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Journal articles on the topic 'Biofluid dynamic'
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1
Hove, Jay R. "In vivo biofluid dynamic imaging in the developing zebrafish." Birth Defects Research Part C: Embryo Today: Reviews 72, no. 3 (September 2004): 277–89. http://dx.doi.org/10.1002/bdrc.20019.
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Yin, Xuewen, and Junfeng Zhang. "Modeling the dynamic flow–fiber interaction for microscopic biofluid systems." Journal of Biomechanics 46, no. 2 (January 2013): 314–18. http://dx.doi.org/10.1016/j.jbiomech.2012.11.001.
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Dunphy, Katie, Kelly O’Mahoney, Paul Dowling, Peter O’Gorman, and Despina Bazou. "Clinical Proteomics of Biofluids in Haematological Malignancies." International Journal of Molecular Sciences 22, no. 15 (July 27, 2021): 8021. http://dx.doi.org/10.3390/ijms22158021.
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Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.
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Pelliccioni, O., M. Cerrolaza, and R. Surós. "A biofluid dynamic computer code using the general lattice Boltzmann equation." Advances in Engineering Software 39, no. 7 (July 2008): 593–611. http://dx.doi.org/10.1016/j.advengsoft.2007.05.009.
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Lee, Sang Joon, Han Wook Park, and Sung Yong Jung. "Usage of CO2microbubbles as flow-tracing contrast media in X-ray dynamic imaging of blood flows." Journal of Synchrotron Radiation 21, no. 5 (July 31, 2014): 1160–66. http://dx.doi.org/10.1107/s1600577514013423.
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X-ray imaging techniques have been employed to visualize various biofluid flow phenomena in a non-destructive manner. X-ray particle image velocimetry (PIV) was developed to measure velocity fields of blood flows to obtain hemodynamic information. A time-resolved X-ray PIV technique that is capable of measuring the velocity fields of blood flows under real physiological conditions was recently developed. However, technical limitations still remained in the measurement of blood flows with high image contrast and sufficient biocapability. In this study, CO2microbubbles as flow-tracing contrast media for X-ray PIV measurements of biofluid flows was developed. Human serum albumin and CO2gas were mechanically agitated to fabricate CO2microbubbles. The optimal fabricating conditions of CO2microbubbles were found by comparing the size and amount of microbubbles fabricated under various operating conditions. The average size and quantity of CO2microbubbles were measured by using a synchrotron X-ray imaging technique with a high spatial resolution. The quantity and size of the fabricated microbubbles decrease with increasing speed and operation time of the mechanical agitation. The feasibility of CO2microbubbles as a flow-tracing contrast media was checked for a 40% hematocrit blood flow. Particle images of the blood flow were consecutively captured by the time-resolved X-ray PIV system to obtain velocity field information of the flow. The experimental results were compared with a theoretically amassed velocity profile. Results show that the CO2microbubbles can be used as effective flow-tracing contrast media in X-ray PIV experiments.
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Shi, Z. D., S. H. Winoto, and T. S. Lee. "Experimental Investigation of Pulsatile Flows in Tubes." Journal of Biomechanical Engineering 119, no. 2 (May 1, 1997): 213–16. http://dx.doi.org/10.1115/1.2796082.
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Based on cam-piston-valve arrangement, a mechanical pulsatile flow generator is designed to investigate sinusoidal flow and other types of pulsatile flow in straight rigid tube. Measurement reveals the relation between pressure gradient and flow rate. Numerical simulation using the k-ε turbulence model are carried out to compare the pulsatile flow produced by the generator with a sinusoidal flow and a physiological flow in a rigid tube. The results show that the pulsatile flow generated has similar dynamic properties to the physiological flow. Hence, the present setup can be used for in-vitro investigation of biofluid phenomena.
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Schintke, Silvia, and Eleonora Frau. "Modulated 3D Cross-Correlation Dynamic Light Scattering Applications for Optical Biosensing and Time-Dependent Monitoring of Nanoparticle-Biofluid Interactions." Applied Sciences 10, no. 24 (December 16, 2020): 8969. http://dx.doi.org/10.3390/app10248969.
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This paper reviews dynamic light scattering (DLS) of gold nanoparticle-protein interactions for the model protein bovine serum albumin (BSA), as well as in complex biofluids, at the example of mouse serum. DLS data of nanorods of various aspect ratio, of proteins and of mouse serum are discussed in terms of the analysis of their hydrodynamic radii, leading to the distinction of rotational and translational motion as well as to the detection of agglomerates. We address in particular advances obtained by modulated 3D cross correlation dynamic light scattering and recent progress using the CORENN algorithm for analysis of DLS data.
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Settles, Gary S. "Sniffers: Fluid-Dynamic Sampling for Olfactory Trace Detection in Nature and Homeland Security—." Journal of Fluids Engineering 127, no. 2 (February 10, 2005): 189–218. http://dx.doi.org/10.1115/1.1891146.
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Vertebrates aim their noses at regions of interest and sniff in order to acquire olfactory trace signals that carry information on food, reproduction, kinship, danger, etc. Invertebrates likewise position antennae in the surrounding fluid to acquire such signals. Some of the fluid dynamics of these natural sensing processes has been examined piecemeal, but the overall topic of sniffing is not well investigated or understood. It is, however, important for several human purposes, especially sampling schemes for sensors to detect chemical and biological traces in the environment. After establishing some background, a general appraisal is given of nature’s accomplishments in the fluid dynamics of sniffing. Opportunities are found for innovation through biomimicry. Since few artificial (“electronic”) noses can currently sniff in the natural sense, ways are considered to help them sniff effectively. Security issues such as explosive trace detection, landmine detection, chemical and biological sniffing, and people sampling are examined. Other sniffing applications including medical diagnosis and leak detection are also considered. Several research opportunities are identified in order to advance this topic of biofluid dynamics. Though written from a fluid dynamics perspective, this review is intended for a broad audience.
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RAVI KIRAN, G., G. RADHAKRISHNAMACHARYA, and O. ANWAR BÉG. "PERISTALTIC FLOW AND HYDRODYNAMIC DISPERSION OF A REACTIVE MICROPOLAR FLUID-SIMULATION OF CHEMICAL EFFECTS IN THE DIGESTIVE PROCESS." Journal of Mechanics in Medicine and Biology 17, no. 01 (February 2017): 1750013. http://dx.doi.org/10.1142/s0219519417500130.
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The hydrodynamic dispersion of a solute in peristaltic flow of a reactive incompressible micropolar biofluid is studied as a model of chyme transport in the human intestinal system with wall effects. The long wavelength approximation, Taylor's limiting condition and dynamic boundary conditions at the flexible walls are used to obtain the average effective dispersion coefficient in the presence of combined homogeneous and heterogeneous chemical reactions. The effects of various pertinent parameters on the effective dispersion coefficient are discussed. It is observed that average effective dispersion coefficient increases with amplitude ratio which implies that dispersion is enhanced in the presence of peristalsis. Furthermore, average effective dispersion coefficient is also elevated with the micropolar rheological and wall parameters. Conversely dispersion is found to decrease with cross viscosity coefficient, homogeneous and heterogeneous chemical reaction rates. The present simulations provide an important benchmark for future chemo-fluid-structure interaction (FSI) computational models.
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Nithiarasu, P. "Special issue on biofluid dynamics." International Journal for Numerical Methods in Fluids 57, no. 5 (2008): 473–74. http://dx.doi.org/10.1002/fld.1849.
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Beeler, Kristina, Roland Bruderer, Marco Tognetti, Kamil Sklodowski, Sebastian Mueller, Dominique Kamber, and Lukas Reiter. "90 Unbiased proteomic profiling leads to the discovery of a novel non-invasive blood-based protein panel with significant positive predictive value in pancreatic and colorectal cancers." Journal for ImmunoTherapy of Cancer 9, Suppl 2 (November 2021): A99. http://dx.doi.org/10.1136/jitc-2021-sitc2021.090.
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BackgroundMass spectrometry-based discovery proteomics has recently emerged as a high-throughput method for the proteomic profiling in biofluid samples from large clinical and population screening cohorts. Despite this progress, a significant fraction of the plasma proteome is currently not covered by state-of-the-art discovery approaches and therefore not accessible for biomarker discovery. To close this analytical gap, we present a novel workflow combining automated plasma depletion and FAIMS-DIA-MS to bridge both sensitivity and scalability. We demonstrate the applicability of this workflow to support biomarker discovery and subject stratification in precision oncology in a case-control cohort.MethodsThe plasma samples were depleted in 96-well format using an automated MARS-14 depletion system. The depleted samples were processed to tryptic peptides and analyzed using a Thermo Scientific Orbitrap Exploris 480 equipped with a FAIMS Pro device. Data processing and analysis were performed using Biognosys’ SpectroMine and Spectronaut software.ResultsUsing the unbiased discovery workflow, we investigated a cohort comprising of 180 plasma samples from healthy donors and subjects diagnosed with pancreatic, breast, prostate, colorectal and lung (NSCLC) cancer at either early or late stage of the disease. Overall, the optimized FAIMS-DIA-MS quantified 2,741 proteins across all samples and 1,849 proteins on average per sample measurement. Based on estimated plasma protein concentrations (Human Protein Atlas), quantified proteins span across 8 orders of magnitude, down to single digit pg/mL. Within this dynamic range, we could interrogate the tissue leakage proteome, interleukins and signaling proteins. Using classification algorithms, we were able to select candidates to build protein panels which provide significant positive predictive values associated with different disease stages, especially in the sub-cohorts for pancreatic and colorectal cancer.ConclusionsWe demonstrate the capabilities of a novel discovery workflow for deep, quantitative profiling of plasma samples at large scale, providing a rich proteomic resource for precision oncology.
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Shyy and, W., M. Francois, HS Udaykumar, N. N’dri and, and R. Tran-Son-Tay. "Moving boundaries in micro-scale biofluid dynamics." Applied Mechanics Reviews 54, no. 5 (September 1, 2001): 405–54. http://dx.doi.org/10.1115/1.1403025.
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Many critical issues in biofluid dynamics occur at the boundaries between fluids, solids, or both. These issues can be very complex since in many cases the boundaries are deformable and moving. Furthermore, different characteristic times, lengths, and material properties are often present which make any computational task taxing. The present review focuses on computational modeling techniques for moving boundaries and multi-component systems with emphasis on micro-scale biofluid physics, including i) the dynamics of leukocyte (white blood cell) deformation, recovery, and adhesion; and ii) the thin-film dynamics involving tear–structure interaction in soft contact lens applications. In these problems, multiple length scales exist, and at least one of them is on the order of 10 μm or smaller. After presenting appropriate computational techniques for moving boundaries, recent research on leukocyte deformation, recovery, and adhesion is reviewed in the context of multi-component, multi-time-scale, and micro-macro interactions. The soft contact lens problem is discussed from the viewpoint of large disparities in length scales due to high aspect ratios. Depending on the nature of the problem and the goal of the computation, alternative computational techniques can successfully address the physical and numerical challenges. A major interest of this article is to stress how moving boundary techniques can be applied to provide new insights into the physico-chemical behavior of complex biological systems. To treat different time and length scales with due care in a moving boundary framework is a grand challenge in developing first-principle-based computational capabilities. There are 175 references in this review article.
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Xu, Wenxin, Junfang Wu, Yanpeng An, Chaoni Xiao, Fuhua Hao, Hongbing Liu, Yulan Wang, and Huiru Tang. "Streptozotocin-Induced Dynamic Metabonomic Changes in Rat Biofluids." Journal of Proteome Research 11, no. 6 (May 18, 2012): 3423–35. http://dx.doi.org/10.1021/pr300280t.
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Wan, Chuanling, Youyang Zhan, Rong Xue, Yijie Wu, Xiaojing Li, and Fengkui Pei. "Gd-DTPA-induced dynamic metabonomic changes in rat biofluids." Magnetic Resonance Imaging 44 (December 2017): 15–25. http://dx.doi.org/10.1016/j.mri.2017.01.009.
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Boutopoulos, Ioannis D., Dimitrios S. Lampropoulos, George C. Bourantas, Karol Miller, and Vassilios C. Loukopoulos. "Two-Phase Biofluid Flow Model for Magnetic Drug Targeting." Symmetry 12, no. 7 (July 1, 2020): 1083. http://dx.doi.org/10.3390/sym12071083.
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Magnetic drug targeting (MDT) is a noninvasive method for the medical treatment of various diseases of the cardiovascular system. Biocompatible magnetic nanoparticles loaded with medicinal drugs are carried to a tissue target in the human body (in vivo) under the applied magnetic field. The present study examines the MDT technique in various microchannels geometries by adopting the principles of biofluid dynamics (BFD). The blood flow is considered as laminar, pulsatile and the blood as an incompressible and non-Newtonian fluid. A two-phase model is adopted to resolve the blood flow and the motion of magnetic nanoparticles (MNPs). The numerical results are obtained by utilizing a meshless point collocation method (MPCM) alongside with the moving least squares (MLS) approximation. The numerical results are verified by comparing with published numerical results. We investigate the effect of crucial parameters of MDT, including (1) the volume fraction of nanoparticles, (2) the location of the magnetic field, (3) the strength of the magnetic field and its gradient, (4) the way that MNPs approach the targeted area, and (5) the bifurcation angle of the vessel.
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LIU, XIUMEI, JIE HE, JIYUN ZHAO, ZHENG LONG, WENHUA LI, and BEIBEI LI. "BIOFLUID FLOW THROUGH A THROTTLE VALVE: A COMPUTATIONAL FLUID DYNAMICS STUDY OF CAVITATION." Journal of Mechanics in Medicine and Biology 16, no. 03 (May 2016): 1650034. http://dx.doi.org/10.1142/s0219519416500342.
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Biofluid flow through a throttle valve is investigated numerically and experimentally in our paper. Numerical studies are performed in order to obtain the mass flow rate through the valve under different operating conditions. Pressure drop behind the throttle valve and formation of the vortex flow downstream has been evaluated. The vortices were mainly distributed on top of the valve rod, the corner of the channel and the corner of the valve seat. When valve opening increases, the vortices grow and cause higher pressure drop. In other words, more energy is lost due to these growing vortices and high viscosity of biofluid. Furthermore, experimental flow visualization is conducted to capture cavitation images near the orifice using high-speed camera. The initial position of cavitation occurred near throttle orifice while cavitation zone downstream is caused by circulating bubbles clusters. As the opening of the valve is decreased, the area and strength of vortices in the corner of the channel grow and cause higher pressure drop firstly, then decrease. In addition, there are a lot of bubble clusters on top of the valve rod and the corner of the valve seat, which flowed downstream and collapsed, then filled the entire channel. In general, the valve opening plays very important role in the performance of a throttle valve. The results would help to observe, understand and manage the cavitation phenomenon in a throttle valve, and improve the performance of throttle valves.
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Ahn, Sungsook, Sung Yong Jung, Jin Pyung Lee, Hae Koo Kim, and Sang Joon Lee. "Gold Nanoparticle Flow Sensors Designed for Dynamic X-ray Imaging in Biofluids." ACS Nano 4, no. 7 (July 2010): 3753–62. http://dx.doi.org/10.1021/nn1003293.
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BÉG, O. ANWAR, TASVEER A. BÉG, R. BHARGAVA, S. RAWAT, and D. TRIPATHI. "FINITE ELEMENT STUDY OF TRANSIENT PULSATILE MAGNETO-HEMODYNAMIC NON-NEWTONIAN FLOW AND DRUG DIFFUSION IN A POROUS MEDIUM CHANNEL." Journal of Mechanics in Medicine and Biology 12, no. 04 (September 2012): 1250081. http://dx.doi.org/10.1142/s0219519412500819.
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A numerical study of pulsatile hydromagnetic flow and mass transfer of a non-Newtonian biofluid through a porous channel containing a non-Darcian porous material is undertaken. An extensively-validated biofluid dynamics variational finite element code, BIOFLOW, is employed to obtain comprehensive computational solutions for the flow regime which is described using a spatially two-dimensional momentum equation and a spatially one-dimensional mass transport equation, under appropriate boundary conditions. The Nakamura-Sawada rheological model is employed which provides a higher yield stress than the Casson model. A non-Newtonian model is justified on the basis that blood exhibits deviation from Newtonian behavior at low shear rates. The conduit considered is rigid with a pulsatile pressure applied via an appropriate pressure gradient term. One hundred two-noded line elements have been employed in the computations. The influence of magnetic field on the flow is studied via the magnetohydrodynamic body force parameter (Nm), which defines the ratio of magnetic (Lorentz) retarding force to the viscous hydrodynamic force. Blood vessel blockage effects are simulated with a Darcy-Forchheimer nonlinear drag force model incorporating a Darcian linear impedance for low Reynolds numbers and a Forchheimer quadratic drag for higher Reynolds numbers. Transformed velocity and concentration profiles are plotted for the influence of Reynolds number (Re), Darcy parameter (λ), Forchheimer inertial drag parameter (NF), non-Newtonian parameter (β), and Schmidt number (Sc) and at various times (T). Three-dimensional profiles of velocity varying in space and time are also provided. Applications of the model include magnetic therapy, biomagnetic pharmaco-dynamics and the simulation of diseased arteries.
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Nag, Subhra, and Andrew Resnick. "Biophysics and biofluid dynamics of primary cilia: evidence for and against the flow-sensing function." American Journal of Physiology-Renal Physiology 313, no. 3 (September 1, 2017): F706—F720. http://dx.doi.org/10.1152/ajprenal.00172.2017.
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Primary cilia have been called “the forgotten organelle” for over 20 yr. As cilia now have their own journal and several books devoted to their study, perhaps it is time to reconsider the moniker “forgotten organelle.” In fact, during the drafting of this review, 12 relevant publications have been issued; we therefore apologize in advance for any relevant work we inadvertently omitted. What purpose is yet another ciliary review? The primary goal of this review is to specifically examine the evidence for and against the hypothesized flow-sensing function of primary cilia expressed by differentiated epithelia within a kidney tubule, bringing together differing disciplines and their respective conceptual and experimental approaches. We will show that understanding the biophysics/biomechanics of primary cilia provides essential information for understanding any potential role of ciliary function in disease. We will summarize experimental and mathematical models used to characterize renal fluid flow and incident force on primary cilia and to characterize the mechanical response of cilia to an externally applied force and discuss possible ciliary-mediated cell signaling pathways triggered by flow. Throughout, we stress the importance of separating the effects of fluid shear and stretch from the action of hydrodynamic drag.
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Ye, Ting, and Yu Li. "A Comparative Review of Smoothed Particle Hydrodynamics, Dissipative Particle Dynamics and Smoothed Dissipative Particle Dynamics." International Journal of Computational Methods 15, no. 08 (October 31, 2018): 1850083. http://dx.doi.org/10.1142/s0219876218500834.
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Smoothed particle hydrodynamics (SPH), dissipative particle dynamics (DPD) and smoothed dissipative particle dynamics (SDPD) are three typical and related particle-based methods. They have been increasingly attractive for solving fluid flow problems, especially for the biofluid flow, because of their advantages of ease and flexibility in modeling complex structure fluids. This work aims to review what the exact similarities and differences are among them, by studying four simple fluid flows: (i) self-diffusion of quiescent flow, (ii) time-dependent Coutte flow, (iii) time-dependent Poiseuille flow, and (iv) lid-driven cavity flow. The simulations show that SPH, DPD and SDPD can give the similar results. SPH generates quite smooth results and has zero system temperature due to the absence of thermal fluctuations, suitable for macroscale problems. However, DPD and SDPD have fluctuating results around the reference results and nonzero system temperature with considerable thermal fluctuations, suitable for mesoscale problems. SDPD is more convenient than DPD to some extent, because it is not required to pre-define the force coefficients. SDPD can adopt more diverse equation of state (EOS) than DPD, because its EOS is user-defined unlike the EOS of DPD, inbuilt in the formulations.
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Rodrigues, Filipe B., Lauren M. Byrne, Rosanna Tortelli, Eileanoir B. Johnson, Peter A. Wijeratne, Marzena Arridge, Enrico De Vita, et al. "Mutant huntingtin and neurofilament light have distinct longitudinal dynamics in Huntington’s disease." Science Translational Medicine 12, no. 574 (December 16, 2020): eabc2888. http://dx.doi.org/10.1126/scitranslmed.abc2888.
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The longitudinal dynamics of the most promising biofluid biomarker candidates for Huntington’s disease (HD)—mutant huntingtin (mHTT) and neurofilament light (NfL)—are incompletely defined. Characterizing changes in these candidates during disease progression could increase our understanding of disease pathophysiology and help the identification of effective therapies. In an 80-participant cohort over 24 months, mHTT in cerebrospinal fluid (CSF), as well as NfL in CSF and blood, had distinct longitudinal trajectories in HD mutation carriers compared with controls. Baseline analyte values predicted clinical disease status, subsequent clinical progression, and brain atrophy, better than did the rate of change in analytes. Overall, NfL was a stronger monitoring and prognostic biomarker for HD than mHTT. Nonetheless, mHTT has prognostic value and might be a valuable pharmacodynamic marker for huntingtin-lowering trials.
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Landry, Markita P. "Protein Corona Formation on Hard and Polymeric Nanoparticles – Towards Understanding Biocompatibility, Biodistribution, and Efficacy." ECS Meeting Abstracts MA2022-01, no. 8 (July 7, 2022): 707. http://dx.doi.org/10.1149/ma2022-018707mtgabs.
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Unpredictable protein adsorption on both hard and soft nanoparticles remains a considerable challenge towards effectively applying nanotechnologies in biological environments. Hard nanoparticles form the basis of many chemical nanosensors. Conversely, soft nanoparticles such as lipid nanoparticles (LNPs) are vital for the successful delivery of mRNA-based vaccines, and offer promising applications in neonatal gene therapy, immunotherapy, and protein replacement therapy. Understanding the biological interactions that both hard and soft nanoparticles undergo upon introduction into biological systems is central to optimize the outcomes of nanoparticle-based delivery biotechnologies in clinical settings. Herein, we present a multimodal study of protein corona composition and dynamics, first on ‘hard’ nanoparticles: spherical polystyrene nanoparticles (a previously studied model nanoparticle) and high aspect ratio single-walled carbon nanotubes (SWCNTs, an understudied nanoparticle). These nanoparticles are exposed to two biofluids of interest: blood plasma (relevant for intravenous applications) and cerebrospinal fluid (relevant for brain imaging and sensing applications). To study these protein coronas, we develop a methodology based on quantitative proteomic mass spectrometry [1] and chemical thermodynamic analysis of real-time protein binding to identify protein corona ‘fingerprints’, enabling quantification of protein abundance and enrichment/depletion relative to the native biofluid, transient kinetics [2], and end-state topology. Interestingly, we find that the heavily studied polystyrene nanoparticles are relatively agnostic in the formation of their protein coronas, demonstrating little preference for particular protein classes or physicochemical properties. Conversely, we find that SWCNTs show strong preference for certain protein classes. Our additional work in machine learing-based analysis shows that corona compositions, and more broadly nanoparticle biofouling, can be drastically different for each nanoparticle type [3]. Lastly, we study nano-bio interactions encountered by ‘soft’ nanoparticles: LNPs commonly used for the therapeutic delivery of mRNA. We investigate how modifying (i) the mRNA packaged inside the LNPs and (ii) the ionizable lipid within the LNPs modulate the subsequently formed protein corona in (iii) various biological environments of relevance for delivery applications. Importantly, this workflow is readily translatable across soft polymer-based nanotechnologies of interest, which are understudied due to the experimental complexity of separating nanoparticle-corona complexes from free proteins. This fundamental understanding of protein-LNP interactions could enable more seamless design and clinical application of next-generation LNP carriers to bolster the safe and effective delivery of mRNA and other therapeutics to patients. References Pinals, R.L., et al., Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments. Angewandte Chemie (2020). Pinals, R. L., Yang, D., Lui, A., Cao, W. & Landry, M. P. Corona Exchange Dynamics on Carbon Nanotubes by Multiplexed Fluorescence Monitoring. JACS (2020). Ouassil, N.*, Pinals, R.L.*, O’Donnell, J.T.D., Wang, J., Landry, M.P.‡ Supervised Learning Model to Predict Protein Adsorption to Nanoparticles. Science Advances (2022).
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Konoshenko, Maria Y., Evgeniy A. Lekchnov, Olga E. Bryzgunova, Elena Kiseleva, Inna A. Pyshnaya, and Pavel P. Laktionov. "Isolation of Extracellular Vesicles from Biological Fluids via the Aggregation–Precipitation Approach for Downstream miRNAs Detection." Diagnostics 11, no. 3 (February 24, 2021): 384. http://dx.doi.org/10.3390/diagnostics11030384.
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Extracellular vesicles (EVs) have high potential as sources of biomarkers for non-invasive diagnostics. Thus, a simple and productive method of EV isolation is demanded for certain scientific and medical applications of EVs. Here we aim to develop a simple and effective method of EV isolation from different biofluids, suitable for both scientific, and clinical analyses of miRNAs transported by EVs. The proposed aggregation–precipitation method is based on the aggregation of EVs using dextran blue and the subsequent precipitation of EVs using 1.5% polyethylene glycol solutions. The developed method allows the effective isolation of EVs from plasma and urine. As shown using TEM, dynamic light scattering, and miRNA analyses, this method is not inferior to ultracentrifugation-based EV isolation in terms of its efficacy, lack of inhibitors for polymerase reactions and applicable for both healthy donors and cancer patients. This method is fast, simple, does not need complicated equipment, can be adapted for different biofluids, and has a low cost. The aggregation–precipitation method of EV isolation accessible and suitable for both research and clinical laboratories. This method has the potential to increase the diagnostic and prognostic utilization of EVs and miRNA-based diagnostics of urogenital pathologies.
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Senf, Brian, and Jong-Hoon Kim. "Effect of Viscosity on High-Throughput Deterministic Lateral Displacement (DLD)." Micro 2, no. 1 (January 24, 2022): 100–112. http://dx.doi.org/10.3390/micro2010006.
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Biosample analysis often requires the purification, separation, or fractionation of a biofluid prior to transport to the biosensor. Deterministic lateral displacement (DLD) is a size-based microfluidic separation technique that shows promise for biosample preparation. Recently, high-throughput DLD separation has been demonstrated with airfoil-shaped pillars at higher flow rates, but this also changes separation dynamics as the Reynolds number (Re) increases. In this work, the particle trajectories in the airfoil DLD with two different angle-of-attacks (AoAs) were studied at a range of Re with alterations of fluid viscosity to mimic biological fluids. Previous studies have found that the critical diameter (Dc) decreases as Re climes. We demonstrated that variations of the fluid viscosity do not alter the separation dynamics if the Re is kept constant. As the associated Re of the flow increases, the Dc decreases regardless of viscosity. The negative AoA with an airfoil DLD pillar design provided the stronger Dc shift to negate pressure increases.
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Prakashan, Drishya, Ramya P R, and Sonu Gandhi. "A Systematic Review on the Advanced Techniques of Wearable Point-of-Care Devices and Their Futuristic Applications." Diagnostics 13, no. 5 (February 28, 2023): 916. http://dx.doi.org/10.3390/diagnostics13050916.
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Personalized point-of-care testing (POCT) devices, such as wearable sensors, enable quick access to health monitoring without the use of complex instruments. Wearable sensors are gaining popularity owing to their ability to offer regular and continuous monitoring of physiological data by dynamic, non-invasive assessments of biomarkers in biofluids such as tear, sweat, interstitial fluid and saliva. Current advancements have concentrated on the development of optical and electrochemical wearable sensors as well as advances in non-invasive measurements of biomarkers such as metabolites, hormones and microbes. For enhanced wearability and ease of operation, microfluidic sampling, multiple sensing, and portable systems have been incorporated with materials that are flexible. Although wearable sensors show promise and improved dependability, they still require more knowledge about interaction between the target sample concentrations in blood and non-invasive biofluids. In this review, we have described the importance of wearable sensors for POCT, their design and types of these devices. Following which, we emphasize on the current breakthroughs in the application of wearable sensors in the realm of wearable integrated POCT devices. Lastly, we discuss the present obstacles and forthcoming potentials including the use of Internet of Things (IoT) for offering self-healthcare using wearable POCT.
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Lenton, S., T. Seydel, T. Nylander, C. Holt, M. Härtlein, S. Teixeira, and G. Zaccai. "Dynamic footprint of sequestration in the molecular fluctuations of osteopontin." Journal of The Royal Society Interface 12, no. 110 (September 2015): 20150506. http://dx.doi.org/10.1098/rsif.2015.0506.
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The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core–shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering. The effects of sequestration are quantified on the nanosecond– ångström resolution by elastic incoherent neutron scattering. The molecular fluctuations of the free phosphopeptide are in agreement with a highly flexible protein. An increased resilience to diffusive motions of OPN is corroborated by molecular fluctuations similar to those observed for globular proteins, yet retaining conformational flexibilities. The results bring insight into the modulation of the activity of OPN and phosphopeptides with a role in the control of biomineralization. The quantification of such effects provides an important handle for the future design of new peptides based on the dynamics–activity relationship.
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FAN, JIZHUANG, WEI ZHANG, YANHE ZHU, and JIE ZHAO. "CFD-BASED SELF-PROPULSION SIMULATION FOR FROG SWIMMING." Journal of Mechanics in Medicine and Biology 14, no. 06 (December 2014): 1440012. http://dx.doi.org/10.1142/s0219519414400120.
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Mechanism analysis of frog swimming is an interesting subject in the field of biofluid mechanics and bionics. Computing the hydrodynamic forces acting on a frog is difficult due to its characteristics of explosive propulsion and large range of joint motion. To analyze the flow around the body and vortices in the wake, in this paper, the method based on Computational Fluid Dynamics (CFD) was utilized to solve the velocity and pressure distributions in the flow field and on the frog. The hydrodynamic problem during the propulsive phase of a frog, Xenopus laevis, was calculated using the CFD software FLUENT. A self-propulsion simulation was performed which computed the body velocity from the joint trajectory input and CFD solved the hydrodynamic forces, and visual CFD results of the hydrodynamic forces and flow field structures were obtained.
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Sia, Isaac, Michael A. Crary, John Kairalla, Giselle D. Carnaby, Mark Sheplak, and Timothy McCulloch. "Derivation and measurement consistency of a novel biofluid dynamics measure of deglutitive bolus‐driving function—pharyngeal swallowing power." Neurogastroenterology & Motility 31, no. 1 (September 23, 2018): e13465. http://dx.doi.org/10.1111/nmo.13465.
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Lee, Pey Yee, Junaida Osman, Teck Yew Low, and Rahman Jamal. "Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery." Bioanalysis 11, no. 19 (October 2019): 1799–812. http://dx.doi.org/10.4155/bio-2019-0145.
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Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
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Neofytou, Panagiotis, Maria Theodosiou, Marios G. Krokidis, and Eleni K. Efthimiadou. "Simulation of Colloidal Stability and Aggregation Tendency of Magnetic Nanoflowers in Biofluids." Modelling 3, no. 1 (December 24, 2021): 14–26. http://dx.doi.org/10.3390/modelling3010002.
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A population balance model for the aggregation of iron oxide nanoflowers (IONfs) is presented. The model is based on the fixed pivot technique and is validated successfully for four kinds of aggregation kernels. The extended Derjaguin, Landau, Verwey, and Overbeek (xDLVO) theory is also employed for assessing the collision efficiency of the particles, which is pertinent to the total energy of the interaction. Colloidal stability experiments were conducted on IONfs for two dispersant cases—aqueous phosphate buffered saline solution (PBS) and simulated body fluid (SBF). Dynamic light scattering (DLS) measurements after 24-h of incubation show a significant size increase in plain PBS, whereas the presence of proteins in SBF prevents aggregation by protein corona formation on the IONfs. Subsequent simulations tend to overpredict the aggregation rate, and this can be attributed to the flower-like shape of IONfs, thus allowing patchiness on the surface of the particles that promotes an uneven energy potential and aggregation hindering. In silico parametric study on the effects of the ionic strength shows a prominent dependency of the aggregation rate on the salinity of the dispersant underlying the effect of repulsion forces, which are almost absent in the PBS case, promoting aggregation. In addition, the parametric study on the van der Waals potential energy effect—within common Hamaker-constant values for iron oxides—shows that this is almost absent for high salinity dispersants, whereas low salinity gives a wide range of results, thus underlying the high sensitivity of the model on the potential energy parameters.
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António, Maria, Tânia Lima, Rui Vitorino, and Ana L. Daniel-da-Silva. "Interaction of Colloidal Gold Nanoparticles with Urine and Saliva Biofluids: An Exploratory Study." Nanomaterials 12, no. 24 (December 13, 2022): 4434. http://dx.doi.org/10.3390/nano12244434.
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The use of gold nanoparticles for drug delivery, photothermal or photodynamic therapy, and biosensing enhances the demand for knowledge about the protein corona formed on the surface of nanoparticles. In this study, gold nanospheres (AuNSs), gold nanorods (AuNRs), and gold nanoflowers (AuNFs) were incubated with saliva or urine. After the interaction, the surface of gold nanoparticles was investigated using UV-VIS spectroscopy, zeta potential, and dynamic light scattering. The shifting of the localized surface plasmon resonance (LSPR) band, the increase in hydrodynamic diameter, and the changes in the surface charge of nanoparticles indicated the presence of biomolecules on the surface of AuNSs, AuNRs, and AuNFs. The incubation of AuNFs with saliva led to nanoparticle aggregation and minimal protein adsorption. AuNSs and AuNRs incubated in saliva were analyzed through liquid chromatography with tandem mass spectrometry (LC-MS/MS) to identify the 96 proteins adsorbed on the surface of the gold nanoparticles. Among the 20 most abundant proteins identified, 14 proteins were common in both AuNSs and AuNRs. We hypothesize that the adsorption of these proteins was due to their high sulfur content, allowing for their interaction with gold nanoparticles via the Au-S bond. The presence of distinct proteins on the surface of AuNSs or AuNRs was also investigated and possibly related to the competition between proteins present on the external layers of corona and gold nanoparticle morphology.
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BÉG, O. ANWAR, M. M. RASHIDI, T. A. BÉG, and M. ASADI. "HOMOTOPY ANALYSIS OF TRANSIENT MAGNETO-BIO-FLUID DYNAMICS OF MICROPOLAR SQUEEZE FILM IN A POROUS MEDIUM: A MODEL FOR MAGNETO-BIO-RHEOLOGICAL LUBRICATION." Journal of Mechanics in Medicine and Biology 12, no. 03 (June 2012): 1250051. http://dx.doi.org/10.1142/s0219519411004642.
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The transient squeezing flow of a magneto-micropolar biofluid in a noncompressible porous medium intercalated between two parallel plates in the presence of a uniform strength transverse magnetic field is investigated. The partial differential equations describing the two-dimensional flow regime are transformed into nondimensional, nonlinear coupled ordinary differential equations for linear and angular momentum (micro-inertia). These equations are solved using the robust Homotopy Analysis Method (HAM) and also numerical shooting quadrature. Excellent correlation is achieved. The influence of magnetic field parameter (Ha) , micropolar spin gradient viscosity parameter (Γ) and unsteadiness parameter (S) on linear and angular velocity (micro-rotation) are presented graphically, for specified values of the micropolar vortex viscosity parameter (R), Darcy number (Da i.e. permeability parameter) and medium porosity parameter (ε). Increasing magnetic field (Ha) serves to decelerate both the linear and angular velocity i.e. enhances lubrication. The excellent potential of HAM in bio-lubrication flows is highlighted.
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CAKMAK, ALI, XINJIAN QI, A. ERCUMENT CICEK, ILYA BEDERMAN, LEIGH HENDERSON, MITCHELL DRUMM, and GULTEKIN OZSOYOGLU. "A NEW METABOLOMICS ANALYSIS TECHNIQUE: STEADY-STATE METABOLIC NETWORK DYNAMICS ANALYSIS." Journal of Bioinformatics and Computational Biology 10, no. 01 (February 2012): 1240003. http://dx.doi.org/10.1142/s0219720012400033.
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With the recent advances in experimental technologies, such as gas chromatography and mass spectrometry, the number of metabolites that can be measured in biofluids of individuals has markedly increased. Given a set of such measurements, a very common task encountered by biologists is to identify the metabolic mechanisms that lead to changes in the concentrations of given metabolites and interpret the metabolic consequences of the observed changes in terms of physiological problems, nutritional deficiencies, or diseases. In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study. We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database. The query output space of the SMDA tool is exponentially large in the number of reactions of the network. However, (i) larger numbers of observations exponentially reduce the output size, and (ii) exploratory search and browsing of the query output space is provided to allow users to search for what they are looking for.
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Mahabub, Maria, M. Ferdows, M. Gluam Murtaza, Giulio Lorenzini, and E. E. Tzirtzilakis. "Numerical Study of Unsteady Boundary Layer Flow of a Biomagnetic Fluid over a Horizontal Stretching Sheet with Magnetic Dipole." Mathematical Modelling of Engineering Problems 9, no. 1 (February 28, 2022): 215–23. http://dx.doi.org/10.18280/mmep.090127.
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This paper focuses on the theoretical and numerical investigation of the unsteady, viscous, incompressible, two-dimensional laminar boundary layer flow of a Newtonian biomagnetic fluid over a stretching sheet under the influence of an applied magnetic field in the presence of heat transfer. The magnetic field is induced by a magnetic dipole placed below the stretching sheet. The magnetic field intensity represents the magneto-thermo-mechanical coupling. This allows exclusion of the biofluid that is distant from the sheet at Curie temperature to avoid further magnetization. The unsteadiness of the flow is discernible in the fluid flow properties. The mathematical model of the problem conforms to the principles of Magnetohydrodynamics (MHD) and Ferrohydrodynamics (FHD). In this work, the study is performed on a specific biofluid, human blood. The modified Stokes principle is used to implement the model under the assumption that along with the three thermodynamic variables P, ρ, and T, the Biomagnetic Fluid Dynamics (BFD) fluid behavior can be characterized as a function of magnetization M. To describe the physical problem, a coupled non-linear system of ordinary differential equations subject to appropriate boundary conditions is derived from Navier-Stokes and thermal energy equations by performing non-dimensionalization of the considered variables. To solve these equations, the dsolve routine in the MAPLE software is used. Numerical results for flow profiles and the local skin friction coefficient (Cfx) and the local Nusselt number (Nux) are discussed for different values of unsteadiness parameter (A), biomagnetic interaction parameter (B) and a rational quantity (ϵ). The achieved results are compared with previously published work for steady state flow, and they seem to be in good agreement. It is found that MHD and FHD interaction parameters affect significantly on the velocity, temperature and pressure field. A successful completion will bring interesting results for better understanding of the biomagnetic fluid flow characteristics and can be beneficial to medical and bioengineering applications; particularly for estimating the characteristics of blood flow in stenosed arteries.
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Park, Hee Jin, Hee Young Cho, and Dong Hyun Cha. "The Amniotic Fluid Cell-Free Transcriptome Provides Novel Information about Fetal Development and Placental Cellular Dynamics." International Journal of Molecular Sciences 22, no. 5 (March 5, 2021): 2612. http://dx.doi.org/10.3390/ijms22052612.
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The amniotic fluid (AF) is a complex biofluid that reflects fetal well-being during development. AF con be divided into two fractions, the supernatant and amniocytes. The supernatant contains cell-free components, including placenta-derived microparticles, protein, cell-free fetal DNA, and cell-free fetal RNA from the fetus. Cell-free mRNA (cfRNA) analysis holds a special position among high-throughput analyses, such as transcriptomics, proteomics, and metabolomics, owing to its ease of profiling. The AF cell-free transcriptome differs from the amniocyte transcriptome and alters with the progression of pregnancy and is often associated with the development of various organ systems including the fetal lung, skin, brain, pancreas, adrenal gland, gastrointestinal system, etc. The AF cell-free transcriptome is affected not only by normal physiologies, such as fetal sex, gestational age, and fetal maturity, but also by pathologic mechanisms such as maternal obesity, and genetic syndromes (Down, Edward, Turner, etc.), as well as pregnancy complications (preeclampsia, intrauterine growth restriction, preterm birth, etc.). cfRNA in the amniotic fluid originates from the placenta and fetal organs directly contacting the amniotic fluid as well as from the fetal plasma across the placenta. The AF transcriptome may reflect the fetal and placental development and therefore aid in the monitoring of normal and abnormal development.
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Hyun, S., C. Kleinstreuer, P. W. Longest, and C. Chen. "Particle-Hemodynamics Simulations and Design Options for Surgical Reconstruction of Diseased Carotid Artery Bifurcations." Journal of Biomechanical Engineering 126, no. 2 (April 1, 2004): 188–95. http://dx.doi.org/10.1115/1.1688777.
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Based on the hypothesis that aggravating hemodynamic factors play a key role in the onset of arterial diseases, the methodology of “virtual prototyping” of branching blood vessels was applied to diseased external carotid artery (ECA) segments. The goals were to understand the underlying particle-hemodynamics and to provide various geometric design options for improved surgical reconstruction based on the minimization of critical hemodynamic wall parameters (HWPs). First, a representative carotid artery bifurcation (CAB) and then CABs with stenosed ECAs, i.e., a distally occluded ECA and an ECA stump, were analyzed based on transient three-dimensional blood flow solutions, employing a user-enhanced commercial finite volume code. Specifically, the HWPs, i.e., oscillatory shear index, wall shear stress angle gradient, near-wall residence time of monocytes, and near-wall helicity angle difference were evaluated to compare the merits of each design option, including a reconstructed near-optimal junction which generates the lowest HWP-values. The results provide physical insight to the biofluid dynamics of branching blood vessels and guide vascular surgeons as well as stent manufacturers towards interventions leading to high sustained patency rates.
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Crook, Alexandra A., and Robert Powers. "Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications." Molecules 25, no. 21 (November 4, 2020): 5128. http://dx.doi.org/10.3390/molecules25215128.
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Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids.
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Xie, Liping, Hedele Zeng, Jianjun Sun, and Wei Qian. "Engineering Microneedles for Therapy and Diagnosis: A Survey." Micromachines 11, no. 3 (March 5, 2020): 271. http://dx.doi.org/10.3390/mi11030271.
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Microneedle (MN) technology is a rising star in the point-of-care (POC) field, which has gained increasing attention from scientists and clinics. MN-based POC devices show great potential for detecting various analytes of clinical interests and transdermal drug delivery in a minimally invasive manner owing to MNs’ micro-size sharp tips and ease of use. This review aims to go through the recent achievements in MN-based devices by investigating the selection of materials, fabrication techniques, classification, and application, respectively. We further highlight critical aspects of MN platforms for transdermal biofluids extraction, diagnosis, and drug delivery assisted disease therapy. Moreover, multifunctional MNs for stimulus-responsive drug delivery systems were discussed, which show incredible potential for accurate and efficient disease treatment in dynamic environments for a long period of time. In addition, we also discuss the remaining challenges and emerging trend of MN-based POC devices from the bench to the bedside.
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Lan, Ke, Guoxiang Xie, and Wei Jia. "Towards Polypharmacokinetics: Pharmacokinetics of Multicomponent Drugs and Herbal Medicines Using a Metabolomics Approach." Evidence-Based Complementary and Alternative Medicine 2013 (2013): 1–12. http://dx.doi.org/10.1155/2013/819147.
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Determination of pharmacokinetics (PKs) of multicomponent pharmaceuticals and/or nutraceuticals (polypharmacokinetics, poly-PKs) is difficult due to the vast number of compounds present in natural products, their various concentrations across a wide range, complexity of their interactions, as well as their complex degradation dynamicsin vivo. Metabolomics coupled with multivariate statistical tools that focus on the comprehensive analysis of small molecules in biofluids is a viable approach to address the challenges of poly-PK. This paper discusses recent advances in the characterization of poly-PK and the metabolism of multicomponent xenobiotic agents, such as compound drugs, dietary supplements, and herbal medicines, using metabolomics strategy. We propose a research framework that integrates the dynamic concentration profile of bioavailable xenobiotic molecules that result fromin vivoabsorption and hepatic and gut bacterial metabolism, as well as the human metabolic response profile. This framework will address the bottleneck problem in the pharmacological evaluation of multicomponent pharmaceuticals and nutraceuticals, leading to the direct elucidation of the pharmacological and molecular mechanisms of these compounds.
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Bisson, Mauro, Massimo Bernaschi, Simone Melchionna, Sauro Succi, and Efthimios Kaxiras. "Multiscale Hemodynamics Using GPU Clusters." Communications in Computational Physics 11, no. 1 (January 2012): 48–64. http://dx.doi.org/10.4208/cicp.210910.250311a.
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AbstractThe parallel implementation of MUPHY, a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries, for multi-GPU platforms is presented. Performance tests show excellent results, with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration, all across the range of GPUs. The basic MUPHY scheme combines a hydrokinetic (Lattice Boltzmann) representation of the blood plasma, with a Particle Dynamics treatment of suspended biological bodies, such as red blood cells. To the best of our knowledge, this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries. This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.
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Batool, Syeda Maheen, Tiffaney Hsia, Sirena K. Khanna, Austin S. Gamblin, Yulia Rosenfeld, Dong Gil You, Bob S. Carter, and Leonora Balaj. "Decoding vesicle-based precision oncology in gliomas." Neuro-Oncology Advances 4, Supplement_2 (November 11, 2022): ii53—ii60. http://dx.doi.org/10.1093/noajnl/vdac035.
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Abstract Extracellular vesicles (EVs) represent a valuable tool in liquid biopsy with tremendous clinical potential in diagnosis, prognosis, and therapeutic monitoring of gliomas. Compared to tissue biopsy, EV-based liquid biopsy is a low-cost, minimally invasive method that can provide information on tumor dynamics before, during, and after treatment. Tumor-derived EVs circulating in biofluids carry a complex cargo of molecular biomarkers, including DNA, RNA, and proteins, which can be indicative of tumor growth and progression. Here, we briefly review current commercial and noncommercial methods for the isolation, quantification, and biochemical characterization of plasma EVs from patients with glioma, touching on whole EV analysis, mutation detection techniques, and genomic and proteomic profiling. We review notable advantages and disadvantages of plasma EV isolation and analytical methods, and we conclude with a discussion on clinical translational opportunities and key challenges associated with the future implementation of EV-based liquid biopsy for glioma treatment.
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Singh, Akhileshwar, Krishna Murari Pandey, and Yogesh Singh. "Triggering the Splitting Dynamics of Low-Viscous Fingers through Surface Wettability Inside Bifurcating Channel." Mathematical Problems in Engineering 2022 (February 10, 2022): 1–14. http://dx.doi.org/10.1155/2022/3462844.
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This work presents the splitting dynamics of low-viscous fingers inside the single bifurcating channel through the surface wettability of daughter branches. The propagation of low-viscous fingers inside branching microchannels have importance in many applications, such as microfluidics, biofluid mechanics (pulmonary airway reopening), and biochemical testing. Several numerical simulations are performed where a water finger propagates inside the silicon oil-filled bifurcating channel, and at the bifurcating tip, it splits into two fingers and these fingers propagate into the separate daughter branches. It is noticed that the behaviour of finger splitting at the bifurcating tip depends upon numerous parameters such as surface wettability, capillary number, viscosity ratio, and surface tension. This study aims to trigger the behaviour of finger splitting through the surface wettability of daughter branches θ 1 , θ 2 . Therefore, a series of numerical simulations are performed by considering four different surface wettability configurations of daughter branches, i.e., θ 1 , θ 2 ∈ 78 ° , 78 ° ; 78 ° , 118 ° ; 78 ° , 150 ° ; 150 ° , 150 ° . According to the results obtained from numerical simulations, finger splitting may be categorized into three types based on splitting ratio λ , i.e., symmetrical splitting, nonsymmetrical splitting, and reversal (no) splitting. It is noticed that the surface wettability of both daughter branches is either hydrophilic 78 ° , 78 ° or superhydrophobic 150 ° , 150 ° , providing symmetrical splitting. The surface wettability of one of the daughter branches is hydrophilic and another is hydrophobic 78 ° , 118 ° , providing nonsymmetrical splitting. The surface wettability of one of the daughter branches is hydrophilic and another is superhydrophobic 78 ° , 150 ° , providing reversal splitting. The findings of this investigation may be incorporated in the fields of biochemical testing and occulted pulmonary airways reopening as well as respiratory diseases such as COVID-19.
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González Fernández, Cristina, Jenifer Gómez Pastora, Arantza Basauri, Marcos Fallanza, Eugenio Bringas, Jeffrey J. Chalmers, and Inmaculada Ortiz. "Continuous-Flow Separation of Magnetic Particles from Biofluids: How Does the Microdevice Geometry Determine the Separation Performance?" Sensors 20, no. 11 (May 27, 2020): 3030. http://dx.doi.org/10.3390/s20113030.
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The use of functionalized magnetic particles for the detection or separation of multiple chemicals and biomolecules from biofluids continues to attract significant attention. After their incubation with the targeted substances, the beads can be magnetically recovered to perform analysis or diagnostic tests. Particle recovery with permanent magnets in continuous-flow microdevices has gathered great attention in the last decade due to the multiple advantages of microfluidics. As such, great efforts have been made to determine the magnetic and fluidic conditions for achieving complete particle capture; however, less attention has been paid to the effect of the channel geometry on the system performance, although it is key for designing systems that simultaneously provide high particle recovery and flow rates. Herein, we address the optimization of Y-Y-shaped microchannels, where magnetic beads are separated from blood and collected into a buffer stream by applying an external magnetic field. The influence of several geometrical features (namely cross section shape, thickness, length, and volume) on both bead recovery and system throughput is studied. For that purpose, we employ an experimentally validated Computational Fluid Dynamics (CFD) numerical model that considers the dominant forces acting on the beads during separation. Our results indicate that rectangular, long devices display the best performance as they deliver high particle recovery and high throughput. Thus, this methodology could be applied to the rational design of lab-on-a-chip devices for any magnetically driven purification, enrichment or isolation.
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Stiehm, Michael, Christoph Brandt-Wunderlich, Stefan Siewert, Klaus-Peter Schmitz, Niels Grabow, Leonid Goubergrits, Titus Kühne, Eric K. W. Poon, Andrew Ooi, and Peter Barlis. "Sensitivity analysis of FDA´s benchmark nozzle regarding in vitro imperfections - Do we need asymmetric CFD benchmarks?" Current Directions in Biomedical Engineering 6, no. 3 (September 1, 2020): 78–81. http://dx.doi.org/10.1515/cdbme-2020-3020.
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AbstractModern technologies and methods such as computer simulation, so-called in silico methods, foster the development of medical devices. For accelerating the uptake of computer simulations and to increase credibility and reliability the U.S. Food and Drug Administration organized an inter-laboratory round robin study of a generic nozzle geometry. In preparation of own bench testing experiment using Particle Image Velocimetry, a custom made silicone nozzle was manufactured. By using in silico computational fluid dynamics method the influence of in vitro imperfections, such as inflow variations and geometrical deviations, on the flow field were evaluated. Based on literature the throat Reynolds number was varied Rethroat = 500 ± 50. It could be shown that the flow field errors resulted from variations of inlet conditions can be largely eliminated by normalizing if the Reynolds number is known. Furthermore, a symmetric imperfection of the silicone model within manufacturing tolerance does not affect the flow as much as an asymmetric failure such as an unintended curvature of the nozzle. In brief, we can conclude that geometrical imperfection of the reference experiment should be considered accordingly to in silico modelling. The question arises, if an asymmetric benchmark for biofluid analysis needs to be established. An eccentric nozzle benchmark could be a suitable case and will be further investigated.
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Birknerova, Natalia, Veronika Mancikova, Evan David Paul, Jan Matyasovsky, Pavol Cekan, Vladimir Palicka, and Helena Parova. "Circulating Cell-Free DNA-Based Methylation Pattern in Saliva for Early Diagnosis of Head and Neck Cancer." Cancers 14, no. 19 (October 6, 2022): 4882. http://dx.doi.org/10.3390/cancers14194882.
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Head and neck cancer (HNC) remains one of the leading causes of mortality worldwide due to tumor diagnosis at a late stage, loco-regional aggression, and distant metastases. A standardized diagnostic procedure for HNC is a tissue biopsy that cannot faithfully portray the in-depth tumor dynamics. Therefore, there is an urgent need to develop simple, accurate, and non-invasive methods for cancer detection and follow-up. A saliva-based liquid biopsy allows convenient, non-invasive, and painless collection of high volumes of this biofluid, with the possibility of repetitive sampling, all enabling real-time monitoring of the disease. No approved clinical test for HNC has yet been established. However, epigenetic changes in saliva circulating cell-free DNA (cfDNA) have the potential for a wide range of clinical applications. Therefore, the aim of this review is to present an overview of cfDNA-based methylation patterns in saliva for early detection of HNC, with particular attention to circulating tumor DNA (ctDNA). Due to advancements in isolation and detection technologies, as well as next- and third-generation sequencing, recent data suggest that salivary biomarkers may be successfully applied for early detection of HNC in the future, but large prospective clinical trials are still warranted.
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Andersson, Magnus, and Matts Karlsson. "Model Verification and Error Sensitivity of Turbulence-Related Tensor Characteristics in Pulsatile Blood Flow Simulations." Fluids 6, no. 1 (December 30, 2020): 11. http://dx.doi.org/10.3390/fluids6010011.
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Model verification, validation, and uncertainty quantification are essential procedures to estimate errors within cardiovascular flow modeling, where acceptable confidence levels are needed for clinical reliability. While more turbulent-like studies are frequently observed within the biofluid community, practical modeling guidelines are scarce. Verification procedures determine the agreement between the conceptual model and its numerical solution by comparing for example, discretization and phase-averaging-related errors of specific output parameters. This computational fluid dynamics (CFD) study presents a comprehensive and practical verification approach for pulsatile turbulent-like blood flow predictions by considering the amplitude and shape of the turbulence-related tensor field using anisotropic invariant mapping. These procedures were demonstrated by investigating the Reynolds stress tensor characteristics in a patient-specific aortic coarctation model, focusing on modeling-related errors associated with the spatiotemporal resolution and phase-averaging sampling size. Findings in this work suggest that attention should also be put on reducing phase-averaging related errors, as these could easily outweigh the errors associated with the spatiotemporal resolution when including too few cardiac cycles. Also, substantially more cycles are likely needed than typically reported for these flow regimes to sufficiently converge the phase-instant tensor characteristics. Here, higher degrees of active fluctuating directions, especially of lower amplitudes, appeared to be the most sensitive turbulence characteristics.
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Kiris, C., D. Kwak, S. Rogers, and I.-D. Chang. "Computational Approach for Probing the Flow Through Artificial Heart Devices." Journal of Biomechanical Engineering 119, no. 4 (November 1, 1997): 452–60. http://dx.doi.org/10.1115/1.2798293.
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Computational fluid dynamics (CFD) has become an indispensable part of aerospace research and design. The solution procedure for incompressible Navier–Stokes equations can be used for biofluid mechanics research. The computational approach provides detailed knowledge of the flowfield complementary to that obtained by experimental measurements. This paper illustrates the extension of CFD techniques to artificial heart flow simulation. Unsteady incompressible Navier–Stokes equations written in three-dimensional generalized curvilinear coordinates are solved iteratively at each physical time step until the incompressibility condition is satisfied. The solution method is based on the pseudocompressibility approach. It uses an implicit upwind-differencing scheme together with the Gauss–Seidel line-relaxation method. The efficiency and robustness of the time-accurate formulation of the numerical algorithm are tested by computing the flow through model geometries. A channel flow with a moving indentation is computed and validated by experimental measurements and other numerical solutions. In order to handle the geometric complexity and the moving boundary problems, a zonal method and an overlapped grid embedding scheme are employed, respectively. Steady-state solutions for the flow through a tilting-disk heart valve are compared with experimental measurements. Good agreement is obtained. Aided by experimental data, the flow through an entire Penn State artificial heart model is computed.
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Jonsson, B. F., S. Doney, J. Dunne, and M. L. Bender. "Evaluating Southern Ocean biological production in two ocean biogeochemical models on daily to seasonal time-scales using satellite surface chlorophyll and O<sub>2</sub>/Ar observations." Biogeosciences Discussions 11, no. 6 (June 20, 2014): 9629–65. http://dx.doi.org/10.5194/bgd-11-9629-2014.
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Abstract. We assess the ability of ocean biogeochemical models to represent seasonal structures in biomass and net community production (NCP) in the Southern Ocean. Two models are compared to observations on daily to seasonal time scales in four different sections of the region. We use daily satellite fields of Chlorophyll (Chl) as a proxy for biomass, and in-situ observations of O2 and Ar supersaturation (ΔO2Ar) to estimate NCP. ΔO2Ar is converted to the flux of biologically generated O2 from sea to air ("O2 bioflux"). All data are aggregated to a climatological year with a daily resolution. To account for potential regional differences within the Southern Ocean, we conduct separate analyses of sections south of South Africa, around the Drake Passage, south of Australia, and south of New Zealand. We find that the models simulate the upper range of Chl concentrations well, underestimate spring levels significantly, and show differences in skill between early and late parts of the growing season. While there is a great deal of scatter in the bioflux observations in general, the four sectors each have distinct patterns that the models pick up. Neither model exhibit a significant distinction between the Australian and New Zealand sectors, and between the Drake Passage and African sectors. South of 60° S, the models fail to predict the observed extent of biological O2 undersaturation. We suggest that this shortcoming may be due either to problems with the ecosystem dynamics or problems with the vertical transport of oxygen. Overall, the bioflux observations are in general agreement with the seasonal structures in satellite chlorophyll, suggesting that this seasonality represent changes in carbon biomass and not Chl : C ratios. This agreement is shared in the models and allows us to interpret the seasonal structure of satellite chlorophyll as qualitatively reflecting the integral of biological production over time for the purposes of model assessment.
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Cohen, Roy, Jacquelyn Nelson, Chinatsu Mukai, and Alexander Travis. "Improved monitoring dynamics through use of a tethered enzyme biosensor to detect and quantify neuron-specific enolase activity levels in biofluids." Current Biomarker Findings Volume 7 (September 2017): 1–7. http://dx.doi.org/10.2147/cbf.s135368.
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Belhaj, Mehdi R., Nathan G. Lawler, and Nolan J. Hoffman. "Metabolomics and Lipidomics: Expanding the Molecular Landscape of Exercise Biology." Metabolites 11, no. 3 (March 7, 2021): 151. http://dx.doi.org/10.3390/metabo11030151.
Full textAbstract:
Dynamic changes in circulating and tissue metabolites and lipids occur in response to exercise-induced cellular and whole-body energy demands to maintain metabolic homeostasis. The metabolome and lipidome in a given biological system provides a molecular snapshot of these rapid and complex metabolic perturbations. The application of metabolomics and lipidomics to map the metabolic responses to an acute bout of aerobic/endurance or resistance exercise has dramatically expanded over the past decade thanks to major analytical advancements, with most exercise-related studies to date focused on analyzing human biofluids and tissues. Experimental and analytical considerations, as well as complementary studies using animal model systems, are warranted to help overcome challenges associated with large human interindividual variability and decipher the breadth of molecular mechanisms underlying the metabolic health-promoting effects of exercise. In this review, we provide a guide for exercise researchers regarding analytical techniques and experimental workflows commonly used in metabolomics and lipidomics. Furthermore, we discuss advancements in human and mammalian exercise research utilizing metabolomic and lipidomic approaches in the last decade, as well as highlight key technical considerations and remaining knowledge gaps to continue expanding the molecular landscape of exercise biology.