Biometric Evaluation of the ATC Method for the Determination of the Acute Dermal Toxicity of Chemicals

The new dermal acute toxic class (ATC) method is presented for one specific classification system for chemicals (released by the European Union) according to acute dermal toxicity. It is a stepwise procedure using three animals of one sex per step. Three starting doses are possible. Assuming a Probit model for the dose response relationship probabilities of a correct, of a less and of a more stringent classification are calculated. It is shown that these probabilities depend only weakly on the starting dose. Also, the expected numbers of used and of dead animals are derived in dependence on the LD₅₀ and on the dose response slope β, as well as the starting doses minimizing the expected animal number are proposed. The results demonstrate that the dermal ATC method is a reliable alternative to the classical LD₅₀ test with the use of significantly fewer animals.     

A simplified method for the rapid isolation of cardiac intercalated discs

A simple and rapid method for the isolation of intercalated discs from a single rat heart is described. The outstanding features of this method are (i) a large quantity of starting material is not necessary, (ii) ultracentrifugation and separating gradient steps are not required, (iii) the disc fraction is relatively pure as verified by electron microscopy, and (iv) the starting tissue is rapidly homogenized into buffer, reducing possible damage to membrane structures after animal death. The fraction is rich in intercellular junctions, with gap junctions, fasciae adherentes and maculae adherentes all appearing well preserved. It should prove a useful starting base for further purification of these junctions and of sarcolemma from a specific portion of the cell surface membrane, namely the major area of structural interaction between adjacent cardiac cells.     

A modified method for whole exome resequencing from minimal amounts of starting DNA

Next generation DNA sequencing (NGS) technologies have revolutionized the pace at which whole genome and exome sequences can be generated. However, despite these advances, many of the methods for targeted resequencing, such as the generation of high-depth exome sequences, are somewhat limited by the relatively large amounts of starting DNA that are normally required. In the case of tumour analysis this is particularly pertinent as many tumour biopsies often return submicrogram quantities of DNA, especially when tumours are microdissected prior to analysis. Here, we present a method for exome capture and resequencing using as little as 50 ng of starting DNA. The sequencing libraries generated by this minimal starting amount (MSA-Cap) method generate datasets that are comparable to standard amount (SA) whole exome libraries that use three micrograms of starting DNA. This method, which can be performed in most laboratories using commonly available reagents, has the potential to enhance large scale profiling efforts such as the resequencing of tumour exomes.     

In-depth characterization of genome-scale network reconstructions for the in vitro synthesis in cell-free systems

Cell-free systems containing multiple enzymes are becoming an increasingly interesting tool for one-pot syntheses of biochemical compounds. To extensively explore the enormous wealth of enzymes in the biological space, we present methods for assembling and curing data from databases to apply them for the prediction of pathway candidates for directed enzymatic synthesis. We use Kyoto Encyclopedia of Genes and Genomes to establish single organism models and a pan-organism model that is combining the available data from all organisms listed there. We introduce a filtering scheme to remove data that are not suitable, for example, generic metabolites and general reactions. In addition, a valid stoichiometry of reactions is required for acceptance. The networks created are analyzed by graph theoretical methods to identify a set of metabolites that are potentially reachable from a defined set of starting metabolites. Thus, metabolites not connected to such starting metabolites cannot be produced unless new starting metabolites or reactions are introduced. The network models also comprise stoichiometric and thermodynamic data that allow the definition of constraints to identify potential pathways. The resulting data can be directly applied using existing or future pathway finding tools.     

Biomechanics of leg deformity treatment

At pre-school age, there is a possibility to treat severe varosity and/or valgosity of legs by orthoses. The three points force effect of the orthosis partially corrects the pathologic defect of the leg. If the orthosis is intermittently used for a long time the correction is permanent. Step by step correction of bone deformities are based on remodelling of growth epiphyses and bones that are caused by orthotic bending pre-stressing. According to Hüter-Volkmann's law, the oblique loading regulates the growth of epiphyseal plates of long bone into the direction of the pressure result and the bone remodelling process is started: it means that the bone grows at the tensile part of growth epiphyses more quickly than at pressure one and gradually eliminates the varosity and/or valgosity defect. The knowledge of stress values for starting of the bone remodelling process is principal for clinical praxis. The values of pre-stressing cannot be increased by starting the remodelling process from the ethical point of view but it can be judged on its starting according to the success of the treatment. The aim of this article is to study the bone, ligament stress state and deformations of successful treatment. Method and calculation algorithm of stress state and deformation that are necessary for the starting of the remodelling process at the knee region were verified on a group of eight patients that were fitted by orthoses with bending pre-stressing. The space models of the knee, femur and tibia were composed with the help of X-ray, CT and MRI scan. The calculation algorithm was implemented on a PC and the program can be easily applied at clinical praxis.     

Dynamics,control, and simulation of the jump of a quadruped

Gross body motion of a six-link quadruped model is considered in the sagittal plane. The model includes eight representative muscles of fore- and hind limbs as force generators. The kinematics of the quadruped's long jump are studied, and the translational and the rotational components of the jump are decoupled. Stability of the model is achieved by state feedback. The motion of this model during starting, flight, and landing phases of motion is studied by digital computer simulation. It is shown that in the starting phase feedback is essential for the control of the takeoff velocity, while the jump itself can be carried out without feedback as a ballistic movement.     

Formation of Starting Plasma Flow in an Open Trap Using Arc Plasma Gun

Plasma Physics Reports - The system is described for the formation of the low-temperature starting plasma flow in the GOL-NB trap. The starting plasma is a target for capturing heating neutral...     

miRNAs expression analysis in paired fresh/frozen and dissected formalin fixed and paraffin embedded glioblastoma using real-time pCR

miRNAs are small molecules involved in gene regulation. Each tissue shows a characteristic miRNAs epression profile that could be altered during neoplastic transformation. Glioblastoma is the most aggressive brain tumour of the adult with a high rate of mortality. Recognizing a specific pattern of miRNAs for GBM could provide further boost for target therapy. The availability of fresh tissue for brain specimens is often limited and for this reason the possibility of starting from formalin fixed and paraffin embedded tissue (FFPE) could very helpful even in miRNAs expression analysis. We analysed a panel of 19 miRNAs in 30 paired samples starting both from FFPE and Fresh/Frozen material. Our data revealed that there is a good correlation in results obtained from FFPE in comparison with those obtained analysing miRNAs extracted from Fresh/Frozen specimen. In the few cases with a not good correlation value we noticed that the discrepancy could be due to dissection performed in FFPE samples. To the best of our knowledge this is the first paper demonstrating that the results obtained in miRNAs analysis using Real-Time PCR starting from FFPE specimens of glioblastoma are comparable with those obtained in Fresh/Frozen samples.     

Poly(oxazoline)s with telechelic antimicrobial functions

Poly(2-alkyl-1,3-oxazoline)s (alkyl = methyl, ethyl) with terminal quarternary ammonium groups were synthesized. It could be shown by NMR and ESI-MS that the termination of the living polymerization with N,N-dimethylalkyl(butyl to hexadecyl)amines was quantitative. The novel functions were investigated regarding their antimicrobial potential toward the bacterium Staphylococcus aureus revealing that only quarternary ammonium functions with 12 and more carbons are antibacterial. Using a novel bifunctional initiator, 3-[(tert-butoxycarbonyl)amino]benzyl-p-toluenesulfonate, poly(oxazoline) with a primary amino group at the starting end and an antimicrobial function at the terminal could be synthesized, as confirmed by NMR and ESI-MS measurements. Comparing the bioactivity of polymers with different functions at the starting end and terminated with dimethyldodecylamine revealed that the starting group has a great effect on the antibacterial properties of the distant terminal. The minimal inhibitory concentrations varied from 0.1 mM for polymer derivatives with a BOC-NH-phenyl starting group to 4 mM for poly(oxazoline)s with a free primary amine at the starting end.     

Sluggishness of auditory perception during localization of short moving sound images

During localization of a moving sound source, a shift of the perceived position relative to the actual one of the starting point is an expression of the perception of sluggishness of the auditory system. In this study, the human ability to localize starting points during a gradual or abrupt movement of fused auditory images (FAIs) was compared with the ability to localize the position of a stationary sound image. Sound images moved from the midline of the head in the direction of each of the ears. The subject’s responses were recorded using a graphics table. There was a tendency to shift the starting point of the trajectory in the direction of the movement. This tendency was stronger for gradual rather than for abrupt FAI movement and for shorter stimuli (100 ms) than for long ones (200 ms). The value of the starting point’s displacement depended on the final interaural time delay. The results obtained are discussed in terms of the “snapshots” and “movement detector” theories, as well as in terms of the sluggish and anticipatory ability of auditory perception.     

Large-scale characteristics of the energy landscape in protein-protein interactions

Characterization of intermolecular energy landscapes in protein-protein interactions is important for understanding the mechanisms of these interactions as well as for designing better protein docking methods. A simplified representation of the landscape was used for a systematic study of its large-scale characteristics in a large nonredundant dataset of protein complexes. The focus of the study is on the basic features of the low-resolution energy basins and their distribution on the landscape. The results clearly show that, in general, the number of such basins is small, these basins are well formed, correlated with actual binding modes, and the pattern of basins distribution depends on the type of the complex. For docking studies, the results suggest that adequate starting points for the structural refinement are detectable by low-resolution procedures and the number of such starting points is relatively small.     

Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study

Molecular dynamics simulations of the binding of the heterochiral tripeptide KkN to the transactivation responsive (TAR) RNA of HIV-1 is presented, using an all-atom force field with explicit water. To obtain starting structures for the TAR-KkN complex, semirigid docking calculations were performed that employ an NMR structure of free TAR RNA. The molecular dynamics simulations show that the starting structures in which KkN binds to the major groove of TAR (as it is the case for the Tat-TAR complex of HIV-1) are unstable. On the other hand, the minor-groove starting structures are found to lead to several binding modes, which are stabilized by a complex interplay of stacking, hydrogen bonding, and electrostatic interactions. Although the ligand does not occupy the binding position of Tat protein, it is shown to hinder the interhelical motion of free TAR RNA. The latter is presumably necessary to achieve the conformational change of TAR RNA to bind Tat protein. Considering the time evolution of the trajectories, the binding process is found to be ligand-induced and cooperative. That is, the conformational rearrangement only occurs in the presence of the ligand and the concerted motion of the ligand and a large part of the RNA binding site is necessary to achieve the final low-energy binding state.     

Ageing with fisheries length-frequency data, using information about growth

A new approach to break down fisheries length-frequency data into age groups, using information on relative growth rate with age, is introduced. The method was verified with data used to test previously published methods. Good starting values for the mean lengths of the fish with age in the statistical analysis of distribution mixtures are often critical. Incorporation of relative growth rate information significantly improves the precision of the ageing procedure even when starting values are less accurate.     

Elimination of the initial value parameters when identifying a system close to a Hopf bifurcation

One of the biggest problems when performing system identification of biological systems is that it is seldom possible to measure more than a small fraction of the total number of variables. If that is the case, the initial state, from where the simulation should start, has to be estimated along with the kinetic parameters appearing in the rate expressions. This is often done by introducing extra parameters, describing the initial state, and one way to eliminate them is by starting in a steady state. We report a generalisation of this approach to all systems starting on the centre manifold, close to a Hopf bifurcation. There exist biochemical systems where such data have already been collected, for example, of glycolysis in yeast. The initial value parameters are solved for in an optimisation sub-problem, for each step in the estimation of the other parameters. For systems starting in stationary oscillations, the sub-problem is solved in a straight-forward manner, without integration of the differential equations, and without the problem of local minima. This is possible because of a combination of a centre manifold and normal form reduction, which reveals the special structure of the Hopf bifurcation. The advantage of the method is demonstrated on the Brusselator.     

Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation

We examine properties of adaptive walks on uncorrelated (i.e. random) fitness landscapes starting from moderately fit genotypes under strong selection weak mutation. As an extension of Orr's model for a single step in an adaptive walk under these conditions, we show that the fitness rank of the dominant genotype in a population after the fixation of a beneficial mutation is, on average, (i+6)/4, where i is the fitness rank of the starting genotype. This accounts for the change in rank due to acquiring a new set of single-mutation neighbors after fixing a new allele through natural selection. Under this scenario, adaptive walks can be modeled as a simple Markov chain on the space of possible fitness ranks with an absorbing state at i = 1, from which no beneficial mutations are accessible. We find that these walks are typically short and are often completed in a single step when starting from a moderately fit genotype. As in Orr's original model, these results are insensitive to both the distribution of fitness effects and most biological details of the system under consideration.     

Redox control of catalytic activities of membrane-associated protein tyrosine kinases

Protein tyrosine kinases (PTKs) play key roles in starting the signal transduction network for cellular development and functions. A number of both receptor-type and non-receptor-type PTKs, which are normally at a resting state, are initially activated in association with functions of the cell membrane and membrane rafts. Results of recent studies have suggested that these membrane-associated mechanisms for activation of PTKs consist of the two steps that are under redox control. The first step is activation of cell surface receptors through chemical crosslinkage or aggregation of receptors and membrane rafts, which leads to production of reactive oxygen species (ROS) as second messengers of intracellular signal transduction. The second step involves chemical modification of PTKs at the highly conserved cysteine in the MXXCW motif as a global switch for starting the tyrosine phosphorylation-dependent local switch for activation of the catalytic activity of the enzyme.     

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy of starting models generated either by comparative modeling or by hand-tracing the density. The method can achieve near-atomic resolution starting from density maps at 4-6 Å resolution.     

Etiology and treatment of pneumonia in children]

The most widespread pathogens of pneumonia in children i.e. Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic susceptibility are described. The ways of selecting starting antibacterial drugs for the treatment of community-acquired and hospital pneumonia are recommended proceeding from the original findings and some literature data. Oral drugs for the treatment of uncomplicated pneumonia are shown to be preferential. In the treatment of nosocomial or hospital pneumonia the starting regimen should allow for the previous antibacterial therapy.