Subunit composition of neurofilaments specifies axonal diameter

Neurofilaments (NFs), which are composed of NF-L, NF-M, and NF-H, are required for the development of normal axonal caliber, a property that in turn is a critical determinant of axonal conduction velocity. To investigate how each subunit contributes to the radial growth of axons, we used transgenic mice to alter the subunit composition of NFs. Increasing each NF subunit individually inhibits radial axonal growth, while increasing both NF-M and NF-H reduces growth even more severely. An increase in NF-L results in an increased filament number but reduced interfilament distance. Conversely, increasing NF-M, NF-H, or both reduces filament number, but does not alter nearest neighbor interfilament distance. Only a combined increase of NF-L with either NF-M or NF-H promotes radial axonal growth. These results demonstrate that both NF-M and NF-H play complementary roles with NF-L in determining normal axonal calibers.     

Scalable parallel word search in multicore/multiprocessor systems

This paper presents a parallel algorithm for fast word search to determine the set of biological words of an input DNA sequence. The algorithm is designed to scale well on state-of-the-art multiprocessor/multicore systems for large inputs and large maximum word sizes. The pattern exhibited by many sequential solutions to this problem is a repetitive execution over a large input DNA sequence, and the generation of large amounts of output data to store and retrieve the words determined by the algorithm. As we show, this pattern does not lend itself to straightforward standard parallelization techniques. The proposed algorithm aims to achieve three major goals to overcome the drawbacks of embarrassingly parallel solution techniques: (i) to impose a high degree of cache locality on a problem that, by nature, tends to exhibit nonlocal access patterns, (ii) to be lock free or largely reduce the need for data access locking, and (iii) to enable an even distribution of the overall processing load among multiple threads. We present an implementation and performance evaluation of the proposed algorithm on DNA sequences of various sizes for different organisms on a dual processor quad-core system with a total of 8 cores. We compare the performance of the parallel word search implementation with a sequential implementation and with an embarrassingly parallel implementation. The results show that the proposed algorithm far outperforms the embarrassingly parallel strategy and achieves a speed-up’s of up to 6.9 on our 8-core test system.     

Distribution of movement time in a target-aiming task

Various characteristics of the distribution of movement time were analyzed for a task involving serial and rotary arm movements aimed at a target. For experimental data generated from five Ss, (a) the distribution tended to be unimodal and more peaked than a normal distribution, (b) the skewness of the distribution was predominantly positive and (c) the standard deviation, in addition to the mean, of movement time was significantly affected by the complexity of the task as measured by Fitts' index of difficulty, while the skewness and the kurtosis were not. For the average results for the Ss, a first-order linear model with the standard deviation of movement time as the dependent variable and Fitts' index as the independent one explained 67% of the variation in standard deviation as compared to 98% of the variation in mean movement time accounted for by the Fitts' index.     

Functional identity of the monomeric and multiple forms of elongation-factor 1 from Krebs-II mouse ascites-tumor cells

Highly purified 3H-labelled elongation factor 1 (EF-1) from Krebs II mouse ascites tumour cells was separated into biologically active monomeric and aggregate forms of the enzyme by either gradient centrifugation or gel filtration. When corrected for their content of inactive enzyme both forms of the factor were found to be equally active whether tested in the binding or synthesis reaction. The only form of the enzyme found bound to ribosomes was the monomer; it was therefore concluded that the aggregate form of the enzyme must first dissociate before it reacts with the ribosome. The stoichiometry of the aminoacyl-tRNA binding reaction to ribosomes in the presence of guanosine nucleotides was also studied. It was found that one molecule of aminoacyl-tRNA and of Guo-5'-P2-CH2-P is bound per molecule of EF-1 bound to the ribosome. Following interaction with a release from, the ribosomes, EF-1 was found to be predominantly monomeric.     

Pyrolysis of model compounds of the flame retardant poly(N-dimethylphosphonomethyl acrylamide)

An investigation of the thermal decomposition of N-dimethylphosphonomethyl amides has shown that the major volatile products for decomposition above 300°C are methanol, the methyl ester of the carboxylic acid, the nitrile, the carboxylic acid, the N-methyl amide, and the N,N-dimethyl amide. Also, benzoic acid was the only volatile product detected in the decomposition of α-benzamidomethylphosphonic acid. A mass balance for the decomposition of N-dimethylphosphonomethyl benzamide at 420°C showed methanol and methyl benzoate to be the major volatile products. Methanol and benzonitrile formation increased with an increase in temperature at a faster rate than the other volatile products. The reaction of amides and phosphonates was further studied using sealed tubes in a furnace. Reaction of N-methylbenzamide with dimethyl methylphosphonate at 307°C in a sealed tube produced methyl benzoate and N,N-dimethylbenzamide. N,N-dimethylbenzamide and dimethylmethylphosphonate were also shown to produce methyl benzoate at 310°C. After a 5-min period more methyl benzoate was produced in the N,N-dimethylbenzamide reaction than in the N-methylbenzamide reaction. Also, addition of ethanol to the N,N-dimethylbenzamide/dimethyl methylphosphonate reaction resulted in less ethyl benzoate methyl benzoate after heating at 310°C.     

MINERALOGICAL,BIB‐SEM AND PETROPHYSICAL DATA IN SEAL ROCK ANALYSIS: A CASE STUDY FROM THE VIENNA BASIN,AUSTRIA

The Vienna Basin is a major hydrocarbon province with a long exploration history. Within the basin, secondary migration from Upper Jurassic source rocks into stacked Middle Miocene (Badenian) sandstone reservoirs was formerly considered to have occurred almost entirely along major fault zones. However recent exploration data has suggested that in areas where no major faults are present, oil may have migrated vertically through the sandy mudstone intervals separating individual reservoir units, which are therefore imperfectly sealed. In order to investigate possible secondary migration through the semi‐permeable mudstones, this study links variations in gross depositional environment (GDE) to variations in mudstone properties (e.g. mineralogy and pore size distribution). The study focussed on the mudstones which seal reservoir sandstones referred to locally as the “8.TH” and “16.TH” units. The bulk mineralogical composition of 56 mudstone and sandy mudstone (and minor intercalated muddy sandstone) samples from seal layers in 22 wells was studied by X‐ray diffraction analysis, broad ion beam – scanning electron microscopy (BIB‐SEM), mercury intrusion porosimetry (MICP) and N₂ adsorption. These data are interpreted in the context of GDE maps of the Vienna Basin which were previously established using seismic and well log data. Results indicate that the gross depositional environment strongly controlled the pore space characteristics of the mudstones. The sandy mudstones in the NW part of the study area were influenced by a complex eastward‐prograding deltaic system which deposited coarse detritus into a major palaeo depression (“Zistersdorf Depression”) located in the centre of the basin. Higher overall porosity and a dominance of larger pore size classes, probably resulting in reduced seal quality, were observed for sandy mudstones from well locations within feeder channels and also from within the Zistersdorf Depression. Similarly, sandy mudstones from locations associated with the long‐term input of coarser sediments in shoreline, coastal and proximal offshore settings in the NW and central parts of the study area are considered to be of lower sealing quality compared to fine‐grained mudstones deposited in distal, open‐marine settings which prevailed in the SE part of the study area throughout the Middle Miocene. In general, pore geometries were influenced by mineralogical composition; quartz‐ and detrital carbonate‐rich samples show equidimensional pores, while more elongated pores (with a higher average aspect ratio) characterize clay‐rich samples. Furthermore, matrix mesopores (2‐50 nm) determined by N₂ sorption are more abundant in clay‐rich versus quartz‐rich samples, and show a pronounced positive trend with increasing percentage of illite‐smectite mixed‐layer clay minerals. This study shows that regional‐scale mudstone seals in the Vienna Basin have been influenced by variations in sedimentation associated with lateral variations in gross depositional environment during the Middle Miocene. The observed pore characteristics will serve as input data for future models of secondary migration.     

Model-based determination of changing kinetics in high cell density cultures using respiration data

During high cell density cultivations, very low growth rates and changes in cell metabolism occur. These have to be accounted for in the kinetic modelling. In this work, an optimisation-based approach is presented which recognises the switching to new parameters at a certain growth rate and thereby improves the quality of the model prediction for different time horizon lengths. For the dynamic automatic adjustment to changing kinetics, a moving horizon estimator (MHE) is applied. Experimental data from cultivations of Ustilago maydis are used for the model-based parameter identification. To validate the method, initially offline data are utilised. In the next step, respiration data, which are available online, are used to enable real-time monitoring. The embedded MHE was successfully applied to predict changes in biokinetic constants during membrane bioreactor (MBR) fermentation. Setting suited horizon lengths and parameter bounds was found to be crucial for convergence and parameter estimation. The expected drop in maintenance parameters at low growth rates was confirmed when using an optimum number of data points.