Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses

Students’ conceptions and misconceptions in chemical kinetics in Port Harcourt Metropolis of Nigeria

The purpose of the study was to probe the conception and misconception of senior secondary (SS3) and University (US) chemistry students in chemical kinetics in Rivers State, Nigeria. The study sample was made up of 107 SS3 and 93 US students. Two main instruments were used to collect data for the study. They are the chemical kinetic calculation problem and alternative conceptions test in chemical kinetics. Overall results of the study showed that students’ performance in basic chemical kinetics calculation was generally poor with the mean scores less than one point. Item analyses on the conception test revealed that about 10% of the students were able to identify the correct answers while about 90% could not identify the correct answers. The university students were superior in performance than the secondary students in the conception test. These results were discussed in the study. [African Journal of Chemical Education—AJCE 5(2), July 2015

A novel function for the Caenorhabditis elegans torsin OOC-5 in nucleoporin localization and nuclear import.

Torsin proteins are AAA+ ATPases that localize to the endoplasmic reticular/nuclear envelope (ER/NE) lumen. A mutation that markedly impairs torsinA function causes the CNS disorder DYT1 dystonia. Abnormalities of NE membranes have been linked to torsinA loss of function and the pathogenesis of DYT1 dystonia, leading us to investigate the role of the Caenorhabditis elegans torsinA homologue OOC-5 at the NE. We report a novel role for torsin in nuclear pore biology. In ooc-5-mutant germ cell nuclei, nucleoporins (Nups) were mislocalized in large plaques beginning at meiotic entry and persisted throughout meiosis. Moreover, the KASH protein ZYG-12 was mislocalized in ooc-5 gonads. Nups were mislocalized in adult intestinal nuclei and in embryos from mutant mothers. EM analysis revealed vesicle-like structures in the perinuclear space of intestinal and germ cell nuclei, similar to defects reported in torsin-mutant flies and mice. Consistent with a functional disruption of Nups, ooc-5-mutant embryos displayed impaired nuclear import kinetics, although the nuclear pore-size exclusion barrier was maintained. Our data are the first to demonstrate a requirement for a torsin for normal Nup localization and function and suggest that these functions are likely conserved

A-optimal designs for an additive quadratic mixture model

Quadratic models are widely used in the analysis of experiments involving mixtures. This paper gives A-optimal designs for an additive quadratic mixture model for q ≥ 3 mixture components. It is proved that in these A-optimal designs, vertices of the simplex S q-1 are support points, and other support points shift gradually from barycentres of depth 1 to barycentres of depth 3 as q increases. A-optimal designs with minimal support are also discussed.published_or_final_versio

An integrated approach for identifying wrongly labeled samples when performing classification in microarray data

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Modelling uncertainty in transcriptome measurements enhances network component analysis of yeast metabolic cycle

Using high throughput DNA binding data for transcription factors and DNA microarray time course data, we constructed four transcription regulatory networks and analysed them using a novel extension to the network component analysis (NCA) approach. We incorporated probe level uncertainties in gene expression measurements into the NCA analysis by the application of probabilistic principal component analysis (PPCA), and applied the method to data from yeast metabolic cycle. Analysis shows statistically significant enhancement to periodicity in a large fraction of the transcription factor activities inferred from the model. For several of these we found literature evidence of post-transcriptional regulation. Accounting for probe level uncertainty of microarray measurements leads to improved network component analysis. Transcription factor profiles showing greater periodicity at their activity levels, rather than at the corresponding mRNA levels, for over half the regulators in the networks points to extensive post-transcriptional regulations. ©2009 IEEE.published_or_final_versio

Pushing the envelope: Evaluating speech rhythm with different envelope extraction techniques

The amplitude of the speech signal varies over time, and the speech envelope is an attempt to characterise this variation in the form of an acoustic feature. Although tacitly assumed, the similarity between the speech envelope-derived time series and that of phonetic objects (e.g., vowels) remains empirically unestablished. The current paper, therefore, evaluates several speech envelope extraction techniques, such as the Hilbert transform, by comparing different acoustic landmarks (e.g., peaks in the speech envelope) with manual phonetic annotation in a naturalistic and diverse dataset. Joint speech tasks are also introduced to determine which acoustic landmarks are most closely coordinated when voices are aligned. Finally, the acoustic landmarks are evaluated as predictors for the temporal characterisation of speaking style using classification tasks. The landmark that performed most closely to annotated vowel onsets was peaks in the first derivative of a human audition-informed envelope, consistent with converging evidence from neural and behavioural data. However, differences also emerged based on language and speaking style. Overall, the results show that both the choice of speech envelope extraction technique and the form of speech under study affect how sensitive an engineered feature is at capturing aspects of speech rhythm, such as the timing of vowels

A prediction approach for multichannel EEG signals modeling using local wavelet SVM

Accurate modeling of the multichannel electroencephalogram (EEG) signal is an important issue in clinical practice. In this paper, we propose a new local spatiotemporal prediction method based on support vector machines (SVMs). Combining with the local prediction method, the sequential minimal optimization (SMO) training algorithm, and the wavelet kernel function, a local SMO-wavelet SVM (WSVM) prediction model is developed to enhance the efficiency, effectiveness, and universal approximation capability of the prediction model. Both the spatiotemporal modeling from the measured time series and the details of the nonlinear modeling procedures are discussed. Simulations and experimental results with real EEG signals show that the proposed method is suitable for real signal processing and is effective in modeling the local spatiotemporal dynamics. This method greatly increases the computational speed and more effectively captures the local information of the signal. © 2006 IEEE.published_or_final_versio

Barrier height change in very thin SiO2 films caused by charge injection

In this paper, we report an investigation of barrier height change in gate oxide caused by charge injection. By analyzing the small change in the post-stress Fowler-Nordheim (FN) tunneling current through the oxide layer, the change of the oxide barrier height due to charge injection is determined quantitatively. The barrier height changes associated with different charge-injection directions and measurement polarities for n-channel metal oxide semiconductor field-effect transistors (MOSFETs) are presented. For comparison a measurement on a p-channel MOSFET is also carried out. For all the cases, the barrier height changes always exhibit a power law dependence on injected charge.published_or_final_versio