Pattern recognition techniques for the emerging field of bioinformatics: A review

The emerging field of bioinformatics has recently created much interest in the computer science and engineering communities. With the wealth of sequence data in many public online databases and the huge amount of data generated from the Human Genome Project, computer analysis has become indispensable. This calls for novel algorithms and opens up new areas of applications for many pattern recognition techniques. In this article, we review two major avenues of research in bioinformatics, namely DNA sequence analysis and DNA microarray data analysis. In DNA sequence analysis, we focus on the topics of sequence comparison and gene recognition. For DNA microarray data analysis, we discuss key issues such as image analysis for gene expression data extraction, data pre-processing, clustering analysis for pattern discovery and gene expression time series data analysis. We describe current methods and show how computational techniques could be useful in these areas. It is our hope that this review article could demonstrate how the pattern recognition community could have an impact on the fascinating and challenging area of genomic research.     

Effective immunity to dental caries: enhancement of salivary anti-Streptococcus mutans antibody responses with oral adjuvants

In the present study, we compared the ability of the soluble adjuvants concanavalin A (ConA), muramyl dipeptide (MDP), and peptidoglycan (PG) to enhance immune responses to orally administered particulate antigens of Streptococcus mutans 6715 in gnotobiotic rats. The isotype and levels of antibody in saliva and in serum from experimental rats were determined by an enzyme-linked immunosorbent assay using S. mutans whole cells (WC) as the coating antigen. The specificities of salivary and serum immunoglobulin A (IgA) antibodies to particulate S. mutans antigens, lipoteichoic acid, S. mutans serotype g carbohydrate, and dextran were also determined. When 50 micrograms of ConA was used as the oral adjuvant with S. mutans 6715 WC immunogen, a slight enhancement of immune responses was obtained. A higher dose of ConA suppressed humoral responses to the immunogen. Enhanced immune responses, especially of the IgA isotype, in both serum and saliva were induced in gnotobiotic rats given MDP and either S. mutans 6715 WC or purified cell walls (CW) by gastric intubation. Elevated IgA antibody levels to CW, lipoteichoic acid, and carbohydrate were observed in rats given S. mutans WC and MDP by gastric intubation, whereas oral immunization with S. mutans CW and MDP resulted in higher antibody levels to CW and carbohydrate and lower levels to lipoteichoic acid when compared with the antibody levels in rats given antigen alone. Rats orally immunized with either S. mutans WC or CW and MDP and challenged with virulent S. mutans 6715 exhibited significantly (P less than or equal to 0.05) lower plaque scores, numbers of viable S. mutans in plaque, and caries scores than did rats immunized with antigen alone or in infected-only controls. In another series of experiments, a PG fraction derived from S. mutans 6715 CW was assessed for adjuvant properties. The oral administration of PG and either S. mutans WC or CW induced good salivary and serum IgA antibody responses. The specificity of the antibodies was similar to that obtained in rats given antigen and MDP. Rats receiving either S. mutans WC or CW and PG and challenged with virulent S. mutans 6715 had lower plaque scores, fewer numbers of viable S. mutans in plaque, and lower caries activity than did infected rats receiving S. mutans WC or CW immunogen alone. These results provide evidence that soluble adjuvants derived from the gram-positive bacterial CW, e.g., MDP and PG, are effective oral adjuvants and augment IgA immune responses to particulate S. mutans antigens which are protective against the mucosally associated disease, dental caries.     

Remote sensing of suspended sediment concentrations of large rivers using multi-temporal MODIS images: an example in the Middle and Lower Yangtze River,China

Conventional measurements of suspended sediment concentration (SSC) are expensive, especially for large river systems. This study aims to examine the potential of estimating SSC of large rivers using high temporal resolution Terra Moderate Resolution Imaging Spectroradiometer (MODIS) data. In contrast to a small number of the samples used by previous studies on remote sensing of SSC, a large number of samples (n?=?153) obtained on 63 dates at five sites across the entire Middle and Lower Yangtze River were employed to investigate the relationship between SSC and the water reflectance of MODIS images. The water reflectance difference between Bands 2 and 5 provided a relatively accurate SSC estimate after atmospheric correction, with 25% mean absolute relative error and 29.7% relative root mean square error. The errors were lower for larger SSC values. Thus, there is a potential that the Terra MODIS could be employed to estimate SSC frequently for large turbid river systems.     

An efficient microfluidic sorter: implementation of double meandering micro striplines for magnetic particles switching

The ability to trap, manipulate, and separate magnetic beads has become one of the key requirements in realizing an integrated magnetic lab-on-chip biosensing system. In this article, we present the design and fabrication of an integrated magneto-fluidic device for sorting magnetic particles with a sorting efficiency of up to 95%. The actuation and manipulation of magnetic beads are realized using microfabricated square meandering current-carrying micro striplines. The current is alternated between two neighboring micro striplines to switch the magnetic beads to either one of the two outlets. We performed a series of parametric study to investigate the effect of applied current, flow rate, and switching frequency on the sorting efficiency. Experimental results reveal that the sorting efficiency is proportional to the square of current applied to the stripline, and decreases with increasing buffer flow rate and switching frequency. Such phenomena agree well with our theoretical analysis and simulation result. The fastest switching rate, which is limited by the microchannel geometry and bead velocity, is 2 Hz.     

Dynamic complexes of beta2-adrenergic receptors with protein kinases and phosphatases and the role of gravin

Signals mediated by G-protein-linked receptors display agonist-induced attenuation and recovery involving both protein kinases and phosphatases. The role of protein kinases and phosphatases in agonist-induced attenuation and recovery of beta-adrenergic receptors was explored by two complementary approaches, antisense RNA suppression and co-immunoprecipitation of target elements. Protein phosphatases 2A and 2B are associated with the unstimulated receptor, the latter displaying a transient decrease followed by a 2-fold increase in the levels of association at 30 min following challenge with agonist. Protein kinase A displays a robust, agonist-induced association with beta-adrenergic receptors over the same period. Suppression of phosphatases 2A and 2B with antisense RNA or inhibition of their activity with calyculin A and FK506, respectively, blocks resensitization following agonist removal. Recycling of receptors to the plasma membrane following agonist-promoted sequestration is severely impaired by loss of either phosphatase 2B or protein kinase C. In addition, loss of protein kinase C diminishes association of phosphatase 2B with beta-adrenergic receptors. Overlay assays performed with the RII subunit of protein kinase A and co-immunoprecipitations reveal proteins of the A kinase-anchoring proteins (AKAP) family, including AKAP250 also known as gravin, associated with the beta-adrenergic receptor. Suppression of gravin expression disrupts recovery from agonist-induced desensitization, confirming the role of gravin in organization of G-protein-linked signaling complexes. The Ht31 peptide, which blocks AKAP protein-protein interactions, blocks association of beta-adrenergic receptors with protein kinase A. These data are the first to reveal dynamic complexes of beta-adrenergic receptors with protein kinases and phosphatases acting via an anchoring protein, gravin.     

High-speed switching of monolithic arrays ofgrating-surface-emitting diode lasers

The electrooptic switching properties of injection-coupled coherent two-dimensional grating-surface-emitting (GSE) laser arrays with multiple gain sections and quantum-well active layers are discussed. Within such an array of injection-coupled GSE lasers, a single gain section can act as an intracavity saturable loss element that can modulate the output of the entire array. Experimental results demonstrate efficient subnanosecond switching of high-power GSE laser arrays by operating only one gain section as an intracavity loss modulator     

Smoking and Parkinson''s disease: a dose-response relationship

BACKGROUND: Previous studies questioned the link between early childhood anemia and detrimental child development. OBJECTIVE: A population-based study was conducted to examine the association between early childhood anemia and mild or moderate metal retardation at 10 y of age. DESIGN: The present study linked early childhood nutrition data collected by the Special Supplemental Program for Women, Infants, and Children (WIC) and school records. Hemoglobin values were used to determine the relation between anemia in early life and children's placement in special education classes for mild or moderate mental retardation. Subjects were all participants in the WIC program. A computer program was used to link data from birth, WIC, and school records. RESULTS: Logistic regression showed an increased likelihood of mild or moderate mental retardation associated with anemia, independent of birth weight, maternal education, sex, race-ethnicity, the mother's age, or the child's age at entry into the WIC program. CONCLUSION: These findings support the proposition that efforts to prevent mild and moderate mental retardation should include providing children with adequate nutrition during early childhood.     

Stimulation of the extracellular signal-regulated kinase 1/2 pathway by human beta-3 adrenergic receptor: new pharmacological profile and mechanism of activation

(-)Deprenyl is an irreversible inhibitor of monoamine oxidase B (MAO-B) frequently used as an adjunct therapy in the treatment of Parkinson's Disease. Recent evidence, however, has found that deprenyl's metabolites are associated with an antiapoptotic action within certain neuronal populations. Interestingly, deprenyl's antiapoptotic actions appear not to depend upon the inhibition of MAO-B. Due to a paucity of information surrounding (-)deprenyl's ability to spare neurons in vivo, a series of studies was conducted to further investigate this phenomenon within an apoptotic neuronal death model: kainic acid induced excitotoxicity. Results indicated that (-)deprenyl increased hippocampal neuronal survival compared to saline-matched controls following kainic acid insult. Furthermore, it was discovered that (-)deprenyl treatment could be stopped 14 days following CNS insult by kainate, with evidence of neuronal sparing still present by day 28. In open-field locomotor activity testing of kainate-treated animals, those given subsequent (-)deprenyl treatment showed habituation curves similar to control subjects, while saline-treated animals did not. Given deprenyl's antiapoptotic actions, it is proposed that (-)deprenyl may be beneficial in the treatment of a variety of neurodegenerative diseases where evidence of apoptosis exists, such as Parkinson's and Alzheimer's Disease, by slowing the disease process itself.     

Deficiency in collagen and fibronectin phagocytosis by human buccal mucosa fibroblasts in vitro as a possible mechanism for oral submucous fibrosis

Oral submucous fibrosis (OSF), a chronic oral mucosal condition commonly found in south Asians, is a disorder characterized by a quantitative as well as a qualitative alteration of collagen deposition within the subepithelial layer of the oral mucosa. Since degradation of collagen by fibroblast phagocytosis is an important pathway for physiological remodelling of soft connective tissues, we have investigated phagocytosis of collagen- and fibronectin-coated latex beads by fibroblast cultures with an in vitro model system. Coated fluorescent latex beads were incubated with human oral mucosa fibroblasts and the fluorescence associated with internalized beads was measured by flow cytometry. Cells from normal tissues that had been incubated with beads for 16 h contained a mean of 75% collagen phagocytic cells and 70% fibronectin phagocytic cells; however, about 15% and 10% of phagocytic cells individually contained more than twice the mean number of beads per cell. In contrast, cells from OSF tissues exhibited a 40% reduction of the proportions of collagen phagocytic cells (mean=35%) and a 48% decrease of the proportions of fibronectin phagocytic cells (mean=22%), none of the cells having a high number of beads as compared to normal fibroblasts. OSF lesions appear to contain fibroblasts with marked deficiencies in collagen and fibronectin phagocytosis. To investigate if inhibition of phagocytosis could be demonstrated in vitro, normal fibroblast cultures were incubated with areca nut alkaloids (arecoline, arecaidine). The cultures had a dose-dependent reduction in the proportions of phagocytic cells. On the other hand, corticosteroid used in the treatment of OSF exhibited a dose-dependent enhancement in the proportion of phagocytic cells. Therefore, our hypothesis for OSF, although oversimplified, is that betel nut alkaloids (arecoline, arecaidine) inhibit fibroblast phagocytosis and this provides a mechanism for the development of OSF. The benefit of a local intralesional injection of corticosteroid is also possibly, at least in part, through an enhancement of fibroblast collagen phagocytosis.     

Inhibition of metastases by anticoagulants

Medicare spends more than $200 billion a year; the politics surrounding the Medicare program cannot be fully understood without an adequate appreciation of that fact. An understanding of the political economy of Medicare is perhaps best achieved by thinking along three dimensions: (1) Medicare as redistributive politics; (2) Medicare as special-interest politics; and (3) Medicare as distributive politics. Seeing the extent to which Medicare policies flow from these political processes makes clear that Medicare reform and broader political reform are, at some level, inseparable and indistinguishable.