UWMadScience https://uwmadscience.news.wisc.edu Behind the science & research that makes the news at UW–Madison Mon, 11 Dec 2017 19:52:28 +0000 en-US hourly 1 https://wordpress.org/?v=4.4.13 Reflecting on Lake Mendota https://uwmadscience.news.wisc.edu/uncategorized/reflecting-on-lake-mendota/ https://uwmadscience.news.wisc.edu/uncategorized/reflecting-on-lake-mendota/#respond Mon, 11 Dec 2017 19:52:28 +0000 https://uwmadscience.news.wisc.edu/?p=2824 One table in particular in the Hamel Family Browsing Library offers a view of Lake Mendota and Memorial Union Terrace that seems to help contemplation. (Photo by Léo Kim)

One table in particular in the Hamel Family Browsing Library offers a view of Lake Mendota and Memorial Union Terrace that seems to help contemplation. (Photo by Léo Kim)

The wind-whipped surface of Lake Mendota in early winter provides precisely the kind of visual resting point that helps your concentration while studying, reading or writing. The moving surface catches your eye, giving your mind time to wander in that way that’s productive rather than distracting.

It sure beats checking your Twitter feed for the thousandth time that day.

That’s part of what makes the Hamel Family Browsing Library in Memorial Union such a good place to hunker down and get some work done. It’s deathly silent, cozily lined with wood and, at the front table at least, has a view of Lake Mendota and the Terrace that’s tough to beat.

Tucked into a drawer in that front table are a few anonymous notes from people reflecting on their time at the University of Wisconsin–Madison — or poking fun at their serious predecessors:

The front table harbors notes from contemplative students. (Photo by Eric Hamilton)

The front table harbors notes from contemplative students. (Photo by Eric Hamilton)

hello good man! or lady! I am sure as of now you are studying. However, I just wanted to inform you that you don’t need a grade to make you smart. You don’t need others approval to make you Beautiful. And you don’t need a degree to be successful. You! Are smart, Beautiful, and successful just the way you are. And don’t let anyone tell you different. Semper Amore. Love you Lots.

Reading room note one

Take a break — did you read that note? pretty cool… it prompted me to think about why I’m here… to be honest, I’m not exactly sure why I’m here yet. Although, I am sure that this the coolest place I’ve ever been. The atmosphere here is electric. It embodies all of the souls who have ever been here. Imagine how many people have studied here… how many late nights have been spent here since 1948. How many people have looked out this same window, out at the beautiful terrace and over the blustry, choppy lake. Why were they here — what did they do with their time at Madison? What will you do?

Reading room note 2

what up

Reading room note 3

This reading room was redone during phase one of the Memorial Union renovation. During construction, workers uncovered an ornate ceiling that had once been covered and hardwood floors beneath the carpet. Both were restored. As best we can tell, little has changed since the Union opened in 1928. The original plans for Memorial Union called for a “Library & Reading Room” in the space. It seems to have been designed as a place for quiet reflection and studious work and, though details have changed over the decades, it remains so today.

The Hamel Family Browsing Library was originally called the Library & Reading Room

The Hamel Family Browsing Library was originally called the Library & Reading Room

No doubt that Arthur Peabody, the state architect who designed Memorial Union, envisioned the same view out onto the lake that inspired these anonymous writers to leave behind their thoughts for posterity. Generations since must have looked out and wondered what they would do with their time at UW–Madison — albeit probably not on post-it notes, considering they weren’t invented until the 1970s.

But post-it notes are as good a way to ask as any other: What will you do with your time here?

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Computer modeling offers glimpse into Wisconsin’s future https://uwmadscience.news.wisc.edu/atmospheric-science/great-lakes-changes/ https://uwmadscience.news.wisc.edu/atmospheric-science/great-lakes-changes/#respond Fri, 01 Dec 2017 22:28:43 +0000 https://uwmadscience.news.wisc.edu/?p=2818 What’s more Wisconsin than milk and cheese? I’ll tell you: It’s snow. Fat, fluffy flakes silently piling up on windowsills and those bitter, piercing blizzards are as predictable as NFC North championships in Wisconsin.

But the cold, snowy conditions that are a staple of winter in Wisconsin and the Great Lakes region are on the decline. According to projections from climate scientists at the University of Wisconsin–Madison, by the end of the century our winters could change dramatically, eventually shrinking by up to two months.

“It will be a very different environment for the Great Lakes,” says Michael Notaro, a senior scientist and associate director of the Center for Climatic Research at the University of Wisconsin–Madison’s Nelson Institute for Environmental Studies.

MODISGreatLakesNovember2015

Winds of change

Notaro and his colleagues use computer programs to create models that simulate regional responses to climate change, and their results show a host of changes to Wisconsin’s winter patterns.

Wisconsin is projected to have fewer days with snow on the ground and warming temperatures will accelerate snowmelt. The fringe months of the cold season – October, November, April and May – could all see significant decreases in snowfall, essentially shortening the winter season and prolonging the “limbo” in between seasons.

Lake effect snowstorms are predicted to increase toward mid-century in the Great Lakes but decrease by century’s end. Lake Superior, which is in a colder environment than the other lakes, will sustain or even increase the frequency of lake effect snowstorms. But this, too, is projected to decline toward the end of the century.

Due to warming temperatures, Wisconsin’s winter precipitation will less often fall the form of snow; instead it will fall as rain.

The forces of change are visible after winter subsides, too. Heavy rain events that can dump two-to-three inches are projected to increase in southern Wisconsin, especially in Dane county. Flooding in Lake Delton in 2008 killed three people and caused $763 million in damages. It is just one example of the effects that extreme rain events can have, Notaro says.

The findings that these models generate are valuable to resource managers in the state, Notaro says.

“We [the Center for Climatic Research] largely develop climate change projection, and other groups use that to kind of get a sense of risk management and how they can change a lot of their policies and planning so that they can dampen some of the negative effects of climate change,” Notaro says. “We’ve done about 52 years of solid research in our center, so we have been a very productive research center here for quite a long time.”

Downscaling global trends

The Great Lakes basin, home to over 30 million Americans and Canadians, houses 21 percent of the world’s fresh water supply. But, according to Notaro, the region is difficult to represent in climate models, which usually operate on a global or continental scale.

“The concern is that a lot of the global climate models, at least half of them, don’t even have the Great Lakes in them,” Notaro says. “The ones that do (include the Great Lakes) barely represent them, so it’s kind of an important issue where you need to use a regional model if you want to study Wisconsin, Michigan, New York and the states in that area.”

In order to investigate changes to the Great Lakes Basin, Notaro and his colleagues use a regional model called RegCM4, for Regional Climate Version 4, developed by the National Centre for Theoretical Physics in Italy. The model is able to produce resolution at a 20-25 kilometer scale, providing a high level of detail critical for detecting changes across smaller climate regions.

To achieve higher resolution over smaller areas, researchers like Notaro use a modeling method called dynamical downscaling.

Global climate data, such as jet streams and cyclones, are entered into the regional model and act as a foundation for its operation. The model then runs over a time scale of the researcher’s choosing, using those larger-scale forces to calculate smaller-scale changes in regional climates. The end results explain how global climate change is affecting the Great Lakes.

“So in other words, how is the large scale wind field and temperature, how is that going to change the Great Lakes Basin, the Great Lakes lake effect snow, that’s something that you need a regional model to study,” Notaro says. “It’s a more complicated process.”

 

Photo: http://research.noaa.gov/sites/oar/EasyGalleryImages/12/977/MODISGreatLakesNovember2015.jpg

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How proposed tax changes affect UW–Madison graduate students https://uwmadscience.news.wisc.edu/uncategorized/how-proposed-tax-changes-affect-uw-madison-graduate-students/ https://uwmadscience.news.wisc.edu/uncategorized/how-proposed-tax-changes-affect-uw-madison-graduate-students/#comments Wed, 29 Nov 2017 14:49:27 +0000 https://uwmadscience.news.wisc.edu/?p=2792 In November, the U.S. House of Representatives passed the Tax Cuts and Jobs Act. One of the proposed changes in this bill is the repeal of Section 117(d), a provision that makes graduate school more affordable by not counting tuition waivers as taxable income. Many graduate students are not charged tuition because of their contributions as teaching and research assistants. The waived tuition isn’t income the students see, and currently isn’t taxed as income. But repeal of Section 117(d) would tax the value of this waived tuition as if it were normal income, meaning students would pay tax on more income than they receive.

Prior to the bill’s passage, University of Wisconsin–Madison Chancellor Rebecca Blank sent a letter to Speaker of the House Paul Ryan detailing her concerns about this change’s effects on graduate students at the university:

“At UW–Madison, approximately 5,300 PhD students and 1,900 Master’s degree students would lose this important tax benefit. In turn, their tax liability would skyrocket for “income” they never receive. The result would be that students — particularly from lower income families — might find it prohibitive to pursue graduate work. They would be caught in a position where they can’t afford the tuition, but can’t afford to pay the taxes if they receive tuition remissions either. We urge you to preserve the Section 117(d) qualified tuition reduction.”

The repeal of Section 117(d) is not included in the current version of the Senate’s tax bill. Since any final bill would have to be agreed upon by both chambers of Congress, the repeal of Section 117(d) remains uncertain.

Three graduate students at UW–Madison share how these proposed tax changes would affect them and their research. Interviews have been edited for clarity and length.

Winslow Hansen is a PhD student in Integrative Biology. He grew up in Bozeman, Montana, and his research still takes him out West. He says that the repeal of Section 117(d) would affect how many people from different backgrounds are able to become scientists.

IMG_0241

If I had to do it again making $3,300 less per year, it would be simply infeasible for me to attend graduate school.

Growing up out West I really got to interact a lot with nature because we lived out in the woods. I spent my childhood hiking around, exploring the woods. And I also saw over the last 20 years there was an increase in the number of people in the region and recreating in the region. That made me realize how people and the environment are connected, from my home going up to a global scale. So I became fascinated in trying to understand how people are affected by their environment, how they affect their environment, and what solutions we can come up with so people can explore and enjoy nature for generations to come. It turns out science is a really powerful tool for studying and answering those questions. And once I realized I could add science to my toolkit I never looked back.

I study how changing climate affects wildfires and their ecological impacts in the northern Rocky Mountains and interior Alaska. As conditions out there are warming and drying, and as we see in the news, we’re getting a lot more wildfire in the landscape. And they’re often burning a lot larger than they used to. And this is a real problem, because we have to protect homes from fires. And that costs the federal government a lot of money because they have to pay to fight fires and protect homes. What I’m really trying to do is understand how and why fires are changing and what the consequences of those changes might be for the ecosystems in which they’re burning.

I wanted to think about (the proposed tax changes) in terms of becoming a new professor at some point in the near future. I’m going to need to recruit graduate students. So I wanted to think about how my graduate students would be affected under this tax bill.

If I were starting now I’d make about $18,000 a year. And under the current tax situation I would be charged roughly 4 percent of my total income as federal tax. (Under the proposed tax changes,) that burden would increase to 19 percent of my earnings, which would be an additional $3,300 per year that I would pay to the federal government. I know from personal experience when I started that it’s already very difficult to live on the amount of money that you’re being paid as a graduate student. If I had to do it again making $3,300 less per year, it would be simply infeasible for me to attend graduate school.

This type of change in the tax code would not just affect the numbers of people that are getting into graduate school — which is a problem because graduate school is where we incubate the next leaders of science — but it’s really going to affect the types of people who are going to graduate school. I would expect this is going to disproportionately affect people from lower socioeconomic groups who cannot afford to take on student loans. And it would eliminate one of the few avenues through which we really have social mobility in society. And it would really constrain the types of questions we ask in science. The diversity in thinking that leads to technical breakthroughs that really benefit society. I find that to be quite concerning.

Bridget McFarland is a first-year PhD student in Plant Genetics and Breeding in Natalia de Leon’s lab researching corn’s ability to adapt to different environments. She got into science by working in Iowa cornfields. She says that having a taxable income higher than the stipend she receives would have made her reconsider graduate school.

BMcFarland

Having a taxable income of $60,000 and a stipend of just over $20,000 is definitely frustrating and stressful.

I’m originally from Chicago. I moved to Iowa in my early teens and my mom signed me up to work in the cornfields, and that’s how I became introduced to the world of agriculture. I worked for the USDA for 4 years while I was an undergraduate at Iowa State. I’m interested in crop improvement to benefit society from a sustainable, nutritional and economic standpoint.

We’re looking at how artificial selection for high-yielding corn has affected the corn plants’ ability to adapt in different environments. Corn is grown all throughout the world so being able to understand how the genotype and environment interact will help us breed crops that are better able to produce across the U.S. and the world.

(Under the proposed tax changes,) my taxable income would change from $22,000 to over $60,000. So my take-home income would decrease a great amount. That’s on top of the health insurance, rent, books and other fees I pay.

To be quite honest, I’m not sure I would’ve considered going to graduate school directly after getting my undergraduate degree if I had to take out loans (to cover higher taxes). So I would say it would be concerning to say the least as a researcher. Having a taxable income of $60,000 and a stipend of just over $20,000 is definitely frustrating and stressful.

I think that there are a lot of consequences (of the proposed tax changes), not only for graduate students, but for research universities altogether. I’m not sure how competitive the U.S. will be in terms of research if it becomes more of a struggle for graduate students who are not able to take on the financial burden with the proposed changes.

Carly Ziter is a PhD student researching ecology in the Integrative Biology department. She grew up Windsor, Ontario, just across the river from Detroit, Michigan. Repeal of Section 117(d) would make international students like her reconsider the U.S. for graduate school, she says.

Ziter_Photo

UW–Madison was absolutely my top choice as an institution for graduate school. But had this policy been in place 4 years ago, I would’ve seriously reconsidered coming here.

I’ve been really fascinated with the outdoors since I was a kid. I was always outside, climbing trees, playing in the mud. So that really sparked my enthusiasm and interest in the natural world. I think, too, when you grow up in my generation, I heard a lot about the environmental problems we’re facing. The common refrain was ‘it’s up to your generation to fix it’. If it’s up to us to fix it, I want to be part of that effort.

I study the benefits that people get from nature. So if you think about clean water, flood protection, or temperature control, the ecosystems around us have a huge part in providing these benefits. My dissertation at UW–Madison addresses how green spaces in urban areas in the city of Madison can provide these benefits and how we can create more sustainable cities.

My funding situation is unique. I’ve been partly funded by a UW stipend and partly by the Canadian government. My income averages to about $33,000 per year. On an international tuition waiver of about $25,000, I believe the proposed tax changes would lead to an increase of $2,000 to $3,000 in taxes per year for me.

UW–Madison was absolutely my top choice as an institution for graduate school. But had this policy been in place 4 years ago, I would’ve seriously reconsidered coming here. Facing additional taxes of several thousand dollars I think will cause a lot of international students to reevaluate whether the U.S. is the right place to go to get a graduate education. One of the proposed solutions (for handling higher taxes) is that graduate students will have to get an additional job to make ends meet. As an international student, working outside of your academic position actually violates your academic visa. So an additional job is not an option.

 

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Looking back 100 years at two major biochemistry discoveries https://uwmadscience.news.wisc.edu/history-of-science/biochemistry-centennial/ Fri, 10 Nov 2017 19:37:42 +0000 https://uwmadscience.news.wisc.edu/?p=2780 This year the Department of Biochemistry at the University of Wisconsin–Madison is celebrating the centennial of two major achievements: the discoveries of vitamin B and the link between goiter and iodine. These two important scientific achievements, as well as the stories, personalities, and controversies that accompanied them changed the field of biochemistry at UW–Madison and around the world.

The department’s work with vitamins began with the “single grain experiment” with cows. The experiment, conducted form 1907 to 1911 by Stephen Babcock, E. B. Hart, Elmer McCollum, and Harry Steenbock, fed groups of cows only a single type of grain: either corn, wheat, or oats, and then a last group was fed a combination of all three. They found that the cows that ate corn were healthier than the others.

This finding told the researchers there was something essential in corn that wasn’t present in wheat or oats, and they began supplementing the other two with different additions, like parts of milk, to find what would make a diet complete.

At about the same time as the vitamin B experiments were taking place, scientists in the Department of Agricultural Chemistry (which later became the Department of Biochemistry) discovered that the disease goiter is caused by a lack of iodine in the diet. Because iodine is an essential part of the thyroid hormone, its absence from the diet causes excessive growth of the thyroid gland — the disease goiter.

Elmer McCollum and Marguerite Davis were responsible for the discovery of “fat-soluble A” (which was eventually resolved into vitamins A, E, D, and K), and E. B. Hart and Harry Steenbock confirmed that iodine can alleviate goiter.

These two discoveries and the department’s work in vitamins are just one example of the ground-breaking research that exemplifies the department’s history and makes up the modern research occurring today.

“There really isn’t a vitamin or mineral that’s been discovered that wasn’t somehow touched by a UW–Madison researcher,” Dave Nelson, a Biochemistry Emeritus Professor and the department’s defacto historian, says. “And while we have lots of diverse research taking place in the department, some are still working in this area. For example, we now have visualized at the molecular level how vitamin D works.”

To read the full story about these major developments in UW–Madison’s rich history of research, visit https://biochem.wisc.edu/news/2017/news-biochemistry-discovery-centennial-2017-10-13

 

 

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Mining the cerebellum for its role in speech https://uwmadscience.news.wisc.edu/health/mining-the-cerebellum-for-its-role-in-speech/ Tue, 07 Nov 2017 22:41:01 +0000 https://uwmadscience.news.wisc.edu/?p=2760 The following comes from Adityarup Chakravorty, a science writer at the Waisman Center at the University of Wisconsin–Madison:


Pick a word. Any word.

To be able to speak aloud the word you picked needs exquisite coordination between several parts of the body. The brain, lungs, throat, voice box, tongue and lips must work together to make sure we are saying what we intend to communicate.

How do we do it? Researchers have long thought that a specific part of our brain – the cerebellum – plays a key role in the muscle control we need to speak.

What they don’t know is how the cerebellum influences our speech.

The cerebellum, a small structure at the back of the human brain

The Cerebellum. Located in the back of the brain, it is involved in central regulation of basic movement, like balance and posture.//From Serendip Studio, Bryn Mawr College

“We know that when the cerebellum is damaged, it causes movement disorders in both speech and non-speech actions,” says UW–Madison Waisman Center investigator Ben Parrell. “What we don’t understand is why cerebellar damage leads to these disorders.”

So Parrell, who is a new assistant professor of communication sciences and disorders at UW-Madison, set out to investigate.

In a recent study, he and his colleagues discovered that damage to the cerebellum diminishes our ability to predict consequences of an action and issue specific motor commands to the body – what researchers call “feedforward control.”

Diminished feedforward – or predictive – control could explain speech difficulties often faced by individuals with cerebellar damage.

“If you can correctly predict what will happen after an action – like trying to say a specific word, for example – you can do things more fluidly, more rapidly because you don’t need to monitor outcomes in real time,” says Parrell.

In contrast, without properly functioning feedforward control, we have to instead exercise “feedback control,” which is reactive rather than predictive and it takes more time. “You do things a little bit at a time, monitor what happened, then do a little bit more and monitor again, and so on,” says Parrell.

Imagine trying to carry out a conversation while having to slow down and make sure that each word is being pronounced correctly.

“For the human nervous system, monitoring outcomes and correcting for them takes between 50-200 milliseconds,” says Parrell. Many actions, including speaking, happen in a much shorter time span. “So the idea is that we can’t rely only on the feedback – or reactive – system to produce these actions because it will be just too slow.”

Ben Parrell

Ben Parrell//Courtesy of the Waisman Center at the University of Wisconsin–Madison

Parrell, who conducted the bulk of the study during his time as a postdoc at the University of California, Berkley, tested both the predictive (feedforward) and reactive (feedback) systems in individuals with and without damage to the cerebellum.

Study participants were asked to read specific words, such as “head,” into a microphone. Their voices were recorded, run through a computer program and played back through headphones. This entire process took 12 milliseconds – an imperceptible nugget of time.

When their voices were played back through headphones, the study participants didn’t always hear what they expected. The researchers subtly changed the words they spoke – “head” would sound more like “hid,” for example.

In tests for predictive control, the researchers introduced these changes over multiple trials. It was up to the participants to compensate, changing how they subsequently pronounced the intended word to get it closer to sounding like “head.” For instance, in the next trial, the speaker might say something that sounded more like “had.”

How well participants were able to do this depended greatly on whether they had experienced cerebellar damage.

“We wanted to ask if people with cerebellar damage could adjust their behavior to incorporate this consequence of their action over time,” says Parrell, noting that individuals with cerebellar damage could adjust their behavior, but not to the same degree as those without any damage. “We take that as evidence that their ability to change their predictive control system is impaired, which indicates that the cerebellum is critical for this process.”

But the tests for reactive control said something else entirely.

In these experiments, the changes to the spoken words were varied. “Sometimes ‘head’ sounded like ‘head,’ sometimes it sounded like ‘hid’ and sometimes it sounded like ‘had,’” says Parrell. “We made the change random and unpredictable.”

That meant the study subjects had to depend on their reactive system. “We found that the folks with cerebellar damage responded to these unpredictable changes to a larger extent than those without any damage,” says Parrell. “It was totally unexpected.”

Parrell’s research shows that the cerebellum plays a vital role in our predictive systems, which in turn greatly affects how we speak and communicate. He is now exploring why those with cerebellar damage have improved reactive systems and what that means for their ability to speak the words they want to use.

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Featured image by Jens Maus, via Wikimedia Commons

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Saving time in the publication process: new service helping researchers on campus https://uwmadscience.news.wisc.edu/science-policy/buckysubmit/ Mon, 06 Nov 2017 22:36:02 +0000 https://uwmadscience.news.wisc.edu/?p=2768 A new submission service is assisting researchers at UW–Madison with new compliance procedures for federally funded research manuscripts.

The service operates like this: a researcher goes to the website and follows the links to submit their manuscript file. Once submitted, the staff reviews the manuscript to ensure that it meets the federal funder’s requirements, and then submits the manuscript to the federal agency.

Called BuckySubmit, the clearinghouse was launched in May 2017 through collaboration between the School of Medicine and Public Health and the Office of the Vice Chancellor for Research and Graduate Education. Public Access Compliance Specialist Ryan Schryver and Ebling Information Architecture Librarian Allan Barclay spearheaded the project. Their goal was to simplify the already-complicated compliance procedures that are required for federally funded research grant projects.

“While the point of having rules in place to govern how funding is spent or how human subjects are treated is important from the perspective of protecting people or research investments, the volume of these mandates can often take time away from the research,” Schryver says.

A new mandate passed in 2013 (or 2008 for National Institutes of Health-sponsored research) requires all peer-reviewed manuscripts, derived using funding from federal agencies whose research and development expenditures total over $100 million, to be made publicly accessible. With the new rules, a service to assist principal investigators running research projects with publishing manuscripts proved all the more necessary.

Jean Phillips the director of the Schwerdtfeger Library at the Space Science and Engineering Center, is helping to coordinate submissions for specific agencies and provided feedback to Schryver on the BuckySubmit architecture. She sees an extended potential that BuckySubmit could offer, more than just easing burdens of compliance for researchers. According to Phillips, the BuckySubmit repository could potentially offer a lens through which to study the research being conducted on campus.

Federal funders are interested in tracking publications data to show the reach and impact of taxpayer-funded research, Phillips says. The data offered from a research repository can help the University learn about its own research and publication trends, such as where articles are being published, whether or not students are co-authors on them, new areas of research gaining more attention, and so on.

“In the future, when citing datasets becomes as common as citing papers, we will be able to look at the impact there, too, in new ways,” Phillips says.

 

For more information on BuckySubmit, visit their website: http://ebling.library.wisc.edu/services/public_access/index.html

 

 

 

 

 

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Burned and crumbling scrolls read with help of UW alum https://uwmadscience.news.wisc.edu/computer-science/unraveling-ancient-scrolls/ Wed, 18 Oct 2017 18:58:21 +0000 https://uwmadscience.news.wisc.edu/?p=2744 The documents of antiquity, ancient scrolls, pose all sorts of challenges for scholars trying to read them. This is especially true for the most fragile documents, those seared but not completely destroyed by fire, sometimes thousands of years ago.

But now scholars have a new resource to non-invasively read ancient scrolls without unrolling them and possibly damaging or destroying the brittle texts that provide a direct window to human experience in the ancient world.

The technology, developed by University of Kentucky computer science Professor and UW-Madison alumnus Brent Seales, was dramatically unveiled in 2015 when the Israeli Antiquities Authority revealed the text – the Book of Leviticus, the oldest copy of the Hebrew Bible outside of the Dead Sea Scrolls – from a badly burned and crumbling 2,000-year-old scroll. The scroll was recovered in the charred ruins of a synagogue at En-Gedi, an oasis on the shore of the Dead Sea in Israel.

The En-Gedi synagogue ruins in Israel

The En-Gedi synagogue ruins in Israel

The technology to “virtually unwrap” the scrolls depends on tomography, used most famously in medicine to non-invasively obtain a cross section of the human body. Adapting advanced tomography, image processing and computer vision techniques, Seales’ team coupled those methodologies to a “pipeline” of software algorithms. The software, devised by Seales’ group, allows for the reading of discrete layers of text and recreation of the hidden pages of a manuscript.

Seales’ group is now laboring to read scrolls recovered from the “Villa of the Papyri,” a house in Roman Herculaneum buried beneath 30 meters of volcanic ash from the eruption of Mount Vesuvius in A.D. 79. The house contained the only complete library that survives from the Greco-Roman world.

Seales, who graduated from UW-Madison with a doctorate in computer science in 1991, will discuss his technology and the promise it holds for reading otherwise inaccessible texts at a special meeting of the Madison Biblical Archaeology Society at 7 p.m. Friday, Oct. 20. The event, which is free and open to the public, will be held at Upper House, 365 East Campus Mall.


Images: University of Kentucky (featured) and By Ziko van Dijk, Wikimedia Commons

 

 

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Testing new treatment methods for spinal cord injuries https://uwmadscience.news.wisc.edu/chemistry/testing-new-treatment-methods-for-spinal-cord-injuries/ Mon, 16 Oct 2017 21:33:22 +0000 https://uwmadscience.news.wisc.edu/?p=2740 Researchers in Dr. Amgad Hanna’s Lab at UW–Madison are experimenting with new treatment options to help restore function after spinal cord injuries.

The treatment involves an injection of Interleukin-10, an anti-inflammatory protein, to a damaged nerve tissue site. In the standard method of application, the protein is injected and disperses throughout the system and is consequentially removed in a matter of hours. But UW–Madison researchers have employed the use of mineral coated micro-particles, laced with Interleukin-10, to create a sustained, localized release of the drug.

According to Dan Hellenbrand, a research assistant in the lab, the micro-particles remain at the injury site and keep the protein bioactive, which is essential for the sustained local release and therapeutic effect.

A micro-particle is basically a small polymer-like particle that are coated with a calcium phosphate, and the calcium phosphate is actually what the protein binds to, that’s what keeps them at the injury site,” Hellenbrand says.

Following a spinal cord injury, secondary damage occurs from over-inflammation of the injured tissue. Interleukin-10 supports the recovery of the tissue by reducing proinflammatory cytokines that cause the tissue to inflame.

Hellenbrand and his associates test the treatment on rats, which receive a contusion to the spine. Following the injury, the rats are injected with the protein-laced micro-particles and are observed for signs of recovery.

“In this case we looked at one month after injury. All rats do regain the ability to walk, but I’d say if they are left alone and don’t have a treatment, their walking is extremely poor. And with the treatment they’re walking very close to normal.”

The Hanna Lab coordinates about two to three research projects at a time, and uses the assistance of about a dozen undergraduate students on projects as well as two medical students at most times. 

The micro particles come from another lab on campus, Dr. William Murphy’s lab in biomedical engineering. The researchers in the Hannah Lab regularly partner with Murphy’s lab on projects.

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Gotta Catch ‘Em All: UW researchers developing plant identification app https://uwmadscience.news.wisc.edu/botany/gotta-catch-em-all-uw-researchers-developing-plant-identification-app/ Wed, 11 Oct 2017 18:31:04 +0000 https://uwmadscience.news.wisc.edu/?p=2729 Imagine you are walking down a trail or a sidewalk when you come across a gorgeous flower. It’s so pretty that you want to remember what it is for later, maybe to plant in your home garden or show to a friend.

So you take out your smartphone, open up your Plant ID app, input the plant’s characteristics, and violà! You now have the scientific name, statewide distribution, and any other facts about the species that you could want.

This is the goal for Catherine Woodward, a botanist and professor at the University of Wisconsin–Madison who is helping to develop a mobile application for identifying Wisconsin plant life.

The idea, Woodward says, is to provide naturalists, educators and anyone else curious about plants with an accessible, easy-to-navigate database as a reference when they are out interacting with plant life and want to learn more about specific organisms.

For a final project, one of her former dendrology students decided to create an app for identifying Wisconsin tree species. This “kind of spiraled into this idea” of creating an app for all the plants in Wisconsin, Woodward says.

According to Woodward, the final product will have the capacity to identify 1,800 different plant species. It will also include maps that show the range and distribution of species, drawing on data housed in the Wisconsin State Herbarium in Birge Hall on UW–Madison’s campus.

“The really unique thing about this app is that it will allow you to collect what you see,” Woodward says, describing a feature of the app that will allow users to develop a searchable catalog or checklist of plants they have identified.

Citizen science is a special component of the application. Through the app, users can collect and submit data to the State Herbarium, where the staff can validate user’s sightings. It will also, contribute to the herbarium and the Wisconsin Department of Natural Resources’ own records of Wisconsin plant life. Sightings of species that are listed as endangered or invasive will also be tagged and prioritized for review; a huge asset to researchers who may be investigating the data.

Woodward also hopes the app will be a tool for educators in Wisconsin and provides a fun and easy way to introduce younger age groups to plant life and botany.

“Because it’s icon based, it’s useful to kids. You can look at the picture and say ‘Oh it looks like that;’ you don’t have to read technical botanical terms to use it,” she says, adding, “I think this will help people overcome their fear because the goal is for it to be fun, not just something that you need or you find necessary for your career, but something that’s actually fun to do.”

The app is being developed by the Field Day Lab, a team of researchers and developers with the Wisconsin Institute for Discovery. The team also works with Wisconsin DNR, who will be testing the app. The beta release is scheduled for this fall. The final version of the app will be available at either a small fee or free of charge, says Woodward.

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Communicating immune health through pop-culture https://uwmadscience.news.wisc.edu/health/gameoftcells/ Fri, 06 Oct 2017 21:16:23 +0000 https://uwmadscience.news.wisc.edu/?p=2722 In the hit HBO television series “Game of Thrones,” the show’s heroes are constantly struggling against a persistent enemy to the north of The Wall, a massive wall of ice that separates the wild northern lands from the southern kingdoms and their inhabitants. Their foes, called white walkers, are zombie-inspired snow creatures whose minions possess human corpses and turn them against their former friends and the living.

In their possession of human bodies, white walkers act similarly to the HIV virus, which possess human t-cells and turn them against other cells in the body. The analogy was adopted by Rob Striker, an associate professor in the Department of Medicine, as the impetus for his website “Game Of T-Cells,” to help explain how HIV works.

“My thesis advisor has recently become a national academy member, and when I worked in his lab I questioned if he spent too much time thinking about titles of paper, how to present data, and analogies on how things worked that we were studying,” Striker says. “I didn’t really recognize that as really important scientific thought, but I now think that analogies are super important in getting people to think about data in different ways.”

Striker is a researcher studying the HIV virus, and had been wanting for some time to develop a way to popularize research on the CD4/CD8 ratio that he says is often overlooked in discussions about immune health and disease.

The CD4/CD8 lymphocyte cell ratio, according to Striker, is a measurement of immune system health. Those with an HIV infection will see a higher amount of CD8 cells in the body.

“The goal is to get people to be measuring the ratio and to be thinking about how do we get ratios to improve, what do the ratios mean, and how do we get as many people involved as possible,” Striker says.

And this mode of communication can be beneficial, says Department of Life Science Chair Dominique Broussard.

“The main [benefit] is that it is easier to reach people when you use channels they enjoy — using pop culture can make science messages resonate with audiences in ways that traditional channels cannot achieve,” Broussard says.

Striker intends to continuously update the site, adding more “houses” to help explain the functions of specific cells, and will be adding videos and additional blog posts to keep new information flowing into the website.

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