GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.     

Kinetic study of angiotensin converting enzyme activity by capillary electrophoresis after in-line reaction at the capillary inlet

The in-capillary reaction of angiotensin converting enzyme (ACE) with the tripeptide substrate hippuryl-L-histidyl-L-leucine was studied. ACE activity was determined by the quantitation of the product, hippuric acid, at 230 nm. Reaction occurred at the capillary inlet during a predetermined waiting period, followed by the electrophoretic separation of the compounds. When the set-up was reversed, i.e. reaction at the opposite side after short-end injection of enzyme and substrate, separation was achieved in less than 5 min. Using the Lineweaver-Burk equation, an average Michaelis constant for ACE from rabbit lung was calculated to be 1.16 +/- 0.12 mM, a value consistent with previously reported data.     

High-resolution laser ablation-inductively coupled plasma-mass spectrometry imaging of cisplatin-induced nephrotoxic side effects

Two-dimensional elemental mapping (bioimaging) via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was performed on 5 μm thick formalin-fixed, paraffin-embedded kidney tissue sections from Cynomolgus monkeys administered with increasing pharmacological doses of cisplatin. Laterally resolved pixels of 1 μm were achieved, enabling elemental analysis on a (sub-)cellular level. Zones of high Pt response were observed in the renal cortex, where proximal tubules are present, the epithelium of which is responsible for partial reabsorption of cisplatin. Histopathological evaluation, of hematoxylin and eosin-stained serial sections, adjacent to the sections probed via LA-ICP-MS, revealed minimal to mild cisplatin-related lesions (<100 μm) in the renal cortex. Necrotic proximal tubules with sloughed epithelial cells in their lumen could be linked directly to the areas with the highest accumulation of cisplatin, indicating a direct link between cellular concentration and toxicity, thereby providing more insight into the mechanisms through which renal damage occurs.     

Synthesis and metal complexation studies of [2n]thiacalix[m]arene[m]pyrazine

Novel [2_n]thiacalixarenepyrazine and [2_n]thiacalixarenetriazine systems were synthesised by one-pot S_NAr reactions. A screening of the metal-complexing ability of [2₆]hexathiacalix[3]arene[3]pyrazine revealed its affinity for Cu^I, Cu^II and Ag^I metal salts.     

Molecular Fluorescence Imaging Spectroscopy for Mapping Low Concentrations of Red Lake Pigments: Van Gogh's Painting The Olive Orchard

Vincent van Gogh used fugitive red lake pigments that have faded in some paintings. Mapping their distribution is key to understanding how his paintings have changed with time. While red lake pigments can be identified from microsamples, in situ identification and mapping remain challenging. This paper explores the ability of molecular fluorescence imaging spectroscopy to identify and, more importantly, map residual non‐degraded red lakes. The high sensitivity of this method enabled identification of the emission spectra of eosin (tetrabromine fluorescein) lake mixed with lead or zinc white at lower concentrations than elemental X‐ray fluorescence (XRF) spectroscopy used on account of bromine. The molecular fluorescence mapping of residual eosin and two carmine red lakes in van Gogh's The Olive Orchard is demonstrated and compared with XRF imaging spectroscopy. The red lakes are consistent with the composition of paint tubes known to have been used by van Gogh.     

On the Validity of Entropy Production Principles for Linear Electrical Circuits

We explain the (non-)validity of close-to-equilibrium entropy production principles in the context of linear electrical circuits. Both the minimum and the maximum entropy production principles are understood within dynamical fluctuation theory. The starting point are Langevin equations obtained by combining Kirchoff’s laws with a Johnson-Nyquist noise at each dissipative element in the circuit. The main observation is that the fluctuation functional for time averages, that can be read off from the path-space action, is in first order around equilibrium given by an entropy production rate. That allows to understand beyond the schemes of irreversible thermodynamics (1) the validity of the least dissipation, the minimum entropy production, and the maximum entropy production principles close to equilibrium; (2) the role of the observables’ parity under time-reversal and, in particular, the origin of Landauer’s counterexample (1975) from the fact that the fluctuating observable there is odd under time-reversal; (3) the critical remark of Jaynes (1980) concerning the apparent inappropriateness of entropy production principles in temperature-inhomogeneous circuits.     

Proactive heuristic procedures for robust project scheduling: An experimental analysis

Solution-robust project scheduling is a growing research field aiming at constructing proactive schedules to cope with multiple disruptions during project execution. When stochastic activity durations are considered, including time buffers between activities is a proven method to improve the stability of a baseline schedule.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Lower Semi-continuous Function Frames

It has never been systematically studied under which algebraic actions lower semi-continuity is a stable property. This is despite the fact that this continuity variant is commonly used, in different branches of mathematics. In this note we propose an abstraction of the lower semi-continuous function frame on a topological space and describe this as the Eilenberg–Moore algebras of a Hom-functor monad. We also point out the connection with approach frames and with classical frame theory. Thereby we obtain several different characterizations of the introduced category.