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Genome-wide association study for complex diseases will generate massive amount of single nucleotide polymorphisms (SNPs) data. Univariate statistical test (i.e. Fisher exact test) was used to single out non-associated SNPs. However, the disease-susceptible SNPs may have little marginal effects in population and are unlikely to retain after the univariate tests. Also, model-based methods are impractical...
Near-infrared spectroscopy (NIRS) is a useful technique for noninvasive measurement of muscle oxygenation. However, analyses of the dynamic changes in muscle metabolism based only on experimental observations of NIRS are difficult. Therefore, we constructed a mathematical model of muscle metabolism, comprising of the ATP synthesizing systems and O2 diffusion system, to identify the mechanisms responsible...
A framework for modeling the activation of skeletal muscle is presented for studying functional electrical stimulation. A mathematical model of the cellular responses of skeletal muscle, created at AgResearch (Ruakura, New Zealand www.agresearch.co.nz), has been integrated with an anatomical, finite element model of the semitendinosus muscle, which was constructed from CT scans of the hind limb of...
We prove that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. We derive the optimal exon length distribution, which minimizes the probability of error in the genome...
This paper presents a novel electrocardiographic inverse approach for imaging the 3-D ventricular activation sequence based on the modeling and estimation of the equivalent current density throughout the entire myocardial volume. The spatio-temporal coherence of the ventricular excitation process is utilized to derive the activation time from the estimated time course of the equivalent current density...
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship...
Platelet-rich plasma (PRP) has been gaining increasing popularity in orthopedics and oral and maxillofacial surgery because of its potential efficacy in enhancing bone regeneration. To maximally augment bone healing using PRP and to control the bioavailability of the relevant growth factors, we have designed an alginate hydrogel-based PRP-delivery system. The bioactivity of the growth factors released...
In this paper we analyze a popular divisive normalization model of V1 with respect to the relationship between its underlying coding strategy and the extraclassical physiological responses of its constituent modeled neurons. Specifically we are interested in whether the optimization goal of redundancy reduction naturally leads to reasonable neural responses, including reasonable distributions of responses...
Neuroblastoma is a childhood cancer of the nervous system. Current prognostic classification of this disease partly relies on morphological characteristics of the cells from H&E-stained images. In this work, an automated cell nuclei segmentation method is developed. This method employs morphological top-hat by reconstruction algorithm coupled with hysteresis thresholding to both detect and segment...
Delivery of antisense oligonucleotides, AON, presents many of the same challenges as delivery of any nucleic acid: charge, stability, cell uptake, endolysosomal escape, and entry into the nucleus. Here we demonstrate efficient delivery of AON after loading into biodegradable polymer vesicles or 'polymersomes'. We focus on AON delivery to muscle cells in vitro and in vivo because of the emergence of...
The subcellular location plays a pivotal role in the functionality of proteins. In this paper we develop a multi-stage linear classifier fusion system based on Efron's bootstrap sampling for predicting subcellular locations of yeast proteins. Three different types of classifiers, i.e. the Naive Bayes (NB) classifier, radial basis function (RBF) network, and multilayer perceptron (MLP), are utilized...
This paper presents a novel device which provides the opportunity to perform high-throughput biochemical assays on different individual cells. In particular, the proposed device is suited to screen the rare cells in biological samples for early stage cancer diagnosis and explore their biochemical functionality. In the process, single cells are precisely positioned and captured in activated micropores...
A novel microfluidic device is presented which creates a linear serial dilution of two input fluid streams. This platform facilitates higher productivity as a component of a high throughput cytotoxicity testing strategy. A modeling solution is presented to create custom linear dilution schemes. The featured device creates a serial dilution of two solutions in the range of 1:9 through 9:1 across nine...
For applications in cell biology, the ability to produce patterns of adhesion proteins for directing cell patterning is of particular interest. Often though, these patterns require extensive clean room facilities and intricate chrome masks to achieve very small feature sizes. We have developed a modified lift-off method for rapid prototyping of simple PLL structures that have features on a micron...
The objective of this study was to evaluate the gene expression of four bone-related adhesive proteins during the early healing of bone defect and bone-implant interface in animal experiments. T-shaped hollow pure titanium implants with dual acid-etched surfaces were placed into femurs of 17 Sprague-Dawley rats, and bone defects with the same size were made in the same site in 15 rats. Newly formed...
Three dimensional cultures in a microfabricated environment provide in vivo-like conditions to cells, and have used in a variety of applications in basic and clinical studies. Also, the analysis of the contractility of cardiomyocytes is important for understanding the mechanism of heart failure as well as the molecular alterations in diseased heart cells. This paper presents a realistic computational...
Contrast-enhanced magnetic resonance imaging (MRI) is useful to study the infiltration of immune cells, in particular macrophages. Contrast agents, for example ultra-small superparamagnetic iron oxide (USPIO) particles, administered intravenously into the blood stream will be engulfed by macrophages circulating in the circulation system. When a transplanted heart rejects, macrophages and other immune...
This modeling study investigates the functional role of pacemaker neurons in generating stable rhythms in the pre-Botzinger complex, a subcircuit of the respiratory pattern-generating circuitry in mammals. While the presence of pacemakers within the network is without doubt, the percentage and significance of such pacemakers is still unresolved. Here we revisited earlier network simulations by varying...
TASERs deliver electrical pulses that can temporarily incapacitate subjects. The goal of this paper is to analyze the distribution of currents in muscle layers and understand the electro-muscular incapacitation safety and efficacy of TASERs. The analyses describe skeletal muscle and motor nerve activation, cell electroporation and current and electric field distributions through skin, fat and muscle...
Tissue engineered constructs have the potential to be used as replacements for current bone graft technologies. One component necessary for bone tissue engineering is a readily available, osteogenic cell source. Human dermal fibroblasts may have the potential to differentiate along an osteoblastic lineage, making them a candidate for use in bone tissue engineering applications. The objective of this...
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