Tuning membership functions of kernel fuzzy classifiers by maximizing margins

We propose two methods for tuning membership functions of a kernel fuzzy classifier based on the idea of SVM (support vector machine) training. We assume that in a kernel fuzzy classifier a fuzzy rule is defined for each class in the feature space. In the first method, we tune the slopes of the membership functions at the same time so that the margin between classes is maximized under the constraints that the degree of membership to which a data sample belongs is the maximum among all the classes. This method is similar to a linear all-at-once SVM. We call this AAO tuning. In the second method, we tune the membership function of a class one at a time. Namely, for a class the slope of the associated membership function is tuned so that the margin between the class and the remaining classes is maximized under the constraints that the degrees of membership for the data belonging to the class are large and those for the remaining data are small. This method is similar to a linear one-against-all SVM. This is called OAA tuning. According to the computer experiment for fuzzy classifiers based on kernel discriminant analysis and those with ellipsoidal regions, usually both methods improve classification performance by tuning membership functions and classification performance by AAO tuning is slightly better than that by OAA tuning.     

Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications

The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.

This minireview describes the development of NIR chemical probes for various protein-tag systems.     

Unique Thermal Structural Phase Transitions Exhibited by Unsymmetrical Organometallic Gold(III)-Dithiolene Complexes with Pentylthio and Hexylthio Groups

Unsymmetrical gold(III)-dithiolene complexes are potential candidates for molecular materials that exhibit thermal structural phase transitions. In this study, unsymmetrical ppy-gold(III) (ppy⁻=C-deprotonated-2-phenylpyridine(−)) complexes [AuC5] and [AuC6] coordinated by dithiolene ligands containing tetrathiafulvalene (TTF) skeletons with pentylthio (2-{bis(pentylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) and hexylthio groups (2-{bis(hexylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) were synthesized. Both complexes exhibited a large absorption band at approximately 508 nm, owing to intramolecular ligand-to-ligand charge transfer. One-dimensional columnar structures with head-to-tail molecular arrangements around the metal ions were constructed in the crystals. The flexible alkylthio groups were intercalated into crystalline spaces between dithiolene ligands in the columns. [AuC5] exhibits a simple phase transition at 198 °C between crystalline and isotropic phases irreversibly. The crystalline phase of [AuC6] observed at 25 °C melted at 148 °C. Another crystalline phase grew above 148 °C with a very slow crystallization rate from the liquid phase and was completely transformed into an isotropic phase at 200 °C.     

Total synthesis and biological evaluation of pacidamycin D and its 3'-hydroxy analogue

Full details of the total synthesis of pacidamycin D (4) and its 3'-hydroxy analogue 32 are described. The chemically labile Z-oxyacyl enamide moiety is the most challenging chemical structure found in uridylpeptide natural products. Key elements of our approach to the synthesis of 4 include the efficient and stereocontrolled construction of the Z-oxyvinyl halides 6 and 7 and their copper-catalyzed cross-coupling with the tetrapeptide carboxamide 5, a thermally unstable compound containing a number of potentially reactive functional groups. This synthetic route also allowed us to easily prepare 3'-hydroxy analogue 32. The assemblage by cross-coupling of the Z-oxyvinyl halide 6 and the carboxamide 5 at a late stage of the synthesis provided ready access to a range of uridylpeptide antibiotics and their analogues, despite their inherent labile nature with potential epimerization, simply by altering the tetrapeptide moiety.     

Boron 1s photoelectron spectrum of 11BF3: vibrational structure and linewidth

The boron 1s photoelectron spectrum of (11)BF(3) has been measured at a photon energy of 400 eV and a resolution of about 55 meV. The pronounced vibrational structure seen in the spectrum has been analyzed to give the harmonic and anharmonic vibrational frequencies of the symmetric stretching mode, 128.1 and 0.15 meV, as well as the change in equilibrium BF bond length upon ionization, -5.83 pm. A similar change in bond length has been observed for PF(3) and SiF(4), but a much smaller change for CF(4). Theoretical calculations for BF(3) that include the effects of electron correlation give results that are in reasonable accord with the experimental values. The Lorentzian (lifetime) width of the boron 1s core hole in BF(3) is found to be 72 meV, comparable to the value of 77 meV that has been reported for CF(4).     

Triethylborane-induced radical allylation reaction with zirconocene-olefin complex

[reaction: see text] Allylzirconium reagents are effective for radical allylation of alpha-halo carbonyl compounds. The key steps would be homolytic cleavage of the zirconium-carbon bond and halogen abstraction by the resulting Cp(2)ZrCl(III). Zirconocene-olefin complex can be also utilized for the allylation of alpha-halo compounds.     

Highly efficient near-infrared-emitting lanthanide(III) complexes formed by heterogeneous self-assembly of Ag(I), Ln(III), and thiacalix[4]arene-p-tetrasulfonate in aqueous solution (Ln(III) = Nd(III), Yb(III))

Heterogeneous self-assembly of thiacalix[4]arene-p-tetrasulfonate (TCAS), Ag(I), and Ln(III) (= Nd(III), Yb(III)) in aqueous solutions conveniently afforded ternary complexes emitting Ln(III)-centered luminescence in the near-infrared (NIR) region. A solution-state study revealed that the Ag(I)-Nd(III)-TCAS system gave a complex Ag(I)(4)·Nd(III)·TCAS(2) in a wide pH range of 6-12. In contrast, the Ag(I)-Yb(III)-TCAS system gave Ag(I)(2)·Yb(III)(2)·TCAS(2) at a pH of around 6 and Ag(I)(2)·Yb(III)·TCAS(2) at a pH of approximately 9.5. The structures of the Yb(III) complexes were proposed based on comparison with known Ag(I)-Tb(III)-TCAS complexes that show the same self-assembly behavior. In Ag(I)(2)·Yb(III)(2)·TCAS(2), two TCAS ligands sandwiched a cyclic array of a Ag(I)-Ag(I)-Yb(III)-Yb(III) core. In Ag(I)(2)·Yb(III)·TCAS(2), Yb(III) was accommodated in an O(8) cube consisting of eight phenolate O(-) groups from two TCAS ligands linked by two S-Ag-S linkages. Crystallographic analysis of Ag(I)(4)·Nd(III)·TCAS(2) revealed that the structure was similar to Ag(I)(2)·Yb(III)·TCAS(2) but that it had four instead of two S-Ag-S linkages. The number of water molecules coordinating to Ln(III) (q) estimated on the basis of the luminescent lifetimes was as follows: Ag(I)(4)·Nd(III)·TCAS(2), 0; Ag(I)(2)·Yb(III)(2)·TCAS(2), 2.4; and Ag(I)(2)·Yb(III)·TCAS(2), 0. These findings were compatible with the solution-state structures. The luminescent quantum yield (Φ) for Ag(I)(4)·Nd(III)·TCAS(2) was 4.9 × 10(-4), which is the second largest value ever reported in H(2)O. These findings suggest that the O(8) cube is an ideal environment to circumvent deactivation via O-H oscillation of coordinating water. The Φ values for Ag(I)(2)·Yb(III)(2)·TCAS(2) and Ag(I)(2)·Yb(III)·TCAS(2) were found to be 3.8 × 10(-4) and 3.3 × 10(-3), respectively, reflecting the q value. Overall, these results indicate that the ternary systems have the potential for a noncovalent strategy via self-assembly of the multidentate ligand, Ln(III), and an auxiliary metal ion to obtain a highly efficient NIR-emissive Ln(III) complex that usually relies on elaborate covalent linkage of a chromophore and multidentate ligands to expel coordinating water.     

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order M?ller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.     

Systematic study of protein detection mechanism of self-assembling 19F NMR/MRI nanoprobes toward rational design and improved sensitivity

(19)F NMR/MRI probe is expected to be a powerful tool for selective sensing of biologically active agents owing to its high sensitivity and no background signals in live bodies. We have recently reported a unique supramolecular strategy for specific protein detection using a protein ligand-tethered self-assembling (19)F probe. This method is based on a recognition-driven disassembly of the nanoprobes, which induced a clear turn-on signal of (19)F NMR/MRI. In the present study, we conducted a systematic investigation of the relationship between structure and properties of the probe to elucidate the mechanism of this turn-on (19)F NMR sensing in detail. Newly synthesized (19)F probes showed three distinct behaviors in response to the target protein: off/on, always-on, and always-off modes. We clearly demonstrated that these differences in protein response could be explained by differences in the stability of the probe aggregates and that "moderate stability" of the aggregates produced an ideal turn-on response in protein detection. We also successfully controlled the aggregate stability by changing the hydrophobicity/hydrophilicity balance of the probes. The detailed understanding of the detection mechanism allowed us to rationally design a turn-on (19)F NMR probe with improved sensitivity, giving a higher image intensity for the target protein in (19)F MRI.