Efficient selection of discriminative genes from microarray gene expression data for cancer diagnosis

A new mutual information (MI)-based feature-selection method to solve the so-called large p and small n problem experienced in a microarray gene expression-based data is presented. First, a grid-based feature clustering algorithm is introduced to eliminate redundant features. A huge gene set is then greatly reduced in a very efficient way. As a result, the computational efficiency of the whole feature-selection process is substantially enhanced. Second, MI is directly estimated using quadratic MI together with Parzen window density estimators. This approach is able to deliver reliable results even when only a small pattern set is available. Also, a new MI-based criterion is proposed to avoid the highly redundant selection results in a systematic way. At last, attributed to the direct estimation of MI, the appropriate selected feature subsets can be reasonably determined. © 2005 IEEE

Practical iron-catalyzed atom/group transfer and insertion reactions

Iron-catalyzed reactions are receiving a surge of interest owing to the natural abundance and biocompatibility of Fe and the urge to develop practically useful sustainable catalysis for fine chemical industries. This article is a brief account of our studies on the C-O and C-N bond formation reactions catalyzed by Fe complexes supported by oligopyridine, macrocyclic tetraaza, and fluorinated porphyrin ligands. The working principle is the in situ generation of reactive Fe=O and Fe=NR intermediates supported by these oxidatively robust N-donor ligands for oxygen atom/nitrogen group transfer and insertion reactions. The catalytic reactions include C-H bond oxidation of saturated hydrocarbons (up to 87 % yield), epoxidation of alkenes (up to 96 % yield), cis-dihydroxylation of alkenes (up to 99 % yield), epoxidation-isomerization (E-I) reaction of aryl alkenes (up to 94 % yield), amination of C-H bonds (up to 95 % yield), aziridination of alkenes (up to 95 % yield), sulfimidation of sulfides (up to 96 % yield), and amide formation from aldehydes (up to 89 % yield). Many of these catalytic reactions feature high regio- and diastereoselectivity and/or high product yields and substrate conversions, and recyclability of the catalyst, demonstrating the applicability of Fe-catalyzed oxidative organic transformation reactions in practical organic synthesis. © 2012 IUPAC.published_or_final_versio

cis-Oxoruthenium complexes supported by chiral tetradentate amine (N4) ligands for hydrocarbon oxidations

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Prostate lesion detection and localization based on locality alignment discriminant analysis

Prostatic adenocarcinoma is one of the most commonly occurring cancers among men in the world, and it also the most curable cancer when it is detected early. Multiparametric MRI (mpMRI) combines anatomic and functional prostate imaging techniques, which have been shown to produce high sensitivity and specificity in cancer localization, which is important in planning biopsies and focal therapies. However, in previous investigations, lesion localization was achieved mainly by manual segmentation, which is time-consuming and prone to observer variability. Here, we developed an algorithm based on locality alignment discriminant analysis (LADA) technique, which can be considered as a version of linear discriminant analysis (LDA) localized to patches in the feature space. Sensitivity, specificity and accuracy generated by the proposed algorithm in five prostates by LADA were 52.2%, 89.1% and 85.1% respectively, compared to 31.3%, 85.3% and 80.9% generated by LDA. The delineation accuracy attainable by this tool has a potential in increasing the cancer detection rate in biopsies and in minimizing collateral damage of surrounding tissues in focal therapies

Practical manganese-catalysed highly enantioselective cis-dihydroxylation of electron-deficient alkenes and detection of a cis-dioxomanganese(v) intermediate by high resolution ESI-MS analysis

A practical protocol has been developed for asymmetric cis-dihydroxylation of electron-deficient alkenes with Oxone catalysed by a manganese complex bearing a chiral tetradentate N 4-donor ligand affording cis-diols in up to 95% yield with up to 96% ee. Analysis of the reaction mixture by high resolution ESI-MS revealed the formation of a cis-dioxomanganese(v) intermediate. © 2011 The Royal Society of Chemistry.link_to_subscribed_fulltex

Cis-dihydroxylation of alkenes with oxone catalyzed by iron complexes of a macrocyclic tetraaza ligand and reaction mechanism by ESI-MS spectrometry and DFT calculations

[FeIII(L-N4Me2)Cl2]+ (1, L-N4Me2 = N,N′-dimethyl-2,11-diaza[3.3](2,6) pyridinophane) is an active catalyst for cis-dihydroxylation of various types of alkenes with oxone at room temperature using limiting amounts of alkene substrates. In the presence of 0.7 or 3.5 mol % of 1, reactions of electron-rich alkenes, including cyclooctene, styrenes, and linear alkenes, with oxone (2 equiv) for 5 min resulted in up to >99% substrate conversion and afforded cis-diol products in up to 67% yield, with cis-diol/epoxide molar ratio of up to 16.8:1. For electron-deficient alkenes including α,β-unsaturated esters and α,β-unsaturated ketones, their reactions with oxone (2 equiv) catalyzed by 1 (3.5 mol %) for 5 min afforded cis-diols in up to 99% yield with up to >99% substrate conversion. A large-scale cis-dihydroxylation of methyl cinnamate (9.7 g) with oxone (1 equiv) afforded the cis-diol product (8.4 g) in 84% yield with 85% substrate conversion. After catalysis, the L-N4Me2 ligand released due to demetalation can be reused to react with newly added Fe(ClO4)2•4H2O to generate an iron catalyst in situ, which could be used to restart the catalytic alkene cis-dihydroxylation. Mechanistic studies by ESI-MS, isotope labeling studies, and DFT calculations on the 1-catalyzed cis-dihydroxylation of dimethyl fumarate with oxone reveal possible involvement of cis-HO-Fe V O and/or cis-O FeV O species in the reaction; the cis-dihydroxylation reactions involving cis-HO-FeV O and cis-O FeV O species both proceed by a concerted but highly asynchronous mechanism, with that involving cis-HO-FeV O being more favorable due to a smaller activation barrier. © 2010 American Chemical Society.link_to_subscribed_fulltex

Flavonoid dimers as bivalent modulators for P-glycoprotein-based multidrug resistance: Structure-activity relationships

We recently described the modulatory activities of apigenin homodimers linked by ethylene glycol units in multidrug-resistant breast cancer and leukemic cells overexpressing ABCB1 (P-glycoprotein, P-gp). To further improve the potency of these dimers, a small library of flavonoid homodimers and hetero-dimers were synthesized, and their in vitro activity in reversing cellular resistance to paclitaxel, along with structure activity relationships (SAR), were evaluated using a P-gp-expressing human breast cancer cell line. Among these synthesized homodimers, many showed more potent reversing activity than that of the parent compound and verapamil. Two compounds in particular showed promising reversing activity at sub-micro-molar concentrations with no cytotoxic effects. Regarding SAR trends, flavonoid dimers with nonpolar and hydrophobic sub-stituents (e.g., methyl and ethyl groups) generally showed more potent resistance-reversing activity than that of dimers with polar and hydrophilic substituents (e.g. hydroxy groups) at the C3, C6, and C7 positions, but not at C5. In terms of sub-stituent steric bulk at C6, it was found that the flavonoid dimer with methyl groups was optimal, with bulkier substituents leading to lower reversing activity. Comparisons of flavonoid heterodimers with the corresponding homodimers revealed that the two binding sites on P-gp for flavonoid moieties are quite similar to each other. Besides paclitaxel, these new compounds also increased drug accumulation and enhanced the cytotoxicity of other cancer drugs such as doxorubicin, vincris-tine, and vinblastine by decreasing the IC 50 values 4 45-fold. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.link_to_subscribed_fulltex