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https://www.readbyqxmd.com/read/28207632/are-we-ready-for-epitope-based-hla-matching-in-clinical-organ-transplantation
#1
Rene J Duquesnoy
This overview describes recent developments demonstrating the significance of epitopes in HLA antibody responses and matching for organ transplantation. HLA epitopes are defined by molecular modeling and amino acid comparisons between HLA alleles and the HLAMatchmaker algorithm considers eplets as essential components. Each allele represents a distinct string of eplets and matching is done by aligning donor and recipient strings. Evidence is summarized how mismatched eplet loads affect antibody responses and transplant outcomes...
February 15, 2017: Transplantation
https://www.readbyqxmd.com/read/28155662/an-ensemble-micro-neural-network-approach-for-elucidating-interactions-between-zinc-finger-proteins-and-their-target-dna
#2
Shayoni Dutta, Spandan Madan, Harsh Parikh, Durai Sundar
BACKGROUND: The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp DNA sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp DNA sequences...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28141523/the-plausibility-of-a-string-quartet-performance-in-virtual-reality
#3
Ilias Bergstrom, Sergio Azevedo, Panos Papiotis, Nuno Saldanha, Mel Slater
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)...
January 27, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28128622/search-for-an-ultralight-scalar-dark-matter-candidate-with-the-auriga-detector
#4
Antonio Branca, Michele Bonaldi, Massimo Cerdonio, Livia Conti, Paolo Falferi, Francesco Marin, Renato Mezzena, Antonello Ortolan, Giovanni A Prodi, Luca Taffarello, Gabriele Vedovato, Andrea Vinante, Stefano Vitale, Jean-Pierre Zendri
A search for a new scalar field, called moduli, has been performed using the cryogenic resonant-mass AURIGA detector. Predicted by string theory, moduli may provide a significant contribution to the dark matter (DM) component of our Universe. If this is the case, the interaction of ordinary matter with the local DM moduli, forming the Galaxy halo, will cause an oscillation of solid bodies with a frequency corresponding to the mass of moduli. In the sensitive band of AURIGA, some 100 Hz at around 1 kHz, the expected signal, with Q=△f/f∼10^{6}, is a narrow peak, △f∼1  mHz...
January 13, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28121936/fatal-remote-cerebellar-hemorrhage-after-supratentorial-unruptured-aneurysm-surgery-in-patient-with-previous-cerebellar-infarction-a-case-report
#5
Eun-Jeong Koh, Jung-Soo Park
RATIONALE: Remote cerebellar hemorrhage (RCH) is a rare complication of supratentorial and spinal surgeries, seldom requiring intervention but occasionally causing significant morbidity or even mortality. Although a number of theories have been proposed, the exact pathophysiology of RCH remains incompletely understood. PATIENT CONCERNS: We present a 62-year-old patient with RCH encountered following surgical clipping of an unruptured middle cerebral artery bifurcation aneurysm in a patient with previous cerebellar infarction...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28106446/exacerbating-the-cosmological-constant-problem-with-interacting-dark-energy-models
#6
M C David Marsh
Future cosmological surveys will probe the expansion history of the Universe and constrain phenomenological models of dark energy. Such models do not address the fine-tuning problem of the vacuum energy, i.e., the cosmological constant problem (CCP), but can make it spectacularly worse. We show that this is the case for "interacting dark energy" models in which the masses of the dark matter states depend on the dark energy sector. If realized in nature, these models have far-reaching implications for proposed solutions to the CCP that require the number of vacua to exceed the fine-tuning of the vacuum energy density...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28101923/how-suboptimal-is-suboptimal-choice
#7
Jay E Hinnenkamp, Timothy A Shahan, Gregory J Madden
In a frequently used suboptimal-choice procedure pigeons choose between an alternative that delivers three food pellets with p = 1.0 and an alternative that delivers ten pellets with p = 0.2. Because pigeons reliably choose the probabilistic (suboptimal) alternative, the procedure has been proposed as a nonhuman analog of human gambling. The present experiments were conducted to evaluate two potential threats to the validity of this procedure. Experiments 1 and 2 evaluated if pigeons obtained food at a lower unit price (i...
January 2017: Journal of the Experimental Analysis of Behavior
https://www.readbyqxmd.com/read/28054814/entrainment-to-an-auditory-signal-is-attention-involved
#8
Richard Kunert, Suzanne R Jongman
Many natural auditory signals, including music and language, change periodically. The effect of such auditory rhythms on the brain is unclear however. One widely held view, dynamic attending theory, proposes that the attentional system entrains to the rhythm and increases attention at moments of rhythmic salience. In support, 2 experiments reported here show reduced response times to visual letter strings shown at auditory rhythm peaks, compared with rhythm troughs. However, we argue that an account invoking the entrainment of general attention should further predict rhythm entrainment to also influence memory for visual stimuli...
January 2017: Journal of Experimental Psychology. General
https://www.readbyqxmd.com/read/28036207/new-solutions-for-non-abelian-cosmic-strings
#9
Mark Hindmarsh, Kari Rummukainen, David J Weir
We study the properties of classical vortex solutions in a non-Abelian gauge theory. A system of two adjoint Higgs fields breaks the SU(2) gauge symmetry to Z_{2}, producing 't Hooft-Polyakov monopoles trapped on cosmic strings, termed beads; there are two charges of monopole and two degenerate string solutions. The strings break an accidental discrete Z_{2} symmetry of the theory, explaining the degeneracy of the ground state. Further symmetries of the model, not previously appreciated, emerge when the masses of the two adjoint Higgs fields are degenerate...
December 16, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/28028716/evaluation-of-the-health-status-of-six-volunteers-from-the-mars-500-project-using-pulse-analysis
#10
Hong-Zhi Shi, Quan-Chun Fan, Jian-Yi Gao, Jun-Lian Liu, Gui-E Bai, Tao Mi, Shuang Zhao, Yu Liu, Dong Xu, Zhi-Feng Guo, Yong-Zhi Li
OBJECTIVE: To comprehensively evaluate the health status of 6 volunteers from the Mars 500 Project through analyzing their pulse graphs and determining the changes in cardiovascular function, degree of fatigue and autonomic nervous function. METHODS: Six volunteers were recruited; all were male aged 26-38 years (average 31.83±4.96 years). Characteristic parameters reflflecting the status of cardiovascular functions were extracted, which included left ventricular contraction, vascular elasticity and peripheral resistance...
December 27, 2016: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/28009201/loops-and-strings-in-a-superconducting-lattice-gauge-simulator
#11
G K Brennen, G Pupillo, E Rico, T M Stace, D Vodola
We propose an architecture for an analog quantum simulator of electromagnetism in 2+1 dimensions, based on an array of superconducting fluxonium devices. The encoding is in the integer (spin-1) representation of the quantum link model formulation of compact U(1) lattice gauge theory. We show how to engineer Gauss' law via an ancilla mediated gadget construction, and how to tune between the strongly coupled and intermediately coupled regimes. The witnesses to the existence of the predicted confining phase of the model are provided by nonlocal order parameters from Wilson loops and disorder parameters from 't Hooft strings...
December 9, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27997192/stabilization-and-antifouling-of-polymer-films-on-a-planar-surface-by-co2-pressurization
#12
Xiaofei Xu, Yibing Dai
In this article, we study the dewetting phenomenon of a polymer and carbon dioxide (CO2) mixture on a planar surface by combining density functional theory and the string method. It is found that dewetting is a first-order discontinuous phase transition. When the pressure is lower than the completely dewetting pressure (Pd), CO2 stabilizes the polymer films. The density fluctuation of the polymer decreases significantly with the inclusion of CO2. When the pressure is above Pd, the polymer film is depleted far away from the surface, leaving a thick layer of pure CO2 in the region near the surface...
January 4, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27982620/one-loop-one-point-functions-in-gauge-gravity-dualities-with-defects
#13
Isak Buhl-Mortensen, Marius de Leeuw, Asger C Ipsen, Charlotte Kristjansen, Matthias Wilhelm
We initiate the calculation of loop corrections to correlation functions in 4D defect conformal field theories (dCFTs). More precisely, we consider N=4 SYM theory with a codimension-one defect separating two regions of space, x_{3}>0 and x_{3}<0, where the gauge group is SU(N) and SU(N-k), respectively. This setup is made possible by some of the real scalar fields acquiring a nonvanishing and x_{3}-dependent vacuum expectation value for x_{3}>0. The holographic dual is the D3-D5 probe brane system where the D5-brane geometry is AdS_{4}×S^{2} and a background gauge field has k units of flux through the S^{2}...
December 2, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27982059/the-role-of-the-unusual-threonine-string-in-the-conversion-of-prion-protein
#14
Romany Abskharon, Fei Wang, Kayla J Vander Stel, Kumar Sinniah, Jiyan Ma
The conversion of normal prion protein (PrP) into pathogenic PrP conformers is central to prion disease, but the mechanism remains unclear. The α-helix 2 of PrP contains a string of four threonines, which is unusual due to the high propensity of threonine to form β-sheets. This structural feature was proposed as the basis for initiating PrP conversion, but experimental results have been conflicting. We studied the role of the threonine string on PrP conversion by analyzing mouse Prnp(a) and Prnp(b) polymorphism that contains a polymorphic residue at the beginning of the threonine string, and PrP mutants in which threonine 191 was replaced by valine, alanine, or proline...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27911542/higher-loop-amplitude-monodromy-relations-in-string-and-gauge-theory
#15
Piotr Tourkine, Pierre Vanhove
The monodromy relations in string theory provide a powerful and elegant formalism to understand some of the deepest properties of tree-level field theory amplitudes, like the color-kinematics duality. This duality has been instrumental in tremendous progress on the computations of loop amplitudes in quantum field theory, but a higher-loop generalization of the monodromy construction was lacking. In this Letter, we extend the monodromy relations to higher loops in open string theory. Our construction, based on a contour deformation argument of the open string diagram integrands, leads to new identities that relate planar and nonplanar topologies in string theory...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27908056/reconstruction-of-piano-hammer-force-from-string-velocity
#16
Antoine Chaigne
A method is presented for reconstructing piano hammer forces through appropriate filtering of the measured string velocity. The filter design is based on the analysis of the pulses generated by the hammer blow and propagating along the string. In the five lowest octaves, the hammer force is reconstructed by considering two waves only: the incoming wave from the hammer and its first reflection at the front end. For the higher notes, four- or eight-wave schemes must be considered. The theory is validated on simulated string velocities by comparing imposed and reconstructed forces...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27896358/emergence-of-ordered-network-mesophases-in-kinetic-pathways-of-order-order-transition-for-linear-abc-triblock-terpolymers
#17
Tongjie Sun, Ping Tang, Feng Qiu, An-Chang Shi
Applying the string method to the self-consistent field theory (SCFT) of ABC linear triblock copolymers, we developed a new strategy to design kinetic pathways for the formation of stable or metastable network mesophases in order-order transition (OOT) processes. The design principle regarding the kinetic pathways between distinct mesophases is based on the matching relationships of both domain spacing and dominant Fourier components of the density distributions. The results suggest that complex ordered network mesophases, such as alternating diamond (D(A)) and alternating plumber's nightmare (P(A)) could be obtained in kinetic pathways between simple phases covering lamellae, cylinders and spheres...
December 6, 2016: Soft Matter
https://www.readbyqxmd.com/read/27858430/branes-in-extended-spacetime-brane-worldvolume-theory-based-on-duality-symmetry
#18
Yuho Sakatani, Shozo Uehara
We propose a novel approach to the brane worldvolume theory based on the geometry of extended field theories: double field theory and exceptional field theory. We demonstrate the effectiveness of this approach by showing that one can reproduce the conventional bosonic string and membrane actions, and the M5-brane action in the weak-field approximation. At a glance, the proposed 5-brane action without approximation looks different from the known M5-brane actions, but it is consistent with the known nonlinear self-duality relation, and it may provide a new formulation of a single M5-brane action...
November 4, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27835022/lightest-visible-sector-supersymmetric-particle-is-likely-to-be-unstable
#19
Bobby S Acharya, Sebastian A R Ellis, Gordon L Kane, Brent D Nelson, Malcolm J Perry
We argue, based on typical properties of known solutions of string or M theory, that the lightest supersymmetric particle of the visible sector is likely to be unstable. In other words, dark matter is probably not a particle with standard model quantum numbers, such as a weakly interacting massive particle. The argument is simple and based on the typical occurrence of (a) hidden sectors, (b) interactions between the standard model (visible) sector and these hidden sectors, and (c) the lack of an argument against massive neutral hidden sector particles being lighter than the lightest visible supersymmetric particle...
October 28, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27827320/stories-of-victimization-self-positioning-and-construction-of-gender-in-narratives-of-abused-women
#20
Karin Jarnkvist, Lotta Brännström
The objective of this article is to analyze how women who have been victims of intimate partner violence (IPV) position themselves in relation to the image of the "ideal victim" and how gender is constructed in that positioning. There is a need for a gender analysis framework to understand how various forms of femininity are constructed and how narratives linked to this can either maintain a woman in an abusive relationship or encourage her to leave. Christie's theory of the "ideal victim" and Connell's gender theory are applied in this study, in which the narratives of 14 female IPV victims in Sweden are analyzed using a narrative method...
November 8, 2016: Journal of Interpersonal Violence
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