A Life Table Regression Analysis for Complex Survey Data

A methodology for obtaining maximum likelihood estimates of life table regression coefficients from complex survey data is presented. Certain of the issues of writing a likelihood for survey data are presented and discussed. The proposed methodology includes consideration of the sampling design in any inference by using design based variance estimates for the parameters. An example is given using data from the 1973 United States National Survey of Family Growth.     

Using a Wetland Bioreactor to Remediate Ground Water Contaminated with Nitrate (mg/L) and Perchlorate (μg/L)

Wetland plants and their rhizospheric microorganisms were used to remove perchlorate from nitrate-contaminated ground water. A wetland bioreactor was constructed with the wetland plants Typha spp., Scirpus spp., and Cyperus spp. These plants provided a habitat and a food source for the indigenous denitrifying microorganisms presumed responsible for the perchlorate and nitrate removal. Ground water contaminated with nitrate (68 mg/L) was collected from a well and injected with concentrations of potassium perchlorate similar to those found in several local wells (50 and 100 μg/L). The water flowed continuously through the wetland bioreactor with hydraulic retention times (HRT) ranging from 0.5 to 400 h. Because microbial denitrification depends, in part, on the nature and amount of carbon available to the microorganisms, four carbon sources (dried leaf matter, dried algae, milk replacement starter, and sodium acetic acid) were evaluated. Analyses for perchlorate

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Work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract W-7405-Eng-18. concentration in ground water were performed using negative electrospray mass spectrometry/mass spectrometry. Of the carbon sources tested, sodium acetic acid was the most efficient at accelerating the nitrate and perchlorate removal rates. The HRT required to remove perchlorate (100 μg/L) to below the detection limit, without carbon source amendment, was 4 d. With the addition of sodium acetic acid (0.26 g/L) the required HRT decreased to 0.5 d. These results suggest that denitrifying microorganisms, supported in a wetland bioreactor amended with a carbon source, remove perchlorate from nitrate contaminated ground water.     

Environment Under the Federal Employees Health Benefits Program: A Report of the Bureau of Research and Planning, California Medical Association

Active and retired federal employees, together with their dependents, represent the single largest group of persons enrolled in any voluntary health insurance program in the United States. The extent of their coverage and enrollment is of particular interest to physicians in California since this state has the largest proportion of all federal employees enrolled among all states. Of the almost 5(3/4) million federal employees and their dependents, enrollment in California was almost 609,000 or slightly over 10 per cent of all those covered. Better than 3 out of 5 individuals covered were enrolled in service type plans both in the U.S. and in California. Of all persons enrolled in comprehensive group practice and individual practice plans in the U.S., almost one-half were in California alone. Almost 4 out of 5 individuals enrolled were in high option plans. "... an indication that most employees were satisfied with their initial choice of plans."     

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in hominoidea

Summary A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.     

Sequence alignments and pair hidden Markov models using evolutionary history

This work presents a novel pairwise statistical alignment method based on an explicit evolutionary model of insertions and deletions (indels). Indel events of any length are possible according to a geometric distribution. The geometric distribution parameter, the indel rate, and the evolutionary time are all maximum likelihood estimated from the sequences being aligned. Probability calculations are done using a pair hidden Markov model (HMM) with transition probabilities calculated from the indel parameters. Equations for the transition probabilities make the pair HMM closely approximate the specified indel model. The method provides an optimal alignment, its likelihood, the likelihood of all possible alignments, and the reliability of individual alignment regions. Human alpha and beta-hemoglobin sequences are aligned, as an illustration of the potential utility of this pair HMM approach.     

Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants

Likelihood methods and methods using invariants are procedures for inferring the evolutionary relationships among species through statistical analysis of nucleic acid sequences. A likelihood-ratio test may be used to determine the feasibility of any tree for which the maximum likelihood can be computed. The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is essentially a form of the likelihood-ratio method. In the case of a small number of species (four or five), these methods may be used to find a confidence set for the correct tree. An exact version of Lake's asymptotic chi 2 test has been mentioned by Holmquist et al. Under very general assumptions, a one-sided exact test is appropriate, which greatly increases power.     

Probabilism and Phylogenetic Inference

The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the task of the historical sciences being one of explanation, not prediction. Thus, frequency probability methods of estimation are inappropriate for making historical inferences. Maximum likelihood estimation procedures are deconstructed from numerous perspectives in spite of their supposed impressive technicalities. Charges of parsimony's inconsistency are rendered mute, because its justification lies elsewhere, yet maximum likelihood is still subject to Wald's dilemma if realism is of any interest. Although all epistemologies make assumptions, the models employed by maximum likelihood are problematic and deterministic, as opposed to the unproblematic background knowledge characteristic of cladistics. Apart from issues of logical and sampling dependencies, the requirements of frequency probability theory are non-trivial and the maximum likelihood estimation of phylogeny can neither escape, nor satisfy the tenets of calculus independence (e.g. i.i.d.) inherent in the multiplicative relations of the method. If phylogeneticists are to maintain a rational foundation for their epistemology, neo-justificationist appeals to some metaphysical truth must be abandoned in favour of the realism of sophisticated falsification.     

On the maximum likelihood method in molecular phylogenetics

Summary The efficiency of obtaining the correct tree by the maximum likelihood method (Felsenstein 1981) for inferring trees from DNA sequence data was compared with trees obtained by distance methods. It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolutionary rate differs among lineages.     

Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)

Background  

In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades.     

Maximum likelihood inference of protein phylogeny and the origin of chloroplasts

Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.