Proton beam writing of microstructures in Agar gel for patterned cell growth

A rather useful prerequisite for many biological and biophysical studies, e.g., for cell-cell communication or neuronal networks, is confined cell growth on micro-structured surfaces. Solidified Agar layers have smooth surfaces which are electrically neutral and thus inhibit receptor binding and cell adhesion. For the first time, Agar microstructures have been manufactured using proton beam writing (PBW). In the irradiated Agar material the polysaccharides are split into oligosaccharides which can easily be washed off leaving Agar-free areas for cell adhesion. The beam diameter of 1 μm allows the fabrication of compartments accommodating single cells which are connected by micrometer-sized channels. Using the external beam the production process is very fast. Up to 50 Petri dishes can be produced per day which makes this technique very suitable for biological investigations which require large throughputs.     

Systematic determination of intrinsic reaction parameters in enzyme immobilizates

For the rational design of processes using immobilized enzymes a mechanistic kinetic model is required, which accounts for all kinetic and thermodynamic phenomena, including the enzyme reaction, the mass transfer of the reactants between both phases, and their diffusion inside the immobilizate. For the example of enzymes immobilized in hydrogel beads suspended in an organic solvent, such a mechanistic kinetic model was obtained by a model-based experimental analysis approach. It was proven that the usually applied concentration measurements in the bulk phase are not sufficient to draw mechanistic conclusions. The most suitable measurement technique was found to be the quantification of the concentration along the radius of the hydrogel bead. These line scans, achieved by two-photon laser scanning microscopy, for the first time allowed to estimate intrinsic reaction and mass transfer parameters simultaneously. Thus, the obtained intrinsic parameter estimates for the biphasic hydrogel system could be directly compared with those obtained in individual systems. This comparison revealed for the first time that the enzyme reaction was not significantly affected by the mild hydrogel encapsulation. However, a significant impact on the transport parameters was found that underlines the need for analyzing the real reaction system using mechanistic models.     

Sparse matrix operations on several multi-core architectures

This paper compares various contemporary multicore-based microprocessor architectures from different vendors with different memory interconnects regarding performance, speedup, and parallel efficiency. Sparse matrix decomposition is used as a benchmark application. The example matrix used in the experiments comes from an electrical engineering application, where numerical simulation of physical processes plays an important role in the design of industrial products.     

Capillary zone electrophoresis for gliadin separation: applications in a spelt breeding program

Gliadins of 27 European spelt [Triticum aestivum ssp. spelta (L.) Thell.] cultivars (cvs) were separated by capillary zone electrophoresis (CZE). A great amount of diversity was found within the CZE gliadin patterns of these cvs; however, only 15 had unique patterns, whereas 2 triples and 3 pairs were identical, i.e., differences were within the uncertainty of the method and environmental effects. Two of these identical pairs were attributed to mislabeling: affected were one of the two Swiss spelt cvs 'Ostar' and 'Sertel', and the German spelt cv 'Steiners Roter Tiroler'. The German cv 'Franckenkorn' showed considerable similarity with the Belgian cv 'Rouquin'. CZE gliadin patterns of 12 modern German bread wheat cvs were distinctly different from those of spelt cvs selected from old land varieties like the Swiss cv 'Oberkulmer Rotkorn'. In the gliadin patterns of 11 spelt cvs, bread wheat elements were found. 7 of the 24 cvs not mislabeled are known to be progeny of wheat/spelt crosses, 4 cvs are described as pure spelt, and the pedigrees of 13 are unknown. Wheat elements were spotted in only 4 of the 7 wheat/spelt crosses and in none of the 4 pure spelt cvs. The results suggest that crossing spelt with modern wheat may be, but is not necessarily, reflected in the gliadin pattern.

High-Speed Prefix-Preserving IP Address Anonymization for Passive Measurement Systems

Passive network measurement and packet header trace collection are vital tools for network operation and research. To protect a user's privacy, it is necessary to anonymize header fields, particularly IP addresses. To preserve the correlation between IP addresses, prefix-preserving anonymization has been proposed. The limitations of this approach for a high-performance measurement system are the need for complex cryptographic computations and potentially large amounts of memory. We propose a new prefix-preserving anonymization algorithm, top-hash subtree-replicated anonymization (TSA), that features three novel improvements: precomputation, replicated subtrees, and top hashing. TSA makes anonymization practical to be implemented on network processors or dedicated logic at Gigabit rates. The performance of TSA is compared with a conventional cryptography based prefix-preserving anonymization scheme which utilizes caching. TSA performs better as it requires no online cryptographic computation and a small number of memory lookups per packet. Our analytic comparison of the susceptibility to attacks between conventional anonymization and our approach shows that TSA performs better for small scale attacks and comparably for medium scale attacks. The processing cost for TSA is reduced by two orders of magnitude and the memory requirements are a few Megabytes. The ability to tune the memory requirements and security level makes TSA ideal for a broad range of network systems with different capabilities     

A methodology for specifying PET VOIs using multimodalitytechniques

Volume-of-interest (VOI) extraction for radionuclide and anatomical measurements requires correct identification and delineation of the anatomical feature being studied. The authors have developed a toolset for specifying three dimensional (3-D) VOIs on a multislice positron emission tomography (PET) dataset. The software is particularly suited for specifying cerebral cortex VOIs which represent a particular gyrus or deep brain structure. A registered 3-D magnetic resonance image (MRI) dataset is used to provide high-resolution anatomical information, both as oblique two-dimensional (2-D) sections and as volume renderings of a segmented cortical surface. VOIs are specified indirectly in two dimensions by drawing a stack of 2-D regions on the MRI data. The regions are tiled together to form closed triangular mesh surface models, which are subsequently transformed into the observation space of the PET scanner. Quantification by this method allows calculation of radionuclide activity in the VOIs, as well as their statistical uncertainties and correlations. The methodology for this type of analysis and validation results are presented     

Heavy-Water (D2O) Take-Up-Induced Lattice Expansion in the High-Temperature Proton Conductor Ba3Ca1.18Nb1.82O9−δ

Dimensional changes of the high-temperature proton conductor Ba₃Ca_1.18Nb_1.82O_9−δ, when exposed to D₂O vapor, were investigated using length-change and precision density measurements. Such information is essential for possible applications of proton conductors in solid oxide fuel cells and humidity and hydrogen sensors. A linear increase of the sample lengths with increases in the deuterium content was observed. Comparison of the present D₂O data with those that were previously obtained for H₂O showed that there was a small isotope effect in the lattice expansion. The fact that the length-change-versus-hydrogen-isotope-concentration curves were almost isotope independent supported the validity of the take-up reaction H₂O( g ) + V_Oö+ Ox_O is an ⇄ 2OH_O. In regard to the latter equation, it was found that small islands of silver, palladium, nickel, and platinum act as catalytic promoters of the reaction and lead, for given heavy-water-steam exposure conditions, to an increase of water absorption of up to 100%, when compared with samples without the catalytic surface layers.     

Commentary: Achieving phosphorus reduction targets for Lake Erie

Harmful Algal Blooms (HABs), which were largely absent from Lake Erie from the 1980s until the mid-late 1990s, have been growing steadily worse in intensity. While much of the phosphorus loading into the lake prior to 1972 was caused by point-source pollution, approximately 88% to 93% of current loading comes from nonpoint sources, of which agriculture is the dominant land use. A reduction target of 860?metric?tons, or 40% of the total phosphorus spring loading in 2008, has been set with the expectation that such a reduction could limit the size and associated impact of HABs in 9 out of every 10?years. We review the effectiveness of recommended practices aimed at reducing phosphorus loss in agriculture and pair this knowledge with behavioral data on likely adoption to identify how best to achieve the reduction target. The data suggests that the target is feasible as a majority of the farming population is willing to consider many of the recommended practices. However, increases in adoption over time have been minimal, and farmers will need better cost-benefit information, site-specific decision support tools, and technical assistance in order to more rapidly adopt and execute the placement of recommended practices. A combination of voluntary and mandatory approaches may be needed, but policies and programs promoting voluntary adoption should be designed to better target known barriers and maximize voluntary program effectiveness.     

A bifunctional enzyme catalyzes the first two steps in N-acetylneuraminic acid biosynthesis of rat liver. Purification and characterization of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase

Biosynthesis of N-acetylneuraminic acid (Neu5Ac), a prominent component of glycoconjugates, is initiated by the action of UDP-N-acetylglucosamine 2-epimerase (UDP-GlcNAc 2-epimerase, EC 5.1. 3.14) and N-acetylmannosamine kinase (ManNAc kinase, EC 2.7.1.60). We demonstrate for the first time that the two activities are parts of one bifunctional enzyme in rat liver. The enzyme was purified to homogeneity from rat liver cytosol using salmine sulfate precipitation and chromatography on phenyl-Sepharose, ATP-agarose, and Mono Q. The purification resulted in one polypeptide with an apparent molecular mass of 75 kDa. Immunoprecipitation with a polyclonal antibody against the polypeptide reduced both enzyme activities in equal amounts. Gel filtration analysis of purified UDP-GlcNAc 2-epimerase/ManNAc kinase showed that the polypeptide self-associates as a dimer and as a hexamer with apparent molecular masses of 150 and 450 kDa, respectively. The hexamer was fully active for both enzyme activities, whereas the dimer catalyzed only the phosphorylation of N-acetylmannosamine (ManNAc). Incubation of the dimer with UDP-N-acetylglucosamine led to reassembly of the fully active hexamer; maximal quantities of the hexamer were produced after incubation for 3 h. Kinetic analysis of purified hexameric and dimeric enzyme revealed significantly lower Michaelis constants (93 +/- 3 to 121 +/- 15 microM for ManNAc and 1.18 +/- 0. 13 to 1.67 +/- 0.20 mM for ATP) and higher cooperativity (Hill coefficients of 1.42 +/- 0.16 to 1.17 +/- 0.06 for ManNAc and 1.30 +/- 0.09 to 1.05 +/- 0.14 for ATP) for the hexamer for both substrates of ManNAc kinase. The Michaelis constant of UDP-GlcNAc 2-epimerase for its substrate was 11 +/- 2 microM. The Hill coefficient of 0.45 +/- 0.07 represents strongly negative cooperativity in substrate binding. UDP-GlcNAc 2-epimerase was feedback inhibited by CMP-Neu5Ac. Complete inhibition was achieved with 60 microM CMP-Neu5Ac, and highly positive cooperativity (Hill coefficient of 4.1) was found for inhibitor binding.