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Biofluid dynamics

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https://www.readbyqxmd.com/read/28709282/hybrid-smoothed-dissipative-particle-dynamics-and-immersed-boundary-method-for-simulation-of-red-blood-cells-in-flows
#1
Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi
In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. The smoothed dissipative particle dynamics (SDPD), a particle-based method, is one of the easy and flexible methods to model such complex structure fluids. It couples the best features of the smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD), with parameters having specific physical meaning (coming from SPH discretization of the Navier-Stokes equations), combined with thermal fluctuations in a mesoscale simulation, in a similar manner to the DPD...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28700536/fully-implantable-battery-free-wireless-optoelectronic-devices-for-spinal-optogenetics
#2
Vijay K Samineni, Jangyeol Yoon, Kaitlyn E Crawford, Yu Ra Jeong, Kajanna C McKenzie, Gunchul Shin, Zhaoqian Xie, Saranya S Sundaram, Yuhang Li, Min Young Yang, Jeonghyun Kim, Di Wu, Yeguang Xue, Xue Feng, Yonggang Huang, Aaron D Mickle, Anthony Banks, Jeong Sook Ha, Judith P Golden, John A Rogers, Robert W Gereau
The advent of optogenetic tools has allowed unprecedented insights into the organization of neuronal networks. Although recently developed technologies have enabled implementation of optogenetics for studies of brain function in freely moving, untethered animals, wireless powering and device durability pose challenges in studies of spinal cord circuits where dynamic, multidimensional motions against hard and soft surrounding tissues can lead to device degradation. We demonstrate here a fully implantable optoelectronic device powered by near-field wireless communication (NFC) technology, with a thin and flexible open-architecture that provides excellent mechanical durability, robust sealing against biofluid penetration and fidelity in wireless activation, thereby allowing for long-term optical stimulation of the spinal cord without constraint on the natural behaviors of the animals...
June 8, 2017: Pain
https://www.readbyqxmd.com/read/28674896/blood-and-plasma-proteomics-targeted-quantitation-and-posttranslational-redox-modifications
#3
Julie A Reisz, Katelyn M Chessler, Monika Dzieciatkowska, Angelo D'Alessandro, Kirk C Hansen
Proteome profiling using mass spectrometry is extensively utilized to understand the physiological characteristics of cells, tissues, fluids, and many other biological matrices. From the earliest days of the proteomics era, exploratory analyses of the blood protein complement have attracted a great deal of interest, owing to the pivotal importance of blood cells and biofluids (serum, plasma) for research and biomedical purposes. Once challenged by the high dynamic range of protein concentrations, low sensitivity of mass spectrometers, and poor annotation of proteomics databases, the techniques in this field have quickly evolved in recent years, particularly in the areas of absolute quantification of proteins and in mapping of posttranslational modifications...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507240/mathematical-methods-in-medicine-neuroscience-cardiology-and-pathology
#4
José M Amigó, Michael Small
The application of mathematics, natural sciences and engineering to medicine is gaining momentum as the mutual benefits of this collaboration become increasingly obvious. This theme issue is intended to highlight the trend in the case of mathematics. Specifically, the scope of this theme issue is to give a general view of the current research in the application of mathematical methods to medicine, as well as to show how mathematics can help in such important aspects as understanding, prediction, treatment and data processing...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28332230/screening-and-identification-of-multiple-constituents-and-their-metabolites-of-zhi-zi-chi-decoction-in-rat-urine-and-bile-by-ultra-high-performance-liquid-chromatography-quadrupole-time-of-flight-mass-spectrometry
#5
Wei Feng, Qiuju Dong, Minyan Liu, Si Li, Ting Liu, Xinguo Wang, Liying Niu
Zhi-zi-chi decoction (ZZCD) is a classical formula widely used in Chinese clinical application. In the present study, a novel and efficient strategy has been developed for screening and identification of multiple constituents and their metabolites of ZZCD using ultra-high-performance liquid chromatography combined with triple time-of-flight mass spectrometry. The novel approach of an online data acquisition method dependent on multiple mass defect filter and dynamic background subtraction is combined with multiple data processing techniques...
March 23, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28317393/structural-analysis-of-two-different-stent-configurations
#6
M Simão, J M Ferreira, J Mora-Rodriguez, H M Ramos
Two different stent configurations (i.e. the well known Palmaz-Schatz (PS) and a new stent configuration) are mechanically investigated. A finite element model was used to study the two geometries under combining loads and a computational fluid dynamic model based on fluid structure interaction was developed investigating the plaque and the artery wall reactions in a stented arterial segment. These models determine the stress and displacement fields of the two stents under internal pressure conditions. Results suggested that stent designs cause alterations in vascular anatomy that adversely affect arterial stress distributions within the wall, which have impact in the vessel responses such as the restenosis...
March 20, 2017: Computer Methods in Biomechanics and Biomedical Engineering
https://www.readbyqxmd.com/read/28314103/computational-study-of-the-forces-driving-aggregation-of-ultrasmall-nanoparticles-in-biological-fluids
#7
Sergio A Hassan
Nanoparticle (NP) aggregation can lead to prolonged retention in tissues or embolism, among other adverse effects. Successful use in biomedicine thus requires the capability to make NPs with limited aggregative potential. Rational design is presently a challenge due to incomplete knowledge of their interactions in biofluids. Recently, ultrasmall gold NPs passivated with endogenous antioxidant glutathione have shown promise for use in vivo. Computer simulations are here conducted to identify the forces underlying aggregation (or lack thereof) of these NPs in a cell culture...
April 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28268867/fea-modeling-and-fluid-flow-simulation-of-human-rectum-with-inserted-bowel-catheters
#8
Yong Zhang, Tina VanRiper, Brian Rague, Drew Weidman
In this project, fluid flow and fluid-structure interaction are studied for the human lower gastrointestinal (GI) region. The study consists of two steps. First, we apply meshing methods to discretize both the human lower GI model and the catheter model at sufficient resolution suitable for importing into a Finite Element Analysis (FEA) tool. For model discretization, 3D models of the colon reconstructed from human MRI slices are used to obtain the valid inlet and outlet boundary surfaces. To resolve the viscous boundary layer in flow studies, a special structure of the near-wall volumetric mesh is built by triangular prisms that construct quasi-structured, multiple near-boundary sub-layers...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227065/fea-modeling-and-fluid-flow-simulation-of-human-rectum-with-inserted-bowel-catheters
#9
Yong Zhang, Tina VanRiper, Brian Rague, Drew Weidman, Yong Zhang, Tina VanRiper, Brian Rague, Drew Weidman, Tina VanRiper, Drew Weidman, Brian Rague, Yong Zhang
In this project, fluid flow and fluid-structure interaction are studied for the human lower gastrointestinal (GI) region. The study consists of two steps. First, we apply meshing methods to discretize both the human lower GI model and the catheter model at sufficient resolution suitable for importing into a Finite Element Analysis (FEA) tool. For model discretization, 3D models of the colon reconstructed from human MRI slices are used to obtain the valid inlet and outlet boundary surfaces. To resolve the viscous boundary layer in flow studies, a special structure of the near-wall volumetric mesh is built by triangular prisms that construct quasi-structured, multiple near-boundary sub-layers...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28197582/wearable-microfluidics-fabric-based-digital-droplet-flowmetry-for-perspiration-analysis
#10
Yahui Yang, Siyuan Xing, Zecong Fang, Ruya Li, Helen Koo, Tingrui Pan
The latest development in wearable technologies has attracted much attention. In particular, collection and analysis of body fluids has been a focus. In this paper, we have reported a wearable microfluidic platform made using conventional fabric materials and laser micromachining to measure the flow rate on a patterned fabric surface, referred to as digital droplet flowmetry (DDF). The proposed wearable DDF is capable of collecting and measuring continuous perspiration with high precision (96% on average) in a real-time fashion over a defined area of skin...
February 15, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28177202/biofluid-triggered-burst-release-from-an-adaptive-covalently-assembled-dipeptide-nanocontainer-for-emergency-treatment
#11
Jinbo Fei, He Zhang, Anhe Wang, Chenchen Qin, Huimin Xue, Junbai Li
The construction of quickly dissociating containers holding bioactive components that meet the extreme requirements of emergency treatment is highly desirable but remains a great challenge. Here the use of small-molecule-induced dynamic covalent assembly is reported for simple and tunable fabrication of a biocompatible diphenylalanine-based nanocontainer toward rapidly responsive cargo delivery. The assembled nanocontainer can adaptively encapsulate various charged or neutral molecules. Upon biofluid trigger, the encapsulated molecules and bioactive proteins are released in a burst (within 5 s) from the nanocontainer due to highly sensitive deprotonation-mediated disruption of hydrogen bonding...
February 8, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28095303/gd-dtpa-induced-dynamic-metabonomic-changes-in-rat-biofluids
#12
Chuanling Wan, Youyang Zhan, Rong Xue, Yijie Wu, Xiaojing Li, Fengkui Pei
OBJECTIVES: The purposes of this study were (1) to detect the dynamic metabonomic changes induced by gadopentetate dimeglumine (Gd-DTPA) and (2) to investigate the potential metabolic disturbances associated with the pathogenesis of nephrogenic systemic fibrosis (NSF) at the early stage. METHODS: A nuclear magnetic resonance (NMR)-based metabolomics approach was used to investigate the urinary and serum metabolic changes induced by a single tail vein injection of Gd-DTPA (dosed at 2 and 5mmol/kg body weight) in rats...
January 14, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28079878/a-complete-workflow-for-high-resolution-spectral-stitching-nanoelectrospray-direct-infusion-mass-spectrometry-based-metabolomics-and-lipidomics
#13
Andrew D Southam, Ralf J M Weber, Jasper Engel, Martin R Jones, Mark R Viant
Metabolomic and lipidomic studies measure and discover metabolic and lipid profiles in biological samples, enabling a better understanding of the metabolism of specific biological phenotypes. Accurate biological interpretations require high analytical reproducibility and sensitivity, and standardized and transparent data processing. Here we describe a complete workflow for nanoelectrospray ionization (nESI) direct-infusion mass spectrometry (DIMS) metabolomics and lipidomics. After metabolite and lipid extraction from tissues and biofluids, samples are directly infused into a high-resolution mass spectrometer (e...
February 2016: Nature Protocols
https://www.readbyqxmd.com/read/27813239/combined-tissue-and-fluid-proteomics-with-tandem-mass-tags-to-identify-low-abundance-protein-biomarkers-of-disease-in-peripheral-body-fluid-an-alzheimer-s-disease-case-study
#14
Claire L Russell, Amanda Heslegrave, Vikram Mitra, Henrik Zetterberg, Jennifer M Pocock, Malcolm A Ward, Ian Pike
RATIONALE: Ideal biomarkers are present in readily accessible samples including plasma and cerebrospinal fluid (CSF), and are directly derived from diseased tissue, therefore likely to be of relatively low abundance. Traditional unbiased proteomic approaches for biomarker discovery have struggled to detect low-abundance markers due to the high dynamic range of proteins, the predominance of hyper-abundant proteins, and the use of data-dependent acquisition mass spectrometry (MS). To overcome these limitations and improve biomarker discovery in peripheral fluids, we have developed TMTcalibrator™; a novel MS workflow combining isobarically labelled diseased tissue digests in parallel with an appropriate set of labelled body fluids to increase the chance of identifying low-abundance, tissue-derived biomarkers...
January 30, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/27649337/lithotripter-shock-wave-interaction-with-a-bubble-near-various-biomaterials
#15
S W Ohl, E Klaseboer, A J Szeri, B C Khoo
Following previous work on the dynamics of an oscillating bubble near a bio-material (Ohl et al 2009 Phys. Med. Biol. 54 6313-36) and the interaction of a bubble with a shockwave (Klaseboer et al 2007 J. Fluid Mech. 593 33-56), the present work concerns the interaction of a gas bubble with a traveling shock wave (such as from a lithotripter) in the vicinity of bio-materials such as fat, skin, muscle, cornea, cartilage, and bone. The bubble is situated in water (to represent a water-like biofluid). The bubble collapses are not spherically symmetric, but tend to feature a high speed jet...
October 7, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27633951/detergents-friends-not-foes-for-high-performance-membrane-proteomics-toward-precision-medicine
#16
REVIEW
Xi Zhang
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples...
September 16, 2016: Proteomics
https://www.readbyqxmd.com/read/27630182/defining-glomerular-disease-in-mechanistic-terms-implementing-an-integrative-biology-approach-in-nephrology
#17
Laura H Mariani, William F Pendergraft, Matthias Kretzler
Advances in biomedical research allow for the capture of an unprecedented level of genetic, molecular, and clinical information from large patient cohorts, where the quest for precision medicine can be pursued. An overarching goal of precision medicine is to integrate the large-scale genetic and molecular data with deep phenotypic information to identify a new mechanistic disease classification. This classification can ideally be used to meet the clinical goal of the right medication for the right patient at the right time...
November 7, 2016: Clinical Journal of the American Society of Nephrology: CJASN
https://www.readbyqxmd.com/read/27154709/direct-detection-of-circulating-free-dna-extracted-from-serum-samples-of-breast-cancer-using-locked-nucleic-acid-molecular-beacon
#18
Zhen Gui, Quanbo Wang, Jinchang Li, Mingchen Zhu, Lili Yu, Tang Xun, Feng Yan, Huangxian Ju
As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB)...
July 1, 2016: Talanta
https://www.readbyqxmd.com/read/27094208/analyses-of-endothelial-cells-and-endothelial-progenitor-cells-released-microvesicles-by-using-microbead-and-q-dot-based-nanoparticle-tracking-analysis
#19
Jinju Wang, Yun Zhong, Xiaotang Ma, Xiang Xiao, Chuanfang Cheng, Yusen Chen, Ifeanyi Iwuchukwu, Kenneth J Gaines, Bin Zhao, Shiming Liu, Jeffrey B Travers, Ji C Bihl, Yanfang Chen
Accurate analysis of specific microvesicles (MVs) from biofluids is critical and challenging. Here we described novel methods to purify and detect MVs shed from endothelial cells (ECs) and endothelial progenitor cells (EPCs) by combining microbeads with fluorescence quantum dots (Q-dots) coupled nanoparticle tracking analysis (NTA). In the in vitro screening systems, we demonstrated that 1) anti-CD105 (EC marker) and anti-CD34 (EPC marker) conjugated-microbeads had the highest sensitivity and specificity for isolating respective MVs, which were confirmed with negative controls, CD41 and CD235a; 2) anti-CD144 (EC marker) and anti-KDR (EPC marker) conjugated-Q-dots exhibited the best sensitivity and specificity for their respective MV NTA detection, which were confirmed with positive control, anti-Annexin V (MV universal marker)...
April 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27038173/dynamic-assessment-of-functional-lipidomic-analysis-in-human-urine
#20
Hannah E Rockwell, Fei Gao, Emily Y Chen, Justice McDaniel, Rangaprasad Sarangarajan, Niven R Narain, Michael A Kiebish
The development of enabling mass spectrometry platforms for the quantification of diverse lipid species in human urine is of paramount importance for understanding metabolic homeostasis in normal and pathophysiological conditions. Urine represents a non-invasive biofluid that can capture distinct differences in an individual's physiological status. However, currently there is a lack of quantitative workflows to engage in high throughput lipidomic analysis. This study describes the development of a MS/MS(ALL) shotgun lipidomic workflow and a micro liquid chromatography-high resolution tandem mass spectrometry (LC-MS/MS) workflow for urine structural and mediator lipid analysis, respectively...
July 2016: Lipids
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