Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.     

Mechanical and Corrosion Properties of ZrB2–SiC Composite Ceramics with Oxide Additions

Powder Metallurgy and Metal Ceramics - Hot pressing was used to produce compact ceramic samples with the following composition (wt.%): 60 ZrB2 + 20 SiC + 20 (Al2O3 + 32 t-ZrO2). The tetragonal...     

Influence of hydrogen on the thermoelectric voltage signal in a Pt/WO<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>/6<Emphasis Type="Italic">H</Emphasis>-SiC/Ni/Pt layered structure

The possibility of detecting H₂ by registering the thermal electromotive force signal, which arises between the surfaces of 6H-SiC plates with a thickness of 400 μm, is established. The working surface of the plates is modified by deposition of a WO _x film and catalytic Pt. An ohmic contact (Ni/Pt) is created on the rear surface of the plate, and this surface is maintained at a stabilized temperature of 350°C. The temperature gradient through the plate thickness arises due to the cooling of the working surface with the air medium. The delivery of H₂ into this medium up to a concentration of 2% gives rise to a 15-fold increase in the electric signal, which considerably exceeds the Pt/WO _x /SiC/Ni/Pt system’s response registered in the usual way by measuring the current–voltage dependence. In this case, an additional power source for the registration of the thermal electromotive force is not required.     

Algorithms for Graphs Embeddable with Few Crossings per Edge

We consider graphs that can be embedded on a surface of bounded genus such that each edge has a bounded number of crossings. We prove that many optimization problems, including maximum independent set, minimum vertex cover, minimum dominating set and many others, admit polynomial time approximation schemes when restricted to such graphs. This extends previous results by Baker and Eppstein to a much broader class of graphs. We also prove that for the considered class of graphs, there are balanced separators of size where n is a number of vertices in the graph. On the negative side, we prove that it is intractable to recognize the graphs embeddable in the plane with at most one crossing per edge.     

The Phase Diagram and the Structure of the Charge-Density-Wave State in High Magnetic Field

The properties of a charge-density wave (CDW) state in quasi-one-dimensional metals in magnetic field below the transition temperature are studied using the mean-field theory. We calculate the phase diagram and show that the CDW state with shifted wave vector in high magnetic field (CDW_x phase) has at least double-cosine modulation on the most part of the phase diagram. The transition from CDW₀ to CDW_x state below the critical temperature is accompanied by a jump of the CDW order parameter and of the wave vector rather than by their continuous increase. This implies a first order transition between these CDW states and explains the strong hysteresis accompanying this transition in many experiments. We examine how the phase diagram changes in the case of imperfect nesting. The results are applicable to different families of organic metals.     

Mitochondrial DNA as a Candidate Marker of Multiple Organ Failure after Cardiac Surgery

Assess the level of mitochondrial DNA depending on the presence of multiple organ failure in patients after heart surgery. The study included 60 patients who underwent surgical treatment of valvular heart disease using cardiopulmonary bypass. Uncomplicated patients were included in the 1st group (n = 30), patients with complications and multiple organ failure (MOF) were included in the 2nd group (n = 30). Serum mtDNA levels were determined by quantitative real-time polymerase chain reaction with fluorescent dyes. Mitochondrial DNA gene expression did not differ between group before surgery. Immediately after the intervention, cytochrome B gene expression was higher in the group with MOF, and it remained high during entire follow-up period. A similar trend was observed in cytochrome oxidase gene expression. Increased NADH levels of gene expressions during the first postoperative day were noted in both groups, the expression showed tendency to increase on the third postoperative day. mtDNA gene expression in the “MOF present” group remained at a higher level compared with the group without complications. A positive correlation was reveled between the severity of MOF according to SOFA score and the level of mtDNA (r = 0.45; p = 0.028) for the end-point “First day”. The ROC analysis showed that mtDNA circulating in plasma (AUC = 0.605) can be a predictor of MOF development. The level of mtDNA significantly increases in case of MOF, irrespective of its cause. (2) The expression of mtDNA genes correlates with the level of MOF severity on the SOFA score.     

Conjugates of Methylene Blue with Cycloalkaneindoles as New Multifunctional Agents for Potential Treatment of Neurodegenerative Disease

The development of multi-target-directed ligands (MTDLs) would provide effective therapy of neurodegenerative diseases (ND) with complex and nonclear pathogenesis. A promising method to create such potential drugs is combining neuroactive pharmacophoric groups acting on different biotargets involved in the pathogenesis of ND. We developed a synthetic algorithm for the conjugation of indole derivatives and methylene blue (MB), which are pharmacophoric ligands that act on the key stages of pathogenesis. We synthesized hybrid structures and performed a comprehensive screening for a specific set of biotargets participating in the pathogenesis of ND (i.e., cholinesterases, NMDA receptor, mitochondria, and microtubules assembly). The results of the screening study enabled us to find two lead compounds (4h and 4i) which effectively inhibited cholinesterases and bound to the AChE PAS, possessed antioxidant activity, and stimulated the assembly of microtubules. One of them (4i) exhibited activity as a ligand for the ifenprodil-specific site of the NMDA receptor. In addition, this lead compound was able to bypass the inhibition of complex I and prevent calcium-induced mitochondrial depolarization, suggesting a neuroprotective property that was confirmed using a cellular calcium overload model of neurodegeneration. Thus, these new MB-cycloalkaneindole conjugates constitute a promising class of compounds for the development of multitarget neuroprotective drugs which simultaneously act on several targets, thereby providing cognitive stimulating, neuroprotective, and disease-modifying effects.     

Modification of the chemical composition,morphology, and antireflection properties of WSe x films formed by pulsed laser deposition

We have studied the possibility of controlling important structural characteristics of WSe _x films, which belong to the class of layered materials and have good prospects for application in modern nano- and optoelectronic devices. It is established that, by using thermal treatment and ion irradiation during pulsed laser deposition (PLD) in the shadow of an antidroplet shield, it is possible to vary the Se/W atomic ratio from 5 to 1.5, change the character of atomic packing, and obtain films with either smooth or rough surfaces. An increase in the height of parabolic protrusions on the surface up to 200–500 nm leads to a decrease in the optical reflection coefficient in a broad wavelength range from 30% (typical of smooth films) to 6%, which can favor a significant increase in the efficiency of solar cells based on semiconductor films of this type.