Biomedical Engineering and Bioengineering Commons^™

Toward Measuring Network Aesthetics Based On Symmetry, Zengqiang Chen, Matthias Dehmer, Frank Emmert-Streib, Abbe Mowshowitz, Yongtang Shi

Publications and Research

In this exploratory paper, we discuss quantitative graph-theoretical measures of network aesthetics. Related work in this area has typically focused on geometrical features (e.g., line crossings or edge bendiness) of drawings or visual representations of graphs which purportedly affect an observer’s perception. Here we take a very different approach, abandoning reliance on geometrical properties, and apply information-theoretic measures to abstract graphs and networks directly (rather than to their visual representaions) as a means of capturing classical appreciation of structural symmetry. Examples are used solely to motivate the approach to measurement, and to elucidate our symmetry-based mathematical theory of network aesthetics.

A Drosophila Model To Examine Collective Migration During Retinogenesis, Caroline Pena, Stephanie Zhang, Mildred Kamara, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

Retinal dysfunction is often caused by aberrant neural cell migration during development. In this study, we observed the migration of neural cells of the Drosophila melanogaster after marking cells of the 3rd instar larvae with the GAL4-UAS expression system when exposed to a concentration gradient of FGF-8 through the use of a microfluidic device. The glial and neuronal cell ratio in the developing brain was determined through immunofluorescent staining and observation. In future studies, a microfluidic device that mimics the developing Drosophila brain and retina will be designed in order to better understand the biological factors that affect the migration …

Collective Behaviour In Video Viewing: A Thermodynamic Analysis Of Gaze Position, Kate Burleson-Lesser, Flaviano Morone, Paul Deguzman, Lucas C. Parra, Hernan Makse

Publications and Research

Videos and commercials produced for large audiences can elicit mixed opinions. We wondered whether this diversity is also reflected in the way individuals watch the videos. To answer this question, we presented 65 commercials with high production value to 25 individuals while recording their eye movements, and asked them to provide preference ratings for each video. We find that gaze positions for the most popular videos are highly correlated. To explain the correlations of eye movements, we model them as ªinteractionsº between individuals. A thermodynamic analysis of these interactions shows that they approach a ªcritical º point such that any …

Influence Of Fibroblasts On Metastatic Cancer Cell Drug Resistance In A 3d Microfluidic Cell Array, Elizabeth C. Benoy

Dissertations and Theses

Modeling an accurate depiction of the tumor microenvironment, (TME), is essential to observe the effect external factors might have on the tumor in vivo. In cancer therapy specifically, the outcomes of clinical treatments are heavily dependent on drug testing methods despite the cytotoxic effects these methods might have on the patient. Our lab has previously developed a three layered microfluidic cell array (3D μFCA) to reconstruct the relevantly spatial configuration of tumor and microvasculature found in vivo in order to develop a more efficient tool of high throughput drug discovery and screening. In this study, we optimized this device to …

Design Development And Performance Study Of A Novel Assistive Device For Mobility Of Toddlers And Children With Visual Impairments, Joowon Jun

Dissertations and Theses

Being able to see allows mankind tremendous access to learn about the world, and because so much learning comes visually, children with visual impairments are delayed in developing range of skills: learning own languages, doing activities, socializing with peers, and etc. While children with vision can do virtually all the activities and tasks for granted, children with visual impairment require different types of tools or materials to do same tasks most of time. Amongst all the disadvantages that children with visual impairment have, one of the most critical disadvantageous area that visual impairment brings to toddler is learning to walk. …

Automatic Optimum Atlas Selection For Multi-Atlas Image Segmentation Using Joint Label Fusion, Kofi Agyeman

Dissertations and Theses

Multi-atlas image segmentation using label fusion is one of the most accurate state of the art image segmentation techniques available for biomedical imaging applications. Motivated to achieve higher image segmentation accuracy, reduce computational costs and a continuously increasing atlas data size, a robust framework for optimum selection of atlases for label fusion is vital. Although believed not to be critical for weighted label fusion techniques by some works (Sabuncu, M. R. et al., 2010, [1]), others have shown that appropriate atlas selection has several merits and can improve multi-atlas image segmentation accuracy (Aljabar et al., 2009, [2], Van de Velde …

Multi-Scale Assessment Of Bone Mechanics And The Mineral Phase Of Intramuscular Bone Of Atlantic Herring Fish, Svetlana Zeveleva

Dissertations and Theses

Bone tissue is a complex composite structure made up of a soft organic phase consisting of collagen I and non-collagenous proteins, and a hard inorganic phase consisting of mineral nanoplatelets. Given it’s compositional properties, bone is a unique stiff, tough, and strong biomaterial, making it exceptionally difficult to synthesize ex vivo. While the complete hierarchical structure may change with age and population, the basic building block components of mineralized collagen fibrils, are preserved. This study uses a model of intramuscular bone of the Atlantic herring fish, which present a simple structure, and no process of remodeling.

A multi-scale approach …

Interaction Between The Stress Phase Angle (Spa) And The Oscillatory Shear Index (Osi) Affects Endothelial Cell Gene Expression, Ronny Amaya, Limary M. Cancel, John M. Tarbell

Publications and Research

Hemodynamic forces play an important role in the non-uniform distribution of atherosclerotic lesions. Endothelial cells are exposed simultaneously to fluid wall shear stress (WSS) and solid circumferential stress (CS). Due to variations in impedance (global factors) and geometric complexities (local factors) in the arterial circulation a time lag arises between these two forces that can be characterized by the temporal phase angle between CS and WSS (stress phase angle±SPA). Asynchronous flows (SPA close to -180Ê) that are most prominent in coronary arteries have been associated with localization of atherosclerosis. Reversing oscillatory flows characterized by an oscillatory shear index (OSI) that …

The Effects Of Compensatory Auditory Stimulation And High-Definition Transcranial Direct Current Stimulation (Hd-Tdcs) On Tinnitus Perception - A Randomized Pilot Study, Simon Henin, Dovid Fein, Eric Smouha, Lucas C. Parra

Publications and Research

Background Tinnitus correlates with elevated hearing thresholds and reduced cochlear compression. We hypothesized that reduced peripheral input leads to elevated neuronal gain resulting in the perception of a phantom sound. Objective The purpose of this pilot study was to test whether compensating for this peripheral deficit could reduce the tinnitus percept acutely using customized auditory stimulation. To further enhance the effects of auditory stimulation, this intervention was paired with high-definition transcranial direct current stimulation (HD-tDCS).

Methods A randomized sham-controlled, single blind study was conducted in a clinical setting on adult participants with chronic tinnitus (n = 14). Compensatory auditory stimulation …

Electro-Chemotactic Fields Induce Cooperative Movement Of Cns Cells, Shawn Mishra, Stephen Redenti, Maribel Vazquez

Publications and Research

Vision loss in adults with Age Related Macular Degeneration (AMD) is attributed to damage of retinal photoreceptor cells that initiate vision by absorbing light. Mouse models have suggested that transplantation of precursor cells may be a novel approach to restore vision. This project uses a combination of electrotactic and chemotactic stimuli to promote and guide CNS cell migration within a microdevice model.

Mechanotransduction Modulates The Effect Of Mechanical Forces (Fluid Shear Stress And Cyclic Strain) On Embryonic Stem Cell Differentiation Toward Vascular Endothelial Cells, Maria Nikmanesh

Dissertations, Theses, and Capstone Projects

The isolation of human ES cells (hES) in 1998 remarkably elevated the interest in the cell therapy capability of ES cells and moved this concept one step closer to reality. Embryonic stem cells with their potential for both self-renewal and directed differentiation have received increasing attention in applications in tissue engineering and repair, cell therapy, and regenerative medicine.

The differentiation of embryonic stem cells into desired lineages depends on the chemical environment of the “niche”, and for certain lineages such as the vascular lineage that must function in a mechanical environment, the timely imposition of mechanical forces is critical. In …

Engineering And Perception, Maribel Vazquez

Open Educational Resources

An introductory seminar to High School and Freshman-Level Undergraduates that describes how several Biomedical Engineering innovations have been motivated by our senses of sight, sound, smell, taste and touch.

Microfluidic Devices In Biotechnology, Maribel Vazquez

Open Educational Resources

This lecture/laboratory course focuses on the fundamentals of modern microfluidic devices with applications to biomedical measurements. Students will review fundamental properties of microfluidic systems including the effects of viscous flow, heat transfer, and electromagnetic phenomena on biological systems. Multiple laboratory modules will expose students to photolithographic and surface treatment techniques required for device development. An end of term project will require students to analyze designs of upcoming biomedical inventions and present their critiques via written report and oral presentation.

Cuny Summer Stem Institute: Experimental Research In Engineering For High School Students, Maribel Vazquez

Open Educational Resources

Summer HS students were engaged in hands-on experimental research in engineering laboratories in mentorship with CCNY Engineering Undergraduate Researchers. This course was part of the Summer STEM Institute directed by Dr. Joe Barba and Mr. Otto Marte.

Kcnq Channel Openers Reverse Depressive Symptoms Via An Active Resilience Mechanism, Allyson K. Friedman, Barbara Juarez, Stacy M. Ku, Hongxing Zhang, Rhodora C. Calizo, Jessica J. Walsh, Depish Chaudhury, Song Zhang, Angel Hawkins, David M. Dietz, James W. Murrogh, Maria Ribadeneira, Erik H. Wong, Rachael L. Neve, Ming-Hu Han

Publications and Research

Less than half of patients suffering from major depressive disorder, a leading cause of disability worldwide, achieve remission with current antidepressants, making it imperative to develop more effective treatment. A new therapeutic direction is emerging from the increased understanding of natural resilience as an active stress-coping process. It is known that potassium (Kþ) channels in the ventral tegmental area (VTA) are an active mediator of resilience. However, no druggable targets have been identified to potentiate active resilience mechanisms. In the chronic social defeat stress model of depression, we report that KCNQ-type Kþ channel openers, including FDA-approved drug retigabine (ezogabine), show …

Mesenchymal Stem Cell Fate: Applying Biomaterials For Control Of Stem Cell Behavior, Hilary J. Anderson, Jugal Kishore Sahoo, Rein V. Ulijn, Matthew J. Dalby

Publications and Research

The materials pipeline for biomaterials and tissue engineering applications is under continuous development. Specifically, there is great interest in the use of designed materials in the stem cell arena as materials can be used to manipulate the cells providing control of behavior. This is important as the ability to “engineer” complexity and subsequent in vitro growth of tissues and organs is a key objective for tissue engineers. This review will describe the nature of the materials strategies, both static and dynamic, and their influence specifically on mesenchymal stem cell fate.

P2x7r-Panx1 Complex Impairs Bone Mechanosignaling Under High Glucose Levels Associated With Type-1 Diabetes, Zeynep Seref-Ferlengez, Stephanie Maung, Mitchell B. Schaffler, David C. Spray, Sylvia O. Suadicani, Mia M. Thi

Publications and Research

Type 1 diabetes (T1D) causes a range of skeletal problems, including reduced bone density and increased risk for bone fractures. However, mechanisms underlying skeletal complications in diabetes are still not well understood.We hypothesize that high glucose levels in T1D alters expression and function of purinergic receptors (P2Rs) and pannexin 1 (Panx1) channels, and thereby impairs ATP signaling that is essential for proper bone response to mechanical loading and maintenance of skeletal integrity. We first established a key role for P2X7 receptor-Panx1 in osteocyte mechanosignaling by showing that these proteins are co-expressed to provide a major pathway for flow-induced ATP release. …

Controlled Microfluidics To Examine Growth-Factor Induced Migration Of Neural Progenitors In The Drosophila Visual System, Cade Beck, Tanya Singh, Angela Farooqi, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

BACKGROUND:

The developing visual system in Drosophila melanogaster provides an excellent model with which to examine the effects of changing microenvironments on neural cell migration via microfluidics, because the combined experimental system enables direct genetic manipulation, in vivo observation, and in vitro imaging of cells, post-embryo. Exogenous signaling from ligands such as fibroblast growth factor (FGF) is well-known to control glia differentiation, cell migration, and axonal wrapping central to vision.

NEW METHOD:

The current study employs a microfluidic device to examine how controlled concentration gradient fields of FGF are able to regulate the migration of vision-critical glia cells with and …

Predicted Molecular Signaling Guiding Photoreceptor Cell Migration Following Transplantation Into Damaged Retina, Uchenna John Unachukwu, Alice Warren, Ze Li, Shawn Mishra, Jing Zhou, Moira Sauane, Hyungsik Lim, Maribel Vazquez, Stephen Redenti

Publications and Research

To replace photoreceptors lost to disease or trauma and restore vision, laboratories around the world are investigating photoreceptor replacement strategies using subretinal transplantation of photoreceptor precursor cells (PPCs) and retinal progenitor cells (RPCs). Significant obstacles to advancement of photoreceptor cell-replacement include low migration rates of transplanted cells into host retina and an absence of data describing chemotactic signaling guiding migration of transplanted cells in the damaged retinal microenvironment. To elucidate chemotactic signaling guiding transplanted cell migration, bioinformatics modeling of PPC transplantation into light-damaged retina was performed. The bioinformatics modeling analyzed whole-genome expression data and matched PPC chemotactic cell-surface receptors to …

Genesis And Growth Of Extracellular Vesicle-Derived Microcalcification In Atherosclerotic Plaques, Joshua D. Hutcheson, Claudia Goettsch, Sergio Bertazzo, Natalia Maldonado, Jessica L. Ruiz, Wilson Goh, Katsumi Yabusaki, Tyler Faits, Carlijn Bouten, Gregory Franck, Thibaut Quillard, Peter Libby, Masanori Aikawa, Sheldon Weinbaum, Elena Aikawa

Publications and Research

Clinical evidence links arterial calcification and cardiovascular risk. Finite-element modelling of the stress distribution within atherosclerotic plaques has suggested that subcellular microcalcifications in the fibrous cap may promote material failure of the plaque, but that large calcifications can stabilize it. Yet the physicochemical mechanisms underlying such mineral formation and growth in atheromata remain unknown. Here, by using three-dimensional collagen hydrogels that mimic structural features of the atherosclerotic fibrous cap, and high-resolution microscopic and spectroscopic analyses of both the hydrogels and of calcified human plaques, we demonstrate that calcific mineral formation and maturation results from a series of events involving the …

Introduction To Biomedical Engineering, Maribel Vazquez

Open Educational Resources

An overview of the field of biomedical engineering designed to acquaint the students with its interdisciplinary nature; research areas presented by the biomedical engineering faculty.

Effect Of Temporal Onset Of Mechanical Loading On Tendon To Bone Healing, Determined With A Novel In-Vivo Device, Mark E. Stasiak

Dissertations, Theses, and Capstone Projects

Background: Exposure to tensile loading has been shown to maintain tendon/ligament homeostasis, with the tensile modulus of the tissue increasing in response to greater loading frequency, and even decreasing in the absence of load. However after injury or surgical repair the effect of tensile load is controversial, with many studies implicating mechanical loading with impaired healing. It is currently unknown when the tensile loading imparted during rehabilitation exercise, can be safely reintroduced after surgical tendon repair or ligament reconstruction, and at what time point it can most benefit the remodeling process. To investigate the effect of tensile loading protocols on …

In Vitro Formation Of Neuroclusters In Microfluidic Devices And Cell Migration As A Function Of Stromal-Derived Growth Factor 1 Gradients, Sean Mccutcheon, Uchenna Unachukwu, Ankush Thakur, Robert Majeska, Stephen Redenti, Maribel Vazquez

Publications and Research

Central nervous system (CNS) cells cultured in vitro as neuroclusters are useful models of tissue regeneration and disease progression. However, the role of cluster formation and collective migration of these neuroclusters to external stimuli has been largely unstudied in vitro. Here, 3 distinct CNS cell types, medulloblastoma (MB), medulloblastoma-derived glial progenitor cells (MGPC), and retinal progenitor cells (RPC), were examined with respect to cluster formation and migration in response to Stromal-Derived Growth Factor (SDF-1). A microfluidic platform was used to distinguish collective migration of neuroclusters from that of individual cells in response to controlled concentration profiles of SDF-1. Cell …

Direct Current Stimulation Modulates Ltp And Ltd: Activity-Dependence And Dendritic Effects, Gregory Kronberg

Dissertations and Theses

Transcranial direct current stimulation (tDCS) has been reported to improve various forms of learning in humans. Stimulation is often applied during training, producing lasting enhancements that are specific to the learned task. These learning effects are thought be mediated by altered synaptic plasticity. However, the effects of DCS during the induction of endogenous synaptic plasticity remain largely unexplored. To model endogenous plasticity I induced long-term potentiation (LTP) and depression (LTD) at Schaffer collateral synapses in CA1 of rat hippocampal slices. When induction was paired with concurrent DCS, the resulting plasticity was biased towards potentiation, such that LTP was enhanced and …

Ultrahigh Field Magnetic Resonance Imaging – Technical Development And Translational Applications, Judy Alper

Dissertations and Theses

Magnetic resonance imaging (MRI) may be used to provide detailed images of the human body with excellent soft tissue contrast. Alongside its current widespread clinical applications for diagnosis and treatment, MRI allows researchers to measure structure and function of different tissue types in order to advance our understanding of human biology and enable new medical applications of MRI. In particular, diseases affecting nerves and vessels, such as trigeminal neuralgia, with uncertain etiology can be studied using multiple MRI modalities so that treatment planning can we more effective and patient outcomes can be improved. Ultrahigh field MRI scanners, such as those …

A Model Microfluidics-Based System For The Human And Mouse Retina., Shawn Mishra, Ankush Thakur, Stephen Redenti, Maribel Vazquez

Publications and Research

The application of microfluidics technologies to the study of retinal function and response holds great promise for development of new and improved treatments for patients with degenerative retinal diseases. Restoration of vision via retinal transplantation therapy has been severely limited by the low numbers of motile cells observed post transplantation. Using modern soft lithographic techniques, we have developed the μRetina, a novel and convenient biomimetic microfluidics device capable of examing the migratory behavior of retinal lineage cells within biomimetic geometries of the human and mouse retina. Coupled computer simulations and experimental validations were used to characterize and confirm the formation …

Egf As A New Therapeutic Target For Medulloblastoma Metastasis, Jennifer Rico-Varela, Tanya Singh, Sean Mccutcheon, Maribel Vazquez

Publications and Research

Medulloblastoma (MB) is a malignant pediatric brain tumor known for its aggressive metastatic potential. Despite the well-documented migration of MB cells to other parts of the brain and spinal column, MB chemotaxis is poorly understood. Herein, we examined the in vitro migratory and cellular responses of MB-derived cells to external signaling of Epidermal Growth Factor (EGF), hepatocyte growth factor (HGF), platelet-derived growth factor (PDGF-BB), and the stromal cellderived factors 1-alpha (SDF-1). Experiments utilized transwell assays and immunocytochemistry to identify receptor activation in MB migration, and used a microfluidic platform to examine directionality, trajectory, and gradient-dependence of motile cells. Data illustrates …

Carboxymethylcellulose Hydrogels Support Cns-Derived Tumor Cell Chemotactic Migration, Tanya Singh, Chandrasekhar Kothapalli, Devika Verma, Steven Nicoll, Maribel Vazquez

Publications and Research

The local microenvironment plays an important role in maintaining the dynamics of the extracellular matrix (ECM) and the cell-ECM relationship. ECM is a complex network of molecules with distinct mechanical and biochemical characteristics. When the mechanisms that are in place to maintain ECM homeostasis are deregulated, most likely, this is the onset of cancer. The ECM becomes highly disorganized and the cell-matrix relationship changes, thus promoting alternations in cell mechanisms and metastasis. Medulloblastoma (MB) is one of the most common, malignant pediatric brain tumors in the United States. In order to gain a better understanding between the cell-ECM relationship and …

Monitoring The Progression Of Spontaneous Articular Cartilage Healing With Infrared Spectroscopy, Megan P. O'Brien, Madhuri Penmatsa, Uday Palukuru, Paul West, Xu Yang, Mathias P. G. Bostrom, Theresa Freeman, Nancy Pleshko

Publications and Research

Objective. Evaluation of early compositional changes in healing articular cartilage is critical for understanding tissue repair and for therapeutic decision-making. Fourier transform infrared imaging spectroscopy (FT-IRIS) can be used to assess the molecular composition of harvested repair tissue. Furthermore, use of an infrared fiber-optic probe (IFOP) has the potential for translation to a clinical setting to provide molecular information in situ. In the current study, we determined the feasibility of IFOP assessment of cartilage repair tissue in a rabbit model, and assessed correlations with gold-standard histology.

Design. Bilateral osteochondral defects were generated in mature white New Zealand rabbits, and …

Contact Analysis For Coupling Of Plates And Screws In Fracture Fixation Of Cortical Bone, Gaffar Gailani, Rachid Moumni, Malek Brahimi

Publications and Research

Internal fixation is a common treatment for bone fracture. Bone fracture occurs due to different reasons such as motor vehicle accidents, falling,…etc. The treatment is performed by fixing plate and screws to the fracture site. Lack of stability of the implants (plates and screws) may lead to delay in healing or failure of treatment. Micro-motion between the implant and the bone may cause formation of fibrous tissue around the screw which will lead to implant loosening. On the other hands, firm fixing of the conventional implants (Dynamic Compression Plates) may lead to delay resorption and delay in healing. Recently, Locked …