Panos N Papapanou

..Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/...

..Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function...

..Elucidation of DOX nephropathy may simultaneously provide insight into the pathogenesis of renal failure and mechanisms of cytotoxicity induced by chemotherapeutic agents...

..This study examined if periodontal treatment can contribute to changes in overall risk and medical expenditures for three chronic conditions [Diabetes Mellitus (DM), Coronary Artery Disease (CAD), and Cerebrovascular Disease (CVD)]...

..We explored the association between subgingival microbial profiles and serum IgG responses to periodontal microbiota in relation to clinical periodontal status...

..These early data point to the usefulness of gene expression profiling techniques in the identification of subclasses of periodontitis with common pathobiology...

..Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories...

..Importantly, the role of periodontal infections as a modifier of systemic health is being increasingly explored...

..This study examined serum immunoglobulin (IgG) responses to periodontal bacteria in patients with periodontitis and periodontitis-free individuals over a 30-month period...

..We investigated the effects of periodontal therapy on gene expression of peripheral blood monocytes...

..This case-control study examined polymorphisms at the interleukin-1 gene in relation to periodontal status, subgingival bacteria and systemic antibodies to periodontal microbiota...

..This study addresses whether checkerboard assessments of serum IgG antibodies to oral bacteria may serve as surrogate markers of clinical periodontal status in epidemiologic studies...

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..We investigated the effect of comprehensive periodontal therapy on the levels of multiple systemic inflammatory biomarkers...

..We hypothesized that a comparison of gene expression signatures between healthy and diseased gingival tissues would provide novel insights in the pathobiology of periodontitis and would inform the design of future studies...

..We investigated the sequential gene expression in the gingiva during the induction and resolution of experimental gingivitis...

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..Various bacterial species are differentially prevalent in periodontal health, gingivitis or periodontitis. We tested the independent associations between three bacterial groupings and gingival inflammation in an epidemiological study...

..We investigated the levels of subgingival plaque bacteria and serum IgG responses in patients with type 1 diabetes and non-diabetic controls of comparable periodontal status...

..We investigated the characteristics of clinical periodontal definitions that were most representative of exposure to bacterial species that are believed to be either markers, or themselves etiologic, of periodontal disease...

..Chronic infections, including periodontal infections, may predispose to cardiovascular disease. We investigated the relationship between periodontal microbiota and hypertension...

..This report summarizes the scientific presentations of the event...

..We explored the association between diabetes mellitus and oral disease in a low-socioeconomic-status urban population...

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..The extent to which the control of periodontal infections results in lower incidence of ASVD events is logistically difficult to assess and has not been addressed in any study so far...

..Tissue factor (TF) and its specific tissue factor pathway inhibitor (TFPI) are produced by vascular cells and are important regulators of the coagulation cascade...

..Ideally, such studies should have a randomized-controlled trial design...

..The receptor for advanced glycation endproducts (RAGE) regulates vascular inflammation and atherogenesis. We hypothesized that RAGE is involved in P. gingivalis's contribution to pro-atherogenic responses in vascular endothelial cells...

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..We examined the extent and severity of radiographic periodontal bone loss in patients with different stages of chronic kidney disease (CKD) and explored a potential dose-response relationship between bone loss and CKD-related biomarkers...

..The purpose of this study was to determine whether radiographically assessed CP is associated with nonstenotic carotid artery plaque as an ultrasound measure of subclinical atherosclerosis...

..CONCLUSIONS: A distinction between the two principal categories of the current periodontitis classification cannot be established by the study of infection patterns...

..In this review, we summarize data on the association between specific periodontal bacterial profiles and tissue gene/protein expression, generated from cell culture models and in vivo studies...

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..01-7.54). Linear regression indicated a significant ( P = .04) association between attachment loss and low birth weight (LBW). CONCLUSION: The data support the notion that periodontitis is independently associated with PTB and LBW...

..In this chapter, we outline the laboratory steps required for the processing of gingival tissue and blood samples in view of hybridization with whole-genome microarrays...

..gingivalis at MOI 1:100. At higher MOI, at least in vitro, P. gingivalis mediates endothelial apoptosis, thereby potentially amplifying proatherogenic mechanisms in the perturbed vasculature...

..In particular, we propose an SVM kernel function that is explicitly heterogeneous. In addition, we describe feature scaling methods for further exploiting prior knowledge of heterogeneity by giving each data type different weights...

..These results suggest that properties of P. gingivalis which render it capable of adhering to/invading other cell types may also be operative in macrophages and play an important role in its atherogenic potential...

..Therefore, mouse lens cell lines conditioned to survive different peroxide stresses have been analyzed to determine their global changes in gene expression...

..Thus, beta-catenin/TCF/Lef-mediated transcriptional events control a subset of the differentiation-associated transcriptional program and thereby participate in maintenance, expansion and stage progression of the epithelial lineage...

..We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods...

..However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported...

..Our methods will be of use in evaluating existing data sets and in helping to design new studies...

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..More advanced users can download the software and source code for local installation. The availability of these tools will permit more widespread application of this powerful learning algorithm in bioinformatics...

..AVAILABILITY: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request...

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..In conclusion, we showed gene expression profiling to be useful in classification and diagnosis, providing insights into pathogenesis and pointing to potential new therapeutic targets of soft tissue sarcoma...

..The increased expression of transcription factors and decreased expression of genes whose products are protective against cell death are hypothesized to underlie the long-term changes that are seen after injury in the neonate...

..This interaction modulates a number of schizophrenia-related phenotypes, providing a framework for understanding the high disease risk associated with this locus, the expression of the phenotype, or both...

..The roles of inflammatory mediation and effect modification were also studied...

..All analyses described in this chapter can be performed using relatively limited computational resources such as a lap top PC with at least 2.0 GB of memory and 2.0 GHz of processing speed...

..We examined whether periodontal treatment or other dental care is associated with adverse birth outcomes within a medical and dental insurance database...

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..Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress...

..CCS/MSP also has typical melanoma features, including immunoreactivity for S100 and HMB45, pigmentation, MITF-M expression, and a propensity for regional lymph node metastases...

..The results support the notion of intrafamilial transfer of mutans streptococci, and suggest that colonization of early acquired strains persists into young adulthood...

..This multi-center study evaluated the potential for sensitization to EMD in a subgroup of periodontal patients treated at least twice with at least 2 months between treatments...

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..Furthermore, IL-4 induces expression of the transcription factor Krox20, which is required for maximal IL-4-induced transcription...

..2 microdeletion...

..Relief of this inhibition lowers the threshold for hippocampal-dependent long-term synaptic potentiation and memory storage in mice...

..Activation of MAPK signaling appears to be a cornerstone in the development of heart disease in both X-linked and autosomal dominant EDMD...

..Activation of MAPK signaling by mutant A-type lamins could be a cornerstone in the development of heart disease in autosomal dominant Emery-Dreifuss muscular dystrophy...

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..The analysis has revealed a small group of antioxidative defense genes that contribute to the survival of T and H cells when exposed to oxidative stress...

..A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO)...

..The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms...

..Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data...

..These data demonstrate that susceptibility to DOX nephropathy represents a founder mutation in the laboratory mouse. Haplotype analysis can be used for identification of the DOXNPH gene and prediction of strain susceptibility pattern...

..Accordingly, these data identify a network of imprinted genes, including Zac1, which controls embryonic growth and which may be the basis for the implementation of a common mechanism of gene regulation during mammalian evolution...

..The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to advance the field...

..Ultimately, a pathobiology-based classification of periodontitis will facilitate correct diagnosis and targeted, efficient therapeutic prevention and intervention strategies. ..