Conditional Maximum Likelihood Estimate and Exact Test of the Common Relative Difference in Combination of 2 × 2 Tables under Inverse Sampling

On the basis of the conditional distribution, given the marginal totals of non-cases fixed for each of independent 2 × 2 tables under inverse sampling, this paper develops the conditional maximum likelihood (CMLE) estimator of the underlying common relative difference (RD) and its asymptotic conditional variance. This paper further provides for the RD an exact interval calculation procedure, of which the coverage probability is always larger than or equal to the desired confidence level and for investigating whether the underlying common RD equals any specified value an exact test procedure, of which Type I error is always less than or equal to the nominal α-level. These exact interval estimation and exact hypothesis testing procedures are especially useful for the situation in which the number of index subjects in a study is small and the asymptotically approximate methods may not be appropriate for use. This paper also notes the condition under which the CMLE of RD uniquely exists and includes a simple example to illustrate use of these techniques.     

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.     

Studies of cadmium uptake in bone and its environmental distribution

Biological Trace Element Research - Rat experiments indicate that oral ingestion of cadmium through drinking water leads to an accumulation of cadmium in bone, in addition to liver and kidney....     

Regeneration of proximal and distal body part in hydra exposed to ultraviolet light (2535 angstroms)

Pelmatohydra oligactis was amputated in the central part of the gastral region and exposed to radiation of ultraviolet rays (2535 angstroms, 12 erg mm(-2)s(-2) for 7, 15 and 20 minutes. The regeneration of the proximal and distal part of the animal which was fixed 8, 24, 48, 72 and 96 hours after the cutting and radiation has been studied cito-histologically. The regeneration of the wounds caused by cutting and those caused by radiation have been compared. It has been found out that the wounds caused by radiation heal much harder and that the radiation-destroyed hypostome needs a longer period to regenerate than the cutting-removed hypostome. It is assumed that radiation-destroyed parts have an inhibitory effect upon environment. But, cito-histological changes concord to a great degree in both cases. The foot regeneration in the animals cut and exposed almost entirely concords the regeneration in the control animals which were cut but not exposed. Namely, both of them, as a rule, remain permanently without a foot. In the paper we have tried to explain these results and brought out the conclusion that hydras do not regenerate the foot because in the bud region there are many zimogen and interstitial cells which are not characteristic of a foot and that is why hydra has a directed growth exclusively toward the distal part, never the opposite. The growth is localized to the hypostome and the bud region. Radiation does not inhibit the process of the budding that has already begun. It is assumed that undamaged cell material travels from the gastroderm toward the bud and serves its formation.     

Confidence Limits on the Ratio of the Mean Failure Times Based on Paired Exponential Observations

This paper discusses interval estimation for the ratio of the mean failure times on the basis of paired exponential observations. This paper considers five interval estimators: the confidence interval using an idea similar to Fieller's theorem (CIFT), the confidence interval using an exact parametric test (CIEP), the confidence interval using the marginal likelihood ratio test (CILR), the confidence interval assuming no matching effect (CINM), and the confidence interval using a locally most powerful test (CIMP). To evaluate and compare the performance of these five interval estimators, this paper applies Monte Carlo simulation. This paper notes that with respect to the coverage probability, use of the CIFT, CILR, or CIMP, although which are all derived based on large sample theory, can perform well even when the number of pairs n is as small as 10. As compared with use of the CILR, this paper finds that use of the CIEP with equal tail probabilities is likely to lose efficiency. However, this loss can be reduced by using the optimal tail probabilities to minimize the average length when n is small (<20). This paper further notes that use of the CIMP is preferable to the CIEP in a variety of situations considered here. In fact, the average length of the CIMP with use of the optimal tail probabilities can even be shorter than that of the CILR. When the intraclass correlation between failure times within pairs is 0 (i.e., the failure times within the same pair are independent), the CINM, which is derived for two independent samples, is certainly the best one among the five interval estimators considered here. When there is an intraclass correlation but which is small (<0.10), the CIFT is recommended for obtaining a relatively short interval estimate without sacrificing the loss of the coverage probability. When the intraclass correlation is moderate or large, either the CILR or the CIMP with the optimal tail probabilities is preferable to the others. This paper also notes that if the intraclass correlation between failure times within pairs is large, use of the CINM can be misleading, especially when the number of pairs is large.