Thin-type dense sets and related properties

We build on Gruenhage, Natkaniec, and Piotrowski?s study of thin, very thin, and slim dense sets in products, and the related notions of (NC) and (GC) which they introduced. We find examples of separable spaces X such that X² has a thin or slim dense set but no countable one. We characterize ordered spaces that satisfy (GC) and (NC), and we give an example of a separable space which satisfies (GC) but not witnessed by a collection of finite sets. We show that the question of when the topological sum of two countable strongly irresolvable spaces satisfies (NC) is related to the Rudin-Keisler order on βω. We also introduce and study the concepts of <κ-thin and superslim dense sets.     

Quantitative and sensitive detection of rare mutations using droplet-based microfluidics

Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(?) assays and pyrosequencing, while quantitative, cannot detect less than ～1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(?) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(?) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to screen the six common mutations in KRAS codon 12 in parallel in a single experiment.     

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

Background  

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit.     

Photoinduced electron transfer dynamics in porphyrin donor dyads

Intramolecular photoinduced electron transfer (PET) processes occurring in dyads with a free base porphyrin-tetraazaanthracene donor (P) and either a tetracyanonaphthoquinidodimethane (TCQ) or benzoquinone (BQ) acceptor linked by a rigid six σ-bond polynorbornane bridge ([6]) have been investigated. For P[6]BQ, PET in the polar solvent benzonitrile (_s = 25.9) occurs with a rate constant (k_PET) of 1.6 × 10⁸ s⁻¹ but is not evident in solvents less polar than tetrahydrofuran (_s = 7.52). For P[6]TCQ, highly efficient forward PET occurs in both polar and non-polar solvents (k_PET > 2 × 10¹⁰ s⁻¹). For P[6]TCQ the lifetime of the resulting charge-separated state decreases markedly with increasing solvent polarity. The results are discussed in the context of the likely mechanisms for electronic coupling and current theories for PET processes in such linked molecular systems.     

A low temperature study of antiferromagnetic YbVO4 by NMR thermally detected by nuclear orientation

NMR-TDNO results using an external ⁶⁰CoCo (hcp) nuclear orientation thermometer for non-irradiated, single crystal, antiferromagnetic YbVO₄ are compared with those obtained earlier with neutron activated samples using both internal and external γ-ray thermometers. Detailed comparisons are made for the ¹⁷¹Yb (I=1/2, 14.31% abundant) stable nucleus. This strongly asymmetric, largely homogeneous, resonance lineshape was retained and is readily power broadened. Extremely broad, field-dependent homogeneous thermometric responses are observed in the expected frequency range for the quadrupolar stable nucleus ¹⁷³Yb (I=5/2, 16.13% abundant) for both irradiated and non-irradiated samples. This revised version was published online in August 2006 with corrections to the Cover Date.     

Spectral diffusion in the tunneling spectra of ligand-stabilized undecagold clusters

We report diffusion in the tunneling spectra of isolated, ligand-stabilized undecagold (Au11) clusters immobilized by attachment to alpha,omega-alkanedithiolate tethers inserted into alkanethiolate self-assembled monolayers. We use scanning tunneling microscopy and spectroscopy at cryogenic (UHV, 4 K) conditions to measure these clusters' conductance with complete control of their chemical and physical environment; additionally, thermal broadening of their electronic states as well as their mobility is minimized. At low temperature, the Au11 clusters demonstrate Coulomb blockade behavior, with zero-conductance gaps resulting from quantum size effects. Surprisingly, chemically identical and even single particles produced different families of tunneling spectra, comparable to previous results for heterogeneous distributions of particles. We hypothesize that, while these particles are chemically attached to the surface of the SAM for measurement, these assemblies may still be sufficiently dynamic to affect their transport properties significantly.     

A short and stereoselective synthesis of (±)-aristeromycin

A new Stereoselective three-step total synthesis of (±)-aristeromycin starting from readily available 1-hydroxymethyl-3-cyclopentene is described.