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REU Summer Interns Tackle Big Problems in Bioinformatics
Top row left to right: Luiz Mata Lopez, Aditya Girish, Sean Markey, Nathan Jacobi and Olivia Miskala-Dinc. Bottom row left to right: Adam Levav, Nicholas Arellano, Lucy Mettee, Esmma Almousa and Shria Arcot.
Following the genome revolution, bioinformatics has rapidly risen as an essential field of research. To increase our understanding of health and disease, there is a critical need for scientists with interdisciplinary training to process and analyze large-scale genomic datasets.
The Center for Bioinformatics and Computational Biology (CBCB) is working to fill those ranks. This summer, a group of 10 undergraduate students from across the country are collaborating with University of Maryland faculty and graduate students to research real world problems in metagenomics, machine learning, single-cell RNA sequencing, parallel computing, and more.
The students are part of a prestigious 10-week long internship funded by the National Science Foundation and run by faculty in CBCB. Seventy-one students applied for this year’s Research Experiences for Undergraduates (REU) program, called BRIDGE (Bioinformatics Research In Data science for Genomics).
Students are working in pairs to learn about a research problem, propose a plan to tackle a specific research question, and then implement their plan. At the end of the summer, each team will produce a paper and give an oral presentation on their project.
Michael Cummings, a professor of biology and director of CBCB, says initial research experiences are important in developing scientific careers.
“Such experiences were certainly important for me as an undergraduate student, as they provided opportunities to learn and explore in ways not possible in a regular classroom setting,” he says. “The students in this cohort represent a diversity of backgrounds and interests. They are a talented group and it’s evident that their perspectives have expanded through the research experience this summer.”
Harihara Subrahmaniam Muralidharan, a fourth-year computer science doctoral student who is working with the REU students, says it has been fun getting to know the group.
“It’s been a welcome change to have interns working in person in the lab space after a several year hiatus due to COVID,” he says.
Undergraduates Nicholas Arellano and Esmma Almousa are working with Cummings to develop machine learning models that would better predict the progression of Parkinson’s disease. They are specifically working with longitudinal data, which allows researchers to assess multiple disease aspects, such as the timing of disease onset.
“We’re trying to create a better way of giving a prognosis based off repeated measures of a patient’s data taken over a period of time,” says Arellano, a rising junior majoring in bioinformatics at Towson University.
He adds that the REU internship has provided him a unique opportunity to work with this type of data.
Almousa, a rising senior majoring in data science at University of Wisconsin–Madison, says she’s studied similar data for Alzheimer’s disease during her course of studies at her home institution.
Still, she finds the learning experience she’s having at CBCB this summer invaluable.
“I think it’s interesting to look at neurodegenerative diseases because there’s a lot of unanswered questions, like how to slow down or eliminate their progression,” she says. “I think finding predictors of these diseases earlier is so important because it can help with things like adjusting the patient’s lifestyle or determining therapeutic interventions.”
Arellano and Almousa both say they are enjoying participating in the internship, calling it a supportive and flexible environment.
“I really appreciate that we’re able to meet with our mentors a couple times each week just to ask questions and go over the new tools we’ve learned,” Almousa says. “Working with Dr. Cummings has been a really wonderful and eye-opening experience.”
Adam Levav, a rising junior majoring in computer science at the University of Maryland, is working on a project that involves developing methods to identify misassembled DNA sequences.
There are many technologies for sequencing DNA, but none of them can read an organism’s whole sequence in one go because it is too long, he says. Instead, they get fragments of sequences at several different places in the organism’s DNA, called reads.
This gives scientists a long, unordered list of short reads, which they then attempt to assemble. Based on the overlaps between the reads, they piece them together back into a reconstruction of the original DNA, like a jigsaw puzzle. “Any error in our reassembled DNA could completely mess up our understanding of the organism,” Levav explains. “For example, if that missing part of the DNA encoded a critical component in the reproduction of a contagious species of bacteria, then we would be completely unable to develop defenses to that bacteria’s reproduction—or worse, develop incorrect defenses. So it’s important to double-check that our reassembled DNA is correct.”
Levav is working with Lucy Mettee, a rising junior majoring in biomedical engineering at the University of Texas at Dallas. They are being mentored by Muralidharan and Mihai Pop, a professor of computer science and director of the University of Maryland Institute for Advanced Computer Studies.
In addition to conducting research, Muralidharan says the group took a field trip to the Smithsonian National Museum of Natural History to see the exhibit “Genome: Unlocking Life’s Code.”
Other students participating in the CBCB program this summer are: Shria Arcot, a rising junior double majoring in computer science with a specialization in bioinformatics at University of California San Diego; Aditya Girish, a rising junior double majoring in biomathematics and computer science at Rutgers University; Olivia Miskala-Dinc, a rising senior majoring in computer science at the University of Maryland; Luiz Mata Lopez, a rising sophomore majoring in computer science at Montgomery College; Nathan Jacobi, a rising senior majoring in computer science with a focus on data science at the University of Georgia; and Sean Markey, a rising senior double majoring in computer science and physics at the University of Maryland.
—Story by Melissa Brachfeld
Cummings Reappointed as Director of CBCB
Michael Cummings, a professor of biology and expert in molecular evolutionary genetics, has been reappointed as director of the Center for Bioinformatics and Computational Biology (CBCB) for five years, effective July 1, 2022.
“Michael is a valuable asset to our research community—both as a strong computational biologist with a broad range of scientific interests, and as an excellent administrator,” says Mihai Pop, director of the University of Maryland Institute for Advanced Computer Studies (UMIACS), which supports CBCB and six other major centers on the Maryland campus.
In the metrics-based CSRankings, the University of Maryland is ranked fourth in the nation in bioinformatics and computational biology. Cummings says this is due in large part to the many excellent people who make up CBCB.
“Our faculty are highly intelligent and productive, which results in high impact and funding level per faculty member,” he says. “The graduate students and other trainees are creative and enthusiastic. Of course, the broader UMIACS community—staff, faculty, students—help to make our successes possible.”
CBCB is focused on researching questions that arise from the genome revolution, studying pathogen genomics, microbiome research, epigenetics, molecular evolution, transcriptional regulation, metabolic modeling, and more.
One of Cummings’s ongoing projects is an open-source, evolutionary analysis software called BEAGLE. It is an essential component in the software workflow used by many scientists studying the evolutionary history of organisms, including viruses that cause AIDS, influenza, Ebola and now COVID-19.
He is also part of a team that recently received $2.7 million from NIH to study how aging impacts the brain, by using machine learning techniques to interpret multiomics data.
Looking forward, Cummings says that his vision is to continue promoting an inclusive culture and further increase the center’s diversity. He also wants to continue creating a supportive and stimulating environment where all members of the community are productive and feel fulfilled.
Cummings notes that he is currently focused on helping CBCB’s newest faculty, assistant professors Brantley Hall and Erin Molloy, develop and expand their already successful research programs as they move toward tenure and promotion.
Cummings has served has the director of CBCB since 2019. He came to the University of Maryland in 2003 as a visiting associate professor, and was the first person to be hired in CBCB. He completed his doctorate in organismic and evolutionary biology at Harvard University, and postdoctoral research at the University of California, Berkeley.
—Story by Maria Herd
Hall Develops Device to Measure Gut Microbial Metabolism
The human intestines contain a complex and diverse community of microbes that break down food to produce metabolites. Some metabolites are beneficial to human health, such as vitamins, while others can be harmful and lead to obesity or gastrointestinal disorders. A major gap in the microbiome field is measuring and understanding these metabolites.
“There are currently few strategies to measure metabolites produced by the gut microbiome, and even fewer that work in real time,” says Brantley Hall, an assistant professor of cell biology and molecular genetics.
Now Hall has been awarded funding from the National Institutes of Health (NIH) to develop a wearable device that can do exactly that, potentially leading to therapeutic interventions for patients suffering from gastrointestinal disorders like Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease. IBS is one of the most common disorders seen by doctors, affecting one in 10 adults.
The $417K award will be spread over two years, supporting Hall’s work in the Center for Bioinformatics and Computational Biology (CBCB), a lab focused on research questions that arise from the genome revolution.
Hall, who also has an appointment in the University of Maryland Institute for Advanced Computer Studies, says that existing devices are much larger, and his goal is to design a smaller device that can perform the same functions if not better.
He adds that future developments could lead to personalized dietary interventions and improved communication between doctors and patients about their symptoms.
—Story by Maria Herd
Mihai Pop Reappointed as Director of UMIACS
Mihai Pop, a professor of computer science noted for his scientific research and advocacy for equality and inclusion in academia, has been reappointed as director of the University of Maryland Institute for Advanced Computer Studies (UMIACS) for a three-year term, effective July 1, 2022.
As director, Pop will continue to provide leadership to 76 UMIACS faculty members and almost 200 graduate students from eight departments across the UMD campus, as well as two-dozen administrative and technical staff that support the institute’s research, innovation and outreach.
Pop has served as director of UMIACS since November 2018, succeeding Amitabh Varshney, who is now dean of the university’s College of Computer, Mathematical, and Natural Sciences.
“Mihai has positioned UMIACS on a path of excellence,” Varshney said. “I look forward to continuing to work with him to advance the breadth and impact of computing research across our campus, the state of Maryland and beyond.”
With Pop as director, UMIACS has consistently brought in more than $25 million each year in research funding. The bulk of those external awards come from the numerous federal labs and agencies that dot the region.
Examples of projects funded under Pop’s tenure as director include the National Science Foundation’s support for computational epidemiology and fairness in artificial intelligence (AI); the National Institute of Standards and Technology’s funding for research in quantum information science and machine learning; and the Defense Advanced Research Projects Agency’s support of research into deepfake videos and AI system adaptation.
“I am honored and grateful to help guide an organization that has a substantive wealth of scientific knowledge and expertise to draw upon,” Pop said. “Much of our work is interdisciplinary, and all of it is focused on offering computational solutions that will have a positive societal impact.”
Moving forward, Pop plans to further strengthen UMIACS’ partnerships with federal agencies while simultaneously increasing activities with physicians and clinicians at the University of Maryland, Baltimore (UMB).
In 2019, Pop hosted a workshop between UMIACS faculty members and UMB researchers to advance new ideas involving artificial intelligence and health care. The initial results were promising, with several teams receiving awards to use AI in addressing aging, traumatic brain injury, mental illness and more.
Pop is also active in bringing more equality and diversity to the field of computer science and to academia in general. He instituted specialized workshops in UMIACS to support early-career faculty members and publicly called for greater recognition and support for this same group.
“The voice of a fresh Ph.D. assistant professor is often louder than that of the most experienced lecturer or research scientist on our campus,” Pop wrote in a 2018 op-ed article in The Faculty Voice. “It is high time for a change. Our campus cannot excel if we continue to ignore and undervalue the many faculty who shoulder the bulk of our teaching, and who represent a critical driving force in our research programs.”
Pop has continuously committed UMIACS resources in support of the Iribe Initiative for Inclusion and Diversity in Computing and other efforts that enhance participation in the discipline by people from diverse backgrounds. This includes sponsoring activities like Technica, the world’s largest hackathon for underrepresented genders; the Diversity in Computing Summit; and the Widening Natural Language Processing workshop.
“One of my top priorities as director of UMIACS is to increase the number of women in our institute,” Pop said. “The strength that comes from diversity—in gender, scientific background or academic titles—is the catalyst that propels new ideas and brings robust innovation.”
Pop’s own research interests cover several areas of bioinformatics, primarily related to the development of computational algorithms for analyzing biological data generated by high-throughput experimental techniques, such as sequencing technologies.
Part of Pop’s research focuses on the computational analysis of the microbial communities inhabiting our world and our bodies—a scientific field called metagenomics. His lab, part of UMIACS’ Center for Bioinformatics and Computational Biology, has developed a number of software tools that are now widely used in the field. He has also been an active participant in a number of large-scale, multinational projects, including the Human Microbiome Project and the GEMS study of diarrheal disease in children from the developing world.
In 2018, Pop made Clarivate Analytics’ list of Highly Cited Researchers, a compilation of influential names in science whose published work in their specialty areas has consistently been judged by their peers to be of particular use and significance. He was also included in the 2014 list.
In 2019, he was named a Fellow of the Association for Computing Machinery, an elite recognition of outstanding science and scholarship that is bestowed upon less than one percent of the organization’s 100,000-plus members. Earlier this year, he was named a Fellow of the International Society for Computational Biology in recognition of his work in developing algorithms for analyzing metagenomic data.
An active educator and mentor, Pop currently advises six graduate students and one high school student. He previously worked with 13 graduate students and six postdocs, and he spent three years as a faculty adviser to a group of UMD freshmen that analyzed the genome of the diamondback terrapin, the university’s mascot.
Pop earned his B.S. in computer science from University Politehnica of Bucharest in Romania in 1994 and his M.S.E. and Ph.D. in computer science from Johns Hopkins University in 1998 and 2000, respectively. He has been at UMD since 2005.
Researcher Awarded $1M From NASA to Develop Disease Forecasting Center and App
NASA has awarded $1 million to a renowned University of Maryland expert on cholera prevention and transmission to develop the first internet and app-based decision-making systems for infectious diseases, followed by a climate disease forecasting center.
The project led by Rita Colwell, a Distinguished University Professor in the University of Maryland Institute for Advanced Computer Studies, will be the application and culmination of her five decades of research on the bacterial infection of the small intestine, typically spread through contaminated water. Known as the 19th century’s pandemic, cholera has killed hundreds of millions of people and still takes 130,000 lives every year, mostly in underdeveloped countries with poor sanitation or areas hit by natural disasters.
Colwell discovered that the source of Vibrio cholerae bacteria is water abundant with plankton, and that it can linger there between epidemics by entering a state of dormancy. Her discoveries helped establish a new field—bacterial zoonosis—and changed scientists’ understanding of how diseases can be transmitted from aquatic organisms to humans.
She also developed state-of-the art techniques using satellite images to predict outbreaks, so that countries with limited budgets can mobilize health care workers and resources to stop the disease. Through remote sensing, computational biology and genomics, Colwell’s scientific advancements have saved thousands of lives and improved public health on a global scale.
Now her life’s work will become digestible in one app, and lay the framework for the first climate-related disease forecasting center, a collaboration that will include NASA, the United Nations, NOAA, the United Kingdom and the University of Florida. It will be located at the University of Maryland.
“This project is truly exciting as it will provide a means of predicting the risk of epidemics on a global basis. The impact may well prove to be enormous as it will enable pre-emptive action, notably to save lives,” she said. “Our newer models to be developed may be able to predict the intensity of given outbreaks, a very important factor for public health intervention.”
Antarpreet Jutla, an associate professor of environmental engineering at the University of Florida and Colwell’s co-principal investigator, said the $1 million award will support their long-term vision of predicting infectious diseases.
Leveraging his mathematical skills, her expertise in microbiology, and NASA’s satellite and weather data, Jutla and Colwell have over the past decade developed interactive maps for locations all over the world—the Chesapeake Bay, Zimbabwe, Mozambique, Senegal, Ethiopia, Bangladesh and Yemen—that can predict outbreaks with 90% accuracy.
Their sophisticated models are currently in use, with the latest prediction of an outbreak in war-torn Ukraine. Colwell also warns that “climate change is bringing cholera to new parts of the world, making this type of prediction system more important than ever before, especially because it provides an opportunity for early intervention.”
—Story by Maria Herd
Cummings Awarded $2.7M to Study Impacts of Aging on the Brain
Michael Cummings, a professor of biology with an appointment in the University of Maryland Institute for Advanced Computer Studies (UMIACS), is part of a team funded by the National Institutes of Health (NIH) to study how aging impacts the brain.
Working with medical experts at the University of Maryland, Baltimore (UMB), Cummings will continue his research on aging and traumatic brain injury in mice, which could eventually contribute toward treatments for age-related diseases like dementia and Alzheimer’s.
The $2.7M award will be spread across four years, supporting his team’s ongoing work that uses machine learning techniques to interpret “multiomics” data, where the data sets of different omics groups—genome, proteome, transcriptome, epigenome, and microbiome—are combined during analysis.
The collaboration was spurred by a state funding initiative called AI + Medicine for High Impact (AIM-HI), which joins faculty from both universities to tackle major issues that require cross-campus expertise in artificial intelligence and medicine. The initiative supports projects that have high potential for scientific breakthroughs and are likely to secure larger federal awards.
“The AIM-HI funding allowed us to show that machine learning could effectively be applied to multiomics data, with hundreds of thousands of variables quantifying the amounts of different proteins and lipids,” explains Cummings.
For their latest project, his team will develop software tools that can assess the brain’s changes in lipids and proteins, then characterize and test those tools.
Their results will be used to make inferences about biochemical pathways, which can help scientists identify potential interventions to mitigate the negative effects of aging on the brain.
Cummings notes that he met his UMB collaborators—Maureen Kane, an associate professor of pharmaceutical sciences, and Marta Lipinski, an associate professor of anesthesiology—at a meeting that was organized by UMIACS Director Mihai Pop intended to stimulate collaborative research proposals.
“Interdisciplinary research supported by new advances in computing will continue to open new doors of discovery,” says Pop. “This work by Michael and his collaborators in Baltimore is a perfect example of that.”
—Story by Maria Herd
CBCB Alums Named to TIME Magazine’s List of 100 Most Influential People
Two genomics experts who completed their doctoral training at the University of Maryland’s Center for Bioinformatics and Computational Biology (CBCB) were just named toTIME magazine’s annual list of 100 most influential people for their landmark work completing the sequencing of the human genome.
Michael Schatz, a Bloomberg Distinguished Professor of Computer Science and Biology at Johns Hopkins University (JHU), and Adam Phillippy, a bioinformatician at the National Human Genome Research Institute (NHGRI), were recognized for leading an international team in achieving the feat that scientists have been working toward for more than two decades.
Their team, the Telomere-to-Telomere (T2T) Consortium, used a mixture of new "long read" DNA sequencing technologies to map a gap-free sequence of the roughly three billion bases, or “letters,” in human DNA.
In making the announcement for TIME, Jennifer Doudna, a biochemist and winner of the 2020 Nobel Prize in Chemistry, explained that the team had uncovered the human genome’s “dark matter” that was missed by earlier sequencing.
“The complete human genome sequence is an invaluable resource that may provide new insights into the origin of diseases and how we can treat them,” Doudna wrote. “It also offers the most complete look yet at the genetic script underlying the very nature of who we are as human beings.”
The Human Genome Project announced it had finished decoding the basic chemical instructions for life in 2003, but skipped a significant section composed of highly repetitive sequences because they were mostly considered “junk DNA” at the time. Today, researchers know there’s more to it, which makes T2T’s work crucial.
Their findings were published earlier this year in the academic journal Science. Sergey Koren, another CBCB alum who completed his computer science Ph.D. in 2012, was a co-first author on the paper.
Phillippy and Schatz graduated with their Ph.D.s in computer science in 2010, working closely with their adviser Steven Salzberg. Now at JHU, Salzburg was CBCB’s founding director.
Schatz was co-advised by Mihai Pop, another genomics expert who is a professor of computer science and director of the University of Maryland Institute for Advanced Computer Studies.
“The success of the T2T project demonstrates the power of interdisciplinary science and represents the culmination of decades of advances in computational techniques for analyzing genomes, many of which were pioneered by Adam and Mike,” says Pop.
He adds that the pair fostered a collegial and collaborative environment in CBCB that still characterizes the center to this day, contributing to the success of many other outstanding scientists.
Looking forward, Schatz says he is excited about the possibilities of using their new genomic technology to improve many aspects of society, from agriculture to health care, and especially a better understanding of cancer.
Developing Algorithms to Predict the Spread of Infectious Diseases
The past 20 years have seen numerous epidemics break out across the globe: SARS, H1N1, Ebola, Zika, and most recently, COVID-19. These diseases have impacted the lives of billions, and lead to millions of deaths around the world. A multitude of factors can cause an infectious disease to develop and spread, including climate and poor sanitation, but even with knowledge of these factors it is difficult to predict when outbreaks will occur. Using previous research on the prediction of cholera outbreaks, however, researchers at the University of Maryland have developed algorithms that can predict the spread of infectious diseases from a local to global scale.
Early work on the prediction of infectious diseases began in the 1970s and 1980s, with the study of cholera in the Chesapeake Bay. Researchers then examined factors like water temperature and salinity as predictors of cholera outbreaks, and later studies integrated the use of satellite sensor data on a number of environmental and infrastructural measures as predictive factors.
Rita Colwell, Distinguished University Professor at the University of Maryland Institute for Advanced Computer Studies (UMIACS) and a pioneer in infectious disease outbreak prediction research—including the work above—sought to utilize and expand on prior satellite sensor models to forecast outbreaks of other diseases, including the risk of COVID-19 in the U.S.
The algorithms—developed using weighted averages from a public dataset—analyze several thresholds on weather, climate, and sociological, epidemiological, and environmental processes related to the abundance, survival, and emergence of new pathogens. The algorithms can also be applied to new pathways of pathogen emergence or transmission using common pathogen footprints. This tool can give public health officials a much-needed advantage to combat disease, and has the potential to help save millions of lives. Colwell expects that satellite sensors will become a major international public health tool to monitor communicable diseases.
The project was funded primarily by NASA, with funding also from the National Science Foundation, the British Aid Agency, and the United Nations. Colwell's collaborators include Anwar Huq, a research professor at UMD’s Department of Cell Biology and Molecular Genetics, and Antar Jutla from the College of Engineering, University of Florida.
Their invention, “Predictive Algorithms for Infectious Diseases,” was nominated for a UMD Invention of the Year award in the Information Sciences category. Winners were announced on May 3, 2022, at Innovate Maryland, a campus-wide celebration of innovation and partnerships at UMD.
This article was published by the University of Maryland Division of Research
Pop Named Fellow by International Society for Computational Biology
Mihai Pop, a professor of computer science and the director of the University of Maryland Institute for Advanced Computer Studies (UMIACS), is being recognized for his significant achievements in computational biology and bioinformatics.
The International Society for Computational Biology (ISCB) has selected Pop as a Fellow for 2022. He joins 10 other ISCB members who have distinguished themselves through outstanding contributions to the field.
ISCB selected Pop for his leadership in the development of algorithms for analyzing metagenomic data, particularly in the context of metagenome assembly and identification of structural variants in assembly graphs, and for his important contributions to large community projects.
Much of Pop’s research focuses on the analysis of microbial communities—a scientific field called metagenomics—which involves the application of bioinformatics tools to study the genetic material from environmental, uncultured microorganisms. Recent years have seen a “metagenomic revolution,” made possible by rapid advances in sequencing technologies, Pop says.
His lab, which is part of the Center for Bioinformatics and Computational Biology, has developed a number of software tools that are now widely used in the field.
They’re currently being funded by the National Institutes of Health to develop a suite of computational tools for reconstructing DNA segments.
The $2.6 million award is supporting Pop’s work building software and developing algorithms that can reconstruct nearly-complete microbial genomes from complex mixtures found in the human gut. He says that ultimately this will help scientists better understand the role of certain microbes in human health and disease.
Pop also leads efforts to assemble data at the Human Microbiome Project, which is aimed at surveying the complex microbial communities inhabiting the human body. His 122 publications have been cited(link is external) more than 38,000 times.
The 2022 Fellows will be recognized at the Intelligent Systems for Molecular Biology conference, held this year from July 10–14 in Madison, Wisconsin.
—Story by Maria Herd
Cummings Receives NVIDIA Academic Hardware Grant
Michael Cummings, a professor of biology with an appointment in the University of Maryland Institute for Advanced Computer Studies (UMIACS), recently received an NVIDIA Academic Hardware Grant to assist in the development of software that provides a rapid analysis of biological sequence data.
The grant is part of NVIDIA’s efforts to advance education and research by enabling groundbreaking, innovative, and unique academic research projects with world-class computing resources.
Cummings plans to use the NVIDIA hardware in the continued development of open-source software known as BEAGLE (Broad-platform Evolutionary Analysis General Likelihood Evaluator).
BEAGLE is an essential component in the software workflow of many scientists studying the evolutionary history of organisms, including the viruses that cause AIDS, influenza, Ebola, and now COVID-19. With the ability of high-throughput tools like BEAGLE to produce results quickly, researchers are helping public health agencies react to health threats, Cummings says.
He adds that the new hardware will allow for the development of new algorithms for larger data sets and more complex models.
“I am thankful to have current state-of-the-art hardware for students and other personnel to use in their research,” Cummings says. “As a mentor it is important that my students get experience with the best current hardware where it benefits their research and training. As a researcher, it is necessary to have the best current hardware to develop software and perform analyses at the limits of what is possible.”
Cummings, who is director of the Center for Bioinformatics and Computational Biology, was previously awarded a NVIDIA Global Impact Award to support his lab’s work on BEAGLE.
—Story by Melissa Brachfeld
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