Clustering and Micro-immiscibility in Alcohol-Water Mixtures: Evidence from Molecular Dynamics Simulations

We have investigated the hydrogen-bonded structures in liquid methanol and a 7:3 mole fraction aqueous solution using classical Molecular Dynamics simulations at 298K and ambient pressure. We find that, in contrast to recent predictions from X-ray emission studies, the hydrogen-bonded structure in liquid methanol is dominated by chain and small ring structures. In the methanol-rich solution, we find evidence of micro-immiscibility, supporting recent conclusions derived from neutron diffraction data.Comment: 5 pages, 4 figure

Assessing the quality of a student-generated question repository

We present results from a study that categorizes and assesses the quality of questions and explanations authored by students, in question repositories produced as part of the summative assessment in introductory physics courses over the past two years. Mapping question quality onto the levels in the cognitive domain of Bloom's taxonomy, we find that students produce questions of high quality. More than three-quarters of questions fall into categories beyond simple recall, in contrast to similar studies of student-authored content in different subject domains. Similarly, the quality of student-authored explanations for questions was also high, with approximately 60% of all explanations classified as being of high or outstanding quality. Overall, 75% of questions met combined quality criteria, which we hypothesize is due in part to the in-class scaffolding activities that we provided for students ahead of requiring them to author questions.Comment: 24 pages, 5 figure

The use of electronic voting systems in large group lectures: Challenges and opportunities

We describe pedagogical, technical and operational issues associated with the introduction of an electronic voting system into large first-year undergraduate lectures. The rationale for doing so is to transform the lecture experience from a one-way transmission of information in to a two-way conversation between lecturer and students, mediated by the technology. We discuss some of the logistics involved, such as choice of handset, cost and siting within a lecture theatre as well as the aspects of pedagogy, such as the requirements of a good question for these interactive episodes. We present a number of possible use scenarios and evaluate student and staff experiences of the process

The Changes in Attitudes and Beliefs of First Year Physics Undergraduates: A Study Using the CLASS Survey

Personal attitudes and beliefs towards learning can influence the way students approach and study a subject; as a result, evaluation of attitudes and how these change over time is becoming increasingly common. We have carried out a study looking at the changes in attitudes of first year physics students over two years at the University of Edinburgh. The Colorado Learning Attitudes About Science Survey (CLASS) was used to obtain a measure of expert-like thinking for students both pre- and post- first year teaching. The results have been subdivided to look at the differences between physics `majors' and `non-majors' as well as the differences in attitudes of female and male students. It was found, in line with previous studies, that students' levels of expert-like thinking decline after initial instruction. When the data was subdivided to look in more detail at specific sections of the undergraduate class it was seen that the decrease in expert-like thinking is much more marked in `non-majors' - those students not intending to take physics as a degree - and also greater in female students than their male peers

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

YesRecently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (alpha,beta,gamma,epsilon) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level

Genome-wide screening for DNA variants associated with reading and language traits

This research was funded by: Max Planck Society, the University of St Andrews - Grant Number: 018696, US National Institutes of Health - Grant Number: P50 HD027802, Wellcome Trust - Grant Number: 090532/Z/09/Z, and Medical Research Council Hub Grant Grant Number: G0900747 91070Reading and language abilities are heritable traits that are likely to share some genetic influences with each other. To identify pleiotropic genetic variants affecting these traits, we first performed a genome‐wide association scan (GWAS) meta‐analysis using three richly characterized datasets comprising individuals with histories of reading or language problems, and their siblings. GWAS was performed in a total of 1862 participants using the first principal component computed from several quantitative measures of reading‐ and language‐related abilities, both before and after adjustment for performance IQ. We identified novel suggestive associations at the SNPs rs59197085 and rs5995177 (uncorrected P ≈ 10–7 for each SNP), located respectively at the CCDC136/FLNC and RBFOX2 genes. Each of these SNPs then showed evidence for effects across multiple reading and language traits in univariate association testing against the individual traits. FLNC encodes a structural protein involved in cytoskeleton remodelling, while RBFOX2 is an important regulator of alternative splicing in neurons. The CCDC136/FLNC locus showed association with a comparable reading/language measure in an independent sample of 6434 participants from the general population, although involving distinct alleles of the associated SNP. Our datasets will form an important part of on‐going international efforts to identify genes contributing to reading and language skills.Publisher PDFPeer reviewe

The necessity of historical inquiry in educational research: the case of Religious Education

publication-status: PublishedThis is an Author's Original Manuscript of an article whose final and definitive form, the Version of Record, has been published in the British Journal of Religious Education, July 2010. Available online at: http://www.tandfonline.com/ or DOI: 10.1080/01416200.2010.498612This article explores the mixed fortunes of historical inquiry as a method in educational studies and exposes evidence for the neglect of this method in religious education research in particular. It argues that historical inquiry, as a counterpart to other research methods, can add depth and range to our understanding of education, including religious education, and can illuminate important longer‐term, broader and philosophical issues. The article also argues that many historical voices have remained silent in the existing historiography of religious education because such historiography is too generalised and too biased towards the development of national policy and curriculum and pedagogical theory. To address this limitation in educational research, this article promotes rigorous historical studies that are more substantially grounded in the appropriate historiographical literature and utilise a wide range of original primary sources. Finally, the article explores a specific example of the way in which a historical approach may be fruitfully applied to a particular contemporary debate concerning the nature and purpose of religious education

Complementarity of information sent via different bases

We discuss quantitatively the complementarity of information transmitted by a quantum system prepared in a basis state in one out of several different mutually unbiased bases (MUBs). We obtain upper bounds on the information available to a receiver who has no knowledge of which MUB was chosen by the sender. These upper bounds imply a complementarity of information encoded via different MUBs and ultimately ensure the security in quantum key distribution protocols.Comment: 9 pages, references adde

Correlations of Behavioral Deficits with Brain Pathology Assessed through Longitudinal MRI and Histopathology in the R6/2 Mouse Model of HD

Huntington's disease (HD) is caused by the expansion of a CAG repeat in the huntingtin (HTT) gene. The R6/2 mouse model of HD expresses a mutant version of exon 1 HTT and develops motor and cognitive impairments, a widespread huntingtin (HTT) aggregate pathology and brain atrophy. Despite the vast number of studies that have been performed on this model, the association between the molecular and cellular neuropathology with brain atrophy, and with the development of behavioral phenotypes remains poorly understood. In an attempt to link these factors, we have performed longitudinal assessments of behavior (rotarod, open field, passive avoidance) and of regional brain abnormalities determined through magnetic resonance imaging (MRI) (whole brain, striatum, cortex, hippocampus, corpus callosum), as well as an end-stage histological assessment. Detailed correlative analyses of these three measures were then performed. We found a gender-dependent emergence of motor impairments that was associated with an age-related loss of regional brain volumes. MRI measurements further indicated that there was no striatal atrophy, but rather a lack of striatal growth beyond 8 weeks of age. T2 relaxivity further indicated tissue-level changes within brain regions. Despite these dramatic motor and neuroanatomical abnormalities, R6/2 mice did not exhibit neuronal loss in the striatum or motor cortex, although there was a significant increase in neuronal density due to tissue atrophy. The deposition of the mutant HTT (mHTT) protein, the hallmark of HD molecular pathology, was widely distributed throughout the brain. End-stage histopathological assessments were not found to be as robustly correlated with the longitudinal measures of brain atrophy or motor impairments. In conclusion, modeling pre-manifest and early progression of the disease in more slowly progressing animal models will be key to establishing which changes are causally related. © 2013 Rattray et al

Vascular endothelial growth factor-A165b is protective and restores endothelial glycocalyx in diabetic nephropathy

Diabetic nephropathy is the leading cause of ESRD in high-income countries and a growing problem across the world. Vascular endothelial growth factor-A (VEGF-A) is thought to be a critical mediator of vascular dysfunction in diabetic nephropathy, yet VEGF-A knockout and overexpression of angiogenic VEGF-A isoforms each worsen diabetic nephropathy. We examined the vasculoprotective effects of the VEGF-A isoform VEGF-A165b in diabetic nephropathy. Renal expression of VEGF-A165b mRNA was upregulated in diabetic individuals with well preserved kidney function, but not in those with progressive disease. Reproducing this VEGF-A165b upregulation in mouse podocytes in vivo prevented functional and histologic abnormalities in diabetic nephropathy. Biweekly systemic injections of recombinant human VEGF-A165b reduced features of diabetic nephropathy when initiated during early or advanced nephropathy in a model of type 1 diabetes and when initiated during early nephropathy in a model of type 2 diabetes. VEGF-A165b normalized glomerular permeability through phosphorylation of VEGF receptor 2 in glomerular endothelial cells, and reversed diabetes-induced damage to the glomerular endothelial glycocalyx. VEGF-A165b also improved the permeability function of isolated diabetic human glomeruli. These results show that VEGF-A165b acts via the endothelium to protect blood vessels and ameliorate diabetic nephropathy