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https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#1
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
March 27, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28345378/probing-the-behavior-of-bovine-serum-albumin-upon-binding-to-atenolol-insights-from-spectroscopic-and-molecular-docking-approaches
#2
Tuo-Ying Jiang, Kai-Li Zhou, Yan-Yue Lou, Dong-Qi Pan, Jie-Hua Shi
Molecular interaction of atenolol, a selective β1 receptor antagonist with the major carrier protein, bovine serum albumin (BSA), was investigated under imitated physiological conditions (pH 7.4) by means of fluorescence spectroscopy, UV absorption spectroscopy, Fourier transform infrared spectroscopy (FT-IR), and molecular modeling studies. The steady-state fluorescence spectra manifested that static type, due to formation of the atenolol-BSA complex, was the dominant mechanism for fluorescence quenching...
March 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28344732/autonomic-modulation-in-older-women-using-resistance-exercise-as-a-countermeasure
#3
Hayden Gerhart, Yu Lun Tai, Curtis Fennell, Xián Mayo, J Derek Kingsley
It is unclear if resistance training (RT) can be used to alter declines in autonomic modulation associated with aging. Young women (YW; range 18-25 yrs) and older women (OW; range 50-72 yrs) were compared at baseline. Only OW underwent supervised RT 2 days a week for 12-weeks. Baseline and post-training measurements included heart rate variability (HRV) and complexity (Sample Entropy) to assess autonomic modulation. The 12-weeks of RT consisted of 9 exercises performing 3 sets of 8-12 repetitions. At baseline, group differences in maximal strength, and autonomic modulation were evaluated with a one-way ANOVA with BMI as a covariate...
2017: International Journal of Exercise Science
https://www.readbyqxmd.com/read/28344326/mutual-information-model-for-link-prediction-in-heterogeneous-complex-networks
#4
Hadi Shakibian, Nasrollah Moghadam Charkari
Recently, a number of meta-path based similarity indices like PathSim, HeteSim, and random walk have been proposed for link prediction in heterogeneous complex networks. However, these indices suffer from two major drawbacks. Firstly, they are primarily dependent on the connectivity degrees of node pairs without considering the further information provided by the given meta-path. Secondly, most of them are required to use a single and usually symmetric meta-path in advance. Hence, employing a set of different meta-paths is not straightforward...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28344189/diffusivity-of-the-double-negatively-charged-mono-vacancy-in-silicon
#5
Chidanand Bhoodoo, Lasse Vines, Edouard Monakhov, Bengt Svensson
Lightly-doped silicon (Si) samples of <i>n</i>-type conductivity have been irradiated with 2.0 MeV H<sup>+</sup> ions at a temperature of 30 K and characterized <i>in situ</i> by deep level transient spectroscopy (DLTS) measurements using an on-line setup. Migration of the Si mono-vacancy in its double negative charge state (<i>V</i><sup>2-</sup>) starts to occur at temperatures above ∼70 K and is monitored via trapping of <i>V</i><sup>2-</sup> by interstitial oxygen impurity atoms (O<sub><i>i</i></sub>), leading to the growth of the prominent vacancy-oxygen (<i>V</i>O) center...
March 27, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28342786/pharmaceutical-solvates-hydrates-and-amorphous-forms
#6
REVIEW
Anne Marie Healy, Zelalem Ayenew Worku, Dinesh Kumar, Atif M Madi
Active pharmaceutical ingredients (APIs) may exist in various solid forms, which can lead to differences in the intermolecular interactions, affecting the internal energy and enthalpy, and the degree of disorder, affecting the entropy. Differences in solid forms often lead to differences in thermodynamic parameters and physicochemical properties for example solubility, dissolution rate, stability and mechanical properties of APIs and excipients. Hence, solid forms of APIs play a vital role in drug discovery and development in the context of optimization of bioavailability, filing intellectual property rights and developing suitable manufacturing methods...
March 22, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28340594/species-specific-ecological-niche-modelling-predicts-different-range-contractions-for-lutzomyia-intermedia-and-a-related-vector-of-leishmania-braziliensis-following-climate-change-in-south-america
#7
Shannon McIntyre, Elizabeth F Rangel, Paul D Ready, Bruno M Carvalho
BACKGROUND: Before 1996 the phlebotomine sand fly Lutzomyia neivai was usually treated as a synonym of the morphologically similar Lutzomyia intermedia, which has long been considered a vector of Leishmania braziliensis, the causative agent of much cutaneous leishmaniasis in South America. This report investigates the likely range changes of both sand fly species in response to a stabilisation climate change scenario (RCP4.5) and a high greenhouse gas emissions one (RCP8.5). METHODS: Ecological niche modelling was used to identify areas of South America with climates currently suitable for each species, and then the future distributions of these climates were predicted based on climate change scenarios...
March 24, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28339268/entropy-evolution-in-the-magnetic-phases-of-partially-frustrated-cepdal
#8
S Lucas, K Grube, C-L Huang, A Sakai, S Wunderlich, E L Green, J Wosnitza, V Fritsch, P Gegenwart, O Stockert, H V Löhneysen
In the heavy-fermion metal CePdAl, long-range antiferromagnetic order coexists with geometric frustration of one-third of the Ce moments. At low temperatures, the Kondo effect tends to screen the frustrated moments. We use magnetic fields B to suppress the Kondo screening and study the magnetic phase diagram and the evolution of the entropy with B employing thermodynamic probes. We estimate the frustration by introducing a definition of the frustration parameter based on the enhanced entropy, a fundamental feature of frustrated systems...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28338474/kagome-like-chains-with-anisotropic-ferromagnetic-and-antiferromagnetic-interactions
#9
Dmitry Dmitriev, Valery Krivnov
We consider a spin-$\frac{1}{2}$ kagome-like chain with competing ferro- and antiferromagnetic anisotropic exchange interactions. The ground state phase diagram of this model consists of the ferromagnetic and ferrimagnetic phases. We study the ground state and the low-temperature properties on the phase boundary between these phases. The ground state on this phase boundary is macroscopically degenerate and consists of localized magnon states. We calculate the ground state degeneracy and corresponding residual entropy...
March 24, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28337725/comparison-of-diagnostic-performance-of-four-software-packages-for-phase-dyssynchrony-analysis-in-gated-myocardial-perfusion-spect
#10
Koichi Okuda, Kenichi Nakajima, Shinro Matsuo, Soichiro Kashiwaya, Hiroto Yoneyama, Takayuki Shibutani, Masahisa Onoguchi, Mitsumasa Hashimoto, Seigo Kinuya
BACKGROUND: Phase analysis of gated myocardial perfusion single-photon emission computed tomography (SPECT) for assessment of left ventricular (LV) dyssynchrony was investigated using the following dedicated software packages: Corridor4DM (4DM), cardioREPO (cREPO), Emory Cardiac Toolbox (ECTb), and quantitative gated SPECT (QGS). The purpose of this study was to evaluate the normal values of 95% histogram bandwidth, phase standard deviation (SD), and entropy and to compare the diagnostic performance of the four software packages...
December 2017: EJNMMI Research
https://www.readbyqxmd.com/read/28337495/encapsulation-induced-aggregation-a-self-assembly-strategy-for-weakly-pi-stacking-chromophores
#11
Soumik Sao, Ishita Mukherjee, Priyadarsi De, Debangshu Chaudhuri
Molecular assembly of weakly pi-stacking core-substituted naphthalene diimides (cNDIs) requires the participation of strong side-group interactions. Spatial confinement within a micellar core leads to locally elevated concentrations and reduced entropy that drives a rapid aggregation, often followed by a slower aggregate reorganization. Fast aggregation kinetics leads to self-sorting of aggregates.
March 24, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28336915/a-novel-method-of-evaluating-knee-joint-stability-of-patients-with-knee-osteoarthritis-multiscale-entropy-analysis-with-a-knee-aiming-task
#12
Diange Zhou, Shijie Zhang, Hui Zhang, Long Jiang, Jue Zhang, Jing Fang
Deteriorating knee stability is a local risk factor that reflects the occurrence and aggregative of osteoarthritis (OA). Despite the many biomechanics-based methods for assessing the structural stability of knee joints in clinics, these methods have many limitations. The stability of the knee joint relies on not only biomechanical factors, but also proprioception and the central nervous system. In this study, we attempt to depict the stability of knee joint from a holistic viewpoint, and a novel index of knee joint stability (IKJS) was thus extracted...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336314/non-linear-van-t-hoff-behavior-in-pulmonary-surfactant-model-membranes
#13
Ernanni D Vieira, Luis G M Basso, Antonio J Costa-Filho
Pulmonary surfactant exhibits phase coexistence over a wide range of surface pressure and temperature. Less is known about the effect of temperature on pulmonary surfactant models. Given the lack of studies on this issue, we used electron paramagnetic resonance (EPR) and nonlinear least-squares (NLLS) simulations to investigate the thermotropic phase behavior of the matrix that mimics the pulmonary surfactant lipid complex, i.e. the lipid mixture composed of dipalmitoyl phosphatidylcholine (DPPC), palmitoyl-oleoyl phosphatidylcholine (POPC) and palmitoyl-oleoyl phosphatidylglycerol (POPG)...
March 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28335804/symbolic-time-series-analysis-of-electroencephalographic-eeg-epileptic-seizure-and-brain-dynamics-with-eye-open-and-eye-closed-subjects-during-resting-states
#14
Lal Hussain, Wajid Aziz, Jalal S Alowibdi, Nazneen Habib, Muhammad Rafique, Sharjil Saeed, Syed Zaki Hassan Kazmi
OBJECTIVE: Epilepsy is a neuronal disorder for which the electrical discharge in the brain is synchronized, abnormal and excessive. To detect the epileptic seizures and to analyse brain activities during different mental states, various methods in non-linear dynamics have been proposed. This study is an attempt to quantify the complexity of control and epileptic subject with and without seizure as well as to distinguish eye-open (EO) and eye-closed (EC) conditions using threshold-based symbolic entropy...
March 23, 2017: Journal of Physiological Anthropology
https://www.readbyqxmd.com/read/28335486/implicit-regularization-for-reconstructing-3d-building-rooftop-models-using-airborne-lidar-data
#15
Jaewook Jung, Yoonseok Jwa, Gunho Sohn
With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task...
March 19, 2017: Sensors
https://www.readbyqxmd.com/read/28335480/weighted-kernel-entropy-component-analysis-for-fault-diagnosis-of-rolling-bearings
#16
Hongdi Zhou, Tielin Shi, Guanglan Liao, Jianping Xuan, Jie Duan, Lei Su, Zhenzhi He, Wuxing Lai
This paper presents a supervised feature extraction method called weighted kernel entropy component analysis (WKECA) for fault diagnosis of rolling bearings. The method is developed based on kernel entropy component analysis (KECA) which attempts to preserve the Renyi entropy of the data set after dimension reduction. It makes full use of the labeled information and introduces a weight strategy in the feature extraction. The class-related weights are introduced to denote differences among the samples from different patterns, and genetic algorithm (GA) is implemented to seek out appropriate weights for optimizing the classification results...
March 18, 2017: Sensors
https://www.readbyqxmd.com/read/28335461/design-and-validation-of-a-low-cost-portable-device-to-quantify-postural-stability
#17
Yong Zhu
Measurement of the displacement of the center-of-pressure (COP) is an important tool used in biomechanics to assess postural stability and human balance. The goal of this research was to design and validate a low-cost portable device that can offer a quick indication of the state of postural stability and human balance related conditions. Approximate entropy (ApEn) values reflecting the amount of irregularity hiding in COP oscillations were used to calculate the index. The prototype adopted a portable design using the measurements of the load cells located at the four corners of a low-cost force platform...
March 18, 2017: Sensors
https://www.readbyqxmd.com/read/28335039/brain-temporal-complexity-in-explaining-the-therapeutic-and-cognitive-effects-of-seizure-therapy
#18
Faranak Farzan, Sravya Atluri, Ye Mei, Sylvain Moreno, Andrea J Levinson, Daniel M Blumberger, Zafiris J Daskalakis
Over 350 million people worldwide suffer from depression, a third of whom are medication-resistant. Seizure therapy remains the most effective treatment in depression, even when many treatments fail. The utility of seizure therapy is limited due to its cognitive side effects and stigma. The biological targets of seizure therapy remain unknown, hindering design of new treatments with comparable efficacy. Seizures impact the brains temporal dynamicity observed through electroencephalography. This dynamicity reflects richness of information processing across distributed brain networks subserving affective and cognitive processes...
March 3, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334469/stereoisomerism-of-bis-sigma-zincane-complexes-evidence-for-an-intramolecular-pathway
#19
Mark Richard Crimmin, Olga Ekkert, Andrew White
The first bis(sigma-zincane) complexes, heterotrimetallic species [M(CO)4(2-HZnBDI)2], have been prepared (BDI = 2-{2,6-i-Pr2C6H3NCMe}2CH). For M = Cr a single stereoisomer is observed in solution and the solid-state. For M = Mo and W, cis and trans isomers where found to reversibly interconvert at 297 K. Despite the huge steric demands of the ligand on zinc, in all cases the cis isomer was found to be the most thermodynamically stable. The activation parameters for the isomerization when M = Mo are H‡ = 20...
March 23, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28334282/comprehensive-assessment-of-flexible-ligand-docking-algorithms-current-effectiveness-and-challenges
#20
Sheng-You Huang
Protein-ligand docking has been playing an important role in modern drug discovery. To model drug-target binding in real systems, a number of flexible-ligand docking algorithms with different sampling strategies and scoring methods have been subsequently developed over the past three decades, while rigid-ligand docking is still being used because of its compelling computational efficiency. Here, a comprehensive assessment has been conducted to investigate the effectiveness of flexible-ligand docking versus rigid-ligand docking for three representative docking algorithms (global optimization, incremental construction and multi-conformer docking) in virtual screening and pose prediction on the Directory of Useful Decoys...
March 14, 2017: Briefings in Bioinformatics
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