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Low complexity

Raquel Matoso Silva, Filomena Adega, Helena J Kjöllerström, Kim Labuschagne, Antoinette Kotze, Carlos Fernandes, Raquel Chaves, Maria do Mar Oom
Genets (Genetta) are a genus of African mammalian carnivorans with 14 currently recognized species, although taxonomic uncertainties remain, particularly regarding the number of species within the large-spotted genet complex. This study presents the first banded karyotype and molecular cytogenetic analysis of a genetically identified panther genet, Genetta maculata, the most common and widespread taxon of the large-spotted genet complex, with a wide distribution in sub-Saharan Africa. Sampled in Gauteng Province, South Africa, it could be assigned to the subspecies G...
October 27, 2016: Cytogenetic and Genome Research
Maruška Budič, Blaž Cigić, Maja Šoštarič, Jerica Sabotič, Vladimir Meglič, Janko Kos, Marjetka Kidrič
Aminopeptidases, together with other proteases, execute and regulate the total and specifically limited protein breakdown involved in plant physiology, raising the possibility of their involvement in response to drought. We have identified, in leaves of Phaseolus vulgaris L., five aminopeptidases (E.C.3.4.11) whose levels of activity changed when three week old plants were subjected to drought. First, second and third trifoliate leaves were investigated separately. The aminopeptidases were first identified then isolated using ion exchange chromatography of leaf extracts...
October 13, 2016: Plant Physiology and Biochemistry: PPB
Zhengrong Yang, Qingxian Zhou, Leo Mok, Anukriti Singh, Douglas J Swartz, Ina L Urbatsch, Christie G Brouillette
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains...
October 23, 2016: Biochimica et Biophysica Acta
Erica H Craig, Jennifer R Adams, Lisette P Waits, Mark R Fuller, Diana M Whittington
Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles...
2016: PloS One
Simone Farina, Ivan Guala, Silvia Oliva, Luigi Piazzi, Rodrigo Pires da Silva, Giulia Ceccherelli
Habitat structure plays an important mediating role in predator-prey interactions. However the effects are strongly dependent on regional predator pools, which can drive predation risk in habitats with very similar structure in opposite directions. In the Mediterranean Sea predation on juvenile sea urchins is commonly known to be regulated by seagrass structure. In this study we test whether the possibility for juvenile Paracentrotus lividus to be predated changes in relation to the fragmentation of the seagrass Posidonia oceanica (four habitat classes: continuous, low-fragmentation, high-fragmentation and rocks), and to the spatial arrangement of such habitat classes at a landscape scale...
2016: PloS One
Cannada Andrew Lewis, Justus Aaron Calvin, Edward F Valeev
We describe the Clustered Low Rank (CLR) framework for block-sparse and block-low-rank tensor representation and computation. The CLR framework exploits the tensor structure revealed by basis clustering; computational savings arise from low-rank compression of tensor blocks and performing block arithmetic in the low-rank form whenever beneficial. The precision is rigorously controlled by 2 parameters, avoiding ad-hoc heuristics, such as domains: one controls the CLR block rank truncation and the other controls screening of small contributions in arithmetic operations on CLR tensors to propagate sparsity through expressions...
October 26, 2016: Journal of Chemical Theory and Computation
Qing-Ju Jiao, Yan Huang, Hong-Bin Shen
Biological networks are effective tools for studying molecular interactions. Modular structure, in which genes or proteins may tend to be associated with functional modules or protein complexes, is a remarkable feature of biological networks. Mining modular structure from biological networks enables us to focus on a set of potentially important nodes, which provides a reliable guide to future biological experiments. The first fundamental challenge in mining modular structure from biological networks is that the quality of the observed network data is usually low owing to noise and incompleteness in the obtained networks...
October 26, 2016: Molecular BioSystems
K Müller, S Datta, M Ahmad, J-H Choi, T Moore, L Pung, C Niebler, G E Gold, A Maier, R Fahrig
PURPOSE: In the last years, dual-energy CT imaging has shown clinical value, thanks to its ability to differentiate materials based on their atomic number and to exploit different properties of images acquired at two different energies. C-arm CT systems are used to guide procedures in the interventional suite. Until now, there are no commercially available systems that employ dual-energy material decomposition. This paper explores the feasibility of implementing a fast kV-switching technique on a clinically available angiographic system for acquiring dual-energy C-arm CT images...
October 2016: Medical Physics
Vaibhav Jain, Prabal K Maiti, Prasad V Bharatam
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details...
September 28, 2016: Journal of Chemical Physics
S Orioli, P Faccioli
Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for clustering microstates into macrostates. The result is a lower dimensional stochastic model which, by construction, provides the optimal coarse-grained Markovian representation of the system's relaxation kinetics...
September 28, 2016: Journal of Chemical Physics
Matteo Barborini, Leonardo Guidoni
The correct description of the ground state electronic and geometrical properties of multi-centre transition metal complexes necessitates of a high-level description of both dynamical and static correlation effects. In di-metallic complexes, the ground state low spin properties can be computed starting from single-determinants High-Spin (HS) and Broken Symmetry (BS) states by reconstructing an approximated low spin potential energy surface through the extended broken symmetry approach, based on the Heisenberg Hamiltonian...
September 28, 2016: Journal of Chemical Physics
Eiji Arima, Huanfei Wen, Yoshitaka Naitoh, Yan Jun Li, Yasuhiro Sugawara
The atomic force microscopy (AFM) is a very important tool for imaging and investigating the complex force interactions on sample surfaces with high spatial resolution. In the AFM, two types of detection systems of the tip-sample interaction forces have been used: an optical detection system and an electrical detection system. In optical detection systems, such as optical beam deflection system or optical fiber interferometer system, both the lateral and the vertical tip-sample forces can be measured simultaneously...
September 2016: Review of Scientific Instruments
M Y Pustylnik, M A Fink, V Nosenko, T Antonova, T Hagl, H M Thomas, A V Zobnin, A M Lipaev, A D Usachev, V I Molotkov, O F Petrov, V E Fortov, C Rau, C Deysenroth, S Albrecht, M Kretschmer, M H Thoma, G E Morfill, R Seurig, A Stettner, V A Alyamovskaya, A Orr, E Kufner, E G Lavrenko, G I Padalka, E O Serova, A M Samokutyayev, S Christoforetti
New complex-plasma facility, Plasmakristall-4 (PK-4), has been recently commissioned on board the International Space Station. In complex plasmas, the subsystem of μm-sized microparticles immersed in low-pressure weakly ionized gas-discharge plasmas becomes strongly coupled due to the high (10(3)-10(4) e) electric charge on the microparticle surface. The microparticle subsystem of complex plasmas is available for the observation at the kinetic level, which makes complex plasmas appropriate for particle-resolved modeling of classical condensed matter phenomena...
September 2016: Review of Scientific Instruments
Wissam A Saidi, Joshua J Choi
Hybrid organic-inorganic perovskites, as well as the perovskites in general, are known for their phase complexity evidenced by the stabilization of different polymorphs, and thus an understanding of their regions of stability and transitions can be important for their photovoltaic and optoelectronic technologies. Here we use a multiscale approach based on first-principles calculations with van der Waals corrections and classical force-field molecular dynamics to determine the finite-temperature properties of the tetragonal and cubic phases of CH3NH3PbI3...
October 14, 2016: Journal of Chemical Physics
Jodi L Connell, Eric T Ritschdorff, Jason B Shear
Advances in microscopic three-dimensional (µ3D) printing provide a means to microfabricate an almost limitless range of arbitrary geometries, offering new opportunities to rapidly prototype complex architectures for microfluidic and cellular applications. Such 3D lithographic capabilities present the tantalizing prospect for engineering micromechanical components - for example, pumps and valves - for cellular environments comprised of smart materials whose size, shape, permeability, stiffness, and other attributes might be modified in real time to precisely manipulate ultra-low-volume samples...
October 26, 2016: Analytical Chemistry
Weiwei Ye, Yifan Xu, Lihao Zheng, Yu Zhang, Mo Yang, Peilong Sun
Histamine is an indicator of food quality and indispensable in the efficient functioning of various physiological systems. Rapid and sensitive determination of histamine is urgently needed in food analysis and clinical diagnostics. Traditional histamine detection methods require qualified personnel, need complex operation processes, and are time-consuming. In this study, a biofunctionalized nanoporous alumina membrane based electrochemical biosensor with magnetic nanoparticles (MNPs) concentration and signal amplification was developed for histamine determination...
October 22, 2016: Sensors
Y Kobayashi, H Kori
We investigate synchronization in complex networks of noisy phase oscillators. We find that, while too weak a coupling is not sufficient for the whole system to synchronize, too strong a coupling induces a nontrivial type of phase slip among oscillators, resulting in synchronization failure. Thus, an intermediate coupling range for synchronization exists, which becomes narrower when the network is more heterogeneous. Analyses of two noisy oscillators reveal that nontrivial phase slip is a generic phenomenon when noise is present and coupling is strong...
September 2016: Chaos
Anna L Gould, Kevin Rossi, C Richard A Catlow, Francesca Baletto, Andrew J Logsdail
We present a study of the transitional pathways between high-symmetry structural motifs for AgAu nanoparticles, with a specific focus on controlling the energetic barriers through chemical design. We show that the barriers can be altered by careful control of the elemental composition and chemical arrangement, with core@shell and vertex-decorated arrangements being specifically influential on the barrier heights. We also highlight the complexity of the potential and free energy landscapes for systems where there are low-symmetry geometric motifs that are energetically competitive to the high-symmetry arrangements...
October 26, 2016: Journal of Physical Chemistry Letters
Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé
BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH...
2016: PeerJ
Christian O Häusler, Michael Hanke
Here we present an annotation of locations and temporal progression depicted in the movie "Forrest Gump", as an addition to a large public functional brain imaging dataset ( The annotation provides information about the exact timing of each of the 870 shots, and the depicted location after every cut with a high, medium, and low level of abstraction. Additionally, four classes are used to distinguish the differences of the depicted time between shots. Each shot is also annotated regarding the type of location (interior/exterior) and time of day...
2016: F1000Research
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