How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?

We recently used computational phylogenetic methods on lexical data to test between two scenarios for the peopling of the Pacific. Our analyses of lexical data supported a pulse-pause scenario of Pacific settlement in which the Austronesian speakers originated in Taiwan around 5,200 years ago and rapidly spread through the Pacific in a series of expansion pulses and settlement pauses. We claimed that there was high congruence between traditional language subgroups and those observed in the language phylogenies, and that the estimated age of the Austronesian expansion at 5,200 years ago was consistent with the archaeological evidence. However, the congruence between the language phylogenies and the evidence from historical linguistics was not quantitatively assessed using tree comparison metrics. The robustness of the divergence time estimates to different calibration points was also not investigated exhaustively. Here we address these limitations by using a systematic tree comparison metric to calculate the similarity between the Bayesian phylogenetic trees and the subgroups proposed by historical linguistics, and by re-estimating the age of the Austronesian expansion using only the most robust calibrations. The results show that the Austronesian language phylogenies are highly congruent with the traditional subgroupings, and the date estimates are robust even when calculated using a restricted set of historical calibrations.     

Outcome Discrepancies and Selective Reporting: Impacting the Leading Journals?

BackgroundSelective outcome reporting of either interesting or positive research findings is problematic, running the risk of poorly-informed treatment decisions. We aimed to assess the extent of outcome and other discrepancies and possible selective reporting between registry entries and published reports among leading medical journals.MethodsRandomized controlled trials published over a 6-month period from July to December 31^st, 2013, were identified in five high impact medical journals: The Lancet, British Medical Journal, New England Journal of Medicine, Annals of Internal Medicine and Journal of American Medical Association were obtained. Discrepancies between published studies and registry entries were identified and related to factors including registration timing, source of funding and presence of statistically significant results.ResultsOver the 6-month period, 137 RCTs were found. Of these, 18% (n = 25) had discrepancies related to primary outcomes with the primary outcome changed in 15% (n = 20). Moreover, differences relating to non-primary outcomes were found in 64% (n = 87) with both omission of pre-specified non-primary outcomes (39%) and introduction of new non-primary outcomes (44%) common. No relationship between primary or non-primary outcome change and registration timing (prospective or retrospective; P = 0.11), source of funding (P = 0.92) and presence of statistically significant results (P = 0.92) was found.ConclusionsDiscrepancies between registry entries and published articles for primary and non-primary outcomes were common among trials published in leading medical journals. Novel approaches are required to address this problem.     

How Accurate Are the Fusion of Cone-Beam CT and 3-D Stereophotographic Images?

Background

Cone-beam Computed Tomography (CBCT) and stereophotography are two of the latest imaging modalities available for three-dimensional (3-D) visualization of craniofacial structures. However, CBCT provides only limited information on surface texture. This can be overcome by combining the bone images derived from CBCT with 3-D photographs. The objectives of this study were 1) to evaluate the feasibility of integrating 3-D Photos and CBCT images 2) to assess degree of error that may occur during the above processes and 3) to identify facial regions that would be most appropriate for 3-D image registration.

Methodology

CBCT scans and stereophotographic images from 29 patients were used for this study. Two 3-D images corresponding to the skin and bone were extracted from the CBCT data. The 3-D photo was superimposed on the CBCT skin image using relatively immobile areas of the face as a reference. 3-D colour maps were used to assess the accuracy of superimposition were distance differences between the CBCT and 3-D photo were recorded as the signed average and the Root Mean Square (RMS) error.

Principal Findings:

The signed average and RMS of the distance differences between the registered surfaces were −0.018 (±0.129) mm and 0.739 (±0.239) mm respectively. The most errors were found in areas surrounding the lips and the eyes, while minimal errors were noted in the forehead, root of the nose and zygoma.

Conclusions

CBCT and 3-D photographic data can be successfully fused with minimal errors. When compared to RMS, the signed average was found to under-represent the registration error. The virtual 3-D composite craniofacial models permit concurrent assessment of bone and soft tissues during diagnosis and treatment planning.     

How Small Are the Smallest Selectable Domains of Form?

Two lines of Drosophila melanogaster from the same base population were selected in opposite directions to produce simultaneous antagonistic changes in two very small (less than 0.2 mm) and closely adjacent (less than 0.3 mm) dimensions within the base of the wing. Wing dimensions near the targeted area became differentiated by large positive and negative percentage differences, while only small homogeneous percentage changes occurred in the remainder of the wing. If very small regions of morphology (less than 100 cells across) can respond to selection almost independently, even in small population samples, then the control of developmental detail must involve many genes, and the diversity of possible outcomes in development and adaptation must be large.     

Visual Cortex: How Are Faces and Objects Represented?

The way in which information about complex objects and faces is represented in visual cortex is controversial. One model posits that information is processed in modules, highly specialized for different categories of objects; an opposing model appeals to a distributed representation across a large network of visual areas. A recent paper uses a novel imaging technique to address this controversy.     

How frugal is Mother Nature with haplotypes?

Motivation: Inference of haplotypes from genotype data is crucialand challenging for many vitally important studies. The first,and most critical step, is the ascertainment of a biologicallysound model to be optimized. Many models that have been proposedrely partially or entirely on reducing the number of uniquehaplotypes in the solution. Results: This article examines the parsimony of haplotypes usingknown haplotypes as well as genotypes from the HapMap project.Our study reveals that there are relatively few unique haplotypes,but not always the least possible, for the datasets with knownsolutions. Furthermore, we show that there are frequently verylarge numbers of parsimonious solutions, and the number increasesexponentially with increasing cardinality. Moreover, these solutionsare quite varied, most of which are not consistent with thetrue solutions. These results quantify the limitations of thePure Parsimony model and demonstrate the imperative need toconsider additional properties for haplotype inference models.At a higher level, and with broad applicability, this articleillustrates the power of combinatorial methods to tease outimperfections in a given biological model. Contact: weixiong.zhang{at}wustl.edu Associate Editor: Alex Bateman     

How Many Endobains Are There?

Oxidative metabolism is very active in brain, where large amounts of chemical energy as ATP molecules are consumed, mostly required to maintain cellular Na+/K+ gradients through the participation of the sodium pump (Na+,K+-ATPase), whose activity is selectively and potently inhibited by the alkaloid ouabain. Na+/K+ gradients are involved in nerve impulse propagation, in neurotransmitter release and cation homeostasis in the nervous system. Likewise, enzyme activity modulation is crucial for maintaining normal blood pressure and cardiovascular contractility as well as renal sodium excretion. The present article reviews the progress in disclosing putative ouabain-like substances, examines their denomination according to different research teams, tissue or biological fluid sources, extraction and purification, assays, biological properties and chemical and biophysical features. When data is available, comparison with ouabain itself is mentioned. Likewise, their potential action in normal physiology as well as in experimental and human pathology is summarized.     

How Conservative Are Evolutionary Anthropologists?

The application of evolutionary theory to human behavior has elicited a variety of critiques, some of which charge that this approach expresses or encourages conservative or reactionary political agendas. In a survey of graduate students in psychology, Tybur, Miller, and Gangestad (Human Nature, 18, 313-328, 2007) found that the political attitudes of those who use an evolutionary approach did not differ from those of other psychology grad students. Here, we present results from a directed online survey of a broad sample of graduate students in anthropology that assays political views. We found that evolutionary anthropology graduate students were very liberal in their political beliefs, overwhelmingly voted for a liberal U.S. presidential candidate in the 2008 election, and identified with liberal political parties; in this, they were almost indistinguishable from non-evolutionary anthropology students. Our results contradict the view that evolutionary anthropologists hold conservative or reactionary political views. We discuss some possible reasons for the persistence of this view in terms of the sociology of science.