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https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#1
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333646/recurrent-neural-networks-with-auxiliary-memory-units
#2
Jianyong Wang, Lei Zhang, Quan Guo, Zhang Yi
Memory is one of the most important mechanisms in recurrent neural networks (RNNs) learning. It plays a crucial role in practical applications, such as sequence learning. With a good memory mechanism, long term history can be fused with current information, and can thus improve RNNs learning. Developing a suitable memory mechanism is always desirable in the field of RNNs. This paper proposes a novel memory mechanism for RNNs. The main contributions of this paper are: 1) an auxiliary memory unit (AMU) is proposed, which results in a new special RNN model (AMU-RNN), separating the memory and output explicitly and 2) an efficient learning algorithm is developed by employing the technique of error flow truncation...
March 21, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28333452/mixed-lanthanide-porous-coordination-polymers-showing-range-tunable-ratiometric-luminescence-for-o2-sensing
#3
Jia-Wen Ye, Jiao-Min Lin, Zong-Wen Mo, Chun-Ting He, Hao-Long Zhou, Jie-Peng Zhang, Xiao-Ming Chen
Luminescent porous coordination polymers (PCPs) are emerging as attractive oxygen-sensing materials, but they are mostly based on single-wavelength luminometry. Here, we report a special mixed-lanthanide strategy for self-referenced ratiometric oxygen sensing. A series of isostructural, pure-lanthanide, or mixed-lanthanide PCPs, MCF-53(Tb/Eux), were synthesized by solvothermal reactions. Single-crystal X-ray diffraction revealed that MCF-53(Tb/Eux) is composed of complicated two-dimensional coordination networks, which interdigitate to form a three-dimensional supramolecular structure retaining one-dimensional ultra-micropores...
March 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28323125/minocycline-hepatotoxicity-clinical-characterization-and-identification-of-hla-b%C3%A2-35-02-as-a-risk-factor
#4
Thomas Jacob Urban, Paola Nicoletti, Naga Chalasani, Jose Serrano, Andrew Stolz, Ann Daly, Guruprasad Aithal, John Dillon, Victor Navarro, Joseph Odin, Huiman Barnhart, David Ostrov, Nanye Long, Elizabeth Theresa Cirulli, Paul Brent Watkins, Robert John Fontana
BACKGROUND & AIMS: Minocycline hepatotoxicity can present with prominent autoimmune features in previously healthy individuals. The aim of this study was to identify genetic determinants of minocycline DILI in a well-phenotyped cohort of patients. METHODS: Caucasian patients with minocycline DILI underwent genome-wide genotyping and were compared to unexposed population controls. Human leukocyte antigen (HLA) binding of minocycline was assessed using AutoDock Vina...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28320311/a-receptor-based-analysis-of-local-ecosystems-in-the-human-brain
#5
Skirmantas Janušonis
BACKGROUND: As a complex system, the brain is a self-organizing entity that depends on local interactions among cells. Its regions (anatomically defined nuclei and areas) can be conceptualized as cellular ecosystems, but the similarity of their functional profiles is poorly understood. The study used the Allen Human Brain Atlas to classify 169 brain regions into hierarchically-organized environments based on their expression of 100 G protein-coupled neurotransmitter receptors, with no a priori reference to the regions' positions in the brain's anatomy or function...
March 20, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28317367/-role-of-small-noncoding-rna-in-the-regulation-of-bacterial-virulence
#6
Wang Lu, Zheng Xin, Wang Shida, Li Jiyao, Xu Xin
In the long-term interaction between pathogens and host, the pathogens regulate the expression of related viru-lence genes to fit the host environment in response to the changes in the host microenvironment. Gene expression was believed to be controlled mainly at the level of transcription initiation by repressors or activators. Recent studies have revealed that small noncoding RNAs (sRNAs) are key regulators in bacterial pathogenesis. sRNA in bacteria is a noncoding RNA with length ranging from 50 to 500 nucleotides...
August 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28315725/vibration-training-after-chronic-spinal-cord-injury-evidence-for-persistent-segmental-plasticity
#7
Chu-Ling Yen, Colleen L McHenry, Michael A Petrie, Shauna Dudley-Javoroski, Richard K Shields
H-reflex paired-pulse depression is gradually lost within the first year post-SCI, a process believed to reflect reorganization of segmental interneurons after the loss of normal descending (cortical) inhibition. This reorganization co-varies in time with the development of involuntary spasms and spasticity. The purpose of this study is to determine whether long-term vibration training may initiate the return of H-reflex paired-pulse depression in individuals with chronic, complete SCI. Five men with SCI received twice-weekly vibration training (30Hz, 0...
March 15, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28297983/memory-effects-on-epidemic-evolution-the-susceptible-infected-recovered-epidemic-model
#8
M Saeedian, M Khalighi, N Azimi-Tafreshi, G R Jafari, M Ausloos
Memory has a great impact on the evolution of every process related to human societies. Among them, the evolution of an epidemic is directly related to the individuals' experiences. Indeed, any real epidemic process is clearly sustained by a non-Markovian dynamics: memory effects play an essential role in the spreading of diseases. Including memory effects in the susceptible-infected-recovered (SIR) epidemic model seems very appropriate for such an investigation. Thus, the memory prone SIR model dynamics is investigated using fractional derivatives...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28295526/pharmacological-treatments-in-asthma-affected-horses-a-pair-wise-and-network-meta-analysis
#9
L Calzetta, P Roncada, D di Cave, L Bonizzi, A Urbani, E Pistocchini, P Rogliani, M G Matera
BACKGROUND: Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyperresponsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma results from several small studies, and no head-to-head clinical trials have been conducted among the available medications...
March 10, 2017: Equine Veterinary Journal
https://www.readbyqxmd.com/read/28295053/intrinsic-optimization-using-stochastic-nanomagnets
#10
Brian Sutton, Kerem Yunus Camsari, Behtash Behin-Aein, Supriyo Datta
This paper draws attention to a hardware system which can be engineered so that its intrinsic physics is described by the generalized Ising model and can encode the solution to many important NP-hard problems as its ground state. The basic constituents are stochastic nanomagnets which switch randomly between the ±1 Ising states and can be monitored continuously with standard electronics. Their mutual interactions can be short or long range, and their strengths can be reconfigured as needed to solve specific problems and to anneal the system at room temperature...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28292833/mesoscale-architecture-shapes-initiation-and-richness-of-spontaneous-network-activity
#11
Samora Okujeni, Steffen Kandler, Ulrich Egert
Spontaneous activity in the absence of external input, including propagating waves of activity, is a robust feature of neuronal networks in vivo and in vitro. The neurophysiological and anatomical requirements for initiation and persistence of such activity, however, are poorly understood, as is their role in the function of neuronal networks. Computational network studies indicate that clustered connectivity may foster the generation, maintenance and richness of spontaneous activity. Since this mesoscale architecture cannot be systematically modified in intact tissue, testing these predictions is impracticable in vivo...
March 14, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28291047/the-impact-of-pre-exposure-prophylaxis-among-men-who-have-sex-with-men-an-individual-based-model
#12
Parastu Kasaie, Jeff Pennington, Maunank S Shah, Stephen A Berry, Danielle German, Colin P Flynn, Chris Beyrer, David W Dowdy
OBJECTIVES: Pre-exposure prophylaxis (PrEP) is recommended for preventing HIV infection among individuals at high risk, including men who have sex with men (MSM). Although its individual-level efficacy is proven, questions remain regarding population-level impact of PrEP implementation. DESIGN: We developed an agent-based simulation of HIV transmission among MSM, accounting for demographics, sexual contact network, HIV disease stage and use of antiretroviral therapy...
March 10, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28288700/externally-induced-frontoparietal-synchronization-modulates-network-dynamics-and-enhances-working-memory-performance
#13
Ines R Violante, Lucia M Li, David W Carmichael, Romy Lorenz, Robert Leech, Adam Hampshire, John C Rothwell, David J Sharp
Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high...
March 14, 2017: ELife
https://www.readbyqxmd.com/read/28286099/tinnitus-and-hyperacusis-contributions-of-paraflocculus-reticular-formation-and-stress
#14
Yu-Chen Chen, Guang-Di Chen, Ben Auerbach, Senthilvelan Manohar, Kelly Radziwon, Richard Salvi
Tinnitus and hyperacusis are common and potentially serious hearing disorders associated with noise-, age- or drug-induced hearing loss. Accumulating evidence suggests that tinnitus and hyperacusis are linked to excessive neural activity in a distributed brain network that not only includes the central auditory pathway, but also brain regions involved in arousal, emotion, stress and motor control. Here we examine electrophysiological changes in two novel non-auditory areas implicated in tinnitus and hyperacusis: the caudal pontine reticular nucleus (PnC), involved in arousal, and the paraflocculus lobe of the cerebellum (PFL), implicated in head-eye coordination and gating tinnitus and we measure the changes in corticosterone stress hormone levels...
March 7, 2017: Hearing Research
https://www.readbyqxmd.com/read/28282439/iterative-free-energy-optimization-for-recurrent-neural-networks-inferno
#15
Alexandre Pitti, Philippe Gaussier, Mathias Quoy
The intra-parietal lobe coupled with the Basal Ganglia forms a working memory that demonstrates strong planning capabilities for generating robust yet flexible neuronal sequences. Neurocomputational models however, often fails to control long range neural synchrony in recurrent spiking networks due to spontaneous activity. As a novel framework based on the free-energy principle, we propose to see the problem of spikes' synchrony as an optimization problem of the neurons sub-threshold activity for the generation of long neuronal chains...
2017: PloS One
https://www.readbyqxmd.com/read/28280569/experimental-measurements-of-water-molecule-binding-energies-for-the-second-and-third-solvation-shells-of-ca-h2o-n-2-complexes
#16
E Bruzzi, A J Stace
Further understanding of the biological role of the Ca(2+) ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca(2+) ion in [Ca(H2O) n ](2+) complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay...
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28277672/linear-and-star-poly-ionic-liquid-assemblies-surface-monolayers-and-multilayers
#17
Andrew J Erwin, Weinan Xu, Hongkun He, Krzysztof Matyjaszewski, Vladimir V Tsukruk
The surface morphology and organization of poly(ionic liquid)s (PILs), poly[1-(4-vinylbenzyl)-3-butylimidazolium bis-(trifluoromethylsulfonyl)imide] (poly(VBBI+Tf2N-), are explored in conjunction to their molecular architecture, preparation conditions, and post-assembly treatments. The formation of stable PIL Langmuir and Langmuir-Blodgett (LB) monolayers at the air-water and air-solid interfaces is demonstrated. The hydrophobic Tf2N- is shown to be a critical agent governing assembly morphology, as observed in the reversible condensation of LB monolayers into dense nanodroplets...
March 9, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28275738/long-range-allosteric-signaling-in-red-light-regulated-diguanylyl-cyclases
#18
Geoffrey Gourinchas, Stefan Etzl, Christoph Göbl, Uršula Vide, Tobias Madl, Andreas Winkler
Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28273610/efficacy-of-a-ketogenic-diet-in-resistant-myoclono-astatic-epilepsy-a-french-multicenter-retrospective-study
#19
Elodie Stenger, Mickael Schaeffer, Claude Cances, Jacques Motte, Stéphane Auvin, Dorothée Ville, Hélène Maurey, Rima Nabbout, Anne de Saint-Martin
OBJECTIVE: Recent studies have suggested that the early introduction of a ketogenic diet (KD) could improve seizure control in myoclono-astatic epilepsy (MAE). This multicenter study sought to identify the benefits of KD use on seizure control and epilepsy and on developmental outcomes in children with resistant MAE. METHODS: Fifty children who were diagnosed with severe MAE in the French network of Reference Centers for Rare Epilepsies and who were treated with KD between 2000 and 2013 were included in this study...
February 20, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28273330/interventions-for-hereditary-haemochromatosis-an-attempted-network-meta-analysis
#20
REVIEW
Elena Buzzetti, Maria Kalafateli, Douglas Thorburn, Brian R Davidson, Emmanuel Tsochatzis, Kurinchi Selvan Gurusamy
BACKGROUND: Hereditary haemochromatosis is a genetic disorder related to proteins involved in iron transport, resulting in iron load and deposition of iron in various tissues of the body. This iron overload leads to complications including liver cirrhosis (and related complications such as liver failure and hepatocellular carcinoma), cardiac failure, cardiac arrhythmias, impotence, diabetes, arthritis, and skin pigmentation. Phlebotomy (venesection or 'blood letting') is the currently recommended treatment for hereditary haemochromatosis...
March 8, 2017: Cochrane Database of Systematic Reviews
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