Computational fluid dynamics modeling of Bacillus anthracis spore deposition in rabbit and human respiratory airways.

Three-dimensional computational fluid dynamics and Lagrangian particle deposition models were developed to compare the deposition of aerosolized Bacillus anthracis spores in the respiratory airways of a human with that of the rabbit, a species commonly used in the study of anthrax disease. The respiratory airway geometries for each species were derived respectively from computed tomography (CT) and µCT images. Both models encompassed airways that extended from the external nose to the lung with a total of 272 outlets in the human model and 2878 outlets in the rabbit model. All simulations of spore deposition were conducted under transient, inhalation-exhalation breathing conditions using average species-specific minute volumes. Two different exposure scenarios were modeled in the rabbit based upon experimental inhalation studies. For comparison, human simulations were conducted at the highest exposure concentration used during the rabbit experimental exposures. Results demonstrated that regional spore deposition patterns were sensitive to airway geometry and ventilation profiles. Due to the complex airway geometries in the rabbit nose, higher spore deposition efficiency was predicted in the nasal sinus compared to the human at the same air concentration of anthrax spores. In contrast, higher spore deposition was predicted in the lower conducting airways of the human compared to the rabbit lung due to differences in airway branching pattern. This information can be used to refine published and ongoing biokinetic models of inhalation anthrax spore exposures, which currently estimate deposited spore concentrations based solely upon exposure concentrations and inhaled doses that do not factor in species-specific anatomy and physiology for deposition.

A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling.

In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFD) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the Modified Newton's Method with nonlinear Krylov accelerator developed by Carlson and Miller [1, 2, 3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a "pressure-drop" residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD-ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural pressure applied to the multiple sets of ODEs. In both the simplified geometry and in the imaging-based geometry, the performance of the method was comparable to that of monolithic schemes, in most cases requiring only a single CFD evaluation per time step. Thus, this new accelerator allows us to begin combining pulmonary CFD models with lower-dimensional models of pulmonary mechanics with little computational overhead. Moreover, because the CFD and lower-dimensional models are totally separate, this framework affords great flexibility in terms of the type and breadth of the adopted lower-dimensional model, allowing the biomedical researcher to appropriately focus on model design. Research funded by the National Heart and Blood Institute Award 1RO1HL073598.

A semiautomated approach for artefact removal in serial tissue cryosections.

Thinly sliced serial tissue sections of an organ can be imaged using optical microscopy at a resolution detailing individual cells. When the tissue sections are first subjected to in situ hybridization or immunohistochemistry, these data sets can be analysed for changes in gene expression and gene products. Such spatial information is important for understanding the functional effects of experimental or environmental challenges to the organism. However, a critical step in analysing these data sets is mitigating artefacts that result from the preparation of the tissue sections. In this paper, we describe an automated method with manual validation tools that together enable detecting and addressing artefacts including dust particles and air bubbles.

An Anisotropic Fluid-Solid Model of the Mouse Heart.

A critical challenge in biomechanical simulations is the spatial discretization of complex fluid-solid geometries created from imaging. This is especially important when dealing with Lagrangian interfaces, as there must be at a minimum both geometric and topological compatibility between fluid and solid phases, with exact matching of the interfacial nodes being highly desirable. We have developed a solution to this problem and applied the approach to the creation of a 3D fluid-solid mesh of the mouse heart. First, a 50 micron isotropic MRI dataset of a perfusion-fixed mouse heart was segmented into blood, tissue, and background using a customized multimaterial connected fuzzy thresholding algorithm. Then, a multimaterial marching cubes algorithm was applied to produce two compatible isosurfaces, one for the blood-tissue boundary and one for the tissue-background boundary. A multimaterial smoothing algorithm that rigorously conserves volume for each phase simultaneously smoothed the isosurfaces. Next we applied novel automated meshing algorithms to generate anisotropic hybrid meshes with the number of layers and the desired element anisotropy for each material as the only input parameters. As the meshes are scale-invariant within a material and include boundary layer prisms, fluid-structure interaction computations would have a relative error equilibrated over the entire mesh. The resulting model is highly detailed mesh representation of the mouse heart, including features such as chordae and coronary vasculature, that is also maximally efficient to produce the best simulation results for the computational resources available.

A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas.

Acquiring information about the expression of a gene in different cell populations and tissues can provide key insight into the function of the gene. A high-throughput in situ hybridization (ISH) method was recently developed for rapid and reproducible acquisition of gene expression patterns in serial tissue sections at cellular resolution. Characterizing and analysing expression patterns on thousands of sections requires efficient methods for locating cells and estimating the level of expression in each cell. Such cellular quantification is an essential step in both annotating and quantitatively comparing high-throughput ISH results. Here we describe a novel automated and efficient methodology for performing this quantification on postnatal mouse brain.

Automated characterization of gene expression patterns with an atlas of the mouse brain.

A spatio-temporal map of gene activity in the brain would be an important contribution to the understanding of brain development, disease, and function. Such a resource is now possible using high-throughput in situ hybridization, a method for transcriptome-wide acquisition of cellular resolution gene expression patterns in serial tissue sections. However, querying an enormous quantity of image data requires computational methods for describing and organizing gene expression patterns in a consistent manner. In addressing this, we have developed procedures for automated annotation of gene expression patterns in the postnatal mouse brain.

Tumor necrosis factor alpha induces BID cleavage and bypasses antiapoptotic signals in prostate cancer LNCaP cells.

Survival of cancer cells in response to therapy, immune response, or metastasis depends on interactions between pro- and antiapoptotic signals. Two major proapoptotic pathways have been described: (a) a death receptor pathway; and (b) a mitochondrial pathway. We reported previously that Akt and the epidermal growth factor (EGF) receptor send separate, redundant survival signals that act to inhibit the mitochondrial proapoptotic pathway in prostate cancer LNCaP cells. However, it was unclear at what level the pro- and antiapoptotic signals interact in these cells, and it was also unclear whether these signals would inhibit the death receptor pathway. We found that EGF can protect LNCaP cells from apoptosis induced by LY294002 but not from tumor necrosis factor a (TNF-alpha)-induced apoptosis. Furthermore, TNF-alpha induced apoptosis under conditions in which Akt was active. Treatment with TNF-alpha resulted in activation of caspase 8 and cleavage of BID, which in turn induced cytochrome c release and caspase 9-dependent activation of effector caspases. Thus, proapoptotic signals induced by both TNF-alpha and LY294002 converge on mitochondria and trigger cytochrome c release. Because EGF can inhibit cytochrome c release induced by LY294002 but not cytochrome c release induced by TNF-alpha, we suggest that the EGF survival mechanism operates on the mitochondrial pathway at a site upstream of cytochrome c release. The ability of TNF-alpha to bypass survival signals from activated EGF receptor and Akt in prostate cancer cells makes death receptor signaling a promising avenue for therapeutic intervention.

Antiapoptotic signaling in LNCaP prostate cancer cells: a survival signaling pathway independent of phosphatidylinositol 3'-kinase and Akt/protein kinase B.

Constitutive activation of the phosphatidylinositol 3'-kinase (PI3 kinase)-Akt/protein kinase B (PKB) "survival signaling" pathway is a likely mechanism by which many cancers become refractory to cytotoxic therapy. In LNCaP prostate cancer cells, the PTEN phosphoinositide phosphatase is inactivated, leading to constitutive activation of Akt/PKB and resistance to apoptosis. However, apoptosis and inactivation of Akt/PKB can be induced in these cells by treatment with PI3 kinase inhibitors. Surprisingly, androgen, epidermal growth factor, or serum can protect these cells from apoptosis, even in the presence of PI3 kinase inhibitors and without activation of Akt/PKB, indicating the activity of a novel, Akt/PKB-independent survival pathway. This pathway blocks apoptosis at a level prior to caspase 3 activation and release of cytochrome c from mitochondria.

Special protocols for patients with trauma.

The ED care of the patient with trauma can be facilitated by the establishment of protocols to ensure prompt access to lifesaving and limb-saving procedures and care. Specific protocols for patients with trauma support assessment and treatment in both the emergency and long-term phases of care.

Anatomy of the accident scene: a prospective study of injury and mortality.

This study of the accident scene focuses on the effects of vehicular deformity and restraint devices on occupant injury. In 500 patients evaluated in a Level I trauma center, seatbelts significantly reduced the likelihood of individuals' requiring the trauma center (P less than 0.0001). Seatbelts also significantly reduced the mortality rate of those who were transported to the trauma center (P less than 0.04). Dashboard intrusion correlated with pelvic (P less than 0.001) and femur (P less than 0.03) fractures, closed head injuries (P less than 0.001), and intraabdominal injuries (P less than 0.02). Steering wheel deformity correlated with pelvic fractures (P less than 0.001) and closed head injuries (P less than 0.005). Windshield violation correlated with closed head injuries (P less than 0.014) and spinal fractures (P less than 0.03). Irreparable vehicles correlated with pelvic (P less than 0.0001) and femur fractures (P less than 0.01), closed head injuries (P less than 0.0001) and intra-abdominal injuries (P less than 0.0001). The authors conclude that a careful examination of the accident scene for specific mechanisms of injury can lead to better prehospital care, more rapid and consistent diagnosis of injury, and improved patient outcome. Further prospective studies should accumulate data that will improve prehospital care, alert physicians to possible injury, increase community awareness of injury prevention, and improve vehicle construction.

Pott's puffy tumor, frontal sinusitis, frontal bone osteomyelitis, and epidural abscess secondary to a wrestling injury.

A blow sustained to the head while wrestling may produce frontal osteomyelitis and its complications, Pott's puffy tumor and epidural abscess. The symptoms may be minimal and may be manifested only by a mild headache and occasional stuffy nose. A 16-year-old boy was studied one month after a head injury sustained while wrestling, complaining only of recurrent headaches and fever. A fluctuant mass was found in the midfrontal area. Frontal sinusitis, subperiosteal abscesss epidural abscess, and frontal osteomyelitis were found at surgery. The frontal bone involved by the osteomyelitis was debrided, and the epidural abscess was evacuated.