IB Professor James O’Dwyer improves on 35-year old ecology model

Article courtesy of Biomarker Magazine from the University of Illinois Institute for Genomic Biology.

“Well, in our country,” said Alice, still panting a little, “you’d generally get to
somewhere else — if you run very fast for a long time, as we’ve been doing.”
“A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”
-Lewis Carroll, Through the Looking GlassODwyerIGB01

Inspired by the Red Queen in Lewis Carroll’s Through the Looking Glass, collaborators from the University of Illinois and National University of Singapore improved a 35-year-old ecology model to better understand how species evolve over decades to millions of years, as reported in Ecology Letters.

The new model, called a mean field model for competition, incorporates the “Red Queen
Effect,” an evolutionary hypothesis introduced by Lee Van Valen in the 1970s that suggests
organisms must constantly increase their fitness in order to compete with other ever-evolving organisms in an ever-changing environment. The mean field model assumes that new species have competitive advantages that allow them to multiply, but over time new species with even better competitive advantages will evolve and outcompete current species, like a conveyor belt constantly moving backwards.

The model gets its name from field theory, which describes how fields, or a value in space and time, interact with matter. A field is like a mark on a map indicating wind speeds at various locations to measure the wind’s velocity. In this ecological context, the “fields” approximate distributions of species abundances. Ecologists can use models to predict what happens next and diagnose sick ecosystems, said Assistant Professor of Plant Biology James O’Dwyer, who co-authored the study.

CREATING A MODEL ECOLOGY MODEL
The mean field model has improved a fundamental ecology model, called neutral
biodiversity theory, which was introduced by Stephen Hubbell in the 1970s. Neutral theory
does not account for competition between different species, thus considering all species to be selectively equal.

“The neutral model relies on random chance,” said O’Dwyer, who is a member of the Biocomplexity theme. “It’s like a series of coin flips and a species has to hit heads every time to become very abundant. That doesn’t happen very often.”

Neutral theory can predict static distributions and abundances of species reasonably well, but it breaks down when applied to changes in communities and species over time. For instance, the neutral model estimates that certain species of rainforest trees are older than Earth.

“At one end of the spectrum, we have this neutral model with very few parameters and very simple mechanisms and dynamics, but at the other end, we have models where we try to parameterize every detail,” O’Dwyer said. “What’s been hardest is to take one or
two steps down this spectrum from the neutral model without being sucked down to this very complicated end of the spectrum.”

By creating a more realistic model that incorporates species differences, O’Dwyer and co-author Ryan Chisholm, an assistant professor at National University of Singapore, have taken an important step down that spectrum. “Our model is not the ecological equivalent of Einstein’s General Theory of Relativity, which was a conceptual leap for physics,” O’Dwyer said. “It is an incremental step at this point. But we will need those conceptual leaps that incorporate the best parts of different models to really understand complex ecological systems better.”
The Templeton World Charity Foundation
supported O’Dwyer’s work.

You can view the complete Biomarker magazine here

Reflections on the first year of graduate school

matt grobis 2Thanks to our guest blogger, Matt Grobis, who is in his second year working toward a PhD in the Ecology and Evolutionary Biology department at Princeton, researching how groups filter noise from information in their environment (particularly predators) and how group membership affects how the whole group behaves.  Matt earned his B.S. in IB in 2012.

What I thought grad school would be like during college:
“Grad school is where you show up at noon, plan some experiments, run them the next day, then analyze the data. A PhD takes 5-7 years because it takes a while to plan the perfect experiment, one that hasn’t been done before and that answers a hole in the literature. During your first year, you do 5-6 experiments and publish at least one of them.”
When you’re doing lab reports during college, it’s almost guaranteed that the Discussion section will say something like “the study would benefit from more data.” We had three hours to do the lab; imagine how good the data would look if we had three weeks? Then, during your senior thesis, you continually imagine being able to do your research without juggling hours of lectures and homework at the same time. Grad school seemed like a big expanse of time to think about experiments, try them again and again until they’re perfect, and then publish. Any sub-perfect experiments were the fault of the experimenter not being motivated enough.

What I think grad school is like at the end of my 1st year:
“Grad school has cycles. Sometimes you show up at 10am, read articles all day, teach yourself R, and go home early. Sometimes you show up at 8am because you need to run three trials of experiments, and sometimes you swing by at 2pm because you were up until 4am writing revisions for a manuscript due to the journal that day. A PhD takes 5-7 years because literally everything takes longer than you think it will, and nothing works the first time you try.”
Something I didn’t quite grasp during my senior thesis and the beginning of the Fulbright was how much others had helped in making the experiment work out. It’s the difference between trying to find a store in a huge city you’ve never been in versus someone giving you a crude map and telling you roughly where the store should be. My advisor in college steered my thesis ideas towards a project that would answer a question regardless of what the results were, and my collaborator in Germany was the equivalent of a 4th-year PhD student in the U.S., meaning she’d had a lot of experience with figuring out the right way to do an experiment.

What my 1st year was like:
You frequently feel like you know nothing
An incredibly common feeling in grad school is “hm… I’m not sure how to do this.” The first reaction is to ask someone else, maybe an older grad student in the lab, or your friend who’s a lot better at R or Matlab than you are (hi, Sinead). You just don’t know the answer right now, so let’s find it and move on. For our generation especially, Wikipedia and Google make the answers to most of our questions separated by merely seconds from when we decide we want to find out. Grad school, on the other hand, is about constantly being in this zone of wanting to know an answer but not having it. That’s what research is; if we knew the answer, we’d have passed the info along to someone else (government organizations, the medical world, conservation groups, engineers, etc.) and be focusing on finding the answer to a new question.

As frustrating as it can be not knowing how to fit a quadratic curve on a scatterplot in R or who to e-mail for ordering new syringes for the lab, it is very satisfying the next time you have to do it and you know exactly how. And as you read more articles, go to more lectures, and talk with more people, you start seeing the same concepts reappearing… but this time, you understand them a little better.

You spend a long time figuring out how to find the answer to a question
Do you remember those “If you had a million dollars, how would you spend the money?” essay prompts in high school? One of the biggest hurdles I’ve had in planning experiments in grad school is getting out of this mentality of infinite money and time. You read about experiments where the authors make grandiose claims out of six data points and you vow to never publish something so ridiculous. If you’re going to do science, you’re going to do it right, even if it means fewer publications during your PhD. Your experiments will have at least 30 individuals, each assayed on multiple days to control for between-day variation in behavior, and each individual will be exposed to 5 treatment groups to see the full effect of the variable on behavior.

Those are fantastic intentions, and you can often make it work. But it’s really difficult. If you’re like me in college, “really difficult” sounds like something that applied to people who weren’t you; you’ve faced “really difficult” before and gotten an A in the class. Let me reiterate: it is really freaking hard to do this.

Here’s an example from this week: I’ve started a pilot experiment to figure out how the social environment affects how skittish a fish is in a new environment. The idea is to use 8 fish in 3 different groups of 60 fish. Due to poor planning, the videos ended up really dark, and it’s impossible to distinguish who’s who in the video. Not only can I not use the data; if it wasn’t for some quick thinking by marking all tanks where fish had seen the experimental tank, I might have had to scrap the experiment! (In animal behavior research, novelty to an environment is often extremely important.) So even though I’ve been planning these ideas for a few weeks, I nearly messed everything up within the first two days of actually doing anything. It always seems so obvious before you start, and then it never goes how you plan. (Above right is a video still from a trial I can’t use.)

But… that’s just how it goes. You can’t get to the end result without making mistakes. And you can’t make any progress if you don’t try.

You wait (a lot) for clearance to do research
Animal welfare committees are a crucial part of research by instituting ethical requirements for how research should be conducted. They ensure that the research has a bigger point and that your methods are the most humane way to get there (e.g. if mice have to be euthanized, what’s the calmest and least painful way for the animals? If the crickets suddenly start dying during the experiment, what do you do?). If you’re doing fieldwork, you need to get a license for the work; if it’s in another country, you probably need a visa as well.

Ensuring that research will be done properly takes a lot of time. Animal welfare committees have panels of both scientists and non-scientists to get a range of perspectives on the ethics of the work, which means extra time is needed to exchange and explain the reasoning for different viewpoints. For fieldwork, a lot of people want government approval for permits or visas, and there are only so many people reading the proposals. The only advice I can give on this is to start early, be patient, and be courteous with your e-mails. The waiting time (on the order of months) can really help refine your ideas for when you actually start.

You start to understand what makes for an interesting scientific question
For the first few months of grad school, I told people I was interested in how group composition affects predator evasion behavior in schools of fish. It took a lot of thinking and discussing with others to refine those ideas into a broader framework with more applicability than one species of fish under one type of predation risk.

You spend a lot of time thinking in grad school. Your ideas have to stand up to hundreds of hours of mental chewing; the best ideas are the ones that not only hold strong but also generate new ideas the more you learn about them.

——————————————————————————————————–
Doing research has been challenging but I’ve been really happy so far. It’s really quite amazing to be paid to think about and do experiments asking questions nobody in the world knows the answer to yet. I feel like the incredible amount of time stuck, trying to figure out an impasse, has taught me how to find the answers to things I don’t know. This mentality has given me a lot of confidence to approach things I might have shied away from before because it seemed too difficult (e.g. teaching myself linear algebra, taking a metro or bus in a country where I don’t speak the language, etc.). And most importantly, I constantly feel like I’m gaining a better understanding of how the world works, which only makes me more excited to see where grad school takes me.

-Matt

May Berenbaum awarded the National Medal of Science!

University of Illinois professor of entomology May Berenbaum has been awarded the National Medal of Science, the nation’s highest honor for achievement and leadership in advancing the fields of science and technology, according to an announcement from the White House Press Office.berenbaum_mayMedalPhoto Courtesy National Science and Technology Medals Foundation

The National Medal of Science was created in 1959 and is awarded annually to individuals who have made outstanding contributions to science and engineering, according to the release.

“Professor Berenbaum’s work has fundamentally changed what we know, how we study and how the public understands the role of insects in nearly every aspect of human life and development,” said

Phyllis M. Wise, chancellor of the Urbana campus. “This is transformative scholarship on a global scale and has implications for every person on the planet. This is a well-deserved honor and all of us at Illinois offer Professor Berenbaum our sincerest congratulations.”

Berenbaum, a Swanlund Chair and the head of the department of entomology, has been a U. of I. faculty member since 1980. Her research, which studies the chemical mechanisms underlying interactions between insects and their host plants, including the detoxification of natural and synthetic chemicals, has produced hundreds of peer-reviewed scientific publications and 35 book chapters.

She also created the Insect Fear Film Festival, now in its 32nd year on campus. The festival engages and entertains hundreds of viewers each year with feature-length films and shorts, commentary on the films, an insect petting zoo and an insect art contest.

Alumni Profile: Muhammed Fazeel

Muhammed Fazeel

Graduated: May 2012

Favorite IB class and why: Ecology and Human Health (IB 361). Professor Allan held a fantastic class related to health. I especially liked it since he made a conscious effort of making relevant lectures based on current/recent epidemics.

Favorite extra curricular activities (undergraduate research, clubs, etc) and why: Being part of the Illinois Launch program at the Academy for Entrepreneurial Leadership.

Why you chose IB:  Integrative Biology took a broader approach at understanding the world from a biology perspective which I found very stimulating.

How you feel IB helped prepare you for your career:  My time at U of I has given me the basic skills needed to better understand and address problems.

What you’re up to now: Soon after I graduated, I started a biomedical startup in Chicago. We have set up partnerships with a few clinics and our work is set to help several heart patients across America.

 

Writing the self-contained universe

Hi all,

You are not sitting next to me right now as I type these ideas. You’re most likely not in New Jersey, and you might not even be in the U.S. The fact that it’s even possible for you to be reading these words right now highlights an ever-growing need to be able to communicate ideas through writing. It’s the difference between you growing bored and leaving halfway to explore other parts of the internet, and you finishing this blog post (before moving on to explore the rest of the internet!).

In essence, writing is just a means of getting info from Point A to Point B. No matter how many amazing and intelligent ideas you may have in your head, they will have to stay there if you don’t know how to communicate them. Here are a few tips on bridging the gap between you and your reader’s mind when it comes to e-mailing a professor or potential collaborator, writing a grant, or explaining your ideas in general.

1. Who is your reader? Why should they care about your message?
Example: e-mail
As often as possible, put yourself in the head of the person reading what you wrote. Let’s say you’re e-mailing a professor to potentially do a PhD with them. They’ll want to know:

– Who is this person? Is he/she currently an undergraduate? If not, what has she done since then?
– What are his research interests? Of my work, what interests him?
– What are her research qualifications? Has she done research before, or is she just applying to grad school because she hasn’t considered other options?
– Has this applicant actually read up about my lab and thinks he’s a good fit, or is he just sending a template e-mail to every researcher he can find?

The more of these you can answer, the more willing the professor will be to respond. Remember that professors are incredibly busy people. Chances are, they enjoy talking with new people and exchanging ideas. But, their schedules are so packed that the easier you can make an e-mail exchange for them, the less time they have to spend answering these questions themselves. You want a researcher to be nodding her head as she reads the e-mail, her questions being answered as she reads so that by the end, the work has been done for her and she can now focus on writing her response.

2. Does your writing actually address what you wanted to say / the prompt?
Example: grant writing, lab reports
Say you’re working on an NSF-GRFP grant (the National Science Foundation Graduate Research Fellowship). You have phenomenal research ideas that would explain a genetic basis for sociability in humans, and you have told a heartwarming story on how you discovered and decided to pursue science. A few months later, you’re surprised to find your revolutionary ideas were not funded by NSF. What happened?

It’s likely that you didn’t answer every part of the application to the degree NSF was looking for. Consider an introductory biology lab in which the students dissect fish and chicken hearts (diagrams on the right). In their report, they are asked to compare the two hearts and explain how these hearts differ in the ability to support different levels of metabolic demand. Unless they provide comparisons between the two hearts and explain how those differences affect ability to support varying metabolisms, they will not get full credit (no matter how detailed either component of their answers are). Think of it as:

10 points total:
5 – provide 3 differences between the 2 hearts
5 – explain each difference in terms of metabolic potential

You can slam dunk those first 5 points, but if you don’t address the second section, it’s likely you won’t even get a passing grade. Similarly, for the GRFP, regardless of how incredible your ideas are, if you don’t explain how your work has any relevance outside of bullet points in a textbook only people in your field will read, even the very best ideas will get passed down. Again, think from the GRFP officer’s viewpoint: every applicant has good ideas, but NSF wants research fellows who will not only advance science but also help spread its ideas beyond the scientific sphere. Even if you would do outreach if you had the opportunity, if you don’t write about it, the GRFP officer can’t assume you would.

3. If your writing was an isolated universe, would that universe make sense?
Example: course exam
This is one I repeatedly tell my introductory biology students for their lab reports and exams. Imagine your mom somehow stumbled across your biology midterm essays (of all the things she could have discovered in your room) and was reading them. Would she be able to understand what you wrote? In this situation, you have someone who most likely hasn’t taken college-level biology in a few decades, if ever. Do they get lost in your jargon, or is your answer self-contained enough for anyone to be able to pick it up and learn something from it? One of the biggest road blocks to a good scientific talk is losing your audience part way because you assume they understand something they actually don’t. Being able to grab a listener from any background and pull them to a new level of understanding is challenging, but it’s critical for teaching.

4. How long do you think your reader will spend on your writing? If they skimmed it, would they still get your message?
Example: lab report, scientific articles
Many science majors in college are under the misconception that a longer lab report is a better one. The idea, which seems reasonable at first, is that the more information you put down, the larger the net you are casting, which has a better chance of catching the answer your TA is looking for. Unfortunately, it’s not quite like that. Aside from giving yourself more opportunities to write something incorrect and actually lose points, in the scientific world you will almost never be in the situation where you’ve written everything you need and should keep writing more.

Again, think about writing as a communication of ideas. Short and sweet (i.e. efficient) is always preferable to long and winding in science. Scientific articles have abstracts so readers can get the gist of the article without needing the motivation, background, and time to read the entire thing (remember how busy many researchers are!). Articles in the journal Science actually have one-sentence summaries for the particularly busy and researchers in related fields who may want a simplified version of the abstract. Brevity is a much better skill to have than the ability to list everything you know about a topic.

Consider the reader, consider your miniature universe. And if all else fails, just call your reader on Skype.

Photo credits:
– Thinking: Basic College English blog (http://uppampangaenglish.blogspot.com)
– Chicken heart: University of Illinois at Urbana-Champaign Chickscope (http://chickscope.beckman.uiuc.edu/explore/embryology/day02/comparative.html)
– Fish heart: Stanford University Environmental Science Investigation (http://esi.stanford.edu/circulation/circulation5.htm)

Matt Grobis is a PhD student at Princeton University and an alumnus of the IB Honors program at the University of Illinois. For more information about academia advice, summaries of scientific articles, and discourses on metal music, check out mattgrobis.blogspot.com or e-mail him at matt.grobis[at]gmail[dot]com.

Fungus that causes white-nose syndrome in bats proves hardy survivor

Written by Diana Yates, Life Sciences Editor | 217-333-5802; diya@illinois.edu

CHAMPAIGN, Ill. — After taking an in-depth look at the basic biology of a fungus that is decimating bat colonies as it spreads across the U.S., researchers report that they can find little that might stop the organism from spreading further and persisting indefinitely in bat caves.

additional photoPhoto by L. Brian Stauffer

Graduate student Daniel Raudabaugh, left, and mycologist Andrew Miller, of the Illinois Natural History Survey, conducted the first in-depth study of the basic biology of P. destructans, the fungus that causes white-nose syndrome in bats.

Their report appears in the journal PLOS ONE.

The aptly named fungus Pseudogymnoascus (Geomyces) destructans causes white-nose syndrome in bats. The infection strikes bats during their winter hibernation, leaving them weakened and susceptible to starvation and secondary infections. The fungus, believed to have originated in Europe, was first seen in New York in the winter of 2006-2007, and now afflicts bats in more than two dozen states. According to the U.S. Fish and Wildlife Service, P. destructans has killed more than 5.5 million bats in the U.S. and Canada.

The fungus thrives at low temperatures, and spreads to bats whose body temperature drops below 20 degrees Celsius (68 degrees Fahrenheit) when they are hibernating in infected caves. Previous research has shown that the fungus persists in caves even after the bats are gone.

The new study, from researchers at the Illinois Natural History Survey at the University of Illinois, found that the fungus can make a meal out of just about any carbon source likely to be found in caves, said graduate student Daniel Raudabaugh, who led the research under the direction of survey mycologist Andrew Miller.

“It can basically live on any complex carbon source, which encompasses insects, undigested insect parts in guano, wood, dead fungi and cave fish,” Raudabaugh said. “We looked at all the different nitrogen sources and found that basically it can grow on all of them. It can grow over a very wide range of pH; it doesn’t have trouble in any pH unless it’s extremely acidic.”

“P. destructans appears to create an environment that should degrade the structure of keratin, the main protein in skin,” Raudabaugh said. It has enzymes that break down urea and proteins that produce a highly alkaline environment that could burn the skin, he said. Infected bats often have holes in their skin, which can increase their susceptibility to other infections.

The fungus can subsist on other proteins and lipids on the bats’ skin, as well as glandular secretions, the researchers said.

“P. destructans can tolerate naturally occurring inhibitory sulfur compounds, and elevated levels of calcium have no effect on fungal growth,” Raudabaugh said.

The only significant limitation of the fungus besides temperatures above 20 degrees Celsius has to do with its ability to take up water, Raudabaugh said. Its cells are leaky, making it hard for the fungus to absorb water from surfaces, such as dry wood, that have a tendency to cling to moisture. But in the presence of degraded fats or free fatty acids, like those found on the skin of living or dead animals, the fungus can draw up water more easily, he said.

“All in all the news for hibernating bats in the U.S. is pretty grim,” Miller said.

“When the fungus first showed up here in Illinois earlier this year we went from zero to 80 percent coverage in a little more than a month,” he said. The team led by U. of I. researchers that discovered the fungus in the state found a single infected bat in one northern Illinois cave, he said. Several weeks later most of the bats in that cave were infected.

Although many studies have been done on the fungal genome and on the bats, Miller said, Raudabaugh is the first to take an in-depth look at the basic biology of the fungus.

“Dan found that P. destructans can live perfectly happily off the remains of most organisms that co-inhabit the caves with the bats,” Miller said. “This means that whether the bats are there or not, it’s going to be in the caves for a very long time.”

The Illinois Natural History Survey is a division of the Prairie Research Institute at the U. of I.

This study was funded through awards given by the Illinois Department of Natural Resources State Wildlife Grants Program (project number T-78-R-1) and the Section 6 Endangered and Threatened Species Program (project number E-54-R-1) to the Illinois Natural History Survey.

Alumni Profile: Colleen Stoyas

Colleen Stoyas on the Beach

Graduated: May 2011

Favorite IB class and why: I loved my Ecology and Evolution class and the field work it entailed, my Organismal Biology class because of its labs, Coral Reef Ecology and its mandatory lab in Belize, Genes and Behavior, and so many others. I think the class I find myself continually applying to my every day “life” choices is Ecology and Human Health, taught by Dr. Brian Allan. This course investigates human health issues from an ecological perspective and regularly influences my perception of infectious disease outbreaks, grocery purchases, choice of where within a city or area to live (did you know lyme disease most commonly occurs in communities of moderate population size and not in rural areas?), and more.

Favorite extra curricular activities (undergraduate research, clubs, etc) and why: My favorite activity was definitely my undergraduate research on yeast genetics in the Freeman Lab (dept of MCB), and I submitted a distinction project prior to graduation. Outside of the lab I was in a co-ed Honor Fraternity, Phi Sigma Pi, that allowed me to make a great group of friends outside of my science courses and participate in service projects in the Champaign-Urbana community.

Why you chose IB: I chose IB over other Life Sciences majors because of the emphasis on analytical thinking and problem solving. In IB courses you are required to memorize less facts and instead given a set of information and asked to apply the principles you learned to answer questions on that information. This type of learning is extremely engaging and affected not only my studies, but how I approach any information given to me in life. I entered Illinois generally interested in science and was told growing up that I would make a good physician. While taking IB150, I realized that my interest in medicine had been in the discovery portion all along, and not in actually treating patients.

Colleen Stoyas with turtle

How you feel IB helped prepare you for your career: As I mentioned above, IB focuses on teaching analytical thinking and problem solving skills. I once had a project where I was asked to pick a plant on campus, and I had to email my professor a paragraph on that plant every week. Sometimes it seems hard to find a difference in a dormant magnolia tree from week-to-week in January and February, but “no change” was unacceptable. By the end of that semester I was at that tree every single day noticing so many differing events in its immobile life. IB taught me to be observant, patient, and responsive to my environment in addition to the value the knowledge the coursework provided me. These skills have been invaluable in my current career as a PhD student in Biomedical Sciences.

What you’re up to now and what you like about it: I am currently starting my third year as a PhD student in the Biomedical Sciences program at the University of California, San Diego. I am a member of the La Spada Laboratory, a large and diverse environment that studies the genetics of inherited neurodegenerative diseases such as Huntington’s disease. My favorite part of my schooling/job is engaging with leaders in the neurodegeneration field and working at the cutting-edge of scientific discovery.

SIB creates new joint center in genomics with Fujian University.

Professor Ray Ming (plant biology) will direct the new joint center in genomics and biotechnology – the center is a collaboration between Integrative Biology and Fujian Agriculture and Forestry University. With an initial investment of $30 million US, the new center promises to open new collaborations between the two institutions and create new opportunities for student exchanges. Professor Feng Sheng Hu, head of plant biology, was instrumental in negotiating the creation of the new center, which will be open for business in the next two months.

“Girls Do Science!” Summer Camp

Group Photo of Girls Do Science Summer Camp

For the second year in a row, SIB faculty, students and staff led a week-long “Girls Do Science!” camp for girls entering 2nd – 6th grade, in partnership with Orpheum Children’s Science Museum. Camp co-directors were Carla Cáceres (Animal Biology/SIB), Katy Heath (Plant Biology/SIB), and Katie Hicks (Education Director at the Orpheum). Campers explored the Pollinatarium with Lesley Deem, where they learned about insects and ticks, ran through Meadowbrook Park for a scavenger hunt of prairie plants, and participated in SIB faculty research on microbes (Katy Heath), mammals (Karen Sears) and plankton (Carla Cáceres) at the Natural History Building.

Staff and graduate and undergraduate students (too many to name!) from SIB and other units such as the graduate Program in Ecology, Evolution and Conservation Biology, Natural Resources and Environmental Sciences and the Department of Cell and Developmental Biology also participated. The camp was sponsored by grants from the National Science Foundation (DEB 1120804 and DGE 1069157).

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