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https://www.readbyqxmd.com/read/29285348/meeting-the-multiscale-challenge-representing-physiology-processes-over-apinatomy-circuits-using-bond-graphs
#1
B de Bono, S Safaei, P Grenon, P Hunter
We introduce, and provide examples of, the application of the bond graph formalism to explicitly represent biophysical processes between and within modular biological compartments in ApiNATOMY. In particular, we focus on modelling scenarios from acid-base physiology to link distinct process modalities as bond graphs over an ApiNATOMY circuit of multiscale compartments. The embedding of bond graphs onto ApiNATOMY compartments provides a semantically and mathematically explicit basis for the coherent representation, integration and visualisation of multiscale physiology processes together with the compartmental topology of those biological structures that convey these processes...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285347/patient-specific-simulations-for-planning-treatment-in-congenital-heart-disease
#2
Claudio Capelli, Emilie Sauvage, Giuliano Giusti, Giorgia M Bosi, Hopewell Ntsinjana, Mario Carminati, Graham Derrick, Jan Marek, Sachin Khambadkone, Andrew M Taylor, Silvia Schievano
Patient-specific computational models have been extensively developed over the last decades and applied to investigate a wide range of cardiovascular problems. However, translation of these technologies into clinical applications, such as planning of medical procedures, has been limited to a few single case reports. Hence, the use of patient-specific models is still far from becoming a standard of care in clinical practice. The aim of this study is to describe our experience with a modelling framework that allows patient-specific simulations to be used for prediction of clinical outcomes...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285346/subject-specific-multi-poroelastic-model-for-exploring-the-risk-factors-associated-with-the-early-stages-of-alzheimer-s-disease
#3
Liwei Guo, John C Vardakis, Toni Lassila, Micaela Mitolo, Nishant Ravikumar, Dean Chou, Matthias Lange, Ali Sarrami-Foroushani, Brett J Tully, Zeike A Taylor, Susheel Varma, Annalena Venneri, Alejandro F Frangi, Yiannis Ventikos
There is emerging evidence suggesting that Alzheimer's disease is a vascular disorder, caused by impaired cerebral perfusion, which may be promoted by cardiovascular risk factors that are strongly influenced by lifestyle. In order to develop an understanding of the exact nature of such a hypothesis, a biomechanical understanding of the influence of lifestyle factors is pursued. An extended poroelastic model of perfused parenchymal tissue coupled with separate workflows concerning subject-specific meshes, permeability tensor maps and cerebral blood flow variability is used...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285345/intima-heterogeneity-in-stress-assessment-of-atherosclerotic-plaques
#4
Ali C Akyildiz, Lambert Speelman, Bas van Velzen, Raoul R F Stevens, Antonius F W van der Steen, Wouter Huberts, Frank J H Gijsen
Atherosclerotic plaque rupture is recognized as the primary cause of cardiac and cerebral ischaemic events. High structural plaque stresses have been shown to strongly correlate with plaque rupture. Plaque stresses can be computed with finite-element (FE) models. Current FE models employ homogeneous material properties for the heterogeneous atherosclerotic intima. This study aimed to evaluate the influence of intima heterogeneity on plaque stress computations. Two-dimensional FE models with homogeneous and heterogeneous intima were constructed from histological images of atherosclerotic human coronaries (n = 12)...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285344/a-model-for-the-optimization-of-anti-inflammatory-treatment-with-chemerin
#5
Simao Laranjeira, Daniel Regan-Komito, Asif J Iqbal, David R Greaves, Stephen J Payne, Piotr Orlowski
Routine treatment of mild to moderate pain with a combination of non-steroidal anti-inflammatory drugs such as paracetamol in combination with corticoid opioids can lead to severe complications including death from gastrointestinal injury or to drug dependence. There is a need for the development of new safer drugs. Chemerin is a mediator promoting resolution of inflammation and it is then a promising candidate for a new treatment. A pilot experimental work using the zymosan-induced peritonitis model has found that injecting extra chemerin resulted in an approximately 1% reduction in the total number of inflammatory cells recruited...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285343/non-invasive-assessment-of-patient-specific-aortic-haemodynamics-from-four-dimensional-flow-mri-data
#6
Lucian Itu, Dominik Neumann, Viorel Mihalef, Felix Meister, Martin Kramer, Mehmet Gulsun, Marcus Kelm, Titus Kühne, Puneet Sharma
We introduce a parameter estimation framework for automatically and robustly personalizing aortic haemodynamic computations from four-dimensional magnetic resonance imaging data. The framework is based on a reduced-order multiscale fluid-structure interaction blood flow model, and on two calibration procedures. First, Windkessel parameters of the outlet boundary conditions are personalized by solving a system of nonlinear equations. Second, the regional mechanical wall properties of the aorta are personalized by employing a nonlinear least-squares minimization method...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285342/a-study-on-the-predictability-of-acute-lymphoblastic-leukaemia-response-to-treatment-using-a-hybrid-oncosimulator
#7
Eleftherios Ouzounoglou, Eleni Kolokotroni, Martin Stanulla, Georgios S Stamatakos
Efficient use of Virtual Physiological Human (VPH)-type models for personalized treatment response prediction purposes requires a precise model parameterization. In the case where the available personalized data are not sufficient to fully determine the parameter values, an appropriate prediction task may be followed. This study, a hybrid combination of computational optimization and machine learning methods with an already developed mechanistic model called the acute lymphoblastic leukaemia (ALL) Oncosimulator which simulates ALL progression and treatment response is presented...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29285341/simulating-a-virtual-population-s-sensitivity-to-salt-and-uninephrectomy
#8
John S Clemmer, Robert L Hester, W Andrew Pruett
Salt sensitivity, with or without concomitant hypertension, is associated with increased mortality. Reduced functional renal mass plays an important role in causing salt-sensitive hypertension for many individuals. Factors that are important in the condition of decreased renal mass and how they affect blood pressure (BP) or salt sensitivity are unclear. We used HumMod, an integrative mathematical model of human physiology, to create a heterogeneous population of 1000 virtual patients by randomly varying physiological parameters...
February 6, 2018: Interface Focus
https://www.readbyqxmd.com/read/29147560/correction-to-why-an-extended-evolutionary-synthesis-is-necessary
#9
Gerd B Müller
[This corrects the article DOI: 10.1098/rsfs.2017.0015.].
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147559/factors-affecting-the-physical-stability-aggregation-of-peptide-therapeutics
#10
REVIEW
Karolina L Zapadka, Frederik J Becher, A L Gomes Dos Santos, Sophie E Jackson
The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147558/discovery-and-design-of-self-assembling-peptides
#11
REVIEW
Shuguang Zhang
Peptides are ubiquitous in nature and useful in many fields, from agriculture as pesticides, in medicine as antibacterial and antifungal drugs founded in the innate immune systems, to medicinal chemistry as hormones. However, the concept of peptides as materials was not recognized until 1990 when a self-assembling peptide as a repeating segment in a yeast protein was serendipitously discovered. Peptide materials are so called because they have bona fide materials property and are made from simple amino acids with well-ordered nanostructures under physiological conditions...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147557/the-diversity-and-utility-of-amyloid-fibrils-formed-by-short-amyloidogenic-peptides
#12
REVIEW
Zahraa S Al-Garawi, Kyle L Morris, Karen E Marshall, Jutta Eichler, Louise C Serpell
Amyloidogenic peptides are well known for their involvement in diseases such as type 2 diabetes and Alzheimer's disease. However, more recently, amyloid fibrils have been shown to provide scaffolding and protection as functional materials in a range of organisms from bacteria to humans. These roles highlight the incredible tensile strength of the cross-β amyloid architecture. Many amino acid sequences are able to self-assemble to form amyloid with a cross-β core. Here we describe our recent advances in understanding how sequence contributes to amyloidogenicity and structure...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147556/mechanism-of-biosurfactant-adsorption-to-oil-water-interfaces-from-millisecond-scale-tensiometry-measurements
#13
Lingling Kong, Kadi Liis Saar, Raphael Jacquat, Liu Hong, Aviad Levin, Hongze Gang, Ruqiang Ye, Bozhong Mu, Tuomas P J Knowles
Many biological molecules are by their nature amphiphilic and have the ability to act as surfactants, stabilizing interfaces between aqueous and immiscible oil phases. In this paper, we explore the adsorption kinetics of surfactin, a naturally occurring cyclic lipopeptide, at hexadecane/water interfaces and compare and contrast its adsorption behaviour with that of synthetic alkyl benzene sulfonate isomers, through direct measurements of changes in interfacial tension upon surfactant adsorption. We access millisecond time resolution in kinetic measurements by making use of droplet microfluidics to probe the interfacial tension of hexadecane droplets dispersed in a continuous water phase through monitoring their deformation when the droplets are exposed to shear flows in a microfluidic channel with regular corrugations...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147555/what-can-machine-learning-do-for-antimicrobial-peptides-and-what-can-antimicrobial-peptides-do-for-machine-learning
#14
REVIEW
Ernest Y Lee, Michelle W Lee, Benjamin M Fulan, Andrew L Ferguson, Gerard C L Wong
Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147554/geometrical-frustration-as-a-potential-design-principle-for-peptide-based-assemblies
#15
REVIEW
Tao Jiang, Elizabeth L Magnotti, Vincent P Conticello
Two-dimensional peptide and protein assemblies have been the focus of increased scientific research as they display significant potential for the creation of functional nanomaterials. Soluble subunits derived from a variety of protein motifs have been demonstrated to self-assemble into structurally defined nanosheets under environmentally benign conditions in which the components often retain their native structure and function. These types of two-dimensional assemblies may have an advantage for nanofabrication in that their extended planar shapes can be more straightforwardly incorporated into the current formats of nanoscale devices...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147553/crafting-of-functional-biomaterials-by-directed-molecular-self-assembly-of-triple-helical-peptide-building-blocks
#16
REVIEW
Jayati Banerjee, Helena S Azevedo
Collagen is the most abundant extracellular matrix protein in the body and has widespread use in biomedical research, as well as in clinics. In addition to difficulties in the production of recombinant collagen due to its high non-natural imino acid content, animal-derived collagen imposes several major drawbacks-variability in composition, immunogenicity, pathogenicity and difficulty in sequence modification-that may limit its use in the practical scenario. However, in recent years, scientists have shifted their attention towards developing synthetic collagen-like materials from simple collagen model triple helical peptides to eliminate the potential drawbacks...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147552/peptide-based-ambidextrous-bifunctional-gelator-applications-in-oil-spill-recovery-and-removal-of-toxic-organic-dyes-for-waste-water-management
#17
Kingshuk Basu, Nibedita Nandi, Biplab Mondal, Ashkan Dehsorkhi, Ian W Hamley, Arindam Banerjee
A low molecular weight peptide-based ambidextrous gelator molecule has been discovered for efficient control of water pollution. The gelator molecules can gel various organic solvents with diverse polarity, e.g. n-hexane, n-octane, petroleum ether, petrol, diesel, aromatic solvents like chlorobenzene, toluene, benzene, o-xylene and even aqueous phosphate buffer of pH 7.5. These gels have been thoroughly characterized using various techniques including field emission scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction analysis, small angle X-ray scattering and rheological experiments...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147551/development-of-proteolytically-stable-n-methylated-peptide-inhibitors-of-aggregation-of-the-amylin-peptide-implicated-in-type-2-diabetes
#18
Idira Obasse, Mark Taylor, Nigel J Fullwood, David Allsop
Islet amyloid polypeptide, also known as amylin, is the main component of the amyloid deposits present in approximately 90% of people with type 2 diabetes mellitus (T2DM). In this disease, amylin aggregates into multimeric β-pleated sheet structures which cause damage to pancreatic islet β-cells. Inhibitors of early-stage amylin aggregation could therefore provide a disease-modifying treatment for T2DM. In this study, overlapping peptides were designed to target the 'binding' region (RLANFLVHSS, residues 11-20) of human amylin, and their effects on amyloid fibril formation were determined by thioflavin-T assay...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147550/self-assembly-of-nucleopeptides-to-interact-with-dnas
#19
Xuewen Du, Jie Zhou, Xinming Li, Bing Xu
As a novel class of biomaterials, nucleopeptides, via the conjugation of nucleobases and peptides, usually self-assemble to form nanofibres driven mainly by hydrogen bonds. Containing nucleobase(s), nucleopeptides have a unique property-interacting with nucleic acids. Here we report the design and characterization of nucleopeptides that self-assemble in water and are able to interact with single-stranded DNAs (ssDNAs). Containing nucleobases on their side chains, these nucleopeptides bind with the ssDNAs, and the ssDNAs reciprocally affect the self-assembly of nucleopeptides...
December 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/29147549/redox-sensitive-reversible-self-assembly-of-amino-acid-naphthalene-diimide-conjugates
#20
Wathsala Liyanage, Paul W Rubeo, Bradley L Nilsson
Peptide and low molecular weight amino acid-based materials that self-assemble in response to environmental triggers are highly desirable candidates in forming functional materials with tunable biophysical properties. In this paper, we explore redox-sensitive self-assembly of cationic phenylalanine derivatives conjugated to naphthalene diimide (NDI). Self-assembly of the cationic Phe-NDI conjugates into nanofibrils was induced in aqueous solvent at high ionic strength. Under reducing conditions, these self-assembled Phe-NDI conjugate fibrils underwent a morphological change to non-fibril aggregates...
December 6, 2017: Interface Focus
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