Search engine processor: Filtering and organizing peptide spectrum matches

The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs a novel three-tier Bayesian approach that uses layers of spectrum, peptide, and protein logic to lead the data to converge to a single list of reliable protein identifications. SEPro is integrated into the PatternLab for proteomics environment, where an arsenal of tools for analyzing shotgun proteomic data is provided. By using the semi-labeled decoy approach for benchmarking, we show that SEPro significantly outperforms a commercially available competitor.     

A Measure of Dependence for the Stratified Cox Proportional Hazards Regression Model

Kent and O'Quigley (1988) apply the concept of information gain to measure both global and partial dependence between explanatory variables and a censored response within the framework of the proportional hazards regression model of Cox (1972). The definition of this measure is extended to cover also the stratified Cox model.     

黄土半干旱区刺槐和侧柏林地土壤水分有效性及生产力分级研究

采用LI-6200型植物光合测定系统和LI-1600型稳态气孔计,对黄土半干旱区刺槐、侧柏的净光合速率、羧化效率、蒸腾速率、水分利用效率、气孔导度、气孔阻力、胞间CO2浓度和气孔限制值与土壤含水量的关系进行研究;并对林地土壤水分有效性及生产力进行分级与评价．结果表明,刺槐与侧柏林地土壤含水量分别在4．5％和4．0％以下为“无效水”;土壤含水量在4．5％～10．0％和4．0％～8．5％阈值内属于“低产低效水”;在10．0％～13．5％和85％～11．0％阈值内为“中产高效水”;在13．5％～17．0％和11．0％～16．0％阈值内属于“高产中效水”;在17．0％～19．0％和16．0％～19．0％阈值内为“中产低效水”;土壤含水量在19．0％以上也属于“低产低效水”。     

Effects of nutrients and shade on tree‐grass interactions in an East African savanna

Abstract. Savanna trees have a multitude of positive and negative effects on understorey grass production, but little is known about how these effects interact. We report on a fertilization and shading experiment carried out in a Tanzanian tropical dry savanna around Acacia tortilis trees. In two years of study there was no difference in grass production under tree canopies or in open grassland. Fertilization, however, indicate that trees do affect the nutrient limitation of the grass layer with an N‐limited system in open grassland to a P‐limited system under the trees. The N:P ratios of grass gave a reliable indication of the nature of nutrient limitation, but only when assessed at the end of the wet season. Mid‐wet season nutrient concentrations of grasses were higher under than outside the tree canopy, suggesting that factors other than nutrients limit grass production. A shading experiment indicated that light may be such a limiting factor during the wet season when water and nutrients are sufficiently available. However, in the dry season when water is scarce, the effect of shade on plant production became positive. We conclude that whether trees increase or decrease production of the herbaceous layer depends on how positive effects (increased soil fertility) and negative effects (shade and soil water availability) interact and that these interactions may significantly change between wet and dry seasons.     

Plant diversity in a calcareous wooded meadow – The significance of management continuity

Questions: What is the contribution of management continuity during the last 30–40 years to variation in species diversity and composition of a calcareous wooded meadow plant community? Is tree cover related to species diversity and composition of the herbaceous layer? What are the effects of local soil gradients on species diversity? Location: Laelatu calcareous wooded meadow, Western Estonian coastal zone. Methods: Plant community composition was assessed in 150 1 m × 1 m plots, located at 30 sites with known management history within Laelatu meadow (7 ha). Light and soil conditions and relative altitude were measured at each plot. DCA was used to analyse variation in species composition and general linear mixed models to analyse the effects of management and environmental parameters on diversity. Results: Management continuity was the primary determinant of plant community composition, followed by light conditions and soil parameters. Species richness, diversity and evenness are positively dependent on management continuity. Spatial autocorrelation is important as well. Diversity started to decline under the tree canopy where 50% or less irradiation reached the level of the herbaceous layer. We did not find significant effects of soil conditions on small‐scale diversity. Conclusions: Management continuity, together with the cover of the tree layer, are the most important determinants of diversity. Despite grassland stands with different management history are located side by side, the regeneration of diversity and composition of plant communities after restoring regular management practices is a slow process.     

An in vitro and in vivo investigation of the effects of diesel exhaust on human airway lining fluid antioxidants

Breathing high concentrations of diesel exhaust (DE) induces pulmonary inflammation, bronchoconstriction, increased airway reactivity, and oxidative stress in healthy subjects. To examine if these responses occur at environmentally relevant concentrations of DE, we exposed 25 healthy subjects to DE (PM(10) 100 microg/m(3), 0.6 ppm NO(2) for 2-h) and filtered air on separate occasions. Immediately following DE exposure, subjects displayed an increase in subjective symptoms and a mild bronchoconstriction. Six hours following the cessation of DE exposure neither airway inflammation, nor antioxidant depletion (ascorbate, urate, and reduced glutathione), was seen at any level of the respiratory tract. Instead, an increased flux of reduced glutathione into the bronchial (p < 0.01) and nasal airways (p < 0.05) was observed. In separate, in vitro experiments, DE was found to have comparable oxidative activity to the transition metal rich residual oil fly ash (ROFA) particle, significantly depleting lung lining fluid ascorbic acid and reduced glutathione in a transition metal and superoxide-dependent mechanism. Together, these data indicate that even though DE has marked oxidative activity, this effect is not observed to any great extent in the airways of healthy subjects. We interpret these findings as being indicative that the antioxidant network at the air-lung interface in healthy subjects is capable of dealing with the oxidative challenge posed by DE at ambient concentrations.     

A semi-Markov model based on generalized Weibull distribution with an illustration for HIV disease

Multi-state stochastic models are useful tools for studying complex dynamics such as chronic diseases. Semi-Markov models explicitly define distributions of waiting times, giving an extension of continuous time and homogeneous Markov models based implicitly on exponential distributions. This paper develops a parametric model adapted to complex medical processes. (i) We introduced a hazard function of waiting times with a U or inverse U shape. (ii) These distributions were specifically selected for each transition. (iii) The vector of covariates was also selected for each transition. We applied this method to the evolution of HIV infected patients. We used a sample of 1244 patients followed up at the hospital in Nice, France.