Moeller-Plesset perturbation theory calculations that approach spectroscopic accuracy in order to check the information that databases hold on the 40 lowest levels of Al-Like ions of iron group elements (K through Ge), and to provide input for the interpretation of concurrent experiments. Our results indicate problems of the database holdings on the levels of the lowest quartet levels in the lighter elements of the range studied. Themore » results of our calculations of the decay rates of five long-lived levels (3s{sup 2}3p {sup 2}p{sup o}{sub 3/2}, 3s3p{sup 2} {sup 4}P{sup o} J and 3s3p3d {sup 4}F{sup o}{sub 9/2}) are compared with lifetime data from beam-foil, electron beam ion trap and heavy-ion storage ring experiments.« less

Ab initio calculations of the electronic structure of the low-lying states for the ultracold LiYb molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tohme, Samir N.; Korek, Mahmoud, E-mail: mahmoud.korek@bau.edu.lb, E-mail: fkorek@yahoo.com; Awad, Ramadan

Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born–Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ω{sub e}, R{sub e}, B{sub e}, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, E{sub v}, themore » rotational constant, B{sub v}, the centrifugal distortion constant, D{sub v}, and the abscissas of the turning points, R{sub min} and R{sub max}, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.« less

Direct experimental observation of the molecular J eff=3/2 ground state in the lacunar spinel GaTa 4Se 8

DOE PAGES

Jeong, Min Yong; Chang, Seo Hyoung; Kim, Beom Hyun; ...

2017-10-04

Strong spin-orbit coupling lifts the degeneracy of t 2g orbitals in 5d transition-metal systems, leaving a Kramers doublet and quartet with effective angular momentum of J eff = 1/2 and 3/2, respectively. These spin-orbit entangled states can host exotic quantum phases such as topological Mott state, unconventional superconductivity, and quantum spin liquid. The lacunar spinel GaTa 4Se 8 was theoretically predicted to form the molecular J eff = 3/2 ground state. Experimental verification of its existence is an important first step to exploring the consequences of the J eff = 3/2 state. Here, we report direct experimental evidence of themore » J eff = 3/2 state in GaTa 4Se 8 by means of excitation spectra of resonant inelastic x-rays scattering at the Ta L 3 and L 2 edges. In conclusion, we found that the excitations involving the J eff = 1/2 molecular orbital were absent only at the Ta L 2 edge, manifesting the realization of the molecular J eff = 3/2 ground state in GaTa 4Se 8.« less

Direct experimental observation of the molecular J eff=3/2 ground state in the lacunar spinel GaTa 4Se 8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Min Yong; Chang, Seo Hyoung; Kim, Beom Hyun

Strong spin-orbit coupling lifts the degeneracy of t 2g orbitals in 5d transition-metal systems, leaving a Kramers doublet and quartet with effective angular momentum of J eff = 1/2 and 3/2, respectively. These spin-orbit entangled states can host exotic quantum phases such as topological Mott state, unconventional superconductivity, and quantum spin liquid. The lacunar spinel GaTa 4Se 8 was theoretically predicted to form the molecular J eff = 3/2 ground state. Experimental verification of its existence is an important first step to exploring the consequences of the J eff = 3/2 state. Here, we report direct experimental evidence of themore » J eff = 3/2 state in GaTa 4Se 8 by means of excitation spectra of resonant inelastic x-rays scattering at the Ta L 3 and L 2 edges. In conclusion, we found that the excitations involving the J eff = 1/2 molecular orbital were absent only at the Ta L 2 edge, manifesting the realization of the molecular J eff = 3/2 ground state in GaTa 4Se 8.« less

Phylogenetic position of the giant anuran trypanosomes Trypanosoma chattoni, Trypanosoma fallisi, Trypanosoma mega, Trypanosoma neveulemairei, and Trypanosoma ranarum inferred from 18S rRNA gene sequences.

PubMed

Martin, Donald S; Wright, André-Denis G; Barta, John R; Desser, Sherwin S

2002-06-01

Phylogenetic relationships within the kinetoplastid flagellates were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included 5 new gene sequences, Trypanosoma fallisi (2,239 bp), Trypanosoma chattoni (2,180 bp), Trypanosoma mega (2,211 bp), Trypanosoma neveulemairei (2,197 bp), and Trypanosoma ranarum (2,203 bp). Trees produced using maximum-parsimony and distance-matrix methods (least-squares, neighbor-joining, and maximum-likelihood), supported by strong bootstrap and quartet-puzzle analyses, indicated that the trypanosomes are a monophyletic group that divides into 2 major lineages, the salivarian trypanosomes and the nonsalivarian trypanosomes. The nonsalivarian trypanosomes further divide into 2 lineages, 1 containing trypanosomes of birds, mammals, and reptiles and the other containing trypanosomes of fish, reptiles, and anurans. Among the giant trypanosomes, T. chattoni is clearly shown to be distantly related to all the other anuran trypanosome species. Trypanosoma mega is closely associated with T. fallisi and T. ranarum, whereas T. neveulemairei and Trypanosoma rotatorium are sister taxa. The branching order of the anuran trypanosomes suggests that some toad trypanosomes may have evolved by host switching from frogs to toads.

The incidence of dementia and intake of animal products: preliminary findings from the Adventist Health Study.

PubMed

Giem, P; Beeson, W L; Fraser, G E

1993-01-01

We investigated the relationship between animal product consumption and evidence of dementia in two cohort substudies. The first enrolled 272 California residents matched for age, sex, and zip code (1 vegan, 1 lacto-ovo-vegetarian, and 2 'heavy' meat eaters in each of 68 quartets). This design ensured a wide range of dietary exposure. The second included 2,984 unmatched subjects who resided within the Loma Linda, California area. All subjects were enrolled in the Adventist Health Study. The matched subjects who ate meat (including poultry and fish) were more than twice as likely to become demented as their vegetarian counterparts (relative risk 2.18, p = 0.065) and the discrepancy was further widened (relative risk 2.99, p = 0.048) when past meat consumption was taken into account. There was no significant difference in the incidence of dementia in the vegetarian versus meat-eating unmatched subjects. There was no obvious explanation for the difference between the two substudies, although the power of the unmatched sub-study to detect an effect of 'heavy' meat consumption was unexpectedly limited. There was a trend towards delayed onset of dementia in vegetarians in both substudies.

Serendipitous discovery of quadruply imaged quasars: two diamonds

NASA Astrophysics Data System (ADS)

Lucey, John R.; Schechter, Paul L.; Smith, Russell J.; Anguita, T.

2018-05-01

Gravitationally lensed quasars are powerful and versatile astrophysical tools, but they are challengingly rare. In particular, only ˜25 well-characterized quadruple systems are known to date. To refine the target catalogue for the forthcoming Taipan Galaxy Survey, the images of a large number of sources are being visually inspected in order to identify objects that are confused by a foreground star or galaxies that have a distinct multicomponent structure. An unexpected by-product of this work has been the serendipitous discovery of about a dozen galaxies that appear to be lensing quasars, i.e. pairs or quartets of foreground stellar objects in close proximity to the target source. Here, we report two diamond-shaped systems. Follow-up spectroscopy with the IMACS instrument on the 6.5m Magellan Baade telescope confirms one of these as a z = 1.975 quasar quadruply lensed by a double galaxy at z = 0.293. Photometry from publicly available survey images supports the conclusion that the other system is a highly sheared quadruply imaged quasar. In starting with objects thought to be galaxies, our lens finding technique complements the conventional approach of first identifying sources with quasar-like colours and subsequently finding evidence of lensing.

Peridinialean dinoflagellate plate patterns, labels and homologies

USGS Publications Warehouse

Edwards, L.E.

1990-01-01

Tabulation patterns for peridinialean dinoflagellate thecae and cysts have been traditionally expressed using a plate labelling system described by C.A. Kofoid in the early 1900's. This system can obscure dinoflagellate plate homologies and has not always been strictly applied. The plate-labelling system presented here introduces new series labels but incorporates key features and ideas from the more recently proposed systems of G.L. Eaton and F.J.R. Taylor, as modified by W.R. Evitt. Plate-series recognition begins with the cingulum (C-series) and proceeds from the cingulum toward the apex for the three series of the epitheca/epicyst and proceeds from the cingulum toward the antapex for the two series of the hypotheca/hypocyst. The epithecal/epicystal model consists of eight plates that touch the anterior margin of the cingulum (E-series: plates E1-E7, ES), seven plates toward the apex that touch the E-series plates (M-series: R, M1-M6), and up to seven plates near the apex that do not touch E-series plates (D-series: Dp-Dv). The hypothecal/hypocystal model consists of eight plates that touch the posterior margin of the cingulum (H-series: H1-H6,HR,HS) and three plates toward the antapex (T1-T3). Epithecal/epicystal tabulation patterns come in both 8- and 7- models, corresponding to eight and seven plates, respectively, in the E-series. Hypothecal/hypocystal tabulation patterns also come in both 8- and 7-models, corresponding to eight and seven plates, respectively, in the H-series. By convention, the 7-model epitheca/epicyst has no plates E1 and M1; the 7-model hypotheca/hypocyst has no plate H6. Within an 8-model or 7-model, the system emphasizes plates that are presumed to be homologous by giving them identical labels. I introduce the adjectives "monothigmate", "dithigmate," and "trithigmate" to designate plates touching one, two, and three plates, respectively, of the adjacent series. The term "thigmation" applies to the analysis of plate contacts between plate series as a guide to interpretation. Application of the proposed plate labelling system involves: (1) locating the cingulum and identifying the plate series, (2) identifying the landmark plates within each series, (3) assigning appropriate plate numbers to plates in the E- and H-series, (4) assigning appropriate plate numbers to the remaining plates using thigmation and interactions of diagonally opposite pairs of plates (quartets) as guides to interpretation. A "typical" gonyaulacoid tabulation pattern combines a 7-model epitheca/epicyst and an 8-model hypotheca/hypocyst. A "typical" peridinioid tabulation pattern combines an 8-model epitheca/epicyst and a 7-model hypotheca/hypocyst. The group that is presently termed partiform gonyaulacoid (which includes the modern genus Cladopyxis Stein and the fossil Microdinium Cookson and Eisenack) has an 8-model epitheca/epicyst and an 8-model hypotheca/hypocyst. ?? 1990.

Nano opto-mechanical systems (NOMS) as a proposal for tactile displays

NASA Astrophysics Data System (ADS)

Campo, E. M.; Roig, J.; Roeder, B.; Wenn, D.; Mamojka, B.; Omastova, M.; Terentjev, E. M.; Esteve, J.

2011-10-01

For over a decade, special emphasis has been placed in the convergence of different fields of science and technology, in an effort to serve human needs by way of enhancing human capabilities. The convergence of the Nano-Bio-Info-Cogni (NBIC) quartet will provide unique solutions to specific needs. This is the case of, Nano-opto mechanical Systems (NOMS), presented as a solution to tactile perception, both for the visually-impaired and for the general public. NOMS, based on photoactive polymer actuators and devices, is a much sought-after technology. In this scheme, light sources promote mechanical actuation producing a variety of nano-opto mechanical systems such as nano-grippers. In this paper, we will provide a series of specifications that the NOMS team is targeting towards the development of a tactile display using optically-activated smart materials. Indeed, tactile displays remain mainly mechanical, compromising reload speeds and resolution which inhibit 3D tactile representation of web interfaces. We will also discuss how advantageous NOMS tactile displays could be for the general public. Tactile processing based on stimulation delivered through the NOMS tablet, will be tested using neuropsychology methods, in particular event-related brain potentials. Additionally, the NOMS tablet will be instrumental to the development of basic neuroscience research.

The N2O activation by Rh5 clusters. A quantum chemistry study.

PubMed

Olvera-Neria, Oscar; Avilés, Roberto; Francisco-Rodríguez, Héctor; Bertin, Virineya; García-Cruz, Raúl; González-Torres, Julio César; Poulain, Enrique

2015-04-01

Nitrous oxide (N2O) is a by-product of exhaust pipe gases treatment produced by motor vehicles. Therefore, the N2O reduction to N2 is necessary to meet the actual environmental legislation. The N2O adsorption and dissociation assisted by the square-based pyramidal Rh5 cluster was investigated using the density functional theory and the zero-order regular approximation (ZORA). The Rh5 sextet ground state is the most active in N2O dissociation, though the quartet and octet states are also active because they are degenerate. The Rh5 cluster spontaneously activates the N2─O cleavage, and the reaction is highly exothermic ca. -75 kcal mol(-1). The N2─O breaking is obtained for the geometrical arrangement that maximizes the overlap and electron transfers between the N2O and Rh5 frontier orbitals. The Rh5 high activity is due to the Rh 3d orbitals are located between the N2O HOMO and LUMO orbitals, which makes possible the interactions between them. In particular, the O 2p states strongly interact with Rh 3d orbitals, which finally weaken the N2─O bond. The electron transfer is from the Rh5 HOMO orbital to the N2O antibonding orbital.

Measuring the radium quartet (228Ra, 226Ra, 224Ra, 223Ra) in seawater samples using gamma spectrometry.

PubMed

van Beek, P; Souhaut, M; Reyss, J-L

2010-07-01

Radium isotopes are widely used in marine studies (eg. to trace water masses, to quantify mixing processes or to study submarine groundwater discharge). While 228Ra and 226Ra are usually measured using gamma spectrometry, short-lived Ra isotopes (224Ra and 223Ra) are usually measured using a Radium Delayed Coincidence Counter (RaDeCC). Here we show that the four radium isotopes can be analyzed using gamma spectrometry. We report 226Ra, 228Ra, 224Ra, 223Ra activities measured using low-background gamma spectrometry in standard samples, in water samples collected in the vicinity of our laboratory (La Palme and Vaccarès lagoons, France) but also in seawater samples collected in the plume of the Amazon river, off French Guyana (AMANDES project). The 223Ra and 224Ra activities determined in these samples using gamma spectrometry were compared to the activities determined using RaDeCC. Activities determined using the two techniques are in good agreement. Uncertainties associated with the 224Ra activities are similar for the two techniques. RaDeCC is more sensitive for the detection of low 223Ra activities. Gamma spectrometry thus constitutes an alternate method for the determination of short-lived Ra isotopes. 2009 Elsevier Ltd. All rights reserved.

A Song of Our Warming Planet: Using Music to Communicate Critical Concepts in Climate Science

NASA Astrophysics Data System (ADS)

St George, S.; Crawford, D.; Reubold, T.

2014-12-01

When climate science is communicated to the broader public, many of its key findings are shared in the form of conceptual diagrams or information-dense data graphics. In this collaboration, we applied a data sonification approach to express NASA's global temperature record as a musical composition for the cello. The resulting piece, which we titled 'A Song of Our Warming Planet', transformed 133 years of annual global temperature anomalies into a haunting, atonal melody that stretched across almost all of the instrument's range. Since its release in June 2013, the song has been featured by several national and international media outlets, including the New York Times, the Weather Channel, and National Public Radio, and its accompanying video has received more than 140,000 views from nearly every corner of the world. We are currently preparing a new composition for string quartet that will add a geographic dimension to describe both the pace and place of global warming. We believe the success of our initial sonification project is testament to the power of music to reach audiences who respond less enthusiastically to traditional methods used to communicate climate science. We also imagine this approach could be applied more broadly to allow students to create novel, visceral, and memorable encounters with other aspects of the geophysical sciences.

Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT-trnF sequences.

PubMed

Neves, Susana S; Swire-Clark, Ginger; Hilu, Khidir W; Baird, Wm Vance

2005-05-01

Phylogenetic relationships in the genus Eleusine (Poaceae: Chloridoideae) were investigated using nuclear ITS and plastid trnT-trnF sequences. Separate and combined data sets were analyzed using parsimony, distance, and likelihood based methods, including Bayesian. Data congruence was examined using character and topological measures. Significant data heterogeneity was detected, but there was little conflict in the topological substructure measures for triplets and quartets, and resolution and clade support increased in the combined analysis. Data incongruence may be a result of noise and insufficient information in the slower evolving trnT-trnF. Monophyly of Eleusine is strongly supported in all analyses, but basal relationships in the genus remain uncertain. There is good support for a CAIK clade (E. coracana subsp. coracana and africana, E. indica, and E. kigeziensis), with E. tristachya as its sister group. Two putative ITS homeologues (A and B loci) were identified in the allotetraploid E. coracana; the 'B' locus sequence type was not found in the remaining species. Eleusine coracana and its putative 'A' genome donor, the diploid E. indica, are confirmed close allies, but sequence data contradicts the hypothesis that E. floccifolia is its second genome donor. The 'B' genome donor remains unidentified and may be extinct.

Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi.

PubMed Central

Huchon, D; Catzeflis, F M; Douzery, E J

2000-01-01

The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two different molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named 'Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more influenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous-Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous. PMID:10722222

Bioactivity of 2′-deoxyinosine-incorporated aptamer AS1411

PubMed Central

Fan, Xinmeng; Sun, Lidan; Wu, Yun; Zhang, Lihe; Yang, Zhenjun

2016-01-01

Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2′-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2′-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2′-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2′-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2′-deoxyinosine moieties in interactive binding processes. PMID:27194215

Bioactivity of 2'-deoxyinosine-incorporated aptamer AS1411.

PubMed

Fan, Xinmeng; Sun, Lidan; Wu, Yun; Zhang, Lihe; Yang, Zhenjun

2016-05-19

Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2'-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2'-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2'-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2'-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2'-deoxyinosine moieties in interactive binding processes.

Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer

PubMed Central

Pasternak, Anna; Hernandez, Frank J.; Rasmussen, Lars M.; Vester, Birte; Wengel, Jesper

2011-01-01

A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA-U placed in position U3, U7 or U12 increases the thermodynamic stability of TBA by 0.15–0.50 kcal/mol. In contrast, modification of any position within the two G-quartet structural elements is unfavorable for quadruplex formation. The intramolecular folding of the quadruplexes is confirmed by Tm versus ln c analysis. Moreover, circular dichroism and thermal difference spectra of the modified TBAs displaying high thermodynamic stability show bands that are characteristic for antiparallel quadruplex formation. Surface plasmon resonance studies of the binding of the UNA-modified TBAs to thrombin show that a UNA monomer is allowed in many positions of the aptamer without significantly changing the thrombin-binding properties. The biological effect of a selection of the modified aptamers was tested by a thrombin time assay and showed that most of the UNA-modified TBAs possess anticoagulant properties, and that the construct with a UNA-U monomer in position 7 is a highly potent inhibitor of fibrin-clot formation. PMID:20870750

Finale of a Quartet: Hints on Supernova Formation

NASA Astrophysics Data System (ADS)

Fang, Xiao; Thompson, Todd A.; Hirata, Christopher M.

2018-01-01

The origin of Type Ia Supernovae (SNe) is not well understood. Two most popular hypotheses are the single-degenerate scenario, where one white dwarf (WD) accretes matter from its giant companion until the Chandrasekhar limit is reached, and the double-degenerate scenario, where two WDs merge and explode. We focus on the second scenario. It has long been realized that binary WD systems normally take extremely long time to merge via gravitational waves and it is still unclear whether WD mergers can fully account for the observed SN Ia rate. Recent effort has been devoted to the effects of introducing a distant tertiary to the binary system. The standard “Kozai-Lidov” mechanism can lead to high eccentricities of the binary WDs, which could lead to direct collisions or much efficient energy dissipation. Alternatively, we investigate the long-term evolution of the hierarchical quadruple systems, i.e. WD binary with a binary companion, which are basically unexplored, yet they should be numerous. We explore their interesting dynamics and find that the fraction of reaching high eccentricities is largely enhanced, which hints on a higher WD merger rate than predicted from triple systems with the same set of secular and non-secular effects considered. Considering the population of quadruple stellar systems, the quadruple scenario might contribute significantly to the overall rate of Ia SNe.

Different equation-of-motion coupled cluster methods with different reference functions: The formyl radical

NASA Astrophysics Data System (ADS)

Kuś, Tomasz; Bartlett, Rodney J.

2008-09-01

The doublet and quartet excited states of the formyl radical have been studied by the equation-of-motion (EOM) coupled cluster (CC) method. The Sz spin-conserving singles and doubles (EOM-EE-CCSD) and singles, doubles, and triples (EOM-EE-CCSDT) approaches, as well as the spin-flipped singles and doubles (EOM-SF-CCSD) method have been applied, subject to unrestricted Hartree-Fock (HF), restricted open-shell HF, and quasirestricted HF references. The structural parameters, vertical and adiabatic excitation energies, and harmonic vibrational frequencies have been calculated. The issue of the reference function choice for the spin-flipped (SF) method and its impact on the results has been discussed using the experimental data and theoretical results available. The results show that if the appropriate reference function is chosen so that target states differ from the reference by only single excitations, then EOM-EE-CCSD and EOM-SF-CCSD methods give a very good description of the excited states. For the states that have a non-negligible contribution of the doubly excited configurations one is able to use the SF method with such a reference function, that in most cases the performance of the EOM-SF-CCSD method is better than that of the EOM-EE-CCSD approach.

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex

PubMed Central

Lee, Ja Yil; Kim, D. S.

2009-01-01

Guanine-rich DNA sequences can form G-quadruplexes. These four-stranded structures are known to form in several genomic regions and to influence certain biological activities. Sometimes, the instability of G-quadruplexes causes the abnormal biological processes. Mutation is a culprit for the destabilization of G-quadruplexes, but the details of mutated G-quadruplexes are poorly understood. In this article, we investigated the conformational dynamics of single-base mutated human telomeric G-quadruplexes in the presence of K+ with single-molecule FRET spectroscopy. We observed that the replacement of single guanine by thymine in a G-track induces various folded structures, i.e. structural polymorphism. Moreover, direct observation of their dynamics revealed that a single-base mutation causes fast unfolding of folded states under physiological conditions. Furthermore, we found that the degree of destabilization varies according to mutation positions. When the central guanine of a G-track is replaced, the G-quadruplexes unfold quickly at any K+ concentrations and temperature. Meanwhile, outer-quartet mutated G-quadruplexes have heterogeneous dynamics at intermediate K+ concentrations and longstanding folded states at high K+ concentrations. Several factors such as base-stacking interaction and K+ coordination are responsible for the different dynamics according to the mutation position. PMID:19359361

Towards global optimization with adaptive simulated annealing

NASA Astrophysics Data System (ADS)

Forbes, Gregory W.; Jones, Andrew E.

1991-01-01

The structure of the simulated annealing algorithm is presented and its rationale is discussed. A unifying heuristic is then introduced which serves as a guide in the design of all of the sub-components of the algorithm. Simply put this heuristic principle states that at every cycle in the algorithm the occupation density should be kept as close as possible to the equilibrium distribution. This heuristic has been used as a guide to develop novel step generation and temperature control methods intended to improve the efficiency of the simulated annealing algorithm. The resulting algorithm has been used in attempts to locate good solutions for one of the lens design problems associated with this conference viz. the " monochromatic quartet" and a sample of the results is presented. 1 Global optimization in the context oflens design Whatever the context optimization algorithms relate to problems that take the following form: Given some configuration space with coordinates r (x1 . . x) and a merit function written asffr) find the point r whereftr) takes it lowest value. That is find the global minimum. In many cases there is also a set of auxiliary constraints that must be met so the problem statement becomes: Find the global minimum of the merit function within the region defined by E. (r) 0 j 1 2 . . . p and 0 j 1 2 . . . q.

A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

Surface Stresses and a Force Balance at a Contact Line.

PubMed

Liang, Heyi; Cao, Zhen; Wang, Zilu; Dobrynin, Andrey V

2018-06-26

Results of the coarse-grained molecular dynamics simulations are used to show that the force balance analysis at the triple-phase contact line formed at an elastic substrate has to include a quartet of forces: three surface tensions (surface free energies) and an elastic force per unit length. In the case of the contact line formed by a droplet on an elastic substrate an elastic force is due to substrate deformation generated by formation of the wetting ridge. The magnitude of this force f el is proportional to the product of the ridge height h and substrate shear modulus G. Similar elastic line force should be included in the force analysis at the triple-phase contact line of a solid particle in contact with an elastic substrate. For this contact problem elastic force obtained from contact angles and surface tensions is a sum of the elastic forces acting from the side of a solid particle and an elastic substrate. By considering only three line forces acting at the triple-phase contact line, one implicitly accounts the bulk stress contribution as a part of the resultant surface stresses. This "contamination" of the surface properties by a bulk contribution could lead to unphysically large values of the surface stresses in soft materials.

A cell-body groove housing the new flagellum tip suggests an adaptation of cellular morphogenesis for parasitism in the bloodstream form of Trypanosoma brucei.

PubMed

Hughes, Louise; Towers, Katie; Starborg, Tobias; Gull, Keith; Vaughan, Sue

2013-12-15

Flagella are highly conserved organelles present in a wide variety of species. In Trypanosoma brucei the single flagellum is necessary for morphogenesis, cell motility and pathogenesis, and is attached along the cell body. A new flagellum is formed alongside the old during the cell division cycle. In the (insect) procyclic form, the flagella connector (FC) attaches the tip of the new flagellum to the side of the old flagellum, ensuring faithful replication of cell architecture. The FC is not present in the bloodstream form of the parasite. We show here, using new imaging techniques including serial block-face scanning electron microscopy (SBF-SEM), that the distal tip of the new flagellum in the bloodstream form is embedded within an invagination in the cell body plasma membrane, named the groove. We suggest that the groove has a similar function to the flagella connector. The groove is a mobile junction located alongside the microtubule quartet (MtQ) and occurred within a gap in the subpellicular microtubule corset, causing significant modification of microtubules during elongation of the new flagellum. It appears likely that this novel form of morphogenetic structure has evolved to withstand the hostile immune response in the mammalian blood.

Concepts of nuclear α-particle condensation

NASA Astrophysics Data System (ADS)

Funaki, Y.; Horiuchi, H.; von Oertzen, W.; Röpke, G.; Schuck, P.; Tohsaki, A.; Yamada, T.

2009-12-01

Certain aspects of the recently proposed antisymmetrized α-particle product state wave function, or THSR (Tohsaki-Horiuchi-Schuck-Röpke) α-cluster wave function, for the description of the ground state in Be8, the Hoyle state in C12, and analogous states in heavier nuclei are elaborated in detail. For instance, the influence of antisymmetrization in the Hoyle state on the bosonic character of the α particles is studied carefully. It is shown to be weak. Bosonic aspects in Hoyle and similar states in other self-conjugate nuclei are, therefore, predominant. Another issue is the de Broglie wavelength of α particles in the Hoyle state, which is shown to be much larger than the inter-α distance. It is pointed out that the bosonic features of low-density α gas states have measurable consequences, one of which, enhanced multi-α decay properties, has likely already been detected. Consistent with experiment, the width of the proposed analog to the Hoyle state in O16 at the excitation energy of Ex=15.1 MeV is estimated to be very small (34 keV), lending credit to the existence of heavier Hoyle-like states. The intrinsic single-boson density matrix of a self-bound Bose system can, under physically desirable boundary conditions, be defined unambiguously. One eigenvalue then separates out, being close to the number of α particles in the system. Differences between Brink and THSR α-cluster wave functions are worked out. No cluster model of the Brink type can describe the Hoyle state with a single configuration. On the contrary, many superpositions of the Brink type are necessary, implying delocalization toward an α-product state. It is shown that single α-particle orbits in condensates of different nuclei are almost the same. It is thus argued that α-particle (quartet) antisymmetrized product states of the THSR type are a very promising novel and useful concept in nuclear physics.

Interstellar PAH emission in the 11-14 micron region: new insights from laboratory data and a tracer of ionized PAHs

NASA Technical Reports Server (NTRS)

Hudgins, D. M.; Allamandola, L. J.

1999-01-01

The Ames infrared spectral database of isolated, neutral and ionized polycyclic aromatic hydrocarbons (PAHS) shows that aromatic CH out-of-plane bending frequencies are significantly shifted upon ionization. For solo- and duet-CH groups, the shift is pronounced and consistently toward higher frequencies. The solo-CH modes are blueshifted by an average of 27 cm-1 and the duet-CH modes by an average of 17 cm-1. For trio- and quartet-CH groups, the ionization shifts of the out-of-plane modes are more erratic and typically more modest. As a result of these ionization shifts, the solo-CH out-of-plane modes move out of the region classically associated with these vibrations in neutral PAHS, falling instead at frequencies well above those normally attributed to out-of-plane bending, vibrations of any type. In addition, for the compact PAHs studied, the duet-CH out-of-plane modes are shifted into the frequency range traditionally associated with the solo-CH modes. These results refine our understanding of the origin of the dominant interstellar infrared emission feature near 11.2 microns, whose envelope has traditionally been attributed only to the out-of-plane bending of solo-CH groups on PAHS, and provide a natural explanation for the puzzling emission feature near 11.0 microns within the framework of the PAH model. Specifically, the prevalent but variable long-wavelength wing or shoulder that is often observed near 11.4 microns likely reflects the contributions of duet-CH units in PAH cations. Also, these results indicate that the emission between 926 and 904 cm-1 (10.8 and 11.1 microns) observed in many sources can be unambiguously attributed to the out-of-plane wagging, of solo-CH units in moderately sized (fewer than 50 carbon atom) PAH cations, making this emission an unequivocal tracer of ionized interstellar PAHS.

A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study.

PubMed

Schneider, M; Soshnikov, D Yu; Holland, D M P; Powis, I; Antonsson, E; Patanen, M; Nicolas, C; Miron, C; Wormit, M; Dreuw, A; Trofimov, A B

2015-10-14

The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n(5) with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZ basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLÉIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.

Low-Lying Electronic States of AlZn Calculated by MRCI+Q Method

NASA Astrophysics Data System (ADS)

Zhang, Shudong; Wang, Mingxu; Wang, Zifan; Hu, Kun; Dong, Jingping

2017-07-01

Some low-lying electronic states of AlZn have been studied by the ab initio calculation method of multireference configuration interaction (MRCI). The complete potential energy curves (PECs) of the three lowest doublet states (X2Π, A2Σ+, and B2Π) and the two lowest quartet states (a4Σ- and b4Π) are computed in the range of R = 0.1-0.9 nm and these states are correlated to three dissociation limits, X2Π and A2Σ+ to Zn(4s2,1S) + Al(3s23p1,2P), a4Σ- and b4Π to Zn(4s2,1S) + Al(3s13p2,4P), and B2Π to Zn(4s14p1,3P) + Al(3s23p1,2P). The calculated PECs indicate that the A2Σ+ state has a very shallow potential well and the other states show significant binding-state characteristics. The equilibrium internuclear distances Re, dissociation energies De, and term energies Te for the electronic excited states were obtained. All the possible vibrational levels, rotational constants, and spectral constants for the four bound states were computed by solving the radial Schrödinger equation of nuclear motion with the Level8.0 program provided by Le Roy.

Characterization of Prdm9 in equids and sterility in mules.

PubMed

Steiner, Cynthia C; Ryder, Oliver A

2013-01-01

Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy's zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility.

Solid oxygen revisited

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.; Jodl, H. J.; Crespo, Yanier

2018-05-01

The paper provides an up-to-date review of the experimental and theoretical works on solid oxygen published over the past decade. The most important results presented in this review are the following: Detection of magnetic collapse in neutron studies under the delta-epsilon transition. Identification of the lattice structure of the ɛ phase. In this structure the O2 molecules retain their individuality, but there is an additional link leading to the formation of clusters of molecular quartets with the structural formula (O2)4. Discovery of the unique magnetic properties of the delta phase, which hosts three different magnetic structures in the domain of the same crystallographic structure. The extension of the phase diagram to the high-pressure high-temperature region which was previously beyond the reach for experiment; the molecular η and η‧ phases were found and their structures were identified. Behavior of the melting line up to 60 GPa (1750 K). Discovery of a new molecular θ phase in ultrahigh magnetic fields up to over 190 T and the construction of the thermodynamical magnetic-field-temperature H- T phase diagram on the base of the ultrahigh-field magnetization, optical magneto-transmission, and adiabatic magnetocaloric effect measurements. Prediction of the persistence of the molecular state of solid oxygen up to the pressure of 1.9 TPa which is significantly higher than the corresponding limits in solid hydrogen and nitrogen, other generic molecular solids.

Navigating the Path of Totality - Results and Lessons Learned from the 2017 Eclipse Broadcast, Webcast, Mobile App and Online Production

NASA Astrophysics Data System (ADS)

Semper, R.; Higdon, R.

2017-12-01

The 2017 total solar eclipse provided unique opportunity to provide public outreach about astronomy, heliophysics, and scientific discovery. The Navigating the Path of Totality project was designed to produce eclipse related educational resources including live video feeds and distribute them to museums, schools, libraries and the public through online and broadcast media. Using special telescope video camera setups, five feeds were produced including a live one hour English program and in parallel a live one hour Spanish program from Casper, WY with a cutaway to Madras, OR, complete (C1-C4) telescope only feeds from both Madras, OR and Casper, Wy, and a complete (C1-C4) telescope only feed with live musical sonification and accompaniment by the Kronos Quartet. Images from the live feeds were made available on the NASA Website, NASA TV, Exploratorium website, Exploratorium Solar Eclipse mobile app, local television and in museums, libraries and schools worldwide. Associated educational video material including images from the 2016 total eclipse from Micronesia was produced and disseminated. In this talk we will discuss the evaluation results including an examination of the effectiveness of the digital strategy of many mobile channels and mobile apps using different analytics including IBM Watson social media analytics services. We will also present the lessons learned from the project.

Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment.

PubMed

Li, Yaohang; Liu, Hui; Rata, Ionel; Jakobsson, Eric

2013-02-25

The rapidly increasing number of protein crystal structures available in the Protein Data Bank (PDB) has naturally made statistical analyses feasible in studying complex high-order inter-residue correlations. In this paper, we report a context-based secondary structure potential (CSSP) for assessing the quality of predicted protein secondary structures generated by various prediction servers. CSSP is a sequence-position-specific knowledge-based potential generated based on the potentials of mean force approach, where high-order inter-residue interactions are taken into consideration. The CSSP potential is effective in identifying secondary structure predictions with good quality. In 56% of the targets in the CB513 benchmark, the optimal CSSP potential is able to recognize the native secondary structure or a prediction with Q3 accuracy higher than 90% as best scored in the predicted secondary structures generated by 10 popularly used secondary structure prediction servers. In more than 80% of the CB513 targets, the predicted secondary structures with the lowest CSSP potential values yield higher than 80% Q3 accuracy. Similar performance of CSSP is found on the CASP9 targets as well. Moreover, our computational results also show that the CSSP potential using triplets outperforms the CSSP potential using doublets and is currently better than the CSSP potential using quartets.

A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, M.; Wormit, M.; Dreuw, A.

2015-10-14

The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n{sup 5} with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZmore » basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLÉIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.« less

A twice-as-smart synthetic G-quartet: PyroTASQ is both a smart quadruplex ligand and a smart fluorescent probe.

PubMed

Laguerre, Aurélien; Stefan, Loic; Larrouy, Manuel; Genest, David; Novotna, Jana; Pirrotta, Marc; Monchaud, David

2014-09-03

Recent and unambiguous evidences of the formation of DNA and RNA G-quadruplexes in cells has provided solid support for these structures to be considered as valuable targets in oncology. Beyond this, they have lent further credence to the anticancer strategies relying on small molecules that selectively target these higher-order DNA/RNA architectures, referred to as G-quadruplex ligands. They have also shed bright light on the necessity of designing multitasking ligands, displaying not only enticing quadruplex interacting properties (affinity, structural selectivity) but also additional features that make them usable for detecting quadruplexes in living cells, notably for determining whether, when, and where these structures fold and unfold during the cell cycle and also for better assessing the consequences of their stabilization by external agents. Herein, we report a brand new design of such multitasking ligands, whose structure experiences a quadruplex-promoted conformational switch that triggers not only its quadruplex affinity (i.e., smart ligands, which display high affinity and selectivity for DNA/RNA quadruplexes) but also its fluorescence (i.e., smart probes, which behave as selective light-up fluorescent reporters on the basis of a fluorogenic electron redistribution). The first prototype of such multifunctional ligands, termed PyroTASQ, represents a brand new generation of quadruplex ligands that can be referred to as "twice-as-smart" quadruplex ligands.

Iron monocyanide (FeCN): Spin-orbit and vibronic interactions in low-lying electronic states

NASA Astrophysics Data System (ADS)

Jerosimić, Stanka V.; Milovanović, Milan Z.

2018-04-01

The spin-orbit eigenvalues of low-energy quartet and sextet spatially degenerate electronic states of FeCN are reported, together with the combined effect of vibronic and spin-orbit interaction in the lowest-lying 14Δ and 16Δ states of FeCN, by using perturbational and variational method. Spin-orbit constants (ASO) have been calculated in the basis of: (a) two components of each degenerate state, (b) four components of 14Δ and 14Π (16Δ and 16Π) states, and (c) ten components of 16Δ, 16Π, 16Σ+, 14Δ, 14Π, and 14Σ+ states. The present calculations predict the values of ASO= -77 cm-1 for 16Δ and ASO= -108 cm-1 for 14Δ state in the lowest-energy spin-orbit manifolds of each state. The major perturbing state for the 14Δ state is the 14Π state (16Π for the sextet 16Δ). As expected, based on extremely small splitting and shallowness of the bending potential energy curves for the lowest-lying 4,6Δ states, the present study indicate that the vibronic coupling does not create significant splitting of the bending levels, but the influence of anharmonicity in the bending mode is more pronounced. However, the spin-orbit fine structure dominantly influences the spectra of this species.

Magnetic field effects on electron transfer reactions involving sextet-spin ( S = 5/2) intermediates generated on photoexcitation of a Cr(III)-porphyrin complex

NASA Astrophysics Data System (ADS)

Mori, Yukie; Hoshino, Mikio; Hayashi, Hisaharu

The excited trip-sextet ( 6 T 1 ) state of chloro-(3-methylimidazol)-( meso -tetraphenylporphyrinato) chromium(III) (Cr III P) is quenched by 1,1 '-dibenzyl-4,4 '-bipyridinium (BV 2+ ) in acetonitrile through electron transfer to give 5 (Cr III P .+ ) and 2 BV .+ . The intermediate is a geminate ion pair in the sextet (Sx) state 6 [ 5 (Cr III P .+ ) 2 BV .+ ], which decays through either the escape from a solvent cage to give the free ions or the spin conversion to the quartet (Qa) state followed by back electron transfer. The free ion yield ( ΦFI ) increased with increasing magnetic field from 0 to 4 T and then slightly decreased from 4 T to 10 T. These magnetic field effects are explained as follows. Under low fields where the Zeeman splitting of the spin sublevels is lower than or comparable with the electron spin dipole-dipole interaction within 5 (Cr III P .+ ), this interaction effectively induces the Sx ⇔Qa conversion of [ 5 (Cr III P .+ ) 2 BV + ] to result in low ΦFI values. Under high fields where the Zeeman splitting is larger than the dipole-dipole interaction, the Sx Qa conversion is decreased with increasing field to cause higher ΦFI values. The slight decrease in ΦFI above 4 T may be due to the Δg mechanism.

Can Baird's and Clar's Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4nπ- and (4n + 2)π-Rings?

PubMed

Ayub, Rabia; Bakouri, Ouissam El; Jorner, Kjell; Solà, Miquel; Ottosson, Henrik

2017-06-16

Compounds that can be labeled as "aromatic chameleons" are π-conjugated compounds that are able to adjust their π-electron distributions so as to comply with the different rules of aromaticity in different electronic states. We used quantum chemical calculations to explore how the fusion of benzene rings onto aromatic chameleonic units represented by biphenylene, dibenzocyclooctatetraene, and dibenzo[a,e]pentalene modifies the first triplet excited states (T 1 ) of the compounds. Decreases in T 1 energies are observed when going from isomers with linear connectivity of the fused benzene rings to those with cis- or trans-bent connectivities. The T 1 energies decreased down to those of the parent (isolated) 4nπ-electron units. Simultaneously, we observe an increased influence of triplet state aromaticity of the central 4n ring as given by Baird's rule and evidenced by geometric, magnetic, and electron density based aromaticity indices (HOMA, NICS-XY, ACID, and FLU). Because of an influence of triplet state aromaticity in the central 4nπ-electron units, the most stabilized compounds retain the triplet excitation in Baird π-quartets or octets, enabling the outer benzene rings to adapt closed-shell singlet Clar π-sextet character. Interestingly, the T 1 energies go down as the total number of aromatic cycles within a molecule in the T 1 state increases.

An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation.

PubMed

Smouse, Peter E; Whitehead, Michael R; Peakall, Rod

2015-11-01

Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require 'common currency' translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi-parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum-spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N(ep) < (N(en)), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation. © 2015 John Wiley & Sons Ltd.

Anharmonic rattling vibrations effects in the ESR of Er 3+ doped SmB 6 Kondo insulator

DOE PAGES

Lesseux, G. G.; Rosa, P. F. S.; Fisk, Z.; ...

2017-01-23

We report X-band Electron Spin Resonance (ESR) experiments on ≈ 0.2% and ≈ 0.7 % Er 3+ doped SmB 6 at low temperature (4 K - 40 K). The crystal field ground state of Er 3+ in SmB 6 is a Γ 8 quartet with a nearby Γ 6 excited doublet. The angular dependence of the resonances is not consistent with transitions between pure cubic crystal field states. The data were interpreted in terms of a dynamic Jahn-Teller (JT) effect by a coupling to Γ 3 vibrational modes, which we propose to originate from the rattling of the small Ermore » 3+ ions in the large SmB6 cage. Our data show an anisotropic pair of E and E’ resonances at g ≈ 4.4 and two nearly isotropic signals at g ≈ 5.8, one intense and narrow (A vibrational mode) and the other broad and faint, which we attribute to Er 3+ ions at lattice sites which are strongly affected by strain, defects and/or extrinsic Al impurities that inhibits the JT effects. Our results are in general consistent with those previously reported by Sturm et al. In addition to the angular dependence of the lines, we discuss the intensities, g-values and the linewidths of the Er 3+ transitions as a function of temperature.« less

Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy.

PubMed

Shazib, Shahed Uddin Ahmed; Vd'ačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

2014-09-01

The ciliate class Heterotrichea is defined by somatic dikinetids bearing postciliodesmata, by an oral apparatus consisting of a paroral membrane and an adoral zone of membranelles, as well as by features of nuclear division involving extramacronuclear microtubules. Although phylogenetic interrelationships among heterotrichs have been analyzed several times, deeper nodes of the heterotrichean tree of life remain poorly resolved. To cast more light on the evolutionary history of heterotricheans, we performed phylogenetic analyses of multiple loci (18S rRNA gene, ITS1-5.8S rRNA-ITS2 region, and 28S rRNA gene) using traditional tree-building phylogenetic methods and statistical tree topology tests as well as phylogenetic networks, split spectrum analysis and quartet likelihood mapping. This multifaceted approach has shown that (1) Peritromus is very likely an adelphotaxon of all other heterotrichs; (2) Spirostomum and Anigsteinia are sister taxa and their common monophyletic origin is strongly supported by a uniquely posteriorly-thickened paroral membrane; (3) the monotypic family Chattonidiidae should be suppressed because its type genus clusters within the family Condylostomatidae; and (4) new families are needed for Gruberia and Fabrea because their affiliation with Spirostomidae and Climacostomidae, respectively, is not supported by molecular phylogenies nor the fine structure of the paroral membrane. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterization of Prdm9 in Equids and Sterility in Mules

PubMed Central

Steiner, Cynthia C.; Ryder, Oliver A.

2013-01-01

Prdm9 (Meisetz) is the first speciation gene discovered in vertebrates conferring reproductive isolation. This locus encodes a meiosis-specific histone H3 methyltransferase that specifies meiotic recombination hotspots during gametogenesis. Allelic differences in Prdm9, characterized for a variable number of zinc finger (ZF) domains, have been associated with hybrid sterility in male house mice via spermatogenic failure at the pachytene stage. The mule, a classic example of hybrid sterility in mammals also exhibits a similar spermatogenesis breakdown, making Prdm9 an interesting candidate to evaluate in equine hybrids. In this study, we characterized the Prdm9 gene in all species of equids by analyzing sequence variation of the ZF domains and estimating positive selection. We also evaluated the role of Prdm9 in hybrid sterility by assessing allelic differences of ZF domains in equine hybrids. We found remarkable variation in the sequence and number of ZF domains among equid species, ranging from five domains in the Tibetan kiang and Asiatic wild ass, to 14 in the Grevy’s zebra. Positive selection was detected in all species at amino acid sites known to be associated with DNA-binding specificity of ZF domains in mice and humans. Equine hybrids, in particular a quartet pedigree composed of a fertile mule showed a mosaic of sequences and number of ZF domains suggesting that Prdm9 variation does not seem by itself to contribute to equine hybrid sterility. PMID:23613924

Relativistic many-body calculations of energies in a broad range of Lu-like ions from W^3+ to Fm^29+

NASA Astrophysics Data System (ADS)

Safronova, U. I.; Safronova, A. S.

2012-06-01

Energies of the [Xe]4f^145d^3, [Xe]4f^145d^26s, [Xe]4f^145d^26p, and [Xe]4f^145d6s6p states of lutetiumlike ions with Z = 74-100 are determined using second-order relativistic many-body perturbation theory (RMBPT). Our calculations start from a Er-like Dirac-Fock potential ([Xe]4f^14 where [Xe]=1s^22s^22p^63s^23p^63d^104s^24p^64d^105s^25p^6). Second-order Coulomb and Breit-Coulomb interactions are included. Correction for the frequency-dependence of the Breit interaction as well as Lamb shift correction to energies are taken into account in lowest order. The three-electron contributions to the energy are compared with the one- and two-electron contributions. They are found to contribute about 10-20% of the total second-order energy. The ratio of the third-order and second-order corrections to the one-electron contributions is found to be about 5-10%. A detailed discussion of the various contributions to the energy levels is given for Lu-like tungsten (Z=74). Trends of excitation energies including splitting of the doublet and quartet terms as functions of nuclear charge Z = 71--100 are illustrated graphically for some states. This research was sponsored by DOE under the OFES grant DE-FG02-08ER54951.

Determination of low-level Radium isotope activities in fresh waters by gamma spectrometry.

PubMed

Molina Porras, Arnold; Condomines, Michel; Seidel, Jean Luc

2017-02-01

A new portable sampling system was developed to extract Radium isotopes from large volumes (up to 300L) of fresh surface- and ground-waters of low Ra-activities (<5mBq/L). Ra is quantitatively adsorbed on a small amount (6.5g) of MnO 2 -coated acrylic fibers, which are then dried and burned at 600°C in the laboratory. The resulting Mn-oxide powder (about 2cm 3 when compacted) is then analyzed through gamma-ray spectrometry which allows measurement of the whole Ra quartet ( 226 Ra, 228 Ra, 224 Ra and 223 Ra) in a single counting of a few days. The usual relative standard combined uncertainties (1σ) are 2-3% for 226 Ra, 228 Ra and 224 Ra; and less than 10% for 223 Ra. This method was applied to the analysis of Ra in karstic waters of the Lez aquifer, and surface- and ground-waters of the upper and middle Vidourle watershed (South of France). The analyzed waters have relatively low 226 Ra activities (1-4mBq/L) in both cases, regardless of the contrasted geology (Mesozoic limestone vs crystalline Variscan basement), but clearly distinct ( 228 Ra/ 226 Ra) ratios in agreement with the differences in Th/U ratios of the two drained areas. Short-lived Ra isotopes ( 224 Ra and 223 Ra) appear to be mainly influenced by near-surface desorption/recoil processes for most of the sampling sites. Copyright © 2016. Published by Elsevier Ltd.

Prospect of Bioflavonoid Fisetin as a Quadruplex DNA Ligand: A Biophysical Approach

PubMed Central

Sengupta, Bidisha; Pahari, Biswapathik; Blackmon, Laura; Sengupta, Pradeep K.

2013-01-01

Quadruplex (G4) forming sequences in telomeric DNA and c-myc promoter regions of human DNA are associated with tumorogenesis. Ligands that can facilitate or stabilize the formation and increase the stabilization of G4 can prevent tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, steady state and time-resolved fluorescence measurements provide important structural and dynamical insights into the free and bound states of the therapeutically potent plant flavonoid fisetin (3,3′,4′,7-tetrahydroxyflavone) in a G4 DNA matrix. The excited state intra-molecular proton transfer (ESPT) of fisetin plays an important role in observing and understanding the binding of fisetin with the G4 DNA. Differential absorption spectra, thermal melting, and circular dichroism spectroscopic studies provide evidences for the formation of G4 DNA and size exclusion chromatography (SEC) proves the binding and 1∶1 stoichiometry of fisetin in the DNA matrix. Comparative analysis of binding in the presence of EtBr proves that fisetin favors binding at the face of the G-quartet, mostly along the diagonal loop. Time resolved fluorescence anisotropy decay analysis indicates the increase in the restrictions in motion from the free to bound fisetin. We have also investigated the fingerprints of the binding of fisetin in the antiparallel quadruplex using Raman spectroscopy. Preliminary results indicate fisetin to be a prospective candidate as a G4 ligand. PMID:23785423

Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer

PubMed Central

Waugh, Mark G.

2014-01-01

Little is known about the possible oncogenic roles of genes encoding for the phosphatidylinositol 4-kinases, a family of enzymes that regulate an early step in phosphoinositide signalling. To address this issue, the mutational status of all four human phosphatidylinositol 4-kinases genes was analyzed across 852 breast cancer samples using the COSMIC data resource. Point mutations in the phosphatidylinositol 4-kinase genes were uncommon and appeared in less than 1% of the patient samples however, 62% of the tumours had increases in gene copy number for PI4KB which encodes the phosphatidylinositol 4-kinase IIIbeta isozyme. Extending this analysis to subsequent enzymes in the phosphoinositide signalling cascades revealed that the only PIP5K1A, PI3KC2B and AKT3 genes exhibited similar patterns of gene copy number variation. By comparison, gene copy number increases for established oncogenes such as EGFR and HER2/Neu were only evident in 20% of the samples. The PI4KB, PIP5K1A, PI3KC2B and AKT3 genes are related in that they all localize to chromosome 1q which is often structurally and numerically abnormal in breast cancer. These results demonstrate that a gene quartet encoding a potential phosphoinositide signalling pathway is amplified in a subset of breast cancers. PMID:25368680

The effects of DNA supercoiling on G-quadruplex formation.

PubMed

Sekibo, Doreen A T; Fox, Keith R

2017-12-01

Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G3T)n and (G3T4)n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G3T4)n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

PubMed

Platt, Roy N; Faircloth, Brant C; Sullivan, Kevin A M; Kieran, Troy J; Glenn, Travis C; Vandewege, Michael W; Lee, Thomas E; Baker, Robert J; Stevens, Richard D; Ray, David A

2018-03-01

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.

Prehistory of Zodiac Dating: Three Strata of Upper Paleolithic Constellations

NASA Astrophysics Data System (ADS)

Gurshtein, Alex A.

A pattern of archaic proto-constellations is extracted from Aratus' "The Phaenomena" didactic poem list according to a size criterion elaborated earlier, and their symbolism is analyzed. As a result of this approach three celestial symbolical strata are discovered to be probably a reflection of the symbols for the Lower, the Middle and the Upper Worlds; the Under-World creatures have a water character, the Middle World ones are mostly anthropomorphic and flying beings are for the Upper World. The strata excerpted from Aratus' sky seems to be in agreement with the well-known Babylonian division into three god pathways for Ea (Enki), Anu and Enlil. There is a possibility of dating the pattern discovered because of precession's strong influence as far back as 16 thousand years, the result being supported by the comparison of different star group mean sizes. The archaic constellation pattern under consideration is a reasonable background of symbolical meanings for the first Zodiacal generation quartet (7.5 thousand years old) examined by the author previously. The enormous size of the Argo constellation (Ship of Argo and his Argonauts) as well as the large sizes of other southern constellations are explained as due to the existence of an accumulation zone near the South celestial pole. Some extra correlations between the reconstruction proposed and cultural data available are discussed. The paper is the second part of the investigation "On the Origin of the Zodiacal constellations" published in Vistas in Astronomy, vol.36, pp.171-190, 1993.

Creative Change: Art, Music, and Climate Science

NASA Astrophysics Data System (ADS)

Dahlberg, R. A.; Hoffman, J. S.; Maurakis, E. G.

2017-12-01

As part of ongoing climate science education initiatives, the Science Museum of Virginia hosted Creative Change in March 2017. The event featured multidisciplinary programming created by scientists, artists, and students reacting to and interpreting climate change and resiliency through a variety of artistic mediums and informal science education. Creative Change was developed in consideration of studies conducted at Columbia University that indicate traditional educational approaches, which rely heavily on scientific information and data literacy, fail to engage and inspire action in a majority of people. Our informal science education programming developed for Creative Change, by contrast, is inclusive to all ages and backgrounds, integrating scientific data and an artistic human touch. Our goal was to increase public awareness of climate change and resiliency through the humanities in support of the Museum's mission to inspire Virginians to enrich their lives through science. Visitors were invited to attend Coral Reef Fever, a dance performance of coral bleaching; high school and university art exhibitions; climate data performed by a string quartet; poetry, rap, and theater performances; and a panel discussion by artists and scientists on communicating science through the arts and humanities. Based on 26 post- event survey results, we found as a result that visitors enjoyed the event (mean of 9.58 out of 10), learned new information (9.07), and strongly agreed that the arts and humanities should be used more in communicating science concepts (9.77). Funded in part by Bond Bradley Endowment and NOAA ELG Award #NA15SEC0080009.

Measurement of intercolumnar forces between parallel guanosine four-stranded helices.

PubMed Central

Mariani, P; Saturni, L

1996-01-01

The deoxyguanosine-5'-monophosphate in aqueous solution self-associates into stable structures, which include hexagonal and cholesteric columnar phases. The structural unit is a four-stranded helix, composed of a stacked array of Hoogsteen-bonded guanosine quartets. We have measured by osmotic stress method the force per unit length versus interaxial distance between helices in the hexagonal phase under various ionic conditions. Two contributions have been recognized: the first one is purely electrostatic, is effective at large distances, and shows a strong dependence on the salt concentration of the solution. The second contribution is short range, dominates at interaxial separations smaller than about 30-32 A, and rises steeply as the columns approach each other, preventing the coalescence of the helices. This repulsion has an exponential nature and shows a magnitude and a decay length insensitive to the ionic strength of the medium. Because these features are distinctive of the hydration force detected between phospholipid bilayers or between several linear macromolecules (DNA, polysaccharides, collagen), we conclude that the dominant force experienced by deoxyguanosine helices approaching contact is hydration repulsion. The observed decay length of about 0.7 A has been rationalized to emerge from the coupling between the 3-A decay length of water solvent and the helically ordered structure of the hydrophilic groups on the opposing surfaces. The present results agree with recent measurements, also showing the dependence of the hydration force decay on the structure of interacting surfaces and confirm the correlations between force and structure. Images FIGURE 1 PMID:8744324

Structural, (197)Au Mössbauer and solid state (31)P CP/MAS NMR studies on bis (cis-bis(diphenylphosphino)ethylene) gold(I) complexes [Au(dppey)(2)]X for X = PF(6), I.

PubMed

Healy, Peter C; Loughrey, Bradley T; Bowmaker, Graham A; Hanna, John V

2008-07-28

(197)Au Mössbauer spectra for the d(10) gold(i) phosphine complexes, [Au(dppey)(2)]X (X = PF(6), I; dppey = (cis-bis(diphenylphosphino)ethylene), and the single crystal X-ray structure and solid state (31)P CPMAS NMR spectrum of [Au(dppey)(2)]I are reported here. In [Au(dppey)(2)]I the AuP(4) coordination geometry is distorted from the approximately D(2) symmetry observed for the PF(6)(-) complex with Au-P bond lengths 2.380(2)-2.426(2) A and inter-ligand P-Au-P angles 110.63(5)-137.71(8) degrees . Quadrupole splitting parameters derived from the Mössbauer spectra are consistent with the increased distortion of the AuP(4) coordination sphere with values of 1.22 and 1.46 mm s(-1) for the PF(6)(-) and I(-) complexes respectively. In the solid state (31)P CP MAS NMR spectrum of [Au(dppey)(2)]I, signals for each of the four crystallographically independent phosphorus nuclei are observed, with the magnitude of the (197)Au quadrupole coupling being sufficiently large to produce a collapse of (1)J(Au-P) splitting from quartets to doublets. The results highlight the important role played by the counter anion in the determination of the structural and spectroscopic properties of these sterically crowded d(10) complexes.

Numerical Investigation of Three-dimensional Instability of Standing Waves

NASA Astrophysics Data System (ADS)

Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.

2002-11-01

We study the three-dimensional instability of finite-amplitude standing waves under the influence of gravity using the transition matrix method. For accurate calculation of the transition matrices, we apply an efficient high-order spectral element method for nonlinear wave dynamics in complex domain. We consider two types of standing waves: (a) plane standing waves; and (b) standing waves in a circular tank. For the former, in addition to the confirmation of the side-band-like instability, we find a new three-dimensional instability for arbitrary base standing waves. The dominant component of the unstable disturbance is an oblique standing wave, with an arbitrary angle relative to the base flow, whose frequency is approximately equal to that of the base standing wave. Based on direct simulations, we confirm such a three-dimensional instability and show the occurrence of the Fermi-Pasta-Ulam recurrence phenomenon during nonlinear evolution. For the latter, we find that beyond a threshold wave steepness, the standing wave with frequency Ω becomes unstable to a small three-dimensional disturbance, which contains two dominant standing-wave components with frequencies ω1 and ω_2, provided that 2Ω ω1 + ω_2. The threshold wave steepness is found to decrease/increase as the radial/azimuthal wavenumber of the base standing wave increases. We show that the instability of standing waves in rectangular and circular tanks is caused by third-order quartet resonances between base flow and disturbance.

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

PubMed

Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

2016-04-12

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

The DUNDRUM Quartet: validation of structured professional judgement instruments DUNDRUM-3 assessment of programme completion and DUNDRUM-4 assessment of recovery in forensic mental health services

PubMed Central

2011-01-01

Background Moving a forensic mental health patient from one level of therapeutic security to a lower level or to the community is influenced by more than risk assessment and risk management. We set out to construct and validate structured professional judgement instruments for consistency and transparency in decision making Methods Two instruments were developed, the seven-item DUNDRUM-3 programme completion instrument and the six item DUNDRUM-4 recovery instrument. These were assessed for all 95 forensic patients at Ireland's only forensic mental health hospital. Results The two instruments had good internal consistency (Cronbach's alpha 0.911 and 0.887). Scores distinguished those allowed no leave or accompanied leave from those with unaccompanied leave (ANOVA F = 38.1 and 50.3 respectively, p < 0.001). Scores also distinguished those in acute/high security units from those in medium or in low secure/pre-discharge units. Each individual item distinguished these levels of need significantly. The DUNDRUM-3 and DUNDRUM-4 correlated moderately with measures of dynamic risk and with the CANFOR staff rated unmet need (Spearman r = 0.5, p < 0.001). Conclusions The DUNDRUM-3 programme completion items distinguished significantly between levels of therapeutic security while the DUNDRUM-4 recovery items consistently distinguished those given unaccompanied leave outside the hospital and those in the lowest levels of therapeutic security. This data forms the basis for a prospective study of outcomes now underway. PMID:21722396

Radiological characteristics of the knee joint in nail patella syndrome.

PubMed

Tigchelaar, S; Rooy, J de; Hannink, G; Koëter, S; van Kampen, A; Bongers, E

2016-04-01

Nail patella syndrome (NPS) is a skeletal dysplasia with patellofemoral dysfunction as a key symptom. We present the first in-depth radiological evaluation of the knee in a large series of NPS patients and describe the typical malformations. Conventional radiological examination of 95 skeletally mature patients with NPS was performed. Patellar morphology was classified according to the Wiberg classification as modified by Baumgartl and Ficat criteria, and trochlear shape was classified according to the Dejour classification. Patellar aplasia was present in 4/90 (4%), and patellar hypoplasia in 77/90 (86%) of patients. The prevailing patellar shapes were type III, type IV and Hunter's cap. No patellar shape genotype-phenotype association could be found. The malformations of the distal femur comprised shortening of the lateral femoral condyle in 46 out of 84 patients (55%), with a prominent anterior surface of the lateral femoral condyle in 47 out of 84 patients (56%) and a flat anterior surface of the medial femoral condyle in 78 out of 85 patients (92%). The trochlea was type A1 according to the Dejour classification in 79 out of 85 patients (93%). An easily recognisable characteristic quartet of malformations consisting of patellar aplasiaor hypoplasia and the malformations of the distal femur was found in 22 out of 81 patients (27%), with the majority displaying at least three malformations. The distinct malformations of the knee in nail patella syndrome are easily recognisable on conventional radiographs and lead to the correct interpretation of the aberrant morphology which is essential in the treatment of these patellofemoral disorders. ©2016 The British Editorial Society of Bone & Joint Surgery.

Direct experimental observation of the molecular J eff = 3/2 ground state in the lacunar spinel GaTa4Se8.

PubMed

Jeong, Min Yong; Chang, Seo Hyoung; Kim, Beom Hyun; Sim, Jae-Hoon; Said, Ayman; Casa, Diego; Gog, Thomas; Janod, Etienne; Cario, Laurent; Yunoki, Seiji; Han, Myung Joon; Kim, Jungho

2017-10-04

Strong spin-orbit coupling lifts the degeneracy of t 2g orbitals in 5d transition-metal systems, leaving a Kramers doublet and quartet with effective angular momentum of J eff  = 1/2 and 3/2, respectively. These spin-orbit entangled states can host exotic quantum phases such as topological Mott state, unconventional superconductivity, and quantum spin liquid. The lacunar spinel GaTa 4 Se 8 was theoretically predicted to form the molecular J eff  = 3/2 ground state. Experimental verification of its existence is an important first step to exploring the consequences of the J eff  = 3/2 state. Here, we report direct experimental evidence of the J eff  = 3/2 state in GaTa 4 Se 8 by means of excitation spectra of resonant inelastic X-ray scattering at the Ta L 3 and L 2 edges. We find that the excitations involving the J eff  = 1/2 molecular orbital are absent only at the Ta L 2 edge, manifesting the realization of the molecular J eff  = 3/2 ground state in GaTa 4 Se 8 .The strong interaction between electron spin and orbital degrees of freedom in 5d oxides can lead to exotic electronic ground states. Here the authors use resonant inelastic X-ray scattering to demonstrate that the theoretically proposed J eff  = 3/2 state is realised in GaTa 4 Se 8 .

Imino-Oxy Acetic Acid Dealkylation as Evidence for an Inner-Sphere Alcohol Intermediate in the Reaction Catalyzed by Peptidylglycine α-Hydroxylating Monooxygenase (PHM)

PubMed Central

McIntyre, Neil R.; Lowe, Edward W.; Merkler, David J.

2009-01-01

Peptidylglycine α-hydroxylating monooxygenase (PHM, EC 1.14.17.3) catalyzes the stereospecific hydroxylation of a glycyl α-carbon in a reaction that requires O2 and ascorbate. Subsequent dealkylation of the α-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC 4.3.2.5), yields a bioactive amide and glyoxylate. PHM is a non-coupled, type II dicopper monooxygenase which activates O2 at only a single copper atom, CuM. In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The D(V/K)APPARENT, BIAA decreased from 14.7 ± 1.0 as [O2] → 0 to 1.0 ± 0.2 as [O2] → ∞ suggesting the dissociation rate constant from the PHM·BIAA complex decreases as [O2] increases; thereby, reducing the steady-state concentration of [PHM]free. BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked CuII-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA.

PubMed

Lopez, Christopher R; Singh, Shivani; Hambarde, Shashank; Griffin, Wezley C; Gao, Jun; Chib, Shubeena; Yu, Yang; Ira, Grzegorz; Raney, Kevin D; Kim, Nayun

2017-06-02

G-quadruplex or G4 DNA is a non-B secondary DNA structure consisting of a stacked array of guanine-quartets that can disrupt critical cellular functions such as replication and transcription. When sequences that can adopt Non-B structures including G4 DNA are located within actively transcribed genes, the reshaping of DNA topology necessary for transcription process stimulates secondary structure-formation thereby amplifying the potential for genome instability. Using a reporter assay designed to study G4-induced recombination in the context of an actively transcribed locus in Saccharomyces cerevisiae, we tested whether co-transcriptional activator Sub1, recently identified as a G4-binding factor, contributes to genome maintenance at G4-forming sequences. Our data indicate that, upon Sub1-disruption, genome instability linked to co-transcriptionally formed G4 DNA in Top1-deficient cells is significantly augmented and that its highly conserved DNA binding domain or the human homolog PC4 is sufficient to suppress G4-associated genome instability. We also show that Sub1 interacts specifically with co-transcriptionally formed G4 DNA in vivo and that yeast cells become highly sensitivity to G4-stabilizing chemical ligands by the loss of Sub1. Finally, we demonstrate the physical and genetic interaction of Sub1 with the G4-resolving helicase Pif1, suggesting a possible mechanism by which Sub1 suppresses instability at G4 DNA. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Developmental diversity in free-living flatworms

PubMed Central

2012-01-01

Flatworm embryology has attracted attention since the early beginnings of comparative evolutionary biology. Considered for a long time the most basal bilaterians, the Platyhelminthes (excluding Acoelomorpha) are now robustly placed within the Spiralia. Despite having lost their relevance to explain the transition from radially to bilaterally symmetrical animals, the study of flatworm embryology is still of great importance to understand the diversification of bilaterians and of developmental mechanisms. Flatworms are acoelomate organisms generally with a simple centralized nervous system, a blind gut, and lacking a circulatory organ, a skeleton and a respiratory system other than the epidermis. Regeneration and asexual reproduction, based on a totipotent neoblast stem cell system, are broadly present among different groups of flatworms. While some more basally branching groups - such as polyclad flatworms - retain the ancestral quartet spiral cleavage pattern, most flatworms have significantly diverged from this pattern and exhibit unique strategies to specify the common adult body plan. Most free-living flatworms (i.e. Platyhelminthes excluding the parasitic Neodermata) are directly developing, whereas in polyclads, also indirect developers with an intermediate free-living larval stage and subsequent metamorphosis are found. A comparative study of developmental diversity may help understanding major questions in evolutionary biology, such as the evolution of cleavage patterns, gastrulation and axial specification, the evolution of larval types, and the diversification and specialization of organ systems. In this review, we present a thorough overview of the embryonic development of the different groups of free-living (turbellarian) platyhelminths, including the Catenulida, Macrostomorpha, Polycladida, Lecithoepitheliata, Proseriata, Bothrioplanida, Rhabdocoela, Fecampiida, Prolecithophora and Tricladida, and discuss their main features under a consensus phylogeny of the phylum. PMID:22429930

A new method to solve the Nd breakup scattering problem in configuration space

NASA Astrophysics Data System (ADS)

Suslov, Vladimir

2005-11-01

A new computational method for solving the configuration-space Faddeev equations for three nucleon system has been developed. This method is based on the spline-decomposition in the angular variable and a generalization of the Numerov method for the hyperradius. The s-wave calculations of the inelasticity and phase-shift, as well as breakup amplitudes for nd and pd breakup scattering for lab energies 14.1 and 42.0 MeV were performed with the Malfliet -Tjon MT I-III potential. In the case of nd breakup scattering the results are in good agreement with those of the benchmark solution [1],[2]. In the case of pd quartet breakup scattering disagreement for the inelasticities reaches up to 6% as compared with those of the Pisa group [3]. The calculated pd amplitudes fulfill the optical theorem with a good precision. 1. J. L. Friar, B. F. Gibson, G. Berthold, W. Gloeckle, Th. Cornelius, H. Witala, J. Haidenbauer, Y. Koike, G. L. Payne, J. A. Tjon, and W. M. Kloet,: http://link.aip.org/link/?&lcreator=getabs-normal&ldir=FWD&lrel=CITES&fromkey=PRVCAN000069000004044003000001&fromkeyType=CVIPS&fromloc=AIP&toj=PRVCAN&tov=42&top=1838&toloc=APS&tourl=http%3A%2F%2Flink.aps.org%2Fabstract%2FPRC%2Fv42%2FPhys. Rev. C 42, 1838 (1990). 2. Frair J.L, Payne G.L., Gl"ockle W., Hueber D., Witala H.: Phys. Rev. C 51, 2356 (1995) 3. Kievsky A., Viviani M., and Rosati S.: Phys. Rev. C 64, 024002 (2001)

Synthesis, characterization and reactivity of trinuclear Cu(II) complexes derived from disalicylaldehyde malonoyldihydrazone

NASA Astrophysics Data System (ADS)

Koch, Angira; Kumar, Arvind; De, Arjun K.; Phukan, Arnab; Lal, Ram A.

2014-08-01

Three new homotrinuclear copper(II) complexes [Cu3(slmh)(μ-Cl)2(CH3OH)3]ṡ0.5CH3OH (1), [Cu3(slmh)(NO3)2(CH3OH)5]ṡ1.5CH3OH (2) and [Cu3(slmh)(μ-ClO4)2(CH3OH)3]ṡ2CH3OH (3) from disalicylaldehyde malonoyldihydrazone have been synthesized and characterized. The composition of the complexes has been established on the basis of data obtained from analytical and thermoanalytical data. The structure of the complexes has been discussed in the light of molar conductance, electronic, FT-IR and far-IR spectral data, magnetic moment and EPR spectral studies. The molar conductance values for the complexes in DMSO solution indicate that all of them are non-electrolyte. The magnetic moment values for the complexes suggest considerable metal-metal intramolecular interaction between metal ions in the structural unit of the complexes. The EPR spectral features reveal that at RT, the ground state for the complexes is a mixture of the quartet state (S = 3/2) and doublet state (S = ½). At lower temperature, the ground state for the complexes is dx2-y2 with considerable contribution from dz2 orbital. Dihydrazone ligand is present in enol form in all of the complexes. The complexes have distorted square pyramidal stereochemistry. The electron transfer reactions of the complexes have been investigated by cyclic voltammetry. Hydrogen peroxide mediated oxidation of benzyl alcohol catalyzed by complex 1 has been studied.

Ferromagnetic coupling by spin polarization in a trinuclear copper(II) metallacyclophane with a triangular cage-like structure.

PubMed

Dul, Marie-Claire; Ottenwaelder, Xavier; Pardo, Emilio; Lescouëzec, Rodrigue; Journaux, Yves; Chamoreau, Lise-Marie; Ruiz-García, Rafael; Cano, Joan; Julve, Miguel; Lloret, Francesc

2009-06-15

A series of trinuclear copper(II) complexes of general formula A(6)[Cu(3)L(2)] x nH(2)O [L = benzene-1,3,5-tris(oxamate); A = Li(+) (n = 8), 1a; Na(+) (n = 11.5), 1b; and K(+) (n = 8.5), 1c] have been synthesized, and they have been structurally and magnetically characterized. X-ray diffraction on single crystals of 1c shows the presence of three square-planar copper(II)-bis(oxamato) moieties which are connected by a double benzene-1,3,5-triyl skeleton to give a unique metallacyclophane-type triangular cage. The copper basal planes are virtually orthogonal to the two benzene rings, which adopt an almost perfect face-to-face alignment. Complexes 1a-c exhibit a quartet (S = 3/2) ground spin state resulting from the moderate ferromagnetic coupling (J values in the range of +7.3 to +16.5 cm(-1)) between the three Cu(II) ions across the two benzene-1,3,5-tris(amidate) bridges [H = -J(S(1) x S(2) + S(2) x S(3) + S(3) x S(1)) with S(1) = S(2) = S(3) = S(Cu) = 1/2]. Density functional theory calculations on the S = 3/2 Cu(II)(3) ground spin state of 1c support the occurrence of a spin polarization mechanism for the propagation of the exchange interaction, as evidenced by the sign alternation of the spin density in the 1,3,5-substituted benzene spacers.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing.

PubMed

Martin, Hilary C; Batty, Elizabeth M; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

2018-05-01

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing

PubMed Central

Martin, Hilary C; Hussin, Julie; Westall, Portia; Daish, Tasman; Kolomyjec, Stephen; Piazza, Paolo; Bowden, Rory; Hawkins, Margaret; Grant, Tom; Moritz, Craig; Grutzner, Frank; Gongora, Jaime; Donnelly, Peter

2018-01-01

Abstract The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10−9/bp/generation (95% CI 4.1 × 10−9–1.2 × 10−8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species. PMID:29688544

Metabolic syndrome in type 2 diabetes: comparison of WHO, modified ATPIII & IDF criteria.

PubMed

Ahmed, Asma; Khan, Talha Ehsan; Yasmeen, Tahira; Awan, Safia; Islam, Najmul

2012-06-01

To determine the frequency of metabolic syndrome in type 2 diabetes according to three commonly used operational definitions {World Health Organization (WHO), National Cholesterol Education Program Adult Treatment Panel (NCEP ATP III) and International Diabetes Federation( IDF)}. To evaluate the agreement between these classifications in the Pakistani cohort. Data was collected retrospectively of 210 patients with type 2 diabetes visiting outpatient clinics of one of the large tertiary care hospitals at Karachi, Pakistan between June 2008 to November 2008. The prevalence of metabolic syndrome was found to be 81.4% (WHO), 86.7 % (IDF) and 91.9 % (NCEP ATPIII). The degree of agreement (kappa statistic) was found to be highest among IDF & NCEP ATPIII (0.728) as compared to (0.436 & 0.417) between WHO & ATP and WHO & IDF respectively. The most significant predictors for metabolic syndrome were found out to be female gender OR= 8.74 95% CI 1.51-50.53, low HDL cholesterol levels OR = 0.89 95% CI 0.84-0.94 and high systolic blood pressure OR= 1.06 95% CI 1.009-1.11. Our study results suggested that NCEP ATPIII and IDF are the most reliable criteria for diagnosing metabolic syndrome in type 2 diabetic patients, with NECP capturing more patients in comparison to IDF definition. The alarmingly high frequency of metabolic syndrome in type 2 diabetes found in this study suggests that primary prevention strategies should be initiated earlier and early in this ethnic group and our health care system should be geared up to cope with this deadly quartet.

The cell wall pectic polymer rhamnogalacturonan-II is required for proper pollen tube elongation: implications of a putative sialyltransferase-like protein.

PubMed

Dumont, Marie; Lehner, Arnaud; Bouton, Sophie; Kiefer-Meyer, Marie Christine; Voxeur, Aline; Pelloux, Jérôme; Lerouge, Patrice; Mollet, Jean-Claude

2014-10-01

Rhamnogalacturonan-II (RG-II) is one of the pectin motifs found in the cell wall of all land plants. It contains sugars such as 2-keto-3-deoxy-d-lyxo-heptulosaric acid (Dha) and 2-keto-3-deoxy-d-manno-octulosonic acid (Kdo), and within the wall RG-II is mostly found as a dimer via a borate diester cross-link. To date, little is known regarding the biosynthesis of this motif. Here, after a brief review of our current knowledge on RG-II structure, biosynthesis and function in plants, this study explores the implications of the presence of a Golgi-localized sialyltransferase-like 2 (SIA2) protein that is possibly involved in the transfer of Dha or Kdo in the RG-II of Arabidopsis thaliana pollen tubes, a fast-growing cell type used as a model for the study of cell elongation. Two heterozygous mutant lines of arabidopsis (sia2-1+/- and qrt1 × sia2-2+/-) were investigated. sia2-2+/- was in a quartet1 background and the inserted T-DNA contained the reporter gene β-glucuronidase (GUS) under the pollen-specific promoter LAT52. Pollen germination and pollen tube phenotype and growth were analysed both in vitro and in vivo by microscopy. Self-pollination of heterozygous lines produced no homozygous plants in the progeny, which may suggest that the mutation could be lethal. Heterozygous mutants displayed a much lower germination rate overall and exhibited a substantial delay in germination (20 h of delay to reach 30 % of pollen grain germination compared with the wild type). In both lines, mutant pollen grains that were able to produce a tube had tubes that were either bursting, abnormal (swollen or dichotomous branching tip) or much shorter compared with wild-type pollen tubes. In vivo, mutant pollen tubes were restricted to the style, whereas the wild-type pollen tubes were detected at the base of the ovary. This study highlights that the mutation in arabidopsis SIA2 encoding a sialyltransferase-like protein that may transfer Dha or Kdo on the RG-II motif has a dramatic effect on the stability of the pollen tube cell wall. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Electronic structure calculation of single and coupled self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Mlinar, Vladan

There are two main contributions of this thesis. First, from the theoretical point of view, we find that different treatments of the nanostructure-barrier interface in the framework of multiband effective-mass theory, result in the existence of non-physical solutions for the hole energy levels of a nanostructure. Our proposed improvement is an approach based on the envelope-function theory for nanostructures developed by Burt and Foreman. In structures with a large difference of the structural parameters between the constituent materials, such as InAs/GaAs quantum nanostructures, the conventional multiband models lead to non-physical solutions. Second, we investigate underlying physics of the theoretically less investigated QD systems. Variation of electronic and optical properties of InAs/GaAs QDs and QDM grown on [11k] substrates, where k=1,2,3 were analyzed and we found that: (i) The QD size in the growth direction determines the degree of influence of the substrate orientation: the flatter the dots, the larger the difference from the reference [001] case. (ii) The small variation of inter-dot distance in eight QD molecule qualitatively changes the transition energy dependence on the substrate orientation. (iii) Size of the QD in the growth direction determines the influence of the (In,Ga)As capping layer on the optical properties of [11k] grown InAs QDs, where k=1,2,3. Next, two cases of type II QDs where hole is localized outside the dot, were discussed: InP/InGaP QDs and QDMs in an external magnetic field, and InAs QDs capped with Ga(As,Sb). Competition between confinement, quantum mechanical coupling, and strain influence the exciton diamagnetic shift in single QD and double and triple QDM is investigated in details. Available experimental data were successfully described by one of the optically active exciton states of the lowest lying exciton quartet. Finally, the electronic and optical properties of unstrained GaAs self-assembled QDs with precisely known sizes and shape, placed in an external magnetic field are investigated. For magnetic fields applied both, in growth direction and perpendicular to it (B≤50T), we found good agreement between our predicted exciton diamagnetic shift and recent experimental magneto-photoluminescence data.

Contribution of non-resonant wave-wave interactions in the dynamics of long-crested sea wave fields

NASA Astrophysics Data System (ADS)

Benoit, Michel

2017-04-01

Gravity waves fields at the surface of the oceans evolve under the combined effects of several physical mechanisms, of which nonlinear wave-wave interactions play a dominant role. These interactions transfer energy between components within the energy spectrum and allow in particular to explain the shape of the distribution of wave energy according to the frequencies and directions of propagation. In the oceanic domain (deep water conditions), dominant interactions are third-order resonant interactions, between quadruplets (or quartets) of wave components, and the evolution of the wave spectrum is governed by a kinetic equation, established by Hasselmann (1962) and Zakharov (1968). The kinetic equation has a number of interesting properties, including the existence of self-similar solutions and cascades to small and large wavelengths of waves, which can be studied in the framework of the wave (or weak) turbulence theory (e.g. Badulin et al., 2005). With the aim to obtain more complete and precise modelling of sea states dynamics, we investigate here the possibility and consequences of taking into account the non-resonant interactions -quasi-resonant in practice- among 4 waves. A mathematical formalism has recently been proposed to account for these non-resonant interactions in a statistical framework by Annenkov & Shrira (2006) (Generalized Kinetic Equation, GKE) and Gramstad & Stiassnie (2013) (Phase Averaged Equation, PAE). In order to isolate the non-resonant contributions, we limit ourselves here to monodirectional (i.e. long-crested) wave trains, since in this case the 4-wave resonant interactions vanish. The (stochastic) modelling approaches proposed by Annenkov & Shrira (2006) and Gramstad & Stiassnie (2013) are compared to phase-resolving (deterministic) simulations based on a fully nonlinear potential approach (using a high-order spectral method, HOS). We study and compare the evolution dynamics of the wave spectrum at different time scales (i.e. over durations ranging from a few wave periods to 1000 periods), with the aim of highlighting the capabilities and limitations of the GKE-PAE models. Different situations are considered by varying the relative water depth, the initial steepness of the wave field, and the shape of the initial wave spectrum, including arbitrary forms. References: Annenkov S.Y., Shrira V.I. (2006) Role of non-resonant interactions in the evolution of nonlinear random water wave fields. J. Fluid Mech., 561, 181-207. Badulin S.I., Pushkarev A.N., Resio D., Zakharov V.E. (2005) Self-similarity of wind-driven seas. Nonlin. Proc. Geophys., 12, 891-946. Gramstad O., Stiassnie M. (2013) Phase-averaged equation for water waves. J. Fluid Mech., 718, 280- 303. Hasselmann K. (1962) On the non-linear energy transfer in a gravity-wave spectrum. Part 1. General theory. J. Fluid Mech., 12, 481-500. Zakharov V.E. (1968) Stability of periodic waves of finite amplitude on the surface of a deep fluid. J. App. Mech. Tech. Phys., 9(2), 190-194.

Combined experimental and theoretical study on the reactivity of compounds I and II in horseradish peroxidase biomimetics.

PubMed

Ji, Li; Franke, Alicja; Brindell, Małgorzata; Oszajca, Maria; Zahl, Achim; van Eldik, Rudi

2014-10-27

For the exploration of the intrinsic reactivity of two key active species in the catalytic cycle of horseradish peroxidase (HRP), Compound I (HRP-I) and Compound II (HRP-II), we generated in situ [Fe(IV) O(TMP(+.) )(2-MeIm)](+) and [Fe(IV) O(TMP)(2-MeIm)](0) (TMP=5,10,15,20-tetramesitylporphyrin; 2-MeIm=2-methylimidazole) as biomimetics for HRP-I and HRP-II, respectively. Their catalytic activities in epoxidation, hydrogen abstraction, and heteroatom oxidation reactions were studied in acetonitrile at -15 °C by utilizing rapid-scan UV/Vis spectroscopy. Comparison of the second-order rate constants measured for the direct reactions of the HRP-I and HRP-II mimics with the selected substrates clearly confirmed the outstanding oxidizing capability of the HRP-I mimic, which is significantly higher than that of HRP-II. The experimental study was supported by computational modeling (DFT calculations) of the oxidation mechanism of the selected substrates with the involvement of quartet and doublet HRP-I mimics ((2,4) Cpd I) and the closed-shell triplet spin HRP-II model ((3) Cpd II) as oxidizing species. The significantly lower activation barriers calculated for the oxidation systems involving (2,4) Cpd I than those found for (3) Cpd II are in line with the much higher oxidizing efficiency of the HRP-I mimic proven in the experimental part of the study. In addition, the DFT calculations show that all three reaction types catalyzed by HRP-I occur on the doublet spin surface in an effectively concerted manner, whereas these reactions may proceed in a stepwise mechanism with the HRP-II mimic as oxidant. However, the high desaturation or oxygen rebound barriers during CH bond activation processes by the HRP-II mimic predict a sufficient lifetime for the substrate radical formed through hydrogen abstraction. Thus, the theoretical calculations suggest that the dissociation of the substrate radical may be a more favorable pathway than desaturation or oxygen rebound processes. Importantly, depending on the electronic nature of the oxidizing species, that is, (2,4) Cpd I or (3) Cpd II, an interesting region-selective conversion phenomenon between sulfoxidation and H-atom abstraction was revealed in the course of the oxidation reaction of dimethylsulfide. The combined experimental and theoretical study on the elucidation of the intrinsic reactivity patterns of the HRP-I and HRP-II mimics provides a valuable tool for evaluating the particular role of the HRP active species in biological systems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetics, mechanism, and spectroscopy of the reversible binding of nitric oxide to aquated iron(II). An undergraduate text book reaction revisited.

PubMed

Wanat, Alicja; Schneppensieper, Thorsten; Stochel, Grazyna; van Eldik, Rudi; Bill, Eckhard; Wieghardt, Karl

2002-01-14

A detailed kinetic and mechanistic analysis of the classical "brown-ring" reaction of [Fe(H(2)O)(6)](2+) with NO was performed using stopped-flow and laser flash photolysis techniques at ambient and high pressure. The kinetic parameters for the "on" and "off" reactions at 25 degrees C were found to be k(on) = 1.42 x 10(6) M(-1) s(-1), DeltaH(++)(on) = 37.1 +/- 0.5 kJ mol(-1), DeltaS(++)(on) = -3 +/- 2 J K(-1) mol(-1), DeltaV(++)(on) = +6.1 +/- 0.4 cm(3) mol(-1), and k(off) = 3240 +/- 750 s(-1), DeltaH(++)(off) = 48.4 +/- 1.4 kJ mol(-1), DeltaS(++)(off) = -15 +/- 5 J K(-1) mol(-1), DeltaV(++)(off) = +1.3 +/- 0.2 cm(3) mol(-1). These parameters suggest that both reactions follow an interchange dissociative (I(d)) ligand substitution mechanism, which correlates well with the suggested mechanism for the water exchange reaction on [Fe(H(2)O)(6)](2+). In addition, Mössbauer spectroscopy and EPR measurements were performed on the reaction product [Fe(H(2)O)(5)(NO)](2+). The Mössbauer and EPR parameters closely resemble those of the [FeNO](7) units in any of the other well-characterized nitrosyl complexes. It is concluded that its electronic structure is best described by the presence of high-spin Fe(III) antiferromagnetically coupled to NO(-) (S = 1) yielding the observed spin quartet ground state (S = (3)/(2)), i.e., [Fe(III)(H(2)O)(5)(NO(-))](2+), and not [Fe(I)(H(2)O)(5)(NO(+))](2+) as usually quoted in undergraduate text books.

STAT3 and importins are novel mediators of early molecular and cellular responses in experimental duodenal ulceration.

PubMed

Khomenko, Tetyana; Deng, Xiaoming; Ahluwalia, Amrita; Tarnawski, Andrzej; Patel, Khushin N; Sandor, Zsuzsanna; Szabo, Sandor

2014-02-01

Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that directly upregulates VEGF, Ref-1, p21, and anti-apoptotic genes such as Bcl-xL. In this study, we hypothesized that STAT3 signaling is activated and provides a critical protective role that is required for enterocyte survival during the early phases of cysteamine-induced duodenal ulcers. We studied the effect of inhibition of STAT3 activity on cysteamine-induced duodenal ulcers in rats and egr-1 knockout mice using STAT3/DNA binding assay, immunohistochemistry, immunoblot, and quantitative reverse transcriptase PCR analyses. We found that G-quartet oligodeoxynucleotides T40214, a specific inhibitor of STAT3/DNA binding, aggravated cysteamine-induced duodenal ulcers in rats 2.8-fold (p < 0.05). In the pre-ulcerogenic stage, cysteamine induced STAT3 tyrosine phosphorylation, its translocation to nuclei, an increased expression and nuclear translocation of importin α and β in the rat duodenal mucosa. Cysteamine enhanced the binding of STAT3 to its DNA consensus sequences at 6, 12, and 24 h after cysteamine by 1.5-, 1.8-, and 3.5-fold, respectively, and activated the expression of STAT3 target genes such as VEGF, Bcl-xL, Ref-1, and STAT3-induced feedback inhibitor, a suppressor of cytokine signaling 3. We also demonstrated that egr-1 knockout mice, which are more susceptible to cysteamine-induced duodenal ulcers, had lower levels of STAT3 expression, its phosphorylation, expression of importin α or β, and STAT3/DNA binding than wild-type mice in response to cysteamine. Thus, STAT3 represents an important new molecular mechanism in experimental duodenal ulceration.

High-precision measurement of the electron spin g factor of trapped atomic nitrogen in the endohedral fullerene N@C60

NASA Astrophysics Data System (ADS)

Wittmann, J. J.; Can, T. V.; Eckardt, M.; Harneit, W.; Griffin, R. G.; Corzilius, B.

2018-05-01

The electronic g factor carries highly useful information about the electronic structure of a paramagnetic species, such as spin-orbit coupling and dia- or paramagnetic (de-)shielding due to local fields of surrounding electron pairs. However, in many cases, a near "spin-only" case is observed, in particular for light elements, necessitating accurate and precise measurement of the g factors. Such measurement is typically impeded by a "chicken and egg situation": internal or external reference standards are used for relative comparison of electron paramagnetic resonance (EPR) Larmor frequencies. However, the g factor of the standard itself usually is subject to a significant uncertainty which directly limits the precision and/or accuracy of the sought after sample g factor. Here, we apply an EPR reference-free approach for determining the g factor of atomic nitrogen trapped within the endohedral fullerene C60:N@C60 in its polycrystalline state by measuring the 1H NMR resonance frequency of dispersing toluene at room temperature. We found a value of g = 2.00204 (4) with a finally reached relative precision of ∼20 ppm. This accurate measurement allows us to directly compare the electronic properties of N@C60 to those found in atomic nitrogen in the gas phase or trapped in other solid matrices at liquid helium temperature. We conclude that spin-orbit coupling in N@C60 at room temperature is very similar in magnitude and of same sign as found in other inert solid matrices and that interactions between the quartet spin system and the C60 molecular orbitals are thus negligible.

Developing a Standard Definition of Whole-Grain Foods for Dietary Recommendations: Summary Report of a Multidisciplinary Expert Roundtable Discussion12

PubMed Central

Ferruzzi, Mario G.; Jonnalagadda, Satya S.; Liu, Simin; Marquart, Len; McKeown, Nicola; Reicks, Marla; Riccardi, Gabriele; Seal, Chris; Slavin, Joanne; Thielecke, Frank; van der Kamp, Jan-Willem; Webb, Densie

2014-01-01

Although the term “whole grain” is well defined, there has been no universal standard of what constitutes a “whole-grain food,” creating challenges for researchers, the food industry, regulatory authorities, and consumers around the world. As part of the 2010 Dietary Guidelines for Americans, the U.S. Dietary Guidelines Technical Advisory Committee issued a call to action to develop definitions for whole-grain foods that could be universally accepted and applied to dietary recommendations and planning. The Committee’s call to action, and the lack of a global whole-grain food definition, was the impetus for the Whole Grain Roundtable held 3–5 December 2012 in Chicago, Illinois. The objective was to develop a whole-grain food definition that is consistent with the quartet of needs of science, food product formulation, consumer behavior, and label education. The roundtable’s expert panel represented a broad range of expertise from the United States and Europe, including epidemiology and dietary intervention researchers, consumer educators, government policy makers, and food and nutrition scientists from academia and the grain food industry. Taking into account the totality, quality, and consistency of available scientific evidence, the expert panel recommended that 8 g of whole grain/30 g serving (27 g/100 g), without a fiber requirement, be considered a minimum content of whole grains that is nutritionally meaningful and that a food providing at least 8 g of whole grains/30-g serving be defined as a whole-grain food. Having an established whole-grain food definition will encourage manufacturers to produce foods with meaningful amounts of whole grain, allow consistent product labeling and messaging, and empower consumers to readily identify whole-grain foods and achieve whole-grain dietary recommendations. PMID:24618757

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

PubMed Central

Stefl, R; Spacková, N; Berger, I; Koca, J; Sponer, J

2001-01-01

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonstandard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 6-thiopurine (tI) has been investigated using large-scale molecular dynamics simulations. The simulations suggest that a G-DNA stem can incorporate inosines without any marked effect on its structure and dynamics. The all-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties as d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies being stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show dramatic differences in the behavior of d(GGGG)(4) and d(IIII)(4). Whereas vacant d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(IIII)(4) is completely disrupted within the first nanosecond. This is a consequence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruplex could involve entirely different intermediate structures than formation of the guanosine quadruplex, and early association of cations in this process appears to be inevitable. In the simulations, the incorporation of 6-thioguanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structures, in close agreement with experimental data. The main reason is the size of the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accommodate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses. PMID:11159416

Laser photoelectron spectroscopy of MnH - and FeH - : Electronic structures of the metal hydrides, identification of a low-spin excited state of MnH, and evidence for a low-spin ground state of FeH

NASA Astrophysics Data System (ADS)

Stevens, Amy E.; Feigerle, C. S.; Lineberger, W. C.

1983-05-01

The laser photoelectron spectra of MnH- and MnD-, and FeH- and FeD- are reported. A qualitative description of the electronic structure of the low-spin and high-spin states of the metal hydrides is developed, and used to interpret the spectra. A diagonal transition in the photodetachment to the known high-spin, 7Σ+, ground state of MnH is observed. An intense off-diagonal transition to a state of MnH, at 1725±50 cm-1 excitation energy, is attributed to loss of an antibonding electron from MnH-, to yield a low-spin quintet state of MnH. For FeH- the photodetachment to the ground state is an off-diagonal transition, attributed to loss of the antibonding electron from FeH-, to yield a low-spin quartet ground state of FeH. A diagonal transition results in an FeH state at 1945±55 cm-1; this state of FeH is assigned as the lowest-lying high-spin sextet state of FeH. An additional excited state of MnH and two other excited states of FeH are observed. Excitation energies for all the states are reported; vibrational frequencies and bond lengths for the ions and several states of the neutrals are also determined from the spectra. The electron affinity of MnH is found to be 0.869±0.010 eV; and the electron affinity of FeH is determined to be 0.934±0.011 eV. Spectroscopic constants for the various deuterides are also reported.

Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.

PubMed

Martin, Guiomar; Soy, Judit; Monte, Elena

2016-01-01

Members of the PIF quartet (PIFq; PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. However, a comprehensive definition of the PIFq-regulated transcriptome under SD is still lacking. We have recently shown that SD and free-running (LL) conditions correspond to "growth" and "no growth" conditions, respectively, correlating with greater abundance of PIF protein in SD. Here, we present a genomic analysis whereby we first define SD-regulated genes at dawn compared to LL in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, we have identified 349 PIF/SD-regulated genes, approximately 55% induced and 42% repressed by both SD and PIFq. Comparison with available databases indicates that PIF/SD-induced and PIF/SD-repressed sets are differently phased at dawn and mid-morning, respectively. In addition, we found that whereas rhythmicity of the PIF/SD-induced gene set is lost in LL, most PIF/SD-repressed genes keep their rhythmicity in LL, suggesting differential regulation of both gene sets by the circadian clock. Moreover, we also uncovered distinct overrepresented functions in the induced and repressed gene sets, in accord with previous studies in other examined PIF-regulated processes. Interestingly, promoter analyses showed that, whereas PIF/SD-induced genes are enriched in direct PIF targets, PIF/SD-repressed genes are mostly indirectly regulated by the PIFs and might be more enriched in ABA-regulated genes.

G-Quadruplex DNA Motifs in the Malaria Parasite Plasmodium falciparum and Their Potential as Novel Antimalarial Drug Targets.

PubMed

Harris, Lynne M; Monsell, Katelyn R; Noulin, Florian; Famodimu, M Toyin; Smargiasso, Nicolas; Damblon, Christian; Horrocks, Paul; Merrick, Catherine J

2018-03-01

G-quadruplexes are DNA or RNA secondary structures that can be formed from guanine-rich nucleic acids. These four-stranded structures, composed of stacked quartets of guanine bases, can be highly stable and have been demonstrated to occur in vivo in the DNA of human cells and other systems, where they play important biological roles, influencing processes such as telomere maintenance, DNA replication and transcription, or, in the case of RNA G-quadruplexes, RNA translation and processing. We report for the first time that DNA G-quadruplexes can be detected in the nuclei of the malaria parasite Plasmodium falciparum , which has one of the most A/T-biased genomes sequenced and therefore possesses few guanine-rich sequences with the potential to form G-quadruplexes. We show that despite this paucity of putative G-quadruplex-forming sequences, P. falciparum parasites are sensitive to several G-quadruplex-stabilizing drugs, including quarfloxin, which previously reached phase 2 clinical trials as an anticancer drug. Quarfloxin has a rapid initial rate of kill and is active against ring stages as well as replicative stages of intraerythrocytic development. We show that several G-quadruplex-stabilizing drugs, including quarfloxin, can suppress the transcription of a G-quadruplex-containing reporter gene in P. falciparum but that quarfloxin does not appear to disrupt the transcription of rRNAs, which was proposed as its mode of action in both human cells and trypanosomes. These data suggest that quarfloxin has potential for repositioning as an antimalarial with a novel mode of action. Furthermore, G-quadruplex biology in P. falciparum may present a target for development of other new antimalarial drugs. Copyright © 2018 American Society for Microbiology.

Map-based cloning and characterization of Zea mays male sterility33 (ZmMs33) gene, encoding a glycerol-3-phosphate acyltransferase.

PubMed

Xie, Ke; Wu, Suowei; Li, Ziwen; Zhou, Yan; Zhang, Danfeng; Dong, Zhenying; An, Xueli; Zhu, Taotao; Zhang, Simiao; Liu, Shuangshuang; Li, Jinping; Wan, Xiangyuan

2018-06-01

Map-based cloning of maize ms33 gene showed that ZmMs33 encodes a sn-2 glycerol-3-phosphate acyltransferase, the ortholog of rice OsGPAT3, and it is essential for male fertility in maize. Genetic male sterility has been widely studied for its biological significance and commercial value in hybrid seed production. Although many male-sterile mutants have been identified in maize (Zea mays L.), it is likely that most genes that cause male sterility are unknown. Here, we report a recessive genetic male-sterile mutant, male sterility33 (ms33), which displays small, pale yellow anthers, and complete male sterility. Using a map-based cloning approach, maize GRMZM2G070304 was identified as the ms33 gene (ZmMs33). ZmMs33 encodes a novel sn-2 glycerol-3-phosphate acyltransferase (GPAT) in maize. A functional complementation experiment showed that GRMZM2G070304 can rescue the male-sterile phenotype of the ms33-6029 mutant. GRMZM2G070304 was further confirmed to be the ms33 gene via targeted knockouts induced by the clustered regularly interspersed short palindromic repeats (CRISPR)/Cas9 system. ZmMs33 is preferentially expressed in the immature anther from the quartet to early-vacuolate microspore stages and in root tissues at the fifth leaf growth stage. Phylogenetic analysis indicated that ZmMs33 and OsGPAT3 are evolutionarily conserved for anther and pollen development in monocot species. This study reveals that the monocot-specific GPAT3 protein plays an important role in male fertility in maize, and ZmMs33 and mutants in this gene may have value in maize male-sterile line breeding and hybrid seed production.

Tracing the Origin of Radioactivity in Groundwater from the Negev, Israel

NASA Astrophysics Data System (ADS)

Vengosh, A.; Pery, N.; Paytan, A.; Haquin, G.; Enhanany, S.; Pankratov, I.

2004-12-01

In normal groundwater conditions natural radionuclides are typically retained on the aquifer matrix and their activity in the groundwater is low. Radium is exceptional since the ratio between adsorbed and dissolved radium depends the ionic strength of the solution. Under high salinity radium is rapidly desorbed and accumulates in the liquid phase. Here we report the results of a geochemical study that investigates the origin of radioactivity in brackish to saline groundwater from the Negev and Arava Valley, Israel. We use the Ra isotope quartet (226Ra-half life 1600 y, 228Ra - 5.6 y, 224Ra - 3.6 d, 223Ra - 11.4 d) to discriminate between radioactivity derived from a thorium source (high 228Ra/226Ra and 224Ra/223Ra ratios) found in groundwater flowing in the Nubian Sandstone aquifer and an uranium source (low 228Ra/226Ra and 224Ra/223Ra ratios) in groundwater flowing in carbonate (Upper Cretaceous) aquifer. We show that the activity of 226Ra in groundwater from the carbonate aquifer is positively correlated with that of the salinity. In the Nubian Sandstone aquifer, however, no such correlation was found. Instead, we observed an inverse correlation between 228Ra activity and sulfate and a positive correlation with barium contents. Given the high H2S content of the ground water, we hypothesized that sulfate reduction process triggers radium leaching to the water, probably due to barite dissolution and anoxic conditions in the aquifer. These findings indicate that high radioactivity can also be found even in low-saline groundwater and that the isotopic ratios of radium are sensitive tracers for the water-rock interactions and thus reconstructing the flow paths in different aquifer matrix (i.e., carbonate versus sandstone).

Evidence for Widespread Reticulate Evolution within Human Duplicons

PubMed Central

Jackson, Michael S. ; Oliver, Karen ; Loveland, Jane ; Humphray, Sean ; Dunham, Ian ; Rocchi, Mariano ; Viggiano, Luigi ; Park, Jonathan P. ; Hurles, Matthew E. ; Santibanez-Koref, Mauro 

2005-01-01

Approximately 5% of the human genome consists of segmental duplications that can cause genomic mutations and may play a role in gene innovation. Reticulate evolutionary processes, such as unequal crossing-over and gene conversion, are known to occur within specific duplicon families, but the broader contribution of these processes to the evolution of human duplications remains poorly characterized. Here, we use phylogenetic profiling to analyze multiple alignments of 24 human duplicon families that span >8 Mb of DNA. Our results indicate that none of them are evolving independently, with all alignments showing sharp discontinuities in phylogenetic signal consistent with reticulation. To analyze these results in more detail, we have developed a quartet method that estimates the relative contribution of nucleotide substitution and reticulate processes to sequence evolution. Our data indicate that most of the duplications show a highly significant excess of sites consistent with reticulate evolution, compared with the number expected by nucleotide substitution alone, with 15 of 30 alignments showing a >20-fold excess over that expected. Using permutation tests, we also show that at least 5% of the total sequence shares 100% sequence identity because of reticulation, a figure that includes 74 independent tracts of perfect identity >2 kb in length. Furthermore, analysis of a subset of alignments indicates that the density of reticulation events is as high as 1 every 4 kb. These results indicate that phylogenetic relationships within recently duplicated human DNA can be rapidly disrupted by reticulate evolution. This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution. PMID:16252241

A Large-Scale Genetic Screen in Arabidopsis to Identify Genes Involved in Pollen Exine Production1[C][W][OA

PubMed Central

Dobritsa, Anna A.; Geanconteri, Aliza; Shrestha, Jay; Carlson, Ann; Kooyers, Nicholas; Coerper, Daniel; Urbanczyk-Wochniak, Ewa; Bench, Bennie J.; Sumner, Lloyd W.; Swanson, Robert; Preuss, Daphne

2011-01-01

Exine, the outer plant pollen wall, has elaborate species-specific patterns, provides a protective barrier for male gametophytes, and serves as a mediator of strong and species-specific pollen-stigma adhesion. Exine is made of sporopollenin, a material remarkable for its strength, elasticity, and chemical durability. The chemical nature of sporopollenin, as well as the developmental mechanisms that govern its assembly into diverse patterns in different species, are poorly understood. Here, we describe a simple yet effective genetic screen in Arabidopsis (Arabidopsis thaliana) that was undertaken to advance our understanding of sporopollenin synthesis and exine assembly. This screen led to the recovery of mutants with a variety of defects in exine structure, including multiple mutants with novel phenotypes. Fifty-six mutants were selected for further characterization and are reported here. In 14 cases, we have mapped defects to specific genes, including four with previously demonstrated or suggested roles in exine development (MALE STERILITY2, CYP703A2, ANTHER-SPECIFIC PROTEIN6, TETRAKETIDE α-PYRONE REDUCTASE/DIHYDROFLAVONOL-4-REDUCTASE-LIKE1), and a number of genes that have not been implicated in exine production prior to this screen (among them, fatty acid ω-hydroxylase CYP704B1, putative glycosyl transferases At1g27600 and At1g33430, 4-coumarate-coenzyme A ligase 4CL3, polygalacturonase QUARTET3, novel gene At5g58100, and nucleotide-sugar transporter At5g65000). Our study illustrates that morphological screens of pollen can be extremely fruitful in identifying previously unknown exine genes and lays the foundation for biochemical, developmental, and evolutionary studies of exine production. PMID:21849515

Real-Time Study of the Interaction between G-Rich DNA Oligonucleotides and Lead Ion on DNA Tetrahedron-Functionalized Sensing Platform by Dual Polarization Interferometry.

PubMed

Wang, Shuang; Lu, Shasha; Zhao, Jiahui; Huang, Jianshe; Yang, Xiurong

2017-11-29

G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb 2+ . The oriented immobilization of probes greatly decreased the spatial hindrance effect and improved the accessibility of the probes to the Pb 2+ ions. Through real-time monitoring of the whole formation process of the G-quadruplex, we speculated that the probes on the tetrahedron platform initially stood on the sensing surface with a random coil conformation, then the G-rich ssDNA preliminarily formed unstable G-quartets by H-bonding and cation binding, subsequently forming a completely folded and stable quadruplex structure through relatively slow strand rearrangements. On the basis of these studies, we also developed a novel sensing platform for the specific and sensitive determination of Pb 2+ and its chelating agent ethylenediaminetetraacetic acid. This study not only provides a proof-of-concept for conformational dynamics of G-quadruplex-related drugs and pathogenes, but also enriches the biosensor tools by combining nanomaterial with interfaces technique.

Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlahović, Filip; Perić, Marko; Zlatar, Matija, E-mail: matijaz@chem.bg.ac.rs

2015-06-07

Herein, we present the systematic, comparative computational study of the d − d transitions in a series of first row transition metal hexaaqua complexes, [M(H{sub 2}O){sub 6}]{sup n+} (M{sup 2+/3+} = V {sup 2+/3+}, Cr{sup 2+/3+}, Mn{sup 2+/3+}, Fe{sup 2+/3+}, Co{sup 2+/3+}, Ni{sup 2+}) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d{sup 2}, d{supmore » 4}, and low-spin d{sup 6} complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d{sup 5} complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.« less

Isospin symmetry of Tz =±3/2→±1/2 Gamow-Teller transitions in A=41 nuclei

NASA Astrophysics Data System (ADS)

Fujita, Y.; Shimbara, Y.; Adachi, T.; Berg, G. P.; Brown, B. A.; Fujita, H.; Hatanaka, K.; Kamiya, J.; Nakanishi, K.; Sakemi, Y.; Sasaki, S.; Shimizu, Y.; Tameshige, Y.; Uchida, M.; Wakasa, T.; Yosoi, M.

2004-11-01

Under the assumption that isospin T is a good quantum number, isobaric analog states and various analogous transitions are expected in isobars with mass number A . The strengths of Tz =±3/2→±1/2 analogous Gamow-Teller (GT) transitions and analogous M1 transitions within the A=41 isobar quartet are compared in detail. The Tz =+3/2→+1/2 GT transitions from the Jπ = 3/2+ ground state of 41K leading to excited Jπ = 1/2+ , 3/2+ , and 5/2+ states in 41Ca were measured using the ( 3He ,t) charge-exchange reaction. With a high energy resolution of 35 keV , many fragmented states were observed, and the GT strength distribution was determined up to 10 MeV excitation energy ( Ex ) . The main part of the strength was concentrated in the Ex =4 6 MeV region. A shell-model calculation could reproduce the concentration, but not so well details of the strength distribution. The obtained distribution was further compared with two results of 41Ti β decay studying the analogous Tz =-3/2→-1/2 GT strengths. They reported contradicting distributions. One-to-one correspondences of analogous transitions and analog states were assigned up to Ex =6 MeV in the comparison with one of these 41Ti β -decay results. Combining the spectroscopic information of the analog states in 41Ca and 41Sc , the most probable Jπ values were deduced for each pair of analog states. It was found that 5/2+ states carry the main part of the observed GT strength, while much less GT strength was carried by 1/2+ and 3/2+ states. The gross features of the GT strength distributions for each J were similar for the isospin analogous Tz =±3/2→±1/2 transitions, but the details were somewhat different. From the difference of the distributions, isospin-asymmetry matrix elements of ≈8 keV were deduced. The Coulomb displacement energy, which is sensitive to the configuration of states, showed a sudden increase of about 50 keV at the excitation energy of 3.8 MeV . The strengths of several M1 transitions to the IAS in 41Ca were compared with the strengths of analogous GT transitions. It was found that ratios of the M1 and GT transition strengths were similar, suggesting that the contributions of the ℓτ term in M1 transitions are small.

Connectivity patterns and rotamer states of nucleobases determine acid-base properties of metalated purine quartets.

PubMed

Lüth, Marc Sven; Freisinger, Eva; Kampf, Gunnar; Garijo Anorbe, Marta; Griesser, Rolf; Operschall, Bert P; Sigel, Helmut; Lippert, Bernhard

2015-07-01

Potentiometric pH titrations and pD dependent (1)H NMR spectroscopy have been applied to study the acidification of the exocyclic amino group of adenine (A) model nucleobases (N9 position blocked by alkyl groups) when carrying trans-a2Pt(II) (with a=NH3 or CH3NH2) entities both at N1 and N7 positions. As demonstrated, in trinuclear complexes containing central A-Pt-A units, it depends on the connectivity pattern of the adenine bases (N7/N7 or N1/N1) and their rotamer states (head-head or head-tail), how large the acidifying effect is. Specifically, a series of trinuclear complexes with (A-N7)-Pt-(N7-A) and (A-N1)-Pt-(N1-A) cross-linking patterns and terminal 9-alkylguanine ligands (9MeGH, 9EtGH) have been analyzed in this respect, and it is shown that, for example, the 9MeA ligands in trans-,trans-,trans-[Pt(NH3)2(N7-9MeA-N1)2{Pt(NH3)2(9EtGH-N7)}2](ClO4)6·6H2O (4a) and trans-,trans-,trans-[Pt(NH3)2(N7-9EtA-N1)2{Pt(CH3NH2)2(9-MeGH-N7)}2](ClO4)6·3H2O (4b) are more acidic, by ca. 1.3 units (first pKa), than the linkage isomer trans-,trans-,trans-[Pt(CH3NH2)2(N1-9MeA-N7)2{Pt(NH3)2(9MeGH-N7)}2](NO3)6·6.25H2O (1b). Overall, acidifications in these types of complexes amount to 7-9 units, bringing the pKa values of such adenine ligands in the best case close to the physiological pH range. Comparison with pKa values of related trinuclear Pt(II) complexes having different co-ligands at the Pt ions, confirms this picture and supports our earlier proposal that the close proximity of the exocyclic amino groups in a head-head arrangement of (A-N7)-Pt-(N7-A), and the stabilization of the resulting N6H(-)⋯H2N6 unit, is key to this difference. Copyright © 2015 Elsevier Inc. All rights reserved.

European Space Agency announces contest to "Name the Cluster Quartet"

NASA Astrophysics Data System (ADS)

2000-02-01

1. Contest rules The European Space Agency (ESA) is launching a public competition to find the most suitable names for its four Cluster II space weather satellites. The quartet, which are currently known as flight models 5, 6, 7 and 8, are scheduled for launch from Baikonur Space Centre in Kazakhstan in June and July 2000. Professor Roger Bonnet, ESA Director of Science Programme, announced the competition for the first time to the European Delegations on the occasion of the Science Programme Committee (SPC) meeting held in Paris on 21-22 February 2000. The competition is open to people of all the ESA member states (*). Each entry should include a set of FOUR names (places, people, or things from history, mythology, or fiction, but NOT living persons). Contestants should also describe in a few sentences why their chosen names would be appropriate for the four Cluster II satellites. The winners will be those which are considered most suitable and relevant for the Cluster II mission. The names must not have been used before on space missions by ESA, other space organizations or individual countries. One winning entry per country will be selected to go to the Finals of the competition. The prize for each national winner will be an invitation to attend the first Cluster II launch event in mid-June 2000 with their family (4 persons) in a 3-day trip (including excursions to tourist sites) to one of these ESA establishments: ESRIN (near Rome, Italy): winners from France, Ireland, United Kingdom, Belgium. VILSPA (near Madrid, Spain): winners from The Netherlands, Norway, Sweden, Finland. ESTEC (near Amsterdam, The Netherlands): winners from Germany, Denmark, Switzerland, Austria. ESOC (in the Rhine Valley, Germany): winners from Italy, Spain , Portugal. During the first Cluster II launch event (June 2000) the chosen four names for the spacecraft will be announced. The grand prize will be: * a trip for the winner and family (4 people) to Paris where ESA's headquarters are located (including a social event) in early Autumn 2000. * a plaque for the winner. * a plaque and a special edition Cluster II scale model donated to the home town of the winner. Contest details can be found on the Internet at: http://sci.esa.int/cluster/competition Information on the competition can also be requested by normal mail by contacting the address below (**). Entries can be submitted by: * Email: cluster@spd.estec.esa.nl * Normal mail to: "Name the Cluster Quartet", Science Programme Communication Service, SCI-MC, ESA - ESTEC, Postbus 299, 2200 AG Noordwijk ZH , The Netherlands (**) Mailed entries must be postmarked no later than 10 May, 2000. The winners will be notified by letter in late May, 2000. (*) Participants must be nationals of one of the ESA member states 2. Cluster II - Mission to Explore the Sun-Earth Connection. This summer, the European Space Agency (ESA) will be launching Cluster II, a unique scientific mission designed to explore space weather and discover how the Sun affects our world. For the first time, a fleet of four identical scientific spacecraft will fly in group formation along elliptical (egg-shaped) orbits around the planet. This satellite squadron will allow scientists to make the first detailed, three-dimensional, maps of the space environment within 120,000 km of the Earth's surface. The Sun-Earth Connection Most of us are aware that the Sun is an important influence on our lives. It brings us light and warmth, and occasionally causes painful sunburn, or even skin cancer, if we expose ourselves to its ultraviolet rays for a long time. When the Sun disappears at night or during a total eclipse, the Earth becomes cold and dark. But the Sun also influences our lives in other, less obvious, ways. It does this by disturbing the "weather" in space. Every second, millions of tonnes of material are blasted out from the Sun into space in the form of charged particles - mainly electrons and protons. This stream of particles creates a solar wind which travels at supersonic speeds towards the Earth. Occasionally, violent solar storms eject high energy particles which streak across the 150 million kilometre gulf between the Sun and Earth in just a few hours. These storms are most frequent every 11 years. The next peak is expected in 2000, just as Cluster II is inserted into orbit to investigate their effects. "Like the weather on Earth, the Sun is changing", says Prof R. Bonnet, ESA's Director of Science. "Like the weather, it is sometimes difficult to predict its variations. They influence not only the Earth but the whole set of planets in the Solar System and the spacecraft which are orbiting in the interplanetary medium and circling the Earth." Fortunately for us, the Earth's magnetic field creates a giant, protective bubble in space - the magnetosphere. Like a mountain in a gale, the magnetosphere forces most of the particles in the solar wind to flow around it. The gusts in the solar wind mould the Earth's magnetic bubble into a tadpole-shape, creating a tail which stretches millions of kilometres downwind. However, Earth's magnetic defences can be breached by high-energy solar particles. Two weak points above the planet's magnetic poles, known as cusps, allow the solar wind to leak into the magnetosphere and spiral down magnetic field lines into the thin upper atmosphere. Other particles which are trapped in the magnetic bubble can collect and then sweep down into the atmosphere. In either case, the particles collide with molecules of air, creating beautiful curtains of light known as auroras or 'polar lights'. "It's like a never-ending football game" says ESA's Cluster II project scientist, Philippe Escoubet. "The Sun is kicking particles towards us, like footballs. The Earth is the goal and its magnetic field is the goalkeeper. It's always trying to push the 'balls' away, but some get past. When particles score goals they disrupt the Earth. Sometimes the Sun is very quiet, but when it's very active we get a lot of 'balls' coming through." Occasionally, the Earth's magnetic shield is so overwhelmed by particles blasted out during solar storms that the magnetic field fluctuates wildly, creating enormous electrical currents. These can induce major power cuts, like one in 1989 which struck six million Canadians during the middle of winter. Minor gusts in the solar wind can also interrupt short wave radio communications, damage communication satellites which transmit TV signals and telephone calls, and even increase corrosion in oil pipelines. Cluster II investigates Like four ships skimming through a sea of particles, the flotilla of Cluster II spacecraft will spend two years investigating this interaction between our nearest star, the Sun, and our fragile world. They will swim through the various layers and boundaries within the magnetosphere, skim over the Earth's magnetic poles to investigate the cusps, and sail downwind to study the magnetic tail. As well as ploughing through the different regions of the magnetosphere, they will cross the shock wave which marks the edge of Earth's magnetic bubble and enter interplanetary space where the solar wind blows at full force. Eleven identical instruments on board each spacecraft will study all aspects of the Earth's electrical and magnetic environment. Some of these are located on rods which protrude into the surrounding space, sweeping through the sea of charged particles as the spacecraft rotates. The magnetometers, which will measure local magnetic fields, are located on the end of two 5-metre-long booms. Four 50-metre wire antennas send back information on electrical fields and waves. Other instruments on the drum-shaped spacecraft investigate the population of charged particles and the electromagnetic phenomena associated with them. Simultaneous measurements from the Cluster II quartet will provide invaluable snapshots of events taking place inside and outside the magnetosphere. Ground controllers will even be able to trim the spacecraft's courses, altering the distances between them in order to ensure that scientists receive the most detailed information ever obtained about the invisible interaction between the Sun and Earth. "Cluster II will give us the best information yet on how the Sun affects the near-Earth environment," says Philippe Escoubet. "The spacecraft will give us four viewpoints - like having one camera behind the goal at a football match and three others at different angles. It will be the first time this has been done for the Earth's magnetic field. This is very exciting because such unprecedented detail will give us a much better opportunity to understand the space environment which surrounds our planet." Thanks to the Cluster II and SOHO solar observing satellites, ESA is leading Europe to be a major world contributor in the International Solar-Terrestrial Programme (ISTP). This global research project, which includes scientists and spacecraft from ESA, the USA, Russia and Japan, is aimed at understanding all aspects of the Sun-Earth relationship. The intention is to link the processes taking place inside the Sun, its output of energy and the flow of the solar wind, and finally its effects upon our planet. Cluster II - the spacecraft and the mission in brief Cluster II is one of ESA's top priority Cornerstone science missions. It is a replacement for the original Cluster mission, which was tragically destroyed by an explosion during the maiden launch of the Ariane 5 rocket in June 1996. Cluster II is scheduled for launch from Baikonur Cosmodrome in Kazakhstan in the summer of 2000. The four satellites will be put into orbit in pairs, using two Soyuz rockets provided by the Russian-French Starsem company, on 15 June and 13 July. They will then follow highly elliptical, polar orbits which will vary between 19,000 and 119,000 km above the Earth. At times, they will be inside the protection of the magnetosphere, while at others they will be fully exposed to the supersonic solar wind. The four identical spacecraft will investigate the changing space weather around our planet in unprecedented detail. In order to achieve this, each spacecraft carries an identical set of 11 instruments, provided by scientific institutions in different countries. These will measure charged particles, magnetic and electrical fields in near-Earth space, providing the first three-dimensional snapshots of this ever-changing environment. Each cylindrical Cluster II spacecraft, which measures 2.9 metres in diameter and 1.3 metres in height, weighs 1.2 tonnes when it is fully fuelled. Large amounts of fuel are required in order to place the satellites in the correct polar orbits and to enable them to manoeuvre in space. 71 kg of each spacecraft's mass is allocated to the scientific payload. Most of the science instruments are attached to the main drum-shaped body of the satellite, but the Cluster II spacecraft also carries two 5 metre-long experiment booms, four 50 metre-long wire booms, and two antenna booms. Scientific institutions and industrial enterprises in almost all of the 14 ESA member states and the United States have participated in the Cluster II project. Working to strict deadlines, ESA and its European industrial partners, under the leadership of German prime contractor Dornier Satellite Systems, have successfully constructed and tested the Cluster II quartet in less than three years. At the same time, the European ground segment for the mission has been prepared to receive and process the vast amount of data - equivalent to 290 million printed pages - that will be returned to Earth over the mission's two year lifetime. Signals to and from the spacecraft will be sent via a 15 metre antenna located at Villafranca in Spain and processed at the European Space Operations Control Centre (ESOC) at Darmstadt, Germany. The Joint Science Operations Centre at Rutherford Appleton Laboratory in the UK will co-ordinate the scientific investigations. Its main task will be to combine all of the demands from the 11 science instrument teams into an overall plan. The stream of information returned by the 44 instruments will be distributed to eight national data centres, six in Europe, one in the USA and one in China. Paying tribute to everyone who has put so much effort into achieving the remarkable revival of the Cluster mission, ESA's Project Manager John Ellwood said, "In the past two and a half years, a tremendous amount of work has been completed by both scientists and industry. It has been a fantastic achievement to build four satellites in such a short time." "Everything is on schedule for the two launches of Cluster II in mid-2000," he added. "We are confident that this tremendously exciting mission will provide spectacular new insights into the interaction between the Sun and our Earth."

PHOSPHATIDYLSERINE SYNTHASE1 is required for microspore development in Arabidopsis thaliana.

PubMed

Yamaoka, Yasuyo; Yu, Yanbo; Mizoi, Junya; Fujiki, Yuki; Saito, Kyoko; Nishijima, Masahiro; Lee, Youngsook; Nishida, Ikuo

2011-08-01

Phosphatidylserine (PS) has many important biological roles, but little is known about its role in plants, partly because of its low abundance. We show here that PS is enriched in Arabidopsis floral tissues and that genetic disruption of PS biosynthesis decreased heterozygote fertility due to inhibition of pollen maturation. At1g15110, designated PSS1, encodes a base-exchange-type PS synthase. Escherichia coli cells expressing PSS1 accumulated PS in the presence of l-serine at 23°C. Promoter-GUS assays showed PSS1 expression in developing anther pollen and tapetum. A few seeds with pss1-1 and pss1-2 knockout alleles escaped embryonic lethality but developed into sterile dwarf mutant plants. These plants contained no PS, verifying that PSS1 is essential for PS biosynthesis. Reciprocal crossing revealed reduced pss1 transmission via male gametophytes, predicting a rate of 61.6%pss1-1 pollen defects in PSS1/pss1-1 plants. Alexander's staining of inseparable qrt1-1 PSS1/pss1-1 quartets revealed a rate of 42% having three or four dead pollen grains, suggesting sporophytic pss1-1 cell death effects. Analysis with the nuclear stain 4',6-diamidino-2-phenylindole (DAPI) showed that all tetrads from PSS1/pss1-1 anthers retain their nuclei, whereas unicellular microspores were sometimes anucleate. Transgenic Arabidopsis expressing a GFP-LactC2 construct that binds PS revealed vesicular staining in tetrads and bicellular microspores and nuclear membrane staining in unicellular microspores. Hence, distribution and/or transport of PS across membranes were dynamically regulated in pollen microspores. However, among unicellular microspores from PSS1/pss1-2 GFP-LactC2 plants, all anucleate microspores showed little GFP-LactC2 fluorescence, suggesting that pss1-2 microspores are more sensitive to sporophytic defects or show partial gametophytic defects. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

Cyclo[n]pyrroles: Size and Site Specific Binding to G-Quadruplexes

PubMed Central

Baker, Erin Shammel; Lee, Jeong T.

2014-01-01

Inhibiting the enzyme telomerase by stabilizing the G-quadruplex has potential in anticancer drug design. Diprotonated cyclo[n]pyrroles represent a set of expanded porphyrin analogues with structures similar to telomestatin, a natural product known to bind to and stabilize G-quadruplexes. As a first step towards testing whether cyclo[n]pyrroles display a similar function, a series of diprotonated cyclo[n]pyrroles (where n = 6, 7 and 8) was each added to the human telomere repeat sequence d(T2AG3)4 and examined with mass spectrometry, ion mobility and molecular dynamics calculations. Nano-ESI-MS indicated that the smaller the cyclo[n]pyrrole, the stronger it binds to the telomeric sequence. It was also found that cyclo[6]pyrrole bound to d(T2AG3)4 better than octaethylporphyrin, a finding rationalized by cyclo[6]pyrrole having a +2 charge, while octaethylporphyrin bears no charge. Ion mobility measurements were used to measure the collision cross section of each d(T2AG3)4/cyclo[n]pyrrole complex. Only one peak was observed in the arrival time distributions for all complexes and the experimental cross sections indicated that only structures with d(T2AG3)4 in an antiparallel G-quadruplex arrangement and each cyclo[n]pyrrole externally stacked below the G-quartets occur under these experimental conditions. When the cyclo[n]pyrroles were intercalated or nonspecifically bound to the quadruplex or if different conformations than antiparallel were considered for d(T2AG3)4, the theoretical cross sections did not match experiment. On this basis, it is inferred that 1) external stacking represents the dominant binding mode for the interaction of cyclo[n]pyrroles with d(T2AG3)4 and 2) the overall size and charge of the cyclo[n]pyrroles play important roles in defining the binding strength. PMID:16492050

A Mononuclear Fe(III) Single Molecule Magnet with a 3/2↔5/2 Spin Crossover

PubMed Central

Tran, Ba L.; Adhikari, Debashis; Pink, Maren; Heinemann, Frank W.; Sutter, Jörg; Szilagyi, Robert K.

2012-01-01

The air stable complex [(PNP)FeCl2] (1) (PNP = N[2-P(CHMe2)2-4-methylphenyl]2−), prepared from one-electron oxidation of [(PNP)FeCl] with ClCPh3, displays an unusual S = 3/2 to S = 5/2 transition above 80 K as inferred by the dc SQUID magnetic susceptibility measurement. The ac SQUID magnetization data, at zero field and between frequencies 10 and 1042 Hz, clearly reveals complex 1 to undergo a frequency dependent of the out-of-phase signal and thus be a single molecular magnet with a thermally activated barrier of Ueff = 32-36 cm−1 (47 - 52 K). Variable temperature Mössbauer data also corroborate a significant temperature dependence in δ and ΔEQ values for 1, which is in agreement with the system undergoing a change in spin state. Likewise, variable temperature X-band EPR spectra of 1 reveals the S = 3/2 to be likely the ground state with the S = 5/2 being close in energy. Multi-edge XAS absorption spectra suggest the electronic structure of 1 to be highly covalent with an effective iron oxidation state that is more reduced than the typical ferric complexes due to the significant interaction of the phosphine groups in PNP and Cl ligands with iron. A variable temperature single crystal X-ray diffraction study of 1 collected between 30-300 K also reveals elongation of the Fe–P bond lengths and increment in the Cl–Fe–Cl angle as the S = 5/2 state is populated. Theoretical studies show overall similar orbital pictures except for the d(z2) orbital which is the most sensitivity to change in the geometry and bonding where the quartet (4B) and the sextet (6A) states are close in energy. PMID:22817325

The synthesis and electronic structure of a novel [NiS4Fe2(CO)6] radical cluster: implications for the active site of the [NiFe] hydrogenases.

PubMed

Wang, Qiang; Barclay, J Elaine; Blake, Alexander J; Davies, E Stephen; Evans, David J; Marr, Andrew C; McInnes, Eric J L; McMaster, Jonathan; Wilson, Claire; Schröder, Martin

2004-07-19

A novel [NiS4Fe2(CO)6]cluster (1: 'S(4)'=(CH(3)C(6)H(3)S(2))(2)(CH(2))(3)) has been synthesised, structurally characterised and has been shown to undergo a chemically reversible reduction process at -1.31 V versus Fc(+)/Fc to generate the EPR-active monoanion 1(-). Multifrequency Q-, X- and S-band EPR spectra of (61)Ni-enriched 1(-) show a well-resolved quartet hyperfine splitting in the low-field region due to the interaction with a single (61)Ni (I=3/2) nucleus. Simulations of the EPR spectra require the introduction of a single angle of non-coincidence between g(1) and A(1), and g(3) and A(3) to reproduce all of the features in the S- and X-band spectra. This behaviour provides a rare example of the detection and measurement of non-coincidence effects from frozen-solution EPR spectra without the need for single-crystal measurements, and in which the S-band experiment is sensitive to the non-coincidence. An analysis of the EPR spectra of 1(-) reveals a 24 % Ni contribution to the SOMO in 1(-), supporting a delocalisation of the spin-density across the NiFe(2) cluster. This observation is supported by IR spectroscopic results which show that the CO stretching frequencies, nu(CO), shift to lower frequency by about 70 cm(-1) when 1 is reduced to 1(-). Density functional calculations provide a framework for the interpretation of the spectroscopic properties of 1(-) and suggest that the SOMO is delocalised over the whole cluster, but with little S-centre participation. This electronic structure contrasts with that of the Ni-A, -B, -C and -L forms of [NiFe] hydrogenase in which there is considerable S participation in the SOMO.

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants.

PubMed

Eaton, Deren A R; Spriggs, Elizabeth L; Park, Brian; Donoghue, Michael J

2017-05-01

Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead to missing information. There is thus a clear expectation for how missing data should be distributed, with fewer loci recovered between more distantly related samples. This observation has led to a related expectation: that RAD-seq data are insufficiently informative for resolving deeper scale phylogenetic relationships. Here we investigate the relationship between missing information among samples at the tips of a tree and information at edges within it. We re-analyze and review the distribution of missing data across ten RAD-seq data sets and carry out simulations to determine expected patterns of missing information. We also present new empirical results for the angiosperm clade Viburnum (Adoxaceae, with a crown age >50 Ma) for which we examine phylogenetic information at different depths in the tree and with varied sequencing effort. The total number of loci, the proportion that are shared, and phylogenetic informativeness varied dramatically across the examined RAD-seq data sets. Insufficient or uneven sequencing coverage accounted for similar proportions of missing data as dropout from mutation-disruption. Simulations reveal that mutation-disruption, which results in phylogenetically distributed missing data, can be distinguished from the more stochastic patterns of missing data caused by low sequencing coverage. In Viburnum, doubling sequencing coverage nearly doubled the number of parsimony informative sites, and increased by >10X the number of loci with data shared across >40 taxa. Our analysis leads to a set of practical recommendations for maximizing phylogenetic information in RAD-seq studies. [hierarchical redundancy; phylogenetic informativeness; quartet informativeness; Restriction-site associated DNA (RAD) sequencing; sequencing coverage; Viburnum.]. © The authors 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Defects in Peroxisomal 6-Phosphogluconate Dehydrogenase Isoform PGD2 Prevent Gametophytic Interaction in Arabidopsis thaliana1[OPEN

PubMed Central

Hölscher, Christian; Meyer, Tanja; Fischer, Kerstin

2016-01-01

We studied the localization of 6-phosphogluconate dehydrogenase (PGD) isoforms of Arabidopsis (Arabidopsis thaliana). Similar polypeptide lengths of PGD1, PGD2, and PGD3 obscured which isoform may represent the cytosolic and/or plastidic enzyme plus whether PGD2 with a peroxisomal targeting motif also might target plastids. Reporter-fusion analyses in protoplasts revealed that, with a free N terminus, PGD1 and PGD3 accumulate in the cytosol and chloroplasts, whereas PGD2 remains in the cytosol. Mutagenesis of a conserved second ATG enhanced the plastidic localization of PGD1 and PGD3 but not PGD2. Amino-terminal deletions of PGD2 fusions with a free C terminus resulted in peroxisomal import after dimerization, and PGD2 could be immunodetected in purified peroxisomes. Repeated selfing of pgd2 transfer (T-)DNA alleles yielded no homozygous mutants, although siliques and seeds of heterozygous plants developed normally. Detailed analyses of the C-terminally truncated PGD2-1 protein showed that peroxisomal import and catalytic activity are abolished. Reciprocal backcrosses of pgd2-1 suggested that missing PGD activity in peroxisomes primarily affects the male gametophyte. Tetrad analyses in the quartet1-2 background revealed that pgd2-1 pollen is vital and in vitro germination normal, but pollen tube growth inside stylar tissues appeared less directed. Mutual gametophytic sterility was overcome by complementation with a genomic construct but not with a version lacking the first ATG. These analyses showed that peroxisomal PGD2 activity is required for guided growth of the male gametophytes and pollen tube-ovule interaction. Our report finally demonstrates an essential role of oxidative pentose-phosphate pathway reactions in peroxisomes, likely needed to sustain critical levels of nitric oxide and/or jasmonic acid, whose biosynthesis both depend on NADPH provision. PMID:26941195

The risks, needs and stages of recovery of a complete forensic patient cohort in an Australian state.

PubMed

Adams, Jonathon; Thomas, Stuart D M; Mackinnon, Tobias; Eggleton, Damien

2018-02-07

Routine outcome measures are increasingly being mandated across mental health services in Australia and overseas. This requirement includes forensic mental health services, but their utility in such specialist services and the inter-relationships between the measures remain unclear. This study sought to characterise the risks, needs and stages of recovery of an entire cohort of forensic patients in one jurisdiction in Australia. Local expert groups, comprising of members of the forensic patient treating teams, were formed to gather information about the status and needs of all forensic patients in the State of New South Wales, Australia. The expert groups provided demographic information and completed three assessment tools concerning the risks, needs and stages of recovery of each forensic patient. The cohort of 327 forensic patients in NSW appears to be typical of forensic mental health service populations internationally when considering factors such as gender, diagnosis, and index offence. A number of important differences across the three structured tools for forensic patients in different levels of secure service provision are presented. The DUNDRUM Quartet demonstrated interesting findings, particularly in terms of the therapeutic security needs, the treatment completion, and the stages of recovery for the forensic patients in the community. The CANFOR highlighted the level of needs across the forensic patient population, whilst the HCR-20 data showed there was no significant difference in the mean clinical and risk management scores between male forensic patients across levels of security. To the authors' knowledge this is the first study of its kind in New South Wales, Australia. We have demonstrated the utility of using a suite of measures to evaluate the risks, needs, and stages of recovery for an entire cohort of forensic patients. The data set helps inform service planning and development, together with providing various avenues for future research.

What makes the hedonic experience of a meal in a top restaurant special and retrievable in the long term? Meal-related, social and personality factors.

PubMed

Muñoz, Francisco; Hildebrandt, Andrea; Schacht, Annekathrin; Stürmer, Birgit; Bröcker, Felix; Martín-Loeches, Manuel; Sommer, Werner

2018-06-01

Knowing what makes a top gastronomy experience unique and retrievable in the long term is of interest for scientific and economic reasons. Recent attempts to isolate predictors of the hedonic evaluation of food have afforded several factors, such as individual and social attributes, or liking/disliking profiles. However, in these studies relevant variables have been examined in isolation without an integrative perspective. Here we investigated 80 guests enjoying a 23-course meal in a top gastronomy restaurant, in groups of four. Our main question concerned the factors driving the overall evaluation of the meal at its conclusion and after three months. To this aim we administered the Big Five Personality Inventory before the meal, dish-by-dish hedonic ratings, and a multi-dimensional Meal Experience Questionnaire (MEQ) at the end of the meal. Hedonic evaluations of the meal were collected immediately after the meal and three months later. Better immediate overall evaluations were predicted by both the number of peaks in dish-by-dish ratings and by positive ratings of the final dish. Both factors and the number of troughs were also critical for the long-term evaluation after three months. The MEQ dimensions overall interest, valence and distraction predicted immediate evaluations, while the long-term evaluations were determined by interest and high scores on the personality traits agreeableness and conscientiousness. High consistency of the hedonic ratings within quartets indicated the relevance of commensality for the meal experience. The present findings highlight the simultaneous relevance of food- and personality-related factors and commensality for a top gastronomy meal experience in the short and long-run. The uncovered relationships are of theoretical interest and for those involved in designing meals for consumers in various settings. Copyright © 2018 Elsevier Ltd. All rights reserved.

Laser Spectroscopy and Density Functional Study on Niobium Dimer Cation

NASA Astrophysics Data System (ADS)

Aydin, Metin; Lombardi, John R.

2009-06-01

Resonant multiphoton fragmentation spectra of niobium dimer cation (Nb2+) have been obtained by utilizing laser vaporization of a Nb metal target. Ions are mass-selected with a time-of-flight mass spectrometer followed by a mass gate, then fragmented with a pulsed dye laser, and the resulting fragment ions are detected with a second time-of-flight reflectron mass spectrometer and multichannel plate. Photon resonances are detected by monitoring ion current as a function of fragmentation laser wavelength. A rich, but complex spectrum of the cation is obtained. The bands display a characteristic multiplet structure that may be interpreted as due to transitions from the ground state X^{4}{Σ}^{-}({Ω}g) to several excited states, X^{4}{Π}({Ω}u) and X^{4}{Σ}(^{-}{Ω}u). The ground state X^{4}{Σ}^{-}({Ω}g) is derived from the electron configuration ({π}{_u})^{4} (1{σ}{_g})^{2}(2{σ}{_g})^{1} ({δ}{_g})^{2}. The two spin-orbit components are split by 145 cm^{-1} due to a strong second-order isoconfigurational spin-orbit interaction with the low-lying ^{2}{Σ}^{+}({Ω}g) state. The vibrational frequencies of the ground sate and the excited state of Nb2+ are identified as well as molecular spin-orbit constants (A{_S}{_O}) in the excited state. The electronic structure of niobium dimer cation was investigated using density functional theory. For the electronic ground state, the predicted spectroscopic properties were in good agreement with experiment. Calculations on excited states reveal congested manifolds of quartet and doublet electronic states in the range 0-30,000 cm^{-1}, reflecting the multitude of possible electronic promotions among the 4d- and 5s-based molecular orbitals. Comparisons are drawn between Nb^{+}{_2} and the prevalent isoelectronic molecules V^{+}{_2}/NbV^{+}/Nb{_2}/V{_2}/NbV. M. Aydin and John R. Lombardi J. Phys. Chem. A. xx XXXX 2009.

Spin-Controlled Conductivity in a Thiophene-Functionalized Iron-Bis(dicarbollide)

NASA Astrophysics Data System (ADS)

Beach, Benjamin; Sauriol, Dustin; Derosa, Pedro

2016-04-01

The relationship between spin state and conductivity is studied for a thiophene-functionalized iron(III)-bis(dicarbollide) with one or two thiophenes at each end of the cage. Iron has a high ground state spin that can be adjusted by external electromagnetic fields to produce different magnetic states. The hypothesis explored here is that changes in the spin state of these Fe-containing molecules can lead to significant changes in molecular conductivity. Two examples of the possible application of such spin-dependent conductivity are its use as a molecular switch, the basic building block in digital logic, or as a memory bit. The molecules were first optimized using the Becke-3 Lee-Yang-Parr functional (B3LYP) with the 6-31G(d) basis set. A relaxed molecular geometry at each spin state was then placed between gold electrodes to conduct spin-polarized electron transport calculations with the density functional theory/non-equilibrium Green's functions formalism. The revised Perdew-Burke-Ernzerhf solids exchange-correlation functional (PBES) with double zeta polarized basis set was used. The result of these calculations show that the conductivity increases with the spin state. The cage structure is shown to exhibit fully delocalized molecular orbitals (MOs) appropriate for high conductivity and thus, in this system, the conductivity depends on the position of the MOs relative to the Fermi level. Minority spins are responsible for the conductivity of the doublet spin state while majority spins dominate for the quartet and sextet spin states as they are found closer to the Fermi level when they are occupied. Energy calculations predict a difference in energy between the more and the less conductive spin states (sextet and doublet respectively) that is 15-20 times greater than the thermal energy, which would imply stability at room temperature; however, the energy difference is sufficiently small that transitions between spin states can be induced.

Determination of the 1s2{\\ell }2{{\\ell }}^{\\prime } state production ratios {{}^{4}P}^{o}/{}^{2}P, {}^{2}D/{}^{2}P and {{}^{2}P}_{+}/{{}^{2}P}_{-} from fast (1{s}^{2},1s2s\\,{}^{3}S) mixed-state He-like ion beams in collisions with H2 targets

NASA Astrophysics Data System (ADS)

Benis, E. P.; Zouros, T. J. M.

2016-12-01

New results are presented on the ratio {R}m={σ }{T2p}( {}4P)/{σ }{T2p}({}2P) concerning the production cross sections of Li-like 1s2s2p quartet and doublet P states formed in energetic ion-atom collisions by single 2p electron transfer to the metastable 1s2s {}3S component of the He-like ion beam. Spin statistics predict a value of R m = 2 independent of the collision system in disagreement with most reported measurements of {R}m≃ 1{--}9. A new experimental approach is presented for the evaluation of R m having some practical advantages over earlier approaches. It also allows for the determination of the separate contributions of ground- and metastable-state beam components to the measured spectra. Applying our technique to zero-degree Auger projectile spectra from 4.5 MeV {{{B}}}3+ (Benis et al 2002 Phys. Rev. A 65 064701) and 25.3 MeV {{{F}}}7+ (Zamkov et al 2002 Phys. Rev. A 65 062706) mixed state (1{s}2 {}1S,1s2s {}3S) He-like ion collisions with H2 targets, we report new values of {R}m=3.5+/- 0.4 for boron and {R}m=1.8+/- 0.3 for fluorine. In addition, the ratios of {}2D/{}2P and {{}2P}+/{{}2P}- populations from either the metastable and/or ground state beam component, also relevant to this analysis, are evaluated and compared to previously reported results for carbon collisions on helium (Strohschein et al 2008 Phys. Rev. A 77 022706) including a critical comparison to theory.

Subterranean Groundwater Nutrient Input to Coastal Oceans and Coral Reef Sustainability

NASA Astrophysics Data System (ADS)

Paytan, A.; Street, J. H.

2003-12-01

Coral reefs are often referred to as the tropical rain forests of the oceans because of their high productivity and biodiversity. Recent observations in coral reefs worldwide have shown clear degradation in water quality and coral reef health and diversity. The implications of this are severe, including tremendous economic losses mostly though fishing and tourism. Nutrient loading has been implicated as one possible cause for the ecosystem decline. A previously unappreciated potential source of nutrient loading is submarine ground water discharge (SGW). Ground water in many cases has high nutrient content from sewage pollution and fertilizer application for agriculture and landscaping. To better understand the effect of this potential source of nutrient input and degrading water quality, we are exploring the contribution of SGW to the nutrient levels in coral reefs. A key to this approach is determining the amount and source of SGW that flows into the coast as well as its nutrient concentrations. The SGW flux and associated input of chemical dissolved load (nutrient, DOC, trace elements and other contaminants) is quantified using naturally occurring Ra isotopes. Radium isotopes have been shown to be excellent tracers for SGW inputs into estuaries and coastal areas (Moore, 1996; Hussain et al., 1999; Kerst et al., 2000). Measurements of Ra activity within the coral reef, the lagoons and the open waters adjacent to the reef provide valuable information regarding the input of Ra as well as nutrients and possibly pollutant from groundwater discharge. Through this analysis the effect of SGD on the delicate carbon and nutrient balance of the fragile coral reef ecosystem could be evaluated. In addition to quantifying the contribution of freshwater to the nutrient mass balance in the reef, information regarding the length of time a water parcel has remained in the near-shore region over the reef can be estimated using the Ra isotope quartet.

Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops.

PubMed

Olsen, Chris M; Lee, Hui-Ting; Marky, Luis A

2009-03-05

G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular processes and more recently are considered novel targets for drug therapy in aging and anticancer research. In this work, we have investigated the thermodynamic contributions of the loops on the stable formation of G-quadruplexes. Specifically, we use a combination of UV, circular dichroism (CD) and fluorescence spectroscopies, and differential scanning calorimetry (DSC) to determine thermodynamic profiles, including the differential binding of ions and water, for the unfolding of the thrombin aptamer: d(GGT2GGTGTGGT2GG) that is referred to as G2. The sequences in italics, TGT and T2, are known to form loops. Other sequences examined contained base substitutions in the TGT loop (TAT, TCT, TTT, TAPT, and UUU), in the T2 loops (T4, U2), or in both loops (UGU and U2, UUU and U2). The CD spectra of all molecules show a positive band centered at 292 nm, which corresponds to the "chair" conformation. The UV and DSC melting curves of each G-quadruplex show monophasic transitions with transition temperatures (T(M)s) that remained constant with increasing strand concentration, confirming their intramolecular formation. These G-quadruplexes unfold with T(M)s in the range from 43.2 to 56.5 degrees C and endothermic enthalpies from 22.9 to 37.2 kcal/mol. Subtracting the contribution of a G-quartet stack from each experimental profile indicated that the presence of the loops stabilize each G-quadruplex by favorable enthalpy contributions, larger differential binding of K+ ions (0.1-0.6 mol K+/ mol), and a variable uptake/release of water molecules (-6 to 8 mol H2O/mol). The thermodynamic contributions for these specific base substitutions are discussed in terms of loop stacking (base-base stacking within the loops) and their hydration effects.

A theoretical study of the dynamic behavior of alkane hydroxylation by a compound I model of cytochrome P450.

PubMed

Yoshizawa, K; Kamachi, T; Shiota, Y

2001-10-10

Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.

Cardiac resynchronization therapy by multipoint pacing improves response of left ventricular mechanics and fluid dynamics: a three-dimensional and particle image velocimetry echo study.

PubMed

Siciliano, Mariachiara; Migliore, Federico; Badano, Luigi; Bertaglia, Emanuele; Pedrizzetti, Gianni; Cavedon, Stefano; Zorzi, Alessandro; Corrado, Domenico; Iliceto, Sabino; Muraru, Denisa

2017-11-01

To characterize the effect of multipoint pacing (MPP) compared to biventricular pacing (BiV) on left ventricle (LV) mechanics and intraventricular fluid dynamics by three-dimensional echocardiography (3DE) and echocardiographic particle imaging velocimetry (Echo-PIV). In 11 consecutive patients [8 men; median age 65 years (57-75)] receiving cardiac resynchronization therapy (CRT) with a quadripolar LV lead (Quartet,St.Jude Medical,Inc.), 3DE and Echo-PIV data were collected for each pacing configuration (CRT-OFF, BiV, and MPP) at follow-up after 6 months. 3DE data included LV volumes, LV ejection fraction (LVEF), strain, and systolic dyssynchrony index (SDI). Echo-PIV was used to evaluate the directional distribution of global blood flow momentum, ranging from zero, when flow force is predominantly along the base-apex direction, up to 90° when it becomes transversal. MPP resulted in significant reduction in end-diastolic and end-systolic volumes compared with both CRT-OFF (P = 0.02; P = 0.008, respectively) and BiV (P = 0.04; P = 0.03, respectively). LVEF and cardiac output were significant superior in MPP compared with CRT-OFF, but similar between MPP and BiV. Statistical significant differences when comparing global longitudinal and circumferential strain and SDI with MPP vs. CRT-OFF were observed (P = 0.008; P = 0.008; P = 0.01, respectively). There was also a trend towards improvement in strain between BiV and MPP that did not reach statistical significance. MPP reflected into a significant reduction of the deviation of global blood flow momentum compared with both CRT-OFF and BiV (P = 0.002) indicating a systematic increase of longitudinal alignment from the base-apex orientation of the haemodynamic forces. These preliminary results suggest that MPP resulted in significant improvement of LV mechanics and fluid dynamics compared with BiV. However, larger studies are needed to confirm this hypothesis. © Crown copyright 2016.

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

PubMed

Beauregard-Racine, Julie; Bicep, Cédric; Schliep, Klaus; Lopez, Philippe; Lapointe, François-Joseph; Bapteste, Eric

2011-07-20

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches. We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.

Music and Astronomy Under The Stars after 4 years and 50,000 People

NASA Astrophysics Data System (ADS)

Lubowich, Donald A.

2013-01-01

Since 2009 my NASA-funded Music and Astronomy Under the Stars (MAUS) program has brought astronomy to 50,000 music lovers at the National Mall (co-sponsor OSTP); Central Park Jazz, Newport Folk, Ravinia, or Tanglewood music festivals; and classical, folk, pop/rock, opera, Caribbean, or county-western concerts in parks assisted by astronomy clubs (55 events; 28parks). MAUS combines solar, optical, and radio telescope observations; live image projection; large posters/banners (From the Earth to the Universe and Visions of the Universe); videos; and hands-on activities (Night Sky Network; Harvard-Smithsonian CfA); imaging with a cell phone mount; and hand-outs(with info on science museums, astronomy clubs, and citizen science before and after the concerts or at intermission. Yo-Yo-Ma, the Chicago and Boston Symphony Orchestras, the McCoy Tyner Quartet, Ravi Coltrane, Esperanza Spalding, the Stanley Clarke Band, Phish, Blood Sweat and Tears, Deep Purple, Patti Smith, Tony Orlando, and Ronan Tynan performed at these concerts. MAUS reached underserved groups and attracted large enthusiastic crowds. Many young children participated in this family learning experience-often the first time they looked through a telescope. Lessons learned: plan early; create partnerships with parks and astronomy clubs; test equipment; have backup equipment; create professional displays; select the best location to obtain a largest number of participants; use media/www sites to promote the events; use many telescopes for multipletargets; project a live image or video; select equipment that is easy to use, store, set-up, and take down; use hands-on astronomy activities; position the displays for maximum visibility (they became teachable moments); and have educator hand-outs. While < 50% of the participants attended a science museum or took part in astronomy programs in the previous year (based on our survey), they found MAUS enjoyable and understandable; learned about astronomy; wanted to learn more; and increased their interest in science (ave. rating 4.6/5). Taking science directly to people is effective in promoting scienceeducation! Sponsor: NASA grant NNX09AD53G

Evaluation of Two Highly-Multiplexed Custom Panels for Massively Parallel Semiconductor Sequencing on Paraffin DNA

PubMed Central

Kotoula, Vassiliki; Lyberopoulou, Aggeliki; Papadopoulou, Kyriaki; Charalambous, Elpida; Alexopoulou, Zoi; Gakou, Chryssa; Lakis, Sotiris; Tsolaki, Eleftheria; Lilakos, Konstantinos; Fountzilas, George

2015-01-01

Background—Aim Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. Methods Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. Results Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman’s rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8–99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1–95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3–76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. Conclusions Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed. PMID:26039550

Cosmic Interactions

NASA Astrophysics Data System (ADS)

2008-01-01

An image based on data taken with ESO's Very Large Telescope reveals a triplet of galaxies intertwined in a cosmic dance. ESO PR Photo 02/08 ESO PR Photo 02/08 NGC 7173, 7174, and 7176 The three galaxies, catalogued as NGC 7173 (top), 7174 (bottom right) and 7176 (bottom left), are located 106 million light-years away towards the constellation of Piscis Austrinus (the 'Southern Fish'). NGC 7173 and 7176 are elliptical galaxies, while NGC 7174 is a spiral galaxy with quite disturbed dust lanes and a long, twisted tail. This seems to indicate that the two bottom galaxies - whose combined shape bears some resemblance to that of a sleeping baby - are currently interacting, with NGC 7176 providing fresh material to NGC 7174. Matter present in great quantity around the triplet's members also points to the fact that NGC 7176 and NGC 7173 have interacted in the past. Astronomers have suggested that the three galaxies will finally merge into a giant 'island universe', tens to hundreds of times as massive as our own Milky Way. ESO PR Photo 02/08 ESO PR Photo 02b/08 NGC 7173, 7174, and 7176 The triplet is part of a so-called 'Compact Group', as compiled by Canadian astronomer Paul Hickson in the early 1980s. The group, which is the 90th entry in the catalogue and is therefore known as HCG 90, actually contains four major members. One of them - NGC 7192 - lies above the trio, outside of this image, and is another peculiar spiral galaxy. Compact groups are small, relatively isolated, systems of typically four to ten galaxies in close proximity to one another. Another striking example is Robert's Quartet. Compact groups are excellent laboratories for the study of galaxy interactions and their effects, in particular the formation of stars. As the striking image reveals, there are many other galaxies in the field. Some are distant ones, while others seem to be part of the family. Studies made with other telescopes have indeed revealed that the HCG 90 group contains 16 members, most of them much smaller in size than the four members with an entry in the NGC catalogue.

Nuclearity controlled cyanide-bridged bimetallic CrIII-MnII compounds: synthesis, crystal structures, magnetic properties and theoretical calculations.

PubMed

Toma, Luminita; Lescouëzec, Rodrigue; Vaissermann, Jacqueline; Delgado, Fernando S; Ruiz-Pérez, Catalina; Carrasco, Rosa; Cano, Juan; Lloret, Francesc; Julve, Miguel

2004-11-19

The preparation, X-ray crystallography and magnetic investigation of the compounds PPh4[Cr(bipy)(CN)4].2 CH3CN.H2O (1) (mononuclear), [[Cr(bipy)(CN)4]2Mn-(H2O)4].4H2O (2) (trinuclear), [[Cr(bipy)(CN)4]2Mn(H2O)2] (3) (chain) and [[Cr(bipy)(CN)4]2Mn(H2O)].H2O.CH3CN (4) (double chain) [bipy=2,2'-bipyridine; PPh4 (+)=tetraphenylphosphonium] are described herein. The [Cr(bipy)(CN)4]- unit act either as a monodentate (2) or bis-monodentate (3) ligand toward the manganese atom through one (2) or two (3) of its four cyanide groups. The manganese atom is six-coordinate with two (2) or four (3) cyanide nitrogens and four (2) or two (3) water molecules building a distorted octahedral environment. In 4, two chains of 3 are pillared through interchain Mn-N-C-Cr links which replace one of the two trans-coordinated water molecules at the manganese atom to afford a double chain structure where bis- and tris-monodenate coordination modes of [Cr(bipy)(CN)4]- coexist. The magnetic properties of 1-4 were investigated in the temperature range 1.9-300 K. A Curie law behaviour for a magnetically isolated spin quartet is observed for 1. A significant antiferromagnetic interaction between CrIII and MnII through the single cyanide bridge [J=-6.2 cm(-1), the Hamiltonian being defined as H=-J(SCr1.SMn+SCr2.SMn] occurs in 2 leading to a low-lying spin doublet which is fully populated at T <5 K. A metamagnetic behaviour is observed for 3 and 4 [the values of the critical field Hc being ca. 3000 (3) and 1500 Oe (4)] which is associated to the occurrence of weak interchain antiferromagnetic interactions between ferrimagnetic Cr2III MnII chains. The analysis of the exchange pathways in 2-4 through DFT type calculations together with the magnetic bevaviour simulation using the quantum Monte Carlo methodology provided a good understanding of their magnetic properties.

Bringing Astronomy Directly to People Who Do Not Come to Star Parties, Science Museums, or Science Festivals

NASA Astrophysics Data System (ADS)

Lubowich, Donald A.

2013-01-01

My successful programs have included telescope observations, hands-on activities, and edible astronomy demonstrations for: outdoor concerts or music festivals; the National Mall; churches, synagogues, seminaries, or clergy conferences; the Ronald McDonald House of Long Island (New Hyde Park, NY), the Winthrop University Hospital Children’s Medical Center (Mineola, NY); the Fresh Air Fund summer camps; a Halloween star party with costumed kids looking through telescopes; a Super Bowl Star Party; the World Science Festival (NYC); the Princeton University Science and Engineering Expo; the USA Science and Engineering Festival; and the NYC Columbus Day Parade. These outreach activities have reached thousands of people including many young girls. Information was also provided about local science museums, citizen science projects, astronomy educational sites, and astronomy clubs to encourage learning after these events. In 2010 I created Astronomy Night on the National Mall (co-sponsored the White House Office of Science and Technology Policy) with the participation of astronomy clubs, Chandra X-Ray Center, STScI, NASA, NOAO, NSF and the National Air and Space Museum. Since 2009 my NASA-funded Music and Astronomy Under the Stars (MAUS) program has brought astronomy to 50,000 music lovers who attended the Central Park Jazz, Newport Folk, Tanglewood, or Ravinia music festivals or classical, folk, rock, pop, opera, or county-western concerts in local parks assisted by astronomy clubs. MAUS is an evening, nighttime, and cloudy weather traveling astronomy program combining solar, optical, and radio telescope observations; a live image projection system; large outdoor posters and banners; videos; and hands-on activities before and after the concerts or at intermission. Yo-Yo-Ma and the Chicago Symphony or Boston Symphony Orchestras, the McCoy Tyner Quartet with Ravi Coltrane, Esperanza Spalding, the Stanley Clarke Band, Phish, Blood Sweat and Tears, Deep Purple, Patti Smith, Tony Orlando, and Ronan Tynan have performed at these concerts. MAUS attracts large enthusiastic crowds often with young children participating in this family learning experience - often the first time these children looked through a telescope.

Part I: Sound color in the music of Gyorgy Kurtag, Part II: "Leopard's Path," thirteen visions for chamber ensemble

NASA Astrophysics Data System (ADS)

Iachimciuc, Igor

The dissertation is in two parts, a theoretical study and a musical composition. In Part I the music of Gyorgy Kurtag is analyzed from the point of view of sound color. A brief description of what is understood by the term sound color, and various ways of achieving specific coloristic effects, are presented in the Introduction. An examination of Kurtag's approaches to the domain of sound color occupies the chapters that follow. The musical examples that are analyzed are selected from Kurtag's different compositional periods, showing a certain consistency in sound color techniques, the most important of which are already present in the String Quartet, Op. 1. The compositions selected for analysis are written for different ensembles, but regardless of the instrumentation, certain principles of the formation and organization of sound color remain the same. Rather than relying on extended instrumental techniques, Kurtag creates a large variety of sound colors using traditional means such as pitch material, register, density, rhythm, timbral combinations, dynamics, texture, spatial displacement of the instruments, and the overall musical context. Each sound color unit in Kurtag's music is a separate entity, conceived as a complete microcosm. Sound color units can either be juxtaposed as contrasting elements, forming sound color variations, or superimposed, often resulting in a Klangfarbenmelodie effect. Some of the same gestural figures (objets trouves) appear in different compositions, but with significant coloristic modifications. Thus, the principle of sound color variations is not only a strong organizational tool, but also a characteristic stylistic feature of the music of Gyorgy Kurtag. Part II, Leopard's Path (2010), for flute, clarinet, violin, cello, cimbalom, and piano, is an original composition inspired by the painting of Jesse Allen, a San Francisco based artist. The composition is conceived as a cycle of thirteen short movements. Ten of these movements are the musical interpretation of the objects presented in the painting, and are stylistically similar. These movements are scored for the entire ensemble. The other three movements, entitled Interludes, provide a stylistic contrast, and are not directly connected with the painting.

Three-dimensional instability of standing waves

NASA Astrophysics Data System (ADS)

Zhu, Qiang; Liu, Yuming; Yue, Dick K. P.

2003-12-01

We investigate the three-dimensional instability of finite-amplitude standing surface waves under the influence of gravity. The analysis employs the transition matrix (TM) approach and uses a new high-order spectral element (HOSE) method for computation of the nonlinear wave dynamics. HOSE is an extension of the original high-order spectral method (HOS) wherein nonlinear wave wave and wave body interactions are retained up to high order in wave steepness. Instead of global basis functions in HOS, however, HOSE employs spectral elements to allow for complex free-surface geometries and surface-piercing bodies. Exponential convergence of HOS with respect to the total number of spectral modes (for a fixed number of elements) and interaction order is retained in HOSE. In this study, we use TM-HOSE to obtain the stability of general three-dimensional perturbations (on a two-dimensional surface) on two classes of standing waves: plane standing waves in a rectangular tank; and radial/azimuthal standing waves in a circular basin. For plane standing waves, we confirm the known result of two-dimensional side-bandlike instability. In addition, we find a novel three-dimensional instability for base flow of any amplitude. The dominant component of the unstable disturbance is an oblique (standing) wave oriented at an arbitrary angle whose frequency is close to the (nonlinear) frequency of the original standing wave. This finding is confirmed by direct long-time simulations using HOSE which show that the nonlinear evolution leads to classical Fermi Pasta Ulam recurrence. For the circular basin, we find that, beyond a threshold wave steepness, a standing wave (of nonlinear frequency Omega) is unstable to three-dimensional perturbations. The unstable perturbation contains two dominant (standing-wave) components, the sum of whose frequencies is close to 2Omega. From the cases we consider, the critical wave steepness is found to generally decrease/increase with increasing radial/azimuthal mode number of the base standing wave. Finally, we show that the instability we find for both two- and three-dimensional standing waves is a result of third-order (quartet) resonance.

Cation Coordination Alters the Conformation of a Thrombin-Binding G-Quadruplex DNA Aptamer That Affects Inhibition of Thrombin.

PubMed

Zavyalova, Elena; Tagiltsev, Grigory; Reshetnikov, Roman; Arutyunyan, Alexander; Kopylov, Alexey

2016-10-01

Thrombin-binding aptamers are promising anticoagulants. HD1 is a monomolecular antiparallel G-quadruplex with two G-quartets linked by three loops. Aptamer-thrombin interactions are mediated with two TT-loops that bind thrombin exosite I. Several cations were shown to be coordinated inside the G-quadruplex, including K + , Na + , NH 4 + , Ba 2+ , and Sr 2+ ; on the contrary, Mn 2+ was coordinated in the grooves, outside the G-quadruplex. K + or Na + coordination provides aptamer functional activity. The effect of other cations on aptamer functional activity has not yet been described, because of a lack of relevant tests. Interactions between aptamer HD1 and a series of cations were studied. A previously developed enzymatic method was applied to evaluate aptamer inhibitory activity. The structure-function correlation was studied using the characterization of G-quadruplex conformation by circular dichroism spectroscopy. K + coordination provided the well-known high inhibitory activity of the aptamer, whereas Na + coordination supported low activity. Although NH 4 + coordination yielded a typical antiparallel G-quadruplex, no inhibitory activity was shown; a similar effect was observed for Ba 2+ and Sr 2+ coordination. Mn 2+ coordination destabilized the G-quadruplex that drastically diminished aptamer inhibitory activity. Therefore, G-quadruplex existence per se is insufficient for aptamer inhibitory activity. To elicit the nature of these effects, we thoroughly analyzed nuclear magnetic resonance (NMR) and X-ray data on the structure of the HD1 G-quadruplex with various cations. The most reasonable explanation is that cation coordination changes the conformation of TT-loops, affecting thrombin binding and inhibition. HD1 counterparts, aptamers 31-TBA and NU172, behaved similarly with some distinctions. In 31-TBA, an additional duplex module stabilized antiparallel G-quadruplex conformation at high concentrations of divalent cations; whereas in NU172, a different sequence of loops in the G-quadruplex module provided an equilibrium of antiparallel and parallel G-quadruplexes that shifted with cation binding. In conclusion, structures of G-quadruplex aptamers are flexible enough and are fine-tuned with different cation coordination.

Condensed Matter Theories - Volume 22

NASA Astrophysics Data System (ADS)

Reinholz, Heidi; Röpke, Gerd; de Llano, Manuel

2007-09-01

pt. A. Fermi liquids. Pressure comparison between the spherical cellular model and the Thomas-Fermi model / G.A. Baker, Jr. Pair excitations and vertex corrections in Fermi fluids and the dynamic structure function of two-dimension 3He / H.M. Böhm, H. Godfrin, E. Krotscheck, H.J. Lauter, M. Meschke and M. Panholzer. Condensation of helium in wedges / E.S. Hernádez ... [et al.]. Non-Fermi liquid behavior from the Fermi-liquid approach / V.A. Khodel ... [et al.]. Theory of third sound and stability of thin 3He-4He superfluid films / E. Krotscheck and M.D. Miller. Pairing in asymmetrical Fermi systems / K.F. Quader and R. Liao. Ground-state properties of small 3He drops from quantum Monte Carlo simulations / E. Sola, J. Casulleras and J. Boronat. Ground-state energy and compressibility of a disordered two-dimensional electron gas / Tanatar ... [et al.]. Quasiexcitons in photoluminescence of incompressible quantum liquids / A. Wójs, A.G ladysiewicz and J.J. Quinn -- pt. B. Bose liquids. Quantum Boltzmann liquids / K.A. Gernoth, M L. Ristig and T. Lindenau. Condensate fraction in the dynamic structure function of Bose fluids / M. Saarela, F. Mazzanti and V. Apaja -- pt. C. Strongly-correlated electronic systems. Electron gas in high-field nanoscopic transport: metallic carbon nanotubes / F. Green and D. Neilson. Evolution and destruction of the Kondo effect in a capacitively coupled double dot system / D.E. Logan and M.R. Galpin. The method of increments-a wavefunction-based Ab-Initio correlation method for solids / B. Paulus. Fractionally charged excitations on frustrated lattices / E. Runge, F. Pollmann and P. Fulde. 5f Electrons in actinides: dual nature and photoemission spectra / G. Zwicknagl -- pt. D. Magnetism. Magnetism in disordered two-dimensional Kondo-Necklace / W. Brenig. On the de Haas-can Alphen oscillation in 2D / S. Fujita and D.L. Morabito. Dynamics in one-dimensional spin systems-density matrix reformalization group study / S. Nishimoto and M. Arikawa. Frustrated quantum antiferromagnets: application of high-order coupled cluster method / J. Richter ... [et al.]. Vorticity and antivorticity in submicron ferromagnetic films / H. Wang, M. Yan and C.E. Campbell -- pt. E. Conductivity. D-wave checkerboard bose condensate of mobile bipolarons / A.S. Alexandrov. Five possible reasons why high-Tc superconductivity is stalled / M. Grether and M. de Llano. Multistability and Multi 2[Pie symbol]-Kinks in the Frenkel-Kontorova model: an application to arrays of Josephson junctions / K.E. Kürten and C. Krattenthaler. Lowering of Boson-Fermion system energy with a gapped cooper resonant-pair dispersion relation / T.A. Mamedov and M. de Llano. The concept of correlated density and its application / K. Morawetz ... [et al.]. Competing local and non-local phase correlations in Fermionic systems with resonant pairing: the Boson-Fermion scenario / J. Ranninger. Superconducting order parameters in the extended Hubbard model: a simple mean-field study / J.S. Thakur and M.P. Das -- pt. F. Nuclear systems. Distribution of maxima of the antisymmetized wave function for the nucleons of a closed-shell and for the nucleons of all closed-shells in a nucleus / G.S. Anagnostatos. Pairing of strongly correlated nucleons / W.H. Dickhoff. Short range correlations in relativistic nuclear models / P.K. Panda, C. Providência and J. da Providência. Quartetting in attractive Fermi-systems and alpha particle condensation in nuclear systems / P. Schuck ... [et al.]. Alpha-alpha and Alpha-nucleus potentials: an energy-density fucntional approach / Z.F. Shehadeh ... [et al.]. -- pt. G. Density functional theory and MD simulations. Dynamics of metal clusters in rare gas clusters / M. Baer ... [et al.]. Reinhard and E. Suraud. Kohn-Sham calculations combined with an average pair-density functional theory / P. Gori-Giorgi and A. Savin. Correlations, collision frequency and optical properties in laser excited clusters / H. Reinholz, T. Raitza and G. Röpke -- pt. H. Biophysics. Condensed matter physics of biomolecule systems in a differential geometric framework / H. Bohr, J.I. Ipsen and S. Markvorsen. The brain's view of the natural world in motion: computing structure from function using directional Fourier transformations / B.K. Dellen, J.W. Clark and R. Wessel -- pt. I. Quantum information. Control and error prevention in condensed matter quantum computing devices / M.S. Byrd and L.A. Wu. Maxent approaches to qubits / C.M. Sarris, A.N. Proto and F B. Malik -- pt. J. New formalisms. Thermal coherent states, a broader class of mixed coherent states, and generalized thermo-field dynamics / R.F. Bishop and A. Vourdas. Ergodic condition and magnetic models / M. Howard Lee. From thermodynamics to Maxent / A. Plastino and E. M.F. Curado. Recent progress in the density-matrix renormalization group / U. Schollwöck.

Lessons learned from additional research analyses of unsolved clinical exome cases.

PubMed

Eldomery, Mohammad K; Coban-Akdemir, Zeynep; Harel, Tamar; Rosenfeld, Jill A; Gambin, Tomasz; Stray-Pedersen, Asbjørg; Küry, Sébastien; Mercier, Sandra; Lessel, Davor; Denecke, Jonas; Wiszniewski, Wojciech; Penney, Samantha; Liu, Pengfei; Bi, Weimin; Lalani, Seema R; Schaaf, Christian P; Wangler, Michael F; Bacino, Carlos A; Lewis, Richard Alan; Potocki, Lorraine; Graham, Brett H; Belmont, John W; Scaglia, Fernando; Orange, Jordan S; Jhangiani, Shalini N; Chiang, Theodore; Doddapaneni, Harsha; Hu, Jianhong; Muzny, Donna M; Xia, Fan; Beaudet, Arthur L; Boerwinkle, Eric; Eng, Christine M; Plon, Sharon E; Sutton, V Reid; Gibbs, Richard A; Posey, Jennifer E; Yang, Yaping; Lupski, James R

2017-03-21

Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.

Demonstration of the production of oxygen-centered free radicals during electrolysis using E.S.R. spin-trapping techniques: effects on cardiac function in the isolated rat heart.

PubMed

Lecour, S; Baouali, A B; Maupoil, V; Chahine, R; Abadie, C; Javouhey-Donzel, A; Rochette, L; Nadeau, R

1998-03-01

The present study was designed to identify the free radicals generated during the electrolysis of the solution used to perfuse isolated rat heart Langendorff preparations. The high reactivity and very short half-life of oxygen free radicals make their detection and identification difficult. A diamagnetic organic molecule (spin trap) can be used to react with a specific radical to produce a more stable secondary radical or "spin adduct" detected by electron spin resonance (ESR). Isovolumic left ventricular systolic pressure (LVSP) and left ventricular end diastolic pressure (LVEDP) were measured by a fluid-filled latex balloon inserted into the left ventricle. The coronary flow was measured by effluent collection. Electrolysis was performed with constant currents of 0.5, 1, 1.5, 3, 5, 7.5, and 10 mA generated by a Grass stimulator and applied to the perfusion solution for 1 min. A group of experiments was done using a 1.5 mA current and a Krebs-Henseleit (K-H) solution containing free radical scavengers (superoxide dismutase (SOD): 100 IU/ml or mannitol: 50 mM). Heart function rapidly declined in hearts perfused with K-H buffer that had been electrolyzed for 1 min. The addition of mannitol (50 mM) to the perfusion solution had no effect on baseline cardiac function before electrolysis while SOD (100 IU/ml) increased the coronary flow. However, SOD was more effective than the mannitol in protecting the heart against decreased of cardiac function, 5 min after the end of electrolysis. Samples of the K-H medium subjected to electrolysis were collected in cuvettes containing a final concentration of 125 mM 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) and analyzed by spectroscopy. The ESR spectrum consisted of a quartet signal (hyperfine couplings aN = aH = 14.9 G) originating from the hydroxyl adduct signal, DMPO-OH. The intensity of the DMPO-OH signal remained stable during the 60 s of electrolysis and the quantity of free radicals induced by electrolysis was directly proportional to the intensity of the current. The addition of mannitol and SOD to the perfusate scavenged the hydroxyl radicals present in the solution, suggesting that both hydroxyl and superoxide radicals were formed during electrolysis.

Obesity, the deadly quartet and the contribution of the neglected daily organ rest - a new dimension of un-health and its prevention

PubMed Central

2015-01-01

The “deadly quartet”: excessive weight, hypertension, impaired glucose homeostasis, and atherogenic dyslipidemia constitute a greater threat to health than the added effects of smoking and alcohol abuse. It is strongly associated with unrestricted consumption of processed, refined foods. Recent observations from experience in South East Asia shows that the interval between lifestyle changes and associated change in disease pattern is shorter than earlier believed. Recent experience from obesity studies in Africa demonstrates not only dramatic changes in health but also large social consequences from being overweight. Obesity is not only a result of overeating - dozens of other factors are known to contribute. Our palaeolithic forefathers and those living a similar lifestyle today are reported to rarely have diseases and to live a long life. One such group is the Hunzas, living in Northern Pakistan, are reported to live on a daily 1,800-calorie 99% plant-based diet, consisting in 73% of mostly unrefined/unprocessed carbohydrates, 17% fat and 10% protein. They, and most likely also our forefathers, do/did most likely only eat twice a day, at noon and early evening. Calorie-restriction (CR) and also fasting was early recommended and has been so during thousands of years - early Greek medicine and giants such as Hippocrates, Galenus and later also Paracelsus prescribed restrictions in eating and fasting. So did Middle Age physicians and other nutrition experts such as Louis Cornado. Today it is again practiced around the World. Overeating and heavy postprandial metabolism is a great burden to the body causing elevated levels in blood of endotoxin, increased inflammatory and oxidative stress, release of tumor necrosis factor-α, and other pro-inflammatory cytokines, increases in numbers of and activating of leukocytes, a reaction that is potentiated by the presence of large-chain fatty acids and sugars. Various metabolic, uremic, microbiota-derived and environmental poisons accumulate in large amounts in the adipose tissues. High levels of poisons in the adipose tissues decreases the turnover of fats in order to protect other organs. The content in adipose of POPs - altogether 17 dioxins/furans and 18 polychlorinated biphenyl congeners, has been reported to be 2-3 times higher in obese compared to lean persons. Daily fasting consisting in 16 to 18 hours of avoidance of calorie intake offers an interesting alternative. An attractive policy is to abstain from eating between 18:00 in the evening and 10:00 or 12:00 AM, a plan, which I personally have practiced during many years. PMID:26312244

G-Quadruplex Folds of the Human Telomere Sequence Alter the Site Reactivity and Reaction Pathway of Guanine Oxidation Compared to Duplex DNA

PubMed Central

Fleming, Aaron M.; Burrows, Cynthia J.

2013-01-01

Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile of the sites of oxidation and structures of products observed from G-quadruplex and duplex structures of the human telomere sequence was studied in the G-quadruplex folds (hybrid (K+), basket (Na+), and propeller (K+ + 50% CH3CN)) resulting from the sequence 5’-(TAGGGT)4T-3’ and in an appropriate duplex containing one telomere repeat. Oxidations with four oxidant systems consisting of riboflavin photosensitization, carbonate radical generation, singlet oxygen, and the copper Fenton-like reaction were analyzed under conditions of low product conversion to determine relative reactivity. The one-electron oxidants damaged the 5’-G in G-quadruplexes leading to spiroiminodihydantoin (Sp) and 2,2,4-triamino-2H-oxazol-5-one (Z) as major products as well as 8-oxo-7,8-dihydroguanine (OG) and 5-guanidinohydantoin (Gh) in low relative yields, while oxidation in the duplex context produced damage at the 5’- and middle-Gs of GGG sequences and resulted in Gh being the major product. Addition of the reductant N-acetylcysteine (NAC) to the reaction did not alter the riboflavin-mediated damage sites, but decreased Z by 2-fold and increased OG by 5-fold, while not altering the hydantoin ratio. However, NAC completely quenched the CO3•− reactions. Singlet oxygen oxidations of the G-quadruplex showed reactivity at all Gs on the exterior faces of G-quartets and furnished the product Sp, while no oxidation was observed in the duplex context under these conditions, and addition of NAC had no effect. Because a long telomere sequence would have higher-order structures of G-quadruplexes, studies were also conducted with 5’-(TAGGGT)8-T-3’, and it provided similar oxidation profiles to the single G-quadruplex. Lastly, CuII/H2O2-mediated oxidations were found to be indiscriminate in the damage patterns, and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) was found to be a major duplex product, while nearly equal yields of 2Ih and Sp were observed in G-quadruplex contexts. These findings indicate that the nature of the secondary structure of folded DNA greatly alters both the reactivity of G toward oxidative stress as well as the product outcome and suggest that recognition of damage in telomeric sequences by repair enzymes may be profoundly different from that of B-form duplex DNA. PMID:23438298

Discovery of Prehistoric Skies

NASA Astrophysics Data System (ADS)

Gurshtein, A. A.

1995-12-01

It was Charles Francois Dupui, of France, who two centuries ago in his twelve-volume "Origine de tous les cults" (1795) worked out a proposition that all the different religious customs, stories, and dogmas will be found upon examination to have a cradle as one or another aspect of the natural, mainly, astronomical phenomena. It is absolutely correct but he and his spirited followers failed to develop a basic scientific quantitative argument focused on astronomy - chronological distribution of events. It is the first time that a combination of the up-to-date knowledge in archaic symbology and the professional astronomical data for precession and other regular astronomical events constitutes conditions for an absolutely new approach. An astronomical reconstruction of the evolution of the Zodiacal constellations was made, based on the Indo-european and Sumero-Akkadian religio-cultural data, including artifacts such as cult statuettes, cuneiform tablets, cylinder seals and boundary stones. It was argued that the development of 12 houses of the Zodiac in 3 groups of 4 over some six millennia was dictated by the changes made by precession in the positions of the vernal and autumnal equinoxes and the summer and winter solstices. The first quartet of the Zodiacal constellations (Gemini, Virgo, Sagittarius, Pisces) was recognized by the first agriculturists from the Fertile Crescent to learn the four most important Sun positions and to predict the ongoing seasons; it was done as far back as 5,600 B.C. (with a formal error of this determination about +/- 150 years). The second one (Taurus, Leo, Scorpio, Aquarius) was introduced in 2,700 +/- 250 years B.C. by Egyptians with their own animal symbolism that was the etymological root for the term the Zodiac (a circle of animals). This event was followed with the acquaintance of the new calendar and erection of the great pyramids as an eternal sanctuary for their mental triumph. In the first half of 14 century B.C. the Egyptian pharaoh Ekhnaton (Amenhotep 1V) attempted to inaugurate a new four constellation set to fixate the Sun track. The attempt was in vain but it seems the knowledge to go via Moses and the tribes left Egypt for Canaan. According our precessional dating the final design of the Zodiac with 12 houses appeared at 1,200 +/- 400 years B.C. In opposite to the figure 7 which was from the Paleolithic, the first great opus where figure 12 appeared as a sacred one was the Holy Bible. Many other details of the concept proposed are discussed.

Roles of Bridging Ligand Topology and Conformation in Controlling Exchange Interactions between Paramagnetic Molybdenum Fragments in Dinuclear and Trinuclear Complexes.

PubMed

Ung VÂ, V&acaron;n Ân; Cargill Thompson, Alexander M. W.; Bardwell, David A.; Gatteschi, Dante; Jeffery, John C.; McCleverty, Jon A.; Totti, Federico; Ward, Michael D.

1997-07-30

The magnetic properties of two series of dinuclear complexes, and one trinuclear complex, have been examined as a function of the bridging pathway between the metal centers. The first series of dinuclear complexes is [{Mo(V)(O)(Tp)Cl}(2)(&mgr;-OO)], where "OO" is [1,4-O(C(6)H(4))(n)O](2)(-) (n = 1, 1; n = 2, 3), [4,4'-O(C(6)H(3)-2-Me)(2)O](2)(-) (4), or [1,3-OC(6)H(4)O](2)(-) (2) [Tp = tris(3,5-dimethylpyrazolyl)hydroborate]. The second series of dinuclear complexes is [{Mo(I)(NO)(Tp)Cl}(2)(&mgr;-NN)], where "NN" is 4,4'-bipyridyl (5), 3,3'-dimethyl-4,4'-bipyridine (6), 3,8-phenanthroline (7), or 2,7-diazapyrene (8). The trinuclear complex is [{Mo(V)(O)(Tp)Cl}(3)(1,3,5-C(6)H(3)O(3))] (9), whose crystal structure was determined [9.5CH(2)Cl(2): C(56)H(81)B(3)Cl(13)Mo(3)N(18)O(6); monoclinic, P2(1)/n; a = 13.443, b = 41.46(2), c = 14.314(6) Å; beta = 93.21(3) degrees; V = 7995(5) Å(3); Z = 4; R(1) = 0.106]. In these complexes, the sign and magnitude of the exchange coupling constant J is clearly related to both the topology and the conformation of the bridging ligand [where J is derived from H = -JS(1)().S(2)() for 1-8 and H = -J(S(1)().S(2)() + S(2)().S(3)() + S(1)().S(3)()) for 9]. The values are as follows: 1, -80 cm(-)(1); 2, +9.8 cm(-)(1); 3, -13.2 cm(-)(1); 4, -2.8 cm(-)(1); 5, -33 cm(-)(1); 6, -3.5 cm(-)(1); 7, -35.6 cm(-)(1); 8, -35.0 cm(-)(1); 9, +14.4 cm(-)(1). In particular the following holds: (1) J is negative (antiferromagnetic exchange) across the para-substituted bridges ligands of 1 and 3-8 but positive (ferromagnetic exchange) across the meta-substituted bridging ligands of 2 and 9. (2) J decreases in magnitude dramatically as the bridging ligand conformation changes from planar to twisted (compare 3 and 4, or 6 and 8). These observations are consistent with a spin-polarization mechanism for the exchange interaction, propagated across the pi-system of the bridging ligand by via overlap of bridging ligand p(pi) orbitals with the d(pi) magnetic orbitals of the metals. The EPR spectrum of 9 is characteristic of a quartet species and shows weak Deltam(s) = 2 and Deltam(s) = 3 transitions at one-half and one-third, respectively, of the field strength of the principal Deltam(s) = 1 component.

PREFACE: 17th International Conference on Microscopy of Semiconducting Materials 2011

NASA Astrophysics Data System (ADS)

Walther, T.; Midgley, P. A.

2011-11-01

This volume contains invited and contributed papers from the 17th international conference on 'Microscopy of Semiconducting Materials' held at Churchill College, University of Cambridge, on 4-7 April 2011. The meeting was organised under the auspices of the Institute of Physics and supported by the Royal Microscopical Society as well as the Materials Research Society of the USA. This conference series deals with recent advances in semiconductor studies carried out by all forms of microscopy, with an emphasis on electron microscopy and related techniques with high spatial resolution. This time the meeting was attended by 131 delegates from 25 countries world-wide, a record in terms of internationality. As semiconductor devices shrink further new routes of device processing and characterisation need to be developed, and, for the latter, methods that offer sub-nanometre spatial resolution are particularly valuable. The various forms of imaging, diffraction and spectroscopy available in modern microscopes are powerful tools for studying the microstructure, the electronic structure, the chemistry and also electric fields in semiconducting materials. Recent advances in instrumentation, from lens aberration correction in both TEM and STEM instruments, to the development of a wide range of scanning probe techniques, as well as new methods of signal quantification have been presented at this conference. Two examples of topics at this meeting that have attracted a number of interesting studies were: the correlation of microstructural, optical and chemical information at atomic resolution with nanometre-scale resolved maps of the local electrical fields in (In,Al)GaN based semiconductors and tomographic approaches to characterise ensembles of nanowires and stacks of processed layers in devices Figure 1 Figure 1. Opening lecture by Professor Sir Colin J Humphreys. Each manuscript submitted for publication in this proceedings volume has been independently reviewed and revised where necessary. In the end, 61 manuscripts were accepted for publication. The Editors are very grateful to the following colleagues for their rapid and careful reviewing of manuscripts: M Albrecht, J S Barnard, R Beanland, G A Botton, D Cooper, L Clement, A J Craven, A G Cullis, N Daneu, V Grillo, E Grünbaum, A Gustafsson, P-H Jouneau, O L Krivanek, D Larson, M Luysberg, S I Molina, F A Ponce, A Rosenauer, F M Ross, I M Ross, J-L Rouviere, and Z L Wang. Prizes for student presentations at the conference were awarded to Mr Alberto Eljarrat, Universitat de Barcelona, and Mr Thibaud Denneulin, CEA-LETI Grenoble, both of whom are presenting their results also as contributions to this proceedings volume. Entertainment during the conference dinner was provided by the college's string quartet, and after the meal we held the now traditional friendly competition between teams of microscopists; this year teams were asked to construct models of scientific instruments using only cardboard, paper, sticky tape and glue. By unanimous vote, the team who presented the 'Atomic Food Microscope (AFM)' prototype won first prize - the deft 'dipping mode' of the cardboard cantilever (see photo) was a highlight! Figure 2 Figure 2. The prize winning 'Atomic Food Microscope (AFM)' in action! The organisers are very grateful to the following companies who contributed to the success of the meeting by presenting trade stands during an exhibition on the evening of 5 April: Agar Scientific, Bruker, CamScan, FEI, Gatan, Hitachi High Technologies, HREM Research, IOP Publishing, JEOL, Leica Microsystems and MICOS. Finally, we would like to thank the staff of the Institute of Physics for their expert assistance in planning and organising this conference and in particular Claire Garland for her dedicated professional support and her always joyful approach to any issues that arose. October 2011 T Walther P A Midgley

Isomerization and fragmentation reactions of gaseous phenylarsane radical cations and phenylarsanyl cations. A study by tandem mass spectrometry and theoretical calculations.

PubMed

Letzel, Matthias; Kirchhoff, Dirk; Grützmacher, Hans-Friedrich; Stein, Daniel; Grützmacher, Hansjörg

2006-04-28

The unimolecular reactions of radical cations and cations derived from phenylarsane, C6H5AsH2 (1) and dideutero phenylarsane, C6H5AsD2 (1-d2), were investigated by methods of tandem mass spectrometry and theoretical calculations. The mass spectrometric experiments reveal that the molecular ion of phenylarsane, 1*+, exhibits different reactivity at low and high internal excess energy. Only at low internal energy the observed fragmentations are as expected, that is the molecular ion 1*+ decomposes almost exclusively by loss of an H atom. The deuterated derivative 1-d2 with an AsD2 group eliminates selectively a D atom under these conditions. The resulting phenylarsenium ion [C6H5AsH]+, 2+, decomposes rather easily by loss of the As atom to give the benzene radical cation [C6H6]*+ and is therefore of low abundance in the 70 eV EI mass spectrum. At high internal excess energy, the ion 1*+ decomposes very differently either by elimination of an H2 molecule, or by release of the As atom, or by loss of an AsH fragment. Final products of these reactions are either the benzoarsenium ion 4*+, or the benzonium ion [C6H7]+, or the benzene radical cation, [C6H6]*+. As key-steps, these fragmentations contain reductive eliminations from the central As atom under H-H or C-H bond formation. Labeling experiments show that H/D exchange reactions precede these fragmentations and, specifically, that complete positional exchange of the H atoms in 1*+ occurs. Computations at the UMP2/6-311+G(d)//UHF/6-311+G(d) level agree best with the experimental results and suggest: (i) 1*+ rearranges (activation enthalpy of 93 kJ mol(-1)) to a distinctly more stable (DeltaH(r)(298) = -64 kJ mol(-1)) isomer 1 sigma*+ with a structure best represented as a distonic radical cation sigma complex between AsH and benzene. (ii) The six H atoms of the benzene moiety of 1 sigma*+ become equivalent by a fast ring walk of the AsH group. (iii) A reversible isomerization 1+<==>1 sigma*+ scrambles eventually all H atoms over all positions in 1*+. The distonic radical cation 1*+ is predisposed for the elimination of an As atom or an AsH fragment. The calculations are in accordance with the experimentally preferred reactions when the As atom and the AsH fragment are generated in the quartet and triplet state, respectively. Alternatively, 1*(+) undergoes a reductive elimination of H2 from the AsH2 group via a remarkably stable complex of the phenylarsandiyl radical cation, [C6H5As]*+ and an H2 molecule.

Countdown for the Cluster quartet

NASA Astrophysics Data System (ADS)

2000-07-01

Following the successful completion of the Cluster II Flight Readiness Review on 23 June, final launch preparations are progressing smoothly and combined operations with the Soyuz-Fregat launch vehicle are now under way. The dual launches, each involving two Cluster spacecraft built under the prime contractorship of Astrium (former Dornier Satellitensysteme GmbH, Germany), are currently scheduled for 15 July with a launch window opening at 14:40 CEST, 12:40 GMT and lasting 6 minutes, and 9 August from Baikonur Space Centre in Kazakhstan. A number of press events have been organised in various countries to coincide with both launches. The main press centre for the first launch will be located at ESA's European Space Operations Centre (ESOC) at Darmstadt in Germany. Local press centres are also being set up in the other ESA establishments: ESRIN (Italy), ESTEC (The Netherlands), and VILSPA (Spain). See attachment for more detailed information and reply form to register at the various sites. Details of the second launch press event, which will be held in London (UK), will be available at a later date. Cluster II Competition Attracts Record Entries. A highlight of the first launch event at ESOC will be the announcement of the overall winner of ESA's "Name the Cluster quartet" competition and the chosen names of the four Cluster II satellites. Last February, members of the public in all of ESA's 15 member states were asked to suggest the most suitable names for the Cluster II spacecraft. The satellites are currently known as flight models (FM) 5, 6, 7 and 8. Competitors were asked to propose a set of four names (places, people, or things from history, mythology, or fiction, but not living persons) and explain in a few sentences the reasons for their choice. After sifting through more than 5,000 entries from all over Europe and debating at length the merits of the various suggestions, the multinational jury eventually produced a list of 15 national prize winners - one from each ESA member state. These finalists and their families have all won a 3-day trip to attend a special Cluster II launch event in one of these ESA establishments: * ESRIN (near Rome, Italy): winners from France, Ireland, Belgium. * VILSPA (near Madrid, Spain): winners from The Netherlands, Norway, Sweden, Finland. * ESTEC (near Amsterdam, The Netherlands): winners from Germany, Denmark, Switzerland, Austria. * ESOC (in the Rhine Valley, Germany): winners from Italy, Spain, Portugal, United Kingdom. The Lucky 15. The lucky national winners are: Austria: VENTO, NUBO, FULMO, PLUVO entered by Andreas Rosenstingl (Vienna, A). Belgium: ALBATROS, EAGLE, FALCON, HAWK entered by André Borremans (Lembeek, B). Denmark: ORIENTÁLIS, OCCIDENTÁLIS, AQUILÓNIUS, AUSTRÁLIS entered by Mia Stampe (Copenhagen, DK). Finland: UKKO, ILMATAR, KOKKO, LOUHI entered by Ismo Hirvonen (Tampere, FI) France: ADAGIO, ALLEGRO, LARGO, VIVACE entered by Daniel Lellouch (c/o Rehovot, Israel) Germany: TRISTAN & ISOLDE, ROMEO & JULIA entered by Manuela Saal (Köln, D) Ireland: IMBOLC, BELTAINE, LUGHNASA, SAMHAIN entered by Grainne Duncan (Dublin, IR). Italy: GEA, URANO, TETI, CRONO entered by Paola Benna (Avigliana-To, I). Netherlands: KIN, UINAL, TUN, KATUN entered by Ben Jasper Fayer (Hoogeven, NL). Norway: CHLOROS, ERYTHROS, AUREUS, LUTEUS entered by Joar Vatnaland (c/o Leeds, UK). Portugal: IXCHELL, ITZAMNA, MAUINA, RAINBOW entered by Carlos Fernando Carvalhido Oliveira (Porto, P). Spain: DIVEE, BEEDY, EEROT, BROT entered by Sergi Porter (Barcelona, E). Sweden: FLUTE, VIOLIN, CELLO, PIANO entered by Ola Carlström (Huddige, SW). Switzerland: SOLÉA, LUNÉA, EOLIA, ONDÉA entered by Luciana Favre (Riddes, CH). United Kingdom: TANGO, RUMBA, SALSA, SAMBA entered by Raymond Cotton (Bristol, UK). One of these lucky finalists will go on to gain a special grand prize when the winning names for the four spacecraft are announced at the ESOC event to mark the first Cluster II launch. These names will then become the official designations of the satellites. Where to witness the first launch in Europe. On 15 July media representatives are invited to cover the launch from various sites in Europe. ESA will broadcast the launch live, with images from Baikonur and ESA's Operations Centre ESOC in Darmstadt, Germany. ESA programme officials and spokespersons will be on hand at each site for interviews. European Press Centre, Germany: Location: ESA/ ESOC Address: Robert-Bosch Strasse 5, Darmstadt, Germany Opening hours: 13:30 -17:30 Contact point: Jocelyne Landeau-Constantin Tel. + 49 6151 90 2696/ 2459 Fax. + 49 6151 90 2961 France Location: ESA Headquarters Address: 8-10 rue Mario Nikis, 75015 Paris, France Opening hours: 13:30- 17:30 Contact point: Anne-Marie Rémondin Tel. + 33 1 5369 7155 Fax. + 33 1 5369 7690 The Netherlands Location: Noordwijk Space Expo Address: Keplerlaan 3, Noordwijk, The Netherlands Opening hours: 13:30 - 17:30 Contact point: Heidi Graf Tel. (till 14/07): + 31 71 565 3006 on launch date at Noordwijk Space Expo, tel.: + 31 71 364 6446 Fax.: + 31 71 565 5728 Italy Location: ESA/ESRIN Address: Via G. Galilei, Frascati (Rome), Italy Opening hours: 13:30- 17:30 Contact point: Franca Morgia Tel. + 39 06 9418 0951 Fax. +39 06 9418 0952 Spain: Location ESA/VILSPA Satellite Station Address: Villafranca del Castillo, Madrid Opening hours: 13:30-17:30 Contact point: Fany Peña Tel + 34 91 813 1211 Fax. +34 91 813 1212 Media representatives wishing to attend the launch event from any of the sites, are kindly requested to fill out the attached reply form and fax it back to the contact point at the site they have chosen. The live launch video transmission will be available in analogue (PAL) and digital (MPEG-2) format, via satellite. There will be different language versions plus clean, international audio. The exact times of the transmission and the satellite parameters will be posted as from 10 July on the Internet at http://television.esa.int. The launch of the first pair of Clusters on 15 July will be covered live also on the Internet by ESA at http://clusterlaunch.esa.int and also by Spaceflight Now at http://spaceflightnow.com Note for editors. ESA's Cluster II mission will study the complex interaction between the Sun and Earth in unprecedented detail. For the first time, four satellites will fly in close formation above the Earth's poles, studying the magnetic field around our planet and its continual battle with the energetic particles of the solar wind. This groundbreaking mission to explore the magnetosphere and provide the first small-scale, three-dimensional 'map' of near-Earth space is one of the key Cornerstones in ESA's Horizons 2000 long term science programme. For more information on the winning entries, visit the ESA Science Website at: http://sci.esa.int/cluster/competition For interviews with the winners up to 10 July, 2000, please contact: Martine Caparros, tel:+31 71 565 3183, fax: +31 71 565 4101, E-mail: mcaparro@estec.esa.nl Further information on the Cluster II mission - including regular updates from Baikonur - can be found on the Internet at: http://sci.esa.int/cluster/ ESA Communication Department, Media Relations Office Tel: +33(0)1. 53.69.7155 Fax: +33(0)1.53.69 7690 Further information on ESA at http://www.esa.int

Cluster II quartet take the stage together

NASA Astrophysics Data System (ADS)

1999-11-01

This is the only occasion on which all four of ESA's Cluster II spacecraft will be on display together in Europe. Four Spacecraft, One Mission The unique event takes place near the end of the lengthy assembly and test programme, during which each individual spacecraft is being assembled in sequence, one after the other. Two have already completed their assembly and systems testing and are about to be stored in special containers at IABG prior to shipment to the Baikonur launch site in Kazakhstan next spring. In the case of the other two, flight models 5 and 8, installation of the science payloads has finished, but their exhaustive series of environmental tests at IABG have yet to begin. Following delivery to the launch site next April, the satellites will be launched in pairs in June and July 2000. Two Soyuz rockets, each with a newly designed Fregat upper stage, are being provided by the Russian-French Starsem company. This will be the first time ESA satellites have been launched from the former Soviet Union. Cluster II is a replacement for the original Cluster mission, which was lost during the maiden launch of Ariane 5 in June 1996. ESA, given the mission's importance in its overall strategy in the area of the Sun-Earth connection, decided to rebuild this unique project. ESA member states supported that proposal. On 3 April 1997, the Agency's Science Programme Committee agreed. Cluster II was born. European Teamwork Scientific institutions and industrial enterprises in almost all the 14 ESA member states and the United States are taking part in the Cluster II project. Construction of the eight Cluster / Cluster II spacecraft has been a major undertaking for European industry. Built into each 1200 kg satellite are six propellant tanks, two pressure tanks, eight thrusters, 80 metres of pipework, about 5 km of wiring, 380 connectors and more than 14 000 electrical contacts. All the spacecraft were assembled in the giant clean room at the Friedrichshafen plant of prime contractor Dornier Satellitensysteme. On completion, they were sent to IABG in Ottobrunn, near Munich, for intensive vibration, thermal, vacuum and magnetic testing. The European ground segment for the mission is just as important. A vast amount of data - equivalent to 290 million printed pages - will be returned to Earth over the mission's two-year lifetime. Signals to and from the spacecraft will be sent via a 15 metre antenna at Villafranca in Spain and processed at the European Space Operations Centre (ESOC) at Darmstadt, Germany. The main control room at ESOC will be used during the launch and early phases of the mission, with teams of operators working round the clock. About two weeks after the second Cluster II pair are placed in their operational orbits, mission operations will switch to a smaller, dedicated control room at ESOC. The Joint Science Operations Centre at Rutherford Appleton Laboratory in the UK will co-ordinate the scientific investigations. Its main task will be to combine all requirements from the 11 science instrument teams into an overall plan. The flow of information returned by the 44 instruments will be distributed to eight national data centres, six in Europe, one in the USA and the other in China. Solar Maximum Cluster II is part of an international programme to find out more about how the Sun influences the Earth. The four Cluster II satellites will join an armada of spacecraft from many countries, which are already studying the Sun and high speed wind of charged particles (mainly electrons and protons) which it continually blasts into space. Ulysses and SOHO, both joint ESA-NASA missions, and ESA's Cluster II , when it will be there, are the flagships of this armada. The timing of the mission is ideal, since it will take place during a period of peak activity in the Sun's 11-year cycle, when sunspots and solar radiation reach a maximum. Cluster II will measure the effects of this activity on near-Earth space as incoming energetic particles subject the magnetosphere - the region dominated by the Earth's magnetic field - to a buffeting. Each spacecraft carries an identical set of 11 instruments provided by scientific institutions in different countries. Formation Flying Cluster II will be the first space science mission ever to fly four identical spacecraft simultaneously. Once the quartet have been inserted into highly elliptical polar orbits, ranging from 19 000 to 119 000 km above the Earth, they will spend the next two years travelling from the magnetosphere into interplanetary space and back again. Sometimes they will be within a few hundred kilometres of each other, sometimes 20 000 kilometres apart, depending on the physical phenomena to be studied. By orbiting in a tetrahedral (triangular pyramid) formation, they will be able to make the first detailed three-dimensional study of the changes and processes taking place in near-Earth space. As the satellites orbit the Earth, they will investigate the rapid changes which occur in the Earth's magnetosphere when large numbers of electrically charged particles (electrons and protons) in the solar wind reach the Earth. Huge amounts of data will be returned which will help scientists unravel the physical processes and small-scale variations taking place in the near-Earth environment. "Cluster II will give us the best information yet on how the Sun affects the near-Earth environment," said Cluster II project scientist, Philippe Escoubet. "For the first time we will be able to study the Earth's magnetic field from four viewpoints with identical instruments." "It will be like having four cameras at a football match - one behind the goal and three others at different angles," he explained. "This is very exciting because it will help us to understand the space environment which surrounds our planet." How The Sun Affects Our Planet. Such studies are not just of academic interest. The Sun affects our world in many ways. Apart from its familiar output of light, heat and ultraviolet radiation, our nearest star also emits a continuous stream of atomic particles - the solar wind - that sweeps out into space at speeds ranging from 280 to 1 000 km/s (1 800 times faster than Concorde). Sometimes, explosions on the Sun send millions of tonnes of gas towards the Earth. These clouds of high-energy particles can travel the 150 million km between the Sun and Earth in a few days. The most energetic particles of all, created by solar flares, can reach the Earth in just 30 minutes. This activity is particularly noticeable at times of solar maximum. When charged particles from the Sun enter the Earth's upper atmosphere, they create shimmering curtains of coloured light, known as auroras, in the polar night sky. Other effects can be much more serious: * Solar storms affect the Earth's ionosphere, causing disruption of short-wave radio communications, navigation systems on ships and aircraft, and military radar systems. * Surges in electricity transmission lines can cause widespread power blackouts, as happened in Quebec, Canada, in March 1989 when 6 million people were left without electricity as a result of a huge solar-induced magnetic storm. * Damage to microchips and electrical discharges can cause satellites to stop operating, disrupting telephone, TV and data communication services. (Aware of the potential dangers, the designers of the Cluster II spacecraft have built them to survive collisions with high- energy particles from the Earth's radiation belts and the solar wind.) * Radiation levels can become hazardous to astronauts and occupants of high-flying aircraft. * Variations in solar energy output cause global climate changes which affect plant growth, crop production and food supply. * High-energy particles hitting the Earth's upper atmosphere can damage the ozone layer which protects us from harmful ultraviolet radiation.

The physical chemistry of coordinated aqua-, ammine-, and mixed-ligand Co2+ complexes: DFT studies on the structure, energetics, and topological properties of the electron density.

PubMed

Varadwaj, Pradeep R; Marques, Helder M

2010-03-07

Spin-unrestricted DFT-X3LYP/6-311++G(d,p) calculations have been performed on a series of complexes of the form [Co(H(2)O)(6-n)(NH(3))(n)](2+) (n = 0-6) to examine their equilibrium gas-phase structures, energetics, and electronic properties in their quartet electronic ground states. In all cases Co(2+) in the energy-minimised structures is in a pseudo-octahedral environment. The calculations overestimate the Co-O and Co-N bond lengths by 0.04 and 0.08 A, respectively, compared to the crystallographically observed mean values. There is a very small Jahn-Teller distortion in the structure of [Co(H(2)O)(6)](2+) which is in contrast to the very marked distortions observed in most (but not all) structures of this cation that have been observed experimentally. The successive replacement of ligated H(2)O by NH(3) leads to an increase in complex stability by 6 +/- 1 kcal mol(-1) per additional NH(3) ligand. Calculations using UB3LYP give stabilisation energies of the complexes about 5 kcal mol(-1) smaller and metal-ligand bond lengths about 0.005 A longer than the X3LYP values since the X3LYP level accounts for the London dispersion energy contribution to the overall stabilisation energy whilst it is largely missing at the B3LYP level. From a natural population analysis (NPA) it is shown that the formation of these complexes is accompanied by ligand-to-metal charge transfer the extent of which increases with the number of NH(3) ligands in the coordination sphere of Co(2+). From an examination of the topological properties of the electron charge density using Bader's quantum theory of atoms in molecules it is shown that the electron density rho(c) at the Co-O bond critical points is generally smaller than that at the Co-N bond critical points. Hence Co-O bonds are weaker than Co-N bonds in these complexes and the stability increases as NH(3) replaces H(2)O in the metal's coordination sphere. Several indicators, including the sign and magnitude of the Laplacian of the charge density nabla(2)rho(c), the ratio of the local potential and kinetic energy densities, |V(c)|/G(c), the sign of the total energy density H(c), and the delocalisation index delta(Co,X), X = O, N, are used to show that whilst the metal-ligand bonds are predominantly ionic in nature, they gain covalent character as NH(3) replaces H(2)O, and the Co-N bond is significantly more covalent than the Co-O bond. We have shown that the delocalisation index delta(Co,X), X = O, N, is strongly correlated with the zero-point corrected stabilisation energy E demonstrating that delta can be used as a measure of the bond stability in these complexes.

European Space Science Scales New Heights

NASA Astrophysics Data System (ADS)

1995-06-01

Satellites, comprising nine tonnes of hardware and sixty experiments, will be placed in orbit with a view to giving scientists a new perspective on the Sun, the Earth's magnetic environment and the universe in general. ISO, the Infrared Space Observatory, will allow astronomers to study all types of objects in the so1al. system - from nearby planets to the farthermost galaxies - with unparalleled sensitivity through the invisible, cold light of infrared radiation. Soho, the solar observatory, will be the fist satellite to continuously observe the Sun in detail, and will do so for at least two yews. The quartet of identical Cluster satellites will probe the Earth's magnetosphere in order to study the storms that can occur there which disrupt radio communications or electrical power supplies on Earth. As Roger Bonnet, Director of the European Space Agency's science programme, points out: "For the programme, this year marks the culmination often years of endeavour now drawing to a close. This shows that Europe is now taking the lead in in situ exploration of the universe". On 23 May ISO successfully completed final testing which validated the satellite's technical performance. It is currently on its way to Guiana onboard the Ariana. It will be launched from the Space Centre at Kourou by an Ariane 44P launcher in late October. On 14 June Soho will undergo similar checkouts which should give it a clean bill of health for dispatch to the Kennedy Space Center (Florida). It is scheduled for a launch on 30 October by NASA's Atlas rocket. Authorisation to dispatch the Cluster quartet to Kourou should be given in late June with a view to a launch at the end of the year on a flagship launcher: the first Ariane-5, which is set to become the most competitive launcher on the world market, Another milestone in space exploration is in the offing: the journey over the Sun's north pole by ESA's Ulysses probe begins this month and will continue through to September. During this phase, Ulysses will have an unprecedented birds'-eye view of the day star's northern reaches. will it find the same anomaly as that observed last year above the south pole? Will the north magnetic pole prove to be as astonishingly inexistent as its southerly counterpart did last summer? The measurements collected during the next three months will be decisive in continuing the global investigation of the star that heats and sustains life on Earth. Moreover, there; could be other surprises in store for solar astrophysicists. For, at their request, ESA and NASA have decided to extend the Ulysses mission by six yews, from 1995 to 2001, so as to allow them to observe the Sun during a period of magnetic activity. With three new missions - ISO, Soho and Cluster - due to be launched and a fourth - Ulysses - embarking on a critical exploration phase, 1995 marks a crucial stage in the history of European space science. But all this is no mere coincidence. It should rather be seen as the result of a sustained planning effort that started ten years ago and is now coming up to its half-way point. For in 1985, at the request of the scientists themselves, ESA set up a 20-year (1985-2005) programme designed to pave the way for ambitious science missions. In other words, giving Europe the wherewithal to play its proper part in peaceful exploration of the universe. The "Horizon 2000" plan was devised solely according to certain key criteria: scientific excellence, project coherence, balance, technological content and realistic budgeting. Management efficiency in particular has allowed Horizon 2000 today to work to a budget of ECU 343 million (12.8iln of ESA's general budget), equivalent in terms of purchasing power to European space science funding twenty-five yews ago. The missions comprising Horizon 2000 were proposed by the scientific community and then selected by groups of leading research scien16sts. They include qualified beacon projects, "Cornerstone missions", costing the equivalent of about two years' budget and medium-size projects accounting for one years budget. It is on the basis of the Horizon 2000 programme that Europe has: launched the Giotto probe, which successfully encountered Comets Halley (1986) and Grigg-Skjellerup (1992); developed the Hipparcos satellite, whose catalogue of 120 000 stars will be published in late 1996; built the Ulysses probe, which has been exploring the third dimension of the solar system since 1992; and contributed at a rate of 20%to the Hubble Space Telescope programme. It is thanks to Horizon 2000 that Europe is now preparing to launch ISO, Soho and Cluster. It is on the basis of the same long-term plan that Europe will build: Huygens, the probe to be launched in 1997, in co-operation with the United States, to explore the organic planet Titan; XMM, the X-ray telescope scheduled for a launch in 1999; Integral, the gamma-ray observatory due to be launched in 2001 in co-operation with Russia; Rosette, the probe which is to land on Comet Wirtanen in 2012; and FIRST, the submillimetre telescope planned to be in orbit in 2006. After a long and fruitful apprenticeship, European space science therefore now looks set to come into its own. It currently ranks an honourable second place in the world and regularly leads the way in certain specific areas of exploration. Thus Europe is now at the forefront of cometary exploration, fundamental astronomy or "astrometry", solar physics and the physics of interplanetary plasma. So it should also be able to take the lead in infrared astronomy, high- energy astronomy and planetary exploration while continuing to conduct cometary studies with Rosetta. One remarkable fact is that the approach and success of Horizon 2000 have attracted unanimous praise both in and beyond Europe. The programme is being supported by virtually all Europe's scien1ilsts. It is drawing on and inspiring increasing numbers of scientists, including many of the younger generation. Its content and management have been approved by all ESA's Member States. Outside Europe, the stability and solidity of Horizon 2000 have made ESA an extremely credible and reliable partner, arousing ever greater interest in international - including transatlantic - co-operation. Given that the first results look positive, it makes sense to think about continuing the work done to date. Which is why this year, half-way through Horizon 2000, it is time to look ahead to the next twenty-year period and embark on the follow-up programme which will lead to further missions being carried out between 2006 and 2016. At ESA Council meeting to be held in October in Toulouse, European ministers responsible for space will therefore have to take a decision on a "Horizon 2000 PLUS " programme designed to ensure successful European space science over a further ten-year period. The proposal being put forward by ESA's directorate of scientific programmes involves setting up three large-scale missions: * a mission to explore Mercury, the least known of the inner solar planets, 60iln of whose surface has yet to be mapped * an interferometry observatory designed to map the sky a hundred times more accurately than the Hipparcos satellite * a gravitational observatory able to pick up the space time waves emitted by the universe at the precise moment of the Big Bang. In parallel four medium-size missions - their content still to be defined - would be carried out. As with its forerunner, Horizon 2000 PLUS has been defined on the basis of proposals submitted by the scientific community following open competition. In all, I10 mission concepts were proposed by a total of 2500 scientists. These were then examined by peer-review groups, involving 75 scientists in all who announced their final choice on I October 1994. The agency is proposing to start preparing for Horizon 2000 PLUS on the basis of level funding up to the year 2000. This means that ESA would undertake to conduct preliminary Horizon 2000 PLUS technological studies by drawing on the Horizon 2000 budget, even though this ,vas not initially planned and despite the increased demands of the new missions. The Horizon 2000 PLUS proposals also include an extremely ambitious fundamental physics project - gravitational antenna - not originally covered by the European space science programme. Consequently, putting this Cornerstone mission in place could lead to a modest 5% increase in the annual budgets being requested over the period 2001-2005. The European space science programme is part of the driving force for industrial technology, fundamental knowledge and European policy generally. Ten years ago, its development was managed in successive stages without a long-term framework, thus ruling out ambitious projects. Today, the European space science community is working to a 20-year plan which has given it its second-place world ranking and prompted regular breakthroughs in hitherto uncharted areas of advanced technology. The task now is to continue down that road with ever greater rigour, professionalism, stability and effectiveness in order to emulate the programme's current success. Note for TV editors: A betacam tape with new video material on ISO, SOHO and CLUSTER is available upon request. To get a copy please contact the ESA Public Relations Division in Paris (Tel: (33.1) 53.69.71.55 - Fax: (33.1) 53.69.76,90),

Cluster finds giant gas vortices at the edge of Earth's magnetic bubble

NASA Astrophysics Data System (ADS)

2004-08-01

12 August 2004 ESA’s quartet of space-weather watchers, Cluster, has discovered vortices of ejected solar material high above the Earth. The superheated gases trapped in these structures are probably tunnelling their way into the Earth’s magnetic ‘bubble’, the magnetosphere. This discovery possibly solves a 17-year-mystery of how the magnetosphere is constantly topped up with electrified gases when it should be acting as a barrier. hi-res Size hi-res: 1446 Kb Credits: H. Hasegawa (Dartmouth College) Three-dimensional cut-away view of Earth's magnetosphere This figure shows a three-dimensional cut-away view of Earth' s magnetosphere. The curly features sketched on the boundary layer are the Kelvin-Helmholtz vortices discovered by Cluster. They originate where two adjacent flows travel with different speed. In this case, one of the flows is the heated gas inside the boundary layer of the magnetosphere, the other the solar wind just outside it. The arrows show the direction of the magnetic field, in red that associated with the solar wind and in green the one inside Earth’s magnetosphere. The white dashed arrow shows the trajectory followed by Cluster. High resolution version (JPG format) 1446 Kb High resolution version (TIFF format) 15 365 Kb hi-res Size hi-res: 22 Kb Credits: H. Hasegawa (Dartmouth College) Electrified gas varies across the vortices along Cluster’s trajectory This computer simulation shows how the density of the electrified gas is expected to vary across the vortices along Cluster’s trajectory (white dashed line). The density is lower inside the boundary layer (blue region) and higher outside, in the region dominated by the solar wind (shown in red). The density variations measured by the instruments on board Cluster match those predicted by this model. Low resolution version (JPG format) 22 Kb High resolution version (TIFF format) 3438 Kb The Earth’s magnetic field is our planet’s first line of defence against the bombardment of the solar wind. The solar wind itself is launched from the Sun and carries the Sun’s magnetic field throughout the Solar System. Sometimes this magnetic field is aligned with Earth’s and sometimes it points in the opposite direction. When the two fields point in opposite directions, scientists understand how ‘doors’ in Earth’s field can open. This phenomenon, called ‘magnetic reconnection’, allows the solar wind to flow in and collect in the reservoir known as the boundary layer. On the contrary, when the fields are aligned they should present an impenetrable barrier to the flow. However, spacecraft measurements of the boundary layer, dating back to 1987, present a puzzle because they clearly show that the boundary layer is fuller when the fields are aligned than when they are not. So how is the solar wind getting in? Thanks to the data from the four formation-flying spacecraft of ESA’s Cluster mission, scientists have made a breakthrough. On 20 November 2001, the Cluster flotilla was heading around from behind Earth and had just arrived at the dusk side of the planet, where the solar wind slides past Earth’s magnetosphere. There it began to encounter gigantic vortices of gas at the magnetopause, the outer ‘edge’ of the magnetosphere. “These vortices were really huge structures, about six Earth radii across,” says Hiroshi Hasegawa, Dartmouth College, New Hampshire who has been analysing the data with help from an international team of colleagues. Their results place the size of the vortices at almost 40 000 kilometres each, and this is the first time such structures have been detected. These vortices are known as products of Kelvin-Helmholtz instabilities (KHI). They can occur when two adjacent flows are travelling with different speeds, so one is slipping past the other. Good examples of such instabilities are the waves whipped up by the wind slipping across the surface of the ocean. Although KHI-waves had been observed before, this is the first time that vortices are actually detected. When a KHI-wave rolls up into a vortex, it becomes known as a ‘Kelvin Cat’s eye’. The data collected by Cluster have shown density variations of the electrified gas, right at the magnetopause, precisely like those expected when travelling through a ‘Kelvin Cat’s eye’. Scientists had postulated that, if these structures were to form at the magnetopause, they might be able to pull large quantities of the solar wind inside the boundary layer as they collapse. Once the solar wind particles are carried into the inner part of the magnetosphere, they can be excited strongly, allowing them to smash into Earth’s atmosphere and give rise to the aurorae. Cluster’s discovery strengthens this scenario but does not show the precise mechanism by which the gas is transported into Earth’s magnetic bubble. Thus, scientists still do not know whether this is the only process to fill up the boundary layer when the magnetic fields are aligned. For those measurements, Hasegawa says, scientists will have to wait for a future generation of magnetospheric satellites. Notes for editors The results of this investigation have appeared in today’s issue of the scientific journal Nature, in a paper entitled ‘Transport of solar wind into Earth's magnetosphere through rolled-up Kelvin-Helmholtz vortices’, by H. Hasegawa, M. Fujimoto, T.D. Phan, H. Reme, A. Balogh, M.W. Dunlop, C. Hashimoto and R. TanDokoro. More about magnetic reconnection Solar wind particles follow ‘magnetic field lines’, rather like beads on a wire. The ‘doors’ that open in Earth’s magnetosphere during oppositely aligned magnetic configurations are caused by a phenomenon called ‘magnetic reconnection‘. During this process, Earth’s field lines spontaneously break and join themselves to the Sun’s, allowing the solar wind to pass freely into Earth’s magnetosphere. Magnetic reconnections are not possible in the aligned case, however, hence the need for a different mechanism to inject the particles into Earth’s magnetosphere. More about Cluster Cluster is a mission of international co-operation between ESA and NASA. It involves four spacecraft, launched on two Russian rockets during the summer of 2000. They are now flying in formation around Earth, relaying the most detailed ever information about how the solar wind affects our planet in 3D. The solar wind is the perpetual stream of subatomic particles given out by the Sun and it can damage communications satellites and power stations on Earth. The Cluster mission is expected to continue until at least 2005. The ongoing archiving of the Cluster data (or Cluster Active Archive) is part of the International Living with a Star programme (ILWS), in which space agencies worldwide get together to investigate how variations in the Sun affect the environment of Earth and the other planets. In particular, ILWS concentrate on those aspects of the Sun-Earth system that may affect mankind and society. ILWS is a collaborative initiative between Europe, the United States, Russia, Japan and Canada.

ESA unveils Spanish antenna for unique space mission

NASA Astrophysics Data System (ADS)

2000-05-01

The newly refurbished antenna, which is located at the Villafranca del Castillo Satellite Tracking Station site (VILSPA) near Madrid, has been selected as the prime communication link with the Cluster II spacecraft. The VIL-1 antenna will play a vital role in ESA's Cluster mission by monitoring and controlling the four spacecraft and by receiving the vast amounts of data that will be returned to Earth during two years of operations. Scheduled for launch in summer 2000, the Cluster quartet will complete the most detailed investigation ever made into the interaction between our pl0anet's magnetosphere - the region of space dominated by Earth's magnetic field - and the continuous stream of charged particles emitted by the Sun - the solar wind. This exciting venture is now well under way, following completion of the satellite assembly and test programme and two successful verification flights by the newly developed Soyuz-Fregat launch vehicle. The ESA Flight Acceptance Review Board has accordingly given the go-ahead for final launch preparations at the Baikonur Cosmodrome in Kazakhstan. VILSPA, ESA and Cluster II Built in 1975, after an international agreement between the European Space Agency and the Spanish government, VILSPA is part of the European Space Operations Centre (ESOC) Tracking Station Network (ESTRACK). In the last 25 years, VILSPA has supported many ESA and international satellite programmes, including the International Ultraviolet Explorer (IUE), EXOSAT and the Infrared Space Observatory (ISO). In addition to supporting the Cluster II mission, it has been designated as the Science Operations Centre for ESA's XMM Newton mission and for the Far-Infrared Space Telescope (FIRST), which is due to launch in 2007. There are now more than half a dozen large dish antennae installed at VILSPA. One of these is the VIL-1 antenna, a 15 metre diameter dish which operates in the S-band radio frequency (1.8 - 2.7 GHz). This antenna has been modernised recently in order to support the forthcoming Cluster II mission. As a result, VILSPA now has two fully upgraded 15 metre S-band antennae, which should enable the facility to enter the new millennium confident in its ability to support future space programmes. Modernisation of VIL-1 included the replacement of the 60 dish panels, the subreflector, the antenna equipment room and other parts of the main structure. One of the most significant modifications has been the replacement of the Servo and tracking systems, since the Cluster II satellites will move in a highly elliptical orbit and require high speed tracking. Into Orbit The Cluster II mission will be launched by two Soyuz rockets provided by the French-Russian Starsem consortium. After two engine burns by the Fregat upper stage, the spacecraft will separate and use their own propulsion systems to reach their final orbits. Travelling in close formation, the four Cluster spacecraft will swoop to within 19,000 km of the Earth's surface and then retreat to 119,000 km - almost one third of the way to the Moon. The four satellites will be visible for an average of about 10 hours per day from the VILSPA ground station. However, only one satellite at a time can be in communication with the ground, which reduces the available time each day to around two and a half hours per satellite. Further challenges arise from the need to send new instructions to the 11 scientific instruments on each spacecraft, and from the vast amount of data to be returned each day from the 44 experiments. Over two years of operations, this adds up to 580 Gigabytes (580,000,000,000 bytes!) of data - equivalent to 290 million pages of printed text. VILSPA will be just one link in the overall Cluster II communications network. The day-to-day operation of the four spacecraft will be handled by the Operations Control Centre at ESOC (Darmstadt, Germany). All of the Cluster II data exchange between VILSPA and ESOC will be handled by dedicated communication lines. European Teamwork. Industrial enterprises in almost all of the 14 ESA member states and the United States have provided hardware for Cluster II, and several Spanish companies have made important contributions to the project. SENER in Bilbao has designed and built the communication and experiment booms for the spacecraft, while Alcatel Espacio in Tres Cantos (Madrid) has provided on-board transponders and high power amplifiers for the spacecraft. Construction of the eight Cluster / Cluster II spacecraft has been a major undertaking for European industry. Built into each 550 kg satellite are six propellant tanks, two pressure tanks, eight thrusters, 80 metres of pipework, about 5 km of wiring, 380 connectors and more than 14,000 electrical contacts. All of the spacecraft have been assembled at the Friedrichshafen (Germany) plant of prime contractor Dornier Satellitensysteme, and then sent to IABG in Ottobrunn, near Munich, for intensive vibration, thermal, vacuum and magnetic testing. Various companies have also participated in the relocation and upgrading of the VIL-1 antenna hardware. MAN (Germany) was responsible for the dismantling of the Odenwald antenna and installation of the dish at VILSPA, while VITROCISET (Italy) handled the transfer of the antenna 'back-end' equipment, which included the computers to process the satellite telemetry and telecommunications signals. These companies were supported by Spanish contractors and local industry.

Radiation Environment Modeling for Spacecraft Design: New Model Developments

NASA Technical Reports Server (NTRS)

Barth, Janet; Xapsos, Mike; Lauenstein, Jean-Marie; Ladbury, Ray

2006-01-01

A viewgraph presentation on various new space radiation environment models for spacecraft design is described. The topics include: 1) The Space Radiatio Environment; 2) Effects of Space Environments on Systems; 3) Space Radiatio Environment Model Use During Space Mission Development and Operations; 4) Space Radiation Hazards for Humans; 5) "Standard" Space Radiation Environment Models; 6) Concerns about Standard Models; 7) Inadequacies of Current Models; 8) Development of New Models; 9) New Model Developments: Proton Belt Models; 10) Coverage of New Proton Models; 11) Comparison of TPM-1, PSB97, AP-8; 12) New Model Developments: Electron Belt Models; 13) Coverage of New Electron Models; 14) Comparison of "Worst Case" POLE, CRESELE, and FLUMIC Models with the AE-8 Model; 15) New Model Developments: Galactic Cosmic Ray Model; 16) Comparison of NASA, MSU, CIT Models with ACE Instrument Data; 17) New Model Developmemts: Solar Proton Model; 18) Comparison of ESP, JPL91, KIng/Stassinopoulos, and PSYCHIC Models; 19) New Model Developments: Solar Heavy Ion Model; 20) Comparison of CREME96 to CREDO Measurements During 2000 and 2002; 21) PSYCHIC Heavy ion Model; 22) Model Standardization; 23) Working Group Meeting on New Standard Radiation Belt and Space Plasma Models; and 24) Summary.

Comparisons of Multilevel Modeling and Structural Equation Modeling Approaches to Actor-Partner Interdependence Model.

PubMed

Hong, Sehee; Kim, Soyoung

2018-01-01

There are basically two modeling approaches applicable to analyzing an actor-partner interdependence model: the multilevel modeling (hierarchical linear model) and the structural equation modeling. This article explains how to use these two models in analyzing an actor-partner interdependence model and how these two approaches work differently. As an empirical example, marital conflict data were used to analyze an actor-partner interdependence model. The multilevel modeling and the structural equation modeling produced virtually identical estimates for a basic model. However, the structural equation modeling approach allowed more realistic assumptions on measurement errors and factor loadings, rendering better model fit indices.

[Analysis of the stability and adaptability of near infrared spectra qualitative analysis model].

PubMed

Cao, Wu; Li, Wei-jun; Wang, Ping; Zhang, Li-ping

2014-06-01

The stability and adaptability of model of near infrared spectra qualitative analysis were studied. Method of separate modeling can significantly improve the stability and adaptability of model; but its ability of improving adaptability of model is limited. Method of joint modeling can not only improve the adaptability of the model, but also the stability of model, at the same time, compared to separate modeling, the method can shorten the modeling time, reduce the modeling workload; extend the term of validity of model, and improve the modeling efficiency. The experiment of model adaptability shows that, the correct recognition rate of separate modeling method is relatively low, which can not meet the requirements of application, and joint modeling method can reach the correct recognition rate of 90%, and significantly enhances the recognition effect. The experiment of model stability shows that, the identification results of model by joint modeling are better than the model by separate modeling, and has good application value.

Evaluating the Bias of Alternative Cost Progress Models: Tests Using Aerospace Industry Acquisition Programs

DTIC Science & Technology

1992-12-01

suspect :mat, -n2 extent predict:.on cas jas ccsiziveiv crrei:=e amonc e v:arious models, :he fandom *.;aik, learn ha r ur e, i;<ea- variable and Bemis...Functions, Production Rate Adjustment Model, Learning Curve Model. Random Walk Model. Bemis Model. Evaluating Model Bias, Cost Prediction Bias. Cost...of four cost progress models--a random walk model, the tradiuonai learning curve model, a production rate model Ifixed-variable model). and a model

Experience with turbulence interaction and turbulence-chemistry models at Fluent Inc.

NASA Technical Reports Server (NTRS)

Choudhury, D.; Kim, S. E.; Tselepidakis, D. P.; Missaghi, M.

1995-01-01

This viewgraph presentation discusses (1) turbulence modeling: challenges in turbulence modeling, desirable attributes of turbulence models, turbulence models in FLUENT, and examples using FLUENT; and (2) combustion modeling: turbulence-chemistry interaction and FLUENT equilibrium model. As of now, three turbulence models are provided: the conventional k-epsilon model, the renormalization group model, and the Reynolds-stress model. The renormalization group k-epsilon model has broadened the range of applicability of two-equation turbulence models. The Reynolds-stress model has proved useful for strongly anisotropic flows such as those encountered in cyclones, swirlers, and combustors. Issues remain, such as near-wall closure, with all classes of models.

Leadership Models.

ERIC Educational Resources Information Center

Freeman, Thomas J.

This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

SUMMA and Model Mimicry: Understanding Differences Among Land Models

NASA Astrophysics Data System (ADS)

Nijssen, B.; Nearing, G. S.; Ou, G.; Clark, M. P.

2016-12-01

Model inter-comparison and model ensemble experiments suffer from an inability to explain the mechanisms behind differences in model outcomes. We can clearly demonstrate that the models are different, but we cannot necessarily identify the reasons why, because most models exhibit myriad differences in process representations, model parameterizations, model parameters and numerical solution methods. This inability to identify the reasons for differences in model performance hampers our understanding and limits model improvement, because we cannot easily identify the most promising paths forward. We have developed the Structure for Unifying Multiple Modeling Alternatives (SUMMA) to allow for controlled experimentation with model construction, numerical techniques, and parameter values and therefore isolate differences in model outcomes to specific choices during the model development process. In developing SUMMA, we recognized that hydrologic models can be thought of as individual instantiations of a master modeling template that is based on a common set of conservation equations for energy and water. Given this perspective, SUMMA provides a unified approach to hydrologic modeling that integrates different modeling methods into a consistent structure with the ability to instantiate alternative hydrologic models at runtime. Here we employ SUMMA to revisit a previous multi-model experiment and demonstrate its use for understanding differences in model performance. Specifically, we implement SUMMA to mimic the spread of behaviors exhibited by the land models that participated in the Protocol for the Analysis of Land Surface Models (PALS) Land Surface Model Benchmarking Evaluation Project (PLUMBER) and draw conclusions about the relative performance of specific model parameterizations for water and energy fluxes through the soil-vegetation continuum. SUMMA's ability to mimic the spread of model ensembles and the behavior of individual models can be an important tool in focusing model development and improvement efforts.

Seven Modeling Perspectives on Teaching and Learning: Some Interrelations and Cognitive Effects

ERIC Educational Resources Information Center

Easley, J. A., Jr.

1977-01-01

The categories of models associated with the seven perspectives are designated as combinatorial models, sampling models, cybernetic models, game models, critical thinking models, ordinary language analysis models, and dynamic structural models. (DAG)

Pursuing the method of multiple working hypotheses to understand differences in process-based snow models

NASA Astrophysics Data System (ADS)

Clark, Martyn; Essery, Richard

2017-04-01

When faced with the complex and interdisciplinary challenge of building process-based land models, different modelers make different decisions at different points in the model development process. These modeling decisions are generally based on several considerations, including fidelity (e.g., what approaches faithfully simulate observed processes), complexity (e.g., which processes should be represented explicitly), practicality (e.g., what is the computational cost of the model simulations; are there sufficient resources to implement the desired modeling concepts), and data availability (e.g., is there sufficient data to force and evaluate models). Consequently the research community, comprising modelers of diverse background, experience, and modeling philosophy, has amassed a wide range of models, which differ in almost every aspect of their conceptualization and implementation. Model comparison studies have been undertaken to explore model differences, but have not been able to meaningfully attribute inter-model differences in predictive ability to individual model components because there are often too many structural and implementation differences among the different models considered. As a consequence, model comparison studies to date have provided limited insight into the causes of differences in model behavior, and model development has often relied on the inspiration and experience of individual modelers rather than on a systematic analysis of model shortcomings. This presentation will summarize the use of "multiple-hypothesis" modeling frameworks to understand differences in process-based snow models. Multiple-hypothesis frameworks define a master modeling template, and include a a wide variety of process parameterizations and spatial configurations that are used in existing models. Such frameworks provide the capability to decompose complex models into the individual decisions that are made as part of model development, and evaluate each decision in isolation. It is hence possible to attribute differences in system-scale model predictions to individual modeling decisions, providing scope to mimic the behavior of existing models, understand why models differ, characterize model uncertainty, and identify productive pathways to model improvement. Results will be presented applying multiple hypothesis frameworks to snow model comparison projects, including PILPS, SnowMIP, and the upcoming ESM-SnowMIP project.

Research on Multi - Person Parallel Modeling Method Based on Integrated Model Persistent Storage

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Liu, Ying

2018-03-01

This paper mainly studies the multi-person parallel modeling method based on the integrated model persistence storage. The integrated model refers to a set of MDDT modeling graphics system, which can carry out multi-angle, multi-level and multi-stage description of aerospace general embedded software. Persistent storage refers to converting the data model in memory into a storage model and converting the storage model into a data model in memory, where the data model refers to the object model and the storage model is a binary stream. And multi-person parallel modeling refers to the need for multi-person collaboration, the role of separation, and even real-time remote synchronization modeling.

Constructive Epistemic Modeling: A Hierarchical Bayesian Model Averaging Method

NASA Astrophysics Data System (ADS)

Tsai, F. T. C.; Elshall, A. S.

2014-12-01

Constructive epistemic modeling is the idea that our understanding of a natural system through a scientific model is a mental construct that continually develops through learning about and from the model. Using the hierarchical Bayesian model averaging (HBMA) method [1], this study shows that segregating different uncertain model components through a BMA tree of posterior model probabilities, model prediction, within-model variance, between-model variance and total model variance serves as a learning tool [2]. First, the BMA tree of posterior model probabilities permits the comparative evaluation of the candidate propositions of each uncertain model component. Second, systemic model dissection is imperative for understanding the individual contribution of each uncertain model component to the model prediction and variance. Third, the hierarchical representation of the between-model variance facilitates the prioritization of the contribution of each uncertain model component to the overall model uncertainty. We illustrate these concepts using the groundwater modeling of a siliciclastic aquifer-fault system. The sources of uncertainty considered are from geological architecture, formation dip, boundary conditions and model parameters. The study shows that the HBMA analysis helps in advancing knowledge about the model rather than forcing the model to fit a particularly understanding or merely averaging several candidate models. [1] Tsai, F. T.-C., and A. S. Elshall (2013), Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation. Water Resources Research, 49, 5520-5536, doi:10.1002/wrcr.20428. [2] Elshall, A.S., and F. T.-C. Tsai (2014). Constructive epistemic modeling of groundwater flow with geological architecture and boundary condition uncertainty under Bayesian paradigm, Journal of Hydrology, 517, 105-119, doi: 10.1016/j.jhydrol.2014.05.027.

The Influence of a Model's Reinforcement Contingency and Affective Response on Children's Perceptions of the Model

ERIC Educational Resources Information Center

Thelen, Mark H.; And Others

1977-01-01

Assesses the influence of model consequences on perceived model affect and, conversely, assesses the influence of model affect on perceived model consequences. Also appraises the influence of model consequences and model affect on perceived model attractiveness, perceived model competence, and perceived task attractiveness. (Author/RK)

Bayesian Model Averaging of Artificial Intelligence Models for Hydraulic Conductivity Estimation

NASA Astrophysics Data System (ADS)

Nadiri, A.; Chitsazan, N.; Tsai, F. T.; Asghari Moghaddam, A.

2012-12-01

This research presents a Bayesian artificial intelligence model averaging (BAIMA) method that incorporates multiple artificial intelligence (AI) models to estimate hydraulic conductivity and evaluate estimation uncertainties. Uncertainty in the AI model outputs stems from error in model input as well as non-uniqueness in selecting different AI methods. Using one single AI model tends to bias the estimation and underestimate uncertainty. BAIMA employs Bayesian model averaging (BMA) technique to address the issue of using one single AI model for estimation. BAIMA estimates hydraulic conductivity by averaging the outputs of AI models according to their model weights. In this study, the model weights were determined using the Bayesian information criterion (BIC) that follows the parsimony principle. BAIMA calculates the within-model variances to account for uncertainty propagation from input data to AI model output. Between-model variances are evaluated to account for uncertainty due to model non-uniqueness. We employed Takagi-Sugeno fuzzy logic (TS-FL), artificial neural network (ANN) and neurofuzzy (NF) to estimate hydraulic conductivity for the Tasuj plain aquifer, Iran. BAIMA combined three AI models and produced better fitting than individual models. While NF was expected to be the best AI model owing to its utilization of both TS-FL and ANN models, the NF model is nearly discarded by the parsimony principle. The TS-FL model and the ANN model showed equal importance although their hydraulic conductivity estimates were quite different. This resulted in significant between-model variances that are normally ignored by using one AI model.

A Smart Modeling Framework for Integrating BMI-enabled Models as Web Services

NASA Astrophysics Data System (ADS)

Jiang, P.; Elag, M.; Kumar, P.; Peckham, S. D.; Liu, R.; Marini, L.; Hsu, L.

2015-12-01

Serviced-oriented computing provides an opportunity to couple web service models using semantic web technology. Through this approach, models that are exposed as web services can be conserved in their own local environment, thus making it easy for modelers to maintain and update the models. In integrated modeling, the serviced-oriented loose-coupling approach requires (1) a set of models as web services, (2) the model metadata describing the external features of a model (e.g., variable name, unit, computational grid, etc.) and (3) a model integration framework. We present the architecture of coupling web service models that are self-describing by utilizing a smart modeling framework. We expose models that are encapsulated with CSDMS (Community Surface Dynamics Modeling System) Basic Model Interfaces (BMI) as web services. The BMI-enabled models are self-describing by uncovering models' metadata through BMI functions. After a BMI-enabled model is serviced, a client can initialize, execute and retrieve the meta-information of the model by calling its BMI functions over the web. Furthermore, a revised version of EMELI (Peckham, 2015), an Experimental Modeling Environment for Linking and Interoperability, is chosen as the framework for coupling BMI-enabled web service models. EMELI allows users to combine a set of component models into a complex model by standardizing model interface using BMI as well as providing a set of utilities smoothing the integration process (e.g., temporal interpolation). We modify the original EMELI so that the revised modeling framework is able to initialize, execute and find the dependencies of the BMI-enabled web service models. By using the revised EMELI, an example will be presented on integrating a set of topoflow model components that are BMI-enabled and exposed as web services. Reference: Peckham, S.D. (2014) EMELI 1.0: An experimental smart modeling framework for automatic coupling of self-describing models, Proceedings of HIC 2014, 11th International Conf. on Hydroinformatics, New York, NY.

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

USGS Publications Warehouse

Curtis, Gary P.; Lu, Dan; Ye, Ming

2015-01-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the synthetic study and future real-world modeling are discussed.

Automated model integration at source code level: An approach for implementing models into the NASA Land Information System

NASA Astrophysics Data System (ADS)

Wang, S.; Peters-Lidard, C. D.; Mocko, D. M.; Kumar, S.; Nearing, G. S.; Arsenault, K. R.; Geiger, J. V.

2014-12-01

Model integration bridges the data flow between modeling frameworks and models. However, models usually do not fit directly into a particular modeling environment, if not designed for it. An example includes implementing different types of models into the NASA Land Information System (LIS), a software framework for land-surface modeling and data assimilation. Model implementation requires scientific knowledge and software expertise and may take a developer months to learn LIS and model software structure. Debugging and testing of the model implementation is also time-consuming due to not fully understanding LIS or the model. This time spent is costly for research and operational projects. To address this issue, an approach has been developed to automate model integration into LIS. With this in mind, a general model interface was designed to retrieve forcing inputs, parameters, and state variables needed by the model and to provide as state variables and outputs to LIS. Every model can be wrapped to comply with the interface, usually with a FORTRAN 90 subroutine. Development efforts need only knowledge of the model and basic programming skills. With such wrappers, the logic is the same for implementing all models. Code templates defined for this general model interface could be re-used with any specific model. Therefore, the model implementation can be done automatically. An automated model implementation toolkit was developed with Microsoft Excel and its built-in VBA language. It allows model specifications in three worksheets and contains FORTRAN 90 code templates in VBA programs. According to the model specification, the toolkit generates data structures and procedures within FORTRAN modules and subroutines, which transfer data between LIS and the model wrapper. Model implementation is standardized, and about 80 - 90% of the development load is reduced. In this presentation, the automated model implementation approach is described along with LIS programming interfaces, the general model interface and five case studies, including a regression model, Noah-MP, FASST, SAC-HTET/SNOW-17, and FLake. These different models vary in complexity with software structure. Also, we will describe how these complexities were overcome through using this approach and results of model benchmarks within LIS.

Literature review of models on tire-pavement interaction noise

NASA Astrophysics Data System (ADS)

Li, Tan; Burdisso, Ricardo; Sandu, Corina

2018-04-01

Tire-pavement interaction noise (TPIN) becomes dominant at speeds above 40 km/h for passenger vehicles and 70 km/h for trucks. Several models have been developed to describe and predict the TPIN. However, these models do not fully reveal the physical mechanisms or predict TPIN accurately. It is well known that all the models have both strengths and weaknesses, and different models fit different investigation purposes or conditions. The numerous papers that present these models are widely scattered among thousands of journals, and it is difficult to get the complete picture of the status of research in this area. This review article aims at presenting the history and current state of TPIN models systematically, making it easier to identify and distribute the key knowledge and opinions, and providing insight into the future research trend in this field. In this work, over 2000 references related to TPIN were collected, and 74 models were reviewed from nearly 200 selected references; these were categorized into deterministic models (37), statistical models (18), and hybrid models (19). The sections explaining the models are self-contained with key principles, equations, and illustrations included. The deterministic models were divided into three sub-categories: conventional physics models, finite element and boundary element models, and computational fluid dynamics models; the statistical models were divided into three sub-categories: traditional regression models, principal component analysis models, and fuzzy curve-fitting models; the hybrid models were divided into three sub-categories: tire-pavement interface models, mechanism separation models, and noise propagation models. At the end of each category of models, a summary table is presented to compare these models with the key information extracted. Readers may refer to these tables to find models of their interest. The strengths and weaknesses of the models in different categories were then analyzed. Finally, the modeling trend and future direction in this area are given.

Multi-Model Combination techniques for Hydrological Forecasting: Application to Distributed Model Intercomparison Project Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ajami, N K; Duan, Q; Gao, X

2005-04-11

This paper examines several multi-model combination techniques: the Simple Multi-model Average (SMA), the Multi-Model Super Ensemble (MMSE), Modified Multi-Model Super Ensemble (M3SE) and the Weighted Average Method (WAM). These model combination techniques were evaluated using the results from the Distributed Model Intercomparison Project (DMIP), an international project sponsored by the National Weather Service (NWS) Office of Hydrologic Development (OHD). All of the multi-model combination results were obtained using uncalibrated DMIP model outputs and were compared against the best uncalibrated as well as the best calibrated individual model results. The purpose of this study is to understand how different combination techniquesmore » affect the skill levels of the multi-model predictions. This study revealed that the multi-model predictions obtained from uncalibrated single model predictions are generally better than any single member model predictions, even the best calibrated single model predictions. Furthermore, more sophisticated multi-model combination techniques that incorporated bias correction steps work better than simple multi-model average predictions or multi-model predictions without bias correction.« less

Expert models and modeling processes associated with a computer-modeling tool

NASA Astrophysics Data System (ADS)

Zhang, Baohui; Liu, Xiufeng; Krajcik, Joseph S.

2006-07-01

Holding the premise that the development of expertise is a continuous process, this study concerns expert models and modeling processes associated with a modeling tool called Model-It. Five advanced Ph.D. students in environmental engineering and public health used Model-It to create and test models of water quality. Using think aloud technique and video recording, we captured their computer screen modeling activities and thinking processes. We also interviewed them the day following their modeling sessions to further probe the rationale of their modeling practices. We analyzed both the audio-video transcripts and the experts' models. We found the experts' modeling processes followed the linear sequence built in the modeling program with few instances of moving back and forth. They specified their goals up front and spent a long time thinking through an entire model before acting. They specified relationships with accurate and convincing evidence. Factors (i.e., variables) in expert models were clustered, and represented by specialized technical terms. Based on the above findings, we made suggestions for improving model-based science teaching and learning using Model-It.

Illustrating a Model-Game-Model Paradigm for Using Human Wargames in Analysis

DTIC Science & Technology

2017-02-01

Working Paper Illustrating a Model- Game -Model Paradigm for Using Human Wargames in Analysis Paul K. Davis RAND National Security Research...paper proposes and illustrates an analysis-centric paradigm (model- game -model or what might be better called model-exercise-model in some cases) for...to involve stakehold- ers in model development from the outset. The model- game -model paradigm was illustrated in an application to crisis planning

Multi-model analysis of terrestrial carbon cycles in Japan: limitations and implications of model calibration using eddy flux observations

NASA Astrophysics Data System (ADS)

Ichii, K.; Suzuki, T.; Kato, T.; Ito, A.; Hajima, T.; Ueyama, M.; Sasai, T.; Hirata, R.; Saigusa, N.; Ohtani, Y.; Takagi, K.

2010-07-01

Terrestrial biosphere models show large differences when simulating carbon and water cycles, and reducing these differences is a priority for developing more accurate estimates of the condition of terrestrial ecosystems and future climate change. To reduce uncertainties and improve the understanding of their carbon budgets, we investigated the utility of the eddy flux datasets to improve model simulations and reduce variabilities among multi-model outputs of terrestrial biosphere models in Japan. Using 9 terrestrial biosphere models (Support Vector Machine - based regressions, TOPS, CASA, VISIT, Biome-BGC, DAYCENT, SEIB, LPJ, and TRIFFID), we conducted two simulations: (1) point simulations at four eddy flux sites in Japan and (2) spatial simulations for Japan with a default model (based on original settings) and a modified model (based on model parameter tuning using eddy flux data). Generally, models using default model settings showed large deviations in model outputs from observation with large model-by-model variability. However, after we calibrated the model parameters using eddy flux data (GPP, RE and NEP), most models successfully simulated seasonal variations in the carbon cycle, with less variability among models. We also found that interannual variations in the carbon cycle are mostly consistent among models and observations. Spatial analysis also showed a large reduction in the variability among model outputs. This study demonstrated that careful validation and calibration of models with available eddy flux data reduced model-by-model differences. Yet, site history, analysis of model structure changes, and more objective procedure of model calibration should be included in the further analysis.

Conceptual and logical level of database modeling

NASA Astrophysics Data System (ADS)

Hunka, Frantisek; Matula, Jiri

2016-06-01

Conceptual and logical levels form the top most levels of database modeling. Usually, ORM (Object Role Modeling) and ER diagrams are utilized to capture the corresponding schema. The final aim of business process modeling is to store its results in the form of database solution. For this reason, value oriented business process modeling which utilizes ER diagram to express the modeling entities and relationships between them are used. However, ER diagrams form the logical level of database schema. To extend possibilities of different business process modeling methodologies, the conceptual level of database modeling is needed. The paper deals with the REA value modeling approach to business process modeling using ER-diagrams, and derives conceptual model utilizing ORM modeling approach. Conceptual model extends possibilities for value modeling to other business modeling approaches.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Service-oriented model-encapsulation strategy for sharing and integrating heterogeneous geo-analysis models in an open web environment

NASA Astrophysics Data System (ADS)

Yue, Songshan; Chen, Min; Wen, Yongning; Lu, Guonian

2016-04-01

Earth environment is extremely complicated and constantly changing; thus, it is widely accepted that the use of a single geo-analysis model cannot accurately represent all details when solving complex geo-problems. Over several years of research, numerous geo-analysis models have been developed. However, a collaborative barrier between model providers and model users still exists. The development of cloud computing has provided a new and promising approach for sharing and integrating geo-analysis models across an open web environment. To share and integrate these heterogeneous models, encapsulation studies should be conducted that are aimed at shielding original execution differences to create services which can be reused in the web environment. Although some model service standards (such as Web Processing Service (WPS) and Geo Processing Workflow (GPW)) have been designed and developed to help researchers construct model services, various problems regarding model encapsulation remain. (1) The descriptions of geo-analysis models are complicated and typically require rich-text descriptions and case-study illustrations, which are difficult to fully represent within a single web request (such as the GetCapabilities and DescribeProcess operations in the WPS standard). (2) Although Web Service technologies can be used to publish model services, model users who want to use a geo-analysis model and copy the model service into another computer still encounter problems (e.g., they cannot access the model deployment dependencies information). This study presents a strategy for encapsulating geo-analysis models to reduce problems encountered when sharing models between model providers and model users and supports the tasks with different web service standards (e.g., the WPS standard). A description method for heterogeneous geo-analysis models is studied. Based on the model description information, the methods for encapsulating the model-execution program to model services and for describing model-service deployment information are also included in the proposed strategy. Hence, the model-description interface, model-execution interface and model-deployment interface are studied to help model providers and model users more easily share, reuse and integrate geo-analysis models in an open web environment. Finally, a prototype system is established, and the WPS standard is employed as an example to verify the capability and practicability of the model-encapsulation strategy. The results show that it is more convenient for modellers to share and integrate heterogeneous geo-analysis models in cloud computing platforms.

Object-oriented biomedical system modelling--the language.

PubMed

Hakman, M; Groth, T

1999-11-01

The paper describes a new object-oriented biomedical continuous system modelling language (OOBSML). It is fully object-oriented and supports model inheritance, encapsulation, and model component instantiation and behaviour polymorphism. Besides the traditional differential and algebraic equation expressions the language includes also formal expressions for documenting models and defining model quantity types and quantity units. It supports explicit definition of model input-, output- and state quantities, model components and component connections. The OOBSML model compiler produces self-contained, independent, executable model components that can be instantiated and used within other OOBSML models and/or stored within model and model component libraries. In this way complex models can be structured as multilevel, multi-component model hierarchies. Technically the model components produced by the OOBSML compiler are executable computer code objects based on distributed object and object request broker technology. This paper includes both the language tutorial and the formal language syntax and semantic description.

Fitting IRT Models to Dichotomous and Polytomous Data: Assessing the Relative Model-Data Fit of Ideal Point and Dominance Models

ERIC Educational Resources Information Center

Tay, Louis; Ali, Usama S.; Drasgow, Fritz; Williams, Bruce

2011-01-01

This study investigated the relative model-data fit of an ideal point item response theory (IRT) model (the generalized graded unfolding model [GGUM]) and dominance IRT models (e.g., the two-parameter logistic model [2PLM] and Samejima's graded response model [GRM]) to simulated dichotomous and polytomous data generated from each of these models.…

Comparing and combining process-based crop models and statistical models with some implications for climate change

NASA Astrophysics Data System (ADS)

Roberts, Michael J.; Braun, Noah O.; Sinclair, Thomas R.; Lobell, David B.; Schlenker, Wolfram

2017-09-01

We compare predictions of a simple process-based crop model (Soltani and Sinclair 2012), a simple statistical model (Schlenker and Roberts 2009), and a combination of both models to actual maize yields on a large, representative sample of farmer-managed fields in the Corn Belt region of the United States. After statistical post-model calibration, the process model (Simple Simulation Model, or SSM) predicts actual outcomes slightly better than the statistical model, but the combined model performs significantly better than either model. The SSM, statistical model and combined model all show similar relationships with precipitation, while the SSM better accounts for temporal patterns of precipitation, vapor pressure deficit and solar radiation. The statistical and combined models show a more negative impact associated with extreme heat for which the process model does not account. Due to the extreme heat effect, predicted impacts under uniform climate change scenarios are considerably more severe for the statistical and combined models than for the process-based model.

An empirical model to forecast solar wind velocity through statistical modeling

NASA Astrophysics Data System (ADS)

Gao, Y.; Ridley, A. J.

2013-12-01

The accurate prediction of the solar wind velocity has been a major challenge in the space weather community. Previous studies proposed many empirical and semi-empirical models to forecast the solar wind velocity based on either the historical observations, e.g. the persistence model, or the instantaneous observations of the sun, e.g. the Wang-Sheeley-Arge model. In this study, we use the one-minute WIND data from January 1995 to August 2012 to investigate and compare the performances of 4 models often used in literature, here referred to as the null model, the persistence model, the one-solar-rotation-ago model, and the Wang-Sheeley-Arge model. It is found that, measured by root mean square error, the persistence model gives the most accurate predictions within two days. Beyond two days, the Wang-Sheeley-Arge model serves as the best model, though it only slightly outperforms the null model and the one-solar-rotation-ago model. Finally, we apply the least-square regression to linearly combine the null model, the persistence model, and the one-solar-rotation-ago model to propose a 'general persistence model'. By comparing its performance against the 4 aforementioned models, it is found that the accuracy of the general persistence model outperforms the other 4 models within five days. Due to its great simplicity and superb performance, we believe that the general persistence model can serve as a benchmark in the forecast of solar wind velocity and has the potential to be modified to arrive at better models.

A Primer for Model Selection: The Decisive Role of Model Complexity

NASA Astrophysics Data System (ADS)

Höge, Marvin; Wöhling, Thomas; Nowak, Wolfgang

2018-03-01

Selecting a "best" model among several competing candidate models poses an often encountered problem in water resources modeling (and other disciplines which employ models). For a modeler, the best model fulfills a certain purpose best (e.g., flood prediction), which is typically assessed by comparing model simulations to data (e.g., stream flow). Model selection methods find the "best" trade-off between good fit with data and model complexity. In this context, the interpretations of model complexity implied by different model selection methods are crucial, because they represent different underlying goals of modeling. Over the last decades, numerous model selection criteria have been proposed, but modelers who primarily want to apply a model selection criterion often face a lack of guidance for choosing the right criterion that matches their goal. We propose a classification scheme for model selection criteria that helps to find the right criterion for a specific goal, i.e., which employs the correct complexity interpretation. We identify four model selection classes which seek to achieve high predictive density, low predictive error, high model probability, or shortest compression of data. These goals can be achieved by following either nonconsistent or consistent model selection and by either incorporating a Bayesian parameter prior or not. We allocate commonly used criteria to these four classes, analyze how they represent model complexity and what this means for the model selection task. Finally, we provide guidance on choosing the right type of criteria for specific model selection tasks. (A quick guide through all key points is given at the end of the introduction.)

Women's Endorsement of Models of Sexual Response: Correlates and Predictors.

PubMed

Nowosielski, Krzysztof; Wróbel, Beata; Kowalczyk, Robert

2016-02-01

Few studies have investigated endorsement of female sexual response models, and no single model has been accepted as a normative description of women's sexual response. The aim of the study was to establish how women from a population-based sample endorse current theoretical models of the female sexual response--the linear models and circular model (partial and composite Basson models)--as well as predictors of endorsement. Accordingly, 174 heterosexual women aged 18-55 years were included in a cross-sectional study: 74 women diagnosed with female sexual dysfunction (FSD) based on DSM-5 criteria and 100 non-dysfunctional women. The description of sexual response models was used to divide subjects into four subgroups: linear (Masters-Johnson and Kaplan models), circular (partial Basson model), mixed (linear and circular models in similar proportions, reflective of the composite Basson model), and a different model. Women were asked to choose which of the models best described their pattern of sexual response and how frequently they engaged in each model. Results showed that 28.7% of women endorsed the linear models, 19.5% the partial Basson model, 40.8% the composite Basson model, and 10.9% a different model. Women with FSD endorsed the partial Basson model and a different model more frequently than did non-dysfunctional controls. Individuals who were dissatisfied with a partner as a lover were more likely to endorse a different model. Based on the results, we concluded that the majority of women endorsed a mixed model combining the circular response with the possibility of an innate desire triggering a linear response. Further, relationship difficulties, not FSD, predicted model endorsement.

The Use of Modeling-Based Text to Improve Students' Modeling Competencies

ERIC Educational Resources Information Center

Jong, Jing-Ping; Chiu, Mei-Hung; Chung, Shiao-Lan

2015-01-01

This study investigated the effects of a modeling-based text on 10th graders' modeling competencies. Fifteen 10th graders read a researcher-developed modeling-based science text on the ideal gas law that included explicit descriptions and representations of modeling processes (i.e., model selection, model construction, model validation, model…

Performance and Architecture Lab Modeling Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

DOE PAGES

Lu, Dan; Ye, Ming; Curtis, Gary P.

2015-08-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict themore » reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally, limitations of applying MLBMA to the synthetic study and future real-world modeling are discussed.« less

Takagi-Sugeno-Kang fuzzy models of the rainfall-runoff transformation

NASA Astrophysics Data System (ADS)

Jacquin, A. P.; Shamseldin, A. Y.

2009-04-01

Fuzzy inference systems, or fuzzy models, are non-linear models that describe the relation between the inputs and the output of a real system using a set of fuzzy IF-THEN rules. This study deals with the application of Takagi-Sugeno-Kang type fuzzy models to the development of rainfall-runoff models operating on a daily basis, using a system based approach. The models proposed are classified in two types, each intended to account for different kinds of dominant non-linear effects in the rainfall-runoff relationship. Fuzzy models type 1 are intended to incorporate the effect of changes in the prevailing soil moisture content, while fuzzy models type 2 address the phenomenon of seasonality. Each model type consists of five fuzzy models of increasing complexity; the most complex fuzzy model of each model type includes all the model components found in the remaining fuzzy models of the respective type. The models developed are applied to data of six catchments from different geographical locations and sizes. Model performance is evaluated in terms of two measures of goodness of fit, namely the Nash-Sutcliffe criterion and the index of volumetric fit. The results of the fuzzy models are compared with those of the Simple Linear Model, the Linear Perturbation Model and the Nearest Neighbour Linear Perturbation Model, which use similar input information. Overall, the results of this study indicate that Takagi-Sugeno-Kang fuzzy models are a suitable alternative for modelling the rainfall-runoff relationship. However, it is also observed that increasing the complexity of the model structure does not necessarily produce an improvement in the performance of the fuzzy models. The relative importance of the different model components in determining the model performance is evaluated through sensitivity analysis of the model parameters in the accompanying study presented in this meeting. Acknowledgements: We would like to express our gratitude to Prof. Kieran M. O'Connor from the National University of Ireland, Galway, for providing the data used in this study.

A simple computational algorithm of model-based choice preference.

PubMed

Toyama, Asako; Katahira, Kentaro; Ohira, Hideki

2017-08-01

A broadly used computational framework posits that two learning systems operate in parallel during the learning of choice preferences-namely, the model-free and model-based reinforcement-learning systems. In this study, we examined another possibility, through which model-free learning is the basic system and model-based information is its modulator. Accordingly, we proposed several modified versions of a temporal-difference learning model to explain the choice-learning process. Using the two-stage decision task developed by Daw, Gershman, Seymour, Dayan, and Dolan (2011), we compared their original computational model, which assumes a parallel learning process, and our proposed models, which assume a sequential learning process. Choice data from 23 participants showed a better fit with the proposed models. More specifically, the proposed eligibility adjustment model, which assumes that the environmental model can weight the degree of the eligibility trace, can explain choices better under both model-free and model-based controls and has a simpler computational algorithm than the original model. In addition, the forgetting learning model and its variation, which assume changes in the values of unchosen actions, substantially improved the fits to the data. Overall, we show that a hybrid computational model best fits the data. The parameters used in this model succeed in capturing individual tendencies with respect to both model use in learning and exploration behavior. This computational model provides novel insights into learning with interacting model-free and model-based components.

Airborne Wireless Communication Modeling and Analysis with MATLAB

DTIC Science & Technology

2014-03-27

research develops a physical layer model that combines antenna modeling using computational electromagnetics and the two-ray propagation model to...predict the received signal strength. The antenna is modeled with triangular patches and analyzed by extending the antenna modeling algorithm by Sergey...7  2.7. Propagation Modeling : Statistical Models ............................................................8  2.8. Antenna Modeling

Marginal and Random Intercepts Models for Longitudinal Binary Data with Examples from Criminology

ERIC Educational Resources Information Center

Long, Jeffrey D.; Loeber, Rolf; Farrington, David P.

2009-01-01

Two models for the analysis of longitudinal binary data are discussed: the marginal model and the random intercepts model. In contrast to the linear mixed model (LMM), the two models for binary data are not subsumed under a single hierarchical model. The marginal model provides group-level information whereas the random intercepts model provides…

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

Model compilation: An approach to automated model derivation

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Baudin, Catherine; Iwasaki, Yumi; Nayak, Pandurang; Tanaka, Kazuo

1990-01-01

An approach is introduced to automated model derivation for knowledge based systems. The approach, model compilation, involves procedurally generating the set of domain models used by a knowledge based system. With an implemented example, how this approach can be used to derive models of different precision and abstraction is illustrated, and models are tailored to different tasks, from a given set of base domain models. In particular, two implemented model compilers are described, each of which takes as input a base model that describes the structure and behavior of a simple electromechanical device, the Reaction Wheel Assembly of NASA's Hubble Space Telescope. The compilers transform this relatively general base model into simple task specific models for troubleshooting and redesign, respectively, by applying a sequence of model transformations. Each transformation in this sequence produces an increasingly more specialized model. The compilation approach lessens the burden of updating and maintaining consistency among models by enabling their automatic regeneration.

A composite computational model of liver glucose homeostasis. I. Building the composite model.

PubMed

Hetherington, J; Sumner, T; Seymour, R M; Li, L; Rey, M Varela; Yamaji, S; Saffrey, P; Margoninski, O; Bogle, I D L; Finkelstein, A; Warner, A

2012-04-07

A computational model of the glucagon/insulin-driven liver glucohomeostasis function, focusing on the buffering of glucose into glycogen, has been developed. The model exemplifies an 'engineering' approach to modelling in systems biology, and was produced by linking together seven component models of separate aspects of the physiology. The component models use a variety of modelling paradigms and degrees of simplification. Model parameters were determined by an iterative hybrid of fitting to high-scale physiological data, and determination from small-scale in vitro experiments or molecular biological techniques. The component models were not originally designed for inclusion within such a composite model, but were integrated, with modification, using our published modelling software and computational frameworks. This approach facilitates the development of large and complex composite models, although, inevitably, some compromises must be made when composing the individual models. Composite models of this form have not previously been demonstrated.

The applicability of turbulence models to aerodynamic and propulsion flowfields at McDonnell-Douglas Aerospace

NASA Technical Reports Server (NTRS)

Kral, Linda D.; Ladd, John A.; Mani, Mori

1995-01-01

The objective of this viewgraph presentation is to evaluate turbulence models for integrated aircraft components such as the forebody, wing, inlet, diffuser, nozzle, and afterbody. The one-equation models have replaced the algebraic models as the baseline turbulence models. The Spalart-Allmaras one-equation model consistently performs better than the Baldwin-Barth model, particularly in the log-layer and free shear layers. Also, the Sparlart-Allmaras model is not grid dependent like the Baldwin-Barth model. No general turbulence model exists for all engineering applications. The Spalart-Allmaras one-equation model and the Chien k-epsilon models are the preferred turbulence models. Although the two-equation models often better predict the flow field, they may take from two to five times the CPU time. Future directions are in further benchmarking the Menter blended k-w/k-epsilon and algorithmic improvements to reduce CPU time of the two-equation model.

The determination of third order linear models from a seventh order nonlinear jet engine model

NASA Technical Reports Server (NTRS)

Lalonde, Rick J.; Hartley, Tom T.; De Abreu-Garcia, J. Alex

1989-01-01

Results are presented that demonstrate how good reduced-order models can be obtained directly by recursive parameter identification using input/output (I/O) data of high-order nonlinear systems. Three different methods of obtaining a third-order linear model from a seventh-order nonlinear turbojet engine model are compared. The first method is to obtain a linear model from the original model and then reduce the linear model by standard reduction techniques such as residualization and balancing. The second method is to identify directly a third-order linear model by recursive least-squares parameter estimation using I/O data of the original model. The third method is to obtain a reduced-order model from the original model and then linearize the reduced model. Frequency responses are used as the performance measure to evaluate the reduced models. The reduced-order models along with their Bode plots are presented for comparison purposes.

BioModels: expanding horizons to include more modelling approaches and formats

PubMed Central

Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi

2018-01-01

Abstract BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. PMID:29106614

Modelling, teachers' views on the nature of modelling, and implications for the education of modellers

NASA Astrophysics Data System (ADS)

Justi, Rosária S.; Gilbert, John K.

2002-04-01

In this paper, the role of modelling in the teaching and learning of science is reviewed. In order to represent what is entailed in modelling, a 'model of modelling' framework is proposed. Five phases in moving towards a full capability in modelling are established by a review of the literature: learning models; learning to use models; learning how to revise models; learning to reconstruct models; learning to construct models de novo. In order to identify the knowledge and skills that science teachers think are needed to produce a model successfully, a semi-structured interview study was conducted with 39 Brazilian serving science teachers: 10 teaching at the 'fundamental' level (6-14 years); 10 teaching at the 'medium'-level (15-17 years); 10 undergraduate pre-service 'medium'-level teachers; 9 university teachers of chemistry. Their responses are used to establish what is entailed in implementing the 'model of modelling' framework. The implications for students, teachers, and for teacher education, of moving through the five phases of capability, are discussed.

Modelling land use change with generalized linear models--a multi-model analysis of change between 1860 and 2000 in Gallatin Valley, Montana.

PubMed

Aspinall, Richard

2004-08-01

This paper develops an approach to modelling land use change that links model selection and multi-model inference with empirical models and GIS. Land use change is frequently studied, and understanding gained, through a process of modelling that is an empirical analysis of documented changes in land cover or land use patterns. The approach here is based on analysis and comparison of multiple models of land use patterns using model selection and multi-model inference. The approach is illustrated with a case study of rural housing as it has developed for part of Gallatin County, Montana, USA. A GIS contains the location of rural housing on a yearly basis from 1860 to 2000. The database also documents a variety of environmental and socio-economic conditions. A general model of settlement development describes the evolution of drivers of land use change and their impacts in the region. This model is used to develop a series of different models reflecting drivers of change at different periods in the history of the study area. These period specific models represent a series of multiple working hypotheses describing (a) the effects of spatial variables as a representation of social, economic and environmental drivers of land use change, and (b) temporal changes in the effects of the spatial variables as the drivers of change evolve over time. Logistic regression is used to calibrate and interpret these models and the models are then compared and evaluated with model selection techniques. Results show that different models are 'best' for the different periods. The different models for different periods demonstrate that models are not invariant over time which presents challenges for validation and testing of empirical models. The research demonstrates (i) model selection as a mechanism for rating among many plausible models that describe land cover or land use patterns, (ii) inference from a set of models rather than from a single model, (iii) that models can be developed based on hypothesised relationships based on consideration of underlying and proximate causes of change, and (iv) that models are not invariant over time.

Investigation of prospective teachers' knowledge and understanding of models and modeling and their attitudes towards the use of models in science education

NASA Astrophysics Data System (ADS)

Aktan, Mustafa B.

The purpose of this study was to investigate prospective science teachers' knowledge and understanding of models and modeling, and their attitudes towards the use of models in science teaching through the following research questions: What knowledge do prospective science teachers have about models and modeling in science? What understandings about the nature of models do these teachers hold as a result of their educational training? What perceptions and attitudes do these teachers hold about the use of models in their teaching? Two main instruments, semi-structured in-depth interviewing and an open-item questionnaire, were used to obtain data from the participants. The data were analyzed from an interpretative phenomenological perspective and grounded theory methods. Earlier studies on in-service science teachers' understanding about the nature of models and modeling revealed that variations exist among teachers' limited yet diverse understanding of scientific models. The results of this study indicated that variations also existed among prospective science teachers' understanding of the concept of model and the nature of models. Apparently the participants' knowledge of models and modeling was limited and they viewed models as materialistic examples and representations. I found that the teachers believed the purpose of a model is to make phenomena more accessible and more understandable. They defined models by referring to an example, a representation, or a simplified version of the real thing. I found no evidence of negative attitudes towards use of models among the participants. Although the teachers valued the idea that scientific models are important aspects of science teaching and learning, and showed positive attitudes towards the use of models in their teaching, certain factors like level of learner, time, lack of modeling experience, and limited knowledge of models appeared to be affecting their perceptions negatively. Implications for the development of science teaching and teacher education programs are discussed. Directions for future research are suggested. Overall, based on the results, I suggest that prospective science teachers should engage in more modeling activities through their preparation programs, gain more modeling experience, and collaborate with their colleagues to better understand and implement scientific models in science teaching.

Validation of Groundwater Models: Meaningful or Meaningless?

NASA Astrophysics Data System (ADS)

Konikow, L. F.

2003-12-01

Although numerical simulation models are valuable tools for analyzing groundwater systems, their predictive accuracy is limited. People who apply groundwater flow or solute-transport models, as well as those who make decisions based on model results, naturally want assurance that a model is "valid." To many people, model validation implies some authentication of the truth or accuracy of the model. History matching is often presented as the basis for model validation. Although such model calibration is a necessary modeling step, it is simply insufficient for model validation. Because of parameter uncertainty and solution non-uniqueness, declarations of validation (or verification) of a model are not meaningful. Post-audits represent a useful means to assess the predictive accuracy of a site-specific model, but they require the existence of long-term monitoring data. Model testing may yield invalidation, but that is an opportunity to learn and to improve the conceptual and numerical models. Examples of post-audits and of the application of a solute-transport model to a radioactive waste disposal site illustrate deficiencies in model calibration, prediction, and validation.

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, Robert M.

2008-01-01

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Using the Model Coupling Toolkit to couple earth system models

USGS Publications Warehouse

Warner, J.C.; Perlin, N.; Skyllingstad, E.D.

2008-01-01

Continued advances in computational resources are providing the opportunity to operate more sophisticated numerical models. Additionally, there is an increasing demand for multidisciplinary studies that include interactions between different physical processes. Therefore there is a strong desire to develop coupled modeling systems that utilize existing models and allow efficient data exchange and model control. The basic system would entail model "1" running on "M" processors and model "2" running on "N" processors, with efficient exchange of model fields at predetermined synchronization intervals. Here we demonstrate two coupled systems: the coupling of the ocean circulation model Regional Ocean Modeling System (ROMS) to the surface wave model Simulating WAves Nearshore (SWAN), and the coupling of ROMS to the atmospheric model Coupled Ocean Atmosphere Prediction System (COAMPS). Both coupled systems use the Model Coupling Toolkit (MCT) as a mechanism for operation control and inter-model distributed memory transfer of model variables. In this paper we describe requirements and other options for model coupling, explain the MCT library, ROMS, SWAN and COAMPS models, methods for grid decomposition and sparse matrix interpolation, and provide an example from each coupled system. Methods presented in this paper are clearly applicable for coupling of other types of models. ?? 2008 Elsevier Ltd. All rights reserved.

Generalized Multilevel Structural Equation Modeling

ERIC Educational Resources Information Center

Rabe-Hesketh, Sophia; Skrondal, Anders; Pickles, Andrew

2004-01-01

A unifying framework for generalized multilevel structural equation modeling is introduced. The models in the framework, called generalized linear latent and mixed models (GLLAMM), combine features of generalized linear mixed models (GLMM) and structural equation models (SEM) and consist of a response model and a structural model for the latent…

Frequentist Model Averaging in Structural Equation Modelling.

PubMed

Jin, Shaobo; Ankargren, Sebastian

2018-06-04

Model selection from a set of candidate models plays an important role in many structural equation modelling applications. However, traditional model selection methods introduce extra randomness that is not accounted for by post-model selection inference. In the current study, we propose a model averaging technique within the frequentist statistical framework. Instead of selecting an optimal model, the contributions of all candidate models are acknowledged. Valid confidence intervals and a [Formula: see text] test statistic are proposed. A simulation study shows that the proposed method is able to produce a robust mean-squared error, a better coverage probability, and a better goodness-of-fit test compared to model selection. It is an interesting compromise between model selection and the full model.

Premium analysis for copula model: A case study for Malaysian motor insurance claims

NASA Astrophysics Data System (ADS)

Resti, Yulia; Ismail, Noriszura; Jaaman, Saiful Hafizah

2014-06-01

This study performs premium analysis for copula models with regression marginals. For illustration purpose, the copula models are fitted to the Malaysian motor insurance claims data. In this study, we consider copula models from Archimedean and Elliptical families, and marginal distributions of Gamma and Inverse Gaussian regression models. The simulated results from independent model, which is obtained from fitting regression models separately to each claim category, and dependent model, which is obtained from fitting copula models to all claim categories, are compared. The results show that the dependent model using Frank copula is the best model since the risk premiums estimated under this model are closely approximate to the actual claims experience relative to the other copula models.

Utilizing Biological Models to Determine the Recruitment of the IRA by Modeling the Voting Behavior of Sinn Fein

DTIC Science & Technology

2006-03-01

models, the thesis applies a biological model, the Lotka - Volterra predator- prey model, to a highly suggestive case study, that of the Irish Republican...Model, Irish Republican Army, Sinn Féin, Lotka - Volterra Predator Prey Model, Recruitment, British Army 16. PRICE CODE 17. SECURITY CLASSIFICATION OF...weaknesses of sociological and biological models, the thesis applies a biological model, the Lotka - Volterra predator-prey model, to a highly suggestive

Right-Sizing Statistical Models for Longitudinal Data

PubMed Central

Wood, Phillip K.; Steinley, Douglas; Jackson, Kristina M.

2015-01-01

Arguments are proposed that researchers using longitudinal data should consider more and less complex statistical model alternatives to their initially chosen techniques in an effort to “right-size” the model to the data at hand. Such model comparisons may alert researchers who use poorly fitting overly parsimonious models to more complex better fitting alternatives, and, alternatively, may identify more parsimonious alternatives to overly complex (and perhaps empirically under-identified and/or less powerful) statistical models. A general framework is proposed for considering (often nested) relationships between a variety of psychometric and growth curve models. A three-step approach is proposed in which models are evaluated based on the number and patterning of variance components prior to selection of better-fitting growth models that explain both mean and variation/covariation patterns. The orthogonal, free-curve slope-intercept (FCSI) growth model is considered as a general model which includes, as special cases, many models including the Factor Mean model (FM, McArdle & Epstein, 1987), McDonald's (1967) linearly constrained factor model, Hierarchical Linear Models (HLM), Repeated Measures MANOVA, and the Linear Slope Intercept (LinearSI) Growth Model. The FCSI model, in turn, is nested within the Tuckerized factor model. The approach is illustrated by comparing alternative models in a longitudinal study of children's vocabulary and by comparison of several candidate parametric growth and chronometric models in a Monte Carlo study. PMID:26237507

Right-sizing statistical models for longitudinal data.

PubMed

Wood, Phillip K; Steinley, Douglas; Jackson, Kristina M

2015-12-01

Arguments are proposed that researchers using longitudinal data should consider more and less complex statistical model alternatives to their initially chosen techniques in an effort to "right-size" the model to the data at hand. Such model comparisons may alert researchers who use poorly fitting, overly parsimonious models to more complex, better-fitting alternatives and, alternatively, may identify more parsimonious alternatives to overly complex (and perhaps empirically underidentified and/or less powerful) statistical models. A general framework is proposed for considering (often nested) relationships between a variety of psychometric and growth curve models. A 3-step approach is proposed in which models are evaluated based on the number and patterning of variance components prior to selection of better-fitting growth models that explain both mean and variation-covariation patterns. The orthogonal free curve slope intercept (FCSI) growth model is considered a general model that includes, as special cases, many models, including the factor mean (FM) model (McArdle & Epstein, 1987), McDonald's (1967) linearly constrained factor model, hierarchical linear models (HLMs), repeated-measures multivariate analysis of variance (MANOVA), and the linear slope intercept (linearSI) growth model. The FCSI model, in turn, is nested within the Tuckerized factor model. The approach is illustrated by comparing alternative models in a longitudinal study of children's vocabulary and by comparing several candidate parametric growth and chronometric models in a Monte Carlo study. (c) 2015 APA, all rights reserved).

Model averaging techniques for quantifying conceptual model uncertainty.

PubMed

Singh, Abhishek; Mishra, Srikanta; Ruskauff, Greg

2010-01-01

In recent years a growing understanding has emerged regarding the need to expand the modeling paradigm to include conceptual model uncertainty for groundwater models. Conceptual model uncertainty is typically addressed by formulating alternative model conceptualizations and assessing their relative likelihoods using statistical model averaging approaches. Several model averaging techniques and likelihood measures have been proposed in the recent literature for this purpose with two broad categories--Monte Carlo-based techniques such as Generalized Likelihood Uncertainty Estimation or GLUE (Beven and Binley 1992) and criterion-based techniques that use metrics such as the Bayesian and Kashyap Information Criteria (e.g., the Maximum Likelihood Bayesian Model Averaging or MLBMA approach proposed by Neuman 2003) and Akaike Information Criterion-based model averaging (AICMA) (Poeter and Anderson 2005). These different techniques can often lead to significantly different relative model weights and ranks because of differences in the underlying statistical assumptions about the nature of model uncertainty. This paper provides a comparative assessment of the four model averaging techniques (GLUE, MLBMA with KIC, MLBMA with BIC, and AIC-based model averaging) mentioned above for the purpose of quantifying the impacts of model uncertainty on groundwater model predictions. Pros and cons of each model averaging technique are examined from a practitioner's perspective using two groundwater modeling case studies. Recommendations are provided regarding the use of these techniques in groundwater modeling practice.

Examination of various turbulence models for application in liquid rocket thrust chambers

NASA Technical Reports Server (NTRS)

Hung, R. J.

1991-01-01

There is a large variety of turbulence models available. These models include direct numerical simulation, large eddy simulation, Reynolds stress/flux model, zero equation model, one equation model, two equation k-epsilon model, multiple-scale model, etc. Each turbulence model contains different physical assumptions and requirements. The natures of turbulence are randomness, irregularity, diffusivity and dissipation. The capabilities of the turbulence models, including physical strength, weakness, limitations, as well as numerical and computational considerations, are reviewed. Recommendations are made for the potential application of a turbulence model in thrust chamber and performance prediction programs. The full Reynolds stress model is recommended. In a workshop, specifically called for the assessment of turbulence models for applications in liquid rocket thrust chambers, most of the experts present were also in favor of the recommendation of the Reynolds stress model.

Comparative study of turbulence models in predicting hypersonic inlet flows

NASA Technical Reports Server (NTRS)

Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

1992-01-01

A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared wery well with the experimental data, and performed better than the Thomas model near the walls.

Comparative study of turbulence models in predicting hypersonic inlet flows

NASA Technical Reports Server (NTRS)

Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

1992-01-01

A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared very well with the experimental data, and performed better than the Thomas model near the walls.

[The reliability of dento-maxillary models created by cone-beam CT and rapid prototyping:a comparative study].

PubMed

Lv, Yan; Yan, Bin; Wang, Lin; Lou, Dong-hua

2012-04-01

To analyze the reliability of the dento-maxillary models created by cone-beam CT and rapid prototyping (RP). Plaster models were obtained from 20 orthodontic patients who had been scanned by cone-beam CT and 3-D models were formed after the calculation and reconstruction of software. Then, computerized composite models (RP models) were produced by rapid prototyping technique. The crown widths, dental arch widths and dental arch lengths on each plaster model, 3-D model and RP model were measured, followed by statistical analysis with SPSS17.0 software package. For crown widths, dental arch lengths and crowding, there were significant differences(P<0.05) among the 3 models, but the dental arch widths were on the contrary. Measurements on 3-D models were significantly smaller than those on other two models(P<0.05). Compared with 3-D models, RP models had more numbers which were not significantly different from those on plaster models(P>0.05). The regression coefficient among three models were significantly different(P<0.01), ranging from 0.8 to 0.9. But between RP and plaster models was bigger than that between 3-D and plaster models. There is high consistency within 3 models, while some differences were accepted in clinic. Therefore, it is possible to substitute 3-D and RP models for plaster models in order to save storage space and improve efficiency.

Smart Frameworks and Self-Describing Models: Model Metadata for Automated Coupling of Hydrologic Process Components (Invited)

NASA Astrophysics Data System (ADS)

Peckham, S. D.

2013-12-01

Model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System) and ESMF (Earth System Modeling Framework) have developed mechanisms that allow heterogeneous sets of process models to be assembled in a plug-and-play manner to create composite "system models". These mechanisms facilitate code reuse, but must simultaneously satisfy many different design criteria. They must be able to mediate or compensate for differences between the process models, such as their different programming languages, computational grids, time-stepping schemes, variable names and variable units. However, they must achieve this interoperability in a way that: (1) is noninvasive, requiring only relatively small and isolated changes to the original source code, (2) does not significantly reduce performance, (3) is not time-consuming or confusing for a model developer to implement, (4) can very easily be updated to accommodate new versions of a given process model and (5) does not shift the burden of providing model interoperability to the model developers, e.g. by requiring them to provide their output in specific forms that meet the input requirements of other models. In tackling these design challenges, model framework developers have learned that the best solution is to provide each model with a simple, standardized interface, i.e. a set of standardized functions that make the model: (1) fully-controllable by a caller (e.g. a model framework) and (2) self-describing. Model control functions are separate functions that allow a caller to initialize the model, advance the model's state variables in time and finalize the model. Model description functions allow a caller to retrieve detailed information on the model's input and output variables, its computational grid and its timestepping scheme. If the caller is a modeling framework, it can compare the answers to these queries with similar answers from other process models in a collection and then automatically call framework service components as necessary to mediate the differences between the coupled models. This talk will first review two key products of the CSDMS project, namely a standardized model interface called the Basic Model Interface (BMI) and the CSDMS Standard Names. The standard names are used in conjunction with BMI to provide a semantic matching mechanism that allows output variables from one process model to be reliably used as input variables to other process models in a collection. They include not just a standardized naming scheme for model variables, but also a standardized set of terms for describing the attributes and assumptions of a given model. To illustrate the power of standardized model interfaces and metadata, a smart, light-weight modeling framework written in Python will be introduced that can automatically (without user intervention) couple a set of BMI-enabled hydrologic process components together to create a spatial hydrologic model. The same mechanisms could also be used to provide seamless integration (import/export) of data and models.

A model-averaging method for assessing groundwater conceptual model uncertainty.

PubMed

Ye, Ming; Pohlmann, Karl F; Chapman, Jenny B; Pohll, Greg M; Reeves, Donald M

2010-01-01

This study evaluates alternative groundwater models with different recharge and geologic components at the northern Yucca Flat area of the Death Valley Regional Flow System (DVRFS), USA. Recharge over the DVRFS has been estimated using five methods, and five geological interpretations are available at the northern Yucca Flat area. Combining the recharge and geological components together with additional modeling components that represent other hydrogeological conditions yields a total of 25 groundwater flow models. As all the models are plausible given available data and information, evaluating model uncertainty becomes inevitable. On the other hand, hydraulic parameters (e.g., hydraulic conductivity) are uncertain in each model, giving rise to parametric uncertainty. Propagation of the uncertainty in the models and model parameters through groundwater modeling causes predictive uncertainty in model predictions (e.g., hydraulic head and flow). Parametric uncertainty within each model is assessed using Monte Carlo simulation, and model uncertainty is evaluated using the model averaging method. Two model-averaging techniques (on the basis of information criteria and GLUE) are discussed. This study shows that contribution of model uncertainty to predictive uncertainty is significantly larger than that of parametric uncertainty. For the recharge and geological components, uncertainty in the geological interpretations has more significant effect on model predictions than uncertainty in the recharge estimates. In addition, weighted residuals vary more for the different geological models than for different recharge models. Most of the calibrated observations are not important for discriminating between the alternative models, because their weighted residuals vary only slightly from one model to another.

Meta-Modeling: A Knowledge-Based Approach to Facilitating Model Construction and Reuse

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Dungan, Jennifer L.

1997-01-01

In this paper, we introduce a new modeling approach called meta-modeling and illustrate its practical applicability to the construction of physically-based ecosystem process models. As a critical adjunct to modeling codes meta-modeling requires explicit specification of certain background information related to the construction and conceptual underpinnings of a model. This information formalizes the heretofore tacit relationship between the mathematical modeling code and the underlying real-world phenomena being investigated, and gives insight into the process by which the model was constructed. We show how the explicit availability of such information can make models more understandable and reusable and less subject to misinterpretation. In particular, background information enables potential users to better interpret an implemented ecosystem model without direct assistance from the model author. Additionally, we show how the discipline involved in specifying background information leads to improved management of model complexity and fewer implementation errors. We illustrate the meta-modeling approach in the context of the Scientists' Intelligent Graphical Modeling Assistant (SIGMA) a new model construction environment. As the user constructs a model using SIGMA the system adds appropriate background information that ties the executable model to the underlying physical phenomena under investigation. Not only does this information improve the understandability of the final model it also serves to reduce the overall time and programming expertise necessary to initially build and subsequently modify models. Furthermore, SIGMA's use of background knowledge helps eliminate coding errors resulting from scientific and dimensional inconsistencies that are otherwise difficult to avoid when building complex models. As a. demonstration of SIGMA's utility, the system was used to reimplement and extend a well-known forest ecosystem dynamics model: Forest-BGC.

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: 1' = 400' HORIZONTAL, 1' = 100' VERTICAL), AND GREENVILLE BRIDGE MODEL (MODEL SCALE: 1' = 360' HORIZONTAL, 1' = 100' VERTICAL). - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

Bayesian Data-Model Fit Assessment for Structural Equation Modeling

ERIC Educational Resources Information Center

Levy, Roy

2011-01-01

Bayesian approaches to modeling are receiving an increasing amount of attention in the areas of model construction and estimation in factor analysis, structural equation modeling (SEM), and related latent variable models. However, model diagnostics and model criticism remain relatively understudied aspects of Bayesian SEM. This article describes…

Evolution of computational models in BioModels Database and the Physiome Model Repository.

PubMed

Scharm, Martin; Gebhardt, Tom; Touré, Vasundra; Bagnacani, Andrea; Salehzadeh-Yazdi, Ali; Wolkenhauer, Olaf; Waltemath, Dagmar

2018-04-12

A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable. We analysed 13734 models from BioModels Database and the Physiome Model Repository. For each model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database. We observed continuous updates in the majority of models. Surprisingly, even the early models are still being modified. We furthermore detected that many updates target annotations, which improves the information one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are available from GitHub https://github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at https://hub.docker.com/r/binfalse/bives-statsgenerator/ . The website https://most.bio.informatik.uni-rostock.de/ provides interactive access to model versions and their evolutionary statistics. The reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a model's provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the maintainers of model repositories to offer transparent model provenance to their users.

Large-watershed flood simulation and forecasting based on different-resolution distributed hydrological model

NASA Astrophysics Data System (ADS)

Li, J.

2017-12-01

Large-watershed flood simulation and forecasting is very important for a distributed hydrological model in the application. There are some challenges including the model's spatial resolution effect, model performance and accuracy and so on. To cope with the challenge of the model's spatial resolution effect, different model resolution including 1000m*1000m, 600m*600m, 500m*500m, 400m*400m, 200m*200m were used to build the distributed hydrological model—Liuxihe model respectively. The purpose is to find which one is the best resolution for Liuxihe model in Large-watershed flood simulation and forecasting. This study sets up a physically based distributed hydrological model for flood forecasting of the Liujiang River basin in south China. Terrain data digital elevation model (DEM), soil type and land use type are downloaded from the website freely. The model parameters are optimized by using an improved Particle Swarm Optimization(PSO) algorithm; And parameter optimization could reduce the parameter uncertainty that exists for physically deriving model parameters. The different model resolution (200m*200m—1000m*1000m ) are proposed for modeling the Liujiang River basin flood with the Liuxihe model in this study. The best model's spatial resolution effect for flood simulation and forecasting is 200m*200m.And with the model's spatial resolution reduction, the model performance and accuracy also become worse and worse. When the model resolution is 1000m*1000m, the flood simulation and forecasting result is the worst, also the river channel divided based on this resolution is differs from the actual one. To keep the model with an acceptable performance, minimum model spatial resolution is needed. The suggested threshold model spatial resolution for modeling the Liujiang River basin flood is a 500m*500m grid cell, but the model spatial resolution with a 200m*200m grid cell is recommended in this study to keep the model at a best performance.

Computational Models for Calcium-Mediated Astrocyte Functions.

PubMed

Manninen, Tiina; Havela, Riikka; Linne, Marja-Leena

2018-01-01

The computational neuroscience field has heavily concentrated on the modeling of neuronal functions, largely ignoring other brain cells, including one type of glial cell, the astrocytes. Despite the short history of modeling astrocytic functions, we were delighted about the hundreds of models developed so far to study the role of astrocytes, most often in calcium dynamics, synchronization, information transfer, and plasticity in vitro , but also in vascular events, hyperexcitability, and homeostasis. Our goal here is to present the state-of-the-art in computational modeling of astrocytes in order to facilitate better understanding of the functions and dynamics of astrocytes in the brain. Due to the large number of models, we concentrated on a hundred models that include biophysical descriptions for calcium signaling and dynamics in astrocytes. We categorized the models into four groups: single astrocyte models, astrocyte network models, neuron-astrocyte synapse models, and neuron-astrocyte network models to ease their use in future modeling projects. We characterized the models based on which earlier models were used for building the models and which type of biological entities were described in the astrocyte models. Features of the models were compared and contrasted so that similarities and differences were more readily apparent. We discovered that most of the models were basically generated from a small set of previously published models with small variations. However, neither citations to all the previous models with similar core structure nor explanations of what was built on top of the previous models were provided, which made it possible, in some cases, to have the same models published several times without an explicit intention to make new predictions about the roles of astrocytes in brain functions. Furthermore, only a few of the models are available online which makes it difficult to reproduce the simulation results and further develop the models. Thus, we would like to emphasize that only via reproducible research are we able to build better computational models for astrocytes, which truly advance science. Our study is the first to characterize in detail the biophysical and biochemical mechanisms that have been modeled for astrocytes.

Computational Models for Calcium-Mediated Astrocyte Functions

PubMed Central

Manninen, Tiina; Havela, Riikka; Linne, Marja-Leena

2018-01-01

The computational neuroscience field has heavily concentrated on the modeling of neuronal functions, largely ignoring other brain cells, including one type of glial cell, the astrocytes. Despite the short history of modeling astrocytic functions, we were delighted about the hundreds of models developed so far to study the role of astrocytes, most often in calcium dynamics, synchronization, information transfer, and plasticity in vitro, but also in vascular events, hyperexcitability, and homeostasis. Our goal here is to present the state-of-the-art in computational modeling of astrocytes in order to facilitate better understanding of the functions and dynamics of astrocytes in the brain. Due to the large number of models, we concentrated on a hundred models that include biophysical descriptions for calcium signaling and dynamics in astrocytes. We categorized the models into four groups: single astrocyte models, astrocyte network models, neuron-astrocyte synapse models, and neuron-astrocyte network models to ease their use in future modeling projects. We characterized the models based on which earlier models were used for building the models and which type of biological entities were described in the astrocyte models. Features of the models were compared and contrasted so that similarities and differences were more readily apparent. We discovered that most of the models were basically generated from a small set of previously published models with small variations. However, neither citations to all the previous models with similar core structure nor explanations of what was built on top of the previous models were provided, which made it possible, in some cases, to have the same models published several times without an explicit intention to make new predictions about the roles of astrocytes in brain functions. Furthermore, only a few of the models are available online which makes it difficult to reproduce the simulation results and further develop the models. Thus, we would like to emphasize that only via reproducible research are we able to build better computational models for astrocytes, which truly advance science. Our study is the first to characterize in detail the biophysical and biochemical mechanisms that have been modeled for astrocytes. PMID:29670517

Assessing the impact of land use change on hydrology by ensemble modeling (LUCHEM). I: Model intercomparison with current land use

USGS Publications Warehouse

Breuer, L.; Huisman, J.A.; Willems, P.; Bormann, H.; Bronstert, A.; Croke, B.F.W.; Frede, H.-G.; Graff, T.; Hubrechts, L.; Jakeman, A.J.; Kite, G.; Lanini, J.; Leavesley, G.; Lettenmaier, D.P.; Lindstrom, G.; Seibert, J.; Sivapalan, M.; Viney, N.R.

2009-01-01

This paper introduces the project on 'Assessing the impact of land use change on hydrology by ensemble modeling (LUCHEM)' that aims at investigating the envelope of predictions on changes in hydrological fluxes due to land use change. As part of a series of four papers, this paper outlines the motivation and setup of LUCHEM, and presents a model intercomparison for the present-day simulation results. Such an intercomparison provides a valuable basis to investigate the effects of different model structures on model predictions and paves the ground for the analysis of the performance of multi-model ensembles and the reliability of the scenario predictions in companion papers. In this study, we applied a set of 10 lumped, semi-lumped and fully distributed hydrological models that have been previously used in land use change studies to the low mountainous Dill catchment, Germany. Substantial differences in model performance were observed with Nash-Sutcliffe efficiencies ranging from 0.53 to 0.92. Differences in model performance were attributed to (1) model input data, (2) model calibration and (3) the physical basis of the models. The models were applied with two sets of input data: an original and a homogenized data set. This homogenization of precipitation, temperature and leaf area index was performed to reduce the variation between the models. Homogenization improved the comparability of model simulations and resulted in a reduced average bias, although some variation in model data input remained. The effect of the physical differences between models on the long-term water balance was mainly attributed to differences in how models represent evapotranspiration. Semi-lumped and lumped conceptual models slightly outperformed the fully distributed and physically based models. This was attributed to the automatic model calibration typically used for this type of models. Overall, however, we conclude that there was no superior model if several measures of model performance are considered and that all models are suitable to participate in further multi-model ensemble set-ups and land use change scenario investigations. ?? 2008 Elsevier Ltd. All rights reserved.

Benchmarking test of empirical root water uptake models

NASA Astrophysics Data System (ADS)

dos Santos, Marcos Alex; de Jong van Lier, Quirijn; van Dam, Jos C.; Freire Bezerra, Andre Herman

2017-01-01

Detailed physical models describing root water uptake (RWU) are an important tool for the prediction of RWU and crop transpiration, but the hydraulic parameters involved are hardly ever available, making them less attractive for many studies. Empirical models are more readily used because of their simplicity and the associated lower data requirements. The purpose of this study is to evaluate the capability of some empirical models to mimic the RWU distribution under varying environmental conditions predicted from numerical simulations with a detailed physical model. A review of some empirical models used as sub-models in ecohydrological models is presented, and alternative empirical RWU models are proposed. All these empirical models are analogous to the standard Feddes model, but differ in how RWU is partitioned over depth or how the transpiration reduction function is defined. The parameters of the empirical models are determined by inverse modelling of simulated depth-dependent RWU. The performance of the empirical models and their optimized empirical parameters depends on the scenario. The standard empirical Feddes model only performs well in scenarios with low root length density R, i.e. for scenarios with low RWU compensation. For medium and high R, the Feddes RWU model cannot mimic properly the root uptake dynamics as predicted by the physical model. The Jarvis RWU model in combination with the Feddes reduction function (JMf) only provides good predictions for low and medium R scenarios. For high R, it cannot mimic the uptake patterns predicted by the physical model. Incorporating a newly proposed reduction function into the Jarvis model improved RWU predictions. Regarding the ability of the models to predict plant transpiration, all models accounting for compensation show good performance. The Akaike information criterion (AIC) indicates that the Jarvis (2010) model (JMII), with no empirical parameters to be estimated, is the best model. The proposed models are better in predicting RWU patterns similar to the physical model. The statistical indices point to them as the best alternatives for mimicking RWU predictions of the physical model.

Modeling uncertainty: quicksand for water temperature modeling

USGS Publications Warehouse

Bartholow, John M.

2003-01-01

Uncertainty has been a hot topic relative to science generally, and modeling specifically. Modeling uncertainty comes in various forms: measured data, limited model domain, model parameter estimation, model structure, sensitivity to inputs, modelers themselves, and users of the results. This paper will address important components of uncertainty in modeling water temperatures, and discuss several areas that need attention as the modeling community grapples with how to incorporate uncertainty into modeling without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.

Energy modeling. Volume 2: Inventory and details of state energy models

NASA Astrophysics Data System (ADS)

Melcher, A. G.; Underwood, R. G.; Weber, J. C.; Gist, R. L.; Holman, R. P.; Donald, D. W.

1981-05-01

An inventory of energy models developed by or for state governments is presented, and certain models are discussed in depth. These models address a variety of purposes such as: supply or demand of energy or of certain types of energy; emergency management of energy; and energy economics. Ten models are described. The purpose, use, and history of the model is discussed, and information is given on the outputs, inputs, and mathematical structure of the model. The models include five models dealing with energy demand, one of which is econometric and four of which are econometric-engineering end-use models.

Advances in Geoscience Modeling: Smart Modeling Frameworks, Self-Describing Models and the Role of Standardized Metadata

NASA Astrophysics Data System (ADS)

Peckham, Scott

2016-04-01

Over the last decade, model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System) and ESMF (Earth System Modeling Framework) have developed mechanisms that make it much easier for modelers to connect heterogeneous sets of process models in a plug-and-play manner to create composite "system models". These mechanisms greatly simplify code reuse, but must simultaneously satisfy many different design criteria. They must be able to mediate or compensate for differences between the process models, such as their different programming languages, computational grids, time-stepping schemes, variable names and variable units. However, they must achieve this interoperability in a way that: (1) is noninvasive, requiring only relatively small and isolated changes to the original source code, (2) does not significantly reduce performance, (3) is not time-consuming or confusing for a model developer to implement, (4) can very easily be updated to accommodate new versions of a given process model and (5) does not shift the burden of providing model interoperability to the model developers. In tackling these design challenges, model framework developers have learned that the best solution is to provide each model with a simple, standardized interface, i.e. a set of standardized functions that make the model: (1) fully-controllable by a caller (e.g. a model framework) and (2) self-describing with standardized metadata. Model control functions are separate functions that allow a caller to initialize the model, advance the model's state variables in time and finalize the model. Model description functions allow a caller to retrieve detailed information on the model's input and output variables, its computational grid and its timestepping scheme. If the caller is a modeling framework, it can use the self description functions to learn about each process model in a collection to be coupled and then automatically call framework service components (e.g. regridders, time interpolators and unit converters) as necessary to mediate the differences between them so they can work together. This talk will first review two key products of the CSDMS project, namely a standardized model interface called the Basic Model Interface (BMI) and the CSDMS Standard Names. The standard names are used in conjunction with BMI to provide a semantic matching mechanism that allows output variables from one process model or data set to be reliably used as input variables to other process models in a collection. They include not just a standardized naming scheme for model variables, but also a standardized set of terms for describing the attributes and assumptions of a given model. Recent efforts to bring powerful uncertainty analysis and inverse modeling toolkits such as DAKOTA into modeling frameworks will also be described. This talk will conclude with an overview of several related modeling projects that have been funded by NSF's EarthCube initiative, namely the Earth System Bridge, OntoSoft and GeoSemantics projects.

[A review on research of land surface water and heat fluxes].

PubMed

Sun, Rui; Liu, Changming

2003-03-01

Many field experiments were done, and soil-vegetation-atmosphere transfer(SVAT) models were stablished to estimate land surface heat fluxes. In this paper, the processes of experimental research on land surface water and heat fluxes are reviewed, and three kinds of SVAT model(single layer model, two layer model and multi-layer model) are analyzed. Remote sensing data are widely used to estimate land surface heat fluxes. Based on remote sensing and energy balance equation, different models such as simplified model, single layer model, extra resistance model, crop water stress index model and two source resistance model are developed to estimate land surface heat fluxes and evapotranspiration. These models are also analyzed in this paper.