Data processing for image-based chemical sensors: unsupervised region of interest selection and background noise compensation

Natural olfaction suggests that numerous replicas of small sensors can achieve large sensitivity. This concept of sensor redundancy can be exploited by use of optical chemical sensors whose use of image sensors enables the simultaneous measurement of several spatially distributed indicators. Digital image sensors split the framed scene into hundreds of thousands of pixels each corresponding to a portion of the sensing layer. The signal from each pixel can be regarded as an independent sensor, which leads to a highly redundant sensor array. Such redundancy can eventually be exploited to increase the signal-to-noise ratio. In this paper we report an algorithm for reduction of the noise of pixel signals. For this purpose, the algorithm processes the output of groups of pixels whose signals share the same time behavior, as is the case for signals related to the same indicator. To define these groups of pixels, unsupervised clustering, based on classification of the indicator colors, is proposed here. This approach to signal processing is tested in experiments on the chemical sensitivity of replicas of eight indicators spotted on to a plastic substrate. Results show that the groups of pixels can be defined independently of the geometrical arrangement of the sensing spots, and substantial improvement of the signal-to-noise ratio is obtained, enabling the detection of volatile compounds at any location on the distributed sensing layer.     

Design and synthesis of fluorescent pilicides and curlicides: bioactive tools to study bacterial virulence mechanisms

Pilicides and curlicides are compounds that block the formation of the virulence factors pili and curli, respectively. To facilitate studies of the interaction between these compounds and the pili and curli assembly systems, fluorescent pilicides and curlicides have been synthesized. This was achieved by using a strategy based on structure-activity knowledge, in which key pilicide and curlicide substituents on the ring-fused dihydrothiazolo 2-pyridone central fragment were replaced by fluorophores. Several of the resulting fluorescent compounds had improved activities as measured in pili- and curli-dependent biofilm assays. We created fluorescent pilicides and curlicides by introducing coumarin and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores at two positions on the peptidomimetic pilicide and curlicide central fragment. Fluorescence images of the uropathogenic Escherichia coli (UPEC) strain UTI89 grown in the presence of these compounds shows that the compounds are strongly associated with the bacteria with a heterogeneous distribution.     

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings

Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.     

Preconcentration and matrix isolation of heavy metals through a two-stage solvent extraction in a flow system

Metal ions (Cd, Cu, Pb, Co and Ni) in trace amounts were isolated from sample matrices and concentrated by extraction in a flow system. The sample flow was first mixed with buffer and reagent (carbamates) and the combined aqueous flow was next segmented with trichlorotrifluoroethane (Freon 113). The metal complexes were extracted into the organic phase in a 2-m long coil which was followed by a separator with a teflon membrane. The organic phase passed on to a second segmentor where an acidic, aqueous mercury(II) solution was added. Back-extraction to the aqueous solution took place in a 1-m long coil. The Freon was removed in a second membrane separator and the aqueous phase was collected and analyzed by graphite-furnace atomic absorption spectrometer. The enrichment factors were of the order of 15–20 and the recoveries were 90–100% from the sub-μg l^?1 level up to 20–50 μg l^?1. The recoveries decrease at concentrations above 50 μg l^?1, presumably because of slow dissolution of precipitated complexes in the sample solutions. The observed recoveries for copper were generally somewhat lower, being in the range 80–90%.     

Neighbours of Einstein's equations: Connections and curvatures

Once the action for Einstein's equations is rewritten as a functional of anSO(3, ) connection and a conformal factor of the metric, it admits a family of neighbours having the same number of degrees of freedom and a precisely defined metric tensor. This paper analyzes the relation between the Riemann tensor of that metric and the curvature tensor of theSO(3) connection. The relation is very complicated in general. The Einstein case is distinguished by the fact that two naturalSO(3) metrics on theGL(3) fibres coincide. In the general case the theory is bimetric on the fibres.     

Shape coexistence in the neutron deficient Pb isotopes and the configuration-constrained shell correction approach

Calculations of shape-isomeric states in neutron deficient lead isotopes have been performed using the configuration-constrained shell correction method with a Woods-Saxon average potential and a monopole pairing interaction. This approach enables us to decompose the ground state potential energy surface in separate parts characterized uniquely by the number of occupied intruder orbitals. The calculations reproduce the positions of the excited 0⁺ intruder states. The isotope¹⁹⁶Pb is discussed in detail.     

Construction of isarithms and isarithmic maps by computers

The most important consideration in map construction is that the finished map shall give an objective picture of the actuality it represents. It is also important that the map can be produced quickly and efficiently with a minimum of manual labor. The coordinate mapping method fulfils these requirements to a very high degree. This article deals with isarithmic mapping methods adapted to the coordinate mapping method and to computers and automatic data processing.