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https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#1
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329460/model-based-comparison-of-the-normal-and-fontan-circulatory-systems-part-iii
#2
Raymond L Watrous, Alvin J Chin
BACKGROUND: For patients with the Fontan circulatory arrangement, angiotensin-converting enzyme inhibition, guanylate cyclase activation, phosphodiesterase 5 inhibition, and endothelin receptor antagonism have so far resulted in little or no improvement in [Formula: see text] or peak cardiac index (CI), suggesting that our understanding of the factors that most impact the exercise hemodynamics is incomplete. METHODS: To facilitate comparisons with clinical reports of the exercise performance of preadolescent Fontan patients, we rescaled our previously reported computational models of a two-year-old normal child and similarly aged Fontan patient, extended our Fontan model to capture the nonlinear relationship between flow and resistance quantified from previous computational fluid dynamic analyses of the total cavopulmonary connection (TCPC), and added respiration as well as skeletal muscle contraction...
March 2017: World Journal for Pediatric & Congenital Heart Surgery
https://www.readbyqxmd.com/read/28328515/solving-multiextremal-problems-by-using-recurrent-neural-networks
#3
Alaeddin Malek, Najmeh Hosseinipour-Mahani
In this paper, a neural network model for solving a class of multiextremal smooth nonconvex constrained optimization problems is proposed. Neural network is designed in such a way that its equilibrium points coincide with the local and global optimal solutions of the corresponding optimization problem. Based on the suitable underestimators for the Lagrangian of the problem, one give geometric criteria for an equilibrium point to be a global minimizer of multiextremal constrained optimization problem with or without bounds on the variables...
March 16, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28328514/dynamic-uncertain-causality-graph-for-knowledge-representation-and-reasoning-utilization-of-statistical-data-and-domain-knowledge-in-complex-cases
#4
Qin Zhang, Quanying Yao
The dynamic uncertain causality graph (DUCG) is a newly presented framework for uncertain causality representation and probabilistic reasoning. It has been successfully applied to online fault diagnoses of large, complex industrial systems, and decease diagnoses. This paper extends the DUCG to model more complex cases than what could be previously modeled, e.g., the case in which statistical data are in different groups with or without overlap, and some domain knowledge and actions (new variables with uncertain causalities) are introduced...
March 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28327745/dynamics-of-miura-patterned-foldable-sheets-in-shear-flow
#5
Sarit Dutta, Michael D Graham
We study the dynamics of piecewise rigid sheets containing predefined crease lines in shear flow. The crease lines act like hinge joints along which the sheet may fold rigidly, i.e. without bending any other crease line. We choose the crease lines such that they tessellate the sheet into a two-dimensional array of parallelograms. Specifically, we focus on a particular arrangement of crease lines known as a Miura-pattern in the origami community. When all the hinges are fully open the sheet is planar, whereas when all are closed the sheet folds over itself to form a compact flat structure...
March 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28327183/modeling-multi-mutation-and-drug-resistance-analysis-of-some-case-studies
#6
Mitra Shojania Feizabadi
BACKGROUND: Drug-induced resistance is one the major obstacles that may lead to therapeutic failure during cancer treatment. Different genetic alterations occur when tumor cells divide. Among new generations of tumor cells, some may express intrinsic resistance to a specific chemotherapeutic agent. Also, some tumor cells may carry a gene that can develop resistance induced by the therapeutic drug. The methods by which the therapeutic approaches need to be revised in the occurrence of drug induced resistance is still being explored...
March 21, 2017: Theoretical Biology & Medical Modelling
https://www.readbyqxmd.com/read/28326054/dynamical-constants-and-time-universals-a-first-step-toward-a-metrical-definition-of-ordered-and-abnormal-cognition
#7
REVIEW
Mark A Elliott, Naomi du Bois
From the point of view of the cognitive dynamicist the organization of brain circuitry into assemblies defined by their synchrony at particular (and precise) oscillation frequencies is important for the correct correlation of all independent cortical responses to the different aspects of a given complex thought or object. From the point of view of anyone operating complex mechanical systems, i.e., those comprising independent components that are required to interact precisely in time, it follows that the precise timing of such a system is essential - not only essential but measurable, and scalable...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28326032/a-dynamic-circuit-hypothesis-for-the-pathogenesis-of-blepharospasm
#8
David A Peterson, Terrence J Sejnowski
Blepharospasm (sometimes called "benign essential blepharospasm," BEB) is one of the most common focal dystonias. It involves involuntary eyelid spasms, eye closure, and increased blinking. Despite the success of botulinum toxin injections and, in some cases, pharmacologic or surgical interventions, BEB treatments are not completely efficacious and only symptomatic. We could develop principled strategies for preventing and reversing the disease if we knew the pathogenesis of primary BEB. The objective of this study was to develop a conceptual framework and dynamic circuit hypothesis for the pathogenesis of BEB...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28325893/a-robust-empirical-seasonal-prediction-of-winter-nao-and-surface-climate
#9
L Wang, M Ting, P J Kushner
A key determinant of winter weather and climate in Europe and North America is the North Atlantic Oscillation (NAO), the dominant mode of atmospheric variability in the Atlantic domain. Skilful seasonal forecasting of the surface climate in both Europe and North America is reflected largely in how accurately models can predict the NAO. Most dynamical models, however, have limited skill in seasonal forecasts of the winter NAO. A new empirical model is proposed for the seasonal forecast of the winter NAO that exhibits higher skill than current dynamical models...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325767/cohesive-properties-of-the-caulobacter-crescentus-holdfast-adhesin-are-regulated-by-a-novel-c-di-gmp-effector-protein
#10
Kathrin S Sprecher, Isabelle Hug, Jutta Nesper, Eva Potthoff, Mohamed-Ali Mahi, Matteo Sangermani, Volkhard Kaever, Torsten Schwede, Julia Vorholt, Urs Jenal
When encountering surfaces, many bacteria produce adhesins to facilitate their initial attachment and to irreversibly glue themselves to the solid substrate. A central molecule regulating the processes of this motile-sessile transition is the second messenger c-di-GMP, which stimulates the production of a variety of exopolysaccharide adhesins in different bacterial model organisms. In Caulobacter crescentus, c-di-GMP regulates the synthesis of the polar holdfast adhesin during the cell cycle, yet the molecular and cellular details of this control are currently unknown...
March 21, 2017: MBio
https://www.readbyqxmd.com/read/28325438/fetal-ecg-extraction-via-type-2-adaptive-neuro-fuzzy-inference-systems
#11
Hajar Ahmadieh, Babak Mohammadzadeh Asl
BACKGROUND AND OBJECTIVE: We proposed a noninvasive method for separating the fetal ECG (FECG) from maternal ECG (MECG) by using Type-2 adaptive neuro-fuzzy inference systems. METHODS: The method can extract FECG components from abdominal signal by using one abdominal channel, including maternal and fetal cardiac signals and other environmental noise signals, and one chest channel. The proposed algorithm detects the nonlinear dynamics of the mother's body. So, the components of the MECG are estimated from the abdominal signal...
April 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28325043/a-molecular-level-insight-of-the-effect-of-hofmeister-anions-on-the-interfacial-surface-tension-of-a-model-protein
#12
Soohaeng Yoo Willow, Sotiris S Xantheas
The effect of the Hofmeister anions on the precipitation of proteins is often discussed using liquid-vapor coexisting systems with the assumption that the liquid-vapor interface mimics the liquid-protein interface. Solvated proteins, however, have both hydrophobic and hydrophilic regions on their surfaces rather than just a pure hydrophobic one. Using a solvated parallel β-sheet layer consisting of both hydrophobic and positively charged hydrophilic surfaces, we investigated the adsorption of kosmotropic (SO4(2-)) and chaotropic (ClO4(-)) anions towards protein's hydrophobic and hydrophilic surfaces via Born-Oppenheimer molecular dynamics simulations using the BLYP density functional theory...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28324611/automated-analysis-of-intracellular-dynamic-processes
#13
Yao Yao, Ihor Smal, Ilya Grigoriev, Maud Martin, Anna Akhmanova, Erik Meijering
The study of intracellular dynamic processes is of fundamental importance for understanding a wide variety of diseases and developing effective drugs and therapies. Advanced fluorescence microscopy imaging systems nowadays allow the recording of virtually any type of process in space and time with super-resolved detail and with high sensitivity and specificity. The large volume and high information content of the resulting image data, and the desire to obtain objective, quantitative descriptions and biophysical models of the processes of interest, require a high level of automation in data analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323481/the-emergence-of-life-as-a-first-order-phase-transition
#14
Cole Mathis, Tanmoy Bhattacharya, Sara Imari Walker
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase is distinguished by selection on replicators...
March 2017: Astrobiology
https://www.readbyqxmd.com/read/28323163/cerebrospinal-and-interstitial-fluid-transport-via-the-glymphatic-pathway-modeled-by-optimal-mass-transport
#15
Vadim Ratner, Yi Gao, Hedok Lee, Rena Elkin, Maiken Nedergaard, Helene Benveniste, Allen Tannenbaum
The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns...
March 16, 2017: NeuroImage
https://www.readbyqxmd.com/read/28323105/automated-workflows-for-modelling-chemical-fate-kinetics-and-toxicity
#16
José Vicente Sala Benito, Alicia Paini, Andrea-Nicole Richarz, Thorsten Meinl, Michael R Berthold, Mark T D Cronin, Andrew P Worth
Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA)...
March 17, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28322876/predator-prey-subsidy-population-dynamics-on-stepping-stone-domains
#17
Lulan Shen, Robert A Van Gorder
Predator-prey-subsidy dynamics on stepping-stone domains are examined using a variety of network configurations. Our problem is motivated by the interactions between arctic foxes (predator) and lemmings (prey) in the presence of seal carrion (subsidy) provided by polar bears. We use the n-Patch Model, which considers space explicitly as a "Stepping Stone" system. We consider the role that the carrying capacity, predator migration rate, input subsidy rate, predator mortality rate, and proportion of predators surviving migration play in the predator-prey-subsidy population dynamics...
March 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322874/reconstructing-the-genotype-to-fitness-map-for-the-bacterial-chemotaxis-network-and-its-emergent-behavioural-phenotypes
#18
Alberto Nakauma, G Sander van Doorn
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes...
March 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322858/a-neuroendocrine-account-of-facial-mimicry-and-its-dynamic-modulation
#19
REVIEW
Eline J Kraaijenvanger, Dennis Hofman, Peter A Bos
Facial expressions are considered central in conveying information about one's emotional state. During social encounters, facial expressions of another individual is often automatically imitated by the observer, a process referred to as 'facial mimicry'. This process is assumed to facilitate prosocial behaviour and is thought to rely on the mirror neuron system, known for its involvement in both observation and execution of motor actions. However, recent studies have revealed mimicry to be a more dynamic process than previously conceptualized, leaving mere perception-action coupling insufficient to explain its behavioural flexibility...
March 16, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28322855/reconstitutions-of-plasmid-partition-systems-and-their-mechanisms
#20
REVIEW
Adam C Brooks, Ling Chin Hwang
Bacterial plasmid and chromosome segregation systems ensure that genetic material is efficiently transmitted to progeny cells. Cell-based studies have shed light on the dynamic nature and the molecular basis of plasmid partition systems. In vitro reconstitutions, on the other hand, have proved to be an invaluable tool for studying the minimal components required to elucidate the mechanism of DNA segregation. This allows us to gain insight into the biological and biophysical processes that enable bacterial cells to move and position DNA...
March 16, 2017: Plasmid
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