Statistical Estimation and Model Selection of Species-Accumulation Functions

Abstract:  Soberón and Llorente (1993) proposed pure-birth stochastic processes as theoretical models for species-accumulation curves, and these processes have frequently been used to describe the progress of biological inventories. We describe, in algorithmic form, an alternative statistical analysis based on a likelihood approach ( Díaz-Francés & Gorostiza 2002 ) that provides mathematical rigor to the ideas in Soberón and Llorente (1993) and improves the estimation of the models by incorporating the facts that the variance of the error is not constant and that the observations are correlated. Additionally, we used the likelihood ratios between candidate models as an objective procedure for model selection, allowing comparison between the goodness of fit of various models. The software for these statistical methods can now be downloaded off the Internet. We used two examples of butterfly data sets to illustrate the use of the methods and the software.     

Agrobacterium-mediated transformation of Nicotiana attenuata, a model ecological expression system

Summary. Research into the genetic basis of the ecological sophistication of plants is hampered by the availability of transformable systems with a wealth of well-described ecological interactions. We present an Agrobacterium-mediated transformation system for the model ecological expression system, Nicotiana attenuata, a native tobacco that occupies the post-fire niche in the Great Basin Desert of North America. We describe a transformation vector and a transformation procedure that differs from the standard cultivated tobacco transformation protocols in its use of selectable markers, explants, media and cultivation conditions. We illustrate its utility in the transformations with genes coding for key enzymes in the oxylipin cascade (lipoxygenase, allene oxide synthase, hydroperoxide lyase) in antisense orientations and present high-throughput screens useful for the detection of altered phenotypes for the oxylipin cascade (green leaf volatiles and jasmonic acid after wounding). Received 14 March 2002; accepted 10 May 2002     

Understanding the opposition

Current debates about sex selection start from a paradox: on the one hand, the ‘liberal’ argument in favour of sex selection is often thought to be sound; but on the other hand there is widespread public opposition to sex selection. So it is worth spending some time examining the arguments against sex selection. Four different types of argument are identified: (i) religious arguments; (ii) consequentialist arguments, mainly concerning disturbance to the sex ratio; (iii) arguments to the effect that sex selection involves a failure to respect the autonomy of a child; (iv) arguments to the effect that the motivation for sex selection brings with it an instrumental attitude to children not compatible with a child's need for unconditional acceptance and love. In the end the conclusion is reached that none of these arguments provide decisive arguments against the liberal thesis that sex selection ought to be permitted, especially where 'family balancing' is envisaged. In the light of this conclusion the issue of fetal sexing followed by selective feticide as a method of sex selection is discussed. It is argued that sex selection is not in general a good reason for abortion, but that this practice may become unstoppable. Copyright © 2006 John Wiley & Sons, Ltd.     

Evaluation of Solvita compost stability and maturity tests for assessment of quality of end-products from mixed latrine style compost toilets

It is challenging and expensive to monitor and test decentralized composting toilet systems, yet critical to prevent the mismanagement of potentially harmful and pathogenic end-product. Recent studies indicate that mixed latrine composting toilets can be inhibited by high ammonia content, a product of urea hydrolysis. Urine-diverting vermicomposting toilets are better able to accomplish the goals of remote site human waste management by facilitating the consumption of fecal matter by earthworms, which are highly sensitive to ammonia. The reliability of Solvita® compost stability and maturity tests were evaluated as a means of determining feedstock suitability for vermicomposting (ammonia) and end-product stability/completeness (carbon dioxide). A significant linear regression between Solvita® ammonia and free ammonia gas was found. Solvita® ranking of maturity did not correspond to ranking assigned by ammonium:nitrate standards. Solvita® ammonia values 4 and 5 contained ammonia levels below earthworm toxicity limits in 80% and 100% of samples respectively indicative of their use in evaluating feedstock suitability for vermicomposting. Solvita® stability tests did not correlate with carbon dioxide evolution tests nor ranking of stability by the same test, presumably due to in situ inhibition of decomposition and microbial respiration by ammonia which were reported by the Solvita® CO₂ test as having high stability values.     

p53 sequence polymorphisms in late-stage leukemic Mytilus edulis are homologous with M. trossulus p53

Mytilus edulis and M. trossulus are key species in marine intertidal communities that develop a leukemia-like haemic neoplasia at increased incidences at some polluted sites. The tumor-suppressor p53, known to be involved in this disease, was proposed as a biomarker based on sequence polymorphisms in M. trossulus. In this study, p53 mRNA sequence variations in normal and diseased M. edulis were compared with those reported previously for M. trossulus for caged individuals of both species submerged in Burrard Inlet (49°20′16.57″N 123°13′51.37″) in 2007 and 2010. Thirty-seven single nucleotide polymorphisms (SNPs) were detected in M. edulis p53 that formed high linkage disequilibrium blocks associated with late-stage leukemia (p < 0.05). These were found at loci that were more homologous with M. trossulus than with healthy M. edulis p53-predicted haplotypes. Increased susceptibility to this cancer might be due to, in part, p53 alleles containing these SNPs.     

环境因素对六氯苯厌氧降解活性的影响

在厌氧污泥具备了较好的六氯苯（HCB）降解能力的基础上,采用标准血清瓶实验方法考察了反应温度、初始pH、摇床转速和营养元素等环境因素对厌氧污泥降解HCB活性的影响。实验设计的反应温度为25、30、35和40℃;初始pH为5.0、6.0、7.0和8.0;摇床转速为0和150r·min-1;营养元素有葡萄糖和维生素b12。用HCB浓度随时间的减少来表征微生物对其的降解活性。结果表明,反应温度对HCB的降解速率有很大影响,适宜温度为35℃左右。初始pH对HCB降解活性没有显著影响,但显示出有随初始pH增大而HCB降解活性增加的趋势。与静置条件相比,一定的混合作用有利于提高HCB的降解活性。有葡萄糖存在条件下,维生素b12对HCB的降解活性有明显的促进作用。温度及外加碳源（葡萄糖）是影响HCB厌氧降解活性的重要因素,并推测葡萄糖在HCB降解过程中提供电子供体方面发挥了重要作用。     

Determinants of exposure to fine particulate matter (PM2.5) for waiting passengers at bus stops

This research evaluates commuter exposure to particulate matter during pre-journey commute segments for passengers waiting at bus stops by investigating 840 min of simultaneous exposure levels, both inside and outside seven bus shelters in Buffalo, New York. A multivariate regression model is used to estimate the relation between exposure to particulate matter (PM_2.5 measured in μg m^?3) and three vectors of determinants: time and location, physical setting and placement, and environmental factors. Four determinants have a statistically significant effect on particulate matter: time of day, passengers’ waiting location, land use near the bus shelter, and the presence of cigarette smoking at the bus shelter. Model results suggest that exposure to PM_2.5 inside a bus shelter is 2.63 μg m^?3 (or 18 percent) higher than exposure outside a bus shelter, perhaps due in part to the presence of cigarette smoking. Morning exposure levels are 6.51 μg m^?3 (or 52 percent) higher than afternoon levels. Placement of bus stops can affect exposure to particulate matter for those waiting inside and outside of shelters: air samples at bus shelters located in building canyons have higher particulate matter than bus shelters located near open space.     

Signal-transfer modeling for regional assessment of forest responses to environmental changes in the southeastern United States

Stochastic transfer of information in a hierarchy of simulators is offered as a conceptual approach for assessing forest responses to changing climate and air quality across 13 southeastern states of the USA. This assessment approach combines geographic information system and Monte Carlo capabilities with several scales of computer modeling for southern pine species and eastern deciduous forests. Outputs, such as forest production, evapotranspiration and carbon pools, may be compared statistically for alternative equilibrium or transient scenarios providing a statistical basis for decision making in regional assessments. This revised version was published online in July 2006 with corrections to the Cover Date.     

An In Situ Bioreactor for the Treatment of Petroleum Hydrocarbons in Groundwater

Two pilot tests of an aerobic in situ bioreactor (ISBR) have been conducted at field sites contaminated with petroleum hydrocarbons. The two sites differed with respect to hydrocarbon concentrations. At one site, concentrations were low but persistent, and at the other site concentrations were high enough to be inhibitory to biodegradation. The ISBR unit is designed to enhance biodegradation of hydrocarbons by stimulating indigenous microorganisms. This approach builds on existing Bio‐Sep^® bead technology, which provides a matrix that can be rapidly colonized by the active members of the microbial community and serves to concentrate indigenous degraders. Oxygen and nutrients are delivered to the bioreactor to maintain conditions favorable for growth and reproduction, and contaminated groundwater is treated as it is circulated through the bed of Bio‐Sep^® beads. Groundwater moving through the system also transports degraders released from Bio‐Sep^® beads away from the bioreactor, potentially increasing biodegradation rates throughout the aquifer. Groundwater sampling, Bio‐Traps, and molecular biological tools were used to assess ISBR performance during the two pilot tests. Groundwater monitoring indicated that contaminant concentrations decreased at both sites, and the microbial data suggested that these decreases were due to degradation by indigenous microorganisms rather than dilution or dispersion mechanisms. Taken together, these lines of evidence showed that the ISBR system effectively increased the number and activity of indigenous microbial degraders and enhanced bioremediation at the test sites. © 2013 Wiley Periodicals, Inc.