Survey of Research Approaches Utilised in The Scholarship of Teaching and Learning Publications

The Scholarship of Teaching and Learning (SoTL) has been described as the fastest growing academic development movement in higher education. As this field of inquiry matures, there is a need to understand how SoTL research is conducted. The purpose of our study was to inform this debate by investigating research approaches used in SoTL publications. We analysed 223 empirical research studies published from 2012 to 2014 in three explicitly focused SoTL journals. We classified the studies as either qualitative, quantitative, or mixed methods using an analytical framework devised from existing literature on research methods. We found that the use of the three research designs was fairly evenly distributed across the papers examined: qualitative (37.2%), quantitative (29.6%), and mixed methods (33.2%). However, there was an over-reliance on data collection from a single source in 83.9% of papers analysed, and this source was primarily students. There was some, but limited, evidence of the use of triangulation through the use of multiple data collection instruments (e.g. survey, assessment tasks, grade databases). Similarly, only one-third of publications classified as mixed methods integrated the analysis and interpretation of the qualitative and quantitative data equally within the study. We conclude that current SoTL research is characterised by methodological pluralism but could be advanced through inclusion of more diverse approaches, such as close reading, and adoption of strategies known to enhance the quality of research, for example, triangulation and visual representation

Multi-omic data integration elucidates Synechococcus adaptation mechanisms to fluctuations in light intensity and salinity

Synechococcus sp. PCC 7002 is a fast-growing cyanobacterium which flourishes in freshwater and marine environments, owing to its ability to tolerate high light intensity and a wide range of salinities. Harnessing the properties of cyanobacteria and understanding their metabolic efficiency has become an imperative goal in recent years owing to their potential to serve as biocatalysts for the production of renewable biofuels. To improve characterisation of metabolic networks, genome-scale models of metabolism can be integrated with multi-omic data to provide a more accurate representation of metabolic capability and refine phenotypic predictions. In this work, a heuristic pipeline is constructed for analysing a genome-scale metabolic model of Synechococcus sp. PCC 7002, which utilises flux balance analysis across multiple layers to observe flux response between conditions across four key pathways. Across various conditions, the detection of significant patterns and mechanisms to cope with fluctuations in light intensity and salinity provides insights into the maintenance of metabolic efficiency

Hybrid architecture for shallow accumulation mode AlGaAs/GaAs heterostructures with epitaxial gates

Accumulation mode devices with epitaxially grown gates have excellent electrical stability due to the absence of dopant impurities and surface states. We overcome typical fabrication issues associated with epitaxially gated structures (e.g., gate leakage and high contact resistance) by using separate gates to control the electron densities in the Ohmic and Hall bar regions. This hybrid gate architecture opens up a way to make ultrastable nanoscale devices where the separation between the surface gates and the 2D electron gas is small. In this work, we demonstrate that the hybrid devices made from the same wafer have reproducible electrical characteristics, with identical mobility and density traces over a large range of 2D densities. In addition, thermal cycling does not influence the measured electrical characteristics. As a demonstration of concept, we have fabricated a hybrid single-electron transistor on a shallow (50 nm) AlGaAs/GaAs heterostructure that shows clear Coulomb blockade oscillations in the low temperature conductance.This project was supported by the Australian Government under the Australia-India Strategic Research Fund and by the Australian Research Council (ARC) DP scheme. A.R.H. acknowledges an ARC Outstanding Researcher Award. Devices were fabricated using the facilities at the NSW Node of the Australian National Fabrication Facility (ANFF). J.R., A.L., and A.D.W. acknowledge support from Mercur Pr-2013-0001, BMBF-Q.com-H 16KIS0109, and DFH/UFA CDFA-05-06.Copyright (2015) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in MacLeod SJ, See AM, Hamilton AR, Farrer I, Ritchie DA, Ritzmann J, Ludwig A, Wieck AD, Applied Physics Letters 106, 012105 (2015) and may be found at http://dx.doi.org/10.1063/1.4905210

Reproducibility of 3-dimensional ultrasound readings of volume of carotid atherosclerotic plaque

<p>Abstract</p> <p>Background</p> <p>Non-invasive 3-dimensional (3D) ultrasound (US) has emerged as the predominant approach for evaluating the progression of carotid atherosclerosis and its response to treatment. The aim of this study was to investigate the quality of a central reading procedure concerning plaque volume (PV), measured by 3D US in a multinational US trial.</p> <p>Methods</p> <p>Two data sets of 45 and 60 3D US patient images of plaques (mean PV, 71.8 and 39.8 μl, respectively) were used. PV was assessed by means of manual planimetry. The intraclass correlation coefficient (ICC) was applied to determine reader variabilities. The repeatability coefficient (RC) and the coefficient of variation (CV) were used to investigate the effect of number of slices (S) in manual planimetry and plaque size on measurement variability.</p> <p>Results</p> <p>Intra-reader variability was small as reflected by ICCs of 0.985, 0.967 and 0.969 for 3 appointed readers. The ICC value generated between the 3 readers was 0.964, indicating that inter-reader variability was small, too. Subgroup analyses showed that both intra- and inter-reader variabilities were lower for larger than for smaller plaques. Mean CVs were similar for the 5S- and 10S-methods with a RC of 4.7 μl. The RC between both methods as well as the CVs were comparatively lower for larger plaques.</p> <p>Conclusion</p> <p>By implementing standardised central 3D US reading protocols and strict quality control procedures highly reliable ultrasonic re-readings of plaque images can be achieved in large multicentre trials.</p

Formation of regulatory modules by local sequence duplication

Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms

Isolation and Characterization of Two Novel Colorectal Cancer Cell Lines, Containing a Subpopulation with Potential Stem-Like Properties: Treatment Options by MYC/NMYC Inhibition

Schulte am Esch J, Windmöller BA, Hanewinkel J, et al. Isolation and Characterization of Two Novel Colorectal Cancer Cell Lines, Containing a Subpopulation with Potential Stem-Like Properties: Treatment Options by MYC/NMYC Inhibition. Cancers. 2020;12(9): 2582.Cancer stem cells (CSC) are crucial mediators of cancer relapse. Here, we isolated two primary human colorectal cancer cell lines derived from a rectal neuroendocrine carcinoma (BKZ-2) and a colorectal adenocarcinoma (BKZ-3), both containing subpopulations with potential stem-like properties. Protein expression of CSC-markers prominin-1 and CD44 antigen was significantly higher for BKZ-2 and BKZ-3 in comparison to well-established colon carcinoma cell lines. High sphere-formation capacity further confirmed the existence of a subpopulation with potential stem-like phenotype. Epithelial–mesenchymal transition markers as well as immune checkpoint ligands were expressed more pronounced in BKZ-2. Both cell populations demonstrated N-myc proto-oncogene (NMYC) copy number gain. Myc proto-oncogene (MYC)/NMYC activity inhibitor all-trans retinoic acid (ATRA) significantly reduced the number of tumor spheres for both and the volume of BKZ-2 spheres. In contrast, the sphere volume of ATRA-treated BKZ-3 was increased, and only BKZ-2 cell proliferation was reduced in monolayer culture. Treatment with KJ-Pyr-9, a specific inhibitor of MYC/NMYC-myc-associated factor X interaction, decreased survival by the induction of apoptosis of both. In summary, here, we present the novel colorectal cancer cell lines BKZ-2 and BKZ-3 as promising cellular in vitro models for colorectal carcinomas and identify the MYC/NMYC molecular pathway involved in CSC-induced carcinogenesis with relevant therapeutic potential

Alternative regression models to assess increase in childhood BMI

<p>Abstract</p> <p>Background</p> <p>Body mass index (BMI) data usually have skewed distributions, for which common statistical modeling approaches such as simple linear or logistic regression have limitations.</p> <p>Methods</p> <p>Different regression approaches to predict childhood BMI by goodness-of-fit measures and means of interpretation were compared including generalized linear models (GLMs), quantile regression and Generalized Additive Models for Location, Scale and Shape (GAMLSS). We analyzed data of 4967 children participating in the school entry health examination in Bavaria, Germany, from 2001 to 2002. TV watching, meal frequency, breastfeeding, smoking in pregnancy, maternal obesity, parental social class and weight gain in the first 2 years of life were considered as risk factors for obesity.</p> <p>Results</p> <p>GAMLSS showed a much better fit regarding the estimation of risk factors effects on transformed and untransformed BMI data than common GLMs with respect to the generalized Akaike information criterion. In comparison with GAMLSS, quantile regression allowed for additional interpretation of prespecified distribution quantiles, such as quantiles referring to overweight or obesity. The variables TV watching, maternal BMI and weight gain in the first 2 years were directly, and meal frequency was inversely significantly associated with body composition in any model type examined. In contrast, smoking in pregnancy was not directly, and breastfeeding and parental social class were not inversely significantly associated with body composition in GLM models, but in GAMLSS and partly in quantile regression models. Risk factor specific BMI percentile curves could be estimated from GAMLSS and quantile regression models.</p> <p>Conclusion</p> <p>GAMLSS and quantile regression seem to be more appropriate than common GLMs for risk factor modeling of BMI data.</p