Making Methods Relevant: Undergraduate Research Methods and the Content Analysis Project

Teachers of undergraduate research methods classes may struggle at times to keep their courses engaging and to have students view the material as relevant to the occupations they will soon enter. This article discusses a content analysis assignment and how it offers a way for students to demonstrate critical thinking and acquire data analysis skills. Through the use of multiple high-impact learning practices, the assignment requires students, individually or in a group, to identify data appropriate for content analysis and then, with faculty guidance, develop research questions, manage the data, conceptualize and operationalize themes, perform content analysis, draw conclusions from the data, and assess the validity and reliability of their work. We discuss the benefits and potential pitfalls of the assignment and analyze data (both quantitative and qualitative) derived from student evaluations of their content analysis project

Detecting Solar System Analogs through Joint Radial Velocity/Astrometric Surveys

Earth-mass exoplanets on year-long orbits and cool gas giants (CGG) on decade-long orbits lie at the edge of current detection limits. The Terra Hunting Experiment (THE) will take nightly radial velocity (RV) observations on HARPS3 of at least 40 bright nearby G and K dwarfs for 10 years, with a target 1$\sigma$ measurement error of $\sim$0.3 m/s, in search of exoplanets that are Earth-like in mass and temperature. However, RV observations can only provide minimum mass estimates, due to the mass-inclination degeneracy. Astrometric observations of these same stars, with sufficient precision, could break this degeneracy. Gaia will soon release $\sim$100-200 astrometric observations of the THE stars with a 10 year baseline and $\sim$34.2 $\mu$as 1$\sigma$ along-scan measurement error. The Nancy Grace Roman Space Telescope will be capable of precision astrometry using its wide field imager (target $\sim$5-20 $\mu$as 1$\sigma$ measurement error for bright stars) and could extend the astrometric observational baseline to $\sim$25 years. We simulate and model an observing program that combines data from these three telescopes. We find that (1) THE RVs and Gaia astrometry can detect Earth-like and CGG-like exoplanets around bright Sun-like stars at 10 parsecs and that (2) adding Roman astrometry improves the detection precision for CGG masses and periods by a factor up to $\sim$10 and $\sim$4, respectively. Such a survey could provide insight into the prevalence of Solar System analogs, exoplanet architectures reminiscent of the mass and orbital separation hierarchy of our Solar System, for the nearest Sun-like stars.Comment: 21 pages, 10 figures. Revised based on comments from anonymous reviewer at AAS Journals. Code available at https://github.com/dyahalomi/rv_and_astrometr

A VLT/FLAMES study of the peculiar intermediate-age large magellanic cloud star cluster NGC 1846. I. Kinematics

In this paper we present high-resolution VLT/FLAMES observations of red giant stars in the massive intermediate-age Large Magellanic Cloud star cluster NGC 1846, which, on the basis of its extended main-sequence turnoff (EMSTO), possesses an internal ag

Hydroxyl radical is produced via the Fenton reaction in submitochondrial particles under oxidative stress: implications for diseases associated with iron accumulation

Mitochondrial dysfunction and reactive oxygen species (ROS) are often implicated in diseases involving oxidative stress and elevated iron. As mitochondria produce ATP by oxidative phosphorylation, ROS by-products are generated from the electron transport chain. Although superoxide and hydrogen peroxide have been thoroughly investigated, little evidence documents hydroxyl radical (HO•) production in mitochondria. In order to determine whether HO• is generated under oxidative stress conditions by a Fenton-type mechanism, bovine heart submitochondrial particles were examined for HO• in the presence and absence of iron ligands, antioxidant enzymes and HO• scavengers. HO• was measured as 2,3- and 2,5-dihydroxybenzoic acid (DHBA), using HPLC with electrochemical detection. The iron ligand desferrioxamine significantly decreased DHBAs, indicating that HO• generation required iron redox-cycling. In addition, results from exogenous SOD and catalase, exogenous hydrogen peroxide, and HO•-scavenger studies support a Fenton-type reaction mechanism. The results indicate that increased HO• levels occur in mitochondria under oxidative stress and that the HO• levels can be modulated with antioxidant enzymes and iron ligands. Our findings together with reports on iron accumulation in degenerative diseases highlight the importance of developing mitochondrial-targeted antioxidants for the therapeutic intervention of diseases associated with mitochondrial dysfunction and oxidative stress

Is dietary Vitamin A associated with myopia from adolescence to young adulthood?

Purpose: Potential links may exist between vitamin A intake and myopia via various pathways. In this study, we examined the association between dietary vitamin A intake during adolescence and myopia in early adulthood. Methods: We performed a prospective analysis utilizing data collected from participants of the Raine Study Gen2. Dietary vitamin A intake, determined via food frequency questionnaires completed at ages 14, 17, and 20 years, was compared with ophthalmic measurements collected at year 20. Low vitamin A levels were defined as \u3c600 \u3eµg/day. Regression models were used to adjust for ocular sun exposure level, educational level, and parental myopia as potential confounders. Results: A total of 642 subjects were analyzed. Although those with adequate vitamin A intakes were less likely to be myopic (P = 0.03), this association became insignificant when adjusted for potential confounding factors in logistic regression modeling (odds ratio, 0.59; 95% confidence interval, 0.98–2.52; P = 0.06). Conclusions: There were no significant associations between total vitamin A intakes during adolescence and year 20 refractive errors after adjustment for confounders. Replication of this finding and further investigations are essential to rule out the suggestion that sufficient vitamin A intake during adolescence is associated with lower risk of myopia in early adulthood. Translational Relevance: Our findings are not definitive that ingesting foods high in vitamin A during childhood and adolescence does not have a role for preventing myopia in early adulthood

The Thresher : lucky imaging without the waste

JAH acknowledges funding from the Science and Technology Facilities Council of the United Kingdom.In traditional lucky imaging (TLI), many consecutive images of the same scene are taken with a high frame-rate camera, and all but the sharpest images are discarded before constructing the final shift-and-add image. Here, we present an alternative image analysis pipeline – The Thresher – for these kinds of data, based on online multi-frame blind deconvolution. It makes use of all available data to obtain the best estimate of the astronomical scene in the context of reasonable computational limits; it does not require prior estimates of the point-spread functions in the images, or knowledge of point sources in the scene that could provide such estimates. Most importantly, the scene it aims to return is the optimum of a justified scalar objective based on the likelihood function. Because it uses the full set of images in the stack, The Thresher outperforms TLI in signal-to-noise ratio; as it accounts for the individual-frame PSFs, it does this without loss of angular resolution. We demonstrate the effectiveness of our algorithm on both simulated data and real Electron-Multiplying CCD images obtained at the Danish 1.54-m telescope (hosted by ESO, La Silla). We also explore the current limitations of the algorithm, and find that for the choice of image model presented here, non-linearities in flux are introduced into the returned scene. Ongoing development of the software can be viewed at https://github.com/jah1994/TheThresher.Publisher PDFPeer reviewe

Chemical tagging can work: Identification of stellar phase-space structures purely by chemical-abundance similarity

Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were in fact born together (in the same molecular cloud), long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ~100,000 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space. We recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon; the prospects for future data sets appear very good.Comment: accepted for publication in the Ap

Quality of DNA Extracted from Mouthwashes

Background A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes. Methodology Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR). Principal Findings Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1–10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22–7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4–14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an ~200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5). Conclusions This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. Whilst the level of degradation did not significantly prevent successful amplification of short PCR fragments, previous studies suggest that such DNA degradation would compromise more demanding applications