3,126 research outputs found
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Three-dimensional RNA models fitted into crystallographic density maps
exhibit pervasive conformational ambiguities, geometric errors and steric
clashes. To address these problems, we present enumerative real-space
refinement assisted by electron density under Rosetta (ERRASER), coupled to
Python-based hierarchical environment for integrated 'xtallography' (PHENIX)
diffraction-based refinement. On 24 data sets, ERRASER automatically corrects
the majority of MolProbity-assessed errors, improves the average Rfree factor,
resolves functionally important discrepancies in noncanonical structure and
refines low-resolution models to better match higher-resolution models
Long-term behavioural rewriting of maladaptive drinking memories via reconsolidation-update mechanisms
BACKGROUND: Alcohol use disorders can be conceptualised as a learned pattern of maladaptive alcohol-consumption behaviours. The memories encoding these behaviours centrally contribute to long-term excessive alcohol consumption and are therefore an important therapeutic target. The transient period of memory instability sparked during memory reconsolidation offers a therapeutic window to directly rewrite these memories using targeted behavioural interventions. However, clinically-relevant demonstrations of the efficacy of this approach are few. We examined key retrieval parameters for destabilising naturalistic drinking memories and the ability of subsequent counterconditioning to effect long-term reductions in drinking. METHODS: Hazardous/harmful beer-drinking volunteers (N = 120) were factorially randomised to retrieve (RET) or not retrieve (No RET) alcohol reward memories with (PE) or without (No PE) alcohol reward prediction error. All participants subsequently underwent disgust-based counterconditioning of drinking cues. Acute responses to alcohol were assessed pre- and post-manipulation and drinking levels were assessed up to 9 months. RESULTS: Greater long-term reductions in drinking were found when counterconditioning was conducted following retrieval (with and without PE), despite a lack of short-term group differences in motivational responding to acute alcohol. Large variability in acute levels of learning during counterconditioning was noted. 'Responsiveness' to counterconditioning predicted subsequent responses to acute alcohol in RET + PE only, consistent with reconsolidation-update mechanisms. CONCLUSIONS: The longevity of behavioural interventions designed to reduce problematic drinking levels may be enhanced by leveraging reconsolidation-update mechanisms to rewrite maladaptive memory. However, inter-individual variability in levels of corrective learning is likely to determine the efficacy of reconsolidation-updating interventions and should be considered when designing and assessing interventions
Single to Double Hump Transition in the Equilibrium Distribution Function of Relativistic Particles
We unveil a transition from single peaked to bimodal velocity distribution in
a relativistic fluid under increasing temperature, in contrast with a
non-relativistic gas, where only a monotonic broadening of the bell-shaped
distribution is observed. Such transition results from the interplay between
the raise in thermal energy and the constraint of maximum velocity imposed by
the speed of light. We study the Bose-Einstein, the Fermi-Dirac, and the
Maxwell-J\"uttner distributions, all exhibiting the same qualitative behavior.
We characterize the nature of the transition in the framework of critical
phenomena and show that it is either continuous or discontinuous, depending on
the group velocity. We analyze the transition in one, two, and three
dimensions, with special emphasis on two-dimensions, for which a possible
experiment in graphene, based on the measurement of the Johnson-Nyquist noise,
is proposed.Comment: 5 pages, 5 figure
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis
<p>Abstract</p> <p>Background</p> <p>ARNT, a member of the basic helix-loop-helix family of transcription factors, is located on human chromosome 1q21–q24, a region which showed well replicated linkage to type 2 diabetes. We hypothesized that common polymorphisms in the <it>ARNT </it>gene might increase the susceptibility to type 2 diabetes through impaired glucose-stimulated insulin secretion.</p> <p>Methods</p> <p>We selected 9 single nucleotide polymorphisms to tag common variation across the <it>ARNT </it>gene. Additionally we searched for novel variants in functional coding domains in European American and African American samples. Case-control studies were performed in 191 European American individuals with type 2 diabetes and 187 nondiabetic European American control individuals, and in 372 African American individuals with type 2 diabetes and 194 African American control individuals. Metabolic effects of <it>ARNT </it>variants were examined in 122 members of 26 European American families from Utah and in 225 unrelated individuals from Arkansas. Gene expression was tested in 8 sibling pairs discordant for type 2 diabetes.</p> <p>Results</p> <p>No nonsynonymous variants or novel polymorphisms were identified. No SNP was associated with type 2 diabetes in either African Americans or European Americans, but among nondiabetic European American individuals, <it>ARNT </it>SNPs rs188970 and rs11204735 were associated with acute insulin response (AIR<sub>g</sub>; p =< 0.005). SNP rs2134688 interacted with body mass index to alter β-cell compensation to insulin resistance (disposition index; p = 0.004). No significant difference in <it>ARNT </it>mRNA levels was observed in transformed lymphocytes from sibling pairs discordant for type 2 diabetes.</p> <p>Conclusion</p> <p>Common <it>ARNT </it>variants are unlikely to explain the linkage signal on chromosome 1q, but may alter insulin secretion in nondiabetic subjects. Our studies cannot exclude a role for rare variants or variants of small (< 1.6) effect size.</p
Towards the Formalization of Fractional Calculus in Higher-Order Logic
Fractional calculus is a generalization of classical theories of integration
and differentiation to arbitrary order (i.e., real or complex numbers). In the
last two decades, this new mathematical modeling approach has been widely used
to analyze a wide class of physical systems in various fields of science and
engineering. In this paper, we describe an ongoing project which aims at
formalizing the basic theories of fractional calculus in the HOL Light theorem
prover. Mainly, we present the motivation and application of such formalization
efforts, a roadmap to achieve our goals, current status of the project and
future milestones.Comment: 9 page
Application of Graphene within Optoelectronic Devices and Transistors
Scientists are always yearning for new and exciting ways to unlock graphene's
true potential. However, recent reports suggest this two-dimensional material
may harbor some unique properties, making it a viable candidate for use in
optoelectronic and semiconducting devices. Whereas on one hand, graphene is
highly transparent due to its atomic thickness, the material does exhibit a
strong interaction with photons. This has clear advantages over existing
materials used in photonic devices such as Indium-based compounds. Moreover,
the material can be used to 'trap' light and alter the incident wavelength,
forming the basis of the plasmonic devices. We also highlight upon graphene's
nonlinear optical response to an applied electric field, and the phenomenon of
saturable absorption. Within the context of logical devices, graphene has no
discernible band-gap. Therefore, generating one will be of utmost importance.
Amongst many others, some existing methods to open this band-gap include
chemical doping, deformation of the honeycomb structure, or the use of carbon
nanotubes (CNTs). We shall also discuss various designs of transistors,
including those which incorporate CNTs, and others which exploit the idea of
quantum tunneling. A key advantage of the CNT transistor is that ballistic
transport occurs throughout the CNT channel, with short channel effects being
minimized. We shall also discuss recent developments of the graphene tunneling
transistor, with emphasis being placed upon its operational mechanism. Finally,
we provide perspective for incorporating graphene within high frequency
devices, which do not require a pre-defined band-gap.Comment: Due to be published in "Current Topics in Applied Spectroscopy and
the Science of Nanomaterials" - Springer (Fall 2014). (17 pages, 19 figures
Scalar-field Pressure in Induced Gravity with Higgs Potential and Dark Matter
A model of induced gravity with a Higgs potential is investigated in detail
in view of the pressure components related to the scalar-field excitations. The
physical consequences emerging as an artifact due to the presence of these
pressure terms are analysed in terms of the constraints parting from energy
density, solar-relativistic effects and galactic dynamics along with the dark
matter halos.Comment: 26 pages, 3 figures, Minor revision, Published in JHE
Higher Dimensional Cylindrical or Kasner Type Electrovacuum Solutions
We consider a D dimensional Kasner type diagonal spacetime where metric
functions depend only on a single coordinate and electromagnetic field shares
the symmetries of spacetime. These solutions can describe static cylindrical or
cosmological Einstein-Maxwell vacuum spacetimes. We mainly focus on
electrovacuum solutions and four different types of solutions are obtained in
which one of them has no four dimensional counterpart. We also consider the
properties of the general solution corresponding to the exterior field of a
charged line mass and discuss its several properties. Although it resembles the
same form with four dimensional one, there is a difference on the range of the
solutions for fixed signs of the parameters. General magnetic field vacuum
solution are also briefly discussed, which reduces to Bonnor-Melvin magnetic
universe for a special choice of the parameters. The Kasner forms of the
general solution are also presented for the cylindrical or cosmological cases.Comment: 16 pages, Revtex. Text and references are extended, Published versio
Evolution of Landau Levels into Edge States at an Atomically Sharp Edge in Graphene
The quantum-Hall-effect (QHE) occurs in topologically-ordered states of
two-dimensional (2d) electron-systems in which an insulating bulk-state
coexists with protected 1d conducting edge-states. Owing to a unique
topologically imposed edge-bulk correspondence these edge-states are endowed
with universal properties such as fractionally-charged quasiparticles and
interference-patterns, which make them indispensable components for QH-based
quantum-computation and other applications. The precise edge-bulk
correspondence, conjectured theoretically in the limit of sharp edges, is
difficult to realize in conventional semiconductor-based electron systems where
soft boundaries lead to edge-state reconstruction. Using scanning-tunneling
microscopy and spectroscopy to follow the spatial evolution of bulk
Landau-levels towards a zigzag edge of graphene supported above a graphite
substrate we demonstrate that in this system it is possible to realize
atomically sharp edges with no edge-state reconstruction. Our results single
out graphene as a system where the edge-state structure can be controlled and
the universal properties directly probed.Comment: 16 pages, 4 figure
Extraction of bodily features for gait recognition and gait attractiveness evaluation
This is the author's accepted manuscript. The final publication is available at Springer via
http://dx.doi.org/10.1007/s11042-012-1319-2. Copyright @ 2012 Springer.Although there has been much previous research on which bodily features are most important in gait analysis, the questions of which features should be extracted from gait, and why these features in particular should be extracted, have not been convincingly answered. The primary goal of the study reported here was to take an analytical approach to answering these questions, in the context of identifying the features that are most important for gait recognition and gait attractiveness evaluation. Using precise 3D gait motion data obtained from motion capture, we analyzed the relative motions from different body segments to a root marker (located on the lower back) of 30 males by the fixed root method, and compared them with the original motions without fixing root. Some particular features were obtained by principal component analysis (PCA). The left lower arm, lower legs and hips were identified as important features for gait recognition. For gait attractiveness evaluation, the lower legs were recognized as important features.Dorothy Hodgkin Postgraduate Award and HEFCE
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