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Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory...
October 2016: PLoS Computational Biology
Maria Prokofjeva, Vladimir Tsvetkov, Dmitry Basmanov, Anna Varizhuk, Maria Lagarkova, Igor Smirnov, Kirill Prusakov, Dmitry Klinov, Vladimir Prassolov, Galina Pozmogova, Sergey N Mikhailov
New natural and chemically modified DNA aptamers that inhibit HIV-1 activity at submicromolar concentrations (presumably via preventing viral entry into target cells) are reported. The new DNA aptamers were developed based on known intramolecular G-quadruplexes (G4s) that were functionally unrelated to HIV inhibition [the thrombin-binding aptamer and the fragment of the human oncogene promoter (Bcl2)]. The majority of previously described DNA inhibitors of HIV infection adopt intermolecular structures, and thus their folding variability represents an obvious disadvantage...
October 20, 2016: Nucleic Acid Therapeutics
Hong Sheng Quah, Li Ting Ng, Bruno Donnadieu, Geok Kheng Tan, Jagadese J Vittal
Five lanthanide MOFs with pcu topology have been exfoliated into nanoplatelets of two-dimensional structures via sonication in the dimethylacetamide solvent. These nanosheets are fluorescent under two-photon excitation dominated by the ligand, indicating energy upconversion ability.
October 20, 2016: Inorganic Chemistry
Parthasarathi Dastidar, Koushik Sarkar
A mixed ligand approach was exploited to synthesize a new series of MnII based coordination polymers (CPs), namely, CP1 {[Mn(-dpa)(-4,4-bp)]MeOH}α, CP2 {[Mn3(-dpa)3(2,2-bp)2]}α, CP3 {[Mn3(-dpa)3(1,10-phen)2]2H2O}α, CP4 {[Mn(-dpa)(-4,4-bpe)1.5]H2O}α, CP5 {[Mn2(-dpa)2(-4,4-bpe)2]½DEF}α and CP6 {[Mn(-dpa)(-4,4-bpe)1.5]½DMA}α, [dpa = 3,5-dicarboxy phenyl azide, 2,2-bp = 2,2-bipyridine, 1,10-phen = 1,10-phenanthroline, 4,4-bpe = 1,2-bis(4-pyridyl)ethylene, 4,4-bp = 4,4-bipyridine, DEF = N,N-diethylformamide, DMA = N,N-dimethylacetamide] to develop multifuntional CPs...
October 20, 2016: Chemistry: a European Journal
Sujin Seo, Huiyeong Ju, Seulgi Kim, In-Hyeok Park, Eunji Lee, Shim Sung Lee
Homo- and heteronuclear group 12 metal (Zn(2+), Cd(2+), and Hg(2+)) complexes 1-6 containing a newly designed 18-membered N2O2S2 macrocycle incorporating two pyridine subunits (L) were prepared and structurally characterized. The individual complexes isolated exhibit unusual stoichiometries, geometries, oxidation states, and structural topologies and include an infinite mercurous complex and a heteronuclear dumbbell-shaped complex. Both the Zn(II) complex [Zn(L)][ZnBr4] (1) and the Cd(II) complex [Cd(L)Br2] (2) are mononuclear, with the metal ion located inside the macrocyclic cavity...
October 20, 2016: Inorganic Chemistry
Rahul Shukla, Deepak Chopra
In this article, the existence of NO noncovalent interactions was explored in per-halo substituted ammonia-water complexes. Optimized geometry at the MP2/aug-cc-pVTZ level shows that the NO distance in all complexes is less than the sum of the vdW radii of N and O. The strength of these contacts was directly dependent on the extent of chlorine substitution on N or O atoms. Also, the level of theory and the basis set employed for the binding energy calculations have a direct effect on the strength of the NO contacts...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
Pesia Katan, Shani Kahta, Ayelet Sasson, Rachel Schiff
Graph complexity as measured by topological entropy has been previously shown to affect performance on artificial grammar learning tasks among typically developing children. The aim of this study was to examine the effect of graph complexity on implicit sequential learning among children with developmental dyslexia. Our goal was to determine whether children's performance depends on the complexity level of the grammar system learned. We conducted two artificial grammar learning experiments that compared performance of children with developmental dyslexia with that of age- and reading level-matched controls...
October 19, 2016: Annals of Dyslexia
Vladimir Kozlov, Sergey Vakulenko, Uno Wennergren
This paper considers a model of foodwebs taking into account species extinction and invasion. We show that system stability depends not only on usual parameters (mortality rates, self-limitation coefficients, and resource abundances), but also on an additional parameter ("biodiversity potential"). The main result is as follows. For foodwebs with random parameters, we obtain an estimate of probability that the foodweb exposed to invasion survives. This estimate involves different system parameters, size and its topological properties...
October 19, 2016: Bulletin of Mathematical Biology
Lei Xu, Meng-Ke Zhai, Fei Wang, Lin Sun, Hong-Bin Du
We herein report a series of microporous metal-porphyrinic frameworks (MPFs), denoted as NUPF-2M, based on rare earth (RE) clusters. NUPF-2M represent the first examples of RE cluster-based MPFs, possessing a rarely seen shp-a topology and exhibiting high thermal and thermal stabilities. After a post-metallization process with FeCl3, NUPF-2M is catalytically active as an efficient heterogeneous catalyst for intermolecular N-H carbene insertion.
October 20, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Ricardo Sevilla-Escoboza, Javier M Buldú
We provide the topological structure of a series of N=28 Rössler chaotic oscillators diffusively coupled through one of its variables. The dynamics of the y variable describing the evolution of the individual nodes of the network are given for a wide range of coupling strengths. Datasets capture the transition from the unsynchronized behavior to the synchronized one, as a function of the coupling strength between oscillators. The fact that both the underlying topology of the system and the dynamics of the nodes are given together makes this dataset a suitable candidate to evaluate the interplay between functional and structural networks and serve as a benchmark to quantify the ability of a given algorithm to extract the structural network of connections from the observation of the dynamics of the nodes...
June 2016: Data in Brief
Tomasz Róg, Adam Orłowski, Alicia Llorente, Tore Skotland, Tuulia Sylvänne, Dimple Kauhanen, Kim Ekroos, Kirsten Sandvig, Ilpo Vattulainen
In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24)...
June 2016: Data in Brief
Mei Fang Lin, Wen Hwa Chou, Marcelo V Kitahara, Chao Lun Allen Chen, David John Miller, Sylvain Forêt
Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the "naked-coral" hypothesis...
2016: PeerJ
Ana María Hernández-Hernández, Dolores Viga-de Alva, Rodrigo Huerta-Quintanilla, Efrain Canto-Lugo, Hugo Laviada-Molina, Fernanda Molina-Segui
We use complex network theory to study the differences between the friendship concepts in elementary school and university students. Four friendship networks were identified from surveys. Three of these networks are from elementary schools; two are located in the rural area of Yucatán and the other is in the urban area of Mérida, Yucatán. We analyzed the structure and the communities of these friendship networks and found significant differences among those at the elementary schools compared with those at the university...
2016: PloS One
S A Jafari, Farhad Shahbazi
No abstract text is available yet for this article.
October 19, 2016: Scientific Reports
L J P Xavier, D R da Costa, A Chaves, J M Pereira, G A Farias
We investigate localized states of a quantum ring confinement in monolayer graphene defined by a circular mass-related potential, which can be induced e.g. by interaction with a substrate that breaks the sublattice symmetry, where a circular line defect provides a change in the sign of the induced mass term along the radial direction. Electronic properties are calculated analytically within the Dirac-Weyl approximation in the presence of an external magnetic field. Analytical results are also compared with those obtained by the tight-binding approach...
October 19, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
S Payabvash, S Taleb, J C Benson, A M McKinney
BACKGROUND AND PURPOSE: Acute stroke presentation and outcome depend on both ischemic infarct volume and location. We aimed to determine the association between acute ischemic infarct topology and lesion volume and stroke severity at presentation and discharge. MATERIALS AND METHODS: Patients with acute ischemic stroke who underwent MR imaging within 24 hours of symptom onset or last seen well were included. Infarcts were segmented and coregistered on the Montreal Neurological Institute-152 brain map...
October 6, 2016: AJNR. American Journal of Neuroradiology
Ariel Haimovici, Pablo Balenzuela, Enzo Tagliazucchi
Synchronization of brain activity fluctuations is believed to represent communication between spatially distant neural processes. These inter-areal functional interactions develop in the background of a complex network of axonal connections linking cortical and sub-cortical neurons, termed the human "structural connectome". Theoretical considerations and experimental evidence support the view that the human brain can be modeled as a system operating at a critical point between ordered (sub-critical) and disordered (super-critical) phases...
October 19, 2016: Brain Connectivity
B Li, J Liu, Y Y Zhang, P Q Wang, Y N Yu, R X Kang, H L Wu, X X Zhang, Z Wang, Y Y Wang
Module-based methods have made much progress in deconstructing biological networks. However, it is a great challenge to quantitatively compare the topological structural variations of modules (allosteric modules [AMs]) under different situations. A total of 23, 42, and 15 coexpression modules were identified in baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) in a global anti-ischemic mice network, respectively. Then, we integrated the methods of module-based consensus ratio (MCR) and modified Zsummary module statistic to validate 12 BA, 22 JA, and 8 UA on-modules based on comparing with vehicle...
October 19, 2016: CPT: Pharmacometrics & Systems Pharmacology
Mark O'Driscoll
Accurate and efficient replication of the human genome occurs in the context of an array of constitutional barriers including regional topological constraints imposed by chromatin architecture and processes such as transcription, catenation of the helical polymer and spontaneously generated DNA lesions including base modifications and strand breaks. DNA replication is fundamentally important for tissue development and homeostasis; differentiation programmes are intimately linked with stem cell division. Unsurprisingly, impairments of the DNA replication machinery can have catastrophic consequences for genome stability and cell division...
October 18, 2016: Journal of Pathology
Tristan da Câmara Santa Clara Gomes, Joaquín De La Torre Medina, Matthieu Lemaitre, Luc Piraux
Track-etched polymer membranes with crossed nanochannels have been revealed to be most suitable as templates to produce large surface area and mechanically stable 3D interconnected nanowire (NW) networks by electrodeposition. Geometrically controlled NW superstructures made of NiCo ferromagnetic alloys exhibit appealing magnetoresistive properties. The combination of exact alloy compositions with the spatial arrangement of NWs in the 3D network is decisive to obtain specific magnetic and magneto-transport behavior...
December 2016: Nanoscale Research Letters
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