Indiana Consortium for Innovation in Biomedical Imaging

poster abstractThe Indiana Consortium for Innovation in Biomedical Imaging (Indiana-CIBI) has been established to leverage the biomedical imaging strengths of several major academic institutions throughout Indiana. This initiative provides the environment, infrastructure, and resources necessary for establishing one of the premier translational, research and educational imaging networks in the United States. The Indiana-CIBI will facilitate the identification of crucial clinical problems and unmet research needs; stimulate the development of innovative solutions; and help translate optimized patient care services into practice at partner health-care delivery facilities. The objectives of the Indiana-CIBI include: Providing national leadership in translation from concept to practice. Encouraging targeted problem-driven technology development. Nurturing innovation and progress through facile access to advanced resources. Focusing Indiana state-wide interdisciplinary partnerships in the development of new, innovative imaging technologies and the utilization of imaging resources. Cultivating investigator engagement and channeling intrinsic motivation. The stated objectives of the Indiana-CIBI define the operational model for the consortium. Key steps in the innovation-focused process include: 1) Identification of critical clinical or biomedical research needs by physician or biomedical investigator(s); 2) Creation of innovative solutions through innovation incubator teams, imaging innovation marathons, and crowdsourcing solicitations; 3) Translation to practice through a large medical physics/radiology network; and 4) Translation to advanced core services through the Indiana-CTSI core resource network. Critical success factors for the Indiana-CIBI include tight integration within academic health care facilities, consolidation of fragmented resources, and expansion of critical support resources, eliminating the need to duplicate some types of services across multiple sites in Indiana. For further information regarding the Indiana Consortium for Innovation in Biomedical Imaging and its programs please contact Mark Holland or Gary Hutchins at [email protected]. The Indiana-CIBI is supported, in part, by contributions from the IUPUI Office of the Vice Chancellor for Research

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

Research Center for Quantitative Renal Imaging

poster abstractMission: The mission of the Research Center for Quantitative Renal Imaging is to provide a focused research environment and resource for the development, implementation, and dissemination of innovative, quantitative imaging methods designed to assess the status of and mechanisms associated with acute and chronic kidney disease and evaluate efficacy of therapeutic interventions. Nature of the Center: This Research Center provides a formal mechanism to link research programs focused on understanding the fundamental mechanisms associated with kidney diseases with those associated with the development of advanced imaging methods and quantitative analyses into a focused effort dedicated toward the development and implementation of quantitative renal imaging methods. Goals of the IUPUI Research Center for Quantitative Renal Imaging: Identify, develop, and implement innovative imaging methods that provide quantitative imaging biomarkers for assessing and inter-relating renal structure, function, hemodynamics and underlying tissue micro-environmental factors contributing to kidney disease. Establish an environment that facilitates and encourages interdisciplinary collaborations among investigators and offers research support to investigators focused on developing and utilizing innovative quantitative imaging methods in support of kidney disease research. Provide a resource to inform the greater research and healthcare communities of advances in quantitative renal imaging and its potential for enhanced patient management and care. Offer an imaging research resource to companies engaged in product development associated with the diagnosis and treatment of kidney diseases. Further Information: For further information regarding the IUPUI Research Center for Quantitative RenalImaging and its funding programs please visit http://www.renalimaging.iupui.edu/ or contact the Center at [email protected]. Acknowledgments: The IUPUI Research Center for Quantitative Renal Imaging is supported by contributions from the IUPUI Signature Center Initiative, the Department of Radiology & Imaging Sciences; the Division of Nephrology, the IUPUI School of Science, the IUPUI School of Engineering & Technology, and the Indiana Clinical and Translational Sciences Institute (CTSI)

A Search for Planets Transiting the M Dwarf Debris Disk Host, AU Microscopii

We present high cadence, high precision multi-band photometry of the young, M1Ve, debris disk star, AU Microscopii. The data were obtained in three continuum filters spanning a wavelength range from 4500\AA to 6600\AA, plus H$\alpha$, over 28 nights in 2005. The lightcurves show intrinsic stellar variability due to starspots with an amplitude in the blue band of 0.051 magnitudes and a period of 4.847 days. In addition, three large flares were detected in the data which all occur near the minimum brightness of the star. We remove the intrinsic stellar variability and combine the lightcurves of all the filters in order to search for transits by possible planetary companions orbiting in the plane of the nearly edge-on debris disk. The combined final lightcurve has a sampling of 0.35 minutes and a standard deviation of 6.8 millimags (mmag). We performed Monte Carlo simulations by adding fake transits to the observed lightcurve and find with 95% significance that there are no Jupiter mass planets orbiting in the plane of the debris disk on circular orbits with periods, P $\le 5$ days. In addition, there are no young Neptune-like planets (with radii 2.5$\times$ smaller than the young Jupiter) on circular orbits with periods, P $\le 3$ days.Comment: accepted to MNRA

FABRICA: A Bioreactor Platform for Printing, Perfusing, Observing, & Stimulating 3D Tissues

We are introducing the FABRICA, a bioprinter-agnostic 3D-printed bioreactor platform designed for 3D-bioprinted tissue construct culture, perfusion, observation, and analysis. The computer-designed FABRICA was 3D-printed with biocompatible material and used for two studies: (1) Flow Profile Study: perfused 5 different media through a synthetic 3D-bioprinted construct and ultrasonically analyzed the flow profile at increasing volumetric flow rates (VFR); (2) Construct Perfusion Study: perfused a 3D-bioprinted tissue construct for a week and compared histologically with a non-perfused control. For the flow profile study, construct VFR increased with increasing pump VFR. Water and other media increased VFR significantly while human and pig blood showed shallow increases. For the construct perfusion study, we confirmed more viable cells in perfused 3D-bioprinted tissue compared to control. The FABRICA can be used to visualize constructs during 3D-bioprinting, incubation, and to control and ultrasonically analyze perfusion, aseptically in real-time, making the FABRICA tunable for different tissues

New sub-millimeter limits on dust in the 55 Cancri planetary system

We present new, high-sensitivity sub-millimeter observations towards 55 Cancri, a nearby G8 star with one, or possibly two, known planetary companion(s). Our 850 $\mu$m map, obtained with the SCUBA instrument on the James Clerk Maxwell Telescope, shows three peaks of emission at the 2.5 mJy level in the vicinity of the star's position. However, the observed peaks are 25\arcsec--40\arcsec away from the star and a deep $R$-band optical image reveals faint point sources that coincide with two of the sub-millimeter peaks. Thus, we do not find evidence for dust emission spatially associated with 55 Cancri. The excess 60 $\mu$m emission detected with ISO may originate from one or more of the 850 $\mu$m peaks that we attribute to background sources. Our new results, together with the HST/NICMOS coronographic images in the near-infrared, place stringent limits on the amount of dust in this planetary system, and argue against the existence of a detectable circumstellar dust disk around 55 Cnc.Comment: 11 pages, 2 PostScript figures, to appear in The Astrophysical Journal Letter

Staged correction of an equinovarus deformity due to pyoderma gangrenosum using a Taylor spatial frame and tibiotalar calcaneal fusion with an intramedullary device

Pyoderma gangrenosum is a rare autoinflammatory syndrome manifested by skin lesions eventually creating ulcers. Surgical management can lead to scarring and contracture at the site of the lesion due to the pathergy phenomenon. A 43-year-old woman presented with a 5-year history of severe equinovarus deformity due to chronic pyoderma gangrenosum on her posteromedial ankle. She underwent a staged fusion. A gradual “closed” correction was performed in a Taylor spatial frame for 8 weeks in order to obviate the need for a surgical release in the area of the ulcer. She was ambulatory and full weight-bearing within 4 weeks of her frame removal. She maintained her correction with an accommodative foot orthosis until she had an uneventful tibiotalar calcaneal fusion with an intramedullary device. This case represents the success of using a Taylor spatial frame for staged fusion involving soft-tissue correction of severe, rigid equinovarus deformity due to pyoderma gangrenosum

Toward three-dimensional echocardiographic determination of regional myofiber structure

As a step toward the goal of relating changes in underlying myocardial structure to observed altered cardiac function in the hearts of individual patients, this study addresses the feasibility of creating echocardiography-derived maps of regional myocardial fiber structure for entire, intact, excised sheep hearts. Backscatter data were obtained from apical echocardiographic images acquired with a clinical ultrasonic imaging system and used to determine local fiber orientations in each of seven hearts. Systematic acquisition across the entire heart volume provided information sufficient to give a complete map for each heart. Results from the echocardiography-derived fiber maps compare favorably with corresponding results derived from diffusion tensor magnetic resonance imaging. The results of this study provide evidence of the feasibility of using echocardiographic methods to generate individualized whole heart fiber maps for patients

Pulmonary Artery Acceleration Time Provides a Reliable Estimate of Invasive Pulmonary Hemodynamics in Children

Background Pulmonary artery acceleration time (PAAT) is a non-invasive method to assess pulmonary hemodynamics, but lacks validity in children. This study sought to evaluate the accuracy of Doppler echocardiography (DE) derived PAAT in predicting right heart catheterization (RHC) derived pulmonary arterial pressure (PAP), pulmonary vascular resistance (PVR) and compliance in children. Methods Prospectively acquired and retrospectively measured DE derived PAAT and RHC derived systolic PAP (sPAP), mean PAP (mPAP), index PVR (PVRi) and compliance were compared by regression analysis in a derivation cohort of 75 children (median age, 5.3 years; 1.3–12.6) with wide ranges of pulmonary hemodynamics. To account for heart rate variability, PAAT was adjusted for right ventricle ejection time (RVET) and corrected by the RR interval. Regression equations incorporating PAAT and PAAT:RVET from the derivation cohort were then evaluated for the accuracy of its predictive values for invasive pulmonary hemodynamics in a validation cohort of 50 age- and weight- matched children with elevated PAP and PVR. Results There were significant inverse correlations between PAAT and RHC derived mPAP (r = −0.82) and PVRi (r= −0.78) and direct correlation (r= 0.78) between PAAT and pulmonary compliance in the derivation cohort. For detection of pulmonary hypertension (PRVi > 3 WU x m2 and mPAP > 25 mmHg), PAAT < 90 msec and PAAT:RVET < 0.31 resulted in a sensitivity of 97% and a specificity of 95%. In the derivation cohort, the regression equations relating PAAT with mPAP and PVRi were: mPAP = 48 – 0.28 x PAAT and PVRi = 9 –0.07 x PAAT. These PAAT integrated equations predicted RHC measured pulmonary hemodynamics in the validation cohort with good correlations (r = 0.88, 0.83 respectively), small biases (<10%), and minimal coefficient of variation (<8%). Conclusions PAAT inversely correlates with RHC measured pulmonary hemodynamics and directly correlates with pulmonary arterial compliance in children. The study established PAAT based regression equations in children to accurately predict RHC derived PAP and PVR