Finding best algorithmic components for clustering microarray data

The analysis of microarray data is fundamental to microbiology. Although clustering has long been realized as central to the discovery of gene functions and disease diagnostic, researchers have found the construction of good algorithms a surprisingly difficult task. In this paper, we address this problem by using a component-based approach for clustering algorithm design, for class retrieval from microarray data. The idea is to break up existing algorithms into independent building blocks for typical sub-problems, which are in turn reassembled in new ways to generate yet unexplored methods. As a test, 432 algorithms were generated and evaluated on published microarray data sets. We found their top performers to be better than the original, component-providing ancestors and also competitive with a set of new algorithms recently proposed. Finally, we identified components that showed consistently good performance for clustering microarray data and that should be considered in further development of clustering algorithms.     

Application of ultrasonic methods to determine elastic anisotropy of polycrystalline copper processed by equal-channel angular pressing

Anisotropy of elastic properties of ultrafine-grained polycrystalline copper after one, two and four passes of equal-channel angular pressing (ECAP) is investigated by means of ultrasonic methods. For each material, Young’s and shear moduli in the principal processing directions are evaluated and the symmetry and orientation of the anisotropy are identified. The relation between the determined symmetry and the processing mechanisms is discussed. It is shown that the material after one and two passes of ECAP exhibits a measurable anisotropy, while the material after the fourth pass behaves isotropically. Within the discussion, it is shown that the origin of the observed anisotropy may be attributed to the spatial arrangement of grain boundaries rather than to the crystallographic texture. In the light of this conclusion, the obtained results correspond well with optical and transmission electron microscopy observations of the microstructures of ECAPed materials documented in the literature.     

Spark plasma sintering of ZrC–SiC ceramics with LiYO2 additive

Spark plasma sintering (SPS) of ZrC–SiC composite powders in the presence of LiYO₂ sintering additive was studied. The starting powders were obtained by a carbothermal reduction (CTR) of natural mineral zircon (ZrSiO₄), which provided an intimate mixing of in-situ created ZrC and SiC powders. This composite powder and LiYO₂ as additive were densified by spark plasma sintering. Microstructural features of the composite were investigated by XRD, SEM/EDS and AFM analysis. The sintered composite material possesses promising mechanical properties and excellent cavitation resistance which was observed with a cavitation erosion test. The values of Vickers microhardness and fracture toughness of the composite material are 20.7 GPa and 5.07 MPam^1/2, respectively.     

Effect of anodic oxidation on the corrosion behavior of Ti-based materials in simulated physiological solution

Anodic oxidation in acetic acid was investigated as a means of improving the corrosion resistance, in simulated physiologic solution, of titanium and two titanium-based alloys, Ti–6Al–7Nb and Nitinol. The composition and the thickness of the surface layers formed by anodization were analyzed using X-ray photoelectron spectroscopy. The electrochemical characteristics were investigated by linear polarization, cyclic polarization, and electrochemical impedance spectroscopy at the open circuit potential. Anodization of all these three metals resulted in the formation of TiO₂ as the main oxide. These layers improved the corrosion behavior in simulated physiological solution, as evidenced by significant increase in polarization resistance and decrease in corrosion current density. Electrochemical impedance results were interpreted based on the two-layer structure of the passive film. Anodization has thus been shown to provide a simple and effective means of improving the corrosion behavior of titanium-based alloys in simulated physiological solution.     

The formation of hydrophobic and corrosion resistant surfaces on copper and bronze by treatment in myristic acid

The surface of freshly etched copper and bronze samples was modified by immersion in ethanol solutions of myristic (tetradecanoic) acid. Modification resulted in the formation of hydrophobic layers with contact angles up to 141°. Two kinds of surface structure were observed. The modified surface of copper was covered by a uniform layer containing nano-grains or knitted-like structure, whereas the modified surface of bronze was covered by a layer with lamellate patterns and nano-grains. The corrosion properties of bare and modified copper and bronze surfaces were tested by potentiodynamic polarization experiments in 0.014 M Na₂SO₄ + 0.024 M NaHCO₃ solution. The deduced effectiveness of corrosion inhibition by the modified layers on copper and bronze was up to 97 and 68%, respectively. Modification of the surface by immersion in an ethanol solution of myristic acid appears to be a promising treatment for improving the corrosion resistance of copper. The same treatment was not very effective when used on bronze.     

Lasioglossins: Three Novel Antimicrobial Peptides from the Venom of the Eusocial Bee Lasioglossum laticeps (Hymenoptera: Halictidae)

Three novel structurally related pentadecapeptides, named lasioglossins, were isolated from the venom of the eusocial bee Lasioglossum laticeps. Their primary sequences were established as H‐Val‐Asn‐Trp‐Lys‐Lys‐Val‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Ala‐Lys‐NH₂ (LL‐I), H‐Val‐Asn‐Trp‐Lys‐Lys‐Ile‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Ala‐Lys‐NH₂ (LL‐II) and H‐Val‐Asn‐Trp‐Lys‐Lys‐Ile‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Val‐Lys‐NH₂ (LL‐III). These lasioglossins exhibited potent antimicrobial activity against both Gram‐positive and Gram‐negative bacteria, low haemolytic and mast cell degranulation activity, and a potency to kill various cancer cells in vitro. The lasioglossin CD spectra were measured in the presence of trifluoroethanol and sodium dodecyl sulfate solution and indicated a high degree of α‐helical conformation. NMR spectroscopy, which was carried out in trifluoroethanol/water confirmed a curved α‐helical conformation with a concave hydrophobic and convex hydrophilic side. To understand the role of this bend on biological activity, we studied lasioglossin analogues in which the Gly in the centre of the molecule was replaced by other amino acid residues (Ala, Lys, Pro). The importance of the N‐terminal part of the molecule to the antimicrobial activity was revealed through truncation of five residues from both the N and C termini of the LL‐III peptide. C‐terminal deamidation of LL‐III resulted in a drop in antimicrobial activity, but esterification of the C terminus had no effect. Molecular modelling of LL‐III and the observed NOE contacts indicated the possible formation of a bifurcated H‐bond between hydrogen from the Lys15 CONH peptide bond and one H of the C‐terminal CONH₂ to the Ile11 oxygen atom. Such interactions cannot form with C‐terminal esterification.     

The synthesis of N-derivatives of 3-aminoperylene and their absorption and fluorescence properties

N-Acetyl and N-triazinyl 3-aminoperylenes were prepared. N-(4,6-Dichloro-1,3,5-triazin-2-yl)-3-aminoperylene was synthesized by the condensation of 3-aminoperylene with cyanuric chloride; other N-triazinyl derivatives were prepared by the successive substitution of chlorine atoms with methoxy or aniline groups. The structure and purity of the compounds were confirmed by elemental analysis, NMR spectroscopy and mass spectrometry. The UV/vis absorption, fluorescence and excitation spectra as well as the fluorescence quantum yields for the compounds were measured in dibutyl ether, 1,4-dioxane, ethyl acetate and acetonitrile; fluorescence lifetimes were measured in ethyl acetate and dimethyl sulfoxide. The influences of both the character of the N-substituent and the solvent polarity upon the spectra and quantum yields are discussed.     

An assessment of in vivo failures of alumina ceramic total hip joint replacements

Several cases of alumina ceramic hip replacement failures are reviewed fractographically. Three main findings are illustrated. Firstly, there is evidence that surgeons can damage the femoral head bore surface during surgery. Secondly, three of the failures described are of extended neck designs which are weaker than those of normal or short length in axial laboratory testing. Under physiological loading, such geometry can lead to levering forces, inappropriate localized contact with the metallic stem and stress concentrations. Delayed failure can ensue, with a fracture pattern quite different from that seen in conventional uniaxial testing. Thirdly, while some failures show head bore surfaces which are clean apart from metallic witness marking, others show brown stains and white deposits suggesting poor conformal contact. We suspect either stems become damaged during surgery before mounting the head or entrapment of debris, pointing to handling care and cleanliness varying between hospitals.     

A spectroscopic and electrochemical investigation of the oxidation pathway of glycyl-d,l-methionine and its N-acetyl derivative induced by gold(III)

The ¹H nuclear magnetic resonance spectroscopy was applied to study the reaction of the dipeptide glycyl-d,l-methionine (H-Gly-d,l-Met-OH) and its N-acetylated derivative (Ac-Gly-d,l-Met-OH) with hydrogen tetrachloridoaurate(III) (H[AuCl₄]). The corresponding peptide and [AuCl₄]^– were reacted in 1:1, 2:1, and 3:1 molar ratios, and all reactions were performed at pD 2.45 in 0.01 M DCl as solvent and at 25°C. It was found that the first step of these reactions is coordination of Au(III) to the thioether sulfur atom with formation of the gold(III)-peptide complex [AuCl₃(R-Gly-Met-OH-S)] (R=H or Ac). This intermediate gold(III) complex further reacts with an additional methionine residue to generate the R-Gly-Met-OH chlorosulfonium cation as the second intermediate product, which readily undergoes hydrolysis to give the corresponding sulfoxide. The oxidation of the methionine residue in the reaction between H-Gly-d,l-Met-OH and [AuCl₄]^– was five times faster (k ₂ = 0.363 ± 0.074 M^-1s^-1) in comparison to the same process with N-acetylated derivative of this peptide (k ₂ = 0.074 ± 0.007 M^-1s^-1). The difference in the oxidation rates between these two peptides can be attributed to the free terminal amino group of H-Gly-d,l-Met-OH dipeptide. The mechanism of this redox process is discussed and, for its clarification, the reaction of the H-Gly-d,l-Met-OH dipeptide with [AuCl₄]^– was additionally investigated by UV-Vis and cyclic voltammetry techniques. From these measurements, it was shown that the [AuCl₂]^– complex under these experimental conditions has a strong tendency to disproportionate, forming [AuCl₄]^– and metallic gold. This study contributes to a better understanding of the mechanism of the Au(III)-induced oxidation of methionine and methionine-containing peptides in relation to the severe toxicity of anti-arthritic and anticancer gold-based drugs.     

固体层状介质中的反射地震记录

反射信号和高速干扰的振幅和波形随着炮检距的增大而变化。反射系数随入射角的变化而变化;薄反射层或厚过渡层的反射系数,透射效应及波的类型的转换也都随着入射角的变化而变化;点源的几何发散也是随着炮检距的变化而变化。反射地震记录的这些复杂性是人所共知的,但是,我们在设计标准模型时通常忽略了这些因素。由大角度所产生的明显影响可在处理时切除,对保留的数据也总是假设波形不变并具有双曲线型的正常时差,在CDP叠加之前常常应用道间平衡和自动增益控制来部分地补偿炮检距对反射的影响。本文的目的是想说明炮检距各种影响的重要性,并且说明分析这些影响的方法。射线参数与截距时间即(p-τ)曲线,以及反射,透射和波型转换系数与射线参数曲线都有助于识别某一特定层状模型中起重要作用的因素。p-τ曲线实际上是由一组易于解释的椭圆累加而构成的。p-τ曲线上的截距时间及斜率表示,x-t图上的一个波至出现的位置。p-τ曲线的曲率与x-t曲线的几何发散度有关。由于射线参数对于任一射线路径来说是固定的,因此也就容易识别出哪些是产生多次波和转换横波的主要射线参数和界面组合。对每个有意义的同相轴制作合成地震记录,就更有利于对资料的分析和解释。对具有较大速度差的地层模型中的高速噪音和具有较小速度差的第三系碎屑岩模型中的信号分析结果,说明了炮检距影响的重要性。