A dual gradient assay for the parametric analysis of cell-surface interactions

Cellular response to microgrooves is addressed using a new assay format, comprising orthogonal gradients of continuously varied groove pitch and depth. Dual layer etch masks are created using a combination of micropatterning and plasma polymer deposition. A silicon substrate with a constant groove width of 8 μm and with ridge width increasing from 8 μm in 0.5 μm steps across 10 mm is fabricated by photolithography. A plasma-polymerized hexane film which is 120 nm thick at one end of these grooves, and 10 nm at the other, is deposited under a diffusion mask. Reactive etching of the patterned sample transfers a gradient of groove pitch and groove depth into the silicon substrate. A silicon master with a gradient of groove depth spanning more than two orders of magnitude (less than 10 nm to over 1000 nm) is used to create an injection molding inlay for mass replication of the screening topography. Polycarbonate replicas are molded for use in cell culture studies, and the functionality of the topography as a high-throughput screening platform is investigated. The response of MDCK, h-TERT fibroblasts, and LE2 endothelial cells is examined, in terms of attachment and morphological response to the variation in topographical cues, with the aim of pinpointing the optimal combination of groove pitch and depth to elicit a tailored response from each cell type. When the range of topographical features screened on a single substrate is considered, this new assay represents a significant step forward in the parametric design and analysis of topographical cues at the biomaterial interface.     

Catalytic Ammonia Decomposition Over Ruthenium Nanoparticles Supported on Nano-Titanates

Nanosized Na₂Ti₃O₇, K₂Ti₆O₁₃ and Cs₂Ti₆O₁₃ materials were prepared and used as supports of ruthenium nanoparticles for catalytic ammonia decomposition. It is shown that these catalysts exhibit higher catalytic activity than ruthenium supported on TiO₂ nanoparticles promoted with cesium. The difference is attributed to the use of nanostructured materials with incorporated alkali metals in the crystal lattice, which apparently gives a higher effect of the promoter. All samples were characterized by X-ray powder diffraction, transmission electron microscopy and N₂ physisorption measurements. Furthermore, the effect of ruthenium loading on the catalytic decomposition of ammonia was investigated.     

Strategy for Optimizing LC-MS Data Processing in Metabolomics: A Design of Experiments Approach

A strategy for optimizing LC-MS metabolomics data processing is proposed. We applied this strategy on the XCMS open source package written in R on both human and plant biology data. The strategy is a sequential design of experiments (DoE) based on a dilution series from a pooled sample and a measure of correlation between diluted concentrations and integrated peak areas. The reliability index metric, used to define peak quality, simultaneously favors reliable peaks and disfavors unreliable peaks using a weighted ratio between peaks with high and low response linearity. DoE optimization resulted in the case studies in more than 57% improvement in the reliability index compared to the use of the default settings. The proposed strategy can be applied to any other data processing software involving parameters to be tuned, e.g., MZmine 2. It can also be fully automated and used as a module in a complete metabolomics data processing pipeline.     

3D Two-Photon Microprinting of Nanoporous Architectures

A photoresist system for 3D two-photon microprinting is presented, which enables the printing of inherently nanoporous structures with mean pore sizes around 50 nm by means of self-organization on the nanoscale. A phase separation between polymerizable and chemically inert photoresist components leads to the formation of 3D co-continuous structures. Subsequent washing-out of the unpolymerized phase reveals the porous polymer structures. To characterize the volume properties of the printed structures, scanning electron microscopy images are recorded from ultramicrotome sections. In addition, the light-scattering properties of the 3D-printed material are analyzed. By adjusting the printing parameters, the porosity can be controlled during 3D printing. As an application example, a functioning miniaturized Ulbricht light-collection sphere is 3D printed and tested.     

Practical perfect hashing in nearly optimal space

A hash function is a mapping from a key universe U   to a range of integers, i.e., h:U?{0,1,…,m−1}$h:U?\{\mathrm{0,1},\dots ,m-1\}$, where m is the range's size. A perfect hash function   for some set S⊆U$S\subseteq U$ is a hash function that is one-to-one on S  , where m≥|S|$m\ge \left|S\right|$. A minimal perfect hash function   for some set S⊆U$S\subseteq U$ is a perfect hash function with a range of minimum size, i.e., m=|S|$m=\left|S\right|$. This paper presents a construction for (minimal) perfect hash functions that combines theoretical analysis, practical performance, expected linear construction time and nearly optimal space consumption for the data structure. For n keys and m=n   the space consumption ranges from 2.62n+o(n)$2.62n+o(n)$ to 3.3n+o(n)$3.3n+o(n)$ bits, and for m=1.23n$m=1.23n$ it ranges from 1.95n+o(n)$1.95n+o(n)$ to 2.7n+o(n)$2.7n+o(n)$ bits. This is within a small constant factor from the theoretical lower bounds of 1.44n$1.44n$ bits for m=n   and 0.89n$0.89n$ bits for m=1.23n$m=1.23n$. We combine several theoretical results into a practical solution that has turned perfect hashing into a very compact data structure to solve the membership problem when the key set S is static and known in advance. By taking into account the memory hierarchy we can construct (minimal) perfect hash functions for over a billion keys in 46 min using a commodity PC. An open source implementation of the algorithms is available at http://cmph.sf.net under the GNU Lesser General Public License (LGPL).     

Evaluation of AVHRR PAL and GIMMS 10‐day composite NDVI time series products using SPOT‐4 vegetation data for the African continent

Global 8 km resolution AVHRR (advanced very high resolution radiometer) NDVI (normalized difference vegetation index) 10‐day composite data sets have been used for numerous local to global scale vegetation time series studies during recent years. AVHRR Pathfinder (PAL) NDVI was available from 1981 until 2001, and the new AVHRR GIMMS NDVI was available from 1981 to the present time. A number of aspects potentially introduce noise in the NDVI data set due to the AVHRR sensor design and data processing. NDVI from SPOT‐4 VGT data is considered an improvement over AVHRR, and for this reason it is important to examine how and if the differences in sensor design and processing influence continental scale NDVI composite products. In this study, the quality of these AVHRR NDVI time series are evaluated by the continental scale 1 km resolution SPOT‐4 vegetation (VGT) 10‐day composite (S10) NDVI data. Three years of AVHRR PAL (1998–2000) and seven years of GIMMS (1998–2004) have been compared to 8 km resampled SPOT‐4 VGT (1998–2004) data. The dynamic range of SPOT‐4 VGT NDVI tends to be higher than the AVHRR PAL NDVI, whereas there is an exact match between AVHRR GIMMS NDVI and SPOT‐4 VGT NDVI. Ortho‐regression analysis on annually integrated values of AVHRR PAL/GIMMS and SPOT‐4 VGT on a continental scale reveals high correlations amongst the AVHRR and the SPOT data set, with lowest RMSE (root mean square error) on the GIMMS/SPOT‐4 VGT compared to the PAL/SPOT‐4 VGT.

Analyses on decade data likewise show that a linear relation exists between Spot‐4 VGT NDVI and the two AVHRR composite products; GIMMS explaining most of the Spot‐4 VGT NDVI variance compared to PAL. These results show that the AVHRR GIMMS NDVI is more consistent with Spot‐4 VGT NDVI compared to AVHRR PAL versus Spot‐4 VGT NDVI (in terms of RMSE and dynamic range) and can therefore be considered the more accurate long time AVHRR data record. Analyses performed on monthly maximum composites and decade composite data, however, reveal intra‐annual variations in the correlation between SPOT‐4 VGT and the two AVHRR data sets, which are attributed to different cloud masking algorithms. The SPOT‐4 VGT cloud‐screening algorithm is insufficient, thereby suppressing the rainy season NDVI.     

Wedge splitting test for a steel-concrete interface

This paper presents a test method designated for the determination of the stress-crack opening relationship of a steel-concrete interface. The method is based on the well known wedge splitting test (WST), and it is illustrated how to obtain the stress-crack opening relationship through an inverse analysis. This inversion method utilizes the cracked hinge model, modified such that it describes the problem at hand. In this paper, pure concrete and steel-concrete composite specimens are tested and compared. It turns out that interfacial cracking of a bimaterial specimen usually behaves as one of the parent materials, in this case concrete. The stress-crack opening relationship of both the concrete and bimaterial specimens are obtained through the proposed inverse analysis. The results show, that interfacial cracking is dominated by the so-called wall-effect and its behavior can be described as quasi-brittle. However, due to the wall-effect, interfacial cracking is more brittle than for the pure concrete.     

Effect of processing additives on (bio)degradability of film-blown poly(ε-caprolactone)

Poly(ε-caprolactone)s (PCL) with slip masterbatch, Erucamide, SiO₂ and Erucamide + CaCO₃ as low-molecular-weight processing additives, were film-blown in a single screw extruder. The films and recycled PCL without additives were exposed to composting, anaerobic sewage sludge (37 and 55°C), pure fungal culture, and chemical hydrolysis at two pH (7 and 10.5) and at two temperatures (room temperature and 50°C). Recycling and addition of processing additives resulted in a slightly slower degradation rate compared with the degradation of pure PCL. The degradations in biotic environment were generally faster than in abiotic environment. Higher degradation rates are observed in more complex environments (composts and anerobic sewage sludge) due to synergism between high temperature and a richer fauna of microorganisms. In the biotic environments, faster reductions in number-average molecular weight (M _n) than in weight-average molecular weight (M _w) were observed. A decrease of M _n with up to 75–80% was estimated for composted pure PCL, while similar samples in anaerobic sludge at 55°C were completely degraded in 50 days. The mechanical properties of the samples subjected to composting exhibited a more rapid enbrittlement compared to the samples subjected to abiotic hydrolysis. The observed increase in crystallinity with increasing degree of degradation is explained by crystallization made possible by chain cleavage in the amorphous phase. © 1998 John Wiley & Sons, Inc. J. Appl. Polym. Sci. 70: 61–74, 1998