The Development of a Content Analysis Model for Assessing Students’ Cognitive Learning in Asynchronous Online Discussions

The purpose of this study was to develop and validate a content analysis model for assessing students\u27 cognitive learning in asynchronous online discussions. It adopted a fully mixed methods design, in which qualitative and quantitative methods were employed sequentially for data analysis and interpretation. Specifically, the design was a sequential exploratory (QUAL→ quan) design with priority given to qualitative data and methods. Qualitative data were 800 online postings collected in two online courses. Quantitative data were 803 online postings from the same two courses but from different discussion topics and different weeks. During the qualitative process, a grounded theory approach was adopted to construct a content analysis model based on qualitative data. During the quantitative process, chi-square tests and confirmative factor analysis (CFA) which used online postings as cases or observations and was the first of its kind were performed to test if the new model fit the quantitative data

Supernova 2007bi as a pair-instability explosion

Stars with initial masses 10 M_{solar} < M_{initial} < 100 M_{solar} fuse progressively heavier elements in their centres, up to inert iron. The core then gravitationally collapses to a neutron star or a black hole, leading to an explosion -- an iron-core-collapse supernova (SN). In contrast, extremely massive stars (M_{initial} > 140 M_{solar}), if such exist, have oxygen cores which exceed M_{core} = 50 M_{solar}. There, high temperatures are reached at relatively low densities. Conversion of energetic, pressure-supporting photons into electron-positron pairs occurs prior to oxygen ignition, and leads to a violent contraction that triggers a catastrophic nuclear explosion. Tremendous energies (>~ 10^{52} erg) are released, completely unbinding the star in a pair-instability SN (PISN), with no compact remnant. Transitional objects with 100 M_{solar} < M_{initial} < 140 M_{solar}, which end up as iron-core-collapse supernovae following violent mass ejections, perhaps due to short instances of the pair instability, may have been identified. However, genuine PISNe, perhaps common in the early Universe, have not been observed to date. Here, we present our discovery of SN 2007bi, a luminous, slowly evolving supernova located within a dwarf galaxy (~1% the size of the Milky Way). We measure the exploding core mass to be likely ~100 M_{solar}, in which case theory unambiguously predicts a PISN outcome. We show that >3 M_{solar} of radioactive 56Ni were synthesized, and that our observations are well fit by PISN models. A PISN explosion in the local Universe indicates that nearby dwarf galaxies probably host extremely massive stars, above the apparent Galactic limit, perhaps resulting from star formation processes similar to those that created the first stars in the Universe.Comment: Accepted version of the paper appearing in Nature, 462, 624 (2009), including all supplementary informatio

A sociological dilemma: race, segregation, and US sociology

US sociology has been historically segregated in that, at least until the 1960s, there were two distinct institutionally organized traditions of sociological thought – one black and one white. For the most part, however, dominant historiographies have been silent on that segregation and, at best, reproduce it when addressing the US sociological tradition. This is evident in the rarity with which scholars such as WEB Du Bois, E Franklin Frazier, Oliver Cromwell Cox, or other ‘African American Pioneers of Sociology’, as Saint-Arnaud calls them, are presented as core sociological voices within histories of the discipline. This article addresses the absence of African American sociologists from the US sociological canon and, further, discusses the implications of this absence for our understanding of core sociological concepts. With regard to the latter, the article focuses in particular on the debates around equality and emancipation and discusses the ways in which our understanding of these concepts could be extended by taking into account the work of African American sociologists and their different interpretations of core themes

Bright X-ray radiation from plasma bubbles in an evolving laser wakefield accelerator

We show that the properties of the electron beam and bright X-rays produced by a laser wakefield accelerator can be predicted if the distance over which the laser self-focuses and compresses prior to self-injection is taken into account. A model based on oscillations of the beam inside a plasma bubble shows that performance is optimised when the plasma length is matched to the laser depletion length. With a 200~TW laser pulse this results in an X-ray beam with median photon energy of 20 keV, $> 10^{9}$ photons per shot and a peak brightness of $4 \times 10^{23}$ photons s$^{-1}$ mrad$^{-2}$ mm$^{-2}$ (0.1 % BW)$^{-1}$

Vocabulary Learning in a Yorkshire Terrier: Slow Mapping of Spoken Words

Rapid vocabulary learning in children has been attributed to “fast mapping”, with new words often claimed to be learned through a single presentation. As reported in 2004 in Science a border collie (Rico) not only learned to identify more than 200 words, but fast mapped the new words, remembering meanings after just one presentation. Our research tests the fast mapping interpretation of the Science paper based on Rico's results, while extending the demonstration of large vocabulary recognition to a lap dog. We tested a Yorkshire terrier (Bailey) with the same procedures as Rico, illustrating that Bailey accurately retrieved randomly selected toys from a set of 117 on voice command of the owner. Second we tested her retrieval based on two additional voices, one male, one female, with different accents that had never been involved in her training, again showing she was capable of recognition by voice command. Third, we did both exclusion-based training of new items (toys she had never seen before with names she had never heard before) embedded in a set of known items, with subsequent retention tests designed as in the Rico experiment. After Bailey succeeded on exclusion and retention tests, a crucial evaluation of true mapping tested items previously successfully retrieved in exclusion and retention, but now pitted against each other in a two-choice task. Bailey failed on the true mapping task repeatedly, illustrating that the claim of fast mapping in Rico had not been proven, because no true mapping task had ever been conducted with him. It appears that the task called retention in the Rico study only demonstrated success in retrieval by a process of extended exclusion

Esperanto for histones : CENP-A, not CenH3, is the centromeric histone H3 variant

The first centromeric protein identified in any species was CENP-A, a divergent member of the histone H3 family that was recognised by autoantibodies from patients with scleroderma-spectrum disease. It has recently been suggested to rename this protein CenH3. Here, we argue that the original name should be maintained both because it is the basis of a long established nomenclature for centromere proteins and because it avoids confusion due to the presence of canonical histone H3 at centromeres

Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs—reduced sensitivity to all hormones and increased selectivity for glucocorticoids—are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR–MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and function and reinforce the importance of permissive mutations in protein evolution

A Morbidity Survey of South African Primary Care

Publication of this article was funded by the Stellenbosch University Open Access Fund.The original publication is available at www.plosone.org/BibliographyBackground: Recent studies have described the burden of disease in South Africa. However these studies do not tell us which of these conditions commonly present to primary care providers, how these conditions may present and how providers make sense of them in terms of their diagnoses. Clinical nurse practitioners are the main primary care providers and need to be better prepared for this role. This study aimed to determine the range and prevalence of reasons for encounter and diagnoses found among ambulatory patients attending public sector primary care facilities in South Africa. Methodology/Principal Findings: The study was a multi-centre prospective cross-sectional survey of consultations in primary care in four provinces of South Africa: Western Cape, Limpopo, Northern Cape and North West. Consultations were coded prior to analysis by using the International Classification of Primary Care-Version 2 in terms of reasons for encounter (REF) and diagnoses. Altogether 18856 consultations were included in the survey and generated 31451 reasons for encounter (RFE) and 24561 diagnoses. Women accounted for 12526 (66.6%) and men 6288 (33.4%). Nurses saw 16238 (86.1%) and doctors 2612 (13.9%) of patients. The top 80 RFE and top 25 diagnoses are reported and ongoing care for hypertension was the commonest RFE and diagnosis. The 20 commonest RFE and diagnoses by age group are also reported. Conclusions/Significance: Ambulatory primary care is dominated by non-communicable chronic diseases. HIV/AIDS and TB are common, but not to the extent predicted by the burden of disease. Pneumonia and gastroenteritis are commonly seen especially in children. Women’s health issues such as family planning and pregnancy related visits are also common. Injuries are not as common as expected from the burden of disease. Primary care providers did not recognise mental health problems. The results should guide the future training and assessment of primary care providers.Stellenbosch University Open Access FundPublishers' Versio

First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus

The relationship between mutation, protein stability and protein function plays a central role in molecular evolution. Mutations tend to be destabilizing, including those that would confer novel functions such as host-switching or antibiotic resistance. Elevated temperature may play an important role in preadapting a protein for such novel functions by selecting for stabilizing mutations. In this study, we test the stability change conferred by single mutations that arise in a G4-like bacteriophage adapting to elevated temperature. The vast majority of these mutations map to interfaces between viral coat proteins, suggesting they affect protein-protein interactions. We assess their effects by estimating thermodynamic stability using molecular dynamic simulations and measuring kinetic stability using experimental decay assays. The results indicate that most, though not all, of the observed mutations are stabilizing

Efficient counting of k-mers in DNA sequences using a bloom filter

<p>Abstract</p> <p>Background</p> <p>Counting <it>k</it>-mers (substrings of length <it>k </it>in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting <it>k</it>-mers in large modern sequence data sets can easily overwhelm the memory capacity of standard computers. In current data sets, a large fraction-often more than 50%-of the storage capacity may be spent on storing <it>k</it>-mers that contain sequencing errors and which are typically observed only a single time in the data. These singleton <it>k</it>-mers are uninformative for many algorithms without some kind of error correction.</p> <p>Results</p> <p>We present a new method that identifies all the <it>k</it>-mers that occur more than once in a DNA sequence data set. Our method does this using a Bloom filter, a probabilistic data structure that stores all the observed <it>k</it>-mers implicitly in memory with greatly reduced memory requirements. We then make a second sweep through the data to provide exact counts of all nonunique <it>k</it>-mers. For example data sets, we report up to 50% savings in memory usage compared to current software, with modest costs in computational speed. This approach may reduce memory requirements for any algorithm that starts by counting <it>k</it>-mers in sequence data with errors.</p> <p>Conclusions</p> <p>A reference implementation for this methodology, BFCounter, is written in C++ and is GPL licensed. It is available for free download at <url>http://pritch.bsd.uchicago.edu/bfcounter.html</url></p