A novel numerical optimization algorithm inspired from weed colonization

This paper introduces a novel numerical stochastic optimization algorithm inspired from colonizing weeds. Weeds are plants whose vigorous, invasive habits of growth pose a serious threat to desirable, cultivated plants making them a threat for agriculture. Weeds have shown to be very robust and adaptive to change in environment. Thus, capturing their properties would lead to a powerful optimization algorithm. It is tried to mimic robustness, adaptation and randomness of colonizing weeds in a simple but effective optimizing algorithm designated as Invasive Weed Optimization (IWO). The feasibility, the efficiency and the effectiveness of IWO are tested in details through a set of benchmark multi-dimensional functions, of which global and local minima are known. The reported results are compared with other recent evolutionary-based algorithms: genetic algorithms, memetic algorithms, particle swarm optimization, and shuffled frog leaping. The results are also compared with different versions of simulated annealing — a generic probabilistic meta-algorithm for the global optimization problem — which are simplex simulated annealing, and direct search simulated annealing. Additionally, IWO is employed for finding a solution for an engineering problem, which is optimization and tuning of a robust controller. The experimental results suggest that results from IWO are better than results from other methods. In conclusion, the performance of IWO has a reasonable performance for all the test functions.     

Contribution of nematodes to the structure and function of the soil food web

As carbon and energy flow through the soil food web they are depleted by the metabolic and production functions of organisms. To be sustained, a "long" food web, with a large biomass at higher trophic levels, must receive a high rate of rhizodeposition or detrital subsidy, or be top-populated by organisms of slow growth and long life cycle. Disturbed soil food webs tend to be bottom heavy and recalcitrant to restoration due to the slow growth of upper predator populations, physical and chemical constraints of the soil matrix, biological imbalances, and the relatively low mobility and invasion potential of soil organisms. The functional roles of nematodes, determined by their metabolic and behavioral activities, may be categorized as ecosystem services, disservices or effect-neutral. Among the disservices attributable to nematodes are overgrazing, which diminishes services of prey organisms, and plant-damaging herbivory, which reduces carbon fixation and availability to other organisms in the food web. Unfortunately, management to ameliorate potential disservices of certain nematodes results in unintended but long-lasting diminution of the services of others. Beneficial roles of nematodes may be enhanced by environmental stewardship that fosters greater biodiversity and, consequently, complementarity and continuity of their services.     

Minimizing false positives in kinase virtual screens

In spite of recent improvements in docking and scoring methods, high false-positive rates remain a common issue in structure-based virtual screening. In this study, the distinctive features of false positives in kinase virtual screens were investigated. A series of retrospective virtual screens on kinase targets was performed on specifically designed test sets, each combining true ligands and experimentally confirmed inactive compounds. A systematic analysis of the docking poses generated for the top-ranking compounds highlighted key aspects differentiating true hits from false positives. The most recurring feature in the poses of false positives was the absence of certain key interactions known to be required for kinase binding. A systematic analysis of 444 crystal structures of ligand-bound kinases showed that at least two hydrogen bonds between the ligand and the backbone protein atoms in the kinase hinge region are present in 90% of the complexes, with very little variability across targets. Closer inspection showed that when the two hydrogen bonds are present, one of three preferred hinge-binding motifs is involved in 96.5% of the cases. Less than 10% of the false positives satisfied these two criteria in the minimized docking poses generated by our standard protocol. Ligand conformational artifacts were also shown to contribute to the occurrence of false positives in a number of cases. Application of this knowledge in the form of docking constraints and post-processing filters provided consistent improvements in virtual screening performance on all systems. The false-positive rates were significantly reduced and the enrichment factors increased by an average of twofold. On the basis of these results, a generalized two-step protocol for virtual screening on kinase targets is suggested.     

Multi-proxy studies in palaeolimnology

Multi-proxy studies are becoming increasingly common in palaeolimnology. Eight basic requirements and challenges for a multi-proxy study are outlined in this essay – definition of research questions, leadership, site selection and coring, data storage, chronology, presentation of results, numerical tools and data interpretation. The nature of proxy data is discussed in terms of physical proxies and biotic proxies. Loss-on-ignition changes and the use of transfer functions are reviewed as examples of problems in the interpretation of data from multi-proxy studies. The importance of pollen analysis and plant macrofossil analysis in multi-proxy studies is emphasised as lake history cannot be interpreted without knowledge of catchment history. Future directions are outlined about how multi-proxy studies can contribute to understanding biotic responses to environmental change.     

Biological weighting functions for DNA damage in sea urchin embryos exposed to ultraviolet radiation

Laboratory experiments examining the effects of ultraviolet radiation (UVR, 290-400 nm) on DNA damage were carried out using the embryos of three species of sea urchins from different habitats; Strongylocentrotus droebachiensis from the Gulf of Maine, Sterechinus neumayeri from the Antarctic, and Evechinus chloroticus from New Zealand. All three species exhibited significant amounts of accumulated DNA damage, measured as cyclobutane pyrimidine dimers (CPD) photoproducts, when exposed to UVR in the laboratory. Biological weighting functions (BWFs) revealed that S. neumayeri has significantly higher sensitivity to UVR-induced DNA damage across most of the UVR spectrum compared to the other two species, and all species were observed to have weightings in the ultraviolet-A (UVA, 320-400 nm) portion of the spectrum. The increased sensitivity to ultraviolet-B (290-320 nm) and UVA in S. neumayeri is correlated with the lowest concentration of UVR absorbing compounds observed in the embryos of the three species of urchin used in this study. Sea urchin embryos and larvae in the respective habitats of the species tested are known to occur within 5 m of the surface of the ocean where both UVB and UVA wavelengths occur. Solar irradiances of UVR at a depth of 5 m, weighted using the urchin DNA damage BWFs, show that E. chloroticus receives the greatest amount of biologically effective UVR despite having the lowest wavelength dependent weightings for DNA damage when compared to the other two species.     

Effect of Semecarpus anacardium Linn. nut milk extract on rat neutrophil functions in adjuvant arthritis

Neutrophils play an important role in the pathogenesis of rheumatoid arthritis (RA) and various inflammatory conditions, by accumulation and liberation of active proteolytic enzymes. The effect of milk extract of Semecarpus anacardium Linn. nuts (SA) at a dosage of 150 mg kg(-1) body weight day(-1) for 14 days on adjuvant arthritis was studied to gain some insight into this intriguing disease in relation to neutrophil functions. The decreased phagocytic function of neutrophils (phagocytic index and avidity index) found in adjuvant arthritis was significantly increased by the administration of the drug SA. Increased levels of reactive oxygen species (superoxide radical, hydroxyl radical, H2O2 and myeloperoxidase), lysosomal enzymes (acid phosphatase and cathepsin D) and increased accumulation of neutrophils in the joints observed in adjuvant arthritic animals were reverted back to near normal levels by treatment with SA. The results of this study indicate that SA can be considered to be a good therapeutic agent for inflammation and arthritis.     

Tools and Techniques for the Assessment of Ecotoxicological Impacts of Contaminants in the Terrestrial Environment

Until recently, only a small number of standardized (mainly acute) tests with earthworms and plants were available for terrestrial risk assessment. However, during the last years various new methods (especially with chronic endpoints such as reproduction) were developed and standardized. Moreover, beyond structural aspects (e.g., the effect on individuals), the question of influences of chemicals on ecological soil functions like litter decomposition has been raised. Later, biological test methods were used in the area of Soil Quality Assessment, where an often unknown and complex contamination of a site-specific field soil has to be evaluated. Due to the variety of soils to be tested, the existing methods had to be adapted. This article briefly summarizes basic principles of method standardization before providing an overview of existing standardized tests for the compartment soil (mainly from Europe), focusing on zoological, plant, and functional methods. After presenting the main features of already standardized tests (in particular those used in soil quality assessment so far) the development of new tests for specific purposes, ideas for a battery of tests and a new, community-based approach assessing the biological quality of field soils are discussed.     

具有两个状态脉冲控制的害虫治理模型的阶一周期解的存在性和吸引性

在文献[10]的基础上,基于害虫治理问题,建立具有两个状态脉冲控制的HollingⅡ功能性反应的害虫治理模型,利用所定义的后继函数和分析的方法研究了系统阶一周期解的存在性和吸引性.     

某私营木制家具制造企业2004 年与2010 年职业病危害因素检测 与评价报告比较和分析

目的:通过比较2个年份职业病危害因素检测与评价报告,评估职业病防治工作的效果。方法:选取两份有代表性的报告,比较和分析职业病危害防护设施的安装、个人防护用品发放与使用、警示标示以及各项检测结果的合格率。结果:该企业2010年各项调查指标相比2004年明显提高。结论:该企业各项职业病防治工作效果显著,劳动环境明显改善,但仍需注意噪声、木粉尘的危害。