Changing Gears

Vaxign 2: Web-based Rational Vaccine Design based on Reverse Vaccinology and Machine Learning

Reverse vaccinology (RV) is a technique that allows the prediction of vaccine candidates from a pathogen’s genome enabling the more efficient development of new vaccines and improvements on existing vaccines. Vaxign2 is the second generation of the first web-based vaccine design program leveraging reverse vaccinology with machine learning via Vaxign-ML. Validation benchmarking has shown Vaxign-ML’s superior prediction performance compared to other RV tools. Vaxign2 has also implemented predictive analyses workflows to empower users to quickly refine prediction results based on different vaccine design rationales. A use case is presented with the successful analysis of SARS-CoV-2, the coronavirus that causes COVID-19.

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Mid-Life Interventions to Reduce Age-Related Fragility Fractures

ckadur

The average age of the general population is increasing with the number of positive correlations that showcase an increase in the number of fractures then an individual can experience with increased age. This review study aims to determine the interventions that should be implemented at the midlife or earlier in order to stabilize the bone mass density throughout the course of an individual’s lifetime. This study was conducted from the analysis of literature regarding a large depth of peer-review journal articles that have been conducted in an attempt to provide a clear picture to reduce the reduction of bone mass density later in life. We are able to see that continuous physical interventions as well as increased supplementation in key areas are able to hold the longevity of bone mass density. It is recommended that by using these techniques, we are able to accrue as much bone mass and then maintain the density to offset the likely-hood of a fracture occurring throughout a lifetime.

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Méliès and the Modern World

ralbayat

This project looks in depth at the work of early filmmaker Georges Méliès who was a pioneer of special effects and story films during the late-nineteenth and early-twentieth centuries. Furthermore, we are looking to highlight the importance of Madeleine Malthête-Méliès, who had perhaps the longest active career of any film historian and whose main concentration was documenting her grandfather Georges Méliès, including locating his many lost films. Our focus has been supporting the publication of a translation of a key historical source that has long been unavailable in English, the late Madeleine Malthête-Méliès’ biography, Georges Méliès, L’Enchanteur, which is under contract with the University of Michigan Press. This book will make Méliès’ work better known to a wider audience including readers of English. We have worked to document the author’s work by arranging English subtitling of a video interview with Madeleine Malthête-Méliès, and have compiled a complete bibliography of the research publication connected with the organization she founded, Les Amis de Georges Méliès. We are summarizing relevant articles for discussion in the introduction to the biography and assisting in the publication of another book, Méliès Boots: Material Contexts for Early Film Manufacturing (University of Michigan Press, under contract). To further show how Georges Méliès has impacted the modern world, we are preparing a short film that will summarize research on Méliès at the University of Michigan undertaken since 2011 told from the point-of-view of a new generation of media makers who draw continuing inspiration from learning about Méliès and his work.

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Evaluating computational methods for predicting protein stability changes upon mutations

rosiekw

Protein-protein interactions (PPIs) are central in biological processes. Most proteins are marginally stable to perform their functions such as binding. Amino acid mutations taking place on proteins may change the protein stability and the affinity of a binding process, which further affects their biological functions. It is reported that amino acid mutations at protein-protein interfaces are frequently implicated in many diseases, including cancer. Therefore, it is of great significance to quantitatively predict the change of protein stability and binding affinity upon mutations, denoted as ddG_stability and ddG_binding. Many tools have been developed for ddG prediction, but there is lacking in a comprehensive comparison of their predictive powers. This study aimed to evaluate the predictive accuracy of a variety of widely used tools for ddG_stability and ddG_binding estimation on a large scale benchmark, placing a guidance on choosing the most accurate tool for ddG prediction.

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Active for Life: The effect of a low-intensity functional circuit training program on endurance among COPD patients

pemma

Patients with Chronic Obstructive Pulmonary Disease (COPD) often lead inactive lifestyles due to breathing difficulties, and sedentary behavior may worsen both symptoms and mortality. The moderate-to-vigorous-intensity exercises emphasized by most fitness programs are not feasible for patients with COPD, but increasing time of light-intensity exercise may be an effective alternative. In this study, a randomized-controlled trial is used to determine whether a light-intensity fitness program called Active for Life (designed by Principal Investigator [PI] Janet Larson) is effective in improving aerobic endurance among COPD patients in the long term (after 52 weeks). Qualified participants are randomly assigned to one of two treatment groups: the Active for Life intervention and the control group. Both groups are guided through physical and behavioral activities with the goal of educating participants about health, but the Active for Life group is focused on functional circuit training (FCT), while the control group involves chair-based movement. All participants undergo ten weeks of lab-based activities according to treatment group, followed by one year of follow-up appointments and self-paced at-home videos. Aerobic endurance is measured by distance walked during the six-minute walk test at baseline, ten weeks, three months, six months, and one year into the program. We hypothesize that engaging participants in the Active for Life program will increase distance walked during the six-minute walk test.

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The Effects of Out-of-Pocket Payments on Emergency and Trauma Surgery Patients’ Livelihoods

pnirali

Every year, 3 million US residents suffer from injuries leading to needing medical care. The trauma care system has greatly improved saving lives from the time of injury, but many patients are left with out-of-pocket (OOP) payments whether or not they had insurance coverage. We do not know what the burden of these OOP payments are, including the long term financial, mental, and physical impact. The specific aims of this study are to 1) measure the OOP payments for patients who had an emergency surgical procedure, 2) quantify whether these OOP payments change on average by the type of insurance a patient has (private, Medicaid, Medicare, uninsured), and 3) understand the hardship caused by OOP payments for these emergency surgical procedures on the patient and their family. This study reports the findings from in-depth qualitative interviews of 30 patients =18 years of age sustaining a traumatic injury requiring treatment at the University of Michigan Hospital trauma center. We expect our mixed-methods analysis to elucidate the downstream effects of large OOP payments not otherwise able to be captured in available databases. Our findings will be one of the first to describe the long-term burden of trauma care and estimate the out-of-pocket payments trauma patients face from patient-level data.

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Modeling Depth of Interaction: A Neural Network Approach

yonghuan

One of the key elements underlying successful second language (L2) learning is the interaction with other language users in the target language (Gass & Varonis, 1985). While the expectation exists that learners will use their linguistic skills in theStudy Abroad (SA) context (e.g., Fraser 2002; Freed, 1990; 2000; Hernández, 2010; Martinsen, 2011; Mendelson 2004; Vande Berg et al., 2009, Whitworth, 2006), it is also known that many SA learners interact substantially less with native speakers (NSs) than they initially anticipate (DeKeyser, 1986; Dewey et al., 2014; Rivers, 1998; Wilkinson, 1998a, 1998b; García-Amaya, 2017). Recent research further shows that SA learners’ target-language use decreases over a six-week SA experience (García-Amaya, 2017; forthcoming). While interaction in the L2 is essential for achieving L2 gains, research has found that learners must negotiate meaning to notice gaps in their acquisition and benefit from their interlocutor(s)’ efforts to adjust interaction and facilitate comprehension (Long 1981, 1983, 1986).

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