Robust DNA microarray image analysis

DNA microarrays are an increasingly important tool that allow biologists to gain insight into the function of thousands of genes in a single experiment. Common to all array-based approaches is the necessity to analyze digital images of the scanned DNA array. The ultimate image analysis goal is to automatically quantify every individual array element (spot), providing information about the amount of DNA bound to a spot. Irrespective of the quantification strategy, the preliminary information to extract about a spot includes the mapping between its location in the digital image and its possibly distorted position in the spot array (gridding). We present a gridding approach divided into a spot-amplification step (matched filter), a rotation estimation step (Radon transform), and a grid spanning step. Quantification of the spots is performed by robustly fitting of a parametric model to pixel intensities with the help of M-estimators. The main advantage of parametric spot fitting is its ability to cope with overlapping spots. If the goodness-of-fit is too bad, a semiparametric spot fitting is employed. We show that our approach is superior to simple quantification strategies such as averaging of the pixel intensities. The system was extensively tested on 1740 images resulting from two DNA libraries.Received: 15 June 2001, Accepted: 21 July 2002, Published online: 3 June 2003 Correspondence to: Norbert Brändle     

Separation of plutonium and neptunium species by capillary electrophoresis-inductively coupled plasma-mass spectrometry and application to natural groundwater samples

Capillary electrophoresis (CE) was coupled to ICPMS in order to combine the good performance of this separation technique with the high sensitivity of the ICPMS for the analysis of plutonium and neptunium oxidation states. The combination of a fused-silica capillary with a MicroMist AR 30-I-FM02 nebulizer and a Cinnabar small-volume cyclonic spray chamber yielded the best separation results. With this setup, it was possible to separate a model element mixture containing neptunium (NpO2(+)), uranium (UO2(2+)), lanthanum (La3+), and thorium (Th4+) in 1 M acetic acid. The same conditions were also suitable for the separation of various oxidation states of plutonium and neptunium in different aqueous samples. All separations were obtained within less than 15 min. A detection limit of 50 ppb identical with 2 x 10(-7) M (3-fold standard deviation of a blank) was achieved. To prove the negligible disturbance of the plutonium and neptunium redox equilibria during the CE separations, plutonium and neptunium speciation by CE-ICPMS in acidic solutions was compared with the results of UV/visible absorption spectroscopy and was found to be in good agreement. The CE-ICPMS system was also applied to study the reduction of Pu(VI) in a humic acid-containing groundwater at different pH values.     

Synthesis and self-assembly of colloidal nanoparticles

We describe recent developments in the synthesis of semiconductor nanoparticles, which lead to a substantial improvement of the luminescence quantum efficiency. Concerning a theoretical model for the growth of an ensemble of nanoparticles, the highest quantum efficiencies are achieved in particles that grow under conditions of a rapid exchange of monomers at the particle surface, leading to a smooth surface structure. Selective etching, core-shell formation and doping of nanoparticles are also discussed as fluorescence-enhancing preparative techniques. Examples of self-assembly of almost-uniformly-sized nanoparticles are given, which result in two-dimensional and three-dimensional superlattices, colloidal crystals and crystalline structures built-up from particles of different sizes. Finally, the self-assembled oriented attachment of quasi-spherical ZnO nanoparticles onto single-crystalline nanorods is presented.     

Micropositioning and microscopic observation of individual picoliter-sized containers within SU-8 microchannels

We describe the fabrication and application of a bioanalytical chip, made of SU-8 photoresist, comprising integrated, high aspect-ratio microfluidic channels, suitable to manipulate and investigate vesicles, cell fragments and biological cells. A central micrometer-sized aperture allows electrical particle counting and planar membrane experiments, microfluids allow (sub)micrometer-sized objects to be transported and addressed with different chemicals. Here we show how lipid vesicles are positioned with micrometer precision within the micro-channels by means of pressure and electrophoretic movement. Our approach is suited for controlling and investigating (bio)chemical synthesis and cellular signalling processes in ultrasmall individual vesicles by electro-optical techniques.     

Mumford-Shah model for one-to-one edge matching.

This paper presents a new algorithm based on the Mumford-Shah model for simultaneously detecting the edge features of two images and jointly estimating a consistent set of transformations to match them. Compared to the current asymmetric methods in the literature, this fully symmetric method allows one to determine one-to-one correspondences between the edge features of two images. The entire variational model is realized in a multiscale framework of the finite element approximation. The optimization process is guided by an estimation minimization-type algorithm and an adaptive generalized gradient flow to guarantee a fast and smooth relaxation. The algorithm is tested on T1 and T2 magnetic resonance image data to study the parameter setting. We also present promising results of four applications of the proposed algorithm: interobject monomodal registration, retinal image registration, matching digital photographs of neurosurgery with its volume data, and motion estimation for frame interpolation.     

Monitoring post-tsunami vegetation recovery in Phang-Nga province,Thailand, based on IKONOS imagery and field investigations – a contribution to the analysis of tsunami vulnerability of coastal ecosystems

A major tsunami in December 2004 devastated the coastal ecosystems along the Andaman Sea coast of Thailand. Since intact coastal ecosystems provide many important services for local communities at the Andaman Sea, it is crucial to investigate to what extent (in terms of percentage area and speed) the affected ecosystems were capable of recovering after the tsunami. Field measurements and multi-date IKONOS imagery were used to estimate the recovery and succession patterns of coastal vegetation types in the Phang-Nga province of Thailand, three years after the tsunami. Thus, this study contributes to a holistic understanding of the ecological vulnerability of the coastal area to tsunamis. A zone-based change detection approach is applied by comparing two change detection techniques: the first method involves the calculation of a recovery rate based on multi-temporal TNDVI (transformed normalized difference vegetation index) images (TNDVI approach), whereas the second approach is a combined approach of the change vector analysis (CVA). Although these two methods provide different types of information (quantitative for the TNDVI approach, qualitative for the CVA), they are comparable in terms of results and accuracies. The results reveal that recovery processes vary based on the type of the ecosystem and, furthermore, are strongly influenced by human activities. Grasslands, coconut plantations and the mixed vegetation cover could recover faster than the mangroves and casuarina forests. Among the forest ecosystems, recovery rates of casuarina forests were higher than for mangroves, but the recovery area was smaller. This study also discusses the potential and some limitations and inaccuracies of applying high-resolution optical imagery for assessing vegetation recovery at a local scale.     

Causalities between CO2, electricity,and other energy variables during phase I and phase II of the EU ETS

The topic of this article is the analysis of the interplay between daily carbon, electricity and gas price data with the European Union Emission Trading System (EU ETS) for CO₂ emissions. In a first step we have performed Granger causality tests for Phase I of the EU ETS (January 2005 until December 2007) and the first year of Phase II of the EU ETS (2008). The analysis includes both spot and forward markets—given the close interactions between the two sets of markets. The results show that during Phase I coal and gas prices, through the clean dark and spark spread, impacted CO₂ futures prices, which in return Granger caused electricity prices. During the first year of the Phase II, the short-run rent capture theory (in which electricity prices Granger cause CO₂ prices) prevailed. On the basis of the qualitative results of the Granger causality tests we obtained the formulation testable equations for quantitative analysis. Standard OLS regressions yielded statistically robust and theoretically coherent results.     

Membranen in der Verfahrenstechnik

Membranes in chemical engineering . In the last 10 years membranes and membrane processes have evolved from a useful laboratory tool to an industrial product of significant technical and commercial impact. In some applications membrane processes have today not only replaced some conventional separation procedures in the chemical process industry, because they are often more economical and yield better quality products, but they have also successfully been utilized to solve mass separation problems where conventional procedures failed or are too expensive. This contribution discusses the state of the art of membranes and membrane processes as well as their major applications, with the main emphasis being placed on more recent developments.     

Regulation of calf renal 25-hydroxyvitamin D-hydroxylase activities by calcium-regulating hormones

Parathyroid hormone and 1,25-dihydroxyvitamin D3 had opposite effects on calf renal 25-hydroxyvitamin D3 24-, 23-, and 1 alpha-hydroxylase activities. Parathyroid hormone administration increased renal 25-hydroxyvitamin D3-1 alpha-hydroxylase activity 7-fold while 25-hydroxyvitamin D3-23- and 24-hydroxylase activities were essentially the same as controls. Administration of 1,25-dihydroxyvitamin D3 increased 25-hydroxyvitamin D3-23-hydroxylase and 24-hydroxylase activities 4-fold and decreased 25-hydroxyvitamin D3-1 alpha-hydroxylase activity to undetectable concentrations. Vitamin D deficiency increased 25-hydroxyvitamin D3-1 alpha -hydroxylase activity 13-fold, and 25-hydroxyvitamin D3-23-hydroxylase and 24-hydroxylase activities were undetectable. These results confirm previous reports with regard to control of renal 25-hydroxyvitamin D3-24-hydroxylase and 1 alpha -hydroxylase in other species and represent new findings relative to the control of 25-hydroxyvitamin D3-23-hydroxylase. Plasma P was lower and 1,25-dihydroxyvitamin D3 higher in calves treated with parathyroid hormone, and Ca and 1,25-dihydroxyvitamin D3 were lower in the vitamin D-deficient calves. 1,25-Dihydroxyvitamin D3-treated calves had higher plasma P and lower Mg than controls. Further studies using this calf model should lead to better understanding of Ca-regulating hormones control of vitamin D metabolism.