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Takeshi Yanai, Masaaki Saitow, Xiao-Gen Xiong, Jakub Chalupský, Yuki Kurashige, Sheng Guo, Sandeep Sharma
We present the development of the multistate multireference second-order perturbation theory (CASPT2) with multi-root references, which are described using the density matrix renormalization group (DMRG) method to handle a large active space. The multistate first-order wave functions are expanded into the internally contracted (IC) basis of the single-state single-reference (SS-SR) scheme, which is shown to be the most feasible variant to use DMRG references. The feasibility of the SS-SR scheme comes from two factors: first, it formally does not require the fourth-order transition reduced density matrix (TRDM); and second, the computational complexity scales linearly with the number of the reference states...
September 7, 2017: Journal of Chemical Theory and Computation
Ningning Wang, Xinyan Yu, Ke Zhang, Chad A Mirkin, Jishan Li
By taking advantage of the optical properties of upconversion nanoparticles (UCNPs), we have designed a luminescence ratiometric nanosensor for measuring nitric oxide (NO) in biological fluids, live cells, and tissues. This nanoconjugate consists of a UCNP core with two strong fluorescence emission peaks at 540 and 656 nm as the upconversion fluorophore, NO-reactive rhodamine B-derived molecules (RdMs) encapsulated within the mesopores of the mSiO2 shell, and a β-cyclodextrin (βCD) layer on the exterior of the particle...
September 5, 2017: Journal of the American Chemical Society
N S Blunt, George H Booth, Ali Alavi
We present developments in the calculation of reduced density matrices (RDMs) in the full configuration interaction quantum Monte Carlo (FCIQMC) method. An efficient scheme is described to allow storage of RDMs across distributed memory, thereby allowing their calculation and storage in large basis sets. We demonstrate the calculation of RDMs for general states by using the recently introduced excited-state FCIQMC approach [N. S. Blunt et al., J. Chem. Phys. 143, 134117 (2015)] and further introduce calculation of transition density matrices in the method...
June 28, 2017: Journal of Chemical Physics
Sevan A Vahanian, Martin R Chavez, Jean Murphy, Patrick Vetere, Farr Nezhat, Anthony M Vintzileos
No abstract text is available yet for this article.
June 8, 2017: Journal of Minimally Invasive Gynecology
Arnab Kar, Ignacio Franco
Practical measures of electronic decoherence, called distilled purities, that are applicable to many-body systems are introduced. While usual measures of electronic decoherence such as the purity employ the full N-particle density matrix which is generally unavailable, the distilled purities are based on the r-body reduced density matrices (r-RDMs) which are more accessible quantities. The r-body distilled purities are derivative quantities of the previously introduced r-body reduced purities [I. Franco and H...
June 7, 2017: Journal of Chemical Physics
Tao Xin, Dawei Lu, Joel Klassen, Nengkun Yu, Zhengfeng Ji, Jianxin Chen, Xian Ma, Guilu Long, Bei Zeng, Raymond Laflamme
Quantum state tomography via local measurements is an efficient tool for characterizing quantum states. However, it requires that the original global state be uniquely determined (UD) by its local reduced density matrices (RDMs). In this work, we demonstrate for the first time a class of states that are UD by their RDMs under the assumption that the global state is pure, but fail to be UD in the absence of that assumption. This discovery allows us to classify quantum states according to their UD properties, with the requirement that each class be treated distinctly in the practice of simplifying quantum state tomography...
January 13, 2017: Physical Review Letters
H Zhao, R J Harris, J Ellis, M Donati, R G Pebody
Human parainfluenza virus (HPIV) infections are one of the commonest causes of upper and lower respiratory tract infections. In order to determine if there have been any recent changes in HPIV epidemiology in England and Wales, laboratory surveillance data between 1998 and 2013 were analysed. The UK national laboratory surveillance database, LabBase, and the newly established laboratory-based virological surveillance system, the Respiratory DataMart System (RDMS), were used. Descriptive analysis was performed to examine the distribution of cases by year, age, sex and serotype, and to examine the overall temporal trend using the χ 2 test...
April 2017: Epidemiology and Infection
J Brendan Ritchie, Stefania Bracci, Hans Op de Beeck
Representational similarity analysis (RSA) is an important part of the methodological toolkit in neuroimaging research. The focus of the approach is the construction of representational dissimilarity matrices (RDMs), which provide a single format for making comparisons between different neural data types, computational models, and behavior. We highlight two issues for the construction and comparison of RDMs. First, the diagonal values of RDMs, which should reflect within condition reliability of neural patterns, are typically not estimated in RSA...
January 7, 2017: NeuroImage
Sandeep Sharma, Gerald Knizia, Sheng Guo, Ali Alavi
We present two efficient and intruder-free methods for treating dynamic correlation on top of general multiconfiguration reference wave functions - including such as obtained by the density matrix renormalization group (DMRG) with large active spaces. The new methods are the second order variant of the recently proposed multireference linearized coupled cluster method (MRLCC) [ Sharma, S.; Alavi, A. J. Chem. Phys. 2015 , 143 , 102815 ] and of N-electron valence perturbation theory (NEVPT2), with expected accuracies similar to MRCI+Q and (at least) CASPT2, respectively...
January 31, 2017: Journal of Chemical Theory and Computation
Shoubing Zhou, Xiu Zhang, Cailian Wang
This study evaluated rituximab-conjugated, doxorubicin-loaded microbubbles (RDMs) in combination with ultrasound as molecular imaging agents for early diagnosis of B cell lymphomas, and as a targeted drug delivery system. Rituximab, a monoclonal CD20 antibody, was attached to the surfaces of doxorubicin-loaded microbubbles. RDM binding to B cell lymphoma cells was assessed using immunofluorescence. The cytotoxic effects of RDMs in combination with ultrasound (RDMs+US) were evaluated in vitro in CD20+ and CD20- cell lines, and its antitumor activities were assessed in Raji (CD20+) and Jurkat (CD20-) lymphoma cell-grafted mice...
January 17, 2017: Oncotarget
Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor Solovyev, Rod A Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L McNally, Nickolai Alexandrov
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer...
January 4, 2017: Nucleic Acids Research
A Eugene DePrince
The direct variational optimization of the ground-state two-electron reduced-density matrix (2-RDM) is typically performed under ensemble N-representability conditions. Accordingly, variationally obtained 2-RDMs for degenerate ground states may not represent a pure state. When considering only ground-state energetics, the ensemble nature of the 2-RDM is of little consequence. However, the use of ensemble densities within an extended random phase approximation (ERPA) yields astonishingly poor estimates of excitation energies, even for simple atomic systems [H...
October 28, 2016: Journal of Chemical Physics
Nikolaus Kriegeskorte, Jörn Diedrichsen
High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behavioural task in question. We would then like to infer which of the candidate BCMs best accounts for measured brain-activity data. Here we describe a method that complements each BCM by a measurement model (MM), which simulates the way the brain-activity measurements reflect neuronal activity (e...
October 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Louise J Walport, Richard J Hopkinson, Rasheduzzaman Chowdhury, Rachel Schiller, Wei Ge, Akane Kawamura, Christopher J Schofield
While the oxygen-dependent reversal of lysine N(ɛ)-methylation is well established, the existence of bona fide N(ω)-methylarginine demethylases (RDMs) is controversial. Lysine demethylation, as catalysed by two families of lysine demethylases (the flavin-dependent KDM1 enzymes and the 2-oxoglutarate- and oxygen-dependent JmjC KDMs, respectively), proceeds via oxidation of the N-methyl group, resulting in the release of formaldehyde. Here we report detailed biochemical studies clearly demonstrating that, in purified form, a subset of JmjC KDMs can also act as RDMs, both on histone and non-histone fragments, resulting in formaldehyde release...
June 23, 2016: Nature Communications
Pallab Kanti Podder, Manoranjan Paul, Manzur Murshed
The emerging High Efficiency Video Coding (HEVC) standard introduces a number of innovative and powerful coding tools to acquire better compression efficiency compared to its predecessor H.264. The encoding time complexities have also increased multiple times that is not suitable for realtime video coding applications. To address this limitation, this paper employs a novel coding strategy to reduce the time complexity in HEVC encoder by efficient selection of appropriate block-partitioning modes based on human visual features (HVF)...
2016: PloS One
Shoubing Zhou, Shiya Zheng, Yongfeng Shan, Lulu Li, Xiu Zhang, Cailian Wang
Doxorubicin (DOX) is one of the most important medicines used for the treatment for B cell lymphoma, yet its clinical efficacy is often limited by severe adverse effects. Drug-loaded microbubbles, combined with ultrasound (US) irradiation, has shown great promise in reducing DOX-induced side effects and improving therapeutic efficacy. Nevertheless, these drug-loaded microbubbles are non-targeted microbubbles with comparatively suboptimal efficiency. Therefore, we synthesized targeted and DOX-loaded microbubbles (DMs), combined with US irradiation, for triggering drug release in lymphoma B cells...
February 2016: Oncology Reports
Seyed-Mahdi Khaligh-Razavi, Johan Carlin, Radoslaw Martin Cichy, Nikolaus Kriegeskorte
Visual processing involves feedforward and recurrent signals. Understanding which computations are performed in the feedforward sweep and which require recurrent processing has been challenging. We used fMRI and MEG to characterize the spatial and temporal components of human visual object representations. In the fMRI experiment, we used brief stimulus presentation (16.7ms) and a backward masking paradigm with short and long interstimulus intervals (ISI) to distinguish the contributions of feedforward and recurrent processing...
2015: Journal of Vision
Nisha Dalal, Virginia Flanagin, Stefan Glasauer
INTRODUCTION: The hippocampus interacts with early visual cortex in a stimulus-dependent way. Previously our lab reported that when participants watched movement through a virtual tunnel there was a weaker correlation between the hippocampus and primary visual cortex than with videos where the phase content was scrambled (Figure S1). The hippocampus may provide an important function in interpreting unpredictable input. Here, we test this hypothesis using a similar fMRI paradigm, together with univariate and representational similarity analyses...
2015: Journal of Vision
David Herrera, Mario Treviño
In two-alternative discrimination tasks, experimenters usually randomize the location of the rewarded stimulus so that systematic behavior with respect to irrelevant stimuli can only produce chance performance on the learning curves. One way to achieve this is to use random numbers derived from a discrete binomial distribution to create a 'full random training schedule' (FRS). When using FRS, however, sporadic but long laterally-biased training sequences occur by chance and such 'input biases' are thought to promote the generation of laterally-biased choices (i...
2015: PloS One
Linda Henriksson, Seyed-Mahdi Khaligh-Razavi, Kendrick Kay, Nikolaus Kriegeskorte
Intrinsic cortical dynamics are thought to underlie trial-to-trial variability of visually evoked responses in animal models. Understanding their function in the context of sensory processing and representation is a major current challenge. Here we report that intrinsic cortical dynamics strongly affect the representational geometry of a brain region, as reflected in response-pattern dissimilarities, and exaggerate the similarity of representations between brain regions. We characterized the representations in several human visual areas by representational dissimilarity matrices (RDMs) constructed from fMRI response-patterns for natural image stimuli...
July 1, 2015: NeuroImage
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