Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method

1. There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. 2. We simulated >32 000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. 3. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. 4. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns

The Sunyaev-Zel'dovich Infrared Experiment: A Millimeter-wave Receiver for Cluster Cosmology

Measurements of the Sunyaev-Zel'dovich (S-Z) effect towards distant clusters of galaxies can be used to determine the Hubble constant and the radial component of cluster peculiar velocities. Determination of the cluster peculiar velocity requires the separation of the two components of the S-Z effect, which are due to the thermal and bulk velocities of the intracluster plasma. The two components can be separated practically only at millimeter (mm) wavelengths. Measurements of the S-Z effect at mm wavelengths are subject to minimal astrophysical confusion and, therefore, provide an important test of results obtained at longer wavelengths. We describe the instrument used to make the first significant detections of the S-Z effect at millimeter wavelengths. This instrument employs new filter, detector, and readout technologies to produce sensitive measurements of differential sky brightness stable on long time scales. These advances allow drift scan observations which achieve high sensitivity while minimizing common sources of systematic error.Comment: 19 pages, 15 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

The BOOMERANG North America Instrument: a balloon-borne bolometric radiometer optimized for measurements of cosmic background radiation anisotropies from 0.3 to 4 degrees

We describe the BOOMERANG North America (BNA) instrument, a balloon-borne bolometric radiometer designed to map the Cosmic Microwave Background (CMB) radiation with 0.3 deg resolution over a significant portion of the sky. This receiver employs new technologies in bolometers, readout electronics, millimeter-wave optics and filters, cryogenics, scan and attitude reconstruction. All these subsystems are described in detail in this paper. The system has been fully calibrated in flight using a variety of techniques which are described and compared. It has been able to obtain a measurement of the first peak in the CMB angular power spectrum in a single balloon flight, few hours long, and was a prototype of the BOOMERANG Long Duration Balloon (BLDB) experiment.Comment: 40 pages, 22 figures, submitted to Ap

Managing affect in learners' questions in undergraduate science

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2012 Society for Research into Higher Education.This article aims to position students' classroom questioning within the literature surrounding affect and its impact on learning. The article consists of two main sections. First, the act of questioning is discussed in order to highlight how affect shapes the process of questioning, and a four-part genesis to question-asking that we call CARE is described: the construction, asking, reception and evaluation of a learner's question. This work is contextualised through studies in science education and through our work with university students in undergraduate chemistry, although conducted in the firm belief that it has more general application. The second section focuses on teaching strategies to encourage and manage learners' questions, based here upon the conviction that university students in this case learn through questioning, and that an inquiry-based environment promotes better learning than a simple ‘transmission’ setting. Seven teaching strategies developed from the authors' work are described, where university teachers ‘scaffold’ learning through supporting learners' questions, and working with these to structure and organise the content and the shape of their teaching. The article concludes with a summary of the main issues, highlighting the impact of the affective dimension of learning through questioning, and a discussion of the implications for future research

Science lives: School choices and ‘natural tendencies’

An analysis of 12 semi-structured interviews with university-based scientists and non-scientists illustrates their life journeys towards, or away from, science and the strengths and impact of life occurrences leading them to choose science or non-science professions. We have adopted narrative approaches and used Mezirow's transformative learning theory framework. The areas of discussion from the result have stressed on three main categories that include ‘smooth transition’, ‘incremental wavering transition' and ‘transformative transition’. The article concludes by discussing the key influences that shaped initial attitudes and direction in these people through natural inclination, environmental inspirations and perceptions of science

The New Zealand rugby injury and performance project. VI. A prospective cohort study of risk factors for injury in rugby union football

Objectives—Although the nature of rugby injury has been well documented, little is known about key risk factors. A prospective cohort study was undertaken to examine the association between potential risk factors and injury risk, measured both as an injury incidence rate and as a proportion of the playing season missed. The latter measure incorporates a measure of injury severity

Original contribution Reduced susceptibility effects in perfusion fMRI with single-shot spin- echo EPI acquisitions at 1.5 Tesla

Abstract Arterial spin labeling (ASL) perfusion contrast is not based on susceptibility effects and can therefore be used to study brain function in regions of high static inhomogeneity. As a proof of concept, single-shot spin-echo echo-planar imaging (EPI) acquisition was carried out with a multislice continuous ASL (CASL) method at 1.5T. A bilateral finger tapping paradigm was used in the presence of an exogenously induced susceptibility artifact over left motor cortex. The spin-echo CASL technique was compared with a regular gradient-echo EPI sequence with the same slice thickness, as well as other imaging methods using thin slices and spin-echo acquisitions. The results demonstrate improved functional sensitivity and efficiency of the spin-echo CASL approach as compared with gradient-echo EPI techniques, and a trend of improved sensitivity as compared with spin-echo EPI approach in the brain regions affected by the susceptibility artifact. ASL images, either with or without subtraction of the control, provide a robust alternative to blood oxygenation level dependant (BOLD) methods for activation imaging in regions of high static field inhomogeneity

Higher C-reactive Protein Levels Predict Postoperative Delirium in Older Patients Undergoing Major Elective Surgery: A Longitudinal Nested Case-Control Study

Background—Delirium is a common, morbid, and costly postoperative complication.. We aimed to identify blood-based postoperative delirium markers in a nested case control study of older surgical patients using a proteomics approach followed by enzyme-linked immunosorbent assay (ELISA) validation. Methods and Materials—The Successful Aging after Elective Surgery Study enrolled dementia-free adults age ≥70 undergoing major scheduled non-cardiac surgery (N=566; 24% delirium). Plasma was collected at 4 timepoints: preoperatively (PREOP), post-anesthesia care unit (PACU), postoperative day 2 (POD2) and 1 month follow-up (PO1MO). Matched pairs were selected for the independent discovery (39 pairs) and replication cohorts (36 pairs), which were subsequently combined into the pooled cohort (75 pairs). iTRAQ-based relative quantitation mass spectrometry proteomics was performed to identify the strongest delirium-related protein, which was selected for ELISA validation. Using the ELISA results, statistical analyses using non-parametric signed-rank tests were performed in all cohorts examining the association between the identified protein and delirium. Results—C-reactive protein (CRP) emerged from the proteomics analysis as the strongest delirium-related protein. ELISA validation confirmed that compared to controls, cases had significantly higher CRP levels (*p\u3c.05, **p\u3c.01) in the discovery, replication, and pooled cohorts at PREOP (median paired difference [mg/L] 1.97*, 0.29, 1.56**, respectively), PACU (2.83, 2.22*, 2.53**, respectively) and POD2 (71.97**, 35.18*, 63.76**, respectively), but not PO1MO (2.72, −0.66, 1.10, respectively). Discussion—Elevated pre- and postoperative plasma levels of CRP were associated with delirium, suggesting that a pre-inflammatory state and heightened inflammatory response to surgery are potential pathophysiological mechanisms of delirium

Technical recommendations for clinical translation of renal MRI: a consensus project of the Cooperation in Science and Technology Action PARENCHIMA

PURPOSE: The potential of renal MRI biomarkers has been increasingly recognised, but clinical translation requires more standardisation. The PARENCHIMA consensus project aims to develop and apply a process for generating technical recommendations on renal MRI. METHODS: A task force was formed in July 2018 focused on five methods. A draft process for attaining consensus was distributed publicly for consultation and finalised at an open meeting (Prague, October 2018). Four expert panels completed surveys between October 2018 and March 2019, discussed results and refined the surveys at a face-to-face meeting (Aarhus, March 2019) and completed a second round (May 2019). RESULTS: A seven-stage process was defined: (1) formation of expert panels; (2) definition of the context of use; (3) literature review; (4) collection and comparison of MRI protocols; (5) consensus generation by an approximate Delphi method; (6) reporting of results in vendor-neutral and vendor-specific terms; (7) ongoing review and updating. Application of the process resulted in 166 consensus statements. CONCLUSION: The process generated meaningful technical recommendations across very different MRI methods, while allowing for improvement and refinement as open issues are resolved. The results are likely to be widely supported by the renal MRI community and thereby promote more harmonisation