Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer

It is known that patients suffering from cancer diseases excrete increased amounts of modified nucleosides with their urine. Especially methylated nucleosides have been proposed to be potential tumor markers for early diagnosis of cancer. For determination of nucleosides in randomly collected urine samples, the nucleosides were extracted using affinity chromatography and then analyzed via reversed phase high-performance liquid chromatography (HPLC) with UV-detection. Eleven nucleosides were quantified in urine samples from 51 breast cancer patients and 65 healthy women.The measured concentrations were used to train a Support Vector Machine (SVM) and a k-nearest-neighbor classifier (k-NN) to discriminate between healthy control subjects and patients suffering from breast cancer. Evaluations of the learned models by computing the leave-one-out error and the prediction error on an independent test set of 29 subjects (15 healthy, 14 breast cancer patients) showed that by using the eleven nucleosides, the occurrence of breast cancer could be forecasted with 86% specificity and 94% sensitivity when using an SVM and 86% for both specificity and sensitivity with the k-NN model.     

Superagonistic fluorinated vitamin D3 analogs stabilize helix 12 of the vitamin D receptor

Side chain fluorination is often used to make analogs of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] resistant to degradation by 24-hydroxylase. The fluorinated nonsteroidal analogs CD578, WU515, and WY1113 have an increased prodifferentiating action on SW480-ADH colon cancer cells, which correlated with stronger induction of vitamin D receptor (VDR)-coactivator interactions and stronger repression of beta-catenin/TCF activity. Cocrystallization of analog CD578 with the zebrafish (z)VDR and an SRC-1 coactivator peptide showed that the fluorine atoms of CD578 make additional contacts with Val444 and Phe448 of activation helix 12 (H12) of the zVDR and with Leu440 of the H11-H12 loop. Consequently, the SRC-1 peptide makes more contacts with the VDR-CD578 complex than with the VDR-1,25(OH)2D3 complex. These data show that fluorination not only affects degradation of an analog but can also have direct effects on H12 stabilization.     

Phase and glass transitions in short-range central potential model systems: the case of C60

Extensive molecular dynamics simulations show that a short-range central potential, suited to model C60, undergoes a high temperature transition to a glassy phase characterized by the positional disorder of the constituent particles. Crystallization, melting, and sublimation, which also take place during the simulation runs, are illustrated in detail. It turns out that vitrification and the mentioned phase transitions occur when the packing fraction of the system-defined in terms of an effective hard-core diameter-equals that of hard spheres at their own glass and melting transition, respectively. A close analogy also emerges between our findings and recent mode coupling theory calculations of structural arrest lines in a similar model of protein solutions. We argue that the conclusions of the present study might hold for a wide class of potentials currently employed to mimic interactions in complex fluids (some of which are of biological interest), suggesting how to achieve at least qualitative predictions of vitrification and crystallization in those systems.     

Integrating the geodesic equations in the Schwarzschild and Kerr space-times using Beltrami's “geometrical” method

We revisit a little known theorem due to Beltrami, through which the integration of the geodesic equations of a curved manifold is accomplished by a method which, even if inspired by the Hamilton-Jacobi method, is purely geometric. The application of this theorem to the Schwarzschild and Kerr metrics leads straightforwardly to the general solution of their geodesic equations. This way of dealing with the problem is, in our opinion, very much in keeping with the geometric spirit of general relativity. In fact, thanks to this theorem we can integrate the geodesic equations by a geometrical method and then verify that the classical conservation laws follow from these equations.     

ac electroosmosis in rectangular microchannels

Motivated by the growing interest in ac electroosmosis as a reliable no moving parts strategy to control fluid motion in microfluidic devices for biomedical applications, such as lab-on-a-chip, we study transient and steady-state electrokinetic phenomena (electroosmosis and streaming currents) in infinitely extended rectangular charged microchannels. With the aid of Fourier series and Laplace transforms we provide a general formal solution of the problem, which is used to study the time-dependent response to sudden ac applied voltage differences in case of finite electric double layer. The Debye-Huckel approximation has been adopted to allow for an algebraic solution of the Poisson-Boltzmann problem in Fourier space. We obtain the expressions of flow velocity profiles, flow rates, streaming currents, as well as expressions of the complex hydraulic and electrokinetic conductances. We analyze in detail the dependence of the electrokinetic conductance on the extension of linear dimensions relative to the Debye length, with an eye on finite electric double layer effects.     

Application of amide-stabilized sulfur ylide reactivity to the stereodivergent synthesis of (R,S)- and (S,R)-reboxetine

A simple access to (R,S)- and (S,R)-reboxetine from a single chiral sulfonium salt 4 is reported. This approach, based on a stabilized sulfur ylide-mediated epoxidation, followed by a regioselective opening reaction, enables the preparation of these two potentially biologically active compounds in 35.6% and 13.7% overall yield.     

Crystal structure and packing analysis of the liquid crystal dimer alpha,omega-bis(4-cyanobiphenyl-4-yloxy)octane

The crystal structure of the liquid crystal dimer α,ω-bis(4-cyanobiphenyl-4'-yloxy)octane has been determined from diffraction data obtained with synchrotron radiation. The structure is triclinic, with the space group P-1 with Z = 2 and the unit cell parameters are a= 7.135(5) Å, b= 12.811(5) Å, c= 15.639(5) Å, α= 75.800(5)°, β= 84.690(5)°, γ= 77.930(5)°. The flexible spacer linking the mesogenic groups is in the all-trans-conformation. Although the molecule has a potential centre of symmetry, it occupies a general position in the cell; this unusual behaviour has been investigated with the aid of a theoretical evaluation of the packing energy.     

Synthesis of Acylboron Compounds

Acylboron compounds are emerging as versatile functional groups with applications in multiple research fields. Their synthesis, however, is still challenging and requires innovative methods. This Minireview provides an overview on the obstacles of acylboron synthesis and highlights notable advances within the last three years on new strategies to overcome the challenges posed by the formation of acyl–boron bonds.     

Polymer thermal and acoustic properties using heterodyne detected transient grating technique

We investigated the acoustic and thermal features of a polymeric system by a heterodyne detected transient grating technique. We studied two polymers characterized by different molecular weights. Transient grating experiments could reveal a reliable series of information on sound velocity, acoustic damping time, and thermal diffusion of the polymers. The temperature and molecular weight dependence of the polymer acoustic and thermal properties are reported. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011