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author:("Yu, guoyang")
1.  Diffuse optical monitoring of hemodynamic changes in piglet brain with closed head injury 
Journal of biomedical optics  2009;14(3):034015.
We used a nonimpact inertial rotational model of a closed head injury in neonatal piglets to simulate the conditions following traumatic brain injury in infants. Diffuse optical techniques, including diffuse reflectance spectroscopy and diffuse correlation spectroscopy (DCS), were used to measure cerebral blood oxygenation and blood flow continuously and noninvasively before injury and up to 6 h after the injury. The DCS measurements of relative cerebral blood flow were validated against the fluorescent microsphere method. A strong linear correlation was observed between the two techniques (R = 0.89, p < 0.00001). Injury-induced cerebral hemodynamic changes were quantified, and significant changes were found in oxy- and deoxy-hemoglobin concentrations, total hemoglobin concentration, blood oxygen saturation, and cerebral blood flow after the injury. The diffuse optical measurements were robust and also correlated well with recordings of vital physiological parameters over the 6-h monitoring period, such as mean arterial blood pressure, arterial oxygen saturation, and heart rate. Finally, the diffuse optical techniques demonstrated sensitivity to dynamic physiological events, such as apnea, cardiac arrest, and hypertonic saline infusion. In total, the investigation corraborates potential of the optical methods for bedside monitoring of pediatric and adult human patients in the neurointensive care unit.
doi:10.1117/1.3146814
PMCID: PMC3169814  PMID: 19566308
diffuse correlation spectroscopy (DCS); diffuse reflectance spectroscopy (DRS); cerebral hemodynamics; cerebral blood flow; traumatic brain injury; near—infrared spectroscopy (NIRS)
2.  A Ground Truth Based Comparative Study on Detecting Epistatic SNPs 
Genome-wide association studies (GWAS) have been widely applied to identify informative SNPs associated with common and complex diseases. Besides single-SNP analysis, the interaction between SNPs is believed to play an important role in disease risk due to the complex networking of genetic regulations. While many approaches have been proposed for detecting SNP interactions, the relative performance and merits of these methods in practice are largely unclear. In this paper, a ground-truth based comparative study is reported involving 9 popular SNP detection methods using realistic simulation datasets. The results provide general characteristics and guidelines on these methods that may be informative to the biological investigators.
doi:10.1109/BIBMW.2009.5332132
PMCID: PMC2998769  PMID: 21151836
Genome-wide association study; single-nucleotide polymorphism; SNP interaction
3.  Fluence Rate-Dependent Intratumor Heterogeneity in Physiologic and Cytotoxic Responses to Photofrin Photodynamic Therapy 
Photodynamic therapy (PDT) can lead to the creation of heterogeneous, response-limiting hypoxia during illumination, which may be controlled in part through illumination fluence rate. In the present report we consider 1) regional differences in hypoxia, vascular response, and cell kill as a function of tumor depth and 2) the role of fluence rate as a mediator of depth-dependent regional intratumor heterogeneity. Intradermal RIF murine tumors were treated with Photofrin-PDT using surface illumination at an irradiance of 75 or 38 mW/cm2. Regional heterogeneity in tumor response was examined through comparison of effects in the surface vs. base of tumors, i.e. along a plane parallel to the skin surface and perpendicular to the incident illumination. 75 mW/cm2-PDT created significantly greater hypoxia in tumor bases relative to their surfaces. Increased hypoxia in the tumor base could not be attributed to regional differences in Photofrin concentration nor effects of fluence rate distribution on photochemical oxygen consumption, but significant depth-dependent heterogeneity in vascular responses and cytotoxic response were detected. At a lower fluence rate of 38 mW/cm2, no detectable regional differences in hypoxia or cytotoxic responses were apparent, and heterogeneity in vascular response was significantly less than that during 75 mW/cm2-PDT. This research suggests that the benefits of low-fluence-rate-PDT are mediated in part by a reduction in intratumor heterogeneity in hypoxic, vascular and cytotoxic responses.
doi:10.1039/b9pp00004f
PMCID: PMC2834171  PMID: 20024165
photodynamic therapy; fluence rate; hypoxia; EF3; blood flow
4.  An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions 
Bioinformatics  2009;25(19):2478-2485.
Motivation: In both genome-wide association studies (GWAS) and pathway analysis, the modest sample size relative to the number of genetic markers presents formidable computational, statistical and methodological challenges for accurately identifying markers/interactions and for building phenotype-predictive models.
Results: We address these objectives via maximum entropy conditional probability modeling (MECPM), coupled with a novel model structure search. Unlike neural networks and support vector machines (SVMs), MECPM makes explicit and is determined by the interactions that confer phenotype-predictive power. Our method identifies both a marker subset and the multiple k-way interactions between these markers. Additional key aspects are: (i) evaluation of a select subset of up to five-way interactions while retaining relatively low complexity; (ii) flexible single nucleotide polymorphism (SNP) coding (dominant, recessive) within each interaction; (iii) no mathematical interaction form assumed; (iv) model structure and order selection based on the Bayesian Information Criterion, which fairly compares interactions at different orders and automatically sets the experiment-wide significance level; (v) MECPM directly yields a phenotype-predictive model. MECPM was compared with a panel of methods on datasets with up to 1000 SNPs and up to eight embedded penetrance function (i.e. ground-truth) interactions, including a five-way, involving less than 20 SNPs. MECPM achieved improved sensitivity and specificity for detecting both ground-truth markers and interactions, compared with previous methods.
Availability: http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm
Contact: djmiller@engr.psu.edu
Supplementary information:Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp435
PMCID: PMC3140808  PMID: 19608708
6.  Transcranial Optical Monitoring of Cerebrovascular Hemodynamics in Acute Stroke Patients 
Optics express  2009;17(5):3884-3902.
“Diffuse correlation spectroscopy” (DCS) is a technology for non-invasive transcranial measurement of cerebral blood flow (CBF) that can be hybridized with “near-infrared spectroscopy” (NIRS). Taken together these methods hold potential for monitoring hemodynamics in stroke patients. We explore the utility of DCS and NIRS to measure effects of head-of-bed (HOB) positioning at 30°, 15°, 0°, −5° and 0° angles in patients with acute ischemic stroke affecting frontal cortex and in controls. HOB positioning significantly altered CBF, oxy-hemoglobin (HbO2) and total-hemoglobin (THC) concentrations. Moreover, the presence of an ipsilateral infarct was a significant effect for all parameters. Results are consistent with the notion of impaired CBF autoregulation in the infarcted hemisphere.
PMCID: PMC2724658  PMID: 19259230
7.  Cerebral hemodynamics in preterm infants during positional intervention measured with diffuse correlation spectroscopy and transcranial Doppler ultrasound 
Optics express  2009;17(15):12571-12581.
Four very low birth weight, very premature infants were monitored during a 12° postural elevation using diffuse correlation spectroscopy (DCS) to measure microvascular cerebral blood flow (CBF) and transcranial Doppler ultrasound (TCD) to measure macrovascular blood flow velocity in the middle cerebral artery. DCS data correlated significantly with peak systolic, end diastolic, and mean velocities measured by TCD (pA =0.036, 0.036, 0.047). Moreover, population averaged TCD and DCS data yielded no significant hemodynamic response to this postural change (p>0.05). We thus demonstrate feasibility of DCS in this population, we show correlation between absolute measures of blood flow from DCS and blood flow velocity from TCD, and we do not detect significant changes in CBF associated with a small postural change (12°) in these patients.
PMCID: PMC2723781  PMID: 19654660

Results 1-7 (7)