1,087 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
Mortality after emergency department intubation
Introduction The purpose of this study is to identify the rate of emergency department (ED) intubation and the mortality associated with ED intubation. Methods We conducted a retrospective chart review of all patients intubated in the ED between 1 January 2004 an
A Comprehensive Analysis of Electric Dipole Moment Constraints on CP-violating Phases in the MSSM
We analyze the constraints placed on individual, flavor diagonal CP-violating
phases in the minimal supersymmetric extension of the Standard Model (MSSM) by
current experimental bounds on the electric dipole moments (EDMs) of the
neutron, Thallium, and Mercury atoms. We identify the four CP-violating phases
that are individually highly constrained by current EDM bounds, and we explore
how these phases and correlations among them are constrained by current EDM
limits. We also analyze the prospective implications of the next generation of
EDM experiments. We point out that all other CP-violating phases in the MSSM
are not nearly as tightly constrained by limits on the size of EDMs. We
emphasize that a rich set of phenomenological consequences is potentially
associated with these generically large EDM-allowed phases, ranging from B
physics, electroweak baryogenesis, and signals of CP-violation at the CERN
Large Hadron Collider and at future linear colliders. Our numerical study takes
into account the complete set of contributions from one- and two-loop EDMs of
the electron and quarks, one- and two-loop Chromo-EDMs of quarks, the Weinberg
3-gluon operator, and dominant 4-fermion CP-odd operator contributions,
including contributions which are both included and not included yet in the
CPsuperH2.0 package. We also introduce an open-source numerical package, 2LEDM,
which provides the complete set of two-loop electroweak diagrams contributing
to the electric dipole moments of leptons and quarks.Comment: 23 pages, 11 figures; v2: references added, minor change
Serotonin and corticosterone rhythms in mice exposed to cigarette smoke and in patients with COPD:implication for COPD-associated neuropathogenesis
The circadian timing system controls daily rhythms of physiology and behavior, and disruption of clock function can trigger stressful life events. Daily exposure to cigarette smoke (CS) can lead to alteration in diverse biological and physiological processes. Smoking is associated with mood disorders, including depression and anxiety. Patients with chronic obstructive pulmonary disease (COPD) have abnormal circadian rhythms, reflected by daily changes in respiratory symptoms and lung function. Corticosterone (CORT) is an adrenal steroid that plays a considerable role in stress and anti-inflammatory responses. Serotonin (5-hydroxytryptamine; 5HT) is a neurohormone, which plays a role in sleep/wake regulation and affective disorders. Secretion of stress hormones (CORT and 5HT) is under the control of the circadian clock in the suprachiasmatic nucleus. Since smoking is a contributing factor in the development of COPD, we hypothesize that CS can affect circadian rhythms of CORT and 5HT secretion leading to sleep and mood disorders in smokers and patients with COPD. We measured the daily rhythms of plasma CORT and 5HT in mice following acute (3 d), sub-chronic (10 d) or chronic (6 mo) CS exposure and in plasma from non-smokers, smokers and patients with COPD. Acute and chronic CS exposure affected both the timing (peak phase) and amplitude of the daily rhythm of plasma CORT and 5HT in mice. Acute CS appeared to have subtle time-dependent effects on CORT levels but more pronounced effects on 5HT. As compared with CORT, plasma 5HT was slightly elevated in smokers but was reduced in patients with COPD. Thus, the effects of CS on plasma 5HT were consistent between mice and patients with COPD. Together, these data reveal a significant impact of CS exposure on rhythms of stress hormone secretion and subsequent detrimental effects on cognitive function, depression-like behavior, mood/anxiety and sleep quality in smokers and patients with COPD
Experimental long-lived entanglement of two macroscopic objects
Entanglement is considered to be one of the most profound features of quantum
mechanics. An entangled state of a system consisting of two subsystems cannot
be described as a product of the quantum states of the two subsystems. In this
sense the entangled system is considered inseparable and nonlocal. It is
generally believed that entanglement manifests itself mostly in systems
consisting of a small number of microscopic particles. Here we demonstrate
experimentally the entanglement of two objects, each consisting of about 10^12
atoms. Entanglement is generated via interaction of the two objects - more
precisely, two gas samples of cesium atoms - with a pulse of light, which
performs a non-local Bell measurement on collective spins of the samples. The
entangled spin state can be maintained for 0.5 millisecond. Besides being of
fundamental interest, the robust, long-lived entanglement of material objects
demonstrated here is expected to be useful in quantum information processing,
including teleportation of quantum states of matter and quantum memory.Comment: Submitted to Nature, June 9, 2001, 11 pages, 3 figures. Contents
changed following referees' suggestion
Cardioprotective effects of lixisenatide in rat myocardial ischemia-reperfusion injury studies
BACKGROUND: Lixisenatide is a glucagon-like peptide-1 analog which stimulates insulin secretion and inhibits glucagon secretion and gastric emptying. We investigated cardioprotective effects of lixisenatide in rodent models reflecting the clinical situation. METHODS: The acute cardiac effects of lixisenatide were investigated in isolated rat hearts subjected to brief ischemia and reperfusion. Effects of chronic treatment with lixisenatide on cardiac function were assessed in a modified rat heart failure model after only transient coronary occlusion followed by long-term reperfusion. Freshly isolated cardiomyocytes were used to investigate cell-type specific mechanisms of lixisenatide action. RESULTS: In the acute setting of ischemia-reperfusion, lixisenatide reduced the infarct-size/area at risk by 36% ratio without changes on coronary flow, left-ventricular pressure and heart rate. Treatment with lixisenatide for 10 weeks, starting after cardiac ischemia and reperfusion, improved left ventricular end-diastolic pressure and relaxation time and prevented lung congestion in comparison to placebo. No anti-fibrotic effect was observed. Gene expression analysis revealed a change in remodeling genes comparable to the ACE inhibitor ramipril. In isolated cardiomyocytes lixisenatide reduced apoptosis and increased fractional shortening. Glucagon-like peptide-1 receptor (GLP1R) mRNA expression could not be detected in rat heart samples or isolated cardiomyocytes. Surprisingly, cardiomyocytes isolated from GLP-1 receptor knockout mice still responded to lixisenatide. CONCLUSIONS: In rodent models, lixisenatide reduced in an acute setting infarct-size and improved cardiac function when administered long-term after ischemia-reperfusion injury. GLP-1 receptor independent mechanisms contribute to the described cardioprotective effect of lixisenatide. Based in part on these preclinical findings patients with cardiac dysfunction are currently being recruited for a randomized, double-blind, placebo-controlled, multicenter study with lixisenatide. TRIAL REGISTRATION: (ELIXA, ClinicalTrials.gov Identifier: NCT01147250
Magnetism, FeS colloids, and Origins of Life
A number of features of living systems: reversible interactions and weak
bonds underlying motor-dynamics; gel-sol transitions; cellular connected
fractal organization; asymmetry in interactions and organization; quantum
coherent phenomena; to name some, can have a natural accounting via
interactions, which we therefore seek to incorporate by expanding the horizons
of `chemistry-only' approaches to the origins of life. It is suggested that the
magnetic 'face' of the minerals from the inorganic world, recognized to have
played a pivotal role in initiating Life, may throw light on some of these
issues. A magnetic environment in the form of rocks in the Hadean Ocean could
have enabled the accretion and therefore an ordered confinement of
super-paramagnetic colloids within a structured phase. A moderate H-field can
help magnetic nano-particles to not only overcome thermal fluctuations but also
harness them. Such controlled dynamics brings in the possibility of accessing
quantum effects, which together with frustrations in magnetic ordering and
hysteresis (a natural mechanism for a primitive memory) could throw light on
the birth of biological information which, as Abel argues, requires a
combination of order and complexity. This scenario gains strength from
observations of scale-free framboidal forms of the greigite mineral, with a
magnetic basis of assembly. And greigite's metabolic potential plays a key role
in the mound scenario of Russell and coworkers-an expansion of which is
suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed
Krishnaswami Alladi, Springer 201
FRASS: the web-server for RNA structural comparison
<p>Abstract</p> <p>Background</p> <p>The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.</p> <p>Results</p> <p>The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.</p> <p>Conclusions</p> <p>The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.</p
Improved Measurements of Partial Rate Asymmetry in B -> h h Decays
We report improved measurements of the partial rate asymmetry (Acp) in B -> h
h decays with 140fb^-1 of data collected with the Belle detector at the KEKB
e+e- collider. Here h stands for a charged or neutral pion or kaon and in total
five decay modes are included: K-+ pi+-, K0s pi-+, K-+ pi0, pi-+ pi0 and K0s
pi0. The flavor of the last decay mode is determined from the accompanying B
meson. Using a data sample 4.7 times larger than that of our previous
measurement, we find Acp(K-+ pi+-) -0.088+-0.035+-0.013, 2.4 sigma from zero.
Results for other decay modes are also presented.Comment: 9 pages, 1 figur
Studies of the Decay B+- -> D_CP K+-
We report studies of the decay B+- -> D_CP K+-, where D_CP denotes neutral D
mesons that decay to CP eigenstates. The analysis is based on a 29.1/fb data
sample of collected at the \Upsilon(4S) resonance with the Belle detector at
the KEKB asymmetric e+ e- storage ring. Ratios of branching fractions of
Cabibbo-suppressed to Cabibbo-favored processes involving D_CP are determined
to be B(B- -> D_1 K-)/B(B- -> D_1 pi-)=0.125 +- 0.036 +- 0.010 and B(B- -> D_2
K-)/B(B- -> D_2 pi-)=0.119 +- 0.028 +- 0.006, where indices 1 and 2 represent
the CP=+1 and CP=-1 eigenstates of the D0 - anti D0 system, respectively. We
also extract the partial rate asymmetries for B+- -> D_CP K+-, finding A_1 =
0.29 +- 0.26 +- 0.05 and A_2 = -0.22 +- 0.24 +- 0.04.Comment: 10 pages, 2 figures, submitted to Physical Review Letter
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