Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins

Hydropathy profile alignment is introduced as a tool in functional genomics. The architecture of membrane proteins is reflected in the hydropathy profile of the amino acid sequence. Both secondary and tertiary structural elements determine the profile which provides enough sensitivity to detect evolutionary links between membrane proteins that are based on structural rather than sequence similarities. Since structure is better conserved than amino acid sequence, the hydropathy profile can detect more distant evolutionary relationships than can be detected by the primary structure. The technique is demonstrated by two approaches in the analysis of a subset of membrane proteins coded on the Escherichia coli and Bacillus subtilis genomes. The subset includes secondary transporters of the 12 helix type. In the first approach, the hydropathy profiles of proteins for which no function is known are aligned with the profiles of all other proteins in the subset to search for structural paralogues with known function. In the second approach, family hydropathy profiles of 8 defined families of secondary transporters that fall into 4 different structural classes (SC-ST1-4) are used to screen the membrane protein set for members of the structural classes. The analysis reveals that over 100 membrane proteins on each genome fall in only two structural classes. The largest structural class, SC-ST1, correlates largely with the Major Facilitator Superfamily defined before, but the number of families within the class has increased up to 57. The second large structural class, SC-ST2 contains secondary transporters for amino acids and amines and consists of 12 families.     

Physical fitness: how to help older patients live stronger and longer. (1)

Most older Americans are not physically fit and do not exercise regularly. This is especially true of older women, who are weaker than men and become disabled and dependent in the later years at a much greater rate. Exercise can increase the body's metabolism and make it more efficient in burning calories. Physical fitness also makes respiration more efficient. Evidence suggests strongly that the physically fit live 2 to 3 years longer and have a better quality of life than sedentary individuals. Any time is the best time for a person of any age to start exercising. Exercise is movement--dancing, walking, lifting a weight, using the body. Older individuals tend to be willing to exercise if they are given appropriate recommendations and follow-up.     

Experience and results of application of remote afterloading system (RALS) optimization program for intracavitary treatment of squamous cell carcinoma of the uterine cervix

An optimization program for a remote after-loading system (RALS) for intracavitary treatment of cancer of the uterine cervix was established in 1982 by Tabushi and his co-workers. This system has been used in our hospital since 1986, using MODULEX. Seventy-three cases of untreated squamous cell carcinoma of the uterine cervix have been treated under RALS, 29 under conventional RALS and 44 under the RALS optimization program. The cumulative 5-year survival rates were obtained for the groups treated under each system by the Kaplan-Meier method. The 5-year survival rate of stage II cases treated under the RALS optimization program was 68.2%, and that of stage III cases 58.5%. On the other hand, that of stage II cases treated under conventional RALS was 56.3%, and that of stage III cases 44.9%. There was no significant difference between these two groups. Local control rates for stage II and III cases were higher than 5 year-survival rates. Among complications, the frequency of grade 2 radiation colitis was 15.9% with the RALS optimization program cases, and that of grade 2 radiation cystitis was 4.5%. We consider the RALS optimization program to be a clinically useful method for the intracavitary treatment of squamous cell carcinoma of the uterine cervix.     

On the necessity of alignment: Reply to Costello and Keane (2001).

In their article, "Testing two theories of conceptual combination: Alignment versus diagnosticity in the comprehension and production of combined concepts," F. J. Costello and M. T. Keane (see record 2000-14052-015) evaluate the role of alignment in the interpretation of noun–noun combinations. They found that participants were not strongly biased to prefer and produce interpretations with alignable differences. Instead, participants sometimes preferred and produced interpretations with nonalignable differences. These results are surprising given that most research has found advantages of alignable differences over nonalignable differences. Costello and Keane also found that feature diagnosticity better predicted their results, and they concluded that alignment does not play an important role in conceptual combination. However, drawing on recent work, the author of the present article gives an alternative interpretation of Costello and Keane's results, showing that alignment is crucial in conceptual combinations. The author also shows that the dual-process model accounts for their results. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Dimensionless numbers for tundish modelling and the Guthrie number (Gu)

Abstract

Modelling the transport phenomena in tundishes has been a vast area of research for the last three decades. Many papers have been published and are available in the literature on this subject. The basics of modelling involve a similarity criterion between the model and the full scale prototype and are well documented in major textbooks. However, the similarity criteria are different for different cases. For example, for fluid flow in a tundish, the Re and Fr similarity is considered, whereas for heat transfer, the Pr and Pe number similarity should be considered. Numerous other examples can be cited. It is really important to know which similarity criteria should be used for a particular case. In this paper, a new dimensionless number Gu has been proposed when dealing with the modelling of inclusions separating out in a tundish. All dimensionless numbers can be represented as a ratio of two characteristic time scales, and this fact is highlighted in the present paper.     

Evaluation, modelling and optimization of the cleaning process of contaminated plastic food refillables

In this study several types of bottle materials (glass, PET (polyethylene terephthalate), PC (polycarbonate), HDPE (high density polyethylene), PP (polypropylene) and PVC (polyvinyl chloride)) were evaluated in order to be used as food refillables, comparing the residual chemical contamination after classical caustic washing. Bottles were contaminated with model chemicals (chloroxylenol and d-limonene) and caustic washed with varied process parameters using a simulated laboratory-scale washing procedure. After washing, the chemical-contaminated bottles were filled with water and stored for 28 days at 37 degrees C. The concentrations of the model chemicals in the water after storage were taken as a measure of chemical contamination. The influence of the cleaning parameters (temperature, caustic and commercial additive concentration) was studied using response surface methodology. Washing temperature showed a significant influence on the removal of absorbed chemicals from surfaces compared with the effect of the caustic and especially the additive concentration. Optimization of caustic cleaning for the cleaning process in question led to better cleaning effectiveness, although none of the different washing conditions were able to remove all absorbed chemicals out of the polymeric resins. Commercially available plastic refillables (PET and PC) showed the best chemical rinsability. Glass bottles, however, had in every case the best rinsing characteristics.     

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures. Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html.     

面向高炉布料操作优化的在线信息检测方法及其应用（下）

2炉喉料层分布检测 炉喉料层分布是否合理,直接影响高炉软熔带形状和炉内反应,因此炉喉料层分布是高炉布料操作的一个主要参考信息.     

面向高炉布料操作优化的在线信息检测方法及其应用(上)

在高炉布料操作优化中,料面温度场分布、炉喉料层分布和高炉炉况是三类重要参考信息,本文针对这三类信息在线检测方法的研究现状进行了综述,并结合图像处理、机理分析、支持向量机和神经网络等多种先进技术,探讨了在常规检测设备条件下炉内信息的模型化检测方法和应用,最后展望了今后的发展方向.     

Characterization of cogon grass (Imperata cylindrica) pollen extract and preliminary analysis of grass group 1, 4 and 5 homologues using monoclonal antibodies to Phleum pratense

In this study, we investigated whether fluorescein isothiocyanate (FITC)-labeling of test DNA and Texas-red (TR) labeling of reference DNA in comparative genomic hybridization (CGH) experiments cause the results to differ from those obtained using the opposite combination (reverse labeling). Analysis was performed on a total of 20 DNA specimens consisting of 13 frozen bone marrow aspirates from patients with acute myeloid leukemia, and fresh peripheral blood samples from seven healthy donors. For CGH, one aliquot from each test DNA sample was labeled using nick-translation with FITC-dUTP and another with TR-dUTP. Afterwards, the FITC-dUTP and TR-dUTP-labeled test DNAs were hybridized to TR-dUTP- and FITC-dUTP-labeled normal reference DNAs, respectively. The results using the two combinations were compared with each other and with the results of G-banding karyotype analysis. Karyotype data was used to detect artifacts known to occur in some chromosome regions in CGH analysis. The control DNAs labeled with FITC or TR showed no DNA copy number changes. Regardless of the fluorochrome employed for labeling, no DNA copy number changes were detected using CGH in patients with normal karyotypes, nor in patients whose karyotype aberrations were present in less than 40% of cells. In the remaining patients, CGH revealed DNA copy number changes that coincided with the results of the G-banding analysis. Hybridization artifacts known to occur in CGH experiments affecting chromosome regions 1p33-pter, 16p, 17p, 19, and 22 were observed in 15-23% of the tumor samples labeled with FITC, but not in samples labeled with TR. In addition, other previously unreported overrepresentations affecting 7q21, 9q34, 16q, 17q, and chromosome 20 were observed at very low frequencies in up to 10% of the samples when FITC was used to label test DNA. However, when TR was used, overrepresentations were observed at 4q13-q21, 11q21-q23, 13q21-qter, and Xq21-q22, whereas 19p was underrepresented. The results demonstrate that TR-labeling confirms abnormalities detected using FITC-labeling and reduces hybridization artifacts in the known problematic regions of the human genome.     

Molecular modelling of Me(2+)-(8-hydroxy-quinolinate)2 complexes using ZINDO and ESSF methods

The Me2+ (8-hydroxy-quinolinate)1-2 system was studied using semi-empirical (ZINDO) and molecular mechanics (ESFF) methods for a range of bivalent metals comprising alkaline earth metals (up to Sr2+) and the first two rows of transition metals. The structural validation of the optimisation calculations showed that ESFF is in general an efficient predictor of the structure of the complexes. On the other hand, ZINDO offers an appropriate tool for describing the mechanisms of complex formation for the studied system. The spectral validation based on the comparison of spectral data with predicted molecular geometric parameters shows that ZINDO offers a better tool for describing the mechanisms of complex formation. Finally, the consistent relationship (in relative terms) between SCF energies and equilibrium constants, and between computed charges at the oxygen ligation atom and pH, showed that ZINDO can be used as a tool for the design of chelating agents. For the system studied the CPU times are not prohibitive, even for a metal-comprehensive investigation.     

Monitoring the abundance of Aedes (Ochlerotatus) albifasciatus (Macquart 1838) (Diptera: Culicidae) to the south of Mar Chiquita Lake, central Argentina, with the aid of remote sensing

Surges in the size of adult populations of the flood-water mosquito Aedes albifasciatus can produce important economical losses because of the way this species irritates livestock. Although this species is also the main vector of west equine encephalitis in Argentina, little is known about the factors affecting its population dynamics, as it is difficult to obtain data on its abundance over a large area. However, the results of intensive study of the mosquito in a few sites might reasonably be extrapolated to a regional scale by the use of remotely sensed data. The adult, larval and pupal stages of Ae. albifasciatus were sampled at five field sites to the south of Mar Chiquita Lake, either once a month (during the dry, cold season) or once a fortnight (during the warm, rainy season), between August 1992 and April 1993. The measured abundance of adults or pre-adults and a meteorological coefficient useful for the estimation of larval abundance each showed significant correlation with various statistics derived from normalized-difference, vegetation indices (NDVI) calculated from satellite (NOAA-AVHRR) imagery. A linear discriminant analysis, using data on NDVI, rainfall and temperature, accurately identified periods with and without pre-adults. The satellite imagery was also useful in the estimation of larval abundance and consequently could be used to predict adult abundance 7 days in advance. Even though the satellite data employed have poor spatial resolution, their high temporal resolution makes them very useful in studies of the population dynamics of mosquitoes in general, at least once the relevant variables and their relationships with mosquito breeding and survival have been identified.     

烧结过程智能优化控制方法及应用(下)

2烧结过程热状态优化控制 烧结是一个机理复杂、参数众多的物理化学过程.烧结过程热状态的好坏直接影响烧结矿的质量和产量.一般来讲,反映烧结终点的热状态参数主要有烧结终点(BTP)和点火温度.     

烧结过程智能优化控制方法及应用(上)

以国内外烧结过程控制技术发展状况为背景,论述了烧结过程智能优化控制的方法及应用,即烧结配料优化方法和烧结过程热状态优化控制(包括烧结终点控制和点火燃烧控制)。分析了上述三个优化控制问题的复杂性,指出了采用模糊控制、神经网络、专家系统等智能方法可以实现烧结过程的优化控制。将提出的智能优化控制方法应用于工业现场,运行结果表明:该方法不仅能在满足烧结矿质量要求的前提下,有效降低配料成本,而且显著改善了工况波动情况,提高了烧结机利用系数及烧结矿质量指标,降低了燃料消耗。最后简要展望了烧结过程控制技术今后的发展方向。