Andreas A. Linninger

University of Illinois at Chicago, Chicago, Illinois, United States

Are you Andreas A. Linninger?

Claim your profile

Publications (156)238.4 Total impact

  • K.M. Yenkie · U.M. Diwekar · A.A. Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Classical reaction kinetics based on deterministic rates laws are not valid for the description of cellular events in which the small number of molecules introduces stochasticity with discrete instead of continuous state transitions. Stochastic models are suitable for simulating transcriptional and translational events inside biological cells, but are impractical for solving inverse problems, which aim to estimate unknown reaction propensities from experimental observations. We introduce a new mathematical framework of Ito stochastic differential equations for the modeling of discrete cellular events and the robust and consistent parameter estimation of cellular dynamics where classical reaction kinetics is invalid. The results supported by case studies on gene expression in B. subtilis cells and viral gene transcription and translation inside non-lytic viral cells demonstrate that the proposed methodology performs as reliable as the gold standard Gillespie algorithm for simulating cellular events. More importantly, the new Ito process framework is ideal for estimating unknown reaction propensities from data as readily as in deterministic parameter estimation by using the novel ‘SPE–simulation free parameter estimation’ approach. Also, the computation time for the stochastic differential equation models is significantly low when compared to discrete event simulations.
    No preview · Article · Jan 2016 · Computers & Chemical Engineering
  • [Show abstract] [Hide abstract]
    ABSTRACT: Purpose: An image filter designed for reconstructing cerebrovascular trees from MR images is described. Current imaging techniques capture major cerebral vessels reliably, but often fail to detect small vessels, whose contrast is suppressed due to limited resolution, slow blood flow rate, and distortions around bifurcations or nonvascular structures. An incomplete view of angioarchitecture limits the information available to physicians. Methods: A novel Hessian-based filter for contrast-enhancement in MR angiography and venography for blood vessel reconstruction without introducing dangling segments is presented. We quantify filter performance with receiver-operating-characteristic and dice-similarity-coefficient analysis. Total extracted vascular length, number-of-segments, volume, surface-to-distance, and positional error are calculated for validation. Results: Reconstruction of cerebrovascular trees from MR images of six volunteers show that the new filter renders more complete representations of subject-specific cerebrovascular networks. Validation with phantom models shows the filter correctly detects blood vessels across all length scales without failing at bifurcations or distorting diameters. Conclusion: The novel filter can potentially improve the diagnosis of cerebrovascular diseases by delivering metrics and anatomy of the vasculature. It also facilitates the automated analysis of large datasets by computing biometrics free of operator subjectivity. The high quality reconstruction enables computational mesh generation for subject-specific hemodynamic simulations. Magn Reson Med, 2016. © 2016 Wiley Periodicals, Inc.
    No preview · Article · Jan 2016 · Magnetic Resonance in Medicine
  • Indu Venugopal · Roxanne Sirhan · Sukhraaj Basati · Andreas A. Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Diagnosis of normal pressure hydrocephalus (NPH) remains challenging due to unambiguous symptoms. Current diagnosis relies mainly on the physician's best judgment making definitive diagnosis both difficult and inaccurate. Therefore, there is a need to develop a sensitive diagnosis technique for NPH. The use of biomarkers has shown great promise in recent disease diagnosis studies. In this paper, a neural cell derived biomarker-myelin basic protein (MBP), is investigated as a biomarker for the accurate diagnosis of NPH. Neural cell derived biomarkers constitute a significant part of the cerebrospinal fluid (CSF) protein composition and are excellent biomarkers for biosensor development. Our biosensor utilizes the interaction between an antibody and an antigen (MBP) for molecular recognition and detection. Information obtained from the interaction is further processed to yield useful quantitative data. The biosensor was constructed using a potentiometric system, containing reference and gold working electrodes. The working electrode was modified using monolayers which could bind to the antibody used for the MBP biomarker detection. The antibody-antigen interaction was monitored and measured using impedance measurements. Sensitivity of MBP detection was found to increase by a factor of up to five upon various molecular modifications of the working electrode. The developed biosensor has been shown to detect MBP levels in the CSF of hydrocephalic rats and is a promising development towards a diagnostic method for NPH.
    No preview · Article · Jan 2016 · Sensor Letters
  • Ying Hsu · Minh Tran · Andreas A. Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Aquaporin-4 water channels play a central role in brain water regulation in neurological disorders. Aquaporin-4 is abundantly expressed at the astroglial endfeet facing the cerebral vasculature and the pial membrane, and both its expression level and subcellular localization significantly influence brain water transport. However, measurements of aquaporin-4 levels in animal models of brain injury often report opposite trends of change at the injury core and the penumbra. Furthermore, aquaporin-4 channels play a beneficial role in brain water clearance in vasogenic edema, but a detrimental role in cytotoxic edema and exacerbate cell swelling. In light of current evidence, we still do not have a complete understanding of the role of aquaporin-4 in brain water transport. In this review, we propose that the regulatory mechanisms of aquaporin-4 at the transcriptional, translational, and post-translational levels jointly regulate water permeability in the short and long time scale after injury. Furthermore, in order to understand why aquaporin-4 channels play opposing roles in cytotoxic and vasogenic edema, we discuss experimental evidence on the dynamically changing osmotic gradients between blood, extracellular space, and the cytosol during the formation of cytotoxic and vasogenic edema. We conclude with an emerging picture of the distinct osmotic environments in cytotoxic and vasogenic edema, and propose that the directions of aquaporin-4-mediated water clearance in these two types of edema are distinct. The difference in water clearance pathways may provide an explanation for the conflicting observations of the roles of aquaporin-4 in edema resolution.
    No preview · Article · Oct 2015 · Croatian Medical Journal
  • [Show abstract] [Hide abstract]
    ABSTRACT: With emerging drug delivery technologies becoming accessible, more options are expected to become available to patients with glioblastoma (GBM) in the near future. It is important for clinicians to be familiar with the underlying mechanisms and limitations of intratumoral drug delivery, and direction of recent research efforts. Tumor-adjacent brain is an extremely complex living matrix that creates challenges with normal tissue intertwining with tumor cells. For convection-enhanced delivery (CED), the role of tissue anisotropy for better predicting the biodistribution of the infusate has recently been studied. Computational predictive methods are now available to better plan CED therapy. Catheter design and placement-in addition to the agent being used-are critical components of any protocol. This paper overviews intratumoral therapies for GBM, highlighting key anatomic and physiologic perspectives, selected agents (especially immunotoxins), and some new developments such as the description of the glymphatic system.
    No preview · Article · Aug 2015 · Journal of Neuro-Oncology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Intramedullary spinal cord tumors have low incidence rates but are associated with difficult treatment options. The majority of patients with these tumors can be initially treated with an attempted resection. Unfortunately, those patients who cannot undergo gross-total resection or have subtotal resection are left with few treatment options, such as radiotherapy and chemotherapy. These adjuvant treatments, however, are associated with the potential for significant adverse side effects and still leave patients with a poor prognosis. To successfully manage these patients and improve both their quality of life and prognosis, novel treatment options must be developed to supplement subtotal resection. New research is underway investigating alternative therapeutic approaches for these patients, including directed, localized drug delivery and nanomedicine techniques. These and other future investigations will hopefully lead to promising new therapies for these devastating diseases.
    Preview · Article · Aug 2015 · Neurosurgical FOCUS
  • Source
    Chih-Yang Hsu · Ben Schneller · Mahsa Ghaffari · Ali Alaraj · Andreas Linninger

    Full-text · Article · Jun 2015
  • Source
    Mahsa Ghaffari · Chih-Yang Hsu · Andreas A Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Unstructured meshes are widely used to delineate the complex geometry of blood vessels in computational fluid dynamics simulation. However, structured parametric meshes can better represent complex geometries with lower grid density thus enabling faster and more precise computations. Current mesh generation methods require user interaction and cannot be used for automatic generation of parametric mesh representations of vascular networks. Our aim is to present a fully automatic algorithm for parametric mesh representation of vascular networks from subject-specific medical images. The methodology requires no user interaction, can create volumetric meshes for non-planar bifurcations and offers full control over the local mesh resolution at the surface and the lumen of the blood vessels. We demonstrate the reliability of our algorithm in terms of mesh quality by evaluating scaled Jacobian and equiangular skewness. The novel method was applied in case studies to reconstruct real image data for the cerebral angioarchitecture. Accurate subject-specific representations of vascular trees are necessary to perform organ-wide hemodynamics for personalized surgical planning of vascular disease.
    Full-text · Conference Paper · May 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Accurate representation of brain anatomical structure is necessary for performing computational hemodynamics simulation to study intracranial diseases. We show in this work an image processing workflow for physiological representations of a subject-specific whole human head reconstruction from medical images. Our workflow provides cerebral vasculatures, CSF space, grey and white matter, skull and scalp. It provides physicians with a complete visualization of the cerebral anatomy and enables computational hemodynamic studies. Magnetic resonance imaging was acquired for one healthy volunteer. Grey and white matter were segmented from T1 images using cortical reconstruction and volumetric segmentation algorithms. Skull and scalp were segmented using morphological operations of T1 images. The cerebrospinal fluid space was segmented using T2 images. MRA and MRV were first processed with in-house vessel enhancement filters before segmentation. To construct computational meshes for hemodynamic simulations, we developed a parametric meshing algorithm to automatically generate surface and volumetric meshes for the vessels. Figure 1 summarizes our results. Panel A exhibits our segmentation for arteries and veins after image filtering. Our vessel filtering suppresses the non-vessel signals enabling automatic vessel segmentation. Panel B demonstrates our parametric computational mesh generation for cerebral vasculature. Panel C shows all the structures we reconstructed from the medical images. Our parametric meshing of the cerebral vasculature allows for hemodynamic simulation for understanding cerebral vascular disease. Additionally, the inclusion of the other intracranial structures allows us to take into account the interactions of vessels with other human head regions. Accurate subject-specific representations of vascular trees are necessary to perform organ-wide hemodynamics for personalized surgical planning of vascular diseases.
    Full-text · Conference Paper · May 2015
  • Kevin M Tangen · Ying Hsu · David C Zhu · Andreas A Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Spinal microstructures are known to substantially affect cerebrospinal fluid patterns, yet their actual impact on flow resistance has not been quantified. Because the length scale of microanatomical aspects is below medical image resolution, their effect on flow is difficult to observe experimentally. Using a computational fluid mechanics approach, we were able to quantify the contribution of micro-anatomical aspects on cerebrospinal fluid (CSF) flow patterns and flow resistance within the entire central nervous system (CNS). Cranial and spinal CSF filled compartments were reconstructed from human imaging data; microscopic trabeculae below the image detection threshold were added artificially. Nerve roots and trabeculae were found to induce regions of microcirculation, whose location, size and vorticity along the spine were characterized. Our CFD simulations based on volumetric flow rates acquired with Cine Phase Contrast MRI in a normal human subject suggest a 2-2.5 fold increase in pressure drop mainly due to arachnoid trabeculae. The timing and phase lag of the CSF pressure and velocity waves along the spinal canal were also computed, and a complete spatio-temporal map encoding CSF volumetric flow rates and pressure was created. Micro-anatomy induced fluid patterns were found responsible for the rapid caudo-cranial spread of an intrathecally administered drug. The speed of rostral drug dispersion is drastically accelerated through pulsatile flow around microanatomy induced vortices. Exploring massive parallelization on a supercomputer, the feasibility of computational drug transport studies was demonstrated. CNS-wide simulations of intrathecal drugs administration can become a practical tool for in silico design, interspecies scaling and optimization of experimental drug trials. Copyright © 2015 Elsevier Ltd. All rights reserved.
    No preview · Article · Mar 2015 · Journal of Biomechanics
  • Eric Lueshen · Indu Venugopal · Tejen Soni · Ali Alaraj · Andreas Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: There is an ongoing struggle to develop efficient drug delivery and targeting methods within the central nervous system. One technique known as intrathecal drug delivery, involves direct drug infusion into the spinal canal and has become standard practice for treating many central nervous system diseases due to reduced systemic toxicity from the drug bypassing the blood-brain barrier. Although intrathecal drug delivery boasts the advantage of reduced systemic toxicity compared to oral and intravenous drug delivery techniques, current intrathecal delivery protocols lack a means of sufficient drug targeting at specific locations of interest within the central nervous system. We previously proposed the method of intrathecal magnetic drug targeting in order to overcome the limited targeting capabilities of standard intrathecal drug delivery protocols, while simultaneously reducing the systemic toxicity as well as the amount of drug required to produce a therapeutic effect. Building off of our previous work, this paper presents the concept of implant-assisted intrathecal magnetic drug targeting. Ferritic stainless steel implants were incorporated within the subarachnoid space of our in vitro human spine model, and the targeting magnet was placed at a physiological distance away from the model and implant to mimic the distance between the epidermis and spinal canal. Computer simulations were performed to optimize implant design for generating high gradient magnetic fields and to study how these fields may aid in therapeutic nanoparticle localization. Experiments aiming to determine the effects of different magnetically-susceptible implants placed within an external magnetic field on the targeting efficiency of gold-coated magnetite nanoparticles were then performed on our in vitro human spine model. Our results indicate that implant-assisted intrathecal magnetic drug targeting is an excellent supplementary technique to further enhance the targeting capabilities of our previously established method of intrathecal magnetic drug targeting.
    No preview · Article · Feb 2015 · Journal of Biomedical Nanotechnology
  • Andreas A. Linninger · Ioannis P. Androulakis

    No preview · Article · Dec 2014 · Computers & Chemical Engineering
  • Martina Heitzig · Andreas A. Linninger · Gürkan Sin · Rafiqul Gani
    [Show abstract] [Hide abstract]
    ABSTRACT: The objective of this work is the development of a generic computer-aided modelling framework to support the development of physiologically-based pharmacokinetic models thereby increasing the efficiency and quality of the modelling process. In particular, the framework systematizes the modelling process by identifying the workflow involved and providing the required methods and tools for model documentation, construction, analysis, identification and discrimination. The application and benefits of the developed framework are demonstrated by a case study related to the whole-body physiologically-based pharmacokinetic modelling of the distribution of the drug cyclosporin A in rats and humans. Four alternative candidate models for rats are derived and discriminated based on experimental data. The model candidate that is best represented by the experimental data is scaled-up to a human being applying physiologically-based scaling laws and identifying model parameters that can be re-fitted by the limited experimental data accessible for humans using sensitivity and identifiability analysis techniques.
    No preview · Article · Dec 2014 · Computers & Chemical Engineering
  • Eric Lueshen · Michael LaRiviere · Bakhtiar Yamini · Andreas Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Convection-enhanced delivery (CED) has emerged as a promising technique for bypassing the blood-brain barrier to deliver therapeutic agents. However, animal studies and clinical trials that utilize the technique suggest that it may require further optimization before it can be safely used in humans. In particular, while volume of distribution in the target tissue can be controlled, the geometrical spread into a desired target region is highly variable from experiment to experiment. In the present paper we have sought to characterize the non-uniform distribution geometry using fluorescent nanoparticles in both a rat model and computer simulations.
    No preview · Article · Dec 2014 · Computers & Chemical Engineering
  • Source
    Joel Buishas · Ian G Gould · Andreas A Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Experimental evidence has cast doubt on the classical model of river-like cerebrospinal fluid (CSF) flow from the choroid plexus to the arachnoid granulations. We propose a novel model of water transport through the parenchyma from the microcirculation as driven by Starling forces. This model investigates the effect of osmotic pressure on water transport between the cerebral vasculature, the extracellular space (ECS), the perivascular space (PVS), and the CSF. A rigorous literature search was conducted focusing on experiments which alter the osmolarity of blood or ventricles and measure the rate of CSF production. Investigations into the effect of osmotic pressure on the volume of ventricles and the flux of ions in the blood, choroid plexus epithelium, and CSF are reviewed. Increasing the osmolarity of the serum via a bolus injection completely inhibits nascent fluid flow production in the ventricles. A continuous injection of a hyperosmolar solution into the ventricles can increase the volume of the ventricle by up to 125%. CSF production is altered by 0.231 μL per mOsm in the ventricle and by 0.835 μL per mOsm in the serum. Water flux from the ECS to the CSF is identified as a key feature of intracranial dynamics. A complete mathematical model with all equations and scenarios is fully described, as well as a guide to constructing a computational model of intracranial water balance dynamics. The model proposed in this article predicts the effects the osmolarity of ECS, blood, and CSF on water flux in the brain, establishing a link between osmotic imbalances and pathological conditions such as hydrocephalus and edema.
    Preview · Article · Oct 2014 · Croatian Medical Journal
  • Sukhraaj Basati · Kevin Tangen · Ying hSU · Hanna Lin · David Frim · Andreas Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Extracranial CSF shunt obstruction is one of the most important problems in hydrocephalus patient management. Despite ongoing research into better shunt design, robust and reliable detection of shunt malfunction remains elusive. The authors present a novel method of correlating degree of tissue ingrowth into ventricular CSF drainage catheters with internal electrical impedance. The impedance based sensor is able to continuously monitor shunt patency using intraluminal electrodes. Prototype obstruction sensors were fabricated for in-vitro analysis of cellular ingrowth into a shunt under static and dynamic flow conditions. Primary astrocyte cell lines and C6 glioma cells were allowed to proliferate up to 7 days within a shunt catheter and the impedance waveform was observed. During cell ingrowth a significant change in the peak-to-peak voltage signal as well as the root-mean-square voltage level was observed, allowing the impedance sensor to potentially anticipate shunt malfunction long before it affects fluid drainage. Finite element modeling was employed to demonstrate that the electrical signal used to monitor tissue ingrowth is contained inside the catheter lumen and does not endanger tissue surrounding the shunt. These results may herald the development of "next generation" shunt technology that allows prediction of malfunction before it affects patient outcome.
    No preview · Article · Jul 2014 · IEEE transactions on bio-medical engineering
  • A Ivanov · C Hsu · A Linninger · S Amin-Hanjani · V Aletich · F Charbel · A Alaraj
    [Show abstract] [Hide abstract]
    ABSTRACT: Improvement in cerebral perfusion post endovascular treatment of vasospasm in patients with aneurysmal subarachnoid haemorrhage (aSAH) is typically assessed by comparison of major vessel diameters on digital subtraction angiography (DSA). In this report we sought to assess relative changes in cerebral blood flow by computational DSA transit time (TT) analysis in patients with cerebral vasospasm before/after endovascular treatment.
    No preview · Article · Jul 2014 · Journal of Neurointerventional Surgery
  • Ian G. Gould · Andreas A. Linninger
    [Show abstract] [Hide abstract]
    ABSTRACT: Objective Oxygen tension in the brain is controlled by the microcirculatory supply of red blood cells, but the effect of non-Newtonian blood flow rheology on tissue oxygenation is not well characterized. This paper assesses different biphasic blood flow models for predicting tissue oxygen tension as a function of microcirulatory hemodynamics.Methods Two existing plasma skimming laws are compared against measured RBC distributions in rat and hamster microcirculatory networks. A novel biphasic blood flow model is introduced. The computational models predict tissue oxygenation in the mesentery, cremaster muscle, and the human secondary cortex.ResultsThis investigation shows deficiencies in prior models, including inconsistent plasma skimming trends and insufficient oxygen perfusion due to the high prevalence (33%) of RBC-free microvessels. Our novel method yields physiologically sound RBC distributions and tissue oxygen tensions within one standard deviation of experimental measurements.ConclusionsA simple, novel biphasic blood flow model is introduced with equal or better predictive power when applied to historic raw data sets. It can overcome limitations of prior models pertaining to trifurcations, anastomoses, and loops. This new plasma skimming law eases the computations of bulk blood flow and hematocrit fields in large microcirculatory networks and converges faster than prior procedures.This article is protected by copyright. All rights reserved.
    No preview · Article · Jul 2014 · Microcirculation (New York, N.Y.: 1994)
  • [Show abstract] [Hide abstract]
    ABSTRACT: OBJECT The use of digital subtraction angiography (DSA) for semiquantitative cerebral blood flow(CBF) assessment is a new technique. The aim of this study was to determine whether patients with aneurysmal subarachnoid hemorrhage (aSAH) with higher Hunt and Hess grades also had higher angiographic contrast transit times (TTs) than patients with lower grades. METHODS A cohort of 30 patients with aSAH and 10 patients without aSAH was included. Relevant clinical information was collected. A method to measure DSA TTs by color-coding reconstructions from DSA contrast-intensity images was applied. Regions of interest (ROIs) were chosen over major cerebral vessels. The estimated TTs included time-to-peak from 0% to 100% (TTP0-100), TTP from 25% to 100% (TTP25-100), and TT from 100% to 10% (TT100-10) contrast intensities. Statistical analysis was used to compare TTs between Group A (Hunt and Hess Grade I-II), Group B (Hunt and Hess Grade III-IV), and the control group. The correlation coefficient was calculated between different ROIs in aSAH groups. RESULTS There was no difference in demographic factors between Group A (n = 10), Group B (n = 20), and the control group (n = 10). There was a strong correlation in all TTs between ROIs in the middle cerebral artery (M1, M2) and anterior cerebral artery (A1, A2). There was a statistically significant difference between Groups A and B in all TT parameters for ROIs. TT100-10 values in the control group were significantly lower than the values in Group B. CONCLUSIONS The DSA TTs showed significant correlation with Hunt and Hess grades. TT delays appear to be independent of increased intracranial pressure and may be an indicator of decreased CBF in patients with a higher Hunt and Hess grade. This method may serve as an indirect technique to assess relative CBF in the angiography suite.
    No preview · Article · Jul 2014 · Journal of Neurointerventional Surgery
  • Source
    Seon Kim · Ying Hsu · Andreas Linninger

    Preview · Article · Mar 2014

Publication Stats

1k Citations
238.40 Total Impact Points

Institutions

  • 1998-2015
    • University of Illinois at Chicago
      • • Department of Bioengineering
      • • Department of Chemical Engineering
      Chicago, Illinois, United States
  • 2005-2007
    • University of Chicago
      Chicago, Illinois, United States
  • 1995-1999
    • Massachusetts Institute of Technology
      • Department of Chemical Engineering
      Cambridge, Massachusetts, United States