Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy

When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units

Spectral Line Imaging Observations of 1E0102.2-7219

E0102-72 is the second brightest X-ray source in the Small Magellanic Cloud and the brightest supernova remnant in the SMC. We observed this SNR for ~140 ksec with the High Energy Transmission Gratings (HETG) aboard the Chandra X-ray Observatory. The small angular size and high surface brightness make this an excellent target for HETG and we resolve the remnant into individual lines. We observe fluxes from several lines which include O VIII Ly$\alpha$, Ly$\beta$, and O VII along with several lines from Ne X, Ne IX and Mg XII. These line ratios provide powerful constraints on the electron temperature and the ionization age of the remnant.Comment: To appear in "Young Supernova Remnants" (11th Annual Astrophysics Conference in Maryland), S. S. Holt & U. Hwang (eds), AIP, New York (2001

The Kinematic and Plasma Properties of X-ray Knots in Cassiopeia A from the Chandra HETGS

We present high-resolution X-ray spectra from the young supernova remnant Cas A using a 70-ks observation taken by the Chandra High Energy Transmission Grating Spectrometer (HETGS). Line emission, dominated by Si and S ions, is used for high-resolution spectral analysis of many bright, narrow regions of Cas A to examine their kinematics and plasma state. These data allow a 3D reconstruction using the unprecedented X-ray kinematic results: we derive unambiguous Doppler shifts for these selected regions, with values ranging between -2500 and +4000 km/s. Plasma diagnostics of these regions, derived from line ratios of resolved He-like triplet lines and H-like lines of Si, indicate temperatures largely around 1 keV, which we model as O-rich reverse-shocked ejecta. The ionization age also does not vary considerably over these regions of the remnant. The gratings analysis was complemented by the non-dispersed spectra from the same dataset, which provided information on emission measure and elemental abundances for the selected Cas A regions. The derived electron density of X-ray emitting ejecta varies from 20 to 200 cm^{-3}. The measured abundances of Mg, Si, S and Ca are consistent with O being the dominant element in the Cas A plasma. With a diameter of 5 arcmin, Cas A is the largest source observed with the HETGS to date. We, therefore, describe the technique we use and some of the challenges we face in the HETGS data reduction from such an extended, complex object.Comment: 26 pages, 16 figures, evised version (minor changes), accepted for publication in ApJ (Oct 20 2006

Questioning and organization studies

This essay identifies a cleavage in the organisation literature that separates ‘questions’ and ‘questioning’ at a very fundamental philosophical level. On the one hand, the objective notion of ‘questions’ has already been well addressed within organization studies, evident in how scholars have scrutinized questions as objects of analysis; for example, paying close attention to the forms and functions of questions as instruments of research. More recently, the linguistic turn within the social sciences has influenced how organization studies researchers have considered organizations as discursive entities, with debate extending to the discursive nature of ‘questions’. On the other hand, the process of ‘questioning’ remains under-researched. From one perspective, questioning the process of questioning is challenging, but, as we submit, this is precisely where American pragmatism can be helpful. As we explore in this essay, the forward-looking quality of pragmatist inquiry is what motors the process of questioning. Our pragmatist-inflected argument is that questioning does not have to always serve critique and position building in the organization studies field. Rather, questioning out of curiosity can build new dialogue and open up new methodological avenues. This may help change the habitual ways in which we explore ideas, problems and situations in organization studies as well as lead to more democratic forms of organizing. Crucially, in this essay we are not looking for ultimate ‘answers’; rather we hope to excite discussion about questioning by giving prominence to something that is so ubiquitous and taken-for-granted as to be invisible to many of us as an object of inquiry

Age constraints in the double pulsar system J0737-3039

We investigate the age constraints that can be placed on the double pulsar system using models for the spin-down of the first-born 22.7-ms pulsar A and the 2.77-s pulsar B with characteristic ages of 210 and 50 Myr respectively. Standard models assuming dipolar spin-down of both pulsars suggest that the time since the formation of B is ~50 Myr, i.e. close to B's characteristic age. However, adopting models which account for the impact of A's relativistic wind on B's spin-down we find that the formation of B took place either 80 or 180 Myr ago, depending the interaction mechanism. Formation 80 Myr ago, closer to B's characteristic age, would result in the contribution from J0737-3039 to the inferred coalescence rates for double neutron star binaries increasing by 40%. The 180 Myr age is closer to A's characteristic age and would be consistent with the most recent estimates of the coalescence rate. The new age constraints do not significantly impact recent estimates of the kick velocity, tilt angle between pre and post-supernova orbital planes or pre-supernova mass of B's progenitor.Comment: 5 pages, 2 figures, 1 table, accepted for publication by MNRA

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

Cue-Induced Dopamine Release Predicts Cocaine Preference: Positron Emission Tomography Studies in Freely Moving Rodents

Positron emission tomography studies in drug-addicted patients have shown that exposure to drug-related cues increases striatal dopamine, which displaces binding of the D2 ligand, [11C]-raclopride. However, it is not known if animals will also show cue-induced displacement of [11C]-raclopride binding. In this study, we use [11C]-raclopride imaging in awake rodents to capture cue-induced changes in dopamine release associated with the conditioned place preference model of drug craving. Ten animals were conditioned to receive cocaine in a contextually distinct environment from where they received saline. Following conditioning, each animal was tested for preference and then received two separate [11C]-raclopride scans. For each scan, animals were confined to the cocaine and/or the saline-paired environment for the first 25 min of uptake, after which they were anesthetized and scanned. [11C]-raclopride uptake in the saline-paired environment served as a within-animal control for uptake in the cocaine-paired environment. Cocaine produced a significant place preference (p = 0.004) and exposure to the cocaine-paired environment decreased [11C]-raclopride binding relative to the saline-paired environment in both the dorsal (20%; p < 0.002) and ventral striatum (22%; p < 0.05). The change in [11C]-raclopride binding correlated with preference in the ventral striatum (R2 = −0.87; p = 0.003). In this region, animals who showed little or no preference exhibited little or no change in [11C]-raclopride binding in the cocaine-paired environment. This noninvasive procedure of monitoring neurochemical events in freely moving, behaving animals advances preclinical molecular imaging by interrogating the degree to which animal models reflect the human condition on multiple dimensions, both biological and behavioral.Chemistry and Chemical Biolog

Statistical Similarities Between WSA‐ENLIL+Cone Model and MAVEN in Situ Observations From November 2014 to March 2016

Normal solar wind flows and intense solar transient events interact directly with the upper Martian atmosphere due to the absence of an intrinsic global planetary magnetic field. Since the launch of the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, there are now new means to directly observe solar wind parameters at the planet’s orbital location for limited time spans. Due to MAVEN’s highly elliptical orbit, in situ measurements cannot be taken while MAVEN is inside Mars’ magnetosheath. To model solar wind conditions during these atmospheric and magnetospheric passages, this research project utilized the solar wind forecasting capabilities of the WSA‐ENLIL+Cone model. The model was used to simulate solar wind parameters that included magnetic field magnitude, plasma particle density, dynamic pressure, proton temperature, and velocity during a four Carrington rotation‐long segment. An additional simulation that lasted 18 Carrington rotations was then conducted. The precision of each simulation was examined for intervals when MAVEN was in the upstream solar wind, that is, with no exospheric or magnetospheric phenomena altering in situ measurements. It was determined that generalized, extensive simulations have comparable prediction capabilities as shorter, more comprehensive simulations. Generally, this study aimed to quantify the loss of detail in long‐term simulations and to determine if extended simulations can provide accurate, continuous upstream solar wind conditions when there is a lack of in situ measurements.Plain Language SummaryIf we ever have a manned mission to Mars, one of the numerous concerns would be space weather conditions and their effects on spacecraft in flight. One particular element of space weather that we like to focus on is solar wind: plasma that is continuously emitted from the Sun. Solar wind can effect communication between Earth and spacecraft, GPS services, and other vital elements of space travel. We therefore want a good understanding of space weather and want to forecast conditions before ever traveling there. Currently, there are not always means to directly measure solar wind, so we rely on numerical models. In this study, we used the model called WSA‐ENLIL+Cone to compare its solar wind measurements and one of our spacecraft orbiting Mars to see how well it did and to see if we can rely on it for solar wind forecasts. As it turns out, the model can be used for forecasting baseline values of different solar wind parameters, for example, temperature, even with limited information. We show in this study that the WSA‐ENLIL+Cone model allows us to forecast solar wind conditions and helps us to understand what is going on at that seemingly barren planet.Key PointsGeneralized, extensive WEC model simulations provide analogous confidence levels and results as detailed, relatively short simulationsWSA‐ENLIL+Cone model succeeds at predicting fast solar wind radial velocityPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142959/1/swe20547.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142959/2/swe20547_am.pd

Comprehension as social and intellectual practice: Rebuilding curriculum in low socioeconomic and cultural minority schools

This article reframes the concept of comprehension as a social and intellectual practice. It reviews current approaches to reading instruction for linguistically and culturally diverse and low socioeconomic students, noting an emphasis on comprehension as autonomous skills. The Four Resources model (Freebody &amp; Luke, 1990) is used to make the case for the integration of comprehension instruction with an emphasis on student cultural and community knowledge, and substantive intellectual and sociocultural content in elementary school curricula. Illustrations are drawn from research underway on the teaching of literacy in primary schools in low SES communities

High Resolution X-Ray Spectra of Capella: Initial Results from the Chandra High Energy Transmission Grating Spectrometer

High resolution spectra of the active binary Capella (G8 III + G1 III) covering the energy range 0.4-8.0 keV (1.5-30 Angstroms) show a large number of emission lines, demonstrating the performance of the HETGS. A preliminary application of plasma diagnostics provides information on coronal temperatures and densities. Lines arising from different elements in a range of ionization states indicate that Capella has plasma with a broad range of temperatures, from log T = 6.3 to 7.2, generally consistent with recent results from observations with the Extreme Ultraviolet Explorer (EUVE) and the Advanced Satellite for Cosmology and Astrophysics (ASCA). The electron density is determined from He-like O VII lines, giving the value N_e=10^10 cm^-3 at T_e=2*10^6 K; He-like lines formed at higher temperatures give only upper limits to the electron density. The density and emission measure from O VII lines together indicate that the coronal loops are significantly smaller than the stellar radius.Comment: 9 pages, 3 figures (1 color) accepted for ApJ