Analysis of contamination in cluster randomized trials of malaria interventions

Background In cluster randomized trials (CRTs) of interventions against malaria, mosquito movement between households ultimately leads to contamination between intervention and control arms, unless they are separated by wide buffer zones. Methods This paper proposes a method for adjusting estimates of intervention effectiveness for contamination and for estimating a contamination range between intervention arms, the distance over which contamination measurably biases the estimate of effectiveness. A sigmoid function is fitted to malaria prevalence or incidence data as a function of the distance of households to the intervention boundary, stratified by intervention status and including a random effect for the clustering. The method is evaluated in a simulation study, corresponding to a range of rural settings with varying intervention effectiveness and contamination range, and applied to a CRT of insecticide treated nets in Ghana. Results The simulations indicate that the method leads to approximately unbiased estimates of effectiveness. Precision decreases with increasing mosquito movement, but the contamination range is much smaller than the maximum distance traveled by mosquitoes. For the method to provide precise and approximately unbiased estimates, at least 50% of the households should be at distances greater than the estimated contamination range from the discordant intervention arm. Conclusions A sigmoid approach provides an appropriate analysis for a CRT in the presence of contamination. Outcome data from boundary zones should not be discarded but used to provide estimates of the contamination range. This gives an alternative to “fried egg” designs, which use large clusters (increasing costs) and exclude buffer zones to avoid bias.

Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

Morphological characters, as presently applied to describe members of the Paguristes tortugae Schmitt, 1933 species complex, appear to be of limited value in inferring phylogenetic relationships within the genus, and may have similarly misinformed understanding of relationships between members of this complex and those presently assigned to the related genera Areopaguristes Rahayu & McLaughlin, 2010 and Pseudopaguristes McLaughlin, 2002. Previously undocumented observations of similarities and differences in color patterns among populations additionally suggest genetic divergences within some species, or alternatively seem to support phylogenetic groupings of some species. In the present study, a Maximum Likelihood (ML) phylogenetic analysis was undertaken based on the H3, 12S mtDNA, and 16S mtDNA sequences of 148 individuals, primarily representatives of paguroid species from the western Atlantic. This molecular analysis supported a polyphyletic Diogenidae Ortmann, 1892, although incomplete taxonomic sampling among the genera of Diogenidae limits the utility of this finding for resolving family level relationships. Several hypotheses regarding the evolutionary relationships among hermit crab genera were refuted by the Kishino-Hasegawa (KH). Shimodaira-Hasegawa (SH) and Approximately Unbiased (AU) tree topology tests, among them the hypothesis that Areopaguristes is monophyletic. A lack of support for the monophyly of Areopaguristes calls into question the phylogenetic validity of gill number for the differentiation of Paguristes, Areopaguristes, and Pseudopaguristes. The study was inconclusive with regard to the relationships among these three genera, but previously unknown diversity within both Paguristes and Areopaguristes was demonstrated. Existence of an undescribed species confounded under the name Paguristes tortugae Schmitt, 1933 was supported by genetics, morphology, and coloration. A second undescribed species with remarkable similarity to Areopaguristes hummi Wass, 1955 was discovered based on genetics and coloration.

Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders

Reanalysis of the dataset used by Khodami et al. (2017) reveals low support values for the key nodes of the copepod (Crustacea) phylogeny and fails to reproduce the results obtained in the study. Maximum likelihood (ML) and Bayesian analyses with the dataset produce phylogenies that are inconsistent with the branching of copepod groups proposed by Khodami et al. (2017). The proposed phylogeny is refuted by the approximately unbiased (AU) statistical test, which undermines several conclusions drawn from the original study.

Unbiased Estimation of Total Rural Loans Advanced and Incurred in an Indian State Along with Unbiased Estimation of Variance in Estimation

Around the year 2000, the problem of reconciling the estimate of loans advanced by the banks and the estimate of loans incurred by the rural farmers was studied in the Indian Statistical Institute. Some approximately unbiased estimates were examined along with approximately unbiased estimates of their approximate variances. Utilizing “Constrained Network” sampling technique exactly unbiased counterparts are presented as alternatives.

Morphology and phylogeny of three karyorelictean ciliates (Protista, Ciliophora), including two novel species, Trachelocerca chinensis sp. n. and Tracheloraphis dragescoi sp. n.

This paper investigates the morphology and infraciliature of three karyorelictean ciliates, Trachelocerca chinensis sp. n., Tracheloraphis dragescoi sp. n. and a rarely known form, Geleia acuta (Dragesco, 1960) Foissner, 1998, which were isolated from the intertidal zone of sandy beaches at Zhanjiang and Qingdao, China. Trachelocerca chinensis sp. n. is distinguished from related forms by having 26–30 somatic kineties, a narrow glabrous stripe and a single nuclear group composed of approximately four to six macronuclei and two micronuclei. Tracheloraphis dragescoi sp. n. can be recognized through its 14–22 somatic kineties, wide glabrous stripe and a single nuclear group composed of about four macronuclei. Phylogenetic analyses based on small-subunit (SSU) rRNA gene sequences indicated that the genera Trachelocerca and Tracheloraphis are closely related but that neither of them appears to be a clearly monophyletic group. Nonetheless, the monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.143, >0.05), although that of Tracheloraphis is rejected (P = 0.011, <0.05). Geleia acuta, meanwhile, branched with Geleia fossata and falls in the Geleia clade.

Correcting the nondetection bias of angle count sampling

The well-known angle count sampling (ACS) has proved to be an efficient sampling technique and has been applied in forest inventories for many decades. However, ACS assumes total visibility of objects; any violation of this assumption leads to a nondetection bias. We present a novel approach, in which the theory of distance sampling is adapted to traditional ACS to correct for the nondetection bias. Two new estimators were developed based on expanding design-based inclusion probabilities by model-based estimates of the detection probabilities. The new estimators were evaluated in a simulation study as well as in a real forest inventory. It is shown that the nondetection bias of the traditional estimator is up to −52.5%, whereas the new estimators are approximately unbiased.

The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.