Annual Review of Biomedical Engineering - Volume 13, 2011

The mammalian olfactory system is able to detect many more odorants than the number of receptors it has by utilizing cross-reactive odorant receptors that generate unique response patterns for each odorant. Mimicking the mammalian system, artificial noses combine cross-reactive sensor arrays with pattern recognition algorithms to create robust odor-discrimination systems. The first artificial nose reported in 1982 utilized a tin-oxide sensor array. Since then, however, a wide range of sensor technologies have been developed and commercialized. This review highlights the most commonly employed sensor types in artificial noses: electrical, gravimetric, and optical sensors. The applications of nose systems are also reviewed, covering areas such as food and beverage quality control, chemical warfare agent detection, and medical diagnostics. A brief discussion of future trends for the technology is also provided.

The definitive treatment for end-stage organ failure is orthotopic transplantation. However, the demand for transplantation far exceeds the number of available donor organs. A promising tissue-engineering/regenerative-medicine approach for functional organ replacement has emerged in recent years. Decellularization of donor organs such as heart, liver, and lung can provide an acellular, naturally occurring three-dimensional biologic scaffold material that can then be seeded with selected cell populations. Preliminary studies in animal models have provided encouraging results for the proof of concept. However, significant challenges for three-dimensional organ engineering approach remain. This manuscript describes the fundamental concepts of whole-organ engineering, including characterization of the extracellular matrix as a scaffold, methods for decellularization of vascular organs, potential cells to reseed such a scaffold, techniques for the recellularization process and important aspects regarding bioreactor design to support this approach. Critical challenges and future directions are also discussed.

High-quality, in vitro screening tools are essential in identifying promising compounds during drug development. Tests with currently used cell-based assays provide an indication of a compound's potential therapeutic benefits to the target tissue, but not to the whole body. Data obtained with animal models often cannot be extrapolated to humans. Multicompartment microfluidic-based devices, particularly those that are physical representations of physiologically based pharmacokinetic (PBPK) models, may contribute to improving the drug development process. These scaled-down devices, termed micro cell culture analogs (μCCAs) or body-on-a-chip devices, can simulate multitissue interactions under near-physiological fluid flow conditions and with realistic tissue-to-tissue size ratios. Because the device can be used with both animal and human cells, it can facilitate cross-species extrapolation. Used in conjunction with PBPK models, the devices permit an estimation of effective concentrations that can be used for studies with animal models or predict the human response. The devices also provide a means for relatively high-throughput screening of drug combinations and, when utilized with a patient's tissue sample, an opportunity for individualized medicine. Here we review efforts made toward the development of microfabricated cell culture systems and give examples that demonstrate their potential use in drug development, such as identifying synergistic drug interactions as well as simulating multiorgan metabolic interactions. In addition to their use in drug development, the devices also can be used to estimate the toxicity of chemicals as occupational hazards and environmental contaminants.

Stem cell technology holds great promises for the cures of devastating diseases, injuries, aging, and even cancers as it is applied in regenerative medicine. Recent breakthroughs in the development of induced pluripotent stem cell techniques and efficient differentiation strategies have generated tremendous enthusiasm and efforts to explore the therapeutic potential of stem cells. Small molecules, which target specific signaling pathways and/or proteins, have been demonstrated to be particularly valuable for manipulating cell fate, state, and function. Such small molecules not only are useful in generating desired cell types in vitro for various applications but also could be further developed as conventional therapeutics to stimulate patients' endogenous cells to repair and regenerate in vivo. Here, we focus on recent progress in the use of small molecules in stem cell biology and regenerative medicine.

In vitro models of traumatic brain injury (TBI) are helping elucidate the pathobiological mechanisms responsible for dysfunction and delayed cell death after mechanical stimulation of the brain. Researchers have identified compounds that have the potential to break the chain of molecular events set in motion by traumatic injury. Ultimately, the utility of in vitro models in identifying novel therapeutics will be determined by how closely the in vitro cascades recapitulate the sequence of cellular events that play out in vivo after TBI. Herein, the major in vitro models are reviewed, and a discussion of the physical injury mechanisms and culture preparations is employed. A comparison between the efficacy of compounds tested in vitro and in vivo is presented as a critical evaluation of the fidelity of in vitro models to the complex pathobiology that is TBI. We conclude that in vitro models were greater than 88% predictive of in vivo results.

Simulating cancer behavior across multiple biological scales in space and time, i.e., multiscale cancer modeling, is increasingly being recognized as a powerful tool to refine hypotheses, focus experiments, and enable more accurate predictions. A growing number of examples illustrate the value of this approach in providing quantitative insights in the initiation, progression, and treatment of cancer. In this review, we introduce the most recent and important multiscale cancer modeling works that have successfully established a mechanistic link between different biological scales. Biophysical, biochemical, and biomechanical factors are considered in these models. We also discuss innovative, cutting-edge modeling methods that are moving predictive multiscale cancer modeling toward clinical application. Furthermore, because the development of multiscale cancer models requires a new level of collaboration among scientists from a variety of fields such as biology, medicine, physics, mathematics, engineering, and computer science, an innovative Web-based infrastructure is needed to support this growing community.

This review presents the state of the art of magnetic resonance imaging (MRI)-guided nanorobotic systems that can perform diagnostic, curative, and reconstructive treatments in the human body at the cellular and subcellular levels in a controllable manner. The concept of an MRI-guided nanorobotic system is based on the use of an MRI scanner to induce the required external driving forces to propel magnetic nanocapsules to a specific target. It is an active targeting mechanism that provides simultaneous propulsion and imaging capabilities, which allow the implementation of real-time feedback control of the targeting process. The architecture of the system comprises four main modules: (a) the nanocapsules, (b) the MRI propulsion module, (c) the MRI tracking module (for image processing), and (d) the controller module. A key concept is the nanocapsule technology, which is based on carriers such as liposomes, polymer micelles, gold nanoparticles, quantum dots, metallic nanoshells, and carbon nanotubes. Descriptions of the significant challenges faced by the MRI-guided nanorobotic system are presented, and promising solutions proposed by the involved research community are discussed. Emphasis is placed on reviewing the limitations imposed by the scaling effects that dominate within the blood vessels and also on reviewing the control algorithms and computational tools that have been developed for real-time propulsion and tracking of the nanocapsules.

Small multicellular model organisms such as the invertebrate nematode C. elegans and the vertebrate zebrafish provide unique opportunities for both basic science and pharmaceutical discovery. In recent years, there have been significant breakthroughs in technologies to manipulate and image these organisms for a variety of purposes ranging from behavioral studies of neuronal circuits to high-throughput screening. Here, we review these advancements with a particular focus on the optically transparent model organisms C. elegans and zebrafish.

This review introduces a novel deformable image registration paradigm that exploits Markov random field formulation and powerful discrete optimization algorithms. We express deformable registration as a minimal cost graph problem, where nodes correspond to the deformation grid, a node's connectivity corresponds to regularization constraints, and labels correspond to 3D deformations. To cope with both iconic and geometric (landmark-based) registration, we introduce two graphical models, one for each subproblem. The two graphs share interconnected variables, leading to a modular, powerful, and flexible formulation that can account for arbitrary image-matching criteria, various local deformation models, and regularization constraints. To cope with the corresponding optimization problem, we adopt two optimization strategies: a computationally efficient one and a tight relaxation alternative. Promising results demonstrate the potential of this approach. Discrete methods are an important new trend in medical image registration, as they provide several improvements over the more traditional continuous methods. This is illustrated with several key examples where the presented framework outperforms existing general-purpose registration methods in terms of both performance and computational complexity. Our methods become of particular interest in applications where computation time is a critical issue, as in intraoperative imaging, or where the huge variation in data demands complex and application-specific matching criteria, as in large-scale multimodal population studies.

The idea of extending the lifetime of our organs is as old as humankind, fueled by major advances in organ transplantation, novel drugs, and medical devices. However, true regeneration of human tissue has become increasingly plausible only in recent years. The human heart has always been a focus of such efforts, given its notorious inability to repair itself following injury or disease. We discuss here the emerging bioengineering approaches to regeneration of heart muscle as a paradigm for regenerative medicine. Our focus is on biologically inspired strategies for heart regeneration, knowledge gained thus far about how to make a “perfect” heart graft, and the challenges that remain to be addressed for tissue-engineered heart regeneration to become a clinical reality. We emphasize the need for interdisciplinary research and training, as recent progress in the field is largely being made at the interfaces between cardiology, stem cell science, and bioengineering.

The ability to clearly observe one's environment in the visible spectrum provides a tremendous evolutionary advantage in most of the world's habitats. The complex optical processing system that has evolved in higher vertebrate animals gathers, focuses, detects, transduces, and interprets incoming visible light. The cornea resides at the front end of this imaging system, where it provides a clear optical aperture, substantial refractive power, and the structural stability required to protect the fragile intraocular components. Nature has resolved these simultaneous design requirements through an exceedingly clever manipulation of common extracellular-matrix structural materials (e.g., collagen and proteoglycans). In this review, we (a) examine the biophysical and optical roles of the cornea, (b) discuss increasingly popular approaches to altering its natural refractive properties with an emphasis on biomechanics, and (c) investigate the fast-rising science of corneal replacement via synthetic biomaterials. We close by considering relevant open problems that would benefit from the increased attention of bioengineers.

The trend toward minimally invasive surgical interventions has created new challenges for visualization during surgical procedures. However, at the same time, the introduction of high-definition digital endoscopy offers the opportunity to apply methods from computer vision to provide visualization enhancements such as anatomic reconstruction, surface registration, motion tracking, and augmented reality. This review provides a perspective on this rapidly evolving field. It first introduces the clinical and technical background necessary for developing vision-based algorithms for interventional applications. It then discusses several examples of clinical interventions where computer vision can be applied, including bronchoscopy, rhinoscopy, transnasal skull-base neurosurgery, upper airway interventions, laparoscopy, robotic-assisted surgery, and Natural Orifice Transluminal Endoscopic Surgery (NOTES). It concludes that the currently reported work is only the beginning. As the demand for minimally invasive procedures rises, computer vision in surgery will continue to advance through close interdisciplinary work between interventionists and engineers.

Diagnostic assays are an important part of health care, both in the clinic and in research laboratories. In addition to improving treatments and clinical outcomes, rapid and reliable diagnostics help track disease epidemiology, curb infectious outbreaks, and further the understanding of chronic illness. Disease markers such as antigens, RNA, and DNA are present at low concentrations in biological samples, such that the majority of diagnostic assays rely on an amplification reaction before detection is possible. Ideally, these amplification reactions would be sensitive, specific, inexpensive, rapid, integrated, and automated. Microfluidic technology currently in development offers many advantages over conventional benchtop reactions that help achieve these goals. The small reaction volumes and energy consumption make reactions cheaper and more efficient in a microfluidic reactor. Additionally, the channel architecture could be designed to perform multiple tests or experimental steps on one integrated, automated platform. This review explores the current research on microfluidic reactors designed to aid diagnostic applications, covering a broad spectrum of amplification techniques and designs.

The development of tools to construct and investigate probabilistic maps of the adult human brain from magnetic resonance imaging (MRI) has led to advances in both basic neuroscience and clinical diagnosis. These tools are increasingly being applied to brain development in adolescence and childhood, and even to neonatal and premature neonatal imaging. Even earlier in development, parallel advances in clinical fetal MRI have led to its growing use as a tool in challenging medical conditions. This has motivated new engineering developments encompassing optimal fast MRI scans and techniques derived from computer vision, the combination of which allows full 3D imaging of the moving fetal brain in utero without sedation. These promise to provide a new and unprecedented window into early human brain growth. This article reviews the developments that have led us to this point, examines the current state of the art in the fields of fast fetal imaging and motion correction, and describes the tools to analyze dynamically changing fetal brain structure. New methods to deal with developmental tissue segmentation and the construction of spatiotemporal atlases are examined, together with techniques to map fetal brain growth patterns.

Control is intrinsic to biological organisms, whose cells are in a constant state of sensing and response to numerous external and self-generated stimuli. Diverse means are used to study the complexity through control-based approaches in these cellular systems, including through chemical and genetic manipulations, input-output methodologies, feedback approaches, and feed-forward approaches. We first discuss what happens in control-based approaches when we are not actively examining or manipulating cells. We then present potential methods to determine what the cell is doing during these times and to reverse-engineer the cellular system. Finally, we discuss how we can control the cell's extracellular and intracellular environments, both to probe the response of the cells using defined experimental engineering-based technologies and to anticipate what might be achieved by applying control-based approaches to affect cellular processes. Much work remains to apply simplified control models and develop new technologies to aid researchers in studying and utilizing cellular and molecular processes.

Over the past two decades, the biomechanical properties of cells have emerged as key players in a broad range of cellular functions, including migration, proliferation, and differentiation. Although much of the attention has focused on the cytoskeletal networks and the cell's microenvironment, relatively little is known about the contribution of the cell nucleus. Here, we present an overview of the structural elements that determine the physical properties of the nucleus and discuss how changes in the expression of nuclear components or mutations in nuclear proteins can not only affect nuclear mechanics but also modulate cytoskeletal organization and diverse cellular functions. These findings illustrate that the nucleus is tightly integrated into the surrounding cellular structure. Consequently, changes in nuclear structure and composition are highly relevant to normal development and physiology and can contribute to many human diseases, such as muscular dystrophy, dilated cardiomyopathy, (premature) aging, and cancer.

Biomolecular motors, in particular motor proteins from the kinesin and myosin families, can be used to explore engineering applications of molecular motors in general. Their outstanding performance enables the experimental study of hybrid systems, where bio-inspired functions such as sensing, actuation, and transport rely on the nanoscale generation of mechanical force. Scaling laws and theoretical studies demonstrate the optimality of biomolecular motor designs and inform the development of synthetic molecular motors.

Cardiovascular devices such as vascular grafts, stents, and heart valves have been widely used to treat cardiovascular diseases. The failure of these devices is usually initiated by the formation of thrombus and neointima on the device surfaces. Antithrombogenic surface modifications have been employed to improve the performance of these devices. In addition to biochemical modifications, tissue engineering approaches hold the promise to fabricate nonthrombogenic biological substitutes for cardiovascular tissues and devices. Endothelial cells (ECs) and stem cells have been used to cover blood-contacting surfaces. Furthermore, for tissue-engineered vascularized tissues and organs, a nonthrombogenic vascular network is essential for mass transfer and the integration of functional tissues and organs into the host upon transplantation. This review discusses the advances in antithrombogenic approaches for surface modifications and cardiovascular tissue engineering.

Cardiovascular disease remains the primary killer worldwide. The heart, essentially an electrically driven mechanical pump, alters its mechanical and electrical properties to compensate for loss of normal mechanical and electrical function. The same adjustment also is performed in the vessels, which constantly adapt their properties to accommodate mechanical and geometrical changes related to aging or disease. Real-time, quantitative assessment of cardiac contractility, conduction, and vascular function before the specialist can visually detect it could be feasible. This new physiologic data could open up interactive therapy regimens that are currently not considered. The eventual goal of this technology is to provide a specific method for estimating the position and severity of contraction defects in cardiac infarcts or angina. This would improve care and outcomes as well as detect stiffness changes and overcome the current global measurement limitations in the progression of vascular disease, at little more cost or risk than that of a clinical ultrasound.

RNA interference (RNAi) technology represents a fundamentally new category of treatments for human disease by addressing targets that are traditionally considered undruggable with existing medicines. The major challenge for RNAi-based therapy is the delivery system that meets human therapeutic needs. Therefore, engineering vectors with good delivery efficiency and safety profile is an intense area of research. Lipid-based nanoparticles for RNAi have yielded successful advances in vivo and to an extent in clinical trials. In this review, we discuss the barriers in developing lipid-based nanoparticles for in vivo RNAi and different strategies to overcome them. Rational designs that address safety concerns and ensure effective delivery will aid the translation of engineered lipid-based nanoparticles toward the clinic in the foreseeable future.