MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees

<p>Abstract</p> <p>Background</p> <p>MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework for designing phylogenetic applications. The problem of interest is generating the all-to-all Robinson-Foulds distance matrix, which has many applications for visualizing and clustering large collections of evolutionary trees. We introduce MrsRF (<it>MapReduce Speeds up RF</it>), a multi-core algorithm to generate a <it>t </it>× <it>t </it>Robinson-Foulds distance matrix between <it>t </it>trees using the MapReduce paradigm.</p> <p>Results</p> <p>We studied the performance of our MrsRF algorithm on two large biological trees sets consisting of 20,000 trees of 150 taxa each and 33,306 trees of 567 taxa each. Our experiments show that MrsRF is a scalable approach reaching a speedup of over 18 on 32 total cores. Our results also show that achieving top speedup on a multi-core cluster requires different cluster configurations. Finally, we show how to use an RF matrix to summarize collections of phylogenetic trees visually.</p> <p>Conclusion</p> <p>Our results show that MapReduce is a promising paradigm for developing multi-core phylogenetic applications. The results also demonstrate that different multi-core configurations must be tested in order to obtain optimum performance. We conclude that RF matrices play a critical role in developing techniques to summarize large collections of trees.</p

Size and shape constancy in consumer virtual reality

With the increase in popularity of consumer virtual reality headsets, for research and other applications, it is important to understand the accuracy of 3D perception in VR. We investigated the perceptual accuracy of near-field virtual distances using a size and shape constancy task, in two commercially available devices. Participants wore either the HTC Vive or the Oculus Rift and adjusted the size of a virtual stimulus to match the geometric qualities (size and depth) of a physical stimulus they were able to refer to haptically. The judgments participants made allowed for an indirect measure of their perception of the egocentric, virtual distance to the stimuli. The data show under-constancy and are consistent with research from carefully calibrated psychophysical techniques. There was no difference in the degree of constancy found in the two headsets. We conclude that consumer virtual reality headsets provide a sufficiently high degree of accuracy in distance perception, to allow them to be used confidently in future experimental vision science, and other research applications in psychology

Echocardiographic predictors of early in-hospital heart failure during first ST-elevation acute myocardial infarction: does myocardial performance index and left atrial volume improve diagnosis over conventional parameters of left ventricular function?

<p>Abstract</p> <p>Background</p> <p>Left ventricular ejection fraction (LVEF) has been considered a major determinant of early outcome in acute myocardial infarction (AMI). Myocardial performance index (MPI) has been associated to early evolution in AMI in a heterogeneous population, including non ST-elevation or previous AMI. Left atrial volume has been related with late evolution after AMI. We evaluated the independent role of clinical and echocardiographic variables including LVEF, MPI and left atrial volume in predicting early in-hospital congestive heart failure (CHF) specifically in patients with a first isolated ST-elevation AMI.</p> <p>Methods</p> <p>Echocardiography was performed within 30 hours of chest pain in 95 patients with a first ST-elevation AMI followed during the first week of hospitalization. Several clinical and echocardiographic variables were analyzed. CHF was defined as Killip class ≥ II. Multivariate regression analysis was used to select independent predictor of in-hospital CHF.</p> <p>Results</p> <p>Early in-hospital CHF occurred in 29 (31%) of patients. LVEF ≤ 0.45 was the single independent and highly significant predictor of early CHF among other clinical and echocardiographic variables (odds ratio 17.0; [95% CI 4.1 - 70.8]; p < 0.0001). MPI alone could not predict CHF in first ST-elevation AMI patients. Left atrial volume was not associated with early CHF in such patients.</p> <p>Conclusion</p> <p>For patients with first, isolated ST-elevation AMI, LVEF assessed by echocardiography still constitutes a strong and accurate independent predictor of early in-hospital CHF, superior to isolated MPI and left atrial volume in this particular subset of patients.</p

Rapid progress on the vertebrate tree of life

<p>Abstract</p> <p>Background</p> <p>Among the greatest challenges for biology in the 21st century is inference of the tree of life. Interest in, and progress toward, this goal has increased dramatically with the growing availability of molecular sequence data. However, we have very little sense, for any major clade, of how much progress has been made in resolving a full tree of life and the scope of work that remains. A series of challenges stand in the way of completing this task but, at the most basic level, progress is limited by data: a limited fraction of the world's biodiversity has been incorporated into a phylogenetic analysis. More troubling is our poor understanding of what fraction of the tree of life is understood and how quickly research is adding to this knowledge. Here we measure the rate of progress on the tree of life for one clade of particular research interest, the vertebrates.</p> <p>Results</p> <p>Using an automated phylogenetic approach, we analyse all available molecular data for a large sample of vertebrate diversity, comprising nearly 12,000 species and 210,000 sequences. Our results indicate that progress has been rapid, increasing polynomially during the age of molecular systematics. It is also skewed, with birds and mammals receiving the most attention and marine organisms accumulating far fewer data and a slower rate of increase in phylogenetic resolution than terrestrial taxa. We analyse the contributors to this phylogenetic progress and make recommendations for future work.</p> <p>Conclusions</p> <p>Our analyses suggest that a large majority of the vertebrate tree of life will: (1) be resolved within the next few decades; (2) identify specific data collection strategies that may help to spur future progress; and (3) identify branches of the vertebrate tree of life in need of increased research effort.</p

Haptic Edge Detection Through Shear

Most tactile sensors are based on the assumption that touch depends on measuring pressure. However, the pressure distribution at the surface of a tactile sensor cannot be acquired directly and must be inferred from the deformation field induced by the touched object in the sensor medium. Currently, there is no consensus as to which components of strain are most informative for tactile sensing. Here, we propose that shape-related tactile information is more suitably recovered from shear strain than normal strain. Based on a contact mechanics analysis, we demonstrate that the elastic behavior of a haptic probe provides a robust edge detection mechanism when shear strain is sensed. We used a jamming-based robot gripper as a tactile sensor to empirically validate that shear strain processing gives accurate edge information that is invariant to changes in pressure, as predicted by the contact mechanics study. This result has implications for the design of effective tactile sensors as well as for the understanding of the early somatosensory processing in mammals

Haptic adaptation to slant: No transfer between exploration modes

Human touch is an inherently active sense: to estimate an object’s shape humans often move their hand across its surface. This way the object is sampled both in a serial (sampling different parts of the object across time) and parallel fashion (sampling using different parts of the hand simultaneously). Both the serial (moving a single finger) and parallel (static contact with the entire hand) exploration modes provide reliable and similar global shape information, suggesting the possibility that this information is shared early in the sensory cortex. In contrast, we here show the opposite. Using an adaptation-and-transfer paradigm, a change in haptic perception was induced by slant-adaptation using either the serial or parallel exploration mode. A unified shape-based coding would predict that this would equally affect perception using other exploration modes. However, we found that adaptation-induced perceptual changes did not transfer between exploration modes. Instead, serial and parallel exploration components adapted simultaneously, but to different kinaesthetic aspects of exploration behaviour rather than object-shape per se. These results indicate that a potential combination of information from different exploration modes can only occur at down-stream cortical processing stages, at which adaptation is no longer effective

Phylogenetic and Biogeographic Analysis of Sphaerexochine Trilobites

BACKGROUND: Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history). Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. METHODOLOGY/PRINCIPAL FINDINGS: Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian. CONCLUSIONS/SIGNIFICANCE: The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species). By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and the Yangtze block (South China) and between Eastern Laurentia and Avalonia

Assessing and reporting heterogeneity in treatment effects in clinical trials: a proposal

Mounting evidence suggests that there is frequently considerable variation in the risk of the outcome of interest in clinical trial populations. These differences in risk will often cause clinically important heterogeneity in treatment effects (HTE) across the trial population, such that the balance between treatment risks and benefits may differ substantially between large identifiable patient subgroups; the "average" benefit observed in the summary result may even be non-representative of the treatment effect for a typical patient in the trial. Conventional subgroup analyses, which examine whether specific patient characteristics modify the effects of treatment, are usually unable to detect even large variations in treatment benefit (and harm) across risk groups because they do not account for the fact that patients have multiple characteristics simultaneously that affect the likelihood of treatment benefit. Based upon recent evidence on optimal statistical approaches to assessing HTE, we propose a framework that prioritizes the analysis and reporting of multivariate risk-based HTE and suggests that other subgroup analyses should be explicitly labeled either as primary subgroup analyses (well-motivated by prior evidence and intended to produce clinically actionable results) or secondary (exploratory) subgroup analyses (performed to inform future research). A standardized and transparent approach to HTE assessment and reporting could substantially improve clinical trial utility and interpretability