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https://www.readbyqxmd.com/read/29035546/the-gradient-adaptive-decomposition-grad-method-optimized-refinement-along-macrostate-borders-in-markov-state-models
#1
Pablo G Romano, Marina Giuseppina Guenza
Markov State Models (MSM) are used to model the kinetics of processes sampled by Molecular Dynamics (MD) simulations. MSM reduce the high dimensionality inherent to MD simulations as they partition the free energy landscape into discrete states, generating a kinetic model as a series of uncorrelated jumps between states. Here, we detail a new method, called GRadient Adaptive Decomposition, which optimizes coarse-grained MSM by refining borders with respect to the gradient along the free energy surface. The proposed method requires only a small number of initial microstates because it corrects for errors produced by limited sampling...
October 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28957659/stem-cell-differentiation-as-a-non-markov-stochastic-process
#2
Patrick S Stumpf, Rosanna C G Smith, Michael Lenz, Andreas Schuppert, Franz-Josef Müller, Ann Babtie, Thalia E Chan, Michael P H Stumpf, Colin P Please, Sam D Howison, Fumio Arai, Ben D MacArthur
Pluripotent stem cells can self-renew in culture and differentiate along all somatic lineages in vivo. While much is known about the molecular basis of pluripotency, the mechanisms of differentiation remain unclear. Here, we profile individual mouse embryonic stem cells as they progress along the neuronal lineage. We observe that cells pass from the pluripotent state to the neuronal state via an intermediate epiblast-like state. However, analysis of the rate at which cells enter and exit these observed cell states using a hidden Markov model indicates the presence of a chain of unobserved molecular states that each cell transits through stochastically in sequence...
September 27, 2017: Cell Systems
https://www.readbyqxmd.com/read/28941875/face-and-gaze-perception-in-borderline-personality-disorder-an-electrical-neuroimaging-study
#3
Cristina Berchio, Camille Piguet, Kornelia Gentsch, Anne-Lise Küng, Tonia A Rihs, Roland Hasler, Jean-Michel Aubry, Alexandre Dayer, Christoph M Michel, Nader Perroud
Humans are sensitive to gaze direction from early life, and gaze has social and affective values. Borderline personality disorder (BPD) is a clinical condition characterized by emotional dysregulation and enhanced sensitivity to affective and social cues. In this study we wanted to investigate the temporal-spatial dynamics of spontaneous gaze processing in BPD. We used a 2-back-working-memory task, in which neutral faces with direct and averted gaze were presented. Gaze was used as an emotional modulator of event-related-potentials to faces...
September 15, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28938855/eeg-resting-state-networks-microstates-source-localization
#4
Anna Custo, Dimitri van der Ville, William M Wells, Ioana M Tomescu, Christoph Michel
Using EEG to elucidate the spontaneous activation of brain resting state networks is non trivial as the signal of interest is of low amplitude and it is difficult to distinguish the underlying neural sources. Using the principles of electric field topographical analysis, it is possible to estimate the meta-stable states of the brain (i.e., the resting state topographies, so-called microstates). We estimated seven resting state topographies explaining the EEG dataset with k-means clustering (N=164, 256 electrodes)...
September 22, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/28936168/mining-time-resolved-functional-brain-graphs-to-an-eeg-based-chronnectomic-brain-aged-index-cbai
#5
Stavros I Dimitriadis, Christos I Salis
The brain at rest consists of spatially and temporal distributed but functionally connected regions that called intrinsic connectivity networks (ICNs). Resting state electroencephalography (rs-EEG) is a way to characterize brain networks without confounds associated with task EEG such as task difficulty and performance. A novel framework of how to study dynamic functional connectivity under the notion of functional connectivity microstates (FCμstates) and symbolic dynamics is further discussed. Furthermore, we introduced a way to construct a single integrated dynamic functional connectivity graph (IDFCG) that preserves both the strength of the connections between every pair of sensors but also the type of dominant intrinsic coupling modes (DICM)...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28931182/-primary-open-angle-glaucoma
#6
Esther M Hoffmann, Verena Prokosch-Willing
Glaucoma leads to blindness but there are diagnostic and therapeutic developments that aid ophthalmologists in the improved mangement of the disease compared to the past. Known risk factors such as age, myopia, dark pigmented skin, genetics, and elevated intraocular pressure play an important role for the individual patient's prognosis, and many yet unknown or not sufficiently investigated risk factors come along. The structured examination of the optic nerve head is crucial for the clincial diagnosis by the ophthalmologist...
September 20, 2017: Klinische Monatsblätter Für Augenheilkunde
https://www.readbyqxmd.com/read/28860987/apathy-in-patients-with-parkinson-s-disease-correlates-with-alteration-of-left-fronto-polar-electroencephalographic-connectivity
#7
Florian Hatz, Antonia Meyer, Ronan Zimmermann, Ute Gschwandtner, Peter Fuhr
Introduction: Quantitative electroencephalography (QEEG) brain frequency and network analyses are known to differentiate between disease stages in Parkinson's disease (PD) and are possible biomarkers. They correlate with cognitive decline. Little is known about changes in brain networks in relation to apathy. Objective/Aims: To analyze changes in brain network connectivities related to apathy. Methods: 40 PD patients (14 PD with mild cognitive deficits and 26 PD with normal cognition) were included. All patients had extensive neuropsychological testing; apathy was evaluated using the apathy evaluation score (AES, median 24...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28844120/development-of-a-biodegradable-flow-resisting-polymer-membrane-for-a-novel-glaucoma-microstent
#8
Stefan Siewert, Karen Falke, Frank Luderer, Thomas Reske, Wolfram Schmidt, Sylvia Pfensig, Michael Stiehm, Ulf Hinze, Boris Chichkov, Niels Grabow, Rudolf Guthoff, Klaus-Peter Schmitz
Within this paper we analyzed the technical feasibility of a novel microstent for glaucoma therapy. For lowering of intraocular pressure, the flexible polyurethane (PUR) implant is designed to drain aqueous humour from the anterior chamber of the eye into subconjunctival, or alternatively suprachoroidal, space. The microstent includes a biodegradable, flow resisting polymer membrane serving as temporary flow resistance for the prevention of early postoperative hypotony. A biodegradable local drug delivery (LDD)-device was designed to prevent fibrous encapsulation...
August 26, 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28817775/electronic-structure-and-properties-of-berkelium-iodates
#9
Mark A Silver, Samantha K Cary, Alejandro J Garza, Ryan E Baumbach, Alexandra A Arico, Gregory A Galmin, Kuan-Wen Chen, Jason A Johnson, Jamie C Wang, Ronald J Clark, Alexander Chemey, Teresa M Eaton, Matthew L Marsh, Kevin Seidler, Shane S Galley, Lambertus van de Burgt, Ashley L Gray, David E Hobart, Kenneth Hanson, Shelley M Van Cleve, Frédéric Gendron, Jochen Autschbach, Gustavo E Scuseria, Laurent Maron, Manfred Speldrich, Paul Kögerler, Cristian Celis-Barros, Dayán Páez-Hernández, Ramiro Arratia-Pérez, Michael Ruf, Thomas E Albrecht-Schmitt
The reaction of (249)Bk(OH)4 with iodate under hydrothermal conditions results in the formation of Bk(IO3)3 as the major product with trace amounts of Bk(IO3)4 also crystallizing from the reaction mixture. The structure of Bk(IO3)3 consists of nine-coordinate Bk(III) cations that are bridged by iodate anions to yield layers that are isomorphous with those found for Am(III), Cf(III), and with lanthanides that possess similar ionic radii. Bk(IO3)4 was expected to adopt the same structure as M(IO3)4 (M = Ce, Np, Pu), but instead parallels the structural chemistry of the smaller Zr(IV) cation...
September 14, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28803910/a-measure-to-quantify-the-degree-of-cooperativity-in-overall-titration-curves
#10
Johannes W R Martini
In the framework of the grand canonical ensemble, different definitions of cooperativity commonly used in the context of ligand binding are not equivalent. A unifying definition is the existence of non-real roots of the binding polynomial. Using this qualitative criterion, an open question is how to quantify the degree of cooperativity. In this work, we introduce a theoretical measure to quantify the degree of cooperativity of a titriation curve. Its definition is based on a minimal energy approach mapping a given binding polynomial to the minimal interaction energy which is required to generate it...
November 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28796192/computational-studies-on-acetylcholinesterases
#11
REVIEW
Yechun Xu, Shanmei Cheng, Joel L Sussman, Israel Silman, Hualiang Jiang
Functions of biomolecules, in particular enzymes, are usually modulated by structural fluctuations. This is especially the case in a gated diffusion-controlled reaction catalyzed by an enzyme such as acetylcholinesterase. The catalytic triad of acetylcholinesterase is located at the bottom of a long and narrow gorge, but it catalyzes the extremely rapid hydrolysis of the neurotransmitter, acetylcholine, with a reaction rate close to the diffusion-controlled limit. Computational modeling and simulation have produced considerable advances in exploring the dynamical and conformational properties of biomolecules, not only aiding in interpreting the experimental data, but also providing insights into the internal motions of the biomolecule at the atomic level...
August 10, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28770364/inter-study-and-inter-individual-consistency-and-variability-of-eeg-erp-microstate-sequences-in-referential-word-production
#12
Marina Laganaro
Periods of stable global electric field at scalp unfolding during a cognitive task can be linked to brain processes and are therefore well suited to investigate simultaneously qualitative and quantitative differences across conditions or populations of interest. The electrophysiological event-related (ERP) spatio-temporal dynamic has been repetitively investigated in referential word production, but the different designs, settings and analyses do not allow to conclude on the reliability of the microstate sequences across studies and individuals...
August 2, 2017: Brain Topography
https://www.readbyqxmd.com/read/28745340/toward-a-quantitative-description-of-microscopic-pathway-heterogeneity-in-protein-folding
#13
Soundhararajan Gopi, Animesh Singh, Swaathiratna Suresh, Suvadip Paul, Sayan Ranu, Athi N Naganathan
How many structurally different microscopic routes are accessible to a protein molecule while folding? This has been a challenging question to address experimentally as single-molecule studies are constrained by the limited number of observed folding events while ensemble measurements, by definition, report only an average and not the distribution of the quantity under study. Atomistic simulations, on the other hand, are restricted by sampling and the inability to reproduce thermodynamic observables directly...
August 9, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28742116/sutureless-microvascular-anastomosis-assisted-by-an-expandable-shape-memory-alloy-stent
#14
Noriko Saegusa, Shunji Sarukawa, Kunihiro Ohta, Kensuke Takamatsu, Mitsuhiro Watanabe, Takashi Sugino, Masahiro Nakagawa, Yasuto Akiyama, Masatoshi Kusuhara, Kazuo Kishi, Keita Inoue
Vascular anastomosis is the highlight of cardiovascular, transplant, and reconstructive surgery, which has long been performed by hand using a needle and suture. However, anastomotic thrombosis occurs in approximately 0.5-10% of cases, which can cause serious complications. To improve the surgical outcomes, attempts to develop devices for vascular anastomosis have been made, but they have had limitations in handling, cost, patency rate, and strength at the anastomotic site. Recently, indwelling metal stents have been greatly improved with precise laser metalwork through programming technology...
2017: PloS One
https://www.readbyqxmd.com/read/28705608/the-impact-of-hearing-aids-and-age-related-hearing-loss-on-auditory-plasticity-across-three-months-an-electrical-neuroimaging-study
#15
Nathalie Giroud, Ulrike Lemke, Philip Reich, Katarina L Matthes, Martin Meyer
The present study investigates behavioral and electrophysiological auditory and cognitive-related plasticity in three groups of healthy older adults (60-77 years). Group 1 was moderately hearing-impaired, experienced hearing aid users, and fitted with new hearing aids using non-linear frequency compression (NLFC on); Group 2, also moderately hearing-impaired, used the same type of hearing aids but NLFC was switched off during the entire period of study duration (NLFC off); Group 3 represented individuals with age-appropriate hearing (NHO) as controls, who were not different in IQ, gender, or age from Group 1 and 2...
June 29, 2017: Hearing Research
https://www.readbyqxmd.com/read/28703587/ionization-and-conformational-equilibria-of-citric-acid-delocalized-proton-binding-in-solution
#16
Sergio Madurga, Miroslava Nedyalkova, Francesc Mas, Josep Lluís Garcés
The microspeciation of citric acid is studied by analyzing NMR titration data. When the site binding (SB) model, which assumes fully localized proton binding to the carboxylic groups, is used to obtain microscopic energy parameters (dissociation constants, pair and triplet interaction energies between charged carboxylate groups), contradictory results are obtained. The resulting macroscopic constants are in very good agreement with the values reported in the literature using potentiometry. However, the found pair interaction energy between the terminal carboxylates and the triplet interaction energy are physically meaningless...
July 31, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28674009/observing-a-quantum-maxwell-demon-at-work
#17
Nathanaël Cottet, Sébastien Jezouin, Landry Bretheau, Philippe Campagne-Ibarcq, Quentin Ficheux, Janet Anders, Alexia Auffèves, Rémi Azouit, Pierre Rouchon, Benjamin Huard
In apparent contradiction to the laws of thermodynamics, Maxwell's demon is able to cyclically extract work from a system in contact with a thermal bath, exploiting the information about its microstate. The resolution of this paradox required the insight that an intimate relationship exists between information and thermodynamics. Here, we realize a Maxwell demon experiment that tracks the state of each constituent in both the classical and quantum regimes. The demon is a microwave cavity that encodes quantum information about a superconducting qubit and converts information into work by powering up a propagating microwave pulse by stimulated emission...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28673879/information-theoretical-analysis-of-resting-state-eeg-microstate-sequences-non-markovianity-non-stationarity-and-periodicities
#18
F von Wegner, E Tagliazucchi, H Laufs
We present an information-theoretical analysis of temporal dependencies in EEG microstate sequences during wakeful rest. We interpret microstate sequences as discrete stochastic processes where each state corresponds to a representative scalp potential topography. Testing low-order Markovianity of these discrete sequences directly, we find that none of the recordings fulfils the Markov property of order 0, 1 or 2. Further analyses show that the microstate transition matrix is non-stationary over time in 80% (window size 10 s), 60% (window size 20 s) and 44% (window size 40 s) of the subjects, and that transition matrices are asymmetric in 14/20 (70%) subjects...
June 30, 2017: NeuroImage
https://www.readbyqxmd.com/read/28673751/intensive-repetitive-transcranial-magnetic-stimulation-changes-eeg-microstates-in-schizophrenia-a-pilot-study
#19
Tomas Sverak, Lenka Albrechtova, Martin Lamos, Irena Rektorova, Libor Ustohal
No abstract text is available yet for this article.
June 30, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28601250/efficacy-safety-and-risk-factors-for-failure-of-standalone-ab-interno-gelatin-microstent-implantation-versus-standalone-trabeculectomy
#20
Matthew B Schlenker, Husayn Gulamhusein, Ina Conrad-Hengerer, Alix Somers, Markus Lenzhofer, Ingeborg Stalmans, Herbert Reitsamer, Fritz H Hengerer, Iqbal Ike K Ahmed
PURPOSE: To compare the efficacy, safety, and risk factors for failure of standalone ab interno gelatin microstent implantation with mitomycin C (MMC) versus trabeculectomy with MMC. DESIGN: International, multicenter, retrospective interventional cohort study. PARTICIPANTS: Three hundred fifty-four eyes of 293 patients (185 microstent and 169 trabeculectomy) with no prior incisional surgery. METHODS: Consecutive eyes with uncontrolled glaucoma underwent microstent or trabeculectomy surgery from January 1, 2011 through July 31, 2015 at 4 academic ophthalmology centers: Toronto, Canada; Frankfurt, Germany; Salzburg, Austria; and Leuven, Belgium...
June 7, 2017: Ophthalmology
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